Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: An R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/> to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.8-0 dated 2015-10-31 and 0.8-1 dated 2015-10-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/NEWS.Rd | 8 ++++++++ src/svds.cpp | 4 +++- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Import/Export Routines for MALDIquant
Description: Functions for reading (tab, csv, Bruker fid, Ciphergen
XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and
writing (tab, csv, mMass MSD, mzML, imzML) different file
formats of mass spectrometry data into/from MALDIquant objects.
Author: Sebastian Gibb [aut, cre],
Pietro Franceschi [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquantForeign versions 0.9 dated 2014-08-11 and 0.10 dated 2015-10-31
MALDIquantForeign-0.10/MALDIquantForeign/DESCRIPTION | 27 - MALDIquantForeign-0.10/MALDIquantForeign/MD5 | 174 ++++----- MALDIquantForeign-0.10/MALDIquantForeign/NAMESPACE | 16 MALDIquantForeign-0.10/MALDIquantForeign/NEWS | 41 ++ MALDIquantForeign-0.10/MALDIquantForeign/R/AllGenerics.R | 4 MALDIquantForeign-0.10/MALDIquantForeign/R/MALDIquantForeign-parallel.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/analyze-functions.R | 13 MALDIquantForeign-0.10/MALDIquantForeign/R/base64encode-functions.R | 13 MALDIquantForeign-0.10/MALDIquantForeign/R/compression-functions.R | 39 -- MALDIquantForeign-0.10/MALDIquantForeign/R/createMassObject-functions.R | 38 +- MALDIquantForeign-0.10/MALDIquantForeign/R/download-function.R | 20 - MALDIquantForeign-0.10/MALDIquantForeign/R/export-functions.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/export-methods.R | 111 +++++ MALDIquantForeign-0.10/MALDIquantForeign/R/exportImzMl-methods.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/exportMsd-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/exportMzMl-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/exportTab-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/R/fileFormats.R | 26 - MALDIquantForeign-0.10/MALDIquantForeign/R/filename-functions.R | 34 - MALDIquantForeign-0.10/MALDIquantForeign/R/filename-methods.R | 5 MALDIquantForeign-0.10/MALDIquantForeign/R/ibd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/import-functions.R | 77 +++- MALDIquantForeign-0.10/MALDIquantForeign/R/importAnalyze-functions.R | 16 MALDIquantForeign-0.10/MALDIquantForeign/R/importAuto-functions.R | 14 MALDIquantForeign-0.10/MALDIquantForeign/R/importBrukerFlex-functions.R | 9 MALDIquantForeign-0.10/MALDIquantForeign/R/importCdf-functions.R | 9 MALDIquantForeign-0.10/MALDIquantForeign/R/importCiphergenXml-functions.R | 13 MALDIquantForeign-0.10/MALDIquantForeign/R/importImzMl-functions.R | 121 +++--- MALDIquantForeign-0.10/MALDIquantForeign/R/importMsd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/importMzMl-functions.R | 18 MALDIquantForeign-0.10/MALDIquantForeign/R/importMzXml-functions.R | 18 MALDIquantForeign-0.10/MALDIquantForeign/R/importTab-functions.R | 25 - MALDIquantForeign-0.10/MALDIquantForeign/R/imzMl-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/list.files-functions.R | 7 MALDIquantForeign-0.10/MALDIquantForeign/R/msd-functions.R | 4 MALDIquantForeign-0.10/MALDIquantForeign/R/msg-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/mzMl-functions.R | 189 +++++++++- MALDIquantForeign-0.10/MALDIquantForeign/R/package.R | 7 MALDIquantForeign-0.10/MALDIquantForeign/R/parseCiphergenXml.R | 5 MALDIquantForeign-0.10/MALDIquantForeign/R/parseMsd.R |only MALDIquantForeign-0.10/MALDIquantForeign/R/parseMzMl.R | 38 -- MALDIquantForeign-0.10/MALDIquantForeign/R/sanitize-functions.R | 4 MALDIquantForeign-0.10/MALDIquantForeign/R/testChecksum-functions.R | 14 MALDIquantForeign-0.10/MALDIquantForeign/R/uuid-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/build/vignette.rds |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/doc/MALDIquantForeign-intro.pdf |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/compressed/csv1.csv.gz |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny1.msd |only MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_continuous.ibd |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_continuous.imzML | 4 MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_processed.ibd |binary MALDIquantForeign-0.10/MALDIquantForeign/inst/exampledata/tiny_processed.imzML | 4 MALDIquantForeign-0.10/MALDIquantForeign/man/MALDIquantForeign-package.Rd | 3 MALDIquantForeign-0.10/MALDIquantForeign/man/MALDIquantForeign-parallel.Rd |only MALDIquantForeign-0.10/MALDIquantForeign/man/base64-encode.Rd | 3 MALDIquantForeign-0.10/MALDIquantForeign/man/export-methods.Rd | 12 MALDIquantForeign-0.10/MALDIquantForeign/man/exportImzMl-methods.Rd |only MALDIquantForeign-0.10/MALDIquantForeign/man/exportMsd-methods.Rd | 13 MALDIquantForeign-0.10/MALDIquantForeign/man/exportMzMl-methods.Rd | 25 - MALDIquantForeign-0.10/MALDIquantForeign/man/exportTab-methods.Rd | 11 MALDIquantForeign-0.10/MALDIquantForeign/man/import-functions.Rd | 13 MALDIquantForeign-0.10/MALDIquantForeign/man/importAnalyze-functions.Rd | 3 MALDIquantForeign-0.10/MALDIquantForeign/man/importBrukerFlex-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importCdf-functions.Rd | 7 MALDIquantForeign-0.10/MALDIquantForeign/man/importCiphergenXml-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importImzMl-functions.Rd | 17 MALDIquantForeign-0.10/MALDIquantForeign/man/importMsd-functions.Rd |only MALDIquantForeign-0.10/MALDIquantForeign/man/importMzMl-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importMzXml-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/importTab-functions.Rd | 5 MALDIquantForeign-0.10/MALDIquantForeign/man/supportedFileFormats-functions.Rd | 6 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_compression-functions.R | 10 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_createMassObject-functions.R | 27 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_download-functions.R | 36 + MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportImzMl-methods.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportMsd-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportMzMl-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_exportTab-methods.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_fileFormats.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_filename-functions.R | 20 + MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_ibd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importBrukerFlex-functions.R | 11 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importCdf-functions.R | 12 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importCiphergenXml-functions.R | 10 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importImzMl-functions.R | 44 +- MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importMsd-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importMzMl-functions.R | 28 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importMzXml-functions.R | 28 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_importTab-functions.R | 26 - MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_list.files-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_msg-functions.R |only MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_sanitize-functions.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_testChecksum-functions.R | 1 MALDIquantForeign-0.10/MALDIquantForeign/tests/testthat/test_uuid-functions.R |only MALDIquantForeign-0.9/MALDIquantForeign/man/cleanFilename.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/composeFilename-methods.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/createMassObject.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/fileExtension.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/mzMlHandlers.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/parseCiphergenXml.Rd |only MALDIquantForeign-0.9/MALDIquantForeign/man/parseMzMl.Rd |only 101 files changed, 995 insertions(+), 561 deletions(-)
More information about MALDIquantForeign at CRAN
Permanent link
Title: Client for the Captricity API
Description: Get text from images of text using Captricity Optical Character
Recognition (OCR) API. Captricity allows you to get text from handwritten
forms --- think surveys --- and other structured paper documents. And it can
output data in form a delimited file keeping field information intact. For more
information, read https://shreddr.captricity.com/developer/overview/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between captr versions 0.1 dated 2015-10-04 and 0.1.2 dated 2015-10-31
DESCRIPTION | 22 +++++++++++++--------- LICENSE |only MD5 | 40 ++++++++++++++++++++++++---------------- NAMESPACE | 2 +- NEWS |only R/set_batch_template.R | 2 +- README.md |only build |only inst/doc |only man/batch_price.Rd | 2 +- man/captr-package.Rd | 6 +++--- man/create_batch.Rd | 2 +- man/get_all.Rd | 2 +- man/get_instance_set.Rd | 2 +- man/get_template_id.Rd | 4 ++-- man/list_instance_sets.Rd | 4 ++-- man/set_batch_template.Rd | 6 +++--- man/set_token.Rd | 4 ++-- man/submit_batch.Rd | 2 +- man/test_readiness.Rd | 2 +- man/track_progress.Rd | 2 +- man/upload_image.Rd | 2 +- vignettes |only 23 files changed, 59 insertions(+), 47 deletions(-)
Title: Ternary Search Tree for Auto-Completion and Spell Checking
Description: A ternary search tree is a type of prefix tree with up to three children and the ability for incremental string search. The package uses this ability for word auto-completion and spell checking. Includes a dataset with the 10001 most frequent English words.
Author: Ricardo Merino [aut, cre],
Samantha Fernandez [ctb]
Maintainer: Ricardo Merino <ricardo.merino.raldua@gmail.com>
Diff between TSTr versions 1.1 dated 2015-10-07 and 1.2 dated 2015-10-31
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- build/TSTr.pdf |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.100.0.0 dated 2015-10-04 and 0.6.200.2.0 dated 2015-10-31
RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/arpack_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/arpack_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/atlas_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/atlas_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/blas_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/blas_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_norm_sparse.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/forward_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/lapack_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/lapack_wrapper.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/superlu_bones.hpp |only RcppArmadillo-0.6.100.0.0/RcppArmadillo/inst/include/armadillo_bits/superlu_wrapper.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/ChangeLog | 23 RcppArmadillo-0.6.200.2.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/MD5 | 889 +-- RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/NEWS.Rd | 21 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo | 34 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/BaseCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/BaseCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Base_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Base_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 28 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Gen_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Gen_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GlueCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/GlueCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Glue_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Glue_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 28 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/OpCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/OpCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Op_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Op_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Proxy.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/ProxyCube.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeMat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SizeMat_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpCol_bones.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpCol_meat.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 11 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 36 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpProxy.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpRow_bones.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpRow_meat.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_bones.hpp | 13 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 11 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_meat.hpp | 11 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/access.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_boost.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_cmath.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng_cxx11.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng_cxx98.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_static_check.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp | 79 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 2402 ++++------ RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup_post.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/cond_rel_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/cond_rel_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 27 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp.cmake |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/constants.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/constants_compat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/debug.hpp | 80 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_arpack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_atlas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_blas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_hdf5.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_lapack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/def_superlu.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diagmat_proxy.hpp | 120 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diagview_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diagview_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diskio_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/distr_param.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOpCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOpCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOp_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eOp_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eglue_core_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eglue_core_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fft_engine.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/field_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 24 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_all.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_any.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_chol.hpp | 35 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_clamp.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cond.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cor.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cov.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cross.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cumprod.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_cumsum.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_det.hpp | 14 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_diagmat.hpp | 42 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_diagvec.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_diff.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_dot.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_gen.hpp | 298 - RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_pair.hpp | 221 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eig_sym.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eigs_gen.hpp | 16 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eigs_sym.hpp | 16 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eps.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_expmat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_eye.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_fft.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_fft2.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_find.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_find_unique.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_flip.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_hist.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_histc.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_inplace_strans.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_inplace_trans.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_interp1.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_inv.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_join.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_kron.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_log_det.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_lu.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_max.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_mean.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_median.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_min.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_misc.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_n_unique.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_nonzeros.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_norm.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_normalise.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_numel.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_ones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_pinv.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_princomp.hpp | 16 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_prod.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_qr.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_qz.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randg.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randi.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randn.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_randu.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_rank.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_repmat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_reshape.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_resize.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_schur.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_shuffle.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_size.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_solve.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sort.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sort_index.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_speye.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_spones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sprandn.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sprandu.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_spsolve.hpp | 19 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_stddev.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_strans.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_sum.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_svd.hpp | 20 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_svds.hpp | 35 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_syl_lyap.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_symmat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_toeplitz.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp | 102 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trans.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trig.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trimat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trunc_exp.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_trunc_log.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_unique.hpp | 14 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_var.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_vectorise.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_zeros.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_conv_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cor_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cor_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cov_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cov_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cross_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_cross_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_hist_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_hist_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_histc_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_histc_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_join_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_join_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_kron_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_kron_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_max_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_max_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_min_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_min_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_mixed_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_relational_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_relational_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_times_meat.hpp | 79 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_toeplitz_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_toeplitz_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_bones.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_meat.hpp | 27 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_misc_bones.hpp | 13 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/gmm_misc_meat.hpp | 13 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_misc.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/include_atlas.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/include_hdf5.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/include_superlu.hpp | 20 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/injector_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/injector_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlueCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlueCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlue_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtGlue_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOpCube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOpCube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOp_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtOp_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mtSpOp_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemm.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemm_mixed.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_gemv.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_herk.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/mul_syrk.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_all_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_all_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_any_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_any_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_chol_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_chol_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_clamp_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_clamp_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cor_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cor_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cov_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cov_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumprod_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumprod_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumsum_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cumsum_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cx_scalar_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cx_scalar_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagmat_bones.hpp | 19 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagmat_meat.hpp | 134 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagvec_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diagvec_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diff_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_diff_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dotext_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_dotext_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_expmat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_expmat_meat.hpp | 14 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_fft_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_fft_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_unique_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_find_unique_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_flip_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_flip_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_hist_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_hist_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_inv_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_inv_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_max_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_max_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_median_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_median_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_min_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_min_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_misc_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_misc_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_nonzeros_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_nonzeros_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_norm_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_norm_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_normalise_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_normalise_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_princomp_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_princomp_meat.hpp | 12 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_prod_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_prod_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_relational_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_relational_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_repmat_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_repmat_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_reshape_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_reshape_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_resize_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_resize_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_shuffle_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_shuffle_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_index_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_index_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_stddev_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_stddev_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_symmat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_symmat_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_toeplitz_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_toeplitz_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_trimat_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_trimat_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_unique_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_unique_meat.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_var_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_var_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_vectorise_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/op_vectorise_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_div.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_minus.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_plus.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_relational.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_schur.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_cube_times.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_div.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_minus.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_ostream.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_plus.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_relational.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_schur.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/podarray_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/podarray_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/promote_type.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/restrictors.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_vec_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/running_stat_vec_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 59 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/span.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spdiagview_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_join_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_diagmat_bones.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_diagmat_meat.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_htrans_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_htrans_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_bones.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_mean_bones.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_mean_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_bones.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_bones.hpp | 18 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_meat.hpp | 107 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_meat.hpp | 7 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_var_bones.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/spop_var_meat.hpp | 9 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/strip.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_bones.hpp | 8 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_each_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem1_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem1_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 10 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/traits.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_elem.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_elem_check.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_mat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_mat_fixed.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/unwrap.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/unwrap_cube.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/unwrap_spmat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/upgrade_val.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wall_clock_bones.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wall_clock_meat.hpp | 6 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_arpack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_atlas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_blas.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_lapack.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_superlu.hpp |only RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xtrans_mat_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xtrans_mat_meat.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_bones.hpp | 5 RcppArmadillo-0.6.200.2.0/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_meat.hpp | 5 459 files changed, 4144 insertions(+), 3685 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver.
Includes support for aggregation, indexing, map-reduce, streaming, 'TLS'
encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.5 dated 2015-07-27 and 0.6 dated 2015-10-31
mongolite-0.5/mongolite/src/Makevars |only mongolite-0.5/mongolite/src/bson/bson-version.c |only mongolite-0.6/mongolite/DESCRIPTION | 6 mongolite-0.6/mongolite/MD5 | 260 mongolite-0.6/mongolite/NAMESPACE | 1 mongolite-0.6/mongolite/NEWS | 6 mongolite-0.6/mongolite/R/iter.R | 2 mongolite-0.6/mongolite/R/mongo.R | 12 mongolite-0.6/mongolite/R/object.R | 12 mongolite-0.6/mongolite/build/vignette.rds |binary mongolite-0.6/mongolite/configure | 115 mongolite-0.6/mongolite/inst/CITATION | 2 mongolite-0.6/mongolite/inst/doc/intro.html | 4 mongolite-0.6/mongolite/src/Makevars.in |only mongolite-0.6/mongolite/src/Makevars.win | 4 mongolite-0.6/mongolite/src/bson/bcon.c | 6 mongolite-0.6/mongolite/src/bson/bson-compat.h | 10 mongolite-0.6/mongolite/src/bson/bson-config.h | 2 mongolite-0.6/mongolite/src/bson/bson-endian.h | 1 mongolite-0.6/mongolite/src/bson/bson-iter.c | 113 mongolite-0.6/mongolite/src/bson/bson-json.c | 30 mongolite-0.6/mongolite/src/bson/bson-macros.h | 81 mongolite-0.6/mongolite/src/bson/bson-memory.c | 20 mongolite-0.6/mongolite/src/bson/bson-memory.h | 1 mongolite-0.6/mongolite/src/bson/bson-oid.c | 36 mongolite-0.6/mongolite/src/bson/bson-reader.c | 36 mongolite-0.6/mongolite/src/bson/bson-stdint.h | 2 mongolite-0.6/mongolite/src/bson/bson-string.c | 16 mongolite-0.6/mongolite/src/bson/bson-thread-private.h | 2 mongolite-0.6/mongolite/src/bson/bson-types.h | 4 mongolite-0.6/mongolite/src/bson/bson-utf8.c | 12 mongolite-0.6/mongolite/src/bson/bson-value.c | 4 mongolite-0.6/mongolite/src/bson/bson-version-functions.c |only mongolite-0.6/mongolite/src/bson/bson-version-functions.h |only mongolite-0.6/mongolite/src/bson/bson-version.h | 33 mongolite-0.6/mongolite/src/bson/bson-writer.c | 12 mongolite-0.6/mongolite/src/bson/bson.c | 235 mongolite-0.6/mongolite/src/bson/bson.h | 1 mongolite-0.6/mongolite/src/client.c | 4 mongolite-0.6/mongolite/src/collection.c | 10 mongolite-0.6/mongolite/src/cursor.c | 4 mongolite-0.6/mongolite/src/mongoc/mongoc-array-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-array.c | 42 mongolite-0.6/mongolite/src/mongoc/mongoc-async-cmd-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-async-cmd.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-async-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-async.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-buffer-private.h | 7 mongolite-0.6/mongolite/src/mongoc/mongoc-buffer.c | 86 mongolite-0.6/mongolite/src/mongoc/mongoc-bulk-operation-private.h | 32 mongolite-0.6/mongolite/src/mongoc/mongoc-bulk-operation.c | 140 mongolite-0.6/mongolite/src/mongoc/mongoc-bulk-operation.h | 7 mongolite-0.6/mongolite/src/mongoc/mongoc-client-pool.c | 100 mongolite-0.6/mongolite/src/mongoc/mongoc-client-pool.h | 4 mongolite-0.6/mongolite/src/mongoc/mongoc-client-private.h | 74 mongolite-0.6/mongolite/src/mongoc/mongoc-client.c | 594 - mongolite-0.6/mongolite/src/mongoc/mongoc-client.h | 18 mongolite-0.6/mongolite/src/mongoc/mongoc-cluster-private.h | 188 mongolite-0.6/mongolite/src/mongoc/mongoc-cluster.c | 3074 +++------- mongolite-0.6/mongolite/src/mongoc/mongoc-collection.c | 352 - mongolite-0.6/mongolite/src/mongoc/mongoc-config.h | 13 mongolite-0.6/mongolite/src/mongoc/mongoc-counters-private.h | 1 mongolite-0.6/mongolite/src/mongoc/mongoc-counters.c | 12 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-array.c | 16 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-cursorid-private.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-cursorid.c | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-private.h | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor-transform.c | 8 mongolite-0.6/mongolite/src/mongoc/mongoc-cursor.c | 386 - mongolite-0.6/mongolite/src/mongoc/mongoc-database.c | 47 mongolite-0.6/mongolite/src/mongoc/mongoc-error.h | 6 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-list.c | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-page-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-page.c | 64 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file-private.h | 1 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file.c | 237 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs-file.h | 68 mongolite-0.6/mongolite/src/mongoc/mongoc-gridfs.c | 17 mongolite-0.6/mongolite/src/mongoc/mongoc-host-list.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-host-list.h | 4 mongolite-0.6/mongolite/src/mongoc/mongoc-index.c | 41 mongolite-0.6/mongolite/src/mongoc/mongoc-index.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-init.c | 10 mongolite-0.6/mongolite/src/mongoc/mongoc-iovec.h | 10 mongolite-0.6/mongolite/src/mongoc/mongoc-list.c | 12 mongolite-0.6/mongolite/src/mongoc/mongoc-log-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-log.c | 163 mongolite-0.6/mongolite/src/mongoc/mongoc-matcher-op-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-matcher-op.c | 45 mongolite-0.6/mongolite/src/mongoc/mongoc-matcher.c | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-memcmp-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-memcmp.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-opcode-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-opcode.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-queue.c | 18 mongolite-0.6/mongolite/src/mongoc/mongoc-read-prefs-private.h | 21 mongolite-0.6/mongolite/src/mongoc/mongoc-read-prefs.c | 359 - mongolite-0.6/mongolite/src/mongoc/mongoc-rpc-private.h | 30 mongolite-0.6/mongolite/src/mongoc/mongoc-rpc.c | 229 mongolite-0.6/mongolite/src/mongoc/mongoc-sasl-private.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc-sasl.c | 32 mongolite-0.6/mongolite/src/mongoc/mongoc-scram.c | 19 mongolite-0.6/mongolite/src/mongoc/mongoc-server-description-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-description.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-description.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-stream-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-server-stream.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-set-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-set.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-socket-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-socket.c | 378 - mongolite-0.6/mongolite/src/mongoc/mongoc-socket.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-ssl.c | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-buffered.c | 44 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-file.c | 24 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-gridfs.c | 14 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-private.h | 11 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-socket.c | 74 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-tls.c | 162 mongolite-0.6/mongolite/src/mongoc/mongoc-stream-tls.h | 3 mongolite-0.6/mongolite/src/mongoc/mongoc-stream.c | 253 mongolite-0.6/mongolite/src/mongoc/mongoc-stream.h | 15 mongolite-0.6/mongolite/src/mongoc/mongoc-thread-private.h | 41 mongolite-0.6/mongolite/src/mongoc/mongoc-topology-description-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-description.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-scanner-private.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology-scanner.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-topology.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-trace.h | 105 mongolite-0.6/mongolite/src/mongoc/mongoc-uri-private.h | 58 mongolite-0.6/mongolite/src/mongoc/mongoc-uri.c | 655 +- mongolite-0.6/mongolite/src/mongoc/mongoc-uri.h | 6 mongolite-0.6/mongolite/src/mongoc/mongoc-util-private.h | 24 mongolite-0.6/mongolite/src/mongoc/mongoc-util.c | 21 mongolite-0.6/mongolite/src/mongoc/mongoc-version-functions.c |only mongolite-0.6/mongolite/src/mongoc/mongoc-version-functions.h |only mongolite-0.6/mongolite/src/mongoc/mongoc-version.h | 9 mongolite-0.6/mongolite/src/mongoc/mongoc-write-command-private.h | 49 mongolite-0.6/mongolite/src/mongoc/mongoc-write-command.c | 969 +-- mongolite-0.6/mongolite/src/mongoc/mongoc-write-concern.c | 57 mongolite-0.6/mongolite/src/mongoc/mongoc-write-concern.h | 2 mongolite-0.6/mongolite/src/mongoc/mongoc.h | 1 mongolite-0.6/mongolite/src/mongoc/utlist.h |only mongolite-0.6/mongolite/src/tests/has_sasl_client_done.c | 3 mongolite-0.6/mongolite/src/win32/ipv6.c | 7 mongolite-0.6/mongolite/tools/winlibs.R | 2 147 files changed, 5825 insertions(+), 4932 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' package.
It also implements the two-stage SEM approach to conduct meta-analytic
structural equation modeling on correlation and covariance matrices.
Author: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Maintainer: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 0.9.4 dated 2015-06-08 and 0.9.6 dated 2015-10-31
DESCRIPTION | 12 - MD5 | 94 ++++---- NAMESPACE | 10 NEWS | 27 ++ R/asyCov.R | 26 ++ R/hidden.R | 90 +------- R/meta2semPlot.R | 2 R/plot.meta.R | 6 R/summary.R | 64 ++++- R/tssem.R | 526 +++++++++++++++++++++++++------------------------ R/zzz.R | 6 data/Aloe14.rda |binary data/BCG.rda |binary data/Becker09.rda |binary data/Becker83.rda |binary data/Becker92.rda |binary data/Becker94.rda |binary data/Berkey98.rda |binary data/Bornmann07.rda |binary data/Cheung00.rda |binary data/Cheung09.rda |binary data/Cooper03.rda |binary data/Digman97.rda |binary data/HedgesOlkin85.rda |binary data/Hox02.rda |binary data/Hunter83.rda |binary data/Jaramillo05.rda |binary data/Mak09.rda |binary data/Norton13.rda |only data/Roorda11.rda |only data/issp05.rda |binary data/issp89.rda |binary data/wvs94a.rda |binary data/wvs94b.rda |binary inst/doc/metaSEM.pdf |binary man/Becker92.Rd | 2 man/Cheung00.Rd | 4 man/Hunter83.Rd | 4 man/Norton13.Rd |only man/Roorda11.Rd |only man/anova.Rd | 8 man/asyCov.Rd | 10 man/issp05.Rd | 1 man/metaSEM-package.Rd | 21 + man/plot.meta.Rd | 2 man/readData.Rd | 3 man/rerun.Rd | 9 man/tssem1.Rd | 40 ++- man/wls.Rd | 6 man/wvs94b.Rd | 4 50 files changed, 537 insertions(+), 440 deletions(-)
Title: Exact Test from the Combinations of Mutually Exclusive
Alterations (CoMEt) Algorithm
Description: An algorithm for identifying combinations of mutually exclusive alterations in cancer genomes. CoMEt represents the mutations in a set M of k genes with a 2^k dimensional contingency table, and then computes the tail probability of observing T(M) exclusive alterations using an exact statistical test.
Author: Max Leiserson [aut, cre],
Hsin-Ta Wu [aut],
Fabio Vandin [ctb],
Vivian Hsiao [ctb],
Benjamin Raphael [ctb]
Maintainer: Max Leiserson <mdml@cs.brown.edu>
Diff between cometExactTest versions 0.1.2 dated 2015-06-24 and 0.1.3 dated 2015-10-31
DESCRIPTION | 9 +-- MD5 | 10 ++- NAMESPACE | 6 +- R/cometexacttest.R | 146 +++++++++++++++++++++++++++++++++++++++++++++++++++-- man/comet.Rd | 20 ++++++- man/figures |only 6 files changed, 176 insertions(+), 15 deletions(-)
More information about cometExactTest at CRAN
Permanent link
Title: Extending R's Dendrogram Functionality
Description: Offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.1.0 dated 2015-07-30 and 1.1.2 dated 2015-10-31
dendextend-1.1.0/dendextend/inst/doc/dendextend-tutorial.pdf |only dendextend-1.1.2/dendextend/ChangeLog | 71 ++ dendextend-1.1.2/dendextend/DESCRIPTION | 12 dendextend-1.1.2/dendextend/MD5 | 53 - dendextend-1.1.2/dendextend/NAMESPACE | 2 dendextend-1.1.2/dendextend/NEWS | 17 dendextend-1.1.2/dendextend/R/ggdend.R | 16 dendextend-1.1.2/dendextend/R/labels.R | 129 +--- dendextend-1.1.2/dendextend/R/prune.R | 5 dendextend-1.1.2/dendextend/R/rect.dendrogram.R | 28 - dendextend-1.1.2/dendextend/R/zzz.R | 2 dendextend-1.1.2/dendextend/README.md | 2 dendextend-1.1.2/dendextend/build/vignette.rds |binary dendextend-1.1.2/dendextend/inst/CITATION | 4 dendextend-1.1.2/dendextend/inst/doc/Cluster_Analysis.R | 44 - dendextend-1.1.2/dendextend/inst/doc/Cluster_Analysis.html | 175 +++--- dendextend-1.1.2/dendextend/inst/doc/FAQ.R | 18 dendextend-1.1.2/dendextend/inst/doc/FAQ.html | 78 +- dendextend-1.1.2/dendextend/inst/doc/Quick_Introduction.R | 2 dendextend-1.1.2/dendextend/inst/doc/Quick_Introduction.html | 51 + dendextend-1.1.2/dendextend/inst/doc/introduction.R | 94 +-- dendextend-1.1.2/dendextend/inst/doc/introduction.html | 304 +++++------ dendextend-1.1.2/dendextend/inst/tests/test-ggdend.R | 29 + dendextend-1.1.2/dendextend/inst/tests/test-labels-assign.R | 47 - dendextend-1.1.2/dendextend/man/ggdend.Rd | 8 dendextend-1.1.2/dendextend/man/identify.dendrogram.Rd | 6 dendextend-1.1.2/dendextend/man/labels-assign.Rd | 24 dendextend-1.1.2/dendextend/man/rect.dendrogram.Rd | 7 28 files changed, 709 insertions(+), 519 deletions(-)
Title: Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Description: Solves the problem of Laplace deconvolution with noisy discrete
non-equally spaced observations on a finite time interval based on expansions
of the convolution kernel, the unknown function and the observed signal over
Laguerre functions basis. It implements the methodology proposed in the paper
"Laplace deconvolution on the basis of time domain data and its application to
Dynamic Contrast Enhanced imaging" by F. Comte, C-A. Cuenod, M. Pensky and Y.
Rozenholc in ArXiv (http://arxiv.org/abs/1405.7107).
Author: Yves Rozenholc (University Paris Descartes), Marianna Pensky (University
of Central Florida)
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between LaplaceDeconv versions 1.0.2 dated 2015-10-29 and 1.0.3 dated 2015-10-31
DESCRIPTION | 18 +++++++++++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 7 +------ R/LagLaplaceDeconvolution.R | 5 +++++ data/EX_DCEMRI_t0.rda |binary data/EX_DCEMRI_t1.rda |binary man/BuildLaguerreSystem.Rd | 14 +++++++------- man/EX_DCEMRI_t0.rda-EX_DCEMRI_t1.rda.Rd | 2 +- man/LagLaplDeconv.Rd | 4 ++-- man/LaguerreLaplaceConvolution.Rd | 12 ++++++------ man/LaplaceConvolution.Rd | 10 +++++----- man/MakeLaguerreMatrix.Rd | 6 +++--- 12 files changed, 54 insertions(+), 46 deletions(-)
Title: Regression Estimation Based on the Compound Covariate Method
Under the Cox Proportional Hazard Model
Description: Calculate regression coefficients and their standard deviations under the Cox proportional hazard model with a large number of covariates. A shrinkage type estimation based on the compound covariate method (Emura, Chen & Chen, 2012 PLoS ONE) and a univariate gene selection method under dependent censoring (Emura & Chen, 2014 Statistical Methods in Medical Research) are implemented. Algorithms for simulating gene expressions in these references are also given.
Author: Takeshi Emura & Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 1.4 dated 2014-04-13 and 2.0 dated 2015-10-31
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++++------ NAMESPACE | 4 +++- R/X.pathway.R |only R/X.tag.R |only man/X.pathway.Rd |only man/X.tag.Rd |only man/cindex.CV.Rd | 35 ++++++++++++++++++++--------------- man/compound.Cox-package.Rd | 19 ++++++++++--------- man/dependCox.reg.CV.Rd | 4 ++-- man/dependCox.reg.Rd | 9 ++++++--- 11 files changed, 59 insertions(+), 44 deletions(-)
Title: Simple Network of Workstations
Description: Support for simple parallel computing in R.
Author: Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between snow versions 0.3-13 dated 2013-09-27 and 0.4-1 dated 2015-10-31
snow-0.3-13/snow/R/pvm.R |only snow-0.4-1/snow/DESCRIPTION | 12 +-- snow-0.4-1/snow/MD5 | 21 +++--- snow-0.4-1/snow/NAMESPACE | 29 +++++++++ snow-0.4-1/snow/R/mpi.R | 44 ++++++------- snow-0.4-1/snow/R/nws.R | 28 ++++---- snow-0.4-1/snow/R/snow.R | 107 ++++++++++++++++++---------------- snow-0.4-1/snow/README | 40 +++++------- snow-0.4-1/snow/inst/RMPISNOW | 2 snow-0.4-1/snow/man/snow-internal.Rd | 26 ++++---- snow-0.4-1/snow/man/snow-rand.Rd | 1 snow-0.4-1/snow/man/snow-startstop.Rd | 20 +++--- 12 files changed, 185 insertions(+), 145 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: An R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/> to solve large scale
eigenvalue/vector problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function which does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. Matrices can be given in either dense
or sparse form.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.7-0 dated 2014-11-02 and 0.8-0 dated 2015-10-31
rARPACK-0.7-0/rARPACK/AUTHORS |only rARPACK-0.7-0/rARPACK/COPYRIGHTS |only rARPACK-0.7-0/rARPACK/NEWS |only rARPACK-0.7-0/rARPACK/R/25_eigs_function.R |only rARPACK-0.7-0/rARPACK/inst/LICENSE |only rARPACK-0.7-0/rARPACK/src/ARPACK |only rARPACK-0.7-0/rARPACK/src/ARPACK.h |only rARPACK-0.7-0/rARPACK/src/Eigs.cpp |only rARPACK-0.7-0/rARPACK/src/Eigs.h |only rARPACK-0.7-0/rARPACK/src/EigsGen.cpp |only rARPACK-0.7-0/rARPACK/src/EigsGen.h |only rARPACK-0.7-0/rARPACK/src/EigsSym.cpp |only rARPACK-0.7-0/rARPACK/src/EigsSym.h |only rARPACK-0.7-0/rARPACK/src/MatOp.h |only rARPACK-0.7-0/rARPACK/src/MatOp_dgeMatrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_dsyMatrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_function.cpp |only rARPACK-0.7-0/rARPACK/src/MatOp_function.h |only rARPACK-0.7-0/rARPACK/src/MatOp_matrix.cpp |only rARPACK-0.7-0/rARPACK/src/MatOp_matrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_sparseMatrix.h |only rARPACK-0.7-0/rARPACK/src/MatOp_symmatrix.cpp |only rARPACK-0.7-0/rARPACK/src/MatOp_symmatrix.h |only rARPACK-0.7-0/rARPACK/src/MatTypes.h |only rARPACK-0.7-0/rARPACK/src/SVDsGen.cpp |only rARPACK-0.7-0/rARPACK/src/SVDsGen.h |only rARPACK-0.7-0/rARPACK/src/SVDsSym.cpp |only rARPACK-0.7-0/rARPACK/src/SVDsSym.h |only rARPACK-0.7-0/rARPACK/src/eigs_funs.cpp |only rARPACK-0.7-0/rARPACK/src/message.cpp |only rARPACK-0.7-0/rARPACK/src/rARPACK-win.def |only rARPACK-0.7-0/rARPACK/src/svds_funs.cpp |only rARPACK-0.7-0/rARPACK/src/wrapper.f |only rARPACK-0.8-0/rARPACK/DESCRIPTION | 22 +- rARPACK-0.8-0/rARPACK/LICENSE | 2 rARPACK-0.8-0/rARPACK/MD5 | 194 +++++++------------------ rARPACK-0.8-0/rARPACK/NAMESPACE | 6 rARPACK-0.8-0/rARPACK/R/00_eigs.R | 112 ++++++++++---- rARPACK-0.8-0/rARPACK/R/10_eigs_real_gen.R | 104 ++++++------- rARPACK-0.8-0/rARPACK/R/20_eigs_real_sym.R | 62 ++++--- rARPACK-0.8-0/rARPACK/R/30_svds.R | 22 +- rARPACK-0.8-0/rARPACK/R/40_svds_real_gen.R | 32 ++-- rARPACK-0.8-0/rARPACK/R/50_svds_real_sym.R | 28 ++- rARPACK-0.8-0/rARPACK/inst/AUTHORS | 22 ++ rARPACK-0.8-0/rARPACK/inst/COPYRIGHTS | 5 rARPACK-0.8-0/rARPACK/inst/NEWS.Rd |only rARPACK-0.8-0/rARPACK/inst/include |only rARPACK-0.8-0/rARPACK/man/eigs.Rd | 30 ++- rARPACK-0.8-0/rARPACK/man/svds.Rd | 7 rARPACK-0.8-0/rARPACK/src/Makevars | 13 - rARPACK-0.8-0/rARPACK/src/Makevars.win | 13 - rARPACK-0.8-0/rARPACK/src/c_interface.c |only rARPACK-0.8-0/rARPACK/src/c_interface.h |only rARPACK-0.8-0/rARPACK/src/eigs_gen.cpp |only rARPACK-0.8-0/rARPACK/src/eigs_sym.cpp |only rARPACK-0.8-0/rARPACK/src/matops.cpp |only rARPACK-0.8-0/rARPACK/src/matops.h |only rARPACK-0.8-0/rARPACK/src/svds.cpp |only 58 files changed, 341 insertions(+), 333 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-8 dated 2015-10-24 and 1.8-9 dated 2015-10-31
ChangeLog | 6 ++++++ DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- man/gamm.Rd | 18 +++++++++++++++++- man/mgcv-parallel.Rd | 10 +++++++++- man/smooth.construct.gp.smooth.spec.Rd | 6 +++--- src/discrete.c | 33 +++++++++------------------------ src/gdi.c | 2 +- src/mat.c | 2 +- 9 files changed, 57 insertions(+), 42 deletions(-)
More information about AlgebraicHaploPackage at CRAN
Permanent link
Title: GUI Tools to Process, Analyze and Plot Fisheries Data
Description: The tools you need to process, analyze, combine, integrate and
plot your fishery data: the georeferenced dataset from the Vessel Monitoring
System (VMS), from the Automatic Information System (AIS) or other tracking
devices, as well as the catches or landings dataset from the Logbook or Vessel
Register. Package 'vmsbase' is equipped by Viewer Tools to visually inspect data
at different steps of the analyses and to produce effective outputs for reports
and scientific publications. Viewers are conceived to show the VMS pings, to
visualize single or multiple tracks for fishing vessels, or to represent the VMS
data on Google Viewer, so that the user can produce easy to interpret and more
realistic visualization of both fishing effort and effort behaviour. Package
'vmsbase' represents the implementation of several R routines which have been
developed by the "Tor Vergata" University of Rome Team involved in the Italian
National Program for the Data Collection Framework for Fisheries Data between
2009-2012.
Author: Lorenzo D'Andrea, Tommaso Russo, Antonio Parisi, Stefano Cataudella
Maintainer: Lorenzo D'Andrea <support@vmsbase.org>
Diff between vmsbase versions 2.0 dated 2015-03-10 and 2.1 dated 2015-10-30
DESCRIPTION | 25 ++- MD5 | 120 +++++++++--------- NAMESPACE | 13 +- R/fun_vms_db_clean.R | 141 ++++++++++++--------- R/gui_main.R | 4 R/gui_vms_db_cut.R | 297 ++++++++++++++++++++++++++-------------------- R/gui_vms_db_dep.R | 12 - R/gui_vms_db_intr.R | 82 ++++-------- R/gui_vms_save_bat.R | 38 +++-- R/latsex2dec.R | 14 -- R/lonsex2dec.R | 14 -- R/saveRawVms.R | 40 +++--- README.md | 23 ++- man/Assign_Area.Rd | 2 man/CountMap.Rd | 2 man/Join2shp.Rd | 2 man/bathymetry.Rd | 2 man/gui_dcf_ind.Rd | 2 man/gui_join_lb_vms.Rd | 2 man/gui_lb_db_create.Rd | 4 man/gui_lb_db_edit.Rd | 4 man/gui_lb_db_stat.Rd | 2 man/gui_lb_editraw.Rd | 6 man/gui_lb_met_cla.Rd | 2 man/gui_lb_met_dis.Rd | 4 man/gui_lb_met_edi.Rd | 4 man/gui_main.Rd | 2 man/gui_mark_fis_poi.Rd | 2 man/gui_out_grid.Rd | 4 man/gui_vms_db_are.Rd | 2 man/gui_vms_db_clean.Rd | 11 - man/gui_vms_db_create.Rd | 4 man/gui_vms_db_cut.Rd | 11 - man/gui_vms_db_dep.Rd | 13 -- man/gui_vms_db_intr.Rd | 11 - man/gui_vms_db_sel.Rd | 11 - man/gui_vms_db_stat.Rd | 11 - man/gui_vms_editraw.Rd | 6 man/gui_vms_met_pred.Rd | 11 - man/gui_vms_save_bat.Rd | 11 - man/gui_vms_view_intrp.Rd | 11 - man/gui_vms_view_ping.Rd | 11 - man/gui_vms_view_track.Rd | 11 - man/gui_vms_viz_adv.Rd | 11 - man/gui_vmsdb_mixsou.Rd | 2 man/harbCoo.Rd | 2 man/kno2kmh.Rd | 2 man/latsex2dec.Rd | 2 man/log_Cla.Rd | 2 man/log_DB.Rd | 2 man/log_File.Rd | 2 man/lonsex2dec.Rd | 2 man/plotNet.Rd | 2 man/polymap.Rd | 2 man/que_vms_DB.Rd | 2 man/rad2deg.Rd | 2 man/saveRawLogBook.Rd | 2 man/saveRawVms.Rd | 2 man/vms_DB.Rd | 2 man/vms_File.Rd | 2 man/vmsbase.Rd | 6 61 files changed, 559 insertions(+), 494 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.1.1 dated 2015-09-18 and 0.1.2 dated 2015-10-30
DESCRIPTION | 10 MD5 | 97 NAMESPACE | 3 NEWS | 12 R/utils.R | 10 R/visClustering.R | 2 R/visConfigure.R | 3 R/visDocumentation.R | 15 R/visEdges.R | 9 R/visGroups.R | 3 R/visHierarchicalLayout.R | 3 R/visInteraction.R | 3 R/visLayout.R | 5 R/visLegend.R |only R/visNetwork.R | 63 R/visNetworkEvents.R | 3 R/visNodes.R | 8 R/visOptions.R | 77 R/visPhysics.R | 5 README.md | 2 inst/doc/Introduction-to-visNetwork.R | 34 inst/doc/Introduction-to-visNetwork.Rmd | 63 inst/doc/Introduction-to-visNetwork.html | 141 - inst/doc/css/prettify.css | 172 - inst/doc/network/index.html | 3112 +++++++++++++++---------------- inst/doc/network/layout.html | 312 +-- inst/doc/network/manipulation.html | 406 ++-- inst/doc/network/nodes.html | 1429 +++++++------- inst/doc/network/physics.html | 446 ++-- inst/examples |only inst/htmlwidgets/lib/vis/vis.map | 2 inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 88 inst/htmlwidgets/visNetwork.js | 396 +++ inst/htmlwidgets/visNetwork.yaml | 2 inst/shiny/server.R | 17 man/visClusteringOutliers.Rd | 2 man/visConfigure.Rd | 3 man/visDocumentation.Rd | 4 man/visEdges.Rd | 9 man/visEvents.Rd | 3 man/visGroups.Rd | 3 man/visHierarchicalLayout.Rd | 3 man/visInteraction.Rd | 3 man/visLayout.Rd | 5 man/visLegend.Rd |only man/visNetwork.Rd | 30 man/visNodes.Rd | 8 man/visOptions.Rd | 37 man/visPhysics.Rd | 5 vignettes/Introduction-to-visNetwork.Rmd | 63 51 files changed, 3893 insertions(+), 3240 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.0.0 dated 2015-09-11 and 1.8.14 dated 2015-10-30
treescape-1.0.0/treescape/man/penEdgeTree.Rd |only treescape-1.0.0/treescape/man/penEdgeTreematch.Rd |only treescape-1.0.0/treescape/man/rcpp_hello_world.Rd |only treescape-1.0.0/treescape/src/rcpp_hello_world.cpp |only treescape-1.8.14/treescape/DESCRIPTION | 11 treescape-1.8.14/treescape/MD5 | 63 treescape-1.8.14/treescape/NAMESPACE | 5 treescape-1.8.14/treescape/R/RcppExports.R | 18 treescape-1.8.14/treescape/R/findGroves.R | 39 treescape-1.8.14/treescape/R/medTree.R | 98 treescape-1.8.14/treescape/R/metrics.R | 133 - treescape-1.8.14/treescape/R/plotGroves.R | 3 treescape-1.8.14/treescape/R/servers.R | 15 treescape-1.8.14/treescape/R/treescape.R | 68 treescape-1.8.14/treescape/README.md | 92 treescape-1.8.14/treescape/inst/shiny/server.R | 1217 +++++++--- treescape-1.8.14/treescape/inst/shiny/ui.R | 679 +++-- treescape-1.8.14/treescape/inst/shiny/www/bootstrap.simplex.css |only treescape-1.8.14/treescape/inst/shiny/www/html/help.html | 180 + treescape-1.8.14/treescape/inst/shiny/www/styles.css |only treescape-1.8.14/treescape/man/findGroves.Rd | 15 treescape-1.8.14/treescape/man/linearMrca.Rd | 10 treescape-1.8.14/treescape/man/medTree.Rd | 31 treescape-1.8.14/treescape/man/multiDist.Rd | 11 treescape-1.8.14/treescape/man/plotGroves.Rd | 4 treescape-1.8.14/treescape/man/treeDist.Rd | 16 treescape-1.8.14/treescape/man/treeVec.Rd | 12 treescape-1.8.14/treescape/man/treescape.Rd | 24 treescape-1.8.14/treescape/man/treescapeServer.Rd | 4 treescape-1.8.14/treescape/src/RcppExports.cpp | 10 treescape-1.8.14/treescape/tests/testthat/testbasics.R | 27 treescape-1.8.14/treescape/vignettes/figs/findgroves-with-emphasis-1.png |only treescape-1.8.14/treescape/vignettes/figs/treescape3d.png |only treescape-1.8.14/treescape/vignettes/figs/treescapeDensiTree.png |only treescape-1.8.14/treescape/vignettes/figs/treescapeTree.png |only treescape-1.8.14/treescape/vignettes/figs/woodmice-tip-emphasis-1.png |only treescape-1.8.14/treescape/vignettes/treescape.Rmd | 48 treescape-1.8.14/treescape/vignettes/treescape.md | 94 38 files changed, 2031 insertions(+), 896 deletions(-)
Title: Datasets for Agresti and Finlay's "Statistical Methods for the
Social Sciences"
Description: Datasets used in "Statistical Methods for the Social Sciences"
(SMSS) by Alan Agresti and Barbara Finlay.
Author: Jeffrey B. Arnold [aut, cre],
Alan Agresti [cph],
Barbara Finlay [cph]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between smss versions 1.0-1 dated 2013-08-22 and 1.0-2 dated 2015-10-30
DESCRIPTION | 15 +----- MD5 | 80 +++++++++++++++++------------------ NEWS | 7 ++- R/crime2005.R | 4 + build/partial.rdb |binary data/UNdata.rda |binary data/anorexia.rda |binary data/birth.rates.rda |binary data/crime2005.rda |binary data/fertility.gdp.rda |binary data/fl.crime.rda |binary data/house.selling.price.2.rda |binary data/house.selling.price.rda |binary data/inc.ed.race.13p1.rda |binary data/income.credit.rda |binary data/mental.impairment.rda |binary data/oecd.data.rda |binary data/statewide.crime.2.rda |binary data/student.survey.rda |binary data/us.pop.size.rda |binary data/zagat.rda |binary inst/extdata/fl-crime.csv | 10 ++-- inst/scripts/download_agresti_csv.sh | 3 - inst/scripts/save_data.R | 2 man/UNdata.Rd | 12 ++--- man/anorexia.Rd | 12 ++--- man/birth.rates.Rd | 8 +-- man/crime2005.Rd | 10 +++- man/fertility.gdp.Rd | 7 +-- man/fl.crime.Rd | 10 ++-- man/house.selling.price.2.Rd | 10 ++-- man/house.selling.price.Rd | 10 ++-- man/inc.ed.race.13p1.Rd | 10 ++-- man/income.credit.Rd | 15 ++---- man/mental.impairment.Rd | 11 ++-- man/oecd.data.Rd | 13 ++--- man/smss-package.Rd | 21 ++++----- man/statewide.crime.2.Rd | 10 +--- man/student.survey.Rd | 9 +-- man/us.pop.size.Rd | 8 ++- man/zagat.Rd | 9 ++- 41 files changed, 154 insertions(+), 152 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that can be indexed similarly to lists, e.g. 'x <- listenv(); x[[2]] <- "b"; names(x)[2] <- "B"; print(x$B)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 0.4.0 dated 2015-08-08 and 0.5.0 dated 2015-10-30
listenv-0.4.0/listenv/.Rinstignore |only listenv-0.5.0/listenv/DESCRIPTION | 8 listenv-0.5.0/listenv/MD5 | 26 +-- listenv-0.5.0/listenv/NAMESPACE | 6 listenv-0.5.0/listenv/NEWS | 12 + listenv-0.5.0/listenv/R/get_variable.R | 4 listenv-0.5.0/listenv/R/listenv.R | 225 +++++++++++++++++++++------ listenv-0.5.0/listenv/R/utils.R | 30 --- listenv-0.5.0/listenv/build |only listenv-0.5.0/listenv/inst |only listenv-0.5.0/listenv/man/as.list.listenv.Rd | 8 listenv-0.5.0/listenv/man/listenv.Rd | 18 +- listenv-0.5.0/listenv/man/map.Rd | 42 ++--- listenv-0.5.0/listenv/tests/get_variable.R | 16 + listenv-0.5.0/listenv/tests/listenv.R | 171 ++++++++++++++++++++ listenv-0.5.0/listenv/vignettes |only 16 files changed, 439 insertions(+), 127 deletions(-)
Title: Kernel Estimator and Bandwidth Selection for Density and Its
Derivatives
Description: Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
Author: Arsalane Chouaib Guidoum
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between kedd versions 1.0.2 dated 2015-01-28 and 1.0.3 dated 2015-10-30
DESCRIPTION | 11 +++++---- MD5 | 53 ++++++++++++++++++++++++------------------------ NAMESPACE | 4 +++ NEWS | 2 + build/vignette.rds |binary inst/doc/Thumbs.db |only inst/doc/intro.Rnw | 2 - inst/doc/intro.pdf |binary inst/doc/kedd.Rnw | 8 +++---- inst/doc/kedd.pdf |binary man/dkde.Rd | 2 - man/h.bcv.Rd | 2 - man/h.ucv.Rd | 2 - man/kedd-package.Rd | 6 ++--- man/kernel.conv.Rd | 2 - man/kernel.fun.Rd | 2 - man/plot.dkde.Rd | 4 +-- man/plot.h.amise.Rd | 2 - man/plot.h.bcv.Rd | 2 - man/plot.h.ccv.Rd | 2 - man/plot.h.mcv.Rd | 2 - man/plot.h.mlcv.Rd | 2 - man/plot.h.tcv.Rd | 2 - man/plot.h.ucv.Rd | 2 - man/plot.kernel.conv.Rd | 2 - man/plot.kernel.fun.Rd | 2 - vignettes/intro.Rnw | 2 - vignettes/kedd.Rnw | 8 +++---- 28 files changed, 68 insertions(+), 60 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are
implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.5.0 dated 2015-10-05 and 0.5.1 dated 2015-10-30
DESCRIPTION | 10 ++++--- MD5 | 42 ++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 8 ++++++ R/downstream.R | 10 +++---- R/gvc.R | 6 ++++ R/nrca.R | 23 ++++++++++++++++++ R/upstream.R | 10 +++---- README.md | 5 +++ inst/doc/gvc.R | 5 ++- inst/doc/gvc.Rmd | 9 +++---- inst/doc/gvc.html | 69 ++++++++++++++++++++---------------------------------- man/dfddva.Rd | 4 +-- man/dfdfva.Rd | 2 - man/downstream.Rd | 14 +++++----- man/e2r.Rd | 4 +-- man/ffddva.Rd | 2 - man/gvc.Rd | 4 +-- man/i2e.Rd | 4 +-- man/nrca.Rd | 25 ++++++++++++++++++- man/upstream.Rd | 14 +++++----- vignettes/gvc.Rmd | 9 +++---- 22 files changed, 167 insertions(+), 114 deletions(-)
Title: Dynamic Nomograms for Linear, Generalized Linear and
Proportional Hazard Models
Description: Demonstrate the results of an lm(), glm() or coxph() model object as a dynamic nomogram that can be displayed in an 'RStudio' panel or web browser.
Author: Amirhossein Jalali, Alberto Alvarez-Iglesias, Davood Roshan Sangachin, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>
Diff between DynNom versions 1.0.1 dated 2015-03-09 and 2.0 dated 2015-10-30
DynNom-1.0.1/DynNom/man/DynNom-package.Rd |only DynNom-2.0/DynNom/DESCRIPTION | 21 - DynNom-2.0/DynNom/MD5 | 15 - DynNom-2.0/DynNom/NAMESPACE | 9 DynNom-2.0/DynNom/R/DynNom.R | 393 +++++------------------------- DynNom-2.0/DynNom/R/DynNom_coxph.R |only DynNom-2.0/DynNom/R/DynNom_glm.R |only DynNom-2.0/DynNom/R/DynNom_lm.R |only DynNom-2.0/DynNom/man/DynNom.Rd | 65 +++- DynNom-2.0/DynNom/man/DynNom.coxph.Rd |only DynNom-2.0/DynNom/man/DynNom.glm.Rd |only DynNom-2.0/DynNom/man/DynNom.lm.Rd |only 12 files changed, 139 insertions(+), 364 deletions(-)
Title: CShapes Dataset and Utilities
Description: Package for CShapes, a GIS dataset of country boundaries (1946-2015). Includes functions for data extraction and the computation of distance matrices and -lists.
Author: Nils B. Weidmann <nils.weidmann@uni-konstanz.de>, Kristian Skrede Gleditsch <ksg@essex.ac.uk>
Maintainer: Nils B. Weidmann <nils.weidmann@uni-konstanz.de>
Diff between cshapes versions 0.4-2 dated 2013-05-07 and 0.5-1 dated 2015-10-30
cshapes-0.4-2/cshapes/inst/shp/cshapes.qpj |only cshapes-0.4-2/cshapes/inst/shp/cshapes.sbn |only cshapes-0.4-2/cshapes/inst/shp/cshapes.sbx |only cshapes-0.4-2/cshapes/inst/shp/cshapes.shp.xml |only cshapes-0.5-1/cshapes/ChangeLog | 5 + cshapes-0.5-1/cshapes/DESCRIPTION | 17 ++-- cshapes-0.5-1/cshapes/MD5 | 22 ++--- cshapes-0.5-1/cshapes/R/cshp.R | 2 cshapes-0.5-1/cshapes/R/distlist.R | 2 cshapes-0.5-1/cshapes/R/distmatrix.R | 2 cshapes-0.5-1/cshapes/inst/shp/cshapes.dbf |binary cshapes-0.5-1/cshapes/inst/shp/cshapes.shp |binary cshapes-0.5-1/cshapes/inst/shp/cshapes_shapefile_documentation.txt | 37 +++++++--- cshapes-0.5-1/cshapes/man/cshapes-package.Rd | 4 - 14 files changed, 53 insertions(+), 38 deletions(-)
Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as defined by Kalbfleisch and Prentice. The underlying survival functions of the event of interest in each group can be estimated using either the (weighted) Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition probabilities in Markov multi-state models. Right-censored and left-truncated data is supported. Moreover, the difference in restricted mean survival can be estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AHR versions 1.2 dated 2015-07-05 and 1.3 dated 2015-10-30
AHR-1.2/AHR/TODO |only AHR-1.3/AHR/DESCRIPTION | 8 ++++---- AHR-1.3/AHR/MD5 | 11 +++++------ AHR-1.3/AHR/R/AHR-package.R | 2 +- AHR-1.3/AHR/R/ahr.R | 34 ++++++++++++++++++++-------------- AHR-1.3/AHR/R/util.R | 2 +- AHR-1.3/AHR/src/prodlim.cpp | 1 - 7 files changed, 31 insertions(+), 27 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.47 dated 2015-06-15 and 1.48 dated 2015-10-29
Changelog | 65 +++++++++ DESCRIPTION | 12 - MD5 | 46 +++--- NAMESPACE | 20 ++ R/Functions.R | 272 +++++++++++++++++++++++---------------- R/blockwiseModulesC.R | 92 +++++++++++-- R/consensusTOM.R | 5 R/empiricalBayesLM.R | 18 ++ R/internalConstants.R | 2 R/labelPoints.R | 8 - R/useNThreads.R | 2 man/WGCNA-package.Rd | 4 man/bicovWeights.Rd | 13 + man/blockSize.Rd | 2 man/blockwiseConsensusModules.Rd | 2 man/consensusKME.Rd | 3 man/consensusProjectiveKMeans.Rd | 5 man/labelPoints.Rd | 8 - man/mergeCloseModules.Rd | 2 man/moduleEigengenes.Rd | 2 man/multiSetMEs.Rd | 6 man/projectiveKMeans.Rd | 5 src/corFunctions-unified.c | 8 - src/networkFunctions.c | 2 24 files changed, 429 insertions(+), 175 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-2 dated 2015-10-01 and 0.1-3 dated 2015-10-29
DESCRIPTION | 24 +++++---- MD5 | 112 ++++++++++++++++++++++++++------------------- NAMESPACE | 9 +++ R/ants-data.R |only R/dispersion.R |only R/download.prism.R | 22 +++++--- R/gaussian.kernel.R |only R/insert.values.R |only R/land.metrics.R | 79 +++++++++++++++++++------------ R/pu-data.R |only R/sample.line.R | 16 ++++-- R/sample.poly.R |only R/shannons.R |only R/similarity.R |only R/tri.R |only data |only inst/NEWS | 15 +++++- man/ants.Rd |only man/bearing.distance.Rd | 12 +++- man/breeding.density.Rd | 30 +++++++----- man/concordance.Rd | 32 ++++++++---- man/conf.interval.Rd | 20 ++++---- man/correlogram.Rd | 23 +++++---- man/csi.Rd | 23 +++++---- man/dispersion.Rd |only man/download.daymet.Rd | 39 ++++++++++----- man/download.hansen.Rd | 20 +++++--- man/download.prism.Rd | 24 ++++++--- man/gaussian.kernel.Rd |only man/group.pdf.Rd | 15 ++++-- man/hexagons.Rd | 16 ++++-- man/idw.smoothing.Rd | 30 +++++++----- man/insert.values.Rd |only man/kl.divergence.Rd | 13 +++-- man/land.metrics.Rd | 67 ++++++++++++++++---------- man/local.min.max.Rd | 20 +++++--- man/loess.boot.Rd | 51 ++++++++++++-------- man/loess.ci.Rd | 26 ++++++---- man/logistic.regression.Rd | 61 ++++++++++++++---------- man/moments.Rd | 40 ++++++++-------- man/nni.Rd | 14 ++++- man/o.ring.Rd | 19 +++++-- man/optimal.k.Rd | 14 ++++- man/outliers.Rd | 24 ++++++--- man/parea.sample.Rd | 21 +++++--- man/plot.loess.boot.Rd | 16 ++++-- man/point.in.poly.Rd | 25 ++++++---- man/pp.subsample.Rd | 48 ++++++++++++------- man/print.loess.boot.Rd | 2 man/pseudo.absence.Rd | 52 ++++++++++++-------- man/pu.Rd |only man/raster.entropy.Rd | 16 ++++-- man/raster.vol.Rd | 21 +++++--- man/sample.line.Rd | 39 ++++++++------- man/sample.poly.Rd |only man/separability.Rd | 61 ++++++++++++++---------- man/shannons.Rd |only man/similarity.Rd |only man/sp.na.omit.Rd | 20 ++++---- man/stratified.random.Rd | 19 +++++-- man/summary.loess.boot.Rd | 2 man/tpi.Rd | 18 ++++--- man/trend.line.Rd | 6 ++ man/tri.Rd |only man/wt.centroid.Rd | 26 ++++++---- man/zonal.stats.Rd | 43 ++++++++++------- 66 files changed, 848 insertions(+), 497 deletions(-)
Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 2.9 dated 2014-09-10 and 3.0 dated 2015-10-29
DESCRIPTION | 14 +++--- LICENCE | 2 MD5 | 62 +++++++++++++------------- NAMESPACE | 17 ++++++- NEWS | 3 + R/STS.R | 8 +-- R/zzz.r | 2 build/vignette.rds |binary demo/Sim.DiffProc.R | 38 ++++++++++++++++ inst/doc/FitSDE.Rnw | 2 inst/doc/FitSDE.pdf |binary inst/doc/Introduction.R | 6 +- inst/doc/Introduction.Rnw | 20 ++++---- inst/doc/Introduction.pdf |binary inst/doc/SDEs.R | 81 +++++++++++++++++++++++++--------- inst/doc/SDEs.Rnw | 102 +++++++++++++++++++++++++++++++------------- inst/doc/SDEs.pdf |binary inst/doc/Thumbs.db |only man/Sim.DiffProc-package.Rd | 21 +++------ man/bridgesde1d.Rd | 1 man/bridgesde2d.Rd | 1 man/bridgesde3d.Rd | 1 man/fitsde.Rd | 2 man/plot2d.Rd | 2 man/snssde1d.Rd | 2 man/snssde2d.Rd | 2 man/snssde3d.Rd | 2 src/Sim.DiffProc.c | 24 ++-------- vignettes/Core_FitSDE.tex | 22 ++++----- vignettes/FitSDE.Rnw | 2 vignettes/Introduction.Rnw | 20 ++++---- vignettes/SDEs.Rnw | 102 +++++++++++++++++++++++++++++++------------- vignettes/Thumbs.db |only 33 files changed, 365 insertions(+), 196 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as Ghostscript is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.4-3 dated 2015-09-20 and 0.4-4 dated 2015-10-29
DESCRIPTION | 21 +++++++++++---------- MD5 | 14 +++++++------- inst/NEWS.Rd | 8 +++++++- man/showtext.auto.Rd | 2 +- man/showtext.begin.Rd | 10 +++++----- man/showtext.end.Rd | 2 +- man/showtext.opts.Rd | 10 +++++----- src/devfuns.c | 35 +++++++++++++++++++---------------- 8 files changed, 56 insertions(+), 46 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.16 dated 2015-04-08 and 1.17 dated 2015-10-29
DESCRIPTION | 8 +- MD5 | 28 ++++--- NAMESPACE | 9 +- R/ancRECON.R | 196 ++++++++++++++++++++++++++++++-------------------- R/corDISC.R | 77 +++++++++++-------- R/corHMM.R | 43 ++++++---- R/corPAINT.R | 67 +++++++++-------- R/lewisMkv.R |only R/rayDISC.R | 82 +++++++++++--------- R/readNexusMorph.R |only man/ancRECON.Rd | 7 - man/corDISC.Rd | 8 +- man/corHMM.Rd | 12 ++- man/corPAINT.Rd | 2 man/lewisMkv.Rd |only man/rayDISC.Rd | 4 - man/readNexusMorph.Rd |only 17 files changed, 319 insertions(+), 224 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids). Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA. 'Analytical methods for disease association studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.1 dated 2015-06-13 and 1.1.1 dated 2015-10-29
DESCRIPTION | 8 MD5 | 22 - NAMESPACE | 5 R/A_ExonPtnAlign_functions.R | 2 R/BIGDAWG.R | 934 +++++++++++++++++++++---------------------- R/update_wrapper.R | 7 build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 6 inst/doc/BIGDAWG.html | 14 man/BIGDAWG.Rd | 6 man/UpdateRelease.Rd | 4 vignettes/BIGDAWG.Rmd | 6 12 files changed, 510 insertions(+), 504 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-20 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-22 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-29 2.1.1
2015-07-28 2.1
2015-05-14 2.0
2015-03-21 1.3
2015-01-10 1.1
2014-12-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-13 1.1.1
2014-05-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-12 1.1.3
2014-01-24 1.1.2
2013-04-06 1.1.1
2013-03-05 1.1
2013-02-25 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-07 1.1.3
2013-09-12 1.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-02 1.1
2013-11-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-12 1.7-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-20 1.01
2012-10-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-28 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-17 0.1.3
2014-12-04 0.1.1
2014-11-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-01 1.0.12
2015-06-19 1.0.8
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation
functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions,
(vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions.
A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the
installation directory for 'dae', describes the use of the package for generating randomized
layouts for experiments. The ANOVA functions facilitate the extraction of information when
the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-2 dated 2015-06-24 and 2.7-5 dated 2015-10-29
dae-2.7-2/dae/R/proj.canon.v3.r |only dae-2.7-2/dae/R/projs.canon.v3.r |only dae-2.7-5/dae/DESCRIPTION | 11 +++-- dae-2.7-5/dae/MD5 | 38 ++++++++++--------- dae-2.7-5/dae/NAMESPACE | 9 ++++ dae-2.7-5/dae/R/Interaction.ABC.Plot.r | 12 ++++-- dae-2.7-5/dae/R/NoReps.r | 59 +++++++++++++++++++++++++++--- dae-2.7-5/dae/R/mat.functions.r | 2 - dae-2.7-5/dae/R/proj.canon.v4.r |only dae-2.7-5/dae/R/projs.canon.v4.r |only dae-2.7-5/dae/build |only dae-2.7-5/dae/inst/NEWS.Rd | 22 +++++++++++ dae-2.7-5/dae/inst/doc/dae-manual.pdf |binary dae-2.7-5/dae/man/dae-package.Rd | 23 ++++------- dae-2.7-5/dae/man/detect.diff.Rd |only dae-2.7-5/dae/man/efficiency.criteria.Rd | 17 +++++--- dae-2.7-5/dae/man/interaction.ABC.plot.Rd | 23 ++++++++--- dae-2.7-5/dae/man/no.reps.Rd | 10 ++--- dae-2.7-5/dae/man/power.exp.Rd | 2 - dae-2.7-5/dae/man/projs.canon.Rd | 27 +++++++++---- dae-2.7-5/dae/man/projs.structure.Rd | 47 ++++++++++++++++------- dae-2.7-5/dae/man/summary.p2canon.Rd | 26 +++++++------ dae-2.7-5/dae/man/summary.pcanon.Rd | 20 +++++----- 23 files changed, 239 insertions(+), 109 deletions(-)
Title: Learning Bayesian Network Classifiers from Data
Description: Implementation of different algorithms for learning discrete Bayesian network classifiers from data, including wrapper algorithms and those based on Chow-Liu's algorithm.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut]
Maintainer: Mihaljevic Bojan <bmihaljevic@fi.upm.es>
Diff between bnclassify versions 0.3.0 dated 2015-07-30 and 0.3.1 dated 2015-10-29
DESCRIPTION | 9 +++--- MD5 | 42 ++++++++++++++++++----------- NAMESPACE | 1 R/0bnclassify-doc.R | 45 ++++++++++++++++++++++++------- R/bnc-dag-operate.R | 10 +++++- R/learn-params-awnb.R | 2 - R/learn-params.R | 2 - README.md | 2 - build/vignette.rds |binary man/bnc.Rd | 4 +- man/cv.Rd | 4 +- man/learn_params.Rd | 53 +++++++++++++++++++++++++------------ man/plot.bnc_dag.Rd | 4 ++ man/wrapper.Rd | 4 +- tests/testthat/test-learn-params.R | 11 +++++++ tests/testthat/test-wrap-grain.R | 6 ++-- vignettes/bnclassify.Rmd | 27 +++++++++++------- vignettes/bnclassify_cache |only 18 files changed, 154 insertions(+), 72 deletions(-)
Title: Augments the Use of 'Asreml' in Fitting Mixed Models
Description: Assists in automating the testing of terms in mixed models when 'asreml' is used
to fit the models. The content falls into the following natural groupings: (i) Data, (ii) Object
manipulation functions, (iii) Model modification functions, (iv) Model testing functions,
(v) Model diagnostics functions, (vi) Prediction production and presentation functions,
(vii) Response transformation functions, and (viii) Miscellaneous functions. A history of the
fitting of a sequence of models is kept in a data frame. Procedures are available for choosing
models that conform to the hierarchy or marginality principle and for displaying predictions
for significant terms in tables and graphs. The package 'asreml' provides a computationally
efficient algorithm for fitting mixed models using Residual Maximum Likelihood. It can be
purchased from 'VSNi' (http://www.vsni.co.uk/) as 'asreml-R', who will supply a zip file for
local installation/updating.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between asremlPlus versions 2.0-0 dated 2015-06-24 and 2.0-2 dated 2015-10-29
DESCRIPTION | 10 ++--- MD5 | 26 +++++++------- NAMESPACE | 8 +++- R/reml.v19.r | 76 +++++++++++++++++++++++++++++++++++++---- R/variogram.faces.v2.r | 6 ++- build |only inst/NEWS.Rd | 14 +++++++ inst/doc/asremlPlus-manual.pdf |binary man/addrm.terms.asrtests.Rd | 10 ++++- man/asremlPlus-package.Rd | 22 +++++------ man/newrcov.asrtests.Rd |only man/pred.present.asreml.Rd | 9 ++-- man/predictionplot.asreml.Rd | 11 +++-- man/testrcov.asrtests.Rd | 13 +++---- man/variofaces.Rd | 11 ++++- 15 files changed, 160 insertions(+), 56 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut]
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan3d versions 0.65-1 dated 2015-05-27 and 1.0-0 dated 2015-10-29
vegan3d-0.65-1/vegan3d/README.md |only vegan3d-1.0-0/vegan3d/DESCRIPTION | 10 - vegan3d-1.0-0/vegan3d/MD5 | 38 ++-- vegan3d-1.0-0/vegan3d/NAMESPACE | 15 + vegan3d-1.0-0/vegan3d/R/ordiplot3d.R | 11 + vegan3d-1.0-0/vegan3d/R/ordirgl.R | 33 +++- vegan3d-1.0-0/vegan3d/R/orditree3d.R |only vegan3d-1.0-0/vegan3d/R/orglellipse.R |only vegan3d-1.0-0/vegan3d/R/orglpoints.R | 18 +- vegan3d-1.0-0/vegan3d/R/orglsegments.R | 20 ++ vegan3d-1.0-0/vegan3d/R/orglspantree.R |only vegan3d-1.0-0/vegan3d/R/orglspider.R | 16 +- vegan3d-1.0-0/vegan3d/R/orgltext.R | 12 + vegan3d-1.0-0/vegan3d/R/rgl.isomap.R | 16 +- vegan3d-1.0-0/vegan3d/R/rgl.renyiaccum.R | 5 vegan3d-1.0-0/vegan3d/R/scores.ordiplot3d.R |only vegan3d-1.0-0/vegan3d/build |only vegan3d-1.0-0/vegan3d/inst |only vegan3d-1.0-0/vegan3d/man/ordiplot3d.Rd | 123 ++++++++------- vegan3d-1.0-0/vegan3d/man/ordirgl.Rd | 208 +++++++++++++++++---------- vegan3d-1.0-0/vegan3d/man/orditree3d.Rd |only vegan3d-1.0-0/vegan3d/man/rgl.isomap.Rd | 32 ++-- vegan3d-1.0-0/vegan3d/man/rgl.renyiaccum.Rd | 6 vegan3d-1.0-0/vegan3d/man/vegan3d-package.Rd |only 24 files changed, 360 insertions(+), 203 deletions(-)
Title: Laplace Deconvolution with Noisy Discrete Non-Equally Spaced
Observations on a Finite Time Interval
Description: Solves the problem of Laplace deconvolution with noisy discrete non-equally spaced observations on a finite time interval based on expansions of the convolution kernel, the unknown function and the observed signal over Laguerre functions basis. It implements the methodology proposed in the paper "Laplace deconvolution on the basis of time domain data and its application to Dynamic Contrast Enhanced imaging" by F. Comte, C-A. Cuenod, M. Pensky and Y. Rozenholc in ArXiv (http://arxiv.org/abs/1405.7107).
Author: Yves Rozenholc (University Paris Descartes), Marianna Pensky (University of Central Florida)
Maintainer: Yves Rozenholc <yves.rozenholc@parisdescartes.fr>
Diff between LaplaceDeconv versions 1.0.1 dated 2015-10-29 and 1.0.2 dated 2015-10-29
DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/LagLaplaceDeconvolution.R | 62 +++++++++++++++++--------------------------- man/LagLaplDeconv.Rd | 36 ++++++++++++------------- 4 files changed, 48 insertions(+), 64 deletions(-)
Title: Statistical Inference of C- And D-Vine Copulas
Description: Functions for statistical inference of canonical vine (C-vine)
and D-vine copulas. Tools for bivariate exploratory data analysis and for bivariate
as well as vine copula selection are provided. Models can be estimated
either sequentially or by joint maximum likelihood estimation.
Sampling algorithms and plotting methods are also included.
Data is assumed to lie in the unit hypercube (so-called copula
data).
Author: Ulf Schepsmeier, Eike Christian Brechmann
Maintainer: Tobias Erhardt
<tobias.erhardt@tum.de>
Diff between CDVine versions 1.3 dated 2015-07-30 and 1.4 dated 2015-10-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/zzz.R | 5 +++++ man/CDVine-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Data Supporting the 'VGAM' Package
Description: Data sets to accompany the VGAM package and
the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015).
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology).
Author: Thomas Yee [aut, cre, cph],
James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAMdata versions 0.9-7 dated 2015-03-17 and 1.0-0 dated 2015-10-29
DESCRIPTION | 20 +++++++++------ MD5 | 68 ++++++++++++++++++++++++++------------------------- NAMESPACE | 6 ++++ NEWS | 18 +++++++++++++ R/family.fishing.R | 51 ++++---------------------------------- data/bb.de.rda |binary data/bd.us.rda |only data/belcap.rda |binary data/crashf.au.rda |binary data/crime.us.rda |binary data/datalist | 1 data/exam1.rda |binary data/fibre15.rda |binary data/fibre1dot5.rda |binary data/gala.rda |binary data/hued.rda |binary data/huie.rda |binary data/huse.rda |binary data/oly12.rda |binary data/prison.us.rda |binary data/profs.nz.rda |binary data/rainfall.rda |binary data/rugby.rda |binary data/rugby.ties.rda |binary data/students.tw.rda |binary data/trapO.rda |binary data/tube10.rda |binary data/ugss.rda |binary data/vtinpat.rda |binary data/wffc.indiv.rda |binary data/wffc.nc.rda |binary data/wffc.rda |binary data/wffc.teams.rda |binary data/xs.nz.rda |binary inst/CITATION | 39 +++++++++++++++++++++++++++++ man/bd.us.Rd |only 36 files changed, 118 insertions(+), 85 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes, and the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
gives details of the statistical framework and VGAM package.
Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 0.9-8 dated 2015-05-11 and 1.0-0 dated 2015-10-29
ChangeLog |only DESCRIPTION | 20 - LICENCE.note |only MD5 | 263 +++++++------- NAMESPACE | 68 +++ NEWS | 63 +++ R/Links.R | 14 R/build.terms.vlm.q | 36 + R/calibrate.q | 15 R/coef.vlm.q | 9 R/confint.vlm.R |only R/family.aunivariate.R | 20 - R/family.basics.R | 30 + R/family.binomial.R | 147 +++++-- R/family.bivariate.R | 66 ++- R/family.categorical.R | 37 + R/family.censored.R | 268 ++++++++++++++ R/family.circular.R | 4 R/family.exp.R | 2 R/family.extremes.R | 14 R/family.genetic.R | 20 - R/family.glmgam.R | 70 ++- R/family.loglin.R | 4 R/family.mixture.R | 8 R/family.nonlinear.R | 4 R/family.normal.R | 758 ++++++++++++++++++++++++++-------------- R/family.others.R | 12 R/family.positive.R | 31 - R/family.qreg.R | 144 ++++--- R/family.rcim.R | 25 + R/family.robust.R | 2 R/family.rrr.R | 317 ++++++++--------- R/family.survival.R | 4 R/family.ts.R | 130 ++++--- R/family.univariate.R | 199 ++++++---- R/family.zeroinf.R | 31 + R/formula.vlm.q | 99 +++++ R/links.q | 797 +++++++++++++++++++++++-------------------- R/model.matrix.vglm.q | 38 +- R/qtplot.q | 20 - R/summary.vglm.q | 39 +- R/vglm.R | 6 R/vglm.fit.q | 2 R/vlm.wfit.q | 2 build/vignette.rds |binary data/Huggins89.t1.rda |binary data/Huggins89table1.rda |binary data/alclevels.rda |binary data/alcoff.rda |binary data/auuc.rda |binary data/backPain.rda |binary data/beggs.rda |binary data/car.all.rda |binary data/cfibrosis.rda |binary data/corbet.rda |binary data/crashbc.rda |binary data/crashf.rda |binary data/crashi.rda |binary data/crashmc.rda |binary data/crashp.rda |binary data/crashtr.rda |binary data/deermice.rda |binary data/ducklings.rda |binary data/finney44.rda |binary data/flourbeetle.rda |binary data/hspider.rda |binary data/lakeO.rda |binary data/leukemia.rda |binary data/marital.nz.rda |binary data/melbmaxtemp.rda |binary data/pneumo.rda |binary data/prinia.rda |binary data/ruge.rda |binary data/toxop.rda |binary data/venice.rda |binary data/venice90.rda |binary data/wine.rda |binary inst/CITATION | 61 ++- inst/doc/categoricalVGAM.pdf |binary inst/doc/crVGAM.R | 4 inst/doc/crVGAM.Rnw | 46 +- inst/doc/crVGAM.pdf |binary man/AA.Aa.aa.Rd | 1 man/AR1.Rd | 11 man/CommonVGAMffArguments.Rd | 29 + man/Links.Rd | 127 +++++- man/SURff.Rd | 2 man/VGAM-package.Rd | 9 man/acat.Rd | 4 man/alaplace3.Rd | 7 man/betabinomUC.Rd | 20 + man/binomialff.Rd | 10 man/binormal.Rd | 10 man/brat.Rd | 4 man/bratUC.Rd | 4 man/cauchit.Rd | 2 man/cens.poisson.Rd | 32 + man/cloglog.Rd | 5 man/confintvglm.Rd |only man/cratio.Rd | 4 man/cumulative.Rd | 6 man/explink.Rd | 2 man/fisherz.Rd | 2 man/foldsqrt.Rd | 2 man/formulavlm.Rd |only man/gengamma.Rd | 10 man/golf.Rd | 22 - man/has.intercept.Rd |only man/identitylink.Rd | 2 man/logc.Rd | 2 man/loge.Rd | 2 man/logit.Rd | 18 man/lognormal.Rd | 6 man/multilogit.Rd | 2 man/multinomial.Rd | 4 man/nbcanlink.Rd | 19 - man/nbolf.Rd | 16 man/negbinomial.Rd | 16 man/notdocumentedyet.Rd | 34 + man/polf.Rd | 17 man/posnormal.Rd | 69 ++- man/probit.Rd | 2 man/propodds.Rd | 2 man/rayleigh.Rd | 3 man/rhobit.Rd | 7 man/sratio.Rd | 6 man/summaryvglm.Rd |only man/tobit.Rd | 100 ++--- man/triangle.Rd | 9 man/undocumented-methods.Rd | 12 man/vcovvlm.Rd |only man/vglm.Rd | 17 man/weibull.mean.Rd |only man/weibullR.Rd | 1 man/wine.Rd | 6 vignettes/crVGAM.Rnw | 46 +- vignettes/crVGAM.bib | 20 + 137 files changed, 3133 insertions(+), 1579 deletions(-)
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with SparseM/Matrix are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within GMRF.
(4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 1.2-1 dated 2015-09-30 and 1.3-0 dated 2015-10-29
ChangeLog | 36 ++++++++++ DESCRIPTION | 8 +- MD5 | 80 +++++++++++------------ R/definitions.R | 2 R/math.R | 103 +++++++++++++++--------------- inst/NEWS | 21 +++++- man/allequal.Rd | 7 -- man/nearestdist.Rd | 10 +- man/operations.Rd | 4 + man/rdist.Rd | 13 +++ tests/constructors.Rout.save | 4 - tests/covmat.Rout.save | 4 - tests/crossprod.Rout.save | 4 - tests/demo_article-jss-example1.Rout.save | 4 - tests/demo_article-jss-example2.Rout.save | 4 - tests/demo_article-jss.Rout.save | 4 - tests/demo_cholesky.Rout.save | 4 - tests/demo_jss15-BYM.Rout.save | 4 - tests/demo_jss15-Leroux.Rout.save | 4 - tests/demo_spam.Rout.save | 4 - tests/demo_timing.Rout.save | 4 - tests/diff.Rout.save | 4 - tests/dim.Rout.save | 4 - tests/displays.Rout.save | 4 - tests/dist.Rout.save | 4 - tests/foreign.Rout.save | 2 tests/helper.Rout.save | 4 - tests/jss_areal_counts.Rout.save | 4 - tests/kronecker.Rout.save | 4 - tests/math.R | 18 ++++- tests/math.Rout.save | 22 +++++- tests/mle.Rout.save | 4 - tests/norm.Rout.save | 4 - tests/ops.Rout.save | 5 - tests/overall.Rout.save | 4 - tests/permutation.Rout.save | 4 - tests/rowcolstats.Rout.save | 4 - tests/solve.Rout.save | 4 - tests/spamlist.Rout.save | 4 - tests/subsetting.Rout.save | 4 - tests/xybind.Rout.save | 4 - 41 files changed, 266 insertions(+), 173 deletions(-)
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Title: Online Principal Component Analysis
Description: Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between onlinePCA versions 1.2 dated 2015-08-12 and 1.3 dated 2015-10-29
DESCRIPTION | 12 ++++---- MD5 | 52 +++++++++++++++++++----------------- NAMESPACE | 12 ++++---- NEWS | 16 ++++++++++- R/batchpca.R | 23 +++++++++++----- R/bsoipca.R |only R/incRpca.R | 2 - R/incRpca.block.R |only R/incRpca.rc.R | 2 - R/perturbationRpca.R | 2 - R/secularRpca.R | 35 +++++++++++++++++------- man/batchpca.Rd | 63 +++++++++++++++++++------------------------- man/bsoipca.Rd |only man/ccipca.Rd | 33 +++++++++++------------ man/coef2fd.Rd | 24 ++++------------ man/create.basis.Rd | 41 +++++++++------------------- man/fd2coef.Rd | 26 ++++-------------- man/ghapca.Rd | 19 ++++--------- man/impute.Rd | 2 - man/incRpca.Rd | 47 ++++++++++++++------------------ man/incRpca.block.Rd |only man/incRpca.rc.Rd | 67 +++++++++++++++++++++-------------------------- man/onlinePCA-package.Rd | 10 ++----- man/perturbationRpca.Rd | 50 ++++++++++++++--------------------- man/secularRpca.Rd | 31 +++++++-------------- man/sgapca.Rd | 19 ++++--------- man/snlpca.Rd | 36 ++++++++----------------- man/updateCovariance.Rd | 10 +++---- man/updateMean.Rd | 13 ++++----- 29 files changed, 293 insertions(+), 354 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation and non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the ML viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.3-0 dated 2015-10-24 and 1.3-2 dated 2015-10-29
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/25-addControlList.R | 19 +++++++++++++------ R/maxBFGS.R | 2 +- R/maxBFGSR.R | 2 +- R/maxCG.R | 2 +- R/maxNM.R | 2 +- R/maxNR.R | 2 +- R/maxOptim.R | 2 +- R/maxSANN.R | 2 +- man/maxNR.Rd | 2 +- 12 files changed, 41 insertions(+), 29 deletions(-)
Title: Purge Training Data from Models
Description: Enables the removal of training data from fitted R models while
retaining predict functionality. The purged models are more portable as their
memory footprints do not scale with the training sample size.
Author: Marc Maier [cre],
Chaoqun Jia [ctb],
MassMutual Advanced Analytics [aut] (http://datascience.massmutual.com)
Maintainer: Marc Maier <mmaier@massmutual.com>
Diff between purge versions 0.1.0 dated 2015-09-02 and 0.2.0 dated 2015-10-28
DESCRIPTION | 22 +++--- MD5 | 12 +-- NAMESPACE | 7 -- R/purge.R | 29 +++++++- man/purge.Rd | 13 +++ tests/purged.filesizes.R | 15 ++++ tests/testthat/test.purge.R | 148 +++++++++++++++++++++++++++++++------------- 7 files changed, 181 insertions(+), 65 deletions(-)
Title: Wild Scale-Enhanced Bootstrap
Description: Perform the Wild Scale-Enhanced (WiSE) bootstrap. Specifically, the user may supply a single or multiple equally-spaced time series and use the WiSE bootstrap to select a wavelet-smoothed model. Conversely, a pre-selected smooth level may also be specified for the time series. Quantities such as the bootstrap sample of wavelet coefficients, smoothed bootstrap samples, and specific hypothesis testing and confidence region results of the wavelet coefficients may be obtained. Additional functions are available to the user which help format the time series before analysis. This methodology is recommended to aid in model selection and signal extraction.
Note: This package specifically uses wavelet bases in the WiSE bootstrap methodology, but the theoretical construct is much more versatile.
Author: Megan Heyman, Snigdhansu Chatterjee
Maintainer: Megan Heyman <heyma029@umn.edu>
Diff between WiSEBoot versions 1.2.0 dated 2015-09-05 and 1.3.0 dated 2015-10-28
DESCRIPTION | 10 +- MD5 | 44 ++++----- NAMESPACE | 5 - NEWS | 17 +++ R/WiSEBoot.R | 53 ++++++++++- R/WiSEHypothesisTest.R | 52 +++++++++-- R/smoothTimeSeries.R | 7 + inst/doc/WiSEBoot_Examples_Vignette.R | 11 +- inst/doc/WiSEBoot_Examples_Vignette.Rnw | 138 ++++++++++++++++++++++--------- inst/doc/WiSEBoot_Examples_Vignette.pdf |binary man/SimulatedSNR0.5Series.Rd | 2 man/SimulatedSNR1.0Series.Rd | 2 man/SimulatedSNR1.5Series.Rd | 2 man/SimulatedSNR2.0Series.Rd | 2 man/SimulatedSmoothSeries.Rd | 2 man/WiSEBoot-package.Rd | 16 +-- man/WiSEBoot.Rd | 38 +++++--- man/WiSEConfidenceRegion.Rd | 17 ++- man/WiSEHypothesisTest.Rd | 31 ++++-- man/padMatrix.Rd | 2 man/padVector.Rd | 2 man/smoothTimeSeries.Rd | 2 vignettes/WiSEBoot_Examples_Vignette.Rnw | 138 ++++++++++++++++++++++--------- 23 files changed, 416 insertions(+), 177 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.2-1 dated 2015-09-09 and 1.2-2 dated 2015-10-28
DESCRIPTION | 16 +-- MD5 | 124 ++++++++++++------------- R/AAA.R | 2 R/DSC_DBSTREAM.R | 2 R/DSC_DStream.R | 2 R/DSD_Memory.R | 4 R/evaluate.R | 23 +++- inst/NEWS | 9 + inst/doc/stream.R | 203 +++++++++++++++--------------------------- inst/doc/stream.Rnw | 90 +++++++----------- inst/doc/stream.pdf |binary inst/doc/stream_extension.pdf |binary man/DSC.Rd | 5 + man/DSC_DBSCAN.Rd | 4 man/DSC_DBSTREAM.Rd | 25 ++--- man/DSC_DStream.Rd | 4 man/DSC_Hierarchical.Rd | 5 + man/DSC_Kmeans.Rd | 4 man/DSC_Macro.Rd | 5 + man/DSC_Micro.Rd | 5 + man/DSC_Reachability.Rd | 4 man/DSC_Sample.Rd | 13 +- man/DSC_Static.Rd | 4 man/DSC_TwoStage.Rd | 4 man/DSC_Window.Rd | 5 + man/DSClassify.Rd | 5 + man/DSD.Rd | 4 man/DSD_BarsAndGaussians.Rd | 5 + man/DSD_Benchmark.Rd | 5 + man/DSD_Cubes.Rd | 5 + man/DSD_Gaussians.Rd | 6 + man/DSD_MG.Rd | 4 man/DSD_Memory.Rd | 4 man/DSD_ReadCSV.Rd | 4 man/DSD_ReadDB.Rd | 4 man/DSD_ScaleStream.Rd | 4 man/DSD_Target.Rd | 5 + man/DSD_UniformNoise.Rd | 5 + man/DSD_mlbenchData.Rd | 5 + man/DSD_mlbenchGenerator.Rd | 5 + man/DSFP.Rd | 5 + man/DSO.Rd | 5 + man/DSO_Sampling.Rd | 4 man/DSO_Window.Rd | 4 man/DST.Rd | 5 + man/MGC.Rd | 6 + man/animation.Rd | 3 man/evaluate.Rd | 31 +++++- man/get_assignment.Rd | 5 + man/get_centers.Rd | 5 + man/get_copy.Rd | 5 + man/get_points.Rd | 5 + man/get_weights.Rd | 5 + man/microToMacro.Rd | 5 + man/nclusters.Rd | 5 + man/plot.Rd | 5 + man/prune_clusters.Rd | 5 + man/recluster.Rd | 5 + man/reset_stream.Rd | 5 + man/save.Rd | 7 + man/update.Rd | 5 + man/write_stream.Rd | 5 + vignettes/stream.Rnw | 90 +++++++----------- 63 files changed, 511 insertions(+), 346 deletions(-)
Title: Sensitivity Indices with Dependent Inputs
Description: Sensitivity indices with dependent correlated inputs, using a
method based on PLS regression.
Author: A. Bouvier [aut], J.-P. Gauchi [aut, cre], E. Volatier [ctb]
Maintainer: Annie Bouvier <annie.bouvier@jouy.inra.fr>
Diff between sivipm versions 1.0-0 dated 2015-04-14 and 1.1-2 dated 2015-10-28
DESCRIPTION | 13 + MD5 | 59 ++++---- NAMESPACE | 9 - NEWS | 36 +++++ R/allmono.R |only R/class-sivip.R |only R/fastregpls2.R |only R/polynome.R | 165 +++++++++++------------ R/regpls2.R | 310 +++++++++++++++++++++++++++------------------ R/sivipm.R | 236 ++++++++++++++++++++++------------ R/vect2poly.R | 6 inst/doc/Vignette.pdf |binary man/cornell1.Rd | 2 man/crpolyX.Rd | 4 man/crpolyXT.Rd | 4 man/poly-class.Rd | 8 + man/polyX-class.Rd | 8 + man/sivip-class.Rd |only man/sivipboot.Rd | 18 ++ man/sivipm-package.Rd | 6 man/sivipm.Rd | 87 ++++++------ man/vect2polyX.Rd | 2 man/vect2polyXT.Rd | 2 src |only tests/exX18Y14.R | 3 tests/exX18Y14.Rout.save | 65 +++++---- tests/exX18Y2.R | 4 tests/exX18Y2.Rout.save | 115 ++++++++-------- tests/exXY180.R | 6 tests/exXY180.Rout.save | 42 +++--- tests/excornell0.R | 20 ++ tests/excornell0.Rout.save | 211 ++++++++++++++++++++---------- tests/excornell1.Rout.save | 31 ++-- 33 files changed, 896 insertions(+), 576 deletions(-)
Title: Ridge Regression and Other Kernels for Genomic Selection
Description: Software for genomic prediction with the RR-BLUP mixed model. One application is to estimate marker effects by ridge regression; alternatively, BLUPs can be calculated based on an additive relationship matrix or a Gaussian kernel.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman <endelman@wisc.edu>
Diff between rrBLUP versions 4.3 dated 2014-03-06 and 4.4 dated 2015-10-28
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- NAMESPACE | 3 ++ NEWS | 5 ++++ R/A.mat.R | 7 ++---- R/GWAS.R | 17 ++++++++------- R/kin.blup.R | 59 +++++++++++++++++++++++++++++++++++-------------------- R/kinship.BLUP.R | 5 +--- man/GWAS.Rd | 6 +++-- man/kin.blup.Rd | 8 +++++-- 10 files changed, 83 insertions(+), 53 deletions(-)
Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between rPref versions 0.6 dated 2015-08-23 and 0.7 dated 2015-10-28
DESCRIPTION | 8 ++--- MD5 | 56 ++++++++++++++++++++------------------ NAMESPACE | 9 ++++++ NEWS | 24 ++++++++-------- R/RcppExports.R | 46 +++++++++++++++---------------- R/base-pref-macros.R | 38 +++++++++++++++----------- R/base-pref.r | 28 +++++++++++++------ R/complex-pref.r | 45 ++++++++++++++----------------- R/general-pref.r |only R/pred-succ.r | 26 ++++++++--------- R/pref-classes.r | 35 +++++++++++++++--------- R/pref-eval.r | 68 +++++++++++++++++++++++++++++------------------ R/rPref.r | 18 +++++++----- R/show-pref.r | 56 ++++++++++++++++++++------------------ R/visualize.r | 22 +++++++-------- inst/test/test-pref.r | 21 ++++++++++++++ inst/test/test-psel.R | 13 ++++++++ inst/test/test-strings.R | 3 +- man/base_pref.Rd | 28 ++++++++++++------- man/base_pref_macros.Rd | 38 +++++++++++++++----------- man/complex_pref.Rd | 32 ++++++++-------------- man/general_pref.Rd |only man/get_btg.Rd | 6 ++-- man/get_hasse_diag.Rd | 4 +- man/plot_front.Rd | 6 ++-- man/pred_succ.Rd | 23 ++++++++------- man/psel.Rd | 41 ++++++++++++++++------------ man/rPref.Rd | 17 ++++++----- man/show.pref.Rd | 29 +++++++++----------- man/show.query.Rd | 5 ++- 30 files changed, 428 insertions(+), 317 deletions(-)
Title: In-Source Documentation for R
Description: A 'Doxygen'-like in-source documentation system
for Rd, collation, and 'NAMESPACE' files.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 4.1.1 dated 2015-04-15 and 5.0.0 dated 2015-10-28
roxygen2-4.1.1/roxygen2/R/parse-registry.R |only roxygen2-4.1.1/roxygen2/man/roxygen.Rd |only roxygen2-4.1.1/roxygen2/src/parser.cpp |only roxygen2-4.1.1/roxygen2/src/roxygen.h |only roxygen2-4.1.1/roxygen2/tests/testthat/test-complete.R |only roxygen2-4.1.1/roxygen2/tests/testthat/test-cpp-parser.R |only roxygen2-5.0.0/roxygen2/DESCRIPTION | 35 roxygen2-5.0.0/roxygen2/MD5 | 211 +- roxygen2-5.0.0/roxygen2/NAMESPACE | 22 roxygen2-5.0.0/roxygen2/R/RcppExports.R | 12 roxygen2-5.0.0/roxygen2/R/alias.R | 2 roxygen2-5.0.0/roxygen2/R/default-data-format.R |only roxygen2-5.0.0/roxygen2/R/family.R | 30 roxygen2-5.0.0/roxygen2/R/minidesc.R | 6 roxygen2-5.0.0/roxygen2/R/object-defaults.R | 29 roxygen2-5.0.0/roxygen2/R/object-from-call.R | 32 roxygen2-5.0.0/roxygen2/R/object.R | 8 roxygen2-5.0.0/roxygen2/R/order-params.R | 1 roxygen2-5.0.0/roxygen2/R/parse-preref.R | 233 +- roxygen2-5.0.0/roxygen2/R/parse.R | 37 roxygen2-5.0.0/roxygen2/R/rc.R | 4 roxygen2-5.0.0/roxygen2/R/rd-file-api.R | 9 roxygen2-5.0.0/roxygen2/R/rd-parse.R | 8 roxygen2-5.0.0/roxygen2/R/rd-tag-api.R | 64 roxygen2-5.0.0/roxygen2/R/roclet-collate.R | 25 roxygen2-5.0.0/roxygen2/R/roclet-namespace.R | 58 roxygen2-5.0.0/roxygen2/R/roclet-rd.R | 311 +-- roxygen2-5.0.0/roxygen2/R/roclet-vignette.R | 1 roxygen2-5.0.0/roxygen2/R/roxygen-tag.R |only roxygen2-5.0.0/roxygen2/R/roxygen.R | 11 roxygen2-5.0.0/roxygen2/R/roxygenize.R | 21 roxygen2-5.0.0/roxygen2/R/safety.R | 16 roxygen2-5.0.0/roxygen2/R/source.R | 4 roxygen2-5.0.0/roxygen2/R/tag-registry.R |only roxygen2-5.0.0/roxygen2/R/template.R | 12 roxygen2-5.0.0/roxygen2/R/usage.R | 5 roxygen2-5.0.0/roxygen2/R/utils.R | 14 roxygen2-5.0.0/roxygen2/README.md | 14 roxygen2-5.0.0/roxygen2/build/vignette.rds |binary roxygen2-5.0.0/roxygen2/inst/doc/collate.R | 10 roxygen2-5.0.0/roxygen2/inst/doc/collate.Rmd | 24 roxygen2-5.0.0/roxygen2/inst/doc/collate.html | 251 --- roxygen2-5.0.0/roxygen2/inst/doc/formatting.R | 8 roxygen2-5.0.0/roxygen2/inst/doc/formatting.Rmd | 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insertions(+), 2712 deletions(-)
Title: Rank-Hazard Plots
Description: Rank-hazard plots (Karvanen and Harrell, Statistics in Medicine 2009) visualize the relative importance of covariates in a proportional hazards model. The key idea is to rank the covariate values and plot the relative hazard as a function of ranks scaled to interval [0,1]. The relative hazard is plotted in respect to the reference hazard, which can bee.g. the hazard related to the median of the covariate.
Author: Juha Karvanen, Nanni Koski
Maintainer: Nanni Koski <nanni.t.koski@student.jyu.fi>
Diff between rankhazard versions 1.0 dated 2014-04-02 and 1.0-2 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 +- man/rankhazardplot.Rd | 3 ++- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-8 dated 2015-10-22 and 0.1-9 dated 2015-10-28
DESCRIPTION | 11 ++-- MD5 | 21 ++++---- NAMESPACE | 2 R/RcppExports.R | 12 ---- R/allPerm.R | 18 +++--- R/initMC.r | 20 +++---- R/nextPerm.R | 19 +++---- R/zzz.R |only man/initMC.Rd | 87 ++++++++++++++++----------------- man/nextPerm.Rd | 74 ++++++++++++++-------------- src/RcppExports.cpp | 33 ------------ src/multicool.cpp | 134 +++++++++++++++++++++++----------------------------- 12 files changed, 186 insertions(+), 245 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms efficiently using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable
matching for two-sided markets, such as the stable marriage
problem and the college-admissions problem. Implements Irving's
Algorithm for the stable roommate problem. Implements the top
trading cycle algorithm for the indivisible goods trading problem.
Author: Jan Tilly, Nick Janetos
Maintainer: Jan Tilly <jtilly@econ.upenn.edu>
Diff between matchingR versions 1.1.1 dated 2015-09-21 and 1.2 dated 2015-10-28
matchingR-1.1.1/matchingR/man/checkPreferenceOrder.Rd |only matchingR-1.1.1/matchingR/man/checkPreferenceOrderOnesided.Rd |only matchingR-1.1.1/matchingR/man/checkStability.Rd |only matchingR-1.1.1/matchingR/man/checkStabilityRoommate.Rd |only matchingR-1.1.1/matchingR/man/checkStabilityTopTradingCycle.Rd |only matchingR-1.1.1/matchingR/man/galeShapleyMatching.Rd |only matchingR-1.1.1/matchingR/man/many2one.Rd |only matchingR-1.1.1/matchingR/man/one2many.Rd |only matchingR-1.1.1/matchingR/man/one2one.Rd |only matchingR-1.1.1/matchingR/man/onesided.Rd |only matchingR-1.1.1/matchingR/man/pkg.env.Rd |only matchingR-1.1.1/matchingR/man/set.column.major.Rd |only matchingR-1.1.1/matchingR/man/set.row.major.Rd |only matchingR-1.1.1/matchingR/man/stableRoommateMatching.Rd |only matchingR-1.1.1/matchingR/man/topTradingCycle.Rd |only matchingR-1.1.1/matchingR/man/validateInputs.Rd |only matchingR-1.1.1/matchingR/man/validateInputsOneSided.Rd |only matchingR-1.2/matchingR/DESCRIPTION | 22 matchingR-1.2/matchingR/MD5 | 107 - matchingR-1.2/matchingR/NEWS.md | 9 matchingR-1.2/matchingR/R/RcppExports.R | 211 +- matchingR-1.2/matchingR/R/deprecated.R |only matchingR-1.2/matchingR/R/galeshapley.R | 740 ++++++---- matchingR-1.2/matchingR/R/matchingR.R | 137 - matchingR-1.2/matchingR/R/roommate.R | 260 ++- matchingR-1.2/matchingR/R/toptradingcycle.R | 117 + matchingR-1.2/matchingR/R/utils.R | 17 matchingR-1.2/matchingR/README.md | 60 matchingR-1.2/matchingR/inst/doc/matchingR-intro.R | 54 matchingR-1.2/matchingR/inst/doc/matchingR-intro.Rmd | 95 - matchingR-1.2/matchingR/inst/doc/matchingR-intro.html | 115 + matchingR-1.2/matchingR/inst/doc/matchingR-performance.R | 28 matchingR-1.2/matchingR/inst/doc/matchingR-performance.Rmd | 28 matchingR-1.2/matchingR/inst/doc/matchingR-performance.html | 84 - matchingR-1.2/matchingR/inst/include/matchingR.h | 17 matchingR-1.2/matchingR/man/cpp_wrapper_galeshapley.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_galeshapley_check_stability.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_irving.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_irving_check_stability.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_ttc.Rd |only matchingR-1.2/matchingR/man/cpp_wrapper_ttc_check_stability.Rd |only matchingR-1.2/matchingR/man/galeShapley.checkPreferences.Rd |only matchingR-1.2/matchingR/man/galeShapley.checkStability.Rd |only matchingR-1.2/matchingR/man/galeShapley.collegeAdmissions.Rd |only matchingR-1.2/matchingR/man/galeShapley.marriageMarket.Rd |only matchingR-1.2/matchingR/man/galeShapley.validate.Rd |only matchingR-1.2/matchingR/man/matchingR-deprecated.Rd |only matchingR-1.2/matchingR/man/matchingR-package.Rd | 74 - matchingR-1.2/matchingR/man/rankIndex.Rd | 4 matchingR-1.2/matchingR/man/roommate.Rd |only matchingR-1.2/matchingR/man/roommate.checkPreferences.Rd |only matchingR-1.2/matchingR/man/roommate.checkStability.Rd |only matchingR-1.2/matchingR/man/roommate.validate.Rd |only matchingR-1.2/matchingR/man/sortIndex.Rd | 4 matchingR-1.2/matchingR/man/sortIndexOneSided.Rd | 13 matchingR-1.2/matchingR/man/toptrading.Rd | 62 matchingR-1.2/matchingR/man/toptrading.checkStability.Rd |only matchingR-1.2/matchingR/src/RcppExports.cpp | 48 matchingR-1.2/matchingR/src/galeshapley.cpp | 163 +- matchingR-1.2/matchingR/src/galeshapley.h | 21 matchingR-1.2/matchingR/src/roommate.cpp | 118 + matchingR-1.2/matchingR/src/roommate.h | 23 matchingR-1.2/matchingR/src/toptradingcycle.cpp | 141 + matchingR-1.2/matchingR/src/toptradingcycle.h | 21 matchingR-1.2/matchingR/src/utils.cpp | 47 matchingR-1.2/matchingR/src/utils.h | 17 matchingR-1.2/matchingR/tests/testthat/test_galeshapley.R | 161 +- matchingR-1.2/matchingR/tests/testthat/test_roommate.R | 64 matchingR-1.2/matchingR/tests/testthat/test_toptradingcycle.R | 17 matchingR-1.2/matchingR/vignettes/bibliography.bib | 2 matchingR-1.2/matchingR/vignettes/matchingR-intro.Rmd | 95 - matchingR-1.2/matchingR/vignettes/matchingR-performance.Rmd | 28 72 files changed, 2131 insertions(+), 1093 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Jeroen Ooms [ctb],
Yixuan Qiu [ctb],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.0.3 dated 2015-10-22 and 0.0.4 dated 2015-10-28
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS |only R/raster.R | 1 - configure | 11 +++++++++++ man/raster_str.Rd | 1 - 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Learning Algorithms for Dynamic Treatment Regimes
Description: Dynamic treatment regimens (DTRs) are sequential decision rules tailored at each stage by time-varying subject-specific features and intermediate outcomes observed in previous stages. This package implements three methods: O-learning (Zhao et. al. 2012,2014), Q-learning (Murphy et. al. 2007; Zhao et.al. 2009) and P-learning (Liu et. al. 2014, 2015) to estimate the optimal DTRs.
Author: Ying Liu, Yuanjia Wang, Donglin Zeng
Maintainer: Ying Liu <yl2802@cumc.columbia.edu>
Diff between DTRlearn versions 1.0 dated 2015-10-23 and 1.1 dated 2015-10-28
DESCRIPTION | 12 ++++----- MD5 | 30 +++++++++++------------ man/DTRlearn-package.Rd | 22 ++++++++++------- man/Olearning.Rd | 27 ++++++++++----------- man/Olearning_Single.Rd | 43 ++++++++++++++++++++++----------- man/Plearning.Rd | 31 +++++++++++------------- man/Qlearning.Rd | 12 ++++----- man/Qlearning_Single.Rd | 16 +++++------- man/make_2classification.Rd | 16 ++++++------ man/make_classification.Rd | 30 +++++++++++++---------- man/plot.linearcl.Rd | 17 ++++++------- man/plot.qlearn.Rd | 27 ++++++--------------- man/predict.linearcl.Rd | 9 ++----- man/predict.qlearn.Rd | 10 +++---- man/predict.rbfcl.Rd | 8 +++--- man/wsvm.Rd | 56 +++++++++++++++++++++++--------------------- 16 files changed, 186 insertions(+), 180 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.5 dated 2015-10-25 and 1.7 dated 2015-10-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/C_CIT_V12.R | 14 ++++++++++++-- man/cit-package.Rd | 4 ++-- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Multivariate Chebyshev Interpolation
Description: Contains methods for creating multivariate Chebyshev
approximation of functions on a hypercube. Some methods for
non-Chebyshev grids are also provided.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research, Oslo, Norway
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between chebpol versions 1.3-1367 dated 2014-09-01 and 1.3-1789 dated 2015-10-28
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- NAMESPACE | 1 + R/chebpol.R | 2 ++ build/vignette.rds |binary inst/doc/chebpol.pdf |binary 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.1 dated 2015-10-21 and 1.2 dated 2015-10-28
DESCRIPTION | 10 +-- MD5 | 23 ++++--- R/RcppExports.R | 4 + R/mgr.R |only R/mkr.R | 156 ++++++++++++++++++++++++---------------------------- R/wgr.R | 116 +++++++++++++++++++++++++++++--------- R/wgr2.R |only inst/CITATION | 2 man/bWGR.Rd | 4 - man/mgr.Rd |only man/mkr.Rd | 25 +++----- man/wgr.Rd | 12 ++-- man/wgr2.Rd |only src/KMUP2.cpp |only src/RcppExports.cpp | 19 ++++++ 15 files changed, 225 insertions(+), 146 deletions(-)
Title: Advanced Analysis of B Cell Receptor Repertoire Data
Description: Methods for advanced analysis of B cell receptor repertoire data, like gene usage, mutations, clones and diversity and their visualisation.
Author: Julia Bischof
Maintainer: Julia Bischof <Julia.Bischof@uksh.de>
Diff between bcRep versions 1.1 dated 2015-10-12 and 1.2.2 dated 2015-10-28
DESCRIPTION | 14 +- MD5 | 79 +++++++++---- NAMESPACE | 6 - R/clones.CDR3Length.R | 4 R/clones.R | 10 + R/clones.filterFunctionality.R |only R/clones.filterJunctionFrame.R |only R/clones.filterSize.R |only R/clones.giniIndex.R |only R/clones.shared.R | 10 + R/clones.shared.summary.R | 2 R/combineIMGT.R |only R/compare.aaDistribution.R |only R/compare.geneUsage.R |only R/compare.trueDiversity.R |only R/geneUsage.R | 34 +++-- R/plotAADistribution.R | 61 ++++++---- R/plotClonesCDR3Length.R | 6 - R/plotClonesCopyNumber.R | 9 + R/plotCompareAADistribution.R |only R/plotCompareGeneUsage.R |only R/plotCompareTrueDiversity.R |only R/plotGeneComb.R | 13 +- R/plotGeneUsage.R | 73 +++++++++--- R/plotTrueDiversity.R | 20 ++- R/sequences.functionality.R | 2 R/sequences.geneComb.R | 43 ++++++- R/sequences.junctionFrame.R | 2 build |only data/aaseqtab2.rda |only inst |only man/aaDistribution.Rd | 7 - man/aaseqtab.Rd | 2 man/aaseqtab2.Rd |only man/bcRep-package.Rd | 198 +++++++++++++++++++--------------- man/clones.Rd | 218 +++++++++++++++++++------------------- man/clones.filterFunctionality.Rd |only man/clones.filterJunctionFrame.Rd |only man/clones.filterSize.Rd |only man/clones.giniIndex.Rd |only man/clones.shared.Rd | 202 +++++++++++++++++------------------ man/combineIMGT.Rd |only man/compare.aaDistribution.Rd |only man/compare.geneUsage.Rd |only man/compare.trueDiversity.Rd |only man/geneUsage.Rd | 10 - man/mutationtab.Rd | 3 man/plotClonesCopyNumber.Rd | 7 - man/sequences.geneComb.Rd | 7 - man/trueDiversity.Rd | 2 vignettes |only 51 files changed, 607 insertions(+), 437 deletions(-)
Title: Diversification Rate Estimation and Fast Simulation of
Reconstructed Phylogenetic Trees under Tree-Wide
Time-Heterogeneous Birth-Death Processes Including
Mass-Extinction Events
Description: Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Author: Sebastian Hoehna and Michael R. May
Maintainer: Sebastian Hoehna <Sebastian.Hoehna@gmail.com>
Diff between TESS versions 2.0.0 dated 2015-06-18 and 2.1.0 dated 2015-10-28
TESS-2.0.0/TESS/vignettes/Bayesian_Diversification_Rate_Analysis.pdf |only TESS-2.1.0/TESS/DESCRIPTION | 10 TESS-2.1.0/TESS/MD5 | 85 ++++-- TESS-2.1.0/TESS/NAMESPACE | 4 TESS-2.1.0/TESS/R/tess.analysis.R | 124 ---------- TESS-2.1.0/TESS/R/tess.plot.output.R | 4 TESS-2.1.0/TESS/R/tess.process.output.R | 2 TESS-2.1.0/TESS/R/tess.sim.age.R | 4 TESS-2.1.0/TESS/R/tess.sim.taxa.R | 29 +- TESS-2.1.0/TESS/R/tess.sim.taxa.age.R | 15 - TESS-2.1.0/TESS/build |only TESS-2.1.0/TESS/inst/doc |only TESS-2.1.0/TESS/man/TESS-package.Rd | 17 + TESS-2.1.0/TESS/man/cettiidae.Rd | 13 - TESS-2.1.0/TESS/man/conifers.Rd | 13 - TESS-2.1.0/TESS/man/mammalia.Rd | 13 - TESS-2.1.0/TESS/man/tess.PosteriorPrediction.Rd | 8 TESS-2.1.0/TESS/man/tess.analysis.Rd | 68 +++-- TESS-2.1.0/TESS/man/tess.likelihood.Rd | 33 ++ TESS-2.1.0/TESS/man/tess.likelihood.rateshift.Rd | 30 +- TESS-2.1.0/TESS/man/tess.mcmc.Rd | 17 + TESS-2.1.0/TESS/man/tess.nTaxa.expected.Rd | 8 TESS-2.1.0/TESS/man/tess.pathSampling.Rd | 15 - TESS-2.1.0/TESS/man/tess.plot.multichain.diagnostics.Rd | 26 +- TESS-2.1.0/TESS/man/tess.plot.output.Rd | 14 - TESS-2.1.0/TESS/man/tess.plot.singlechain.diagnostics.Rd | 14 - TESS-2.1.0/TESS/man/tess.process.output.Rd | 18 - TESS-2.1.0/TESS/man/tess.sim.age.Rd | 2 TESS-2.1.0/TESS/vignettes/Bayesian_Diversification_Rate_Analysis.Rnw |only TESS-2.1.0/TESS/vignettes/ext_figures |only TESS-2.1.0/TESS/vignettes/literature.bib |only TESS-2.1.0/TESS/vignettes/results |only 32 files changed, 313 insertions(+), 273 deletions(-)
Title: Integrates R and Essentia
Description: Contains three functions that query AuriQ Systems' Essentia Database and return the results in R. 'essQuery' takes a single Essentia command and captures the output in R, where you can save the output to a dataframe or stream it directly into additional analysis. 'read.essentia' takes an Essentia script and captures the output csv data into R, where you can save the output to a dataframe or stream it directly into additional analysis. 'capture.essentia' takes a file containing any number of Essentia commands and captures the output of the specified statements into R dataframes. Essentia can be downloaded for free at http://www.auriq.com/documentation/source/install/index.html.
Author: Ben Waxer
Maintainer: Ben Waxer <bwaxer@auriq.com>
Diff between RESS versions 1.2 dated 2015-07-30 and 1.3 dated 2015-10-28
RESS-1.2/RESS/R/essquery.R |only RESS-1.2/RESS/R/readudb.R |only RESS-1.2/RESS/man/read.udb.Rd |only RESS-1.3/RESS/DESCRIPTION | 10 +++++----- RESS-1.3/RESS/MD5 | 16 +++++++++------- RESS-1.3/RESS/NAMESPACE | 1 + RESS-1.3/RESS/R/captureessentia.R |only RESS-1.3/RESS/R/essQuery.R |only RESS-1.3/RESS/R/readessentia.R |only RESS-1.3/RESS/man/RESS-package.Rd | 24 +++++++++++++++--------- RESS-1.3/RESS/man/capture.essentia.Rd |only RESS-1.3/RESS/man/essQuery.Rd | 8 ++++---- RESS-1.3/RESS/man/read.essentia.Rd |only 13 files changed, 34 insertions(+), 25 deletions(-)
More information about randomForest.ddR at CRAN
Permanent link
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: http://bit.ly/1Nwo4CB.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between MCMC.qpcr versions 1.2 dated 2015-05-23 and 1.2.2 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- R/HPDsummary.R | 2 +- R/getNormalizedData.R | 11 ++++++++--- R/mcmc.qpcr.R | 13 +++++++++---- R/mcmc.qpcr.lognormal.R | 13 +++++++++---- man/MCMC.qpcr-package.Rd | 6 +++--- man/getNormalizedData.Rd | 5 ++++- 9 files changed, 54 insertions(+), 30 deletions(-)
Title: Citations for 'Knitr' Markdown Files
Description: Provides the ability to create dynamic citations
in which the bibliographic information is pulled from the web rather
than having to be entered into a local database such as 'bibtex' ahead of
time. The package is primarily aimed at authoring in the R 'markdown'
format, and can provide outputs for web-based authoring such as linked
text for inline citations. Cite using a 'DOI', URL, or
'bibtex' file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between knitcitations versions 1.0.6 dated 2015-05-25 and 1.0.7 dated 2015-10-28
DESCRIPTION | 20 ++++++++++---------- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ NEWS | 6 +++--- R/bibliography.R | 2 +- R/cleanbib.R | 3 ++- R/knitcitations.R | 1 + build/vignette.rds |binary inst/doc/tutorial.pdf |binary man/bibliography.Rd | 2 +- man/cleanbib.Rd | 10 +--------- tests/testthat/test_bib_metadata.R | 1 + tests/testthat/test_cite.R | 14 +++++++++++++- 13 files changed, 47 insertions(+), 38 deletions(-)
Title: Multiple Ordinal Tobit (MOT) Model
Description: Fit right censored Multiple Ordinal Tobit (MOT) model.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between lmmot versions 0.1.2 dated 2014-12-16 and 0.1.3 dated 2015-10-28
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 4 +++- R/lmmot.R | 7 +++---- R/motFisher.R | 5 +++-- R/motGradient.R | 5 +++-- R/motHessian.R | 5 +++-- R/motLogLik.R | 6 ++++-- man/lmmot.Rd | 5 +++-- man/motFisher.Rd | 7 ++++--- man/motGradient.Rd | 7 ++++--- man/motHessian.Rd | 7 ++++--- man/motLogLik.Rd | 7 ++++--- man/print.lmmot.Rd | 3 ++- man/summary.lmmot.Rd | 3 ++- 15 files changed, 61 insertions(+), 48 deletions(-)
Title: Platform for EDGAR Filing Management
Description: EDGAR is the Electronic Data Gathering, Analysis, and Retrieval system which performs automated collection, validation, indexing, acceptance, and forwarding of submissions by companies and others who are required by law to file forms with the U.S. Securities and Exchange Commission (SEC). This package downloads EDGAR quarterly master index, daily master index, filings from SEC.org site and do sentiment analysis of 10-K statements.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 1.0.2 dated 2015-09-24 and 1.0.3 dated 2015-10-28
edgar-1.0.2/edgar/R/downlaod_master_index.R |only edgar-1.0.3/edgar/DESCRIPTION | 10 - edgar-1.0.3/edgar/MD5 | 24 +- edgar-1.0.3/edgar/R/download_filings.R | 2 edgar-1.0.3/edgar/R/download_master_index.R |only edgar-1.0.3/edgar/R/get_wordfrquency.R | 5 edgar-1.0.3/edgar/R/polarity_histogram.R | 87 +++++----- edgar-1.0.3/edgar/R/runEDGAR_shiny.R | 9 - edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/edgar_shiny_functions.R | 14 + edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/server.R | 10 - edgar-1.0.3/edgar/inst/shiny-edgar/edgarapp/ui.R | 2 edgar-1.0.3/edgar/man/RunEdgarShiny.Rd | 5 edgar-1.0.3/edgar/man/negwords.Rd | 8 edgar-1.0.3/edgar/man/poswords.Rd | 8 14 files changed, 99 insertions(+), 85 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy ``And'' Gate (DINA) cognitive diagnostic model parameters using the Gibbs sampler described by Culpepper (2015) DOI: 10.3102/1076998615595403.
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between dina versions 1.0 dated 2015-10-27 and 1.0.1 dated 2015-10-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/DINA_Gibbs.Rd | 18 +++++++++--------- man/DINAsim.Rd | 8 ++++---- man/dina-package.Rd | 2 +- src/DINAcpp101315.cpp | 12 ++++++------ 6 files changed, 28 insertions(+), 28 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included; uses Maarloes Maathius's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.7 dated 2015-07-20 and 1.2.8 dated 2015-10-27
icenReg-1.2.7/icenReg/src/icenReg_files/pavaAlgorithm.cpp |only icenReg-1.2.8/icenReg/DESCRIPTION | 17 icenReg-1.2.8/icenReg/MD5 | 45 icenReg-1.2.8/icenReg/NAMESPACE | 10 icenReg-1.2.8/icenReg/NEWS | 11 icenReg-1.2.8/icenReg/R/Utilities.R | 126 - icenReg-1.2.8/icenReg/R/optCliq.R |only icenReg-1.2.8/icenReg/R/referenceClasses.R |only icenReg-1.2.8/icenReg/R/user_functions.R | 85 - icenReg-1.2.8/icenReg/man/ICNPMLE.Rd |only icenReg-1.2.8/icenReg/man/diag_baseline.Rd | 7 icenReg-1.2.8/icenReg/man/diag_covar.Rd | 4 icenReg-1.2.8/icenReg/man/essIncData.Rd | 18 icenReg-1.2.8/icenReg/man/ic_par.Rd | 6 icenReg-1.2.8/icenReg/man/ic_sp.Rd | 29 icenReg-1.2.8/icenReg/man/optCliq.Rd |only icenReg-1.2.8/icenReg/man/simBVCen.Rd |only icenReg-1.2.8/icenReg/man/simIC_weib.Rd | 4 icenReg-1.2.8/icenReg/src/icenReg.cpp | 4 icenReg-1.2.8/icenReg/src/icenReg_files/basicUtilities.cpp | 269 +++ icenReg-1.2.8/icenReg/src/icenReg_files/bivariateNPMLE.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/bivariateNPMLE.h |only icenReg-1.2.8/icenReg/src/icenReg_files/experimentalCode.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/ic_par.cpp | 174 ++ icenReg-1.2.8/icenReg/src/icenReg_files/ic_par.h | 52 icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_ch.cpp | 702 +++------- icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_ch.h | 145 +- icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_gradDescent.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/myPAVAalgorithm.cpp |only 29 files changed, 1008 insertions(+), 700 deletions(-)
Title: CLUster Evaluation (CLUE)
Description: CLUE is an R package for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms.
Author: Pengyi Yang & Raja Jothi
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between ClueR versions 1.0 dated 2015-02-04 and 1.1 dated 2015-10-27
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NAMESPACE | 7 ++- R/runClue.R | 12 +++-- README.md | 113 ++++++++++++++++++++++++++++++++++++++++++++++++- man/ClueR-package.Rd | 8 ++- man/clustEnrichment.Rd | 2 man/clustOptimal.Rd | 2 man/enrichmentTest.Rd | 2 man/fuzzPlot.Rd | 2 man/runClue.Rd | 6 +- man/temporalSimu.Rd | 2 12 files changed, 152 insertions(+), 34 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
Liang et al hyper-g priors (JASA 2008) or mixtures of
g-priors in GLMS of Li and Clyde 2015. Other model
selection criteria include AIC and BIC. Sampling
probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an MCMC algorithm
samples models using the BAS tree structure as an efficient
hash table. Allows uniform or beta-binomial prior distributions on
models, and may force variables to always be included.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.0.5 dated 2015-09-10 and 1.0.6 dated 2015-10-27
BAS-1.0.5/BAS/R/coefpriors.R |only BAS-1.0.6/BAS/CHANGELOG | 11 + BAS-1.0.6/BAS/DESCRIPTION | 8 - BAS-1.0.6/BAS/INDEX |only BAS-1.0.6/BAS/MD5 | 70 ++++++---- BAS-1.0.6/BAS/NAMESPACE | 5 BAS-1.0.6/BAS/R/bas.R | 17 +- BAS-1.0.6/BAS/R/bas.gglm.R | 64 ++++----- BAS-1.0.6/BAS/R/betapriors.R |only BAS-1.0.6/BAS/R/coefficients.R | 4 BAS-1.0.6/BAS/R/predict.bma.R | 58 ++++++-- BAS-1.0.6/BAS/R/summary.bma.R | 5 BAS-1.0.6/BAS/man/EB.Rd |only BAS-1.0.6/BAS/man/TG-priors.Rd |only BAS-1.0.6/BAS/man/bas.Rd | 12 - BAS-1.0.6/BAS/man/bas.glm.Rd | 73 +++++++---- BAS-1.0.6/BAS/man/beta.prime.Rd |only BAS-1.0.6/BAS/man/cchpriors.Rd |only BAS-1.0.6/BAS/man/coefpriors.Rd | 2 BAS-1.0.6/BAS/man/hyper-g.Rd |only BAS-1.0.6/BAS/man/predict.basglm.Rd |only BAS-1.0.6/BAS/man/predict.bma.Rd | 28 ++-- BAS-1.0.6/BAS/man/robust.Rd |only BAS-1.0.6/BAS/man/summary.bma.Rd | 16 +- BAS-1.0.6/BAS/src/amcmc.c | 4 BAS-1.0.6/BAS/src/bas-glm.h | 4 BAS-1.0.6/BAS/src/bayesreg.c | 6 BAS-1.0.6/BAS/src/betapriorfamily.c |only BAS-1.0.6/BAS/src/betapriorfamily.h |only BAS-1.0.6/BAS/src/deterministic.c | 4 BAS-1.0.6/BAS/src/glm_deterministic.c | 21 +-- BAS-1.0.6/BAS/src/glm_lpy.c | 224 ++++++++++++++++++---------------- BAS-1.0.6/BAS/src/glm_mcmc.c | 71 ++-------- BAS-1.0.6/BAS/src/glm_mcmcbas.c | 30 ++-- BAS-1.0.6/BAS/src/glm_sampleworep.c | 44 ++++-- BAS-1.0.6/BAS/src/hypergeometric1F1.c | 69 ++++++---- BAS-1.0.6/BAS/src/mcmc.c | 4 BAS-1.0.6/BAS/src/mcmc_new.c | 4 BAS-1.0.6/BAS/src/mcmcbas.c | 4 BAS-1.0.6/BAS/src/posisearch.c | 4 BAS-1.0.6/BAS/src/sampleworep.c | 8 - BAS-1.0.6/BAS/src/sampleworep_new.c | 8 - 42 files changed, 490 insertions(+), 392 deletions(-)
Title: Helper Functions for Structural Equation Modelling in OpenMx
Description: Helper functions for making, running, and reporting SEM
and twin models in OpenMx.
If you are just starting, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 0.50 dated 2015-08-27 and 1.0.0 dated 2015-10-27
umx-0.50/umx/man/coef.MxModel.Rd |only umx-1.0.0/umx/DESCRIPTION | 13 umx-1.0.0/umx/INSTALL | 16 umx-1.0.0/umx/MD5 | 257 +++--- umx-1.0.0/umx/NAMESPACE | 28 umx-1.0.0/umx/NEWS | 15 umx-1.0.0/umx/R/build_run_modify.r | 956 +++++++++++++++++++---- umx-1.0.0/umx/R/deprecated.r | 44 - umx-1.0.0/umx/R/fit_and_reporting.r | 778 +++++++++++++++++- umx-1.0.0/umx/R/misc_and_utility.r | 223 ++++- umx-1.0.0/umx/R/xmu.r | 58 - umx-1.0.0/umx/README.md | 15 umx-1.0.0/umx/man/RMSEA.MxModel.Rd | 3 umx-1.0.0/umx/man/RMSEA.Rd | 1 umx-1.0.0/umx/man/RMSEA.summary.mxmodel.Rd | 3 umx-1.0.0/umx/man/confint.MxModel.Rd | 1 umx-1.0.0/umx/man/extractAIC.MxModel.Rd | 1 umx-1.0.0/umx/man/logLik.Rd | 1 umx-1.0.0/umx/man/plot.MxModel.Rd | 14 umx-1.0.0/umx/man/qm.Rd | 9 umx-1.0.0/umx/man/residuals.MxModel.Rd | 1 umx-1.0.0/umx/man/umx-deprecated.Rd | 30 umx-1.0.0/umx/man/umx.Rd | 58 - umx-1.0.0/umx/man/umxACE.Rd | 6 umx-1.0.0/umx/man/umxAdd1.Rd | 3 umx-1.0.0/umx/man/umxCI.Rd | 1 umx-1.0.0/umx/man/umxCI_boot.Rd | 1 umx-1.0.0/umx/man/umxCP.Rd |only umx-1.0.0/umx/man/umxCompare.Rd | 1 umx-1.0.0/umx/man/umxCovData.Rd | 13 umx-1.0.0/umx/man/umxDiagnose.Rd | 12 umx-1.0.0/umx/man/umxDrop1.Rd | 3 umx-1.0.0/umx/man/umxEFA.Rd | 3 umx-1.0.0/umx/man/umxEquate.Rd | 3 umx-1.0.0/umx/man/umxEval.Rd | 14 umx-1.0.0/umx/man/umxExpCov.Rd | 1 umx-1.0.0/umx/man/umxExpMeans.Rd | 1 umx-1.0.0/umx/man/umxFitIndices.Rd | 1 umx-1.0.0/umx/man/umxFixAll.Rd | 3 umx-1.0.0/umx/man/umxGetParameters.Rd | 3 umx-1.0.0/umx/man/umxGxE.Rd |only umx-1.0.0/umx/man/umxHetCor.Rd | 3 umx-1.0.0/umx/man/umxIP.Rd |only umx-1.0.0/umx/man/umxJiggle.Rd | 14 umx-1.0.0/umx/man/umxLabel.Rd | 4 umx-1.0.0/umx/man/umxLatent.Rd | 4 umx-1.0.0/umx/man/umxMI.Rd | 3 umx-1.0.0/umx/man/umxPadAndPruneForDefVars.Rd | 4 umx-1.0.0/umx/man/umxPath.Rd | 91 +- umx-1.0.0/umx/man/umxPlotACE.Rd | 1 umx-1.0.0/umx/man/umxPlotCP.Rd |only umx-1.0.0/umx/man/umxPlotGxE.Rd |only umx-1.0.0/umx/man/umxPlotIP.Rd |only umx-1.0.0/umx/man/umxRAM.Rd | 30 umx-1.0.0/umx/man/umxReRun.Rd | 4 umx-1.0.0/umx/man/umxReduce.Rd | 5 umx-1.0.0/umx/man/umxRun.Rd | 4 umx-1.0.0/umx/man/umxSetParameters.Rd | 3 umx-1.0.0/umx/man/umxStandardizeACE.Rd | 3 umx-1.0.0/umx/man/umxStandardizeModel.Rd | 1 umx-1.0.0/umx/man/umxSummary.MxModel.Rd | 1 umx-1.0.0/umx/man/umxSummary.Rd | 14 umx-1.0.0/umx/man/umxSummaryCP.Rd |only umx-1.0.0/umx/man/umxSummaryGxE.Rd |only umx-1.0.0/umx/man/umxSummaryIP.Rd |only umx-1.0.0/umx/man/umxThresholdMatrix.Rd | 4 umx-1.0.0/umx/man/umxUnexplainedCausalNexus.Rd | 3 umx-1.0.0/umx/man/umxValues.Rd | 4 umx-1.0.0/umx/man/umx_APA_CI.Rd | 9 umx-1.0.0/umx/man/umx_APA_pval.Rd | 25 umx-1.0.0/umx/man/umx_RAM_ordinal_objective.Rd | 4 umx-1.0.0/umx/man/umx_add_variances.Rd | 16 umx-1.0.0/umx/man/umx_aggregate.Rd | 9 umx-1.0.0/umx/man/umx_apply.Rd | 14 umx-1.0.0/umx/man/umx_as_numeric.Rd | 3 umx-1.0.0/umx/man/umx_check.Rd | 14 umx-1.0.0/umx/man/umx_check_OS.Rd | 32 umx-1.0.0/umx/man/umx_check_model.Rd | 14 umx-1.0.0/umx/man/umx_check_multi_core.Rd | 14 umx-1.0.0/umx/man/umx_cont_2_ordinal.Rd | 3 umx-1.0.0/umx/man/umx_cov2raw.Rd | 3 umx-1.0.0/umx/man/umx_cov_diag.Rd | 4 umx-1.0.0/umx/man/umx_default_option.Rd | 15 umx-1.0.0/umx/man/umx_drop_ok.Rd | 1 umx-1.0.0/umx/man/umx_explode.Rd | 39 umx-1.0.0/umx/man/umx_find_object.Rd | 9 umx-1.0.0/umx/man/umx_fix_first_loadings.Rd | 4 umx-1.0.0/umx/man/umx_fix_latents.Rd | 4 umx-1.0.0/umx/man/umx_get_CI_as_APA_string.Rd | 14 umx-1.0.0/umx/man/umx_get_bracket_addresses.Rd | 14 umx-1.0.0/umx/man/umx_get_checkpoint.Rd | 18 umx-1.0.0/umx/man/umx_get_cores.Rd | 14 umx-1.0.0/umx/man/umx_get_optimizer.Rd | 14 umx-1.0.0/umx/man/umx_grep.Rd | 7 umx-1.0.0/umx/man/umx_has_CIs.Rd | 14 umx-1.0.0/umx/man/umx_has_been_run.Rd | 14 umx-1.0.0/umx/man/umx_has_means.Rd | 14 umx-1.0.0/umx/man/umx_has_square_brackets.Rd | 14 umx-1.0.0/umx/man/umx_is_MxMatrix.Rd | 14 umx-1.0.0/umx/man/umx_is_MxModel.Rd | 14 umx-1.0.0/umx/man/umx_is_RAM.Rd | 14 umx-1.0.0/umx/man/umx_is_cov.Rd | 14 umx-1.0.0/umx/man/umx_is_endogenous.Rd | 14 umx-1.0.0/umx/man/umx_is_exogenous.Rd | 14 umx-1.0.0/umx/man/umx_is_ordered.Rd | 14 umx-1.0.0/umx/man/umx_lower2full.Rd | 26 umx-1.0.0/umx/man/umx_make_bin_cont_pair_data.Rd | 3 umx-1.0.0/umx/man/umx_merge_CIs.Rd | 3 umx-1.0.0/umx/man/umx_msg.Rd | 40 umx-1.0.0/umx/man/umx_names.Rd | 40 umx-1.0.0/umx/man/umx_object_as_str.Rd | 11 umx-1.0.0/umx/man/umx_paste_names.Rd | 38 umx-1.0.0/umx/man/umx_pb_note.Rd | 7 umx-1.0.0/umx/man/umx_print.Rd | 49 - umx-1.0.0/umx/man/umx_read_lower.Rd | 3 umx-1.0.0/umx/man/umx_rename.Rd | 44 - umx-1.0.0/umx/man/umx_reorder.Rd | 12 umx-1.0.0/umx/man/umx_residualize.Rd | 3 umx-1.0.0/umx/man/umx_rot.Rd | 44 - umx-1.0.0/umx/man/umx_round.Rd | 3 umx-1.0.0/umx/man/umx_scale.Rd | 3 umx-1.0.0/umx/man/umx_scale_wide_twin_data.Rd | 3 umx-1.0.0/umx/man/umx_set_checkpoint.Rd | 14 umx-1.0.0/umx/man/umx_set_cores.Rd | 15 umx-1.0.0/umx/man/umx_set_optimizer.Rd | 14 umx-1.0.0/umx/man/umx_show.Rd | 13 umx-1.0.0/umx/man/umx_standardize_IP.Rd |only umx-1.0.0/umx/man/umx_string_to_algebra.Rd | 15 umx-1.0.0/umx/man/umx_swap_a_block.Rd | 3 umx-1.0.0/umx/man/umx_time.Rd | 9 umx-1.0.0/umx/man/umx_trim.Rd | 39 umx-1.0.0/umx/man/xmuLabel_Matrix.Rd | 4 umx-1.0.0/umx/man/xmu_dot_make_paths.Rd | 2 umx-1.0.0/umx/man/xmu_dot_make_residuals.Rd | 13 umx-1.0.0/umx/tests/testthat |only umx-1.0.0/umx/tests/testthat.R |only 136 files changed, 2508 insertions(+), 1230 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future. Web applications are provided
(via 'shiny') for the implemented methods to help in designing and deploying the
computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 0.25.3 dated 2015-08-01 and 0.25.4 dated 2015-10-27
distcomp-0.25.3/distcomp/inst/ex/STCoxDefn.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxDefn.rds |only distcomp-0.25.3/distcomp/inst/ex/STCoxMasterSetup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxSite1Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxSite2Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxTest.R |only distcomp-0.25.3/distcomp/inst/ex/STCoxTest.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDDefn.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDDefn.rds |only distcomp-0.25.3/distcomp/inst/ex/SVDMasterSetup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite1Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite2Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite3Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.R |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.rds |only distcomp-0.25.3/distcomp/inst/ex/svd-example-full-new.Rout |only distcomp-0.25.3/distcomp/inst/ex/svd-example-full.Rout |only distcomp-0.25.3/distcomp/inst/webApps/setupSlaveApp |only distcomp-0.25.3/distcomp/man/coxMaster.Rd |only distcomp-0.25.3/distcomp/man/coxSlave.Rd |only distcomp-0.25.3/distcomp/man/makeSlave.Rd |only distcomp-0.25.3/distcomp/man/setupSlave.Rd |only distcomp-0.25.3/distcomp/man/svdMaster.Rd |only distcomp-0.25.3/distcomp/man/svdSlave.Rd |only distcomp-0.25.4/distcomp/DESCRIPTION | 6 distcomp-0.25.4/distcomp/MD5 | 97 distcomp-0.25.4/distcomp/NAMESPACE | 8 distcomp-0.25.4/distcomp/R/coxstuff.R | 16 distcomp-0.25.4/distcomp/R/distcomp.R | 72 distcomp-0.25.4/distcomp/R/svdstuff.R | 25 distcomp-0.25.4/distcomp/README.md | 15 distcomp-0.25.4/distcomp/inst/doc/examples.html | 60 distcomp-0.25.4/distcomp/inst/doc/examples.pdf |binary distcomp-0.25.4/distcomp/inst/doc_src/examples.Rmd | 10 distcomp-0.25.4/distcomp/inst/doc_src/examples.md | 64 distcomp-0.25.4/distcomp/inst/ex/README.Rmd | 70 distcomp-0.25.4/distcomp/inst/ex/README.html | 82 distcomp-0.25.4/distcomp/inst/ex/README.md | 70 distcomp-0.25.4/distcomp/inst/ex/Rprofile |only distcomp-0.25.4/distcomp/inst/ex/STCoxMaster.R |only distcomp-0.25.4/distcomp/inst/ex/STCoxMaster.Rout |only distcomp-0.25.4/distcomp/inst/ex/STCoxSetup.Rout |only distcomp-0.25.4/distcomp/inst/ex/STCoxTest.rds |only distcomp-0.25.4/distcomp/inst/ex/SVDMaster.R |only distcomp-0.25.4/distcomp/inst/ex/SVDMaster.Rout |only distcomp-0.25.4/distcomp/inst/ex/SVDSetup.Rout |only distcomp-0.25.4/distcomp/inst/ex/SVDTestDefn.rds |only distcomp-0.25.4/distcomp/inst/ex/svd-example.R | 3 distcomp-0.25.4/distcomp/inst/ex/svd-example.Rout | 5051 +++++++++- distcomp-0.25.4/distcomp/inst/ex/uis-example.R | 2 distcomp-0.25.4/distcomp/inst/ex/uis-example.Rout | 38 distcomp-0.25.4/distcomp/inst/webApps/definitionApp/defineNewCoxModel/server.R | 4 distcomp-0.25.4/distcomp/inst/webApps/setupWorkerApp |only distcomp-0.25.4/distcomp/man/CoxMaster.Rd |only distcomp-0.25.4/distcomp/man/CoxWorker.Rd |only distcomp-0.25.4/distcomp/man/SVDMaster.Rd |only distcomp-0.25.4/distcomp/man/SVDWorker.Rd |only distcomp-0.25.4/distcomp/man/availableComputations.Rd | 8 distcomp-0.25.4/distcomp/man/distcomp-internal.Rd | 12 distcomp-0.25.4/distcomp/man/makeWorker.Rd |only distcomp-0.25.4/distcomp/man/runDistcompApp.Rd | 8 distcomp-0.25.4/distcomp/man/saveNewComputation.Rd | 2 distcomp-0.25.4/distcomp/man/setupWorker.Rd |only distcomp-0.25.4/distcomp/man/writeCode.Rd | 2 65 files changed, 5380 insertions(+), 345 deletions(-)
Title: Continuous Time Autoregressive Models
Description: Functions to Fit Continuous Time Autoregressive Models with the Kalman Filter.
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port by Zhu Wang with contribution from John Nash, Netlib and NAG authors
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between cts versions 1.0-19 dated 2014-02-26 and 1.0-20 dated 2015-10-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 7 ++++++- build/vignette.rds |binary inst/doc/kf.pdf |binary 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Buckley-James Regression for Survival Data with High-Dimensional
Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Including L_2 boosting with componentwise linear least squares, componentwise smoothing splines, P-splines, regression trees and boosted MARS. Other high-dimensional tools include elastic net and MARS.
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bujar versions 0.1-4 dated 2014-06-24 and 0.1-5 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 7 +++++++ NEWS | 5 +++++ 4 files changed, 20 insertions(+), 8 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.cn versions 1.6.0 dated 2015-02-24 and 1.6.1 dated 2015-10-27
aroma.cn-1.6.0/aroma.cn/R/makeSmoothSplinePredict.DEPRECATED.R |only aroma.cn-1.6.1/aroma.cn/DESCRIPTION | 21 +- aroma.cn-1.6.1/aroma.cn/MD5 | 16 - aroma.cn-1.6.1/aroma.cn/NAMESPACE | 14 + aroma.cn-1.6.1/aroma.cn/NEWS | 11 + aroma.cn-1.6.1/aroma.cn/R/021.dynamic_imports.R | 100 +++++----- aroma.cn-1.6.1/aroma.cn/R/999.DEPRECATED.R |only aroma.cn-1.6.1/aroma.cn/R/CartesianSnpData.R | 4 aroma.cn-1.6.1/aroma.cn/R/PeaksAndValleys.EXTS.R | 12 - aroma.cn-1.6.1/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 6 10 files changed, 96 insertions(+), 88 deletions(-)
Title: Utility Functions for Web Applications
Description: Utility functions for developing web applications. Includes parsers
for application/x-www-form-urlencoded as well as multipart/form-data
and examples of using the parser with either httpuv or rhttpd.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between webutils versions 0.3 dated 2015-01-24 and 0.4 dated 2015-10-27
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- R/demo_httpuv.R | 2 ++ man/demo_httpuv.Rd | 3 ++- man/demo_rhttpd.Rd | 3 ++- man/parse_http.Rd | 3 ++- man/parse_multipart.Rd | 3 ++- man/parse_query.Rd | 3 ++- 9 files changed, 31 insertions(+), 19 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: Functions for estimating split-duration regression models and various associated generic function methods.
Author: Andreas Beger [aut, cre],
Daina Chiba [aut],
Daniel Hill [aut],
Nils Metternich [aut],
Shahryar Minhas [aut],
Michael Ward [cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.13.1 dated 2015-07-09 and 0.14.0 dated 2015-10-27
spduration-0.13.1/spduration/R/attemptDate.R |only spduration-0.13.1/spduration/R/forecast.default.R |only spduration-0.13.1/spduration/R/forecast.spdur.R |only spduration-0.13.1/spduration/R/model.coups.R |only spduration-0.13.1/spduration/R/plot_hazard.r |only spduration-0.13.1/spduration/man/attemptDate.Rd |only spduration-0.13.1/spduration/man/loglog_hazard.Rd |only spduration-0.13.1/spduration/man/weibull_hazard.Rd |only spduration-0.14.0/spduration/DESCRIPTION | 11 spduration-0.14.0/spduration/MD5 | 93 +++--- spduration-0.14.0/spduration/NAMESPACE | 4 spduration-0.14.0/spduration/R/RcppExports.R | 8 spduration-0.14.0/spduration/R/add_duration.R | 89 ------ spduration-0.14.0/spduration/R/attempt_date.R |only spduration-0.14.0/spduration/R/data-docs.R |only spduration-0.14.0/spduration/R/forecast.R | 193 +++++++++++++ spduration-0.14.0/spduration/R/panel_lag.R | 25 - spduration-0.14.0/spduration/R/plot.spdur.R | 264 +++++++++++++------ spduration-0.14.0/spduration/R/predict.spdur.R | 28 -- spduration-0.14.0/spduration/R/spdur.R | 7 spduration-0.14.0/spduration/R/spduration-package.R | 38 -- spduration-0.14.0/spduration/R/sploglog.R | 4 spduration-0.14.0/spduration/R/spweibull.R | 4 spduration-0.14.0/spduration/R/summary.spdur.R | 9 spduration-0.14.0/spduration/README.md | 41 -- spduration-0.14.0/spduration/data/bscoup.rda |only spduration-0.14.0/spduration/man/add_duration.Rd | 3 spduration-0.14.0/spduration/man/attempt_date.Rd |only spduration-0.14.0/spduration/man/bscoup.Rd |only spduration-0.14.0/spduration/man/coups.Rd | 2 spduration-0.14.0/spduration/man/forecast.Rd | 2 spduration-0.14.0/spduration/man/forecast.default.Rd | 2 spduration-0.14.0/spduration/man/forecast.spdur.Rd | 2 spduration-0.14.0/spduration/man/hazard.Rd | 7 spduration-0.14.0/spduration/man/loglog.Rd | 1 spduration-0.14.0/spduration/man/loglog_lnl.Rd | 1 spduration-0.14.0/spduration/man/model.coups.Rd | 2 spduration-0.14.0/spduration/man/plot.spdur.Rd | 21 - spduration-0.14.0/spduration/man/plot_hazard.Rd |only spduration-0.14.0/spduration/man/plot_hazard1.Rd | 16 - spduration-0.14.0/spduration/man/plot_hazard2.Rd | 20 - spduration-0.14.0/spduration/man/spdur.Rd | 2 spduration-0.14.0/spduration/man/sploglog.Rd | 1 spduration-0.14.0/spduration/man/sploglog_lnl.Rd | 1 spduration-0.14.0/spduration/man/spweib_lnl.Rd | 1 spduration-0.14.0/spduration/man/spweibull.Rd | 1 spduration-0.14.0/spduration/man/weib_lnl.Rd | 1 spduration-0.14.0/spduration/man/weibull.Rd | 1 spduration-0.14.0/spduration/src/loglog_lnl.cpp | 3 spduration-0.14.0/spduration/src/sploglog_lnl.cpp | 2 spduration-0.14.0/spduration/src/spweib_lnl.cpp | 2 spduration-0.14.0/spduration/src/weib_lnl.cpp | 2 spduration-0.14.0/spduration/tests |only 53 files changed, 540 insertions(+), 374 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.6 dated 2015-09-05 and 0.10.7 dated 2015-10-27
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- configure | 17 +++++++++-------- 3 files changed, 17 insertions(+), 16 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.4-0 dated 2015-05-04 and 3.5-0 dated 2015-10-27
ncvreg-3.4-0/ncvreg/inst/tests/test.R |only ncvreg-3.5-0/ncvreg/DESCRIPTION | 8 +- ncvreg-3.5-0/ncvreg/MD5 | 43 +++++------ ncvreg-3.5-0/ncvreg/NAMESPACE | 10 +- ncvreg-3.5-0/ncvreg/NEWS | 19 ++++ ncvreg-3.5-0/ncvreg/R/auc.R |only ncvreg-3.5-0/ncvreg/R/convexMin.R | 23 ++--- ncvreg-3.5-0/ncvreg/R/cv.ncvreg.R | 34 ++++---- ncvreg-3.5-0/ncvreg/R/cv.ncvsurv.R | 116 ++++++++++++++++++------------ ncvreg-3.5-0/ncvreg/R/loss.R | 4 - ncvreg-3.5-0/ncvreg/R/ncvreg.R | 31 ++++---- ncvreg-3.5-0/ncvreg/R/ncvsurv.R | 22 ++--- ncvreg-3.5-0/ncvreg/R/plot.cv.ncvreg.R | 2 ncvreg-3.5-0/ncvreg/R/setupLambda.R | 6 - ncvreg-3.5-0/ncvreg/R/setupLambdaCox.R | 10 +- ncvreg-3.5-0/ncvreg/inst/tests/auc.R |only ncvreg-3.5-0/ncvreg/inst/tests/ncvreg.R |only ncvreg-3.5-0/ncvreg/inst/tests/parallel.R | 34 ++++++++ ncvreg-3.5-0/ncvreg/inst/tests/surv.R | 13 +++ ncvreg-3.5-0/ncvreg/man/auc.Rd |only ncvreg-3.5-0/ncvreg/man/cv.ncvreg.Rd | 14 +++ ncvreg-3.5-0/ncvreg/man/cv.ncvsurv.Rd | 43 ++++++++--- ncvreg-3.5-0/ncvreg/man/ncvreg-package.Rd | 4 - ncvreg-3.5-0/ncvreg/man/ncvreg.Rd | 2 ncvreg-3.5-0/ncvreg/src/cox-dh.c | 41 +++++++--- 25 files changed, 310 insertions(+), 169 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-5 dated 2015-10-20 and 0.1-6 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/gimme.R | 18 ++++++++++-------- 3 files changed, 17 insertions(+), 15 deletions(-)
Title: Create a Simple Web API for your R Functions
Description: A set of convenience functions to build simple APIs.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between jug versions 0.1.0 dated 2015-10-27 and 0.1.1 dated 2015-10-27
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/middleware_core.R | 6 +++--- R/middleware_error.R | 1 + R/response.R | 4 ++++ build/vignette.rds |binary inst/doc/jug.Rmd | 4 ++-- inst/doc/jug.html | 2 +- man/Error.Rd | 2 +- man/Middleware.Rd | 2 +- man/MiddlewareHandler.Rd | 2 +- man/RawTestRequest.Rd | 2 +- man/Request.Rd | 2 +- man/Response.Rd | 2 +- vignettes/jug.Rmd | 4 ++-- 15 files changed, 36 insertions(+), 31 deletions(-)
Title: Graph Edge Computations for Spatial Point Patterns
Description: Graphs (or networks) and graph component
calculations for spatial locations in *D.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between spatgraphs versions 2.62 dated 2012-09-26 and 3.0 dated 2015-10-27
spatgraphs-2.62/spatgraphs/R/First.R |only spatgraphs-2.62/spatgraphs/R/adjacency.R |only spatgraphs-2.62/spatgraphs/R/class.R |only spatgraphs-2.62/spatgraphs/R/clip.R |only spatgraphs-2.62/spatgraphs/R/clustering.R |only spatgraphs-2.62/spatgraphs/R/edgelengths.R |only spatgraphs-2.62/spatgraphs/R/mstoperations.R |only spatgraphs-2.62/spatgraphs/R/others.R |only spatgraphs-2.62/spatgraphs/R/plot.R |only spatgraphs-2.62/spatgraphs/R/runif3d.R |only spatgraphs-2.62/spatgraphs/R/spectral.R |only spatgraphs-2.62/spatgraphs/R/summary.R |only spatgraphs-2.62/spatgraphs/R/weights.R |only spatgraphs-2.62/spatgraphs/ToAdd.TXT0 |only spatgraphs-2.62/spatgraphs/change.log |only spatgraphs-2.62/spatgraphs/man/spatgraphs-clip.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-cut.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-legacy.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-mailer.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-other.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-package.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-plot.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-print.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-runif3d.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg2dxf.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg2igraph.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sgc.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-shake.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-shortestPath.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spatcluster.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spatgraph.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spectral.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-weight.Rd |only spatgraphs-2.62/spatgraphs/src/Point.cpp |only spatgraphs-2.62/spatgraphs/src/Point.h |only spatgraphs-2.62/spatgraphs/src/Rextras.cpp |only spatgraphs-2.62/spatgraphs/src/Rextras.h |only spatgraphs-2.62/spatgraphs/src/clustering.cpp |only spatgraphs-2.62/spatgraphs/src/cutprune.cpp |only spatgraphs-2.62/spatgraphs/src/dists.cpp |only spatgraphs-2.62/spatgraphs/src/dists.h |only spatgraphs-2.62/spatgraphs/src/rgraph.cpp |only spatgraphs-3.0/spatgraphs/DESCRIPTION | 22 spatgraphs-3.0/spatgraphs/MD5 | 119 - spatgraphs-3.0/spatgraphs/NAMESPACE | 57 spatgraphs-3.0/spatgraphs/NEWS |only spatgraphs-3.0/spatgraphs/R/RcppExports.R |only spatgraphs-3.0/spatgraphs/R/adjacency_matrix.R |only spatgraphs-3.0/spatgraphs/R/class_sg.R |only spatgraphs-3.0/spatgraphs/R/class_sgc.R |only spatgraphs-3.0/spatgraphs/R/constants.R |only spatgraphs-3.0/spatgraphs/R/cut_sg.R |only spatgraphs-3.0/spatgraphs/R/edgeLengths.R |only spatgraphs-3.0/spatgraphs/R/parse_input_coordinates.R |only spatgraphs-3.0/spatgraphs/R/plot_sg.R |only spatgraphs-3.0/spatgraphs/R/plot_sgc.R |only spatgraphs-3.0/spatgraphs/R/prune_sg.R |only spatgraphs-3.0/spatgraphs/R/set_weights.R |only spatgraphs-3.0/spatgraphs/R/sg2dxf.R | 100 - spatgraphs-3.0/spatgraphs/R/sg2igraph.R | 96 - spatgraphs-3.0/spatgraphs/R/shortestPath.R | 157 +- spatgraphs-3.0/spatgraphs/R/spatcluster.R |only spatgraphs-3.0/spatgraphs/R/spatgraph.R | 245 --- spatgraphs-3.0/spatgraphs/R/spectral_sg.R |only spatgraphs-3.0/spatgraphs/R/verify_parameters.R |only spatgraphs-3.0/spatgraphs/man/SG_GRAPH_PARAMETERS.Rd |only spatgraphs-3.0/spatgraphs/man/adj2sg.Rd |only spatgraphs-3.0/spatgraphs/man/as.sg.Rd |only spatgraphs-3.0/spatgraphs/man/as.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/as.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/cut.sg.Rd |only spatgraphs-3.0/spatgraphs/man/edgeLengths.Rd |only spatgraphs-3.0/spatgraphs/man/is_sg.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sg.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgspectral.Rd |only spatgraphs-3.0/spatgraphs/man/plot3.sg.Rd |only spatgraphs-3.0/spatgraphs/man/print.sg.Rd |only spatgraphs-3.0/spatgraphs/man/print.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/print.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/prune.sg.Rd |only spatgraphs-3.0/spatgraphs/man/sg2adj.Rd |only spatgraphs-3.0/spatgraphs/man/sg2dxf.Rd |only spatgraphs-3.0/spatgraphs/man/sg2igraph.Rd |only spatgraphs-3.0/spatgraphs/man/sg2sparse.Rd |only spatgraphs-3.0/spatgraphs/man/sg2sym.Rd |only spatgraphs-3.0/spatgraphs/man/sg2wadj.Rd |only spatgraphs-3.0/spatgraphs/man/sg_parse_coordinates.Rd |only spatgraphs-3.0/spatgraphs/man/sg_verify_parameters.Rd |only spatgraphs-3.0/spatgraphs/man/shortestPath.Rd |only spatgraphs-3.0/spatgraphs/man/sparse2sg.Rd |only spatgraphs-3.0/spatgraphs/man/spatcluster.Rd |only spatgraphs-3.0/spatgraphs/man/spatgraph.Rd |only spatgraphs-3.0/spatgraphs/man/spectral.sg.Rd |only spatgraphs-3.0/spatgraphs/man/summary.sg.Rd |only spatgraphs-3.0/spatgraphs/man/summary.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/t.sg.Rd |only spatgraphs-3.0/spatgraphs/man/t.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/weight.sg.Rd |only spatgraphs-3.0/spatgraphs/src/Graph.cpp | 1096 ++++---------- spatgraphs-3.0/spatgraphs/src/Graph.h | 97 - spatgraphs-3.0/spatgraphs/src/Pp.cpp | 298 --- spatgraphs-3.0/spatgraphs/src/Pp.h | 107 - spatgraphs-3.0/spatgraphs/src/RcppExports.cpp |only spatgraphs-3.0/spatgraphs/src/cut.cpp |only spatgraphs-3.0/spatgraphs/src/prune.cpp |only spatgraphs-3.0/spatgraphs/src/spatcluster.cpp |only spatgraphs-3.0/spatgraphs/src/spatgraph.cpp |only 110 files changed, 842 insertions(+), 1552 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.21 dated 2015-03-30 and 1.4.22 dated 2015-10-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 10 ++++++++++ R/elda.R | 4 ++-- inst/NEWS | 5 +++++ 5 files changed, 26 insertions(+), 10 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names, default values and
(if so desired) ranges or sets of allowed option values that will be
automatically checked. Settings can then be retrieved, altered and reset
to defaults with ease. For R programmers and package developers it offers
cloning and merging functionality which allows for conveniently defining
global and local options, possibly in a multilevel options hierarchy. See
the package vignette for some examples concerning functions, S4 classes,
and reference classes. There are convenience functions to reset par()
and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between settings versions 0.2.2 dated 2015-06-01 and 0.2.4 dated 2015-10-27
DESCRIPTION | 26 ++++++------ MD5 | 23 +++++----- NAMESPACE | 2 NEWS | 4 + R/options.R | 91 +++++++++++++++++++++++++++++++++++++++++-- inst/doc/settings.R | 14 ++++++ inst/doc/settings.Rmd | 31 ++++++++++++++ inst/doc/settings.html | 32 ++++++++++++++- man/clone_and_merge.Rd | 15 +++++++ man/inlist.Rd |only man/options_manager.Rd | 16 +++++++ tests/testthat/testOptions.R | 20 +++++++++ vignettes/settings.Rmd | 31 ++++++++++++++ 13 files changed, 276 insertions(+), 29 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.1-5 dated 2015-05-11 and 1.2-0 dated 2015-10-27
DESCRIPTION | 10 +- MD5 | 30 ++++-- NAMESPACE | 9 + R/g.analyse.R | 1 R/g.create.sp.mat.R |only R/g.getbout.R |only R/g.loadlog.R |only R/g.part3.R |only R/g.part4.R |only R/g.plot5.R |only R/g.report.part2.R | 6 - R/g.report.part4.R |only R/g.shell.GGIR.R | 95 ++++++++++++++++++-- R/g.sib.det.R |only R/g.sib.plot.R |only R/g.sib.sum.R |only data/datalist | 6 - inst/NEWS.Rd | 192 +++++++++++++++++++++-------------------- man/GGIR-package.Rd | 238 ++++++++++++++++++++++++++-------------------------- man/g.part3.Rd |only man/g.part4.Rd |only man/g.shell.GGIR.Rd | 124 ++++++++++++++++++++++----- 22 files changed, 450 insertions(+), 261 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.7 dated 2015-09-21 and 2.1.7-1 dated 2015-10-27
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++----------- NEWS | 9 ++++- R/advanced.procD.lm.r | 36 +++++++++++----------- R/bilat.symmetry.r | 23 ++++---------- R/geomorph.support.code.r | 75 ++++++++++++++++++++++++++++++---------------- R/gpagen.r | 2 - R/morphol.disparity.r | 7 ++-- R/plotAllometry.r | 50 ++++++++++++++---------------- R/procD.lm.r | 2 - R/procD.pgls.r | 22 +++++++++---- R/readland.nts.r | 6 ++- R/trajectory.analysis.r | 5 +-- R/two.b.pls.r | 17 +++++----- R/warpRefMesh.r | 15 ++++----- README.md |only man/gpagen.Rd | 2 - man/plotAllometry.Rd | 8 ++-- man/procD.pgls.Rd | 4 +- man/two.b.pls.Rd | 11 ++++-- src/geomorph.c | 7 +++- 21 files changed, 195 insertions(+), 153 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.1 dated 2015-09-01 and 1.7.2 dated 2015-10-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/build.dist.struct.R | 3 +-- R/rcbalance-internal.R | 6 ++---- R/rcbalance.R | 6 ++++-- man/dist2net.Rd | 6 +++++- 6 files changed, 21 insertions(+), 18 deletions(-)
Title: Converting Odds Ratio to Relative Risk in Cohort Studies with
Partial Data Information
Description: Convert the Odds Ratio to the Relative Risk in Cohort Studies with Partial Data Information.
Author: Zhu Wang
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between orsk versions 1.0-1 dated 2013-10-10 and 1.0-2 dated 2015-10-27
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 ++- build/vignette.rds |binary 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Normal Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between mclust versions 5.0.2 dated 2015-07-08 and 5.1 dated 2015-10-27
DESCRIPTION | 10 MD5 | 68 ++--- R/bootstrap.R | 4 R/densityMclust.R | 48 ++- R/mclust.R | 34 ++ R/mclustaddson.R | 82 +++--- R/mclustda.R | 148 +++++------ R/mclustdr.R | 12 R/util.R | 5 build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/NEWS | 6 inst/doc/mclust.Rmd | 1 inst/doc/mclust.html | 410 ++++++++++++++++---------------- man/Mclust.Rd | 2 man/MclustDA.Rd | 4 man/bic.Rd | 2 man/clustCombi.Rd | 2 man/diabetes.Rd | 2 man/emControl.Rd | 15 - man/estep.Rd | 2 man/mclustModel.Rd | 4 man/mvn.Rd | 2 man/mvnX.Rd | 2 man/plot.densityMclust.Rd | 36 +- man/summary.mclustBIC.Rd | 4 src/mclustaddson.f | 240 ++++++++++++++++-- vignettes/mclust.Rmd | 1 35 files changed, 698 insertions(+), 448 deletions(-)
Title: Methods that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.14.2 dated 2015-06-24 and 0.15.0 dated 2015-10-27
DESCRIPTION | 8 ++-- MD5 | 64 +++++++++++++++++++---------------- NAMESPACE | 4 ++ NEWS | 22 ++++++++++-- R/rowMads.R | 8 ++-- R/weightedMad.R | 13 ++++--- R/weightedMean.R | 12 +++++- R/weightedMedian.R | 8 +++- R/weightedVar.R | 45 ++++++++++++++++-------- build/vignette.rds |binary inst/doc/matrixStats-methods.html | 4 +- man/matrixStats-package.Rd | 2 - man/weightedMad.Rd | 2 - man/weightedMean.Rd | 2 - man/weightedMedian.Rd | 3 - man/weightedVar.Rd | 11 +++++- src/allocMatrix2.c | 2 - src/binMeans-BINBY-template.h | 3 + src/diff2_TYPE-template.h | 2 - src/logSumExp_internal.c | 36 ++++++++++++------- src/meanOver_TYPE-template.h | 22 +++++++++--- src/productExpSumLog_TYPE-template.h | 7 +++ src/rowDiffs_TYPE-template.h | 2 - src/sumOver_TYPE-template.h | 10 ++++- src/weightedMean_TYPE-template.h | 13 ++++++- src/weightedMedian_TYPE-template.h | 8 ---- tests/reports |only tests/rowWeightedVars.R | 7 ++- tests/weightedMedian.R | 13 +++++++ tests/weightedVar.R |only tests/weightedVar_etal.R | 3 - 31 files changed, 228 insertions(+), 108 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for model validation and calibration.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 2.0 dated 2015-09-16 and 2.1 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 15 ++++++++++++++- R/hdnom.calibrate.R | 2 +- R/hdnom.models.R | 47 ++++++++++++++++++++++++++++++++++++++++++----- README.md | 2 +- TODO | 2 +- inst/doc/hdnom.Rmd | 4 ++-- inst/doc/hdnom.html | 12 ++++++------ man/hdcox.mcp.Rd | 10 +++++----- man/hdnom.calibrate.Rd | 2 +- vignettes/hdnom.Rmd | 4 ++-- 12 files changed, 91 insertions(+), 41 deletions(-)
Title: Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
Author: Maria Ortiz [aut, ctb],
Ander Aramburu [ctb],
Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut, ctb],
Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between calmate versions 0.12.0 dated 2015-02-23 and 0.12.1 dated 2015-10-27
DESCRIPTION | 14 ++++---- MD5 | 10 +++--- NAMESPACE | 3 + NEWS | 6 +++ tests/calmateByTotalAndFracB.R | 68 ++++++++++++++++++++--------------------- tests/thetaAB2TotalAndFracB.R | 28 ++++++++-------- 6 files changed, 68 insertions(+), 61 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between ACNE versions 0.8.0 dated 2015-02-23 and 0.8.1 dated 2015-10-27
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 6 ++++++ NEWS | 4 ++++ man/ACNE-package.Rd | 2 +- 5 files changed, 25 insertions(+), 14 deletions(-)
Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>
Diff between NlcOptim versions 0.1 dated 2015-10-12 and 0.2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/NlcOptim.R | 6 +++++- man/NlcOptim.Rd | 8 +++++++- 4 files changed, 19 insertions(+), 9 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath') and adaptive 'SPUpath' ('aSPUpath') test, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST'), extended version of 'GATES' test for pathway-based association testing ('Gates-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative.
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.37 dated 2015-08-03 and 1.38 dated 2015-10-26
DESCRIPTION | 10 +-- MD5 | 22 ++++--- NAMESPACE | 6 +- R/GEEaSPU.R |only R/aSPUs.R | 21 ++++--- R/aSPUsPath.r | 4 + R/aSPUsim1.R | 6 +- R/aSPUsim2.R | 7 ++ R/util.R | 157 +++++++++++++++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary man/GEEaSPU.Rd |only man/aSPUs.Rd | 20 ++++-- man/aSPUsPath.Rd | 4 + 13 files changed, 223 insertions(+), 34 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-13 dated 2015-09-28 and 0.3-14 dated 2015-10-26
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/ChangeLog | 14 ++++++++++++++ inst/SVN_VERSION | 2 +- man/topo-bin-gIntersection.Rd | 26 ++++++++++++++++++++++++++ src/rgeos_topology_binary.c | 8 ++++---- 7 files changed, 69 insertions(+), 15 deletions(-)
Title: D3 Javascript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.1.1 dated 2015-06-30 and 0.3 dated 2015-10-26
scatterD3-0.1.1/scatterD3/inst/htmlwidgets/lib/d3-3.5.5.min.js |only scatterD3-0.3/scatterD3/DESCRIPTION | 14 scatterD3-0.3/scatterD3/MD5 | 33 scatterD3-0.3/scatterD3/NAMESPACE | 2 scatterD3-0.3/scatterD3/NEWS | 21 scatterD3-0.3/scatterD3/R/scatterD3.R | 85 scatterD3-0.3/scatterD3/README.md | 54 scatterD3-0.3/scatterD3/build/vignette.rds |binary scatterD3-0.3/scatterD3/inst/doc/introduction.R | 6 scatterD3-0.3/scatterD3/inst/doc/introduction.Rmd | 84 scatterD3-0.3/scatterD3/inst/doc/introduction.html | 118 scatterD3-0.3/scatterD3/inst/htmlwidgets/lib/d3-3.5.6.min.js |only scatterD3-0.3/scatterD3/inst/htmlwidgets/lib/d3-legend.min.js |only scatterD3-0.3/scatterD3/inst/htmlwidgets/lib/scatterD3.css | 5 scatterD3-0.3/scatterD3/inst/htmlwidgets/scatterD3.js | 1268 ++++++---- scatterD3-0.3/scatterD3/inst/htmlwidgets/scatterD3.yaml | 6 scatterD3-0.3/scatterD3/man/scatterD3-shiny.Rd | 4 scatterD3-0.3/scatterD3/man/scatterD3.Rd | 40 scatterD3-0.3/scatterD3/vignettes/introduction.Rmd | 84 19 files changed, 1093 insertions(+), 731 deletions(-)
Title: Data Integration Feature for Force.com and Salesforce.com
Description: Insert, update,
retrieve, delete and bulk operate datasets with a SaaS based CRM
Salesforce.com and a PaaS based application platform Force.com from R.
Author: Takekatsu Hiramura [aut, cre],
Steven Mortimer [ctb],
Alexis Iglauer [ctb]
Maintainer: Takekatsu Hiramura <thira@plavox.info>
Diff between RForcecom versions 0.7 dated 2013-10-23 and 0.8 dated 2015-10-26
RForcecom-0.7/RForcecom/man/RForcecom-package.Rd |only RForcecom-0.8/RForcecom/DESCRIPTION | 48 ++- RForcecom-0.8/RForcecom/MD5 | 64 +++-- RForcecom-0.8/RForcecom/NAMESPACE | 58 +++- RForcecom-0.8/RForcecom/R/RForcecom.R |only RForcecom-0.8/RForcecom/R/rforcecom.abortBulkJob.R |only RForcecom-0.8/RForcecom/R/rforcecom.api.R | 19 + RForcecom-0.8/RForcecom/R/rforcecom.bulkQuery.R |only RForcecom-0.8/RForcecom/R/rforcecom.checkBatchStatus.R |only RForcecom-0.8/RForcecom/R/rforcecom.closeBulkJob.R |only RForcecom-0.8/RForcecom/R/rforcecom.create.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.createBulkBatch.R |only RForcecom-0.8/RForcecom/R/rforcecom.createBulkJob.R |only RForcecom-0.8/RForcecom/R/rforcecom.debug.R | 1 RForcecom-0.8/RForcecom/R/rforcecom.delete.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.getBatchDetails.R |only RForcecom-0.8/RForcecom/R/rforcecom.getBulkQueryResult.R |only RForcecom-0.8/RForcecom/R/rforcecom.getObjectDescription.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.getObjectList.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.getServerTimestamp.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.insertBulkAttachments.R |only RForcecom-0.8/RForcecom/R/rforcecom.login.R | 127 ++++++---- RForcecom-0.8/RForcecom/R/rforcecom.logout.R |only RForcecom-0.8/RForcecom/R/rforcecom.query.R | 20 - RForcecom-0.8/RForcecom/R/rforcecom.queryMore.R | 14 - RForcecom-0.8/RForcecom/R/rforcecom.retrieve.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.search.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.submitBulkQuery.R |only RForcecom-0.8/RForcecom/R/rforcecom.update.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.upsert.R | 7 RForcecom-0.8/RForcecom/R/rforcecom.write.csv.R |only RForcecom-0.8/RForcecom/man/RForcecom.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.abortBulkJob.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.api.Rd | 2 RForcecom-0.8/RForcecom/man/rforcecom.bulkQuery.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.checkBatchStatus.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.closeBulkJob.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.createBulkBatch.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.createBulkJob.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.getBatchDetails.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.getBulkQueryResult.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.insertBulkAttachments.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.login.Rd | 70 +---- RForcecom-0.8/RForcecom/man/rforcecom.logout.Rd |only RForcecom-0.8/RForcecom/man/rforcecom.query.Rd | 8 RForcecom-0.8/RForcecom/man/rforcecom.submitBulkQuery.Rd |only 46 files changed, 290 insertions(+), 204 deletions(-)
Title: Talk to the NCBI EUtils
Description: An interface to NCBI databases such as PubMed, GenBank, or GEO
powered by the Entrez Programming Utilities (EUtils). The nine EUtils
provide programmatic access to the NCBI Entrez query and database
system for searching and retrieving biological data.
Author: Gerhard Schöfl <gerhard.schofl@gmail.com>
Maintainer: Gerhard Schöfl <gerhard.schofl@gmail.com>
Diff between reutils versions 0.2.1 dated 2015-08-29 and 0.2.2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 ++++++- R/elink.R | 33 ++++++++++++++++++++------------- R/reutils-package.R | 1 + R/utils.R | 1 + man/elink.Rd | 2 +- 7 files changed, 39 insertions(+), 25 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.4-1786 dated 2015-10-21 and 2.4-1788 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/bccorr.R | 26 ++++++++++++++++++-------- R/cgsolve.R | 4 ++-- exec/lfescript | 10 ++++++++-- inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary src/lfe.c | 4 ++-- src/lfe.h | 4 ++-- 10 files changed, 45 insertions(+), 29 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert <marius.hofert@uwaterloo.ca>,
Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>,
Martin Maechler <maechler@stat.math.ethz.ch>, and
Jun Yan <jun.yan@uconn.edu>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 0.999-13 dated 2015-03-05 and 0.999-14 dated 2015-10-26
copula-0.999-13/copula/R/device.R |only copula-0.999-13/copula/demo/AC-Liouville-demo.R |only copula-0.999-13/copula/demo/GIG-demo.R |only copula-0.999-13/copula/demo/QARClayton.R |only copula-0.999-13/copula/demo/copula_garch.R |only copula-0.999-13/copula/demo/dnac-demo.R |only copula-0.999-13/copula/demo/gof_radial.R |only copula-0.999-13/copula/demo/logL-vis.R |only copula-0.999-13/copula/demo/qrng.R |only copula-0.999-13/copula/demo/tail_compatibility.R |only copula-0.999-13/copula/man/device.Rd |only copula-0.999-14/copula/DESCRIPTION | 32 ++-- copula-0.999-14/copula/MD5 | 120 +++++++++------- copula-0.999-14/copula/NAMESPACE | 111 ++++++++------ copula-0.999-14/copula/R/aux-acopula.R | 5 copula-0.999-14/copula/R/cop_objects.R | 1 copula-0.999-14/copula/R/empcop.R | 2 copula-0.999-14/copula/R/estimation.R | 8 - copula-0.999-14/copula/R/gofTests.R | 2 copula-0.999-14/copula/R/gofTrafos.R | 7 copula-0.999-14/copula/R/graphics.R | 10 - copula-0.999-14/copula/R/nacopula.R | 2 copula-0.999-14/copula/R/normalCopula.R | 5 copula-0.999-14/copula/R/tCopula.R | 3 copula-0.999-14/copula/TODO | 25 +++ copula-0.999-14/copula/build/partial.rdb |only copula-0.999-14/copula/build/vignette.rds |binary copula-0.999-14/copula/demo/00Index | 10 - copula-0.999-14/copula/demo/estimation_via_HAC.R |only copula-0.999-14/copula/demo/gofCopula.R | 17 +- copula-0.999-14/copula/demo/gof_graph.R | 6 copula-0.999-14/copula/demo/retstable.R | 14 + copula-0.999-14/copula/inst/NEWS.Rd | 31 +++- copula-0.999-14/copula/inst/Rsource/GIG.R | 116 ++++++++------- copula-0.999-14/copula/inst/Rsource/dnac.R | 9 - copula-0.999-14/copula/inst/Rsource/utils.R | 2 copula-0.999-14/copula/inst/doc/AC_Liouville.Rmd |only copula-0.999-14/copula/inst/doc/AC_Liouville.html |only copula-0.999-14/copula/inst/doc/AR_Clayton.Rmd |only copula-0.999-14/copula/inst/doc/AR_Clayton.html |only copula-0.999-14/copula/inst/doc/Frank-Rmpfr.pdf |binary copula-0.999-14/copula/inst/doc/GIG.Rmd |only copula-0.999-14/copula/inst/doc/GIG.html |only copula-0.999-14/copula/inst/doc/NALC.Rmd |only copula-0.999-14/copula/inst/doc/NALC.html |only copula-0.999-14/copula/inst/doc/copula_GARCH.Rmd |only copula-0.999-14/copula/inst/doc/copula_GARCH.html |only copula-0.999-14/copula/inst/doc/dNAC.Rmd |only copula-0.999-14/copula/inst/doc/dNAC.html |only copula-0.999-14/copula/inst/doc/logL_visualization.Rmd |only copula-0.999-14/copula/inst/doc/logL_visualization.html |only copula-0.999-14/copula/inst/doc/nacopula-pkg.pdf |binary copula-0.999-14/copula/inst/doc/qrng.Rmd |only copula-0.999-14/copula/inst/doc/qrng.html |only copula-0.999-14/copula/inst/doc/rhoAMH-dilog.Rnw | 3 copula-0.999-14/copula/inst/doc/rhoAMH-dilog.pdf |binary copula-0.999-14/copula/inst/doc/tail_compatibility.Rmd |only copula-0.999-14/copula/inst/doc/tail_compatibility.html |only copula-0.999-14/copula/inst/doc/wild_animals.Rmd |only copula-0.999-14/copula/inst/doc/wild_animals.html |only copula-0.999-14/copula/man/An.Rd | 4 copula-0.999-14/copula/man/Mvdc.Rd | 2 copula-0.999-14/copula/man/coeffG.Rd |only copula-0.999-14/copula/man/contour-methods.Rd | 10 - copula-0.999-14/copula/man/copula-package.Rd | 14 - copula-0.999-14/copula/man/ellipCopula.Rd | 39 +++++ copula-0.999-14/copula/man/fitMvdc.Rd | 7 copula-0.999-14/copula/man/gofCopula.Rd | 19 +- copula-0.999-14/copula/man/pobs.Rd | 5 copula-0.999-14/copula/man/qqplot2.Rd | 10 - copula-0.999-14/copula/tests/estim-ex.R | 21 ++ copula-0.999-14/copula/tests/fitting-ex.R | 1 copula-0.999-14/copula/vignettes/AC_Liouville.Rmd |only copula-0.999-14/copula/vignettes/AR_Clayton.Rmd |only copula-0.999-14/copula/vignettes/GIG.Rmd |only copula-0.999-14/copula/vignettes/NALC.Rmd |only copula-0.999-14/copula/vignettes/copula_GARCH.Rmd |only copula-0.999-14/copula/vignettes/dNAC.Rmd |only copula-0.999-14/copula/vignettes/logL_visualization.Rmd |only copula-0.999-14/copula/vignettes/qrng.Rmd |only copula-0.999-14/copula/vignettes/rhoAMH-dilog.Rnw | 3 copula-0.999-14/copula/vignettes/tail_compatibility.Rmd |only copula-0.999-14/copula/vignettes/wild_animals.Rmd |only 83 files changed, 411 insertions(+), 265 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots
and similar graphics for exploring the properties of experimental designs. The design region is
explored via random sampling, which allows for more flexibility than traditional variance
dispersion graphs. A formula interface is leveraged to provide access to complex model
formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or
multiple model formulae. Instead of using pointwise optimization to find the minimum and
maximum scaled prediction variance curves, which can be inaccurate and time consuming, this
package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.1.1 dated 2015-08-21 and 1.1.2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot.spv.R | 2 +- man/plot.spv.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Gene Network Inference from Time-Series Transcriptomic Data
Description: The Time-Delay Correlation algorithm (TDCor) reconstructs the topology of a gene regulatory network (GRN) from time-series transcriptomic data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was initially developed to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset which was used in this study is included in the package to illustrate how to use it.
Author: Julien Lavenus
Maintainer: Mikael Lucas <mikael.lucas@ird.fr>
Diff between TDCor versions 0.1-1 dated 2015-04-18 and 0.1-2 dated 2015-10-26
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 4 ++++ R/TDCOR.R | 4 ++-- data/LR_dataset.rda |binary data/TF.rda |binary data/l_genes.rda |binary data/l_names.rda |binary data/l_prior.rda |binary data/times.rda |binary man/TDCOR.Rd | 11 +++++++---- man/TDCor-package.Rd | 4 ++-- 12 files changed, 30 insertions(+), 23 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams
(q-gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler).
An implementation of soundex is provided as well. Distances can be computed
between character vectors while taking proper care of encoding or between
integer vectors representing generic sequences.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.3 dated 2015-08-21 and 0.9.4 dated 2015-10-26
DESCRIPTION | 6 +- MD5 | 12 ++-- NEWS | 4 + src/Rstringdist.c | 9 ++- src/jaro.c | 116 ++++++++++++++++++---------------------- src/stringdist.c | 4 + tests/testthat/testStringdist.R | 7 ++ 7 files changed, 86 insertions(+), 72 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.1.1 dated 2015-10-08 and 1.1.2 dated 2015-10-26
DESCRIPTION | 8 +-- MD5 | 10 +-- R/Add_to_data_object.R | 125 ++++++++++++++++++++++++++----------------------- R/Prepare_data.R | 2 man/add_sitestat.Rd | 6 +- man/nodiv-package.Rd | 4 - 6 files changed, 83 insertions(+), 72 deletions(-)
Title: Genome-Wide Association Analysis of a Biomarker Accounting for
Limit of Detection
Description: Genome-wide association (GWAS) analyses
of a biomarker that account for the limit of detection.
Author: Ahmad Vaez, Ilja M. Nolte, Peter J. van der Most
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Diff between lodGWAS versions 1.0-3 dated 2015-02-20 and 1.0-6 dated 2015-10-26
lodGWAS-1.0-3/lodGWAS/R/packaging_v10-0.r |only lodGWAS-1.0-3/lodGWAS/inst/doc/Sample_geno.dose |only lodGWAS-1.0-3/lodGWAS/inst/doc/Sample_geno.map |only lodGWAS-1.0-3/lodGWAS/inst/doc/Sample_pheno.txt |only lodGWAS-1.0-6/lodGWAS/DESCRIPTION | 10 +++---- lodGWAS-1.0-6/lodGWAS/MD5 | 17 ++++++------ lodGWAS-1.0-6/lodGWAS/NAMESPACE | 2 + lodGWAS-1.0-6/lodGWAS/R/packaging_v10-6.r |only lodGWAS-1.0-6/lodGWAS/inst/doc/lodGWAS_changelog_v1_0_6.txt |only lodGWAS-1.0-6/lodGWAS/inst/extdata |only lodGWAS-1.0-6/lodGWAS/man/lodGWAS-package.Rd | 4 +- lodGWAS-1.0-6/lodGWAS/man/lod_GWAS.Rd | 15 +++++++--- 12 files changed, 29 insertions(+), 19 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description:
We provide a set of functions to retrieve information about GIMMS NDVI3g
files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native
binary (ENVI) format directly into R based on the widely applied 'raster'
package; and calculate monthly value composites (e.g. maximum value
composites, MVC) from the bi-monthly input data.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.1.1 dated 2015-10-09 and 0.2.0 dated 2015-10-26
gimms-0.1.1/gimms/R/createHdr.R |only gimms-0.1.1/gimms/man/createHdr.Rd |only gimms-0.2.0/gimms/DESCRIPTION | 8 gimms-0.2.0/gimms/MD5 | 32 +-- gimms-0.2.0/gimms/NAMESPACE | 2 gimms-0.2.0/gimms/R/createHeader.R |only gimms-0.2.0/gimms/R/downloadGimms.R | 30 ++- gimms-0.2.0/gimms/R/monthlyComposite.R | 14 + gimms-0.2.0/gimms/R/monthlyIndices.R | 121 +++++++++---- gimms-0.2.0/gimms/R/rasterizeGimms.R | 43 ++-- gimms-0.2.0/gimms/R/rearrangeFiles.R | 161 ++++++++++-------- gimms-0.2.0/gimms/R/updateInventory.R | 106 ++++++------ gimms-0.2.0/gimms/README.md | 261 +++++++++++++++++++++++++----- gimms-0.2.0/gimms/man/createHeader.Rd |only gimms-0.2.0/gimms/man/downloadGimms.Rd | 17 + gimms-0.2.0/gimms/man/monthlyComposite.Rd | 14 + gimms-0.2.0/gimms/man/monthlyIndices.Rd | 11 + gimms-0.2.0/gimms/man/rasterizeGimms.Rd | 30 +-- gimms-0.2.0/gimms/man/rearrangeFiles.Rd | 8 19 files changed, 568 insertions(+), 290 deletions(-)
Title: Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Description: Local inferential feature significance for multivariate kernel density estimation.
Author: Tarn Duong <tarn.duong@gmail.com> & Matt Wand <Matt.Wand@uts.edu.au>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between feature versions 1.2.12 dated 2015-09-08 and 1.2.13 dated 2015-10-26
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- R/dfltCounts.R |only R/drvkde.R |only R/featureSignif.R | 13 +++++-------- R/plot.fs.R | 36 ++++++++++++++++-------------------- inst/doc/feature.pdf |binary man/feature-package.Rd | 2 +- man/featureSignifGUI.Rd | 4 ++-- man/plot.fs.Rd | 3 ++- 10 files changed, 40 insertions(+), 44 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.1-0 dated 2015-08-16 and 1.1-1 dated 2015-10-26
DESCRIPTION | 9 - MD5 | 56 +++--- NAMESPACE | 3 R/ContingencyTests.R | 5 R/ContrastTest.R | 7 R/CorrelationTests.R | 20 +- R/MTP.R | 3 R/MaximallySelectedStatisticsTests.R | 5 R/helpers.R | 53 ++---- build/vignette.rds |binary inst/NEWS.Rd | 18 +- inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.R | 133 +++++++-------- inst/doc/coin.Rnw | 291 +++++++++++++++++---------------- inst/doc/coin.pdf |binary inst/doc/coin_implementation.pdf |binary man/IndependenceTest.Rd | 6 man/PermutationDistribution-methods.Rd | 11 + man/SymmetryTest.Rd | 4 man/ocarcinoma.Rd | 4 man/pvalue-methods.Rd | 4 tests/Examples/coin-Ex.Rout.save | 10 - tests/regtest_contingency.R | 25 +- tests/regtest_contingency.Rout.save | 29 +-- tests/regtest_distribution.R | 4 tests/regtest_distribution.Rout.save | 8 vignettes/coin.Rnw | 291 +++++++++++++++++---------------- vignettes/coin.Rout.save | 115 +++++-------- 29 files changed, 553 insertions(+), 561 deletions(-)
Title: API for UK Gas Market Information
Description: Allows users to access live UK gas market information via National Grid's API.
Author: Timothy Wong [aut, cre]
Maintainer: Timothy Wong <timothy.wong@hotmail.co.uk>
Diff between ukgasapi versions 0.10 dated 2015-10-18 and 0.13 dated 2015-10-25
DESCRIPTION | 12 +++++------ MD5 | 6 ++--- R/dataItemExplorer.R | 52 +++++++++++++++++++++++------------------------- man/dataItemExplorer.Rd | 19 ++++++----------- 4 files changed, 41 insertions(+), 48 deletions(-)
Title: Create "Table 1" to Describe Baseline Characteristics
Description: Creates "Table 1", i.e., description of baseline patient
characteristics, which is essential in every medical research.
Supports both continuous and categorical variables, as well as
p-values and standardized mean differences. Weighted data are
supported via the survey package. See github for a screencast.
tableone was inspired by descriptive statistics functions in
Deducer , a Java-based GUI package by Ian Fellows. This package
does not require GUI or Java, and intended for command-line users.
Author: Kazuki Yoshida, Justin Bohn.
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between tableone versions 0.7.1 dated 2015-08-12 and 0.7.2 dated 2015-10-25
DESCRIPTION | 8 - MD5 | 14 +- NEWS | 9 + R/modules-smd.R | 8 + R/tableone-package.R | 2 build/vignette.rds |binary inst/doc/smd.html | 254 ++++++++++++++++++++++++------------------------ man/tableone-package.Rd | 2 8 files changed, 155 insertions(+), 142 deletions(-)
Title: Optimization of Sample Configurations using Spatial Simulated
Annealing
Description: Methods to optimize sample configurations using spatial simulated
annealing. Multiple objective functions are implemented for various
purposes, such as variogram estimation, trend estimation, and spatial
interpolation. A general purpose spatial simulated annealing function
enables the user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre],
Lucia Helena Cunha dos Anjos [ths],
Gustavo de Mattos Vasques [ths],
Gerard B M Heuvelink [ths],
Edzer Pebesma [ctb],
Jon Skoien [ctb],
Joshua French [ctb],
Pierre Roudier [ctb],
Dick Brus [ctb],
Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between spsann versions 1.0.1 dated 2015-07-31 and 1.0-2 dated 2015-10-25
DESCRIPTION | 8 ++++---- MD5 | 45 ++++++++++++++++++++++++--------------------- NAMESPACE | 2 ++ R/AAA.R | 8 +++++--- R/SPSANNtools.R | 28 +++++++++++++++++++--------- R/check-spsann-arguments.R | 1 + R/optimACDC.R | 22 +++++++++++++++++----- R/optimCLHS.R |only R/optimCORR.R | 16 ++++++++++++++-- R/optimDIST.R | 4 ++-- R/optimPPL.R | 21 +++++++++++---------- R/optimSPAN.R | 25 +++++++++++++++++++++---- R/plotting-options.R | 8 +++++++- R/prepare-clhs-covars.R |only R/spsann.R | 4 ++-- man/optimACDC.Rd | 28 ++++++++++++++-------------- man/optimCLHS.Rd |only man/optimCORR.Rd | 22 +++++++++++----------- man/optimDIST.Rd | 22 +++++++++++----------- man/optimMKV.Rd | 18 +++++++++--------- man/optimMSSD.Rd | 18 +++++++++--------- man/optimPPL.Rd | 18 +++++++++--------- man/optimSPAN.Rd | 24 ++++++++++++------------ man/optimUSER.Rd | 18 +++++++++--------- man/spsann-package.Rd | 4 ++-- 25 files changed, 215 insertions(+), 149 deletions(-)
Title: Tools for Harnessing MLBAM Gameday Data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert <cpsievert1@gmail.com>
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between pitchRx versions 1.8 dated 2015-10-13 and 1.8.1 dated 2015-10-25
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 22 ++++++++++++++-------- R/animateFX.R | 1 - R/scrape.R | 1 - 5 files changed, 23 insertions(+), 19 deletions(-)
Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions K1, K2, K3 and K4 to characterize
distributions with left and right, symmetric or asymmetric fat tails in market
finance, neuroscience and other disciplines. Two algorithms to estimate with
a high accuracy distribution parameters, quantiles, value-at-risk and expected
shortfall. Also, power hyperbolas and power hyperbolic functions. This is a
major update that breaks compatibility with previous versions.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between FatTailsR versions 1.2-3 dated 2015-07-08 and 1.4-1 dated 2015-10-25
FatTailsR-1.2-3/FatTailsR/R/b_trigohp.R |only FatTailsR-1.2-3/FatTailsR/R/c_logishp.R |only FatTailsR-1.2-3/FatTailsR/R/d_conversion.R |only FatTailsR-1.2-3/FatTailsR/R/e_kiener1.R |only FatTailsR-1.2-3/FatTailsR/R/f_kiener2.R |only FatTailsR-1.2-3/FatTailsR/R/g_kiener3.R |only FatTailsR-1.2-3/FatTailsR/R/h_kiener4.R |only FatTailsR-1.2-3/FatTailsR/R/i_moments.R |only FatTailsR-1.2-3/FatTailsR/R/j_tailskiener.R |only FatTailsR-1.2-3/FatTailsR/R/k_estimation.R |only FatTailsR-1.2-3/FatTailsR/R/l_regression.R |only FatTailsR-1.2-3/FatTailsR/R/m_regression2.R |only FatTailsR-1.2-3/FatTailsR/R/n_regression3.R |only FatTailsR-1.2-3/FatTailsR/R/z_data.R |only FatTailsR-1.2-3/FatTailsR/man/ckiener.Rd |only FatTailsR-1.2-3/FatTailsR/man/estimkappa6.Rd |only FatTailsR-1.2-3/FatTailsR/man/estimkienerX.Rd |only FatTailsR-1.2-3/FatTailsR/man/fitkienerLX.Rd |only FatTailsR-1.4-1/FatTailsR/DESCRIPTION | 29 +-- FatTailsR-1.4-1/FatTailsR/MD5 | 103 ++++++------ FatTailsR-1.4-1/FatTailsR/NAMESPACE | 87 +++++++++- FatTailsR-1.4-1/FatTailsR/NEWS | 69 ++++++-- FatTailsR-1.4-1/FatTailsR/R/a_FatTailsR-package.R | 150 ++++++++++------- FatTailsR-1.4-1/FatTailsR/R/b_data.R |only FatTailsR-1.4-1/FatTailsR/R/c_trigohp.R |only FatTailsR-1.4-1/FatTailsR/R/d_logishp.R |only FatTailsR-1.4-1/FatTailsR/R/e_conversion.R |only FatTailsR-1.4-1/FatTailsR/R/f_kiener1.R |only FatTailsR-1.4-1/FatTailsR/R/g_kiener2.R |only FatTailsR-1.4-1/FatTailsR/R/h_kiener3.R |only FatTailsR-1.4-1/FatTailsR/R/i_kiener4.R |only FatTailsR-1.4-1/FatTailsR/R/j_moments.R |only FatTailsR-1.4-1/FatTailsR/R/k_tailskiener.R |only FatTailsR-1.4-1/FatTailsR/R/l_estimation.R |only FatTailsR-1.4-1/FatTailsR/R/m_laplaceroll.R |only FatTailsR-1.4-1/FatTailsR/R/n_estimation2.R |only FatTailsR-1.4-1/FatTailsR/R/o_regression.R |only FatTailsR-1.4-1/FatTailsR/data/datalist |only FatTailsR-1.4-1/FatTailsR/data/dfData.rda |binary FatTailsR-1.4-1/FatTailsR/data/tData.rda |binary FatTailsR-1.4-1/FatTailsR/data/xData.rda |binary FatTailsR-1.4-1/FatTailsR/data/zData.rda |binary FatTailsR-1.4-1/FatTailsR/man/FatTailsR.Rd | 145 +++++++++-------- FatTailsR-1.4-1/FatTailsR/man/aw2k.Rd | 119 +++++++++++--- FatTailsR-1.4-1/FatTailsR/man/checkquantiles.Rd | 46 ++++- FatTailsR-1.4-1/FatTailsR/man/ckiener1234.Rd |only FatTailsR-1.4-1/FatTailsR/man/dfData.Rd | 56 ------ FatTailsR-1.4-1/FatTailsR/man/dimdim.Rd |only FatTailsR-1.4-1/FatTailsR/man/elevenprobs.Rd | 51 ++---- FatTailsR-1.4-1/FatTailsR/man/estimkiener11.Rd | 118 ++++++------- FatTailsR-1.4-1/FatTailsR/man/exfit0.Rd |only FatTailsR-1.4-1/FatTailsR/man/exphp.Rd | 13 - FatTailsR-1.4-1/FatTailsR/man/extractData.Rd |only FatTailsR-1.4-1/FatTailsR/man/fitkienerX.Rd |only FatTailsR-1.4-1/FatTailsR/man/getDSdata.Rd | 44 ++--- FatTailsR-1.4-1/FatTailsR/man/getnamesk.Rd |only FatTailsR-1.4-1/FatTailsR/man/kashp.Rd | 8 FatTailsR-1.4-1/FatTailsR/man/kiener1.Rd | 96 +++++++++-- FatTailsR-1.4-1/FatTailsR/man/kiener2.Rd | 103 ++++++++++-- FatTailsR-1.4-1/FatTailsR/man/kiener3.Rd | 120 +++++++++++--- FatTailsR-1.4-1/FatTailsR/man/kiener4.Rd | 113 ++++++++++--- FatTailsR-1.4-1/FatTailsR/man/kmoments.Rd | 186 +++++++++++----------- FatTailsR-1.4-1/FatTailsR/man/laplacegaussnorm.Rd | 17 +- FatTailsR-1.4-1/FatTailsR/man/loghp.Rd | 4 FatTailsR-1.4-1/FatTailsR/man/logishp.Rd | 4 FatTailsR-1.4-1/FatTailsR/man/logit.Rd | 44 +++-- FatTailsR-1.4-1/FatTailsR/man/pk2pk.Rd | 80 ++++----- FatTailsR-1.4-1/FatTailsR/man/pprobs0.Rd |only FatTailsR-1.4-1/FatTailsR/man/regkienerLX.Rd | 139 +++++++++------- FatTailsR-1.4-1/FatTailsR/man/roundcoefk.Rd |only FatTailsR-1.4-1/FatTailsR/man/tData.Rd | 6 FatTailsR-1.4-1/FatTailsR/man/xData.Rd | 6 FatTailsR-1.4-1/FatTailsR/man/zData.Rd | 6 73 files changed, 1251 insertions(+), 711 deletions(-)
Title: Measures of the Sturdiness of Regression Coefficients
Description: The sValues package implements the s-values proposed by Ed. Leamer.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between sValues versions 0.1.1 dated 2015-09-13 and 0.1.2 dated 2015-10-25
sValues-0.1.1/sValues/README.md |only sValues-0.1.2/sValues/DESCRIPTION | 9 +-- sValues-0.1.2/sValues/MD5 | 21 ++++--- sValues-0.1.2/sValues/NAMESPACE | 2 sValues-0.1.2/sValues/R/internal_functions.R | 12 +--- sValues-0.1.2/sValues/R/sValues.R | 74 +++++++++++++++------------ sValues-0.1.2/sValues/inst/doc/sValues.R | 3 - sValues-0.1.2/sValues/inst/doc/sValues.Rnw | 3 - sValues-0.1.2/sValues/inst/doc/sValues.pdf |binary sValues-0.1.2/sValues/man/sValues.Rd | 36 ++++++++----- sValues-0.1.2/sValues/tests |only sValues-0.1.2/sValues/vignettes/sValues.Rnw | 3 - 12 files changed, 86 insertions(+), 77 deletions(-)
Title: Mixed Tempered Stable Distribution
Description: We provide detailed functions for univariate Mixed Tempered Stable distribution.
Author: Lorenzo Mercuri, Edit Rroji
Maintainer: Lorenzo Mercuri <lorenzo.mercuri@unimi.it>
Diff between MixedTS versions 1.0.3 dated 2015-07-17 and 1.0.4 dated 2015-10-25
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/MixedTS.R | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.14 dated 2015-10-11 and 0.99.15 dated 2015-10-25
DescTools-0.99.14/DescTools/R/test.DescTools.r |only DescTools-0.99.15/DescTools/DESCRIPTION | 8 DescTools-0.99.15/DescTools/MD5 | 47 +- DescTools-0.99.15/DescTools/NAMESPACE | 4 DescTools-0.99.15/DescTools/NEWS | 17 + DescTools-0.99.15/DescTools/R/DescTools.r | 282 ++++++++++------- DescTools-0.99.15/DescTools/inst/doc/Combinatorics.pdf |binary DescTools-0.99.15/DescTools/inst/doc/TablesInR.pdf |binary DescTools-0.99.15/DescTools/man/Abind.Rd | 11 DescTools-0.99.15/DescTools/man/BarnardTest.Rd |only DescTools-0.99.15/DescTools/man/BubbleLegend.Rd | 36 +- DescTools-0.99.15/DescTools/man/DateFunctions.Rd | 15 DescTools-0.99.15/DescTools/man/DescTools-package.Rd | 2 DescTools-0.99.15/DescTools/man/FindColor.Rd | 23 - DescTools-0.99.15/DescTools/man/Keywords.Rd | 6 DescTools-0.99.15/DescTools/man/PlotFun.Rd | 36 +- DescTools-0.99.15/DescTools/man/PlotMosaic.Rd | 14 DescTools-0.99.15/DescTools/man/Stamp.Rd | 4 DescTools-0.99.15/DescTools/man/StrPos.Rd | 9 DescTools-0.99.15/DescTools/man/SysInfo.Rd | 14 DescTools-0.99.15/DescTools/man/VarCI.Rd | 15 DescTools-0.99.15/DescTools/src/Barnard.c |only DescTools-0.99.15/DescTools/src/aux_fct.cpp | 25 - DescTools-0.99.15/DescTools/src/between.c | 91 +++-- DescTools-0.99.15/DescTools/src/between.h | 16 DescTools-0.99.15/DescTools/tests/misc.R | 26 - 26 files changed, 410 insertions(+), 291 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.3.0 dated 2015-06-16 and 3.3.1 dated 2015-10-25
BUGS | 2 DESCRIPTION | 12 - MD5 | 43 +++--- NAMESPACE | 7 - R/InitMHP.DynMLE.blockdiag.R | 203 +++++++++++++++++--------------- R/combine.networks.R | 108 +++++++++++++++-- R/ergm.godfather.R | 2 R/stergm.EGMME.SA.R | 4 R/stergm.getMCMCsample.R | 4 R/zzz.R | 10 + inst/NEWS.Rd | 74 ++++++++--- inst/doc/STERGM.pdf |binary man/ergm-terms.Rd | 4 man/stergm.Rd | 8 - man/tergm-package.Rd | 5 src/MHproposals_DynMLE.c | 2 src/MHproposals_DynMLE_block.c | 132 ++++++++++++++++++++ src/MHproposals_DynMoME.c | 2 tests/combine.networks.R | 34 +++++ tests/dynamic_MLE.R | 36 +++-- tests/dynamic_MLE_2.R | 38 ++++- tests/dynamic_MLE_blockdiag.R | 27 ++-- tests/dynamic_MLE_blockdiag.bipartite.R |only 23 files changed, 556 insertions(+), 201 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website where registered users can submit and discuss content. This package uses Reddit API to extract Reddit data using Reddit API. Note that due to the API limitations, the number of comments that can extracted is limited to 500 per thread. The package consists of 4 functions, one for extracting relevant URLs, one for extracting features out of given URLs, one that does both together and one that constructs graphs based on the structure of a thread.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 1.1.1 dated 2015-07-04 and 2.0.0 dated 2015-10-25
DESCRIPTION | 12 +-- MD5 | 13 ++- NAMESPACE | 1 R/RedditExtractoR.R | 170 +++++++++++++++++++++++++++++++++++++++++-------- man/construct_graph.Rd |only man/get_reddit.Rd | 5 - man/reddit_content.Rd | 3 man/reddit_urls.Rd | 6 - 8 files changed, 167 insertions(+), 43 deletions(-)
More information about RedditExtractoR at CRAN
Permanent link
Title: Solve Generalized Estimating Equations
Description: GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The "M" in the name "geeM" is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel <lmcda4@lsuhsc.edu>
Diff between geeM versions 0.7.4 dated 2015-05-25 and 0.8.0 dated 2015-10-25
DESCRIPTION | 9 MD5 | 14 - NAMESPACE | 5 R/geem.R | 717 ++++++++++++++++++++++++++++++-------------------------- R/print.R | 142 ++++++----- R/updatealpha.R | 301 ++++++++++++----------- R/utility.R | 54 +++- man/geem.Rd | 332 +++++++++++++------------ 8 files changed, 861 insertions(+), 713 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inversion of a symmetric Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010). Please see an eprint at http://arxiv.org/pdf/1507.06055.pdf for more details.
Author: Giri Gopalan, Luke Bornn
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.1 dated 2015-07-27 and 1.1.2 dated 2015-10-25
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.4 dated 2015-03-10 and 1.5 dated 2015-10-25
cit-1.4/cit/R/C_CIT_V5.R |only cit-1.4/cit/man/cit.Rd |only cit-1.4/cit/man/plotcit.Rd |only cit-1.4/cit/src/cit_v7.cpp |only cit-1.5/cit/DESCRIPTION | 12 ++++++------ cit-1.5/cit/MD5 | 24 +++++++++++++++++------- cit-1.5/cit/NAMESPACE | 4 +++- cit-1.5/cit/R/C_CIT_V12.R |only cit-1.5/cit/man/cit-package.Rd | 10 +++++----- cit-1.5/cit/man/cit.bp.Rd |only cit-1.5/cit/man/cit.cp.Rd |only cit-1.5/cit/man/fdr.cit.Rd |only cit-1.5/cit/man/fdr.od.Rd |only cit-1.5/cit/man/iuq.Rd |only cit-1.5/cit/man/linreg.Rd |only cit-1.5/cit/src/citconlog2_perm_v5.cpp |only cit-1.5/cit/src/citconlog2_v3.cpp |only cit-1.5/cit/src/citconlog2cvr_v3.cpp |only cit-1.5/cit/src/citconlog3_perm_v5.cpp |only cit-1.5/cit/src/citconlog3cvr_perm_v6.cpp |only cit-1.5/cit/src/logisticfunc.cpp |only cit-1.5/cit/src/logisticfunc.h |only 22 files changed, 31 insertions(+), 19 deletions(-)
Title: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda <josef.uyeda@gmail.com>
Diff between bayou versions 1.0.1 dated 2014-07-31 and 1.1.0 dated 2015-10-25
DESCRIPTION | 15 - MD5 | 112 +++++----- NAMESPACE | 6 R/bayou-likelihood.R | 19 - R/bayou-mcmc-utilities.R | 60 ++++- R/bayou-mcmc.R | 14 - R/bayou-package.R | 5 R/bayou-plotting.R | 364 +++++++++++++++------------------- R/bayou-prior.R | 47 ++-- R/bayou-simulation.r | 5 R/bayou-steppingstone.R | 60 +++-- R/conversion-utilities.R | 7 R/probability.R | 12 - man/Lposterior.Rd | 34 +-- man/OU.lik.Rd | 41 +-- man/OU.repar.Rd | 14 - man/OUphenogram.Rd | 40 +-- man/OUwie2bayou.Rd | 14 - man/QG.alpha.Rd | 13 - man/QG.sig2.Rd | 13 - man/bayou-package.Rd | 11 - man/bayou.lik.Rd | 29 +- man/bayou.mcmc.Rd | 102 +++------ man/bayou2OUwie.Rd | 22 -- man/cdpois.Rd | 25 +- man/combine.chains.Rd | 15 - man/dataSim.Rd | 33 +-- man/dhalfcauchy.Rd | 28 +- man/dloc.Rd | 32 +- man/dsb.Rd | 63 ++--- man/gelman.R.Rd | 27 +- man/identifyBranches.Rd | 37 +-- man/load.bayou.Rd | 32 +- man/make.powerposteriorFn.Rd | 29 +- man/make.prior.Rd | 128 +++++------ man/make.refFn.Rd | 46 +--- man/makeTransparent.Rd | 13 - man/overparameterize.startingPoint.Rd |only man/parmap.W.Rd | 28 +- man/pars2simmap.Rd | 28 +- man/phenogram.density.Rd | 47 +--- man/plot.bayouMCMC.Rd | 13 - man/plot.ssMCMC.Rd | 19 - man/plotBayoupars.Rd | 12 - man/plotRegimes.Rd |only man/plotSimmap.mcmc.Rd | 113 ++-------- man/print.bayouFit.Rd | 11 - man/print.priorFn.Rd | 11 - man/print.refFn.Rd | 11 - man/print.ssMCMC.Rd | 10 man/priorSim.Rd | 22 -- man/pull.pars.Rd | 28 +- man/regime.plot.Rd | 27 +- man/set.burnin.Rd | 14 - man/simmap.W.Rd | 34 +-- man/steppingstone.Rd | 98 ++------- man/summary.bayouMCMC.Rd | 17 - src/RcppExports.cpp | 50 +--- 58 files changed, 978 insertions(+), 1182 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.13.2 dated 2015-05-27 and 2.14.0 dated 2015-10-25
DESCRIPTION | 14 MD5 | 40 +- NAMESPACE | 29 + NEWS | 18 - R/999.AromaAffymetrix.R | 6 R/999.DEPRECATED.R | 50 -- R/AffyGenePDInfo.writeCdf.R | 2 R/AffymetrixCdfFile.COUNTS.R | 1 R/AffymetrixCelSet.R | 34 - R/AvgPlm.R | 2 R/DChipGenomeInformation.R | 3 R/DChipSnpInformation.R | 3 R/SnpChipEffectSet.extractAlleleSet.R | 9 R/UnitModel.fitCnProbes.R | 8 inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R | 178 +++++----- inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R | 1 man/ArrayExplorer.Rd | 2 man/DChipGenomeInformation.Rd | 3 man/DChipSnpInformation.Rd | 3 man/Non-documented_objects.Rd | 7 man/nbrOfGroupsPerUnit.AffymetrixCdfFile.Rd | 4 21 files changed, 188 insertions(+), 229 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation and non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the ML viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.2-4 dated 2014-12-31 and 1.3-0 dated 2015-10-24
maxLik-1.2-4/maxLik/man/returnMessage.Rd |only maxLik-1.2-4/maxLik/tests/fitExpDist.R |only maxLik-1.2-4/maxLik/tests/fitExpDist.Rout.save |only maxLik-1.2-4/maxLik/tests/fitNormalDist.R |only maxLik-1.2-4/maxLik/tests/fitNormalDist.Rout.save |only maxLik-1.3-0/maxLik/DESCRIPTION | 20 maxLik-1.3-0/maxLik/MD5 | 116 maxLik-1.3-0/maxLik/NAMESPACE | 12 maxLik-1.3-0/maxLik/NEWS | 17 maxLik-1.3-0/maxLik/R/05-classes.R |only maxLik-1.3-0/maxLik/R/10-MaxControl_class.R |only maxLik-1.3-0/maxLik/R/20-maxControl.R |only maxLik-1.3-0/maxLik/R/25-addControlList.R |only maxLik-1.3-0/maxLik/R/30-addControlDddot.R |only maxLik-1.3-0/maxLik/R/condiNumber.R | 7 maxLik-1.3-0/maxLik/R/logLikAttr.R | 16 maxLik-1.3-0/maxLik/R/maxBFGS.R | 17 maxLik-1.3-0/maxLik/R/maxBFGSR.R | 113 maxLik-1.3-0/maxLik/R/maxBFGSRCompute.R | 88 maxLik-1.3-0/maxLik/R/maxBHHH.R | 4 maxLik-1.3-0/maxLik/R/maxCG.R | 28 maxLik-1.3-0/maxLik/R/maxNM.R | 25 maxLik-1.3-0/maxLik/R/maxNR.R | 95 maxLik-1.3-0/maxLik/R/maxNRCompute.R | 211 + maxLik-1.3-0/maxLik/R/maxOptim.R | 164 - maxLik-1.3-0/maxLik/R/maxSANN.R | 32 maxLik-1.3-0/maxLik/R/openParam.R |only maxLik-1.3-0/maxLik/R/showMaxControl.R |only maxLik-1.3-0/maxLik/R/stdEr.maxLik.R | 4 maxLik-1.3-0/maxLik/R/summary.maxLik.R | 2 maxLik-1.3-0/maxLik/R/sumt.R | 10 maxLik-1.3-0/maxLik/man/activePar.Rd | 13 maxLik-1.3-0/maxLik/man/bread.maxLik.Rd | 21 maxLik-1.3-0/maxLik/man/compareDerivatives.Rd | 49 maxLik-1.3-0/maxLik/man/condiNumber.Rd | 59 maxLik-1.3-0/maxLik/man/estfun.maxLik.Rd | 23 maxLik-1.3-0/maxLik/man/fnSubset.Rd | 83 maxLik-1.3-0/maxLik/man/hessian.Rd | 16 maxLik-1.3-0/maxLik/man/logLik.maxLik.Rd | 4 maxLik-1.3-0/maxLik/man/maxBFGS.Rd | 165 - maxLik-1.3-0/maxLik/man/maxControl.Rd |only maxLik-1.3-0/maxLik/man/maxLik-internal.Rd | 1 maxLik-1.3-0/maxLik/man/maxLik-methods.Rd | 50 maxLik-1.3-0/maxLik/man/maxLik-package.Rd |only maxLik-1.3-0/maxLik/man/maxLik.Rd | 69 maxLik-1.3-0/maxLik/man/maxNR.Rd | 295 +- maxLik-1.3-0/maxLik/man/maximType.Rd | 10 maxLik-1.3-0/maxLik/man/nIter.Rd | 11 maxLik-1.3-0/maxLik/man/nObs.Rd | 15 maxLik-1.3-0/maxLik/man/nParam.Rd | 8 maxLik-1.3-0/maxLik/man/numericGradient.Rd | 33 maxLik-1.3-0/maxLik/man/returnCode.Rd | 42 maxLik-1.3-0/maxLik/man/summary.maxLik.Rd | 51 maxLik-1.3-0/maxLik/man/summary.maxim.Rd | 33 maxLik-1.3-0/maxLik/man/sumt.Rd | 86 maxLik-1.3-0/maxLik/man/vcov.maxLik.Rd | 36 maxLik-1.3-0/maxLik/tests/BFGSR.R | 26 maxLik-1.3-0/maxLik/tests/BFGSR.Rout.save | 68 maxLik-1.3-0/maxLik/tests/constraints.R | 184 + maxLik-1.3-0/maxLik/tests/constraints.Rout.save | 1223 +--------- maxLik-1.3-0/maxLik/tests/examples.R | 35 maxLik-1.3-0/maxLik/tests/examples.Rout.save | 860 +++++-- maxLik-1.3-0/maxLik/tests/finalHessian.Rout.save | 14 maxLik-1.3-0/maxLik/tests/fitNormalDist_privateTest.Rout.save |only maxLik-1.3-0/maxLik/tests/methods.R | 14 maxLik-1.3-0/maxLik/tests/methods.Rout.save | 92 maxLik-1.3-0/maxLik/tests/parameters_privateTest.Rout.save |only 67 files changed, 2417 insertions(+), 2253 deletions(-)
Title: Analysis of Factorial Experiments
Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(),
aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within
(i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating
multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and
computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM
only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums
of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre],
Ben Bolker [aut],
Jake Westfall [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Frederik Aust [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>
Diff between afex versions 0.14-2 dated 2015-08-17 and 0.15-2 dated 2015-10-24
afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-basic.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-bugs.R |only afex-0.14-2/afex/tests/testthat/test-aov_car-basic.car-structural.R |only afex-0.15-2/afex/DESCRIPTION | 40 afex-0.15-2/afex/MD5 | 77 afex-0.15-2/afex/NAMESPACE | 1 afex-0.15-2/afex/NEWS | 956 +++---- afex-0.15-2/afex/R/afex-package.R | 6 afex-0.15-2/afex/R/allFit.R | 176 - afex-0.15-2/afex/R/aov_car.R | 778 ++--- afex-0.15-2/afex/R/compare.2.vectors.R | 186 - afex-0.15-2/afex/R/deprecated.R | 58 afex-0.15-2/afex/R/ems.R | 214 - afex-0.15-2/afex/R/helpers.R | 96 afex-0.15-2/afex/R/ks2013.3-data.R | 56 afex-0.15-2/afex/R/md_12.1-data.R | 90 afex-0.15-2/afex/R/md_15.1-data.R | 122 afex-0.15-2/afex/R/md_16.1-data.R | 68 afex-0.15-2/afex/R/md_16.4-data.R | 68 afex-0.15-2/afex/R/methods.afex_aov.R | 286 +- afex-0.15-2/afex/R/mixed.R | 1328 +++++----- afex-0.15-2/afex/R/nice.R | 286 +- afex-0.15-2/afex/R/obk.long-data.R | 92 afex-0.15-2/afex/R/round_ps.R | 56 afex-0.15-2/afex/R/set_contrasts.R | 90 afex-0.15-2/afex/R/sk2011.1-data.R | 90 afex-0.15-2/afex/R/sk2011.2-data.R | 64 afex-0.15-2/afex/inst/doc/anova_posthoc.R | 2 afex-0.15-2/afex/inst/doc/anova_posthoc.Rmd | 2 afex-0.15-2/afex/inst/doc/anova_posthoc.html | 154 - afex-0.15-2/afex/man/afex-package.Rd | 6 afex-0.15-2/afex/man/afex_aov-methods.Rd | 11 afex-0.15-2/afex/man/mixed.Rd | 6 afex-0.15-2/afex/man/nice.Rd | 11 afex-0.15-2/afex/tests/testthat.R | 8 afex-0.15-2/afex/tests/testthat/test-afex_aov.R | 106 afex-0.15-2/afex/tests/testthat/test-aov_car-basic.R |only afex-0.15-2/afex/tests/testthat/test-aov_car-bugs.R |only afex-0.15-2/afex/tests/testthat/test-aov_car-structural.R |only afex-0.15-2/afex/tests/testthat/test-mixed-bugs.R |only afex-0.15-2/afex/tests/testthat/test-mixed-mw.R | 92 afex-0.15-2/afex/tests/testthat/test-mixed-structure.R | 324 +- afex-0.15-2/afex/vignettes/anova_posthoc.Rmd | 2 43 files changed, 3029 insertions(+), 2979 deletions(-)
Title: R Interface to FOAAS
Description: R access to the FOAAS (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between rfoaas versions 0.1.6 dated 2015-05-31 and 0.1.8 dated 2015-10-24
ChangeLog | 35 ++++++++++++++++++ DESCRIPTION | 8 ++-- MD5 | 14 +++---- NAMESPACE | 3 + R/foaas.R | 15 +++++++ README.md | 2 - man/rfoaas-package.Rd | 27 ++++++++++++- tests/runTestsAgainstFOAAS.R | 83 ++++++++++++++++++++++++------------------- 8 files changed, 135 insertions(+), 52 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.4.0 dated 2015-06-16 and 3.5.1 dated 2015-10-24
ergm-3.4.0/ergm/R/edgelist.R |only ergm-3.4.0/ergm/R/ergm.sample.eta2theta.R |only ergm-3.4.0/ergm/man/vector.namesmatch.Rd |only ergm-3.4.0/ergm/tests/samplike_condoutdeg.R |only ergm-3.5.1/ergm/DESCRIPTION | 21 ergm-3.5.1/ergm/MD5 | 109 ++-- ergm-3.5.1/ergm/NAMESPACE | 38 + ergm-3.5.1/ergm/R/InitErgmTerm.R | 26 ergm-3.5.1/ergm/R/InitMHP.blockdiag.R | 105 +++ ergm-3.5.1/ergm/R/approx.hotelling.diff.test.R | 48 + ergm-3.5.1/ergm/R/build_term_index.R | 617 +++++++++++------------ ergm-3.5.1/ergm/R/ergm.CD.fixed.R | 12 ergm-3.5.1/ergm/R/ergm.MCMCse.R | 141 +---- ergm-3.5.1/ergm/R/ergm.MCMCse.lognormal.R | 113 +--- ergm-3.5.1/ergm/R/ergm.MCMLE.R | 19 ergm-3.5.1/ergm/R/ergm.R | 266 +++++---- ergm-3.5.1/ergm/R/ergm.bridge.R | 5 ergm-3.5.1/ergm/R/ergm.estimate.R | 2 ergm-3.5.1/ergm/R/ergm.llik.R | 5 ergm-3.5.1/ergm/R/ergm.llik.obs.R | 44 - ergm-3.5.1/ergm/R/ergm.model.utils.R | 23 ergm-3.5.1/ergm/R/ergm.san.R | 5 ergm-3.5.1/ergm/R/ergm.utility.R | 2 ergm-3.5.1/ergm/R/formula.utils.R | 82 --- ergm-3.5.1/ergm/R/is.curved.R |only ergm-3.5.1/ergm/R/is.inCH.R | 23 ergm-3.5.1/ergm/R/logLik.ergm.R | 4 ergm-3.5.1/ergm/R/mcmc.diagnostics.ergm.R | 12 ergm-3.5.1/ergm/R/parallel.utils.R | 26 ergm-3.5.1/ergm/inst/NEWS.Rd | 128 +++- ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.html | 35 - ergm-3.5.1/ergm/inst/doc/ergm.pdf |binary ergm-3.5.1/ergm/man/Getting.Started.Rd | 13 ergm-3.5.1/ergm/man/as.edgelist.Rd | 50 - ergm-3.5.1/ergm/man/control.ergm.Rd | 21 ergm-3.5.1/ergm/man/ergm-constraints.Rd | 12 ergm-3.5.1/ergm/man/ergm-package.Rd | 13 ergm-3.5.1/ergm/man/ergm-parallel.Rd | 2 ergm-3.5.1/ergm/man/ergm-terms.Rd | 54 +- ergm-3.5.1/ergm/man/ergm.Rd | 13 ergm-3.5.1/ergm/man/ergm.init.methods.Rd | 12 ergm-3.5.1/ergm/man/ergm.mple.Rd | 2 ergm-3.5.1/ergm/man/ergm_formula_utils.Rd | 38 - ergm-3.5.1/ergm/man/is.curved.Rd |only ergm-3.5.1/ergm/man/mcmc.diagnostics.ergm.Rd | 9 ergm-3.5.1/ergm/man/standardize.network.Rd | 3 ergm-3.5.1/ergm/man/vcov.ergm.Rd | 4 ergm-3.5.1/ergm/src/MHproposals_block.c | 100 +++ ergm-3.5.1/ergm/src/changestats.c | 12 ergm-3.5.1/ergm/src/changestats.h | 2 ergm-3.5.1/ergm/tests/constrain_blockdiag.R | 36 + ergm-3.5.1/ergm/tests/constrain_degrees.R | 3 ergm-3.5.1/ergm/tests/constrain_observed.R | 4 ergm-3.5.1/ergm/tests/constraint_conflict.R | 10 ergm-3.5.1/ergm/tests/estflo.R | 4 ergm-3.5.1/ergm/tests/miss_tests.R | 1 ergm-3.5.1/ergm/tests/off/samplike_condoutdeg.R |only ergm-3.5.1/ergm/tests/target_offset.R | 20 ergm-3.5.1/ergm/tests/termTests.flexible.R | 14 59 files changed, 1289 insertions(+), 1074 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between statnet.common versions 3.2.3 dated 2015-08-05 and 3.3.0 dated 2015-10-24
DESCRIPTION | 14 ++++++++------ MD5 | 11 +++++++---- NAMESPACE | 2 +- NEWS | 9 +++++++-- R/formula.utilities.R |only R/misc.utilities.R | 21 +++++++++++++++++++++ man/formula.utilities.Rd |only man/vector.namesmatch.Rd |only 8 files changed, 44 insertions(+), 13 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Random Effects and/or Sample Selection Models for Panel Count
Data
Description: A high performance package implementing random effects and/or sample selection models for panel count data.
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Diff between PanelCount versions 1.0.1 dated 2015-08-31 and 1.0.9 dated 2015-10-24
DESCRIPTION | 14 ++++++------ MD5 | 34 ++++++++++++++--------------- NAMESPACE | 1 R/CRE.R | 44 ++++++++++++++++++++++++++++++------- R/CRE_SS.R | 63 +++++++++++++++++++++++++++++++++++++++++++----------- R/PLN_RE.R | 28 ++++++++++++++++++------ R/PanelCount.R | 4 ++- R/PoissonRE.R | 24 ++++++++++++++++---- R/ProbitRE.R | 26 +++++++++++++++++----- R/data.R | 4 +-- data/rt.RData |binary man/CRE.Rd | 25 ++++++++++++++++++--- man/CRE_SS.Rd | 31 +++++++++++++++++++++----- man/PLN_RE.Rd | 24 +++++++++++++++++--- man/PanelCount.Rd | 5 ++++ man/PoissonRE.Rd | 14 +++++++++--- man/ProbitRE.Rd | 15 ++++++++++-- man/rt.Rd | 4 +-- 18 files changed, 274 insertions(+), 86 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.4.1 dated 2015-10-17 and 0.4.2 dated 2015-10-24
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++--------- NEWS | 5 ++++ R/qic.R | 6 +++-- R/tcc.R | 12 ++++++----- inst/doc/controlcharts.R | 8 +++---- inst/doc/controlcharts.Rmd | 16 +++++++------- inst/doc/controlcharts.html | 48 ++++++++++++++++++++++---------------------- inst/doc/runcharts.html | 18 ++++++++-------- man/plot.tcc.Rd | 4 +-- vignettes/controlcharts.Rmd | 16 +++++++------- 11 files changed, 85 insertions(+), 76 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-7 dated 2015-07-23 and 1.8-8 dated 2015-10-24
ChangeLog | 55 +++ DESCRIPTION | 6 MD5 | 67 ++-- NAMESPACE | 4 R/bam.r | 268 ++++++++++++++---- R/efam.r | 89 +++--- R/fast-REML.r | 21 - R/gam.fit3.r | 38 +- R/gam.fit4.r | 151 +++++++--- R/gamlss.r | 13 R/mgcv.r | 74 +++-- R/plots.r | 19 - R/smooth.r | 291 ++++++++++++++++++-- R/soap.r | 17 - man/bam.Rd | 13 man/mgcv-package.Rd | 2 man/mgcv-parallel.Rd | 5 man/negbin.Rd | 2 man/plot.gam.Rd | 10 man/predict.bam.Rd | 12 man/predict.gam.Rd | 12 man/single.index.Rd | 2 man/smooth.construct.Rd | 4 man/smooth.construct.gp.smooth.spec.Rd |only man/smooth.construct.sos.smooth.spec.Rd | 3 man/smooth.terms.Rd | 21 - man/smoothCon.Rd | 8 man/t2.Rd | 9 man/uniquecombs.Rd | 22 + man/ziP.Rd | 46 ++- po/R-mgcv.pot | 67 +++- src/gdi.c | 464 ++++++++++++++++++++------------ src/init.c | 4 src/mat.c | 18 - src/mgcv.h | 12 35 files changed, 1343 insertions(+), 506 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and use the utility
methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame,
and apply functions to your tree data. Useful for decision trees, machine learning, finance, conversion
from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.2.1 dated 2015-09-09 and 0.2.4 dated 2015-10-24
DESCRIPTION | 8 MD5 | 34 - NAMESPACE | 2 NEWS | 12 R/node.R | 10 R/node_actives.R | 3 R/node_methods.R | 23 - R/node_methods_traversal.R | 6 data/acme.rda |binary inst/doc/applications.R | 70 --- inst/doc/applications.Rmd | 84 ---- inst/doc/applications.html | 161 +------- inst/doc/data.tree.html | 35 - inst/extdata/flare.json | 758 +++++++++++++++++++------------------- man/NODE_RESERVED_NAMES_CONST.Rd | 2 man/Node.Rd | 1 tests/testthat/test-treeMethods.R | 31 + vignettes/applications.Rmd | 84 ---- 18 files changed, 528 insertions(+), 796 deletions(-)
Title: Cox Regression (Proportional Hazards Model) with Multiple Causes
and Mixed Effects
Description: A high performance package estimating Cox Model when an even has more than one causes. It also supports random and fixed effects, tied events, and time-varying variables.
Author: Jing Peng
Maintainer: Jing Peng <pengjing@live.com>
Diff between CoxPlus versions 1.1.0 dated 2015-09-06 and 1.1.1 dated 2015-10-24
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/fastCox.R | 2 ++ man/CoxPlus.Rd | 5 +++++ 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Interactive Visualization of Topic Models
Description: Tools to create an interactive web-based visualization of a
topic model that has been fit to a corpus of text data using
Latent Dirichlet Allocation (LDA). Given the estimated parameters of
the topic model, it computes various summary statistics as input to
an interactive visualization built with D3.js that is accessed via
a browser. The goal is to help users interpret the topics in their
LDA topic model.
Author: Carson Sievert [aut, cre],
Kenny Shirley [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between LDAvis versions 0.2 dated 2015-01-23 and 0.3.2 dated 2015-10-24
LDAvis-0.2/LDAvis/inst/examples |only LDAvis-0.3.2/LDAvis/DESCRIPTION | 10 +- LDAvis-0.3.2/LDAvis/MD5 | 47 +++++----- LDAvis-0.3.2/LDAvis/NAMESPACE | 4 LDAvis-0.3.2/LDAvis/NEWS | 20 ++++ LDAvis-0.3.2/LDAvis/R/createJSON.R | 65 +++++++++----- LDAvis-0.3.2/LDAvis/R/imports.R |only LDAvis-0.3.2/LDAvis/R/runShiny.R | 2 LDAvis-0.3.2/LDAvis/R/serVis.R | 6 - LDAvis-0.3.2/LDAvis/R/shiny.R |only LDAvis-0.3.2/LDAvis/README.md | 25 ++++- LDAvis-0.3.2/LDAvis/build/vignette.rds |binary LDAvis-0.3.2/LDAvis/inst/doc/details.Rnw | 9 +- LDAvis-0.3.2/LDAvis/inst/doc/details.pdf |binary LDAvis-0.3.2/LDAvis/inst/htmljs/index.html | 7 - LDAvis-0.3.2/LDAvis/inst/htmljs/lda.css | 77 +---------------- LDAvis-0.3.2/LDAvis/inst/htmljs/ldavis.js | 46 ++++------ LDAvis-0.3.2/LDAvis/inst/shiny |only LDAvis-0.3.2/LDAvis/man/TwentyNewsgroups.Rd | 3 LDAvis-0.3.2/LDAvis/man/createJSON.Rd | 126 +++++++++++++--------------- LDAvis-0.3.2/LDAvis/man/jsPCA.Rd | 13 +- LDAvis-0.3.2/LDAvis/man/renderVis.Rd |only LDAvis-0.3.2/LDAvis/man/runShiny.Rd | 25 ++--- LDAvis-0.3.2/LDAvis/man/serVis.Rd | 44 ++++----- LDAvis-0.3.2/LDAvis/man/visOutput.Rd |only LDAvis-0.3.2/LDAvis/vignettes/details.Rnw | 9 +- 26 files changed, 259 insertions(+), 279 deletions(-)
Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms for design and
analysis of probability surveys. The functions are tailored for Generalized
Random Tessellation Stratified survey designs.
Author: Tom Kincaid [aut, cre],
Tony Olsen [aut],
Don Stevens [ctb],
Christian Platt [ctb],
Denis White [ctb],
Richard Remington [ctb]
Maintainer: Tom Kincaid <Kincaid.Tom@epa.gov>
Diff between spsurvey versions 3.0 dated 2015-05-22 and 3.1 dated 2015-10-23
spsurvey-3.0/spsurvey/src/insideGridCell.c |only spsurvey-3.0/spsurvey/src/pickSamplePoints.c |only spsurvey-3.0/spsurvey/vignettes/FL_lakes.tab |only spsurvey-3.0/spsurvey/vignettes/IN_streams.tab |only spsurvey-3.0/spsurvey/vignettes/Luck_Ash_streams.dbf |only spsurvey-3.0/spsurvey/vignettes/Luck_Ash_streams.shp |only spsurvey-3.0/spsurvey/vignettes/Luck_Ash_streams.shx |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.dbf |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.prj |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.shp |only spsurvey-3.0/spsurvey/vignettes/NE_lakes.shx |only spsurvey-3.0/spsurvey/vignettes/NLA_2007.tab |only spsurvey-3.0/spsurvey/vignettes/SC_estuaries.tab |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.dbf |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.prj |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.shp |only spsurvey-3.0/spsurvey/vignettes/UT_ecoregions.shx |only spsurvey-3.0/spsurvey/vignettes/decon_data.tab |only spsurvey-3.0/spsurvey/vignettes/lLuck_Ash_streams.prj |only spsurvey-3.1/spsurvey/DESCRIPTION | 11 spsurvey-3.1/spsurvey/MD5 | 173 ++++------ spsurvey-3.1/spsurvey/NAMESPACE | 19 - spsurvey-3.1/spsurvey/R/AAA.R | 2 spsurvey-3.1/spsurvey/R/SpatialDesign-methods.R | 3 spsurvey-3.1/spsurvey/R/change.analysis.R | 13 spsurvey-3.1/spsurvey/R/change.est.R | 13 spsurvey-3.1/spsurvey/R/changevar.mean.R | 11 spsurvey-3.1/spsurvey/R/changevar.prop.R | 11 spsurvey-3.1/spsurvey/R/changevar.size.R | 11 spsurvey-3.1/spsurvey/build/vignette.rds |binary spsurvey-3.1/spsurvey/data/FL_lakes.rda |binary spsurvey-3.1/spsurvey/data/IN_streams.rda |binary spsurvey-3.1/spsurvey/data/Luck_Ash_streams.rda |binary spsurvey-3.1/spsurvey/data/NE_lakes.rda |binary spsurvey-3.1/spsurvey/data/NLA_2007.rda |binary spsurvey-3.1/spsurvey/data/SC_estuaries.rda |binary spsurvey-3.1/spsurvey/data/UT_ecoregions.rda |binary spsurvey-3.1/spsurvey/data/decon_data.rda |binary spsurvey-3.1/spsurvey/inst/CITATION | 4 spsurvey-3.1/spsurvey/inst/NEWS.Rd | 17 + spsurvey-3.1/spsurvey/inst/doc/Area_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Area_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/Area_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Area_Design.R | 55 ++- spsurvey-3.1/spsurvey/inst/doc/Area_Design.Rnw | 16 spsurvey-3.1/spsurvey/inst/doc/Area_Design.pdf |binary spsurvey-3.1/spsurvey/inst/doc/CDF_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/CDF_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/CDF_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/CDF_Deconvolution.R | 4 spsurvey-3.1/spsurvey/inst/doc/CDF_Deconvolution.Rnw | 14 spsurvey-3.1/spsurvey/inst/doc/CDF_Deconvolution.pdf |binary spsurvey-3.1/spsurvey/inst/doc/CHANGES.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Finite_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Finite_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/Finite_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Finite_Design.R | 55 ++- spsurvey-3.1/spsurvey/inst/doc/Finite_Design.Rnw | 20 - spsurvey-3.1/spsurvey/inst/doc/Finite_Design.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Linear_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Linear_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/inst/doc/Linear_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Linear_Design.R | 55 ++- spsurvey-3.1/spsurvey/inst/doc/Linear_Design.Rnw | 16 spsurvey-3.1/spsurvey/inst/doc/Linear_Design.pdf |binary spsurvey-3.1/spsurvey/inst/doc/README.pdf |binary spsurvey-3.1/spsurvey/inst/doc/Risk_Analysis.R | 4 spsurvey-3.1/spsurvey/inst/doc/Risk_Analysis.Rnw | 16 spsurvey-3.1/spsurvey/inst/doc/Risk_Analysis.pdf |binary spsurvey-3.1/spsurvey/inst/doc/UserGuide.pdf |binary spsurvey-3.1/spsurvey/man/change.analysis.Rd | 13 spsurvey-3.1/spsurvey/man/change.est.Rd | 13 spsurvey-3.1/spsurvey/man/spsurvey-internal.Rd | 5 spsurvey-3.1/spsurvey/src/dbfFileParser.c | 100 ++---- spsurvey-3.1/spsurvey/src/grts.c | 28 - spsurvey-3.1/spsurvey/src/grtsarea.c | 7 spsurvey-3.1/spsurvey/src/grtslin.c | 28 - spsurvey-3.1/spsurvey/src/grtspts.c | 5 spsurvey-3.1/spsurvey/src/insideAreaGridCell.c | 28 - spsurvey-3.1/spsurvey/src/insideLinearGridCell.c | 28 - spsurvey-3.1/spsurvey/src/irsarea.c | 29 - spsurvey-3.1/spsurvey/src/irslin.c | 32 - spsurvey-3.1/spsurvey/src/pickAreaSamplePoints.c | 28 - spsurvey-3.1/spsurvey/src/pickGridCells.c | 11 spsurvey-3.1/spsurvey/src/pickLinearSamplePoints.c | 28 - spsurvey-3.1/spsurvey/src/ranho.c | 5 spsurvey-3.1/spsurvey/src/shapeParser.c | 289 +++++++----------- spsurvey-3.1/spsurvey/src/spsurvey.h | 6 spsurvey-3.1/spsurvey/vignettes/Area_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/Area_Design.Rnw | 16 spsurvey-3.1/spsurvey/vignettes/CDF_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/CDF_Deconvolution.Rnw | 14 spsurvey-3.1/spsurvey/vignettes/Finite_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/Finite_Design.Rnw | 20 - spsurvey-3.1/spsurvey/vignettes/Linear_Analysis.Rnw | 12 spsurvey-3.1/spsurvey/vignettes/Linear_Design.Rnw | 16 spsurvey-3.1/spsurvey/vignettes/Risk_Analysis.Rnw | 16 97 files changed, 743 insertions(+), 677 deletions(-)
Title: An Information About Deputies and Votings in Polish Diet
Description: Set of functions that access information about deputies and votings in Polish diet from webpage http://www.sejm.gov.pl/.
The package was developed as a result of an internship in MI2 Group - http://mi2.mini.pw.edu.pl/, Faculty of Mathematics and Information Science, Warsaw University of Technology.
Author: Piotr Smuda [aut, cre],
Przemyslaw Biecek [aut],
Tomasz Mikolajczyk [ctb]
Maintainer: Piotr Smuda <piotrsmuda@gmail.com>
Diff between sejmRP versions 1.1 dated 2015-09-27 and 1.2 dated 2015-10-23
DESCRIPTION | 11 - MD5 | 67 +++++----- NAMESPACE | 3 R/create_database.R | 6 R/deputies_get_data.R | 2 R/get_deputies_table.R | 28 ++-- R/get_filtered_votes.R | 86 ++++++------- R/get_statements_table.R | 33 ++--- R/get_votes_table.R | 34 ++--- R/get_votings_table.R | 30 ++-- R/safe_html.R |only R/statements_create_table.R | 14 +- R/statements_get_statement.R | 9 - R/statements_get_statements_data.R | 2 R/statements_get_statements_table.R |only R/statements_update_table.R | 33 ++++- R/votes_get_clubs_links.R | 2 R/votes_update_table.R | 12 + R/votings_get_date.R | 2 R/votings_get_votings_links.R | 2 R/votings_update_table.R | 10 + man/create_database.Rd | 3 man/get_deputies_table.Rd | 2 man/get_filtered_votes.Rd | 4 man/get_statements_table.Rd | 4 man/get_votes_table.Rd | 6 man/get_votings_table.Rd | 2 man/safe_html.Rd |only man/statements_get_statement.Rd | 4 man/statements_get_statements_table.Rd |only man/statements_update_table.Rd | 5 man/votes_update_table.Rd | 5 man/votings_update_table.Rd | 5 tests/testthat/test_get_statements_table.R | 2 tests/testthat/test_statements_get_statements_data.R | 2 tests/testthat/test_statements_get_statements_table.R |only vignettes/INSTRUCTION.Rmd | 111 +++++++++--------- 37 files changed, 306 insertions(+), 235 deletions(-)
Title: Functions to Analyze and Visualize Likert Type Items
Description: Functions to analyze and visualize likert type items.
Author: Jason Bryer <jason@bryer.org>, Kimberly Speerschneider
<kimkspeer@gmail.com>
Maintainer: Jason Bryer <jason@bryer.org>
Diff between likert versions 1.2 dated 2014-10-17 and 1.3.0 dated 2015-10-23
DESCRIPTION | 14 ++--- MD5 | 105 +++++++++++++++++++------------------- NAMESPACE | 23 ++++++-- NEWS | 13 ++++ R/likert-package.R | 27 +++++++-- R/likert.R | 37 ++++++++++--- R/plot.histogram.R | 4 + R/plot.likert.bar.r | 115 ++++++++++++++++++++++++++++-------------- R/plot.likert.gap.R | 2 R/plot.likert.heat.r | 2 R/plot.likert.matrix.r | 2 R/shinyLikert.R | 1 R/summary.likert.r | 7 ++ build/vignette.rds |binary data/datalist | 1 data/sasr.rda |only demo/00Index | 1 demo/GroupedFactors.R |only demo/RecodeFactors.R | 2 demo/likert.R | 9 +-- inst/doc/likert-xtable.R | 11 +--- inst/doc/likert-xtable.Rnw | 5 - inst/doc/likert-xtable.pdf |binary inst/shiny/server.R | 2 man/MathAnxiety.Rd | 3 - man/MathAnxietyGender.Rd | 3 - man/abs_formatter.Rd | 3 - man/align.plots.Rd | 3 - man/gap.Rd | 3 - man/label_wrap_mod.Rd | 3 - man/likert-package.Rd | 3 - man/likert.Rd | 9 ++- man/likert.bar.plot.Rd | 20 ++++--- man/likert.density.plot.Rd | 3 - man/likert.heat.plot.Rd | 3 - man/likert.histogram.plot.Rd | 3 - man/likert.matrix.plot.Rd | 3 - man/mass.Rd | 3 - man/pisaitems.Rd | 3 - man/plot.likert.Rd | 3 - man/plot.likert.gap.Rd | 3 - man/print.likert.Rd | 3 - man/print.likert.bar.plot.Rd | 3 - man/print.likert.gap.Rd | 3 - man/print.likert.heat.plot.Rd | 3 - man/print.xlikert.Rd | 3 - man/recode.Rd | 3 - man/reverse.levels.Rd | 3 - man/sasr.Rd |only man/shinyLikert.Rd | 3 - man/summary.likert.Rd | 3 - man/summary.likert.gap.Rd | 3 - man/xtable.likert.Rd | 3 - man/zeroGrob.Rd | 3 - vignettes/likert-xtable.Rnw | 5 - 55 files changed, 322 insertions(+), 176 deletions(-)
Title: Estimation of Diagonal Elements of Sparse Precision-Matrices
Description: Several estimators of the diagonal elements of a sparse precision
(inverse covariance) matrix from a sample of Gaussian vectors for a
given matrix of estimated marginal regression coefficients.
To install package 'gurobi', instructions at
http://user.gurobi.com/download/gurobi-optimizer and
http://www.gurobi.com/documentation/6.0/refman/r_api_overview.html.
Author: Arnak Dalalyan [aut], Samuel Balmand [aut, cre]
Maintainer: Samuel Balmand <Samuel.Balmand@ensg.eu>
Diff between DESP versions 0.1-3 dated 2015-06-16 and 0.1-4 dated 2015-10-23
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- man/DESP-package.Rd | 4 ++-- man/DESP_MST.Rd | 2 +- man/DESP_PML.Rd | 2 +- man/DESP_RML.Rd | 2 +- man/DESP_RV.Rd | 2 +- man/DESP_SPT.Rd | 2 +- src/Makevars | 2 ++ src/scs/scs.mk | 8 +++++++- 11 files changed, 36 insertions(+), 23 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: An implementation of the jDE variant of the Differential Evolution
stochastic algorithm for global optimization of nonlinear programming problems.
Author: Eduardo L. T. Conceicao and Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.0-3 dated 2015-07-19 and 1.0-4 dated 2015-10-23
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- man/JDEoptim.Rd | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Forecast Verification Routines for the SPECS FP7 Project
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between SpecsVerification versions 0.4-0 dated 2015-09-11 and 0.4-1 dated 2015-10-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/Detrend.R | 5 +++-- R/ReliabilityDiagram.R | 23 ++++++++++++++++++++--- man/ClimEns.Rd | 2 +- man/GetDensity.Rd | 2 +- man/PlotDressedEns.Rd | 6 +++--- man/ReliabilityDiagram.Rd | 7 ++++--- 9 files changed, 45 insertions(+), 26 deletions(-)
More information about SpecsVerification at CRAN
Permanent link
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and, for binomial data, the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 2.0.1 dated 2015-06-19 and 2.0.2 dated 2015-10-23
DESCRIPTION | 10 ++-- MD5 | 36 +++++++-------- NAMESPACE | 3 + R/CV.G.Poisson.R | 2 R/CV.Poisson.R | 13 ++++- R/Performance.G.Poisson.R | 2 R/Performance.Poisson.R | 2 man/Analyze.Binomial.Rd | 36 +++++++-------- man/AnalyzeSetUp.Binomial.Rd | 28 ++++++------ man/CV.Binomial.Rd | 12 ++--- man/CV.G.Binomial.Rd | 10 ++-- man/CV.G.Poisson.Rd | 46 ++++++++++---------- man/CV.Poisson.Rd | 61 +++++++++++++------------- man/Performance.G.Binomial.Rd | 10 ++-- man/Performance.G.Poisson.Rd | 84 ++++++++++++++++++------------------ man/Performance.Poisson.Rd | 96 ++++++++++++++++++++++++++---------------- man/SampleSize.Binomial.Rd | 14 +++--- man/SampleSize.Poisson.Rd | 83 ++++++++++++++++++++---------------- man/Sequential-package.Rd | 22 +++++---- 19 files changed, 311 insertions(+), 259 deletions(-)
Title: Hierarchical Clustering with P-Values via Multiscale Bootstrap
Resampling
Description: An implementation of multiscale bootstrap resampling for
assessing the uncertainty in hierarchical cluster analysis.
It provides AU (approximately unbiased) p-value as well as
BP (bootstrap probability) value for each cluster in a dendrogram.
Author: Ryota Suzuki <suzuki@ef-prime.com>, Hidetoshi Shimodaira
<shimo@sigmath.es.osaka-u.ac.jp>
Maintainer: Ryota Suzuki <suzuki@ef-prime.com>
Diff between pvclust versions 1.3-2 dated 2014-12-22 and 2.0-0 dated 2015-10-23
DESCRIPTION | 8 MD5 | 10 NAMESPACE | 6 R/pvclust-internal.R | 347 ++++++++++++++++++++++++++------ R/pvclust.R | 538 +++++++++++++++++++++++---------------------------- man/pvclust.Rd | 79 +++++-- 6 files changed, 591 insertions(+), 397 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.2 dated 2015-07-26 and 1.6.3 dated 2015-10-23
checkmate-1.6.2/checkmate/NEWS |only checkmate-1.6.3/checkmate/DESCRIPTION | 6 checkmate-1.6.3/checkmate/MD5 | 180 +++++----- checkmate-1.6.3/checkmate/NAMESPACE | 3 checkmate-1.6.3/checkmate/R/AssertCollection.r |only checkmate-1.6.3/checkmate/R/asInteger.r | 14 checkmate-1.6.3/checkmate/R/checkAccess.r | 4 checkmate-1.6.3/checkmate/R/checkArray.r | 4 checkmate-1.6.3/checkmate/R/checkAtomic.r | 4 checkmate-1.6.3/checkmate/R/checkAtomicVector.r | 4 checkmate-1.6.3/checkmate/R/checkCharacter.r | 13 checkmate-1.6.3/checkmate/R/checkChoice.r | 4 checkmate-1.6.3/checkmate/R/checkClass.r | 4 checkmate-1.6.3/checkmate/R/checkComplex.r | 4 checkmate-1.6.3/checkmate/R/checkCount.r | 4 checkmate-1.6.3/checkmate/R/checkDataFrame.r | 13 checkmate-1.6.3/checkmate/R/checkDirectory.r | 4 checkmate-1.6.3/checkmate/R/checkEnvironment.r | 4 checkmate-1.6.3/checkmate/R/checkFactor.r | 11 checkmate-1.6.3/checkmate/R/checkFile.r | 5 checkmate-1.6.3/checkmate/R/checkFlag.r | 4 checkmate-1.6.3/checkmate/R/checkFunction.r | 4 checkmate-1.6.3/checkmate/R/checkInt.r | 4 checkmate-1.6.3/checkmate/R/checkInteger.r | 4 checkmate-1.6.3/checkmate/R/checkIntegerish.r | 4 checkmate-1.6.3/checkmate/R/checkList.r | 4 checkmate-1.6.3/checkmate/R/checkLogical.r | 4 checkmate-1.6.3/checkmate/R/checkMatrix.r | 4 checkmate-1.6.3/checkmate/R/checkNamed.r | 4 checkmate-1.6.3/checkmate/R/checkNames.r | 4 checkmate-1.6.3/checkmate/R/checkNull.r | 4 checkmate-1.6.3/checkmate/R/checkNumber.r | 4 checkmate-1.6.3/checkmate/R/checkNumeric.r | 4 checkmate-1.6.3/checkmate/R/checkPathForOutput.r | 4 checkmate-1.6.3/checkmate/R/checkPercentage.r | 4 checkmate-1.6.3/checkmate/R/checkScalar.r | 4 checkmate-1.6.3/checkmate/R/checkScalarNA.r | 4 checkmate-1.6.3/checkmate/R/checkSetEqual.r | 14 checkmate-1.6.3/checkmate/R/checkString.r | 4 checkmate-1.6.3/checkmate/R/checkSubset.r | 4 checkmate-1.6.3/checkmate/R/checkVector.r | 4 checkmate-1.6.3/checkmate/R/helper.r | 16 checkmate-1.6.3/checkmate/build/vignette.rds |binary checkmate-1.6.3/checkmate/inst/NEWS.md |only checkmate-1.6.3/checkmate/inst/README.md |only checkmate-1.6.3/checkmate/inst/doc/checkmate.R | 26 - checkmate-1.6.3/checkmate/inst/doc/checkmate.Rmd | 52 -- checkmate-1.6.3/checkmate/inst/doc/checkmate.html | 39 -- checkmate-1.6.3/checkmate/man/AssertCollection.Rd |only checkmate-1.6.3/checkmate/man/asInteger.Rd | 9 checkmate-1.6.3/checkmate/man/checkAccess.Rd | 5 checkmate-1.6.3/checkmate/man/checkArray.Rd | 5 checkmate-1.6.3/checkmate/man/checkAtomic.Rd | 5 checkmate-1.6.3/checkmate/man/checkAtomicVector.Rd | 5 checkmate-1.6.3/checkmate/man/checkCharacter.Rd | 5 checkmate-1.6.3/checkmate/man/checkChoice.Rd | 5 checkmate-1.6.3/checkmate/man/checkClass.Rd | 5 checkmate-1.6.3/checkmate/man/checkComplex.Rd | 5 checkmate-1.6.3/checkmate/man/checkCount.Rd | 5 checkmate-1.6.3/checkmate/man/checkDataFrame.Rd | 6 checkmate-1.6.3/checkmate/man/checkDirectory.Rd | 5 checkmate-1.6.3/checkmate/man/checkEnvironment.Rd | 5 checkmate-1.6.3/checkmate/man/checkFactor.Rd | 5 checkmate-1.6.3/checkmate/man/checkFile.Rd | 5 checkmate-1.6.3/checkmate/man/checkFlag.Rd | 5 checkmate-1.6.3/checkmate/man/checkFunction.Rd | 6 checkmate-1.6.3/checkmate/man/checkInt.Rd | 5 checkmate-1.6.3/checkmate/man/checkInteger.Rd | 5 checkmate-1.6.3/checkmate/man/checkIntegerish.Rd | 5 checkmate-1.6.3/checkmate/man/checkList.Rd | 5 checkmate-1.6.3/checkmate/man/checkLogical.Rd | 5 checkmate-1.6.3/checkmate/man/checkMatrix.Rd | 5 checkmate-1.6.3/checkmate/man/checkNamed.Rd | 5 checkmate-1.6.3/checkmate/man/checkNames.Rd | 5 checkmate-1.6.3/checkmate/man/checkNull.Rd | 5 checkmate-1.6.3/checkmate/man/checkNumber.Rd | 5 checkmate-1.6.3/checkmate/man/checkNumeric.Rd | 5 checkmate-1.6.3/checkmate/man/checkPathForOutput.Rd | 5 checkmate-1.6.3/checkmate/man/checkPercentage.Rd | 5 checkmate-1.6.3/checkmate/man/checkScalar.Rd | 5 checkmate-1.6.3/checkmate/man/checkScalarNA.Rd | 5 checkmate-1.6.3/checkmate/man/checkSetEqual.Rd | 9 checkmate-1.6.3/checkmate/man/checkString.Rd | 5 checkmate-1.6.3/checkmate/man/checkSubset.Rd | 5 checkmate-1.6.3/checkmate/man/checkVector.Rd | 5 checkmate-1.6.3/checkmate/src/all_missing.h | 1 checkmate-1.6.3/checkmate/src/any_missing.c | 25 - checkmate-1.6.3/checkmate/src/any_missing.h | 1 checkmate-1.6.3/checkmate/src/qassert.c | 10 checkmate-1.6.3/checkmate/tests/testthat/test_AssertCollection.r |only checkmate-1.6.3/checkmate/tests/testthat/test_checkSetEqual.r | 3 checkmate-1.6.3/checkmate/tests/testthat/test_qtest.r | 20 + checkmate-1.6.3/checkmate/tests/testthat/test_qtestr.r | 3 checkmate-1.6.3/checkmate/vignettes/checkmate.Rmd | 57 ++- 94 files changed, 463 insertions(+), 359 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.7.2 dated 2015-02-27 and 1.7.3.0 dated 2015-10-23
DESCRIPTION | 8 MD5 | 135 +-- NAMESPACE | 7 NEWS | 18 R/Contlcmm.R | 1470 ++++++++++++++++++++------------------ R/Jointlcmm.R | 289 ++++++- R/Ordlcmm.R | 1109 +++++++++++++++-------------- R/VarCov.Jointlcmm.R | 2 R/VarCov.lcmm.R | 2 R/VarCov.multlcmm.R | 2 R/VarCovRE.hlme.R | 280 +++---- R/VarExpl.Jointlcmm.R | 2 R/VarExpl.lcmm.R | 2 R/VarExpl.multlcmm.R | 7 R/WaldMult.R | 302 ++++--- R/cuminc.R | 22 R/dynpred.R | 44 - R/epoce.R | 7 R/estimates.Jointlcmm.R | 2 R/estimates.lcmm.R | 2 R/estimates.multlcmm.R | 2 R/hlme.R | 1255 +++++++++++++++++---------------- R/lcmm.R | 19 R/multlcmm.R | 1743 ++++++++++++++++++++++++---------------------- R/plot.R | 8 R/plot.predictlink.R | 4 R/plotbaselinerisk.R | 2 R/plotlinkfunction.R | 2 R/plotlinkfunctionmult.R | 43 - R/plotpostprob.R | 2 R/plotresid.R | 2 R/plotsurvival.R | 2 R/postprob.Jointlcmm.R | 2 R/predictL.Jointlcmm.R | 30 R/predictL.lcmm.R | 20 R/predictL.multlcmm.R | 20 R/predictY.Jointlcmm.R | 51 + R/predictY.hlme.R | 18 R/predictY.lcmm.R | 53 + R/predictY.multlcmm.R | 99 +- R/predictlink.Jointlcmm.R | 30 R/predictlink.lcmm.R | 30 R/predictlink.multlcmm.R | 35 R/print.Jointlcmm.R | 13 R/print.hlme.R | 15 R/print.lcmm.R | 17 R/print.multlcmm.R | 16 R/summary.Jointlcmm.R | 751 ++++++++++--------- R/summary.hlme.R | 400 ++++++---- R/summary.lcmm.R | 526 ++++++++----- R/summary.multlcmm.R | 724 ++++++++++--------- R/summarytable.R | 4 inst |only man/Jointlcmm.Rd | 21 man/hlme.Rd | 20 man/lcmm-package.Rd | 4 man/lcmm.Rd | 25 man/multlcmm.Rd | 27 src/AOptim.f90 | 95 ++ src/Jointhet.f90 | 161 ++-- src/Makevars | 1 src/cvpl.f90 | 147 ++- src/hetmixCont.f90 | 190 +++-- src/hetmixContMult.f90 | 308 ++++---- src/hetmixOrd.f90 | 215 ++++- src/hetmixlin.f90 | 106 ++ src/postprob2.f90 | 2 src/predictCont.f90 | 15 src/predictMult.f90 | 13 69 files changed, 6380 insertions(+), 4620 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.6 dated 2015-07-23 and 1.6.4 dated 2015-10-23
DESCRIPTION | 12 +++++------ MD5 | 52 ++++++++++++++++++++++++------------------------ R/GoogleMapsPlot.R | 26 ++++++++++++------------ R/RcppExports.R |only R/TheilSen.R | 16 ++++++++++++-- R/aqStats.R | 12 +++++------ R/calendarPlot.R | 4 ++- R/checkPrep.R | 32 ++++++++++++++++------------- R/conditionalQuantile.R | 10 +++++---- R/cutData.R | 4 +-- R/importAURN.R | 8 +++++-- R/openColours.R | 4 +-- R/polarAnnulus.R | 3 +- R/scatterPlot.R | 2 - R/summaryPlot.R | 2 - R/timeAverage.R | 19 ++++++++++------- R/timeProp.R | 2 - R/timeVariation.R | 2 - R/utilities.R | 6 +++-- man/TheilSen.Rd | 6 +++-- man/calendarPlot.Rd | 4 ++- man/openColours.Rd | 4 +-- man/polarAnnulus.Rd | 3 +- man/summaryPlot.Rd | 2 - man/timeAverage.Rd | 17 ++++++++------- man/timeVariation.Rd | 2 - src/Cquantile.cpp | 6 +++-- src/RcppExports.cpp |only 28 files changed, 151 insertions(+), 109 deletions(-)
Title: Penalized Likelihood Estimation and Prediction under the Joint
Cox Models Between Tumour Progression and Death for
Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.2 dated 2015-10-03 and 2.3 dated 2015-10-23
DESCRIPTION | 8 +-- MD5 | 10 +-- NAMESPACE | 3 - R/F.window.R | 121 ++++++++++++++++++++++++++--------------------- man/F.window.Rd | 23 ++------ man/joint.Cox-package.Rd | 4 - 6 files changed, 88 insertions(+), 81 deletions(-)
Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between RGA versions 0.2.4 dated 2015-08-31 and 0.3 dated 2015-10-22
RGA-0.2.4/RGA/inst/doc/common-queries.R |only RGA-0.2.4/RGA/inst/doc/common-queries.Rmd |only RGA-0.2.4/RGA/inst/doc/common-queries.html |only RGA-0.2.4/RGA/vignettes/common-queries.Rmd |only RGA-0.3/RGA/DESCRIPTION | 25 +-- RGA-0.3/RGA/MD5 | 163 +++++++++++++------------ RGA-0.3/RGA/NAMESPACE | 18 -- RGA-0.3/RGA/R/accounts.R | 4 RGA-0.3/RGA/R/auth.R | 85 +++++++------ RGA-0.3/RGA/R/convert.R | 108 ++++++---------- RGA-0.3/RGA/R/custom-dims.R | 8 - RGA-0.3/RGA/R/custom-mets.R | 8 - RGA-0.3/RGA/R/custom-sources.R | 4 RGA-0.3/RGA/R/date-ranges.R |only RGA-0.3/RGA/R/env.R |only RGA-0.3/RGA/R/experiments.R | 8 - RGA-0.3/RGA/R/filters.R | 8 - RGA-0.3/RGA/R/ga.R | 23 ++- RGA-0.3/RGA/R/get-data.R | 64 +++++---- RGA-0.3/RGA/R/goals.R | 8 - RGA-0.3/RGA/R/mcf.R | 21 +-- RGA-0.3/RGA/R/metadata.R | 45 +++--- RGA-0.3/RGA/R/mgmt.R | 36 +++-- RGA-0.3/RGA/R/profiles.R | 14 +- RGA-0.3/RGA/R/query.R | 33 ++--- RGA-0.3/RGA/R/realtime.R | 18 -- RGA-0.3/RGA/R/report.R | 74 +++-------- RGA-0.3/RGA/R/request.R | 120 ++++++++---------- RGA-0.3/RGA/R/segments.R | 2 RGA-0.3/RGA/R/unsampled.R | 8 - RGA-0.3/RGA/R/uploads.R |only RGA-0.3/RGA/R/url.R | 29 ++-- RGA-0.3/RGA/R/utils.R | 52 ++----- RGA-0.3/RGA/R/webproperties.R | 14 +- RGA-0.3/RGA/R/zzz.R | 3 RGA-0.3/RGA/README.md | 8 - RGA-0.3/RGA/build/vignette.rds |binary RGA-0.3/RGA/data/ga.rda |binary RGA-0.3/RGA/inst/NEWS.Rd | 17 ++ RGA-0.3/RGA/inst/doc/authorize.Rmd | 18 +- RGA-0.3/RGA/inst/doc/authorize.html | 102 +++++++++------ RGA-0.3/RGA/inst/doc/management-api.html | 52 +++++-- RGA-0.3/RGA/inst/doc/metadata-api.html | 56 +++++--- RGA-0.3/RGA/inst/doc/reporting-api.Rmd | 19 +- RGA-0.3/RGA/inst/doc/reporting-api.html | 73 ++++++----- RGA-0.3/RGA/inst/shiny-examples |only RGA-0.3/RGA/man/authorize.Rd | 6 RGA-0.3/RGA/man/get_custom_dimension.Rd | 5 RGA-0.3/RGA/man/get_custom_metric.Rd | 5 RGA-0.3/RGA/man/get_experiment.Rd | 5 RGA-0.3/RGA/man/get_filter.Rd | 5 RGA-0.3/RGA/man/get_ga.Rd | 16 +- RGA-0.3/RGA/man/get_goal.Rd | 5 RGA-0.3/RGA/man/get_mcf.Rd | 14 +- RGA-0.3/RGA/man/get_profile.Rd | 9 + RGA-0.3/RGA/man/get_realtime.Rd | 4 RGA-0.3/RGA/man/get_unsampled_report.Rd | 5 RGA-0.3/RGA/man/get_upload.Rd |only RGA-0.3/RGA/man/get_webproperty.Rd | 9 + RGA-0.3/RGA/man/list_accounts.Rd | 7 - RGA-0.3/RGA/man/list_custom_dimensions.Rd | 5 RGA-0.3/RGA/man/list_custom_metrics.Rd | 5 RGA-0.3/RGA/man/list_custom_sources.Rd | 5 RGA-0.3/RGA/man/list_dimsmets.Rd | 5 RGA-0.3/RGA/man/list_experiments.Rd | 5 RGA-0.3/RGA/man/list_filters.Rd | 5 RGA-0.3/RGA/man/list_goals.Rd | 5 RGA-0.3/RGA/man/list_profiles.Rd | 7 - RGA-0.3/RGA/man/list_segments.Rd | 5 RGA-0.3/RGA/man/list_unsampled_reports.Rd | 5 RGA-0.3/RGA/man/list_uploads.Rd |only RGA-0.3/RGA/man/list_webproperties.Rd | 9 - RGA-0.3/RGA/man/shiny_dimsmets.Rd |only RGA-0.3/RGA/tests/testthat/test-auth.R | 12 - RGA-0.3/RGA/tests/testthat/test-convert-ga.R | 15 +- RGA-0.3/RGA/tests/testthat/test-convert-mcf.R | 92 +++++++------- RGA-0.3/RGA/tests/testthat/test-convert-mgmt.R | 19 +- RGA-0.3/RGA/tests/testthat/test-metadata.R | 4 RGA-0.3/RGA/tests/testthat/test-url.R | 4 RGA-0.3/RGA/vignettes/authorize.Rmd | 18 +- RGA-0.3/RGA/vignettes/reporting-api.Rmd | 19 +- 81 files changed, 899 insertions(+), 788 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.9.5 dated 2015-10-07 and 1.10.0 dated 2015-10-22
CHANGELOG | 12 ++ DESCRIPTION | 8 - MD5 | 68 ++++++------ NAMESPACE | 7 - R/binning.R | 278 +++++++++++++---------------------------------------- R/kcde.R | 8 - R/kcopula.R | 6 - R/kda.R | 53 +++++----- R/kdde.R | 219 ++++++++++++++++++++++++++++++++++------- R/kde-test.R | 2 R/kde.R | 32 +++--- R/kfe.R | 147 ---------------------------- R/normal.R | 55 ++++------ R/prelim.R | 17 +-- R/selector.R | 86 ++++++++-------- inst/doc/kde.pdf |binary man/Hlscv.Rd | 24 ++-- man/Hns.Rd | 7 - man/Hpi.Rd | 4 man/Hscv.Rd | 4 man/binning.Rd | 18 ++- man/contour.Rd | 2 man/ise.mixt.Rd | 2 man/kcde.Rd | 5 man/kcopula.Rd | 4 man/kda.Rd | 21 ++-- man/kdde.Rd | 13 +- man/kde.Rd | 14 +- man/kroc.Rd | 4 man/ks-internal.Rd | 10 - man/ks-package.Rd | 7 - man/plot.kda.Rd | 6 - man/plot.kdde.Rd | 10 - man/plot.kde.Rd | 6 - man/plotmixt.Rd | 6 - 35 files changed, 538 insertions(+), 627 deletions(-)
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.1 dated 2015-10-10 and 0.8.3 dated 2015-10-22
DESCRIPTION | 10 +-- MD5 | 136 ++++++++++++++++++++++++------------------------ R/BluegillJL.R | 19 +++--- R/BrookTroutTH.R | 8 +- R/ChinookArg.R | 12 ++-- R/CodNorwegian.R | 13 ++-- R/CutthroatAL.R | 35 ++++++------ R/Ecoli.R | 12 +++- R/Mirex.R | 18 ++++-- R/PikeNY.R | 21 +++---- R/PikeNYPartial1.R | 27 ++++----- R/SMBassLS.R | 10 +-- R/SMBassWB.R | 47 ++++++++-------- R/SpotVA1.R | 8 +- R/WR79.R | 12 ++-- R/WhitefishLC.R | 33 ++++++----- R/ageComparisons.R | 16 ++--- R/alkIndivAge.R | 2 R/bcFuns.R | 5 - R/capHistConvert.R | 2 R/catchCurve.R | 2 R/chapmanRobson.R | 2 R/depletion.R | 2 R/growthModels.R | 22 +++---- R/metaM.R | 12 ++-- R/mrClosed.R | 2 R/mrOpen.R | 2 R/psdAdd.R | 6 +- R/psdCI.R | 2 R/psdCalc.R | 6 +- R/psdPlot.R | 6 +- R/psdVal.R | 6 +- R/removal.R | 2 R/srStarts.R | 2 R/stockRecruitment.R | 2 man/BluegillJL.Rd | 19 +++--- man/BrookTroutTH.Rd | 8 +- man/ChinookArg.Rd | 13 ++-- man/CodNorwegian.Rd | 13 ++-- man/CutthroatAL.Rd | 36 +++++++----- man/Ecoli.Rd | 13 +++- man/Mirex.Rd | 19 ++++-- man/PikeNY.Rd | 21 +++---- man/PikeNYPartial1.Rd | 27 ++++----- man/SMBassLS.Rd | 10 +-- man/SMBassWB.Rd | 45 ++++++++------- man/SpotVA1.Rd | 8 +- man/WR79.Rd | 12 ++-- man/WhitefishLC.Rd | 33 ++++++----- man/ageBias.Rd | 6 +- man/agePrecision.Rd | 10 +-- man/alkIndivAge.Rd | 2 man/bcFuns.Rd | 7 +- man/capHistConvert.Rd | 2 man/catchCurve.Rd | 2 man/chapmanRobson.Rd | 2 man/depletion.Rd | 2 man/growthModels.Rd | 22 +++---- man/metaM.Rd | 12 ++-- man/mrClosed.Rd | 2 man/mrOpen.Rd | 2 man/psdAdd.Rd | 6 +- man/psdCI.Rd | 2 man/psdCalc.Rd | 6 +- man/psdPlot.Rd | 6 +- man/psdVal.Rd | 6 +- man/removal.Rd | 2 man/srStarts.Rd | 2 man/stockRecruitment.Rd | 2 69 files changed, 475 insertions(+), 427 deletions(-)
Title: Estimation of Distribution Algorithms Based on Copulas
Description: Provides a platform where EDAs (estimation of
distribution algorithms) based on copulas can be implemented and
studied. The package offers complete implementations of various
EDAs based on copulas and vines, a group of well-known
optimization problems, and utility functions to study the
performance of the algorithms. Newly developed EDAs can be easily
integrated into the package by extending an S4 class with generic
functions for their main components.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez <ygonzalezfernandez@gmail.com>
Diff between copulaedas versions 1.4.1 dated 2014-06-21 and 1.4.2 dated 2015-10-22
copulaedas-1.4.1/copulaedas/src |only copulaedas-1.4.2/copulaedas/DESCRIPTION | 30 ++++--- copulaedas-1.4.2/copulaedas/MD5 | 69 ++++++++-------- copulaedas-1.4.2/copulaedas/NAMESPACE | 10 +- copulaedas-1.4.2/copulaedas/NEWS | 20 +++- copulaedas-1.4.2/copulaedas/R/CEDA.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/EDA.R | 26 +++--- copulaedas-1.4.2/copulaedas/R/VEDA.R | 34 +++----- copulaedas-1.4.2/copulaedas/R/edaCriticalPopSize.R | 28 +++--- copulaedas-1.4.2/copulaedas/R/edaIndepRuns.R | 46 +++++------ copulaedas-1.4.2/copulaedas/R/edaOptimize.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaReplace.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaReport.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaRun.R | 34 ++++---- copulaedas-1.4.2/copulaedas/R/edaSeed.R | 26 +++--- copulaedas-1.4.2/copulaedas/R/edaSelect.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/edaTerminate.R | 24 ++--- copulaedas-1.4.2/copulaedas/R/margins.R | 26 +++--- copulaedas-1.4.2/copulaedas/R/problems.R | 24 ++--- copulaedas-1.4.2/copulaedas/inst/CITATION | 35 ++++---- copulaedas-1.4.2/copulaedas/man/CEDA-class.Rd | 42 +++++----- copulaedas-1.4.2/copulaedas/man/EDA-class.Rd | 20 ++-- copulaedas-1.4.2/copulaedas/man/EDAResult-class.Rd | 18 ++-- copulaedas-1.4.2/copulaedas/man/EDAResults-class.Rd | 14 +-- copulaedas-1.4.2/copulaedas/man/VEDA-class.Rd | 74 +++++++++--------- copulaedas-1.4.2/copulaedas/man/edaCriticalPopSize.Rd | 24 ++--- copulaedas-1.4.2/copulaedas/man/edaIndepRuns.Rd | 6 - copulaedas-1.4.2/copulaedas/man/edaOptimize.Rd | 16 +-- copulaedas-1.4.2/copulaedas/man/edaReplace.Rd | 14 +-- copulaedas-1.4.2/copulaedas/man/edaReport.Rd | 22 ++--- copulaedas-1.4.2/copulaedas/man/edaRun.Rd | 34 ++++---- copulaedas-1.4.2/copulaedas/man/edaSeed.Rd | 20 ++-- copulaedas-1.4.2/copulaedas/man/edaSelect.Rd | 21 ++--- copulaedas-1.4.2/copulaedas/man/edaTerminate.Rd | 32 +++---- copulaedas-1.4.2/copulaedas/man/margins.Rd | 60 +++++++------- copulaedas-1.4.2/copulaedas/man/problems.Rd | 27 +++--- 36 files changed, 502 insertions(+), 494 deletions(-)
Title: Weighted Scores Method for Regression Models with Dependent Data
Description: Has functions to implement the weighted scores method and CL1 information criteria as an intermediate step for variable/correlation selection for longitudinal categorical and count data in Nikoloulopoulos, Joe and Chaganty (2011, Biostatistics, 12: 653-665) and Nikoloulopoulos (2015a,2015b).
Author: A. K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk> and H. Joe <harry.joe@ubc.ca>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Diff between weightedScores versions 0.9.1 dated 2014-11-06 and 0.9.5.1 dated 2015-10-22
DESCRIPTION | 12 - INDEX | 21 +-- MD5 | 58 ++++++-- NAMESPACE | 23 ++- R/CLIC-ord.R |only R/exchmvn.R |only R/mvn.deriv.R |only R/mvnapp.R |only R/ord.reg.univar.R |only R/wtsc-ord.R |only data/arthritis.rda |only man/CLIC.Rd |only man/arthritis.Rd |only man/bcl.Rd | 145 ++++++++++----------- man/cl1.Rd | 273 +++++++++++++++++++++++----------------- man/exchmvn.Rd |only man/godambe.Rd | 354 +++++++++++++++++++++++++++++++--------------------- man/iee.Rd | 169 ++++++++++++------------ man/iee.ord.Rd |only man/marglik.Rd | 104 +++++++-------- man/margmodel.Rd | 149 ++++++++++++--------- man/mvn.deriv.Rd |only man/mvnapp.Rd |only man/scoreCov.Rd | 68 +++++---- man/solvewtsc.Rd | 322 ++++++++++++++++++++++++++++------------------- man/weightMat.Rd | 289 +++++++++++++++++++++++++----------------- man/wtsc.Rd | 149 +++++++++++---------- man/wtsc.wrapper.Rd | 214 ++++++++++++++++--------------- src |only 29 files changed, 1349 insertions(+), 1001 deletions(-)
More information about weightedScores at CRAN
Permanent link
Title: Simple TCGA Data Access for Integrated Statistical Analysis in R
Description: Automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.
Author: Ying-Wooi Wan, Genevera I. Allen, Matthew L. Anderson, Zhandong Liu
Maintainer: Ying-Wooi Wan <yingwoow@bcm.edu>
Diff between TCGA2STAT versions 1.0 dated 2015-07-17 and 1.2 dated 2015-10-22
TCGA2STAT-1.0/TCGA2STAT/man/GeneMerge.Rd |only TCGA2STAT-1.2/TCGA2STAT/DESCRIPTION | 12 TCGA2STAT-1.2/TCGA2STAT/MD5 | 39 +- TCGA2STAT-1.2/TCGA2STAT/NAMESPACE | 2 TCGA2STAT-1.2/TCGA2STAT/R/TCGA2STAT.R | 394 +++++++++++++---------- TCGA2STAT-1.2/TCGA2STAT/build |only TCGA2STAT-1.2/TCGA2STAT/inst |only TCGA2STAT-1.2/TCGA2STAT/man/OMICSBind.Rd |only TCGA2STAT-1.2/TCGA2STAT/man/SampleSplit.Rd | 4 TCGA2STAT-1.2/TCGA2STAT/man/TCGA2STAT-package.Rd | 23 - TCGA2STAT-1.2/TCGA2STAT/man/TumorNormalMatch.Rd | 9 TCGA2STAT-1.2/TCGA2STAT/man/geneinfo.Rd | 4 TCGA2STAT-1.2/TCGA2STAT/man/getTCGA.Rd | 44 +- TCGA2STAT-1.2/TCGA2STAT/vignettes |only 14 files changed, 303 insertions(+), 228 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers. Among available
features there are: pattern searching (e.g., with ICU Java-like regular
expressions or the Unicode Collation Algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski and Bartek Tartanus (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 0.5-5 dated 2015-06-29 and 1.0-1 dated 2015-10-22
DESCRIPTION | 18 - INSTALL | 18 + LICENSE | 58 +++ MD5 | 53 +-- NEWS | 13 R/compare.R | 210 -------------- R/encoding_detection.R | 12 R/join.R | 8 R/sort.R |only R/trans_casemap.R | 4 R/trans_normalization.R | 20 - configure | 20 - man/stri_duplicated.Rd | 2 man/stri_order.Rd | 2 man/stri_unique.Rd | 2 src/Makevars.win | 6 src/install.libs.R.in | 65 ++++ src/stri_compare.cpp | 568 +++++++++------------------------------ src/stri_container_listutf8.cpp | 2 src/stri_cpp.txt | 1 src/stri_encoding_detection.cpp | 86 +++++ src/stri_exports.h |only src/stri_join.cpp | 292 ++++++++++---------- src/stri_sort.cpp |only src/stri_stringi.cpp | 58 ++- src/stri_stringi.h | 277 +------------------ src/stri_sub.cpp | 18 - src/stri_trans_casemap.cpp | 48 ++- src/stri_trans_normalization.cpp | 173 ++++++++++- 29 files changed, 875 insertions(+), 1159 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood
Maintainer: Ben Sherwood <bsherwo2@jhu.edu>
Diff between rqPen versions 1.1 dated 2015-03-15 and 1.2 dated 2015-10-22
DESCRIPTION | 12 - MD5 | 47 ++-- NAMESPACE | 27 ++ NEWS | 9 R/rqPen.R | 460 ++++++++++++++++++++++++++++++++++++++++- man/beta_plots.Rd | 6 man/coef.cv.rq.group.pen.Rd |only man/coef.cv.rq.pen.Rd |only man/cv.rq.group.pen.Rd |only man/cv.rq.pen.Rd | 8 man/cv_plots.Rd | 4 man/getRho.Rd |only man/groupMultLambda.Rd |only man/groupQICD.Rd |only man/group_derivs.Rd |only man/kernel_estimates.Rd |only man/kernel_weights.Rd |only man/mcp.Rd | 4 man/mcp_deriv.Rd | 4 man/model_eval.Rd | 2 man/nonzero.Rd |only man/nonzero.cv.rq.group.pen.Rd |only man/plot.cv.rq.group.pen.Rd |only man/predict.cv.rq.pen.Rd | 2 man/predict.rq.pen.Rd | 4 man/rq.group.fit.Rd |only man/rq.group.lin.prog.Rd |only man/rq.lasso.fit.Rd | 4 man/rq.lasso.fit.mult.Rd |only man/rq.nc.fit.Rd | 9 man/scad.Rd | 4 man/scad_deriv.Rd | 4 32 files changed, 553 insertions(+), 57 deletions(-)
Title: Multiresolution Kriging Based on Markov Random Fields
Description: Functions for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) Moreover, the covariance model for this method
can approximate the Matern covariance family but also allows for a
multi-resolution model and supports efficient computation of the
profile likelihood for estimating covariance parameters. This is
accomplished through compactly supported basis functions and a
Markov random field model for the basis coefficients. These features
lead to sparse matrices for the computations. An extension of this
version over previous ones ( < 5.4 ) is the support for different
geometries besides a rectangular domain.
One benefit of the LatticeKrig model/approach
is the facility to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating non-stationary covariances. Included are
generic methods for prediction, standard errors for prediction,
plotting of the estimated surface and conditional and unconditional
simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between LatticeKrig versions 3.4 dated 2014-08-28 and 5.4 dated 2015-10-22
LatticeKrig-3.4/LatticeKrig/R/LKrig.MRF.precision.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.cyl.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.a.wght.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.alpha.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.centers.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.make.grid.info.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.normalize.basis.R |only LatticeKrig-3.4/LatticeKrig/R/LKrig.setup.R |only LatticeKrig-3.4/LatticeKrig/man/LKinfo.Rd |only LatticeKrig-3.4/LatticeKrig/tests/LKrig.test.NonStationary.R |only LatticeKrig-5.4/LatticeKrig/DESCRIPTION | 23 LatticeKrig-5.4/LatticeKrig/MD5 | 172 ++- LatticeKrig-5.4/LatticeKrig/NAMESPACE | 61 + LatticeKrig-5.4/LatticeKrig/R/BACK |only LatticeKrig-5.4/LatticeKrig/R/GridList.R |only LatticeKrig-5.4/LatticeKrig/R/LKDist.R |only LatticeKrig-5.4/LatticeKrig/R/LKDistComponents.R |only LatticeKrig-5.4/LatticeKrig/R/LKDistGrid.R |only LatticeKrig-5.4/LatticeKrig/R/LKDistGridComponents.R |only LatticeKrig-5.4/LatticeKrig/R/LKGridCheck.R |only LatticeKrig-5.4/LatticeKrig/R/LKGridFindNmax.R |only LatticeKrig-5.4/LatticeKrig/R/LKRectangleFastNormalization.R |only LatticeKrig-5.4/LatticeKrig/R/LKinfoCheck.R |only LatticeKrig-5.4/LatticeKrig/R/LKinfoUpdate.R | 42 LatticeKrig-5.4/LatticeKrig/R/LKrig.MLE.R | 32 LatticeKrig-5.4/LatticeKrig/R/LKrig.R | 362 +++---- LatticeKrig-5.4/LatticeKrig/R/LKrig.basis.R | 119 +- LatticeKrig-5.4/LatticeKrig/R/LKrig.coef.R | 30 LatticeKrig-5.4/LatticeKrig/R/LKrig.cov.R | 87 - LatticeKrig-5.4/LatticeKrig/R/LKrig.cov.plot.R | 6 LatticeKrig-5.4/LatticeKrig/R/LKrig.lnPlike.R | 141 +- LatticeKrig-5.4/LatticeKrig/R/LKrig.make.par.grid.R | 6 LatticeKrig-5.4/LatticeKrig/R/LKrig.misc.R | 56 + LatticeKrig-5.4/LatticeKrig/R/LKrig.precision.R | 67 - LatticeKrig-5.4/LatticeKrig/R/LKrig.quadraticform.R |only LatticeKrig-5.4/LatticeKrig/R/LKrig.sim.R | 54 - LatticeKrig-5.4/LatticeKrig/R/LKrig.sim.conditional.R | 96 + LatticeKrig-5.4/LatticeKrig/R/LKrig.spind2spam.R | 20 LatticeKrig-5.4/LatticeKrig/R/LKrig.traceA.R | 14 LatticeKrig-5.4/LatticeKrig/R/LKrigCovWieghtedObs.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigDefaultFixedFunction.R | 75 + LatticeKrig-5.4/LatticeKrig/R/LKrigDistance.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigFindLambda.R | 132 +- LatticeKrig-5.4/LatticeKrig/R/LKrigLatticeCenters.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigMakewU.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigMakewX.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigNormalizeBasis.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSAR.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetup.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetupAlpha.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetupAwght.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigSetupLattice.R |only LatticeKrig-5.4/LatticeKrig/R/LKrigUnrollGrid.R | 21 LatticeKrig-5.4/LatticeKrig/R/LatticeKrig.R | 69 - LatticeKrig-5.4/LatticeKrig/R/LatticeKrigEasyDefaults.R |only LatticeKrig-5.4/LatticeKrig/R/ModelBox.R |only LatticeKrig-5.4/LatticeKrig/R/ModelCylinder.R |only LatticeKrig-5.4/LatticeKrig/R/ModelInterval.R |only LatticeKrig-5.4/LatticeKrig/R/ModelRectangle.R |only LatticeKrig-5.4/LatticeKrig/R/ModelRing.R |only LatticeKrig-5.4/LatticeKrig/R/Radial.basis.R | 94 - LatticeKrig-5.4/LatticeKrig/R/Tensor.basis.R |only LatticeKrig-5.4/LatticeKrig/R/WendlandFunction.R |only LatticeKrig-5.4/LatticeKrig/R/convertIndexPeriodic.R |only LatticeKrig-5.4/LatticeKrig/R/createLKrigObject.R |only LatticeKrig-5.4/LatticeKrig/R/directionCosines.R |only LatticeKrig-5.4/LatticeKrig/R/predict.LKrig.R | 75 - LatticeKrig-5.4/LatticeKrig/R/predictLKrigFixedFunction.R | 19 LatticeKrig-5.4/LatticeKrig/R/predictSE.LKrig.R | 130 +- LatticeKrig-5.4/LatticeKrig/R/predictSurface.LKrig.R | 102 +- LatticeKrig-5.4/LatticeKrig/R/print.LKinfo.R | 87 + LatticeKrig-5.4/LatticeKrig/R/print.LKrig.R | 49 LatticeKrig-5.4/LatticeKrig/R/print.LatticeKrig.R |only LatticeKrig-5.4/LatticeKrig/R/setDefaultsLKinfo.R |only LatticeKrig-5.4/LatticeKrig/R/triWeight.R |only LatticeKrig-5.4/LatticeKrig/man/LKDistance.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKRing.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKgeometry.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKinfoCheck.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrig.MLE.Rd | 76 + LatticeKrig-5.4/LatticeKrig/man/LKrig.Rd | 491 +++++----- LatticeKrig-5.4/LatticeKrig/man/LKrig.basis.Rd | 138 +- LatticeKrig-5.4/LatticeKrig/man/LKrig.fixed.Rd | 3 LatticeKrig-5.4/LatticeKrig/man/LKrig.internal.Rd | 76 - LatticeKrig-5.4/LatticeKrig/man/LKrig.misc.Rd | 60 + LatticeKrig-5.4/LatticeKrig/man/LKrig.sim.Rd | 21 LatticeKrig-5.4/LatticeKrig/man/LKrigDistance-methods.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigLatticeCenters.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigNormalizeBasisFast.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSAR.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetup.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetupAlpha.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetupAwght.Rd |only LatticeKrig-5.4/LatticeKrig/man/LKrigSetupLattice.Rd |only LatticeKrig-5.4/LatticeKrig/man/LatticeKrig.Rd | 180 ++- LatticeKrig-5.4/LatticeKrig/man/Radial.Basis.Rd | 84 + LatticeKrig-5.4/LatticeKrig/man/gridList-class.Rd |only LatticeKrig-5.4/LatticeKrig/man/setDefaultsLKinfo.Rd |only LatticeKrig-5.4/LatticeKrig/src/LKdist.f |only LatticeKrig-5.4/LatticeKrig/src/LKdistgrid.f |only LatticeKrig-5.4/LatticeKrig/src/dfind1d.f |only LatticeKrig-5.4/LatticeKrig/src/findNorm.f | 3 LatticeKrig-5.4/LatticeKrig/tests/LKrig.FindNorm.test.R | 91 + LatticeKrig-5.4/LatticeKrig/tests/LKrig.FindNorm.test.Rout.save |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.LKCylinder.test.R |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.basis.test.R | 159 ++- LatticeKrig-5.4/LatticeKrig/tests/LKrig.basis.test.Rout.save | 39 LatticeKrig-5.4/LatticeKrig/tests/LKrig.lnPlike.test.Rout.save | 16 LatticeKrig-5.4/LatticeKrig/tests/LKrig.nullspace.test.Rout.save |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.precision.test.R | 226 +--- LatticeKrig-5.4/LatticeKrig/tests/LKrig.precision.test.Rout.save | 39 LatticeKrig-5.4/LatticeKrig/tests/LKrig.se.test.R | 110 +- LatticeKrig-5.4/LatticeKrig/tests/LKrig.se.test.Rout.save | 95 - LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.3D.R |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.3D.Rout.save |only LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.R | 59 - LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.Rout.save | 25 LatticeKrig-5.4/LatticeKrig/tests/LKrig.test.inverse.R |only 118 files changed, 2470 insertions(+), 1762 deletions(-)
Title: Data to Support Fish Stock Assessment (FSA) Package
Description: The datasets to support the Fish Stock Assessment (FSA) package.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSAdata versions 0.3.0 dated 2015-10-06 and 0.3.2 dated 2015-10-22
DESCRIPTION | 11 MD5 | 566 ++++++++++++++++++++++++---------------------- NAMESPACE | 2 R/AHerringChile.R | 2 R/AfricanRivers.R | 9 R/AlewifeLH.R | 14 - R/AnchovetaChile.R | 2 R/BGHRfish.R |only R/BGHRsample.R |only R/BSkateGB.R | 19 - R/BassFL.R | 4 R/BlackDrum2001.R |only R/BloaterLH.R | 17 - R/BlueCatfish.R | 8 R/BlueCrab.R | 2 R/BluefishAge.R | 14 - R/BluegillLM.R | 11 R/BluntnoseIL1.R | 14 - R/BrookTroutNC.R | 19 - R/BrookTroutNEWP.R | 2 R/BrookTroutNEWP1.R | 2 R/BrookTroutOnt.R | 21 - R/BrownTroutVC1.R | 21 - R/BullTroutRML1.R | 19 - R/BullTroutRML2.R | 6 R/BullTroutTC.R | 4 R/CCatfishNB.R |only R/Cabezon.R | 8 R/Casselman1990.R | 13 - R/ChinookKR.R | 17 - R/CiscoTL.R | 25 +- R/CrappieARMS.R | 8 R/CreekChub.R |only R/CreelMN.R | 7 R/Croaker1.R | 12 R/Croaker2.R | 2 R/CutthroatALf.R | 17 - R/DarterOnt.R | 4 R/Deckeretal1999.R | 2 R/EuroPerchTJ.R | 2 R/FHCatfish.R | 8 R/FHCatfishATL.R | 2 R/FSAdata.R | 39 +-- R/FWDrumLE2.R | 4 R/Ghats.R | 9 R/GreensCreekMine.R | 2 R/Hake.R | 11 R/HalibutPAC.R | 17 - R/Herman.R | 6 R/HerringBWE.R | 17 - R/HerringISS.R | 19 - R/HumpbackWFCR.R | 21 - R/InchLake1.R | 14 - R/InchLake2.R | 17 - R/JobfishSIO.R | 2 R/Jonubi2.R | 12 R/KingCrabAK.R | 17 - R/LMBassBL.R | 8 R/LMBassLCB.R | 8 R/LakeTroutALTER.R | 14 - R/LakeTroutEggs.R | 9 R/LakeTroutGIS.R | 15 - R/LakeTroutMI.R | 19 - R/Lizardfish.R | 15 - R/LobsterHI.R | 2 R/Menhaden1.R | 2 R/Morwong1.R | 12 R/Morwong2.R | 12 R/Morwong3.R | 12 R/Morwong4a.R | 10 R/MulletBS.R | 12 R/MuskieSLR.R | 12 R/MuskieWI06MR.R | 23 - R/PSalmonAK.R | 19 - R/Pallid.R | 10 R/Pathfinder.R | 2 R/PikeHL.R | 21 - R/PikeNYPartial2.R | 21 - R/PikeWindermere.R | 21 - R/PygmyWFBC.R | 39 +-- R/RBSmeltErie.R | 4 R/RBSmeltLM.R | 8 R/RBTroutKenai.R | 2 R/RBTroutUNSP.R | 17 - R/RWhitefishAI.R | 2 R/RWhitefishIR.R | 2 R/RedDrum.R | 8 R/Riffleshell.R | 23 - R/RockBassL02.R | 12 R/RuffeSLRH92.R | 30 +- R/RuffeTL89.R | 4 R/SLampreyGL.R | 51 ++-- R/SalmonidsMCCA.R | 2 R/SardineLK.R | 2 R/SardinesPacific.R | 58 ++-- R/SculpinALTER.R | 18 - R/ShadCR.R |only R/ShrimpGuam.R | 2 R/SiscowetMI2004.R |only R/Snapper.R | 51 ++-- R/SnapperHG1.R | 10 R/SnapperHG2.R | 10 R/SockeyeKL.R | 57 ++-- R/SockeyeSR.R | 63 ++--- R/SpotVA2.R | 12 R/SpottedSucker1.R | 2 R/StripedBass1.R | 15 - R/StripedBass2.R | 5 R/StripedBass3.R | 11 R/StripedBass4.R | 12 R/StripedBass5.R | 12 R/StripedBass6.R | 12 R/SturgeonBL.R | 63 ++--- R/SturgeonGB.R |only R/SunfishIN.R | 29 +- R/SunfishLP.R | 55 ++-- R/TPrawnsEG.R | 21 - R/TroutperchLM2.R | 8 R/TroutperchLM3.R | 14 - R/VendaceLP.R | 15 - R/VendaceLP2.R | 13 - R/WShrimpGA.R | 17 - R/WalleyeConsumption.R | 2 R/WalleyeEL.R | 17 - R/WalleyeErie.R | 6 R/WalleyeErie2.R | 21 - R/WalleyeKS.R | 2 R/WalleyeMN06a.R | 9 R/WalleyeMN06b.R | 25 +- R/WalleyePL.R | 23 - R/WalleyePS.R | 16 - R/WalleyeWad.R |only R/WalleyeWyrlng.R |only R/WhiteGrunt1.R | 2 R/WhiteGrunt2.R | 8 R/WhitefishLS.R | 9 R/WhitefishMB.R | 14 - R/WhitefishTB.R | 17 - R/YERockfish.R | 6 R/YPerchCB1.R | 2 R/YPerchCB2.R | 15 - R/YPerchGB.R | 2 R/YPerchGL.R | 15 - R/YPerchRL.R | 2 R/YPerchSB.R | 13 - R/YPerchSB1.R | 6 R/YPerchTL.R | 20 - R/YTFlounder.R | 14 - data/BGHRfish.rdata |only data/BGHRsample.rdata |only data/BlackDrum2001.rdata |only data/CCatfishNB.rdata |only data/CreekChub.rdata |only data/ShadCR.rdata |only data/SiscowetMI2004.rdata |only data/SturgeonGB.rdata |only data/WalleyeWad.rdata |only data/WalleyeWyrlng.rdata |only man/AHerringChile.Rd | 2 man/AfricanRivers.Rd | 9 man/AlewifeLH.Rd | 12 man/BGHRfish.Rd |only man/BGHRsample.Rd |only man/BSkateGB.Rd | 15 - man/BassFL.Rd | 2 man/BlackDrum2001.Rd |only man/BloaterLH.Rd | 15 - man/BlueCatfish.Rd | 6 man/BluefishAge.Rd | 12 man/BluegillLM.Rd | 11 man/BluntnoseIL1.Rd | 12 man/BrookTroutNC.Rd | 15 - man/BrookTroutOnt.Rd | 19 - man/BrownTroutVC1.Rd | 17 - man/BullTroutRML1.Rd | 17 - man/BullTroutRML2.Rd | 4 man/BullTroutTC.Rd | 2 man/CCatfishNB.Rd |only man/Cabezon.Rd | 6 man/Casselman1990.Rd | 13 - man/ChinookKR.Rd | 15 - man/CiscoTL.Rd | 23 - man/CrappieARMS.Rd | 7 man/CreekChub.Rd |only man/CreelMN.Rd | 9 man/Croaker1.Rd | 12 man/Croaker2.Rd | 2 man/CutthroatALf.Rd | 17 - man/DarterOnt.Rd | 4 man/Deckeretal1999.Rd | 2 man/EuroPerchTJ.Rd | 2 man/FHCatfish.Rd | 8 man/FHCatfishATL.Rd | 2 man/FSAdata.Rd | 35 +- man/FWDrumLE2.Rd | 4 man/Ghats.Rd | 11 man/GreensCreekMine.Rd | 2 man/Hake.Rd | 9 man/HalibutPAC.Rd | 17 - man/Herman.Rd | 6 man/HerringBWE.Rd | 15 - man/HerringISS.Rd | 17 - man/HumpbackWFCR.Rd | 19 - man/InchLake1.Rd | 14 - man/InchLake2.Rd | 17 - man/JobfishSIO.Rd | 2 man/Jonubi2.Rd | 12 man/KingCrabAK.Rd | 15 - man/LMBassBL.Rd | 8 man/LMBassLCB.Rd | 8 man/LakeTroutALTER.Rd | 14 - man/LakeTroutEggs.Rd | 11 man/LakeTroutGIS.Rd | 13 - man/LakeTroutMI.Rd | 15 - man/Lizardfish.Rd | 13 - man/LobsterHI.Rd | 2 man/Menhaden1.Rd | 2 man/Morwong1.Rd | 12 man/Morwong2.Rd | 12 man/Morwong3.Rd | 12 man/Morwong4a.Rd | 10 man/MulletBS.Rd | 12 man/MuskieSLR.Rd | 12 man/MuskieWI06MR.Rd | 21 - man/PSalmonAK.Rd | 17 - man/Pallid.Rd | 10 man/Pathfinder.Rd | 2 man/PikeHL.Rd | 19 - man/PikeNYPartial2.Rd | 19 - man/PikeWindermere.Rd | 21 - man/PygmyWFBC.Rd | 39 +-- man/RBSmeltErie.Rd | 4 man/RBSmeltLM.Rd | 8 man/RBTroutKenai.Rd | 2 man/RBTroutUNSP.Rd | 15 - man/RWhitefishAI.Rd | 2 man/RWhitefishIR.Rd | 2 man/RedDrum.Rd | 8 man/Riffleshell.Rd | 21 - man/RockBassLO2.Rd | 12 man/RuffeSLRH92.Rd | 30 +- man/RuffeTL89.Rd | 4 man/SLampreyGL.Rd | 21 - man/SalmonidsMCCA.Rd | 2 man/SardineLK.Rd | 2 man/SardinesPacific.Rd | 18 - man/SculpinALTER.Rd | 18 - man/ShadCR.Rd |only man/ShrimpGuam.Rd | 2 man/SiscowetMI2004.Rd |only man/Snapper.Rd | 17 - man/SnapperHG1.Rd | 11 man/SnapperHG2.Rd | 10 man/SockeyeKL.Rd | 21 - man/SockeyeSR.Rd | 24 - man/SpotVA2.Rd | 12 man/SpottedSucker1.Rd | 2 man/StripedBass1.Rd | 15 - man/StripedBass2.Rd | 5 man/StripedBass3.Rd | 9 man/StripedBass4.Rd | 12 man/StripedBass5.Rd | 12 man/StripedBass6.Rd | 12 man/SturgeonBL.Rd | 33 +- man/SturgeonGB.Rd |only man/SunfishIN.Rd | 25 +- man/SunfishLP.Rd | 18 - man/TPrawnsEG.Rd | 19 - man/TroutperchLM2.Rd | 8 man/TroutperchLM3.Rd | 15 - man/VendaceLP.Rd | 11 man/VendaceLP2.Rd | 11 man/WShrimpGA.Rd | 13 - man/WalleyeConsumption.Rd | 2 man/WalleyeEL.Rd | 15 - man/WalleyeErie.Rd | 2 man/WalleyeErie2.Rd | 21 - man/WalleyeKS.Rd | 2 man/WalleyeMN06a.Rd | 8 man/WalleyeMN06b.Rd | 23 - man/WalleyePL.Rd | 21 - man/WalleyePS.Rd | 16 - man/WalleyeWad.Rd |only man/WalleyeWyrlng.Rd |only man/WhiteGrunt1.Rd | 2 man/WhiteGrunt2.Rd | 8 man/WhitefishLS.Rd | 11 man/WhitefishMB.Rd | 14 - man/WhitefishTB.Rd | 17 - man/YERockfish.Rd | 6 man/YPerchCB1.Rd | 2 man/YPerchCB2.Rd | 13 - man/YPerchGB.Rd | 2 man/YPerchGL.Rd | 15 - man/YPerchRL.Rd | 2 man/YPerchSB.Rd | 13 - man/YPerchSB1.Rd | 6 man/YPerchTL.Rd | 20 - man/YTFlounder.Rd | 14 - 299 files changed, 2130 insertions(+), 1861 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between coneproj versions 1.8 dated 2015-10-03 and 1.9 dated 2015-10-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/coneproj.R | 11 ++++++++--- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Simulating Data to Study Performance of Clustering Algorithms
Description: The utility of this package is in simulating mixtures of Gaussian
distributions with different levels of overlap between mixture
components. Pairwise overlap, defined as a sum of two
misclassification probabilities, measures the degree of
interaction between components and can be readily employed to
control the clustering complexity of datasets simulated from
mixtures. These datasets can then be used for systematic
performance investigation of clustering and finite mixture
modeling algorithms. Among other capabilities of 'MixSim', there
are computing the exact overlap for Gaussian mixtures,
simulating Gaussian and non-Gaussian data, simulating outliers
and noise variables, calculating various measures of agreement
between two partitionings, and constructing parallel
distribution plots for the graphical display of finite mixture
models.
Author: Volodymyr Melnykov [aut],
Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Robert Davies [ctb] (quadratic form probabilities),
Stephen Moshier [ctb] (eigenvalue calculations),
Rouben Rostamian [ctb] (memory allocation)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between MixSim versions 1.1-1 dated 2015-05-24 and 1.1-2 dated 2015-10-22
MixSim-1.1-1/MixSim/NEWS |only MixSim-1.1-2/MixSim/ChangeLog | 6 ++++++ MixSim-1.1-2/MixSim/DESCRIPTION | 34 +++++++++++++++++++++++----------- MixSim-1.1-2/MixSim/MD5 | 11 +++++------ MixSim-1.1-2/MixSim/NAMESPACE | 4 ++++ MixSim-1.1-2/MixSim/cleanup | 3 ++- MixSim-1.1-2/MixSim/src/libAdjRand.c | 26 +++++++++++++++++++++++++- 7 files changed, 65 insertions(+), 19 deletions(-)
Title: Simulating Data for PLS Mode B Structural Models
Description: A set of functions have been implemented to generate random data to perform Monte Carlo simulations on structural models with formative constructs and interaction and nonlinear effects (Two-Step PLS Mode B structural models). The setup of the true model considers a simple structure with three formative exogenous constructs related to one formative endogenous construct. The routines take into account the interaction and nonlinear effects of the exogenous constructs on the endogenous construct.
Author: Alba Martinez-Ruiz <amartine@ucsc.cl> and Claudia Martinez-Araneda <cmartinez@ucsc.cl>
Maintainer: Alba Martinez-Ruiz <amartine@ucsc.cl>
Diff between dgmb versions 1.1 dated 2014-06-25 and 1.2 dated 2015-10-22
DESCRIPTION | 16 ++++++++-------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 4 +++- R/dgmbGui.R | 18 +++++++++--------- inst/docs/dgmb-manual.pdf |binary man/ErrEnLV.Rd | 2 +- man/ExoLVsCor.Rd | 5 ++--- man/ExoMVs.Rd | 3 +-- man/IntPar.Rd | 2 +- man/NIEffects.Rd | 3 +-- man/ToProcess.Rd | 2 +- man/ViewHelp.Rd | 2 +- man/dgmb-package.Rd | 17 +++++++++-------- man/dgmbGui.Rd | 29 +++-------------------------- man/figures |only 15 files changed, 57 insertions(+), 76 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between rjags versions 3-15 dated 2015-04-15 and 4-4 dated 2015-10-22
rjags-3-15/rjags/README |only rjags-4-4/rjags/DESCRIPTION | 17 - rjags-4-4/rjags/INSTALL |only rjags-4-4/rjags/MD5 | 36 +-- rjags-4-4/rjags/NAMESPACE | 9 rjags-4-4/rjags/R/jags.R | 36 ++- rjags-4-4/rjags/R/jags.object.R | 3 rjags-4-4/rjags/R/mcarray.R | 43 +++- rjags-4-4/rjags/R/unix/zzz.R.in | 3 rjags-4-4/rjags/R/windows/zzz.R | 3 rjags-4-4/rjags/configure | 353 ++++++++++++++++++++++++----------- rjags-4-4/rjags/configure.ac | 189 ++++++++++++------ rjags-4-4/rjags/man/adapt.Rd | 8 rjags-4-4/rjags/man/coda.samples.Rd | 19 + rjags-4-4/rjags/man/jags.model.Rd | 7 rjags-4-4/rjags/src/Makevars.in | 4 rjags-4-4/rjags/src/Makevars.win | 2 rjags-4-4/rjags/src/jags.cc | 32 +-- rjags-4-4/rjags/src/jags.cc.orig |only rjags-4-4/rjags/src/parallel.cc | 4 rjags-4-4/rjags/src/parallel.cc.orig |only 21 files changed, 524 insertions(+), 244 deletions(-)
Title: Preparing Experimental Data for Statistical Analysis
Description: Prepares data collected in an experimental design for statistical
analysis (e.g., analysis of variance ;ANOVA) by taking the individual data
files and preparing one table that contains several possibilities for
dependent variables. Most suitable when measuring reaction-times and/or
accuracy, or any other variable in an interval or ratio scale. Functions
included: file_merge(), read_data() and prep(). The file_merge() function
vertically merges individual data files (in a long format) in which each line
is a single trial within the experiment to one single dataset. The
read_data() function reads a file in a txt or csv format that contains a
single dataset in a long format table and creates a data frame from it. The
prep() function aggregates the single dataset according to any combination of
between and within grouping variables (i.e., between-subjects and
within-subjects independent variables, respectively), and returns a data
frame with a number of dependent measures for further analysis for each
experimental cell according to the combination of provided grouping
variables. Dependent measures for each experimental cell include among
others means before and after rejecting all values according to a flexible
standard deviation criterion/s, number of rejected values according to the
flexible standard deviation criterion/s, proportions of rejected values
according to the flexible standard deviation criterion/s, number of values
before rejection, means after rejecting values according to procedures
described in Van Selst & Jolicoeur (1994) (suitable when measuring
reaction-times), standard deviations, medians, means according to any
percentile (e.g., 0.05, 0.25, 0.75, 0.95) and harmonic means. The data frame
prep() returns can also be exported as a txt file to be used for statistical
analysis in other statistical programs.
Author: Ayala S. Allon [aut, cre],
Roy Luria [aut],
Jim Grange [ctb],
Nachshon Meiran [ctb]
Maintainer: Ayala S. Allon <ayalaallon@gmail.com>
Diff between prepdat versions 1.0.2 dated 2015-09-01 and 1.0.3 dated 2015-10-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 5 +++++ NEWS.md | 33 +++++++++++++++++++++++++++++++++ R/prep.R | 16 +++++++--------- README.md | 26 +++++++++++++++++++++++--- 6 files changed, 76 insertions(+), 20 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currenty it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.47 dated 2015-10-08 and 0.48 dated 2015-10-22
ChangeLog | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++++++----- DESCRIPTION | 8 ++--- MD5 | 6 ++-- man/vars.Rd | 3 ++ 4 files changed, 85 insertions(+), 13 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.3.0 dated 2015-10-06 and 0.4.0 dated 2015-10-22
DESCRIPTION | 6 - MD5 | 19 +-- NEWS.md | 9 + R/eval_tt.R |only R/generics.R | 65 +++++++----- R/helpers.R | 254 +++++++++++++++++++++++++++++++++++++++++++++++--- R/kdecop.R | 125 +++++++++++++++--------- R/kdecopula-package.R | 5 README.md | 5 man/kdecop.Rd | 76 +++++++++----- man/kdecopula.Rd | 5 11 files changed, 439 insertions(+), 130 deletions(-)
Title: Optimal Transport in Various Forms
Description: Solve optimal transport problems in statistics. Compute Wasserstein metrics (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p metrics), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, point patterns, and mass vectors.
Author: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de> with substantial contributions of code by Bjoern Baehre and Carsten Gottschlich
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.6-3 dated 2014-10-16 and 0.7-0 dated 2015-10-22
DESCRIPTION | 13 - MD5 | 20 - NAMESPACE | 7 NEWS | 35 +++ R/fundament.R | 481 ++++++++++++++++++++++++++++++++++++---------- R/lilhelpers.R | 10 man/transport-internal.Rd | 2 man/transport.Rd | 21 +- man/trcontrol.Rd | 2 src/revsimplex.c | 129 +++++++++++- src/shortsimplex.c | 11 - 11 files changed, 585 insertions(+), 146 deletions(-)
Title: Get Hourly Meteorological Data from Global Stations
Description: Selectively acquire hourly meteorological data from stations located all over the world.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between stationaRy versions 0.4 dated 2015-10-12 and 0.4.1 dated 2015-10-22
DESCRIPTION | 11 - MD5 | 6 R/get_isd_station_data.R | 3 README.md | 496 ++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 506 insertions(+), 10 deletions(-)
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.3 dated 2015-06-04 and 1.5.4 dated 2015-10-22
DESCRIPTION | 9 ++- MD5 | 86 +++++++++++++++++------------------ NAMESPACE | 41 ++++++++++++---- R/envelope.R | 18 ++++--- R/estfun.ssym.R | 2 R/extra.parameter.R | 53 ++++++++++++++++----- R/itpE.R | 23 ++++++--- R/itpE2.R | 20 ++++---- R/itpE3.R | 19 +++++-- R/itpEC.R | 21 +++++--- R/itpEC2.R | 25 ++++++---- R/ncs.R | 2 R/plot.ssym.R | 4 - R/psp.R | 2 R/ssym.l.R | 119 ++++++++++++++++++++++++++++++++++++++----------- R/ssym.l2.R | 119 +++++++++++++++++++++++++++++++++++++++---------- R/ssym.nl.R | 72 +++++++++++++++++++++-------- R/summary.ssym.R | 10 ++-- man/AIC.ssym.Rd | 2 man/BIC.ssym.Rd | 2 man/Ovocytes.Rd | 4 - man/coef.ssym.Rd | 2 man/envelope.Rd | 10 +++- man/extra.parameter.Rd | 5 +- man/fitted.ssym.Rd | 2 man/influence.ssym.Rd | 3 - man/itpE.Rd | 2 man/itpE2.Rd | 2 man/itpE3.Rd | 2 man/itpEC.Rd | 4 - man/itpEC2.Rd | 2 man/logLik.ssym.Rd | 2 man/ncs.Rd | 2 man/np.graph.Rd | 2 man/plot.ssym.Rd | 2 man/psp.Rd | 2 man/residuals.ssym.Rd | 2 man/rvgs.Rd | 6 +- man/ssym-package.Rd | 8 +-- man/ssym.l.Rd | 12 ++-- man/ssym.l2.Rd | 8 ++- man/ssym.nl.Rd | 9 ++- man/summary.ssym.Rd | 4 - man/vcov.ssym.Rd | 2 44 files changed, 510 insertions(+), 238 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 4.9 dated 2015-09-16 and 5.0 dated 2015-10-22
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/seqminer.R | 8 ++++++-- inst/CITATION | 6 ++++-- 5 files changed, 26 insertions(+), 12 deletions(-)
Title: Robust Ordinal Regression UTADIS
Description: Implementation of Robust Ordinal Regression for value-based sorting with some extensions and additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA) framework.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek <k.ciomek@gmail.com>
Diff between rorutadis versions 0.1.3 dated 2014-07-29 and 0.3.0 dated 2015-10-22
rorutadis-0.1.3/rorutadis/man/removeConstraintsByRestrictions.Rd |only rorutadis-0.3.0/rorutadis/DESCRIPTION | 11 rorutadis-0.3.0/rorutadis/MD5 | 88 rorutadis-0.3.0/rorutadis/NAMESPACE | 9 rorutadis-0.3.0/rorutadis/R/drawing.R | 270 +- rorutadis-0.3.0/rorutadis/R/explanations.R | 217 - rorutadis-0.3.0/rorutadis/R/inconsistencies.R |only rorutadis-0.3.0/rorutadis/R/main.R | 439 +-- rorutadis-0.3.0/rorutadis/R/model.R | 1247 +++------- rorutadis-0.3.0/rorutadis/R/postFactumAnalysis.R | 100 rorutadis-0.3.0/rorutadis/R/problem.R | 9 rorutadis-0.3.0/rorutadis/R/sampling.R |only rorutadis-0.3.0/rorutadis/R/solution.R | 283 +- rorutadis-0.3.0/rorutadis/man/addAssignmentPairwiseAtLeastComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/addAssignmentPairwiseAtMostComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/addAssignmentsLB.Rd | 3 rorutadis-0.3.0/rorutadis/man/addAssignmentsUB.Rd | 3 rorutadis-0.3.0/rorutadis/man/addMaximalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/addMinimalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/buildProblem.Rd | 3 rorutadis-0.3.0/rorutadis/man/calculateAssignments.Rd | 3 rorutadis-0.3.0/rorutadis/man/calculateExtremeClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/calculateStochasticResults.Rd |only rorutadis-0.3.0/rorutadis/man/checkConsistency.Rd | 7 rorutadis-0.3.0/rorutadis/man/compareAssignments.Rd | 9 rorutadis-0.3.0/rorutadis/man/deteriorateAssignment.Rd | 3 rorutadis-0.3.0/rorutadis/man/drawUtilityPlots.Rd | 28 rorutadis-0.3.0/rorutadis/man/explainAssignment.Rd | 10 rorutadis-0.3.0/rorutadis/man/findInconsistencies.Rd |only rorutadis-0.3.0/rorutadis/man/findRepresentativeFunction.Rd | 30 rorutadis-0.3.0/rorutadis/man/findSimpleFunction.Rd |only rorutadis-0.3.0/rorutadis/man/getAssignments.Rd | 19 rorutadis-0.3.0/rorutadis/man/getCharacteristicPoints.Rd | 19 rorutadis-0.3.0/rorutadis/man/getMarginalUtilities.Rd | 19 rorutadis-0.3.0/rorutadis/man/getPreferentialCore.Rd | 3 rorutadis-0.3.0/rorutadis/man/getRestrictions.Rd | 5 rorutadis-0.3.0/rorutadis/man/getThresholds.Rd | 21 rorutadis-0.3.0/rorutadis/man/improveAssignment.Rd | 3 rorutadis-0.3.0/rorutadis/man/investigateUtility.Rd | 5 rorutadis-0.3.0/rorutadis/man/mergeAssignments.Rd | 3 rorutadis-0.3.0/rorutadis/man/plotComprehensiveValue.Rd |only rorutadis-0.3.0/rorutadis/man/plotVF.Rd |only rorutadis-0.3.0/rorutadis/man/removeAssignmentPairwiseAtLeastComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeAssignmentPairwiseAtMostComparisons.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeAssignmentsLB.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeAssignmentsUB.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeMaximalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/removeMinimalClassCardinalities.Rd | 3 rorutadis-0.3.0/rorutadis/man/rorutadis-package.Rd | 4 49 files changed, 1291 insertions(+), 1615 deletions(-)
Title: Read Tabular Data
Description: Read flat/tabular text files from disk (or a connection).
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between readr versions 0.2.1 dated 2015-10-21 and 0.2.2 dated 2015-10-22
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- inst/doc/column-types.html | 4 ++-- inst/doc/locales.html | 4 ++-- src/QiParsers.h | 2 -- src/TokenizerDelim.cpp | 9 ++++++++- src/TokenizerDelim.h | 2 +- src/parse.cpp | 2 +- src/read.cpp | 6 +++--- 9 files changed, 28 insertions(+), 23 deletions(-)
Title: Inverse-Regression Estimation of Radioactive Doses
Description: Radioactive doses estimation using individual chromosomal aberrations information. See Higueras M, Puig P, Ainsbury E, Rothkamm K. (2015). A new inverse regression model applied to radiation biodosimetry. Proceedings of the Royal Society A, 471.
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between radir versions 1.0 dated 2015-01-08 and 1.0.1 dated 2015-10-22
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 13 ++++++++++--- inst/CITATION | 20 ++++++++++++++++++++ man/radir-package.Rd | 19 ------------------- 5 files changed, 40 insertions(+), 32 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.4 dated 2015-06-15 and 0.4.5 dated 2015-10-22
DESCRIPTION | 8 - MD5 | 56 +++++----- NAMESPACE | 3 R/aaa-globals.R | 2 R/augment-rprofile.R | 3 R/clean-search-path.R | 2 R/cranlike-repositories.R | 18 ++- R/dependencies.R | 218 +++++++++++++++++++++++++++-------------- R/downloader.R | 174 +++++++++++++++++++++++++------- R/external.R | 21 +-- R/hooks.R | 2 R/install.R | 23 +++- R/options.R | 12 +- R/packrat-mode.R | 20 +++ R/packrat.R | 45 -------- R/paths.R | 13 +- R/pkg.R | 3 R/restore.R | 15 +- R/snapshot.R | 83 ++++++++------- R/status.R | 2 R/utils.R | 73 ++++++++++++- README.md | 2 inst/resources/init-rprofile.R | 2 inst/resources/init.R | 61 ++++++++--- man/appDependencies.Rd | 8 + man/packrat-external.Rd | 6 - man/packrat-options.Rd | 2 man/repository-management.Rd | 3 man/snapshotImpl.Rd | 7 + 29 files changed, 589 insertions(+), 298 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 3.10.4 dated 2015-05-12 and 3.11.4 dated 2015-10-22
mvabund-3.10.4/mvabund/configure |only mvabund-3.10.4/mvabund/configure.ac |only mvabund-3.10.4/mvabund/src/Makevars.in |only mvabund-3.10.4/mvabund/src/RtoAnovaCpp.cpp |only mvabund-3.10.4/mvabund/src/RtoGlm.cpp |only mvabund-3.10.4/mvabund/src/RtoGlmAnova.cpp |only mvabund-3.10.4/mvabund/src/RtoGlmSmry.cpp |only mvabund-3.10.4/mvabund/src/RtoSmryCpp.cpp |only mvabund-3.11.4/mvabund/DESCRIPTION | 14 mvabund-3.11.4/mvabund/MD5 | 76 +-- mvabund-3.11.4/mvabund/NAMESPACE | 199 ++++--- mvabund-3.11.4/mvabund/R/RcppExports.R |only mvabund-3.11.4/mvabund/R/RcppVersion.R | 28 - mvabund-3.11.4/mvabund/R/anova.manyany.R | 166 ++++-- mvabund-3.11.4/mvabund/R/anova.manyglm.R | 37 - mvabund-3.11.4/mvabund/R/anova.manylm.R | 55 +- mvabund-3.11.4/mvabund/R/anova.traitglm.R | 8 mvabund-3.11.4/mvabund/R/cv.glm1path.R | 41 - mvabund-3.11.4/mvabund/R/default.plot.mvformula.R | 47 + mvabund-3.11.4/mvabund/R/is.wholenumber.R | 8 mvabund-3.11.4/mvabund/R/manyany.R | 4 mvabund-3.11.4/mvabund/R/manyglm.R | 107 ++-- mvabund-3.11.4/mvabund/R/print.anova.manyglm.R | 10 mvabund-3.11.4/mvabund/R/print.summary.manyglm.R | 10 mvabund-3.11.4/mvabund/R/summary.manyglm.R | 550 +++++++++++----------- mvabund-3.11.4/mvabund/R/summary.manylm.R | 468 +++++++++--------- mvabund-3.11.4/mvabund/R/traitglm.R | 91 ++- mvabund-3.11.4/mvabund/R/transAxis.SW.R | 240 ++++----- mvabund-3.11.4/mvabund/README.md |only mvabund-3.11.4/mvabund/cleanup | 17 mvabund-3.11.4/mvabund/data/Tasmania.RData |binary mvabund-3.11.4/mvabund/data/antTraits.RData |binary mvabund-3.11.4/mvabund/data/solberg.RData |binary mvabund-3.11.4/mvabund/data/spider.RData |binary mvabund-3.11.4/mvabund/data/tikus.RData |binary mvabund-3.11.4/mvabund/man/anova.manyany.Rd | 4 mvabund-3.11.4/mvabund/man/traitglm.Rd | 16 mvabund-3.11.4/mvabund/src/Makevars |only mvabund-3.11.4/mvabund/src/Makevars.win | 5 mvabund-3.11.4/mvabund/src/RcppExports.cpp |only mvabund-3.11.4/mvabund/src/Rinterface.cpp |only mvabund-3.11.4/mvabund/src/glm.cpp | 22 mvabund-3.11.4/mvabund/src/io.cpp | 2 mvabund-3.11.4/mvabund/src/mvabund_types.h |only mvabund-3.11.4/mvabund/src/resampTest.h | 36 + mvabund-3.11.4/mvabund/src/simutility.cpp | 4 46 files changed, 1255 insertions(+), 1010 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between multicool versions 0.1-7 dated 2015-08-17 and 0.1-8 dated 2015-10-22
DESCRIPTION | 8 ++--- MD5 | 4 +- R/initMC.r | 94 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 53 insertions(+), 53 deletions(-)
Title: Estimation of ICA Mixture Models
Description: The icamix package provides R functions as well as a C++ library which facilitate the estimation of ICA mixture models. We have developed and implemented the NSMM-ICA algorithm that currently integrates npEM and Fast-ICA for non-parametric estimation of ICA mixture models. We will continue to build in algorithms that interweave the EM step with other types of ICA techniques.
Author: Xiaotian Zhu, David R. Hunter
Maintainer: Xiaotian Zhu <xiaotian.zhu@abbvie.com>
Diff between icamix versions 1.0.2 dated 2015-04-20 and 1.0.4 dated 2015-10-22
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ man/EMFASTICAALG.Rd | 7 ++----- man/ESTIMATEDMEMBER.Rd | 3 +-- man/plot.EMFASTICAALG.Rd | 3 +-- man/plot.summary.EMFASTICAALG.Rd | 3 +-- man/print.EMFASTICAALG.Rd | 3 +-- man/print.summary.EMFASTICAALG.Rd | 3 +-- man/summary.EMFASTICAALG.Rd | 3 +-- 10 files changed, 22 insertions(+), 29 deletions(-)
Title: Hot Deck Imputation Methods for Missing Data
Description: Hot deck imputation methods to resolve missing data.
Author: Dieter William Joenssen [aut, cre, cph]
Maintainer: Dieter William Joenssen <Dieter.Joenssen@googlemail.com>
Diff between HotDeckImputation versions 1.0.0 dated 2014-09-28 and 1.1.0 dated 2015-10-22
DESCRIPTION | 20 MD5 | 33 - NAMESPACE | 4 NEWS | 18 R/HotDeckImputation.R | 781 +++++++++++++++++++++++++-------------- R/SeqentialHotDeck.R | 42 +- R/zzz.R | 22 - man/HotDeckImputation-package.Rd | 6 man/impute.CPS_SEQ_HD.Rd | 4 man/impute.NN_HD.Rd | 36 + man/impute.SEQ_HD.Rd | 2 man/impute.mean.Rd | 2 man/match.d_r_odd.Rd | 5 man/match.d_r_vam.Rd | 5 src/Distmatrix.c | 61 ++- src/VAM.c | 2 src/seq_HD.c | 66 +++ src/test_functions.c |only 18 files changed, 771 insertions(+), 338 deletions(-)
More information about HotDeckImputation at CRAN
Permanent link
Title: Forest Growth Model Utilities
Description: Growth models and forest production require existing data manipulation and the creation of new data, structured from basic forest inventory data. The purpose of this package is provide functions to support these activities.
Author: Clayton Vieira Fraga,
Ana Paula Simiqueli,
Wagner Amorim da Silva Altoe
Maintainer: Clayton Vieira Fraga <altoe.wagner@gmail.com>
Diff between Fgmutils versions 0.1 dated 2015-10-14 and 0.2 dated 2015-10-22
DESCRIPTION | 17 ++++++++++------- MD5 | 25 +++++++++++++++++-------- NAMESPACE | 4 +++- NEWS |only R/check.integer.R |only R/converteCampoParaCharacter.R | 8 ++++---- R/getAnoMedicao.R | 30 ++++++++++++++++++++---------- R/listToDataFrame.R |only R/verificaTipoColuna.R | 4 ++-- man/check.integer.Rd |only man/converteCampoParaCharacter.Rd | 8 ++++---- man/getAnoMedicao.Rd | 20 ++++++++++++-------- man/listToDataFrame.Rd |only man/verificaTipoColuna.Rd | 4 ++-- tests |only 15 files changed, 74 insertions(+), 46 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-57 dated 2015-10-11 and 6.0-58 dated 2015-10-22
DESCRIPTION | 8 - MD5 | 36 +++---- R/extractProb.R | 9 - R/ggplot.R | 153 ++++++++++++++++++-------------- R/pcaNNet.R | 16 ++- R/preProcess.R | 90 +++++++++++++++---- R/train.default.R | 17 +++ R/workflows.R | 11 +- inst/NEWS.Rd | 13 ++ man/confusionMatrix.Rd | 2 man/extractPrediction.Rd | 2 man/models.Rd | 221 ++++++++++++++++++++++++++++++++++++++++++++++- man/pcaNNet.Rd | 2 man/plot.rfe.Rd | 2 man/plot.train.Rd | 4 man/preProcess.Rd | 23 +++- man/sensitivity.Rd | 2 man/train.Rd | 2 man/trainControl.Rd | 4 19 files changed, 476 insertions(+), 141 deletions(-)
Title: Table, Apply, and Split Functionality for Matrix and
'big.matrix' Objects
Description: Extend the bigmemory package with 'table', 'tapply', and 'split' support for 'big.matrix' objects. The functions may also be used with native R matrices for improving speed and memory-efficiency.
Author: Michael J. Kane <kaneplusplus@gmail.com> and John W. Emerson <jayemerson@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigtabulate versions 1.1.2 dated 2013-11-05 and 1.1.4 dated 2015-10-22
bigtabulate-1.1.2/bigtabulate/inst |only bigtabulate-1.1.4/bigtabulate/DESCRIPTION | 24 +++++++-------- bigtabulate-1.1.4/bigtabulate/MD5 | 14 ++++---- bigtabulate-1.1.4/bigtabulate/NAMESPACE | 1 bigtabulate-1.1.4/bigtabulate/R/bigtabulate.R | 8 ++--- bigtabulate-1.1.4/bigtabulate/R/zzz.R | 2 - bigtabulate-1.1.4/bigtabulate/configure | 3 + bigtabulate-1.1.4/bigtabulate/man/bigtabulate-package.Rd | 6 +-- bigtabulate-1.1.4/bigtabulate/src/Makevars |only 9 files changed, 30 insertions(+), 28 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.2.1 dated 2015-06-05 and 2.2.2 dated 2015-10-21
pcnetmeta-2.2.1/pcnetmeta/R/model.binary.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.binary.hom.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.cont.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.cont.hom.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.followup.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.followup.hom.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.py.het.ind.R |only pcnetmeta-2.2.1/pcnetmeta/R/model.py.hom.ind.R |only pcnetmeta-2.2.2/pcnetmeta/DESCRIPTION | 8 +- pcnetmeta-2.2.2/pcnetmeta/MD5 | 42 ++++------ pcnetmeta-2.2.2/pcnetmeta/NAMESPACE | 6 + pcnetmeta-2.2.2/pcnetmeta/R/absolute.plot.R | 56 ++++++-------- pcnetmeta-2.2.2/pcnetmeta/R/contrast.plot.R | 40 ++++++---- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.R | 74 +++++------------- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.cont.R | 76 ++++++------------- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.followup.R | 70 ++++------------- pcnetmeta-2.2.2/pcnetmeta/R/nma.ab.py.R | 70 ++++------------- pcnetmeta-2.2.2/pcnetmeta/R/rank.prob.R | 19 +++- pcnetmeta-2.2.2/pcnetmeta/man/absolute.plot.Rd | 16 +++- pcnetmeta-2.2.2/pcnetmeta/man/contrast.plot.Rd | 12 +-- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.Rd | 24 +++--- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.cont.Rd | 23 +++-- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.followup.Rd | 27 ++++-- pcnetmeta-2.2.2/pcnetmeta/man/nma.ab.py.Rd | 27 ++++-- pcnetmeta-2.2.2/pcnetmeta/man/pcnetmeta-package.Rd | 2 pcnetmeta-2.2.2/pcnetmeta/man/rank.prob.Rd | 11 ++ 26 files changed, 259 insertions(+), 344 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski and Matthias Schmid
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>
Diff between discSurv versions 1.1.0 dated 2015-05-27 and 1.1.1 dated 2015-10-21
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 4 ++++ man/dataLongCompRisks.Rd | 27 +++++++++++++++++++++++++++ man/discSurv-package.Rd | 18 +++++++++++++----- 5 files changed, 53 insertions(+), 14 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 0.9-10 dated 2015-07-10 and 0.9-11 dated 2015-10-21
DESCRIPTION | 9 +-- MD5 | 43 ++++++++++----- NAMESPACE | 7 ++ R/GMRF.R | 23 ++++++++ R/calibratemcmc.R | 15 +++++ R/log_posteriors_and_derivatives_polygonal.R | 3 + R/nonspatial_log_likelihood_and_derivatives.R | 16 +++++ R/outputSummary.R |only R/plottingfunctions.R | 27 +++++++++- R/postprocessing.R | 13 +++- R/spatgrid.R | 70 ++++++++++++++++++++++++++ R/spatsurv.R | 4 - R/spatsurvMisc.R | 5 + R/survsim.R | 2 R/survspat.R | 11 ++-- README.md | 2 data |only man/Summarise.Rd |only man/fs.Rd |only man/fstimes.Rd |only man/getOptCellwidth.Rd |only man/getbb.Rd |only man/print.textSummary.Rd |only man/showGrid.Rd |only man/spatsurv-package.Rd | 2 man/spplot1.Rd | 4 + man/textSummary.Rd |only 27 files changed, 217 insertions(+), 39 deletions(-)
Title: Bias, Precision, and Power for Multi-Level Random Regressions
Description: Calculates bias, precision, and power for multi-level random regressions. Random regressions are types of hierarchical models in which data are structured in groups and (regression) coefficients can vary by groups. Tools to estimate model performance are designed mostly for scenarios where (regression) coefficients vary at just one level. 'MultiRR' provides simulation and analytical tools (based on 'lme4') to study model performance for random regressions that vary at more than one level (multi-level random regressions), allowing researchers to determine optimal sampling designs.
Author: Yimen G. Araya-Ajoy
Maintainer: Yimen G. Araya-Ajoy <yimencr@gmail.com>
Diff between MultiRR versions 1.0 dated 2015-05-13 and 1.1 dated 2015-10-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 6 +++++- man/Anal.MultiRR.Rd | 2 +- man/Bias.Rd | 2 +- man/Imprecision.Rd | 2 +- man/MultiRR-package.Rd | 2 +- man/Plot.Sim.Rd | 2 +- man/Power.Rd | 2 +- man/Sim.MultiRR.Rd | 2 +- man/Summary.Rd | 2 +- 11 files changed, 27 insertions(+), 23 deletions(-)
Title: Enhanced Analytics for Marketers Navigating the Ocean of Web
Data
Description: Provides a web analytics toolbox for marketers using services such as Google Analytics, Facebook Insights, etc.
Author: Felix MIKAELIAN <felix.mikaelian@essec.edu>
Maintainer: Felix MIKAELIAN <felix.mikaelian@essec.edu>
Diff between marketeR versions 0.1.0 dated 2015-09-10 and 0.1.1 dated 2015-10-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/AutoReport.R | 6 +++--- R/WeekSummary.R | 2 +- inst/AutoReport/AutoReport.Rmd | 8 ++++---- 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.3-1709 dated 2015-05-26 and 2.4-1786 dated 2015-10-21
DESCRIPTION | 10 - MD5 | 75 +++++---- NAMESPACE | 13 + R/bccorr.R | 189 +++++++++++++++++++----- R/cgsolve.R | 14 + R/compfactor.R | 4 R/efactory.R | 8 - R/felm.R | 333 +++++++++++++++++++++++++++++++++----------- R/generics.R | 16 +- R/is.estimable.R | 9 - R/kaczmarz.R | 9 - R/startup.R | 7 R/trace.R | 27 ++- R/utils.R | 23 ++- exec/lfescript | 94 ++++++++---- inst/NEWS.Rd | 26 +++ inst/doc/CHANGELOG | 3 inst/doc/identification.pdf |binary inst/doc/lfeguide.txt | 1 inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/bccorr.Rd | 4 man/condfstat.Rd | 4 man/demeanlist.Rd | 8 + man/felm.Rd | 23 ++- man/fevcov.Rd | 8 + man/lfe-package.Rd | 10 - src/Makevars.in | 6 src/demean.c | 11 - src/lfe.c | 12 + src/lfe.h | 4 src/ppf.c |only tests/bctest.Rout.save | 22 +- tests/intact.R |only tests/intact.Rout.save |only tests/interact.Rout.save | 6 tests/verify.R | 5 tests/verify.Rout.save | 11 + tests/weights.R | 1 tests/weights.Rout.save | 28 ++- 40 files changed, 747 insertions(+), 277 deletions(-)
Title: Interface to the Agave API
Description: Provides an interface to the the many computational resources iPlant offers through their RESTful application programming interface, see <http://www.iplantcollaborative.org/> for more information about iPlant, and <http://www.iplantcollaborative.org/ci/iplant-science-apis> for its APIs. Currently, 'rPlant' functions interact with the iPlant Agave API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using 'rPlant', users will have to register with the iPlant Collaborative. See <http://agaveapi.co/> for more information on the Agave API and <http://user.iplantcollaborative.org/> to register with iPlant.
Author: Barb Banbury <darwinthesun@gmail.com> and Kurt Michels <kamichels@math.arizona.edu>, Jeremy M. Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Kurt Michels <kamichels@math.arizona.edu>
Diff between rPlant versions 2.11 dated 2015-09-28 and 2.12 dated 2015-10-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Muscle.R | 6 ++---- 3 files changed, 7 insertions(+), 9 deletions(-)
Title: Read Tabular Data
Description: Read flat/tabular text files from disk (or a connection).
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between readr versions 0.2.0 dated 2015-10-19 and 0.2.1 dated 2015-10-21
DESCRIPTION | 12 ++++-------- MD5 | 16 ++++++++-------- R/encoding.R | 2 +- inst/doc/column-types.html | 4 ++-- inst/doc/locales.html | 4 ++-- man/encoding.Rd | 2 +- src/Collector.cpp | 2 +- src/Iconv.cpp | 16 +++++++++++++++- src/localtime.c | 6 ++++++ 9 files changed, 40 insertions(+), 24 deletions(-)
Title: Nonparametric Combination of Hypothesis Tests
Description: An implementation of nonparametric combination of hypothesis tests.
This package performs nonparametric combination (Pesarin and Salmaso 2010),
a permutation-based procedure for jointly testing multiple hypotheses. The
tests are conducted under the global "sharp" null hypothesis of no effects,
and the component tests are combined on the metric of their p-values. A
key feature of nonparametric combination is that it accounts for the
dependence among tests under the null hypothesis. In addition to the
"NPC" function, which performs nonparametric combination itself, the
package also contains a number of helper functions, many of which calculate
a test statistic given an input of data.
Author: Devin Caughey [aut, cre]
Maintainer: Devin Caughey <devin.caughey@gmail.com>
Diff between NPC versions 1.0.0 dated 2015-04-18 and 1.0.2 dated 2015-10-21
DESCRIPTION | 10 +++---- MD5 | 19 +++++++------ NEWS.md |only R/HarmonicWtdMean.R | 2 - R/KS.R | 7 +++- R/NPC.R | 7 +++- R/NormalCF.R | 2 - R/StudentsT.R | 3 +- man/FWE.Rd | 49 +++++++++++++++++++--------------- man/HoggAdapt.Rd | 24 ++++++++-------- man/t2p.Rd | 74 ++++++++++++++++++---------------------------------- 11 files changed, 96 insertions(+), 101 deletions(-)
Title: Capture-Mark-Recapture Analysis using Multiple Non-Invasive
Marks
Description: Capture-mark-recapture analysis with multiple non-invasive marks. The models implemented in 'multimark' combine encounter history data arising from two different non-invasive ``marks'', such as images of left-sided and right-sided pelage patterns of bilaterally asymmetrical species, to estimate abundance and related demographic parameters while accounting for imperfect detection. Bayesian models are specified using simple formulae and fitted using Markov chain Monte Carlo. Addressing deficiencies in currently available software, 'multimark' also provides a user-friendly interface for performing Bayesian multimodel inference using capture-recapture data consisting of a single conventional mark or multiple non-invasive marks.
Author: Brett T. McClintock [aut, cre],
Acho Arnold [ctb, cph] (C original matrix library,
https://github.com/najela/matrix.h),
Barry Brown [ctb] (Fortran original ranlib library),
James Lovato [ctb] (Fortran original ranlib library),
John Burkardt [ctb] (C original ranlib library,
http://people.sc.fsu.edu/~jburkardt/c_src/ranlib),
Cleve Moler [ctb] (C original linpack library,
http://www.kkant.net/geist/ranlib/)
Maintainer: Brett T. McClintock <brett.mcclintock@noaa.gov>
Diff between multimark versions 1.3.0 dated 2015-07-28 and 1.3.1 dated 2015-10-21
DESCRIPTION | 8 MD5 | 40 NAMESPACE | 54 NEWS | 123 + R/CJS.R | 2830 ++++++++++++++++++++++---------------------- R/Closed.R | 2166 ++++++++++++++++----------------- R/multimark_functions.R | 1634 ++++++++++++------------- inst/CITATION | 86 - man/bobcat.Rd | 50 man/getprobsCJS.Rd | 92 - man/getprobsClosed.Rd | 84 - man/markCJS.Rd | 252 +-- man/markClosed.Rd | 188 +- man/multimarkCJS.Rd | 320 ++-- man/multimarkClosed.Rd | 258 ++-- man/multimarksetup-class.Rd | 108 - man/multimodelCJS.Rd | 200 +-- man/multimodelClosed.Rd | 172 +- man/processdata.Rd | 116 - man/simdataCJS.Rd | 126 - man/simdataClosed.Rd | 122 - 21 files changed, 4505 insertions(+), 4524 deletions(-)
Title: Wrapper Functions for FSL (FMRIB Software Library) from
Functional MRI of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL
(http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used
neuroimaging software, using system commands. The goal is to be able to
interface with FSL completely in R, where you pass R objects of class "nifti",
implemented by package 'oro.nifti', and the function executes an FSL command
and returns an R object of class "nifti" if desired.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 1.4.4 dated 2015-05-21 and 1.5.0 dated 2015-10-21
fslr-1.4.4/fslr/NEWS |only fslr-1.5.0/fslr/DESCRIPTION | 16 ++++++------ fslr-1.5.0/fslr/MD5 | 27 ++++++++++++-------- fslr-1.5.0/fslr/NAMESPACE | 8 ++++++ fslr-1.5.0/fslr/R/dropEmptyImageDimensions.R | 10 ++++++- fslr-1.5.0/fslr/R/fslfill2.R | 2 - fslr-1.5.0/fslr/R/fslhd.R | 35 +++++++++++++++++++++++---- fslr-1.5.0/fslr/R/ortho2.R | 5 ++- fslr-1.5.0/fslr/R/ortho_diff.R |only fslr-1.5.0/fslr/R/readNIfTI2.R |only fslr-1.5.0/fslr/R/rescale_img.R | 4 ++- fslr-1.5.0/fslr/R/writenii.R |only fslr-1.5.0/fslr/README.md | 4 ++- fslr-1.5.0/fslr/build/vignette.rds |binary fslr-1.5.0/fslr/man/cog.Rd | 4 ++- fslr-1.5.0/fslr/man/ortho_diff.Rd |only fslr-1.5.0/fslr/man/readNIfTI2.Rd |only fslr-1.5.0/fslr/man/writeNIfTI2.Rd |only 18 files changed, 85 insertions(+), 30 deletions(-)
Title: Two-Locus Family-Based Association Test with Polytomic Outcome
Description: Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models
defined by some design matrix.
Author: Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca> and Jordie Croteau
<jordie.croteau@crulrg.ulaval.ca>
Maintainer: Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca>
Diff between fat2Lpoly versions 1.1.1 dated 2014-10-17 and 1.2.2 dated 2015-10-21
DESCRIPTION | 16 MD5 | 90 NAMESPACE | 6 R/alleles2sums.R | 88 R/calcule.poids.Chen.R | 70 R/calcule.poids.alphafixe.r | 70 R/converti.terme.R | 16 R/cov.score.interfunction.R | 90 R/cov.score.poly.R | 158 R/design.1locus.R | 56 R/design.dichotomique.R | 66 R/design.endo2disease.R | 82 R/design.full.R | 66 R/design.polytomous.R | 416 R/fat2Lpoly.R | 116 R/fat2Lpoly.withinR.R | 555 R/get.scores.pvalues.R | 144 R/ibd.terms.R | 316 R/ibd.terms.w.r | 300 R/produits.paires.R | 16 R/read.merlin.files.R | 394 R/score.poly.R | 50 R/score.poly.w.r | 62 R/scores.covs.R | 552 data/fat2Lpoly.allSNPs.rda |binary data/ped.x.all.rda |binary inst/extdata/loc1.dat | 12 inst/extdata/loc1.freq | 12 inst/extdata/loc1.ibd |32642 ++++++++++++++++++++++---------------------- inst/extdata/loc1.ped | 1280 - inst/extdata/loc2.dat | 12 inst/extdata/loc2.freq | 18 inst/extdata/loc2.ibd |32642 ++++++++++++++++++++++---------------------- inst/extdata/loc2.ped | 1280 - man/design.1locus.Rd | 102 man/design.dichotomous.Rd | 82 man/design.endo2disease.Rd | 100 man/design.full.Rd | 106 man/fat2Lpoly-internal.Rd | 52 man/fat2Lpoly-package.Rd | 108 man/fat2Lpoly.Rd | 392 man/fat2Lpoly.allSNPs.Rd | 50 man/fat2Lpoly.withinR.Rd | 174 man/get.scores.pvalues.Rd | 108 man/ped.x.all.Rd | 80 man/read.merlin.files.Rd | 182 46 files changed, 36619 insertions(+), 36610 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.1 dated 2015-08-18 and 0.3.2 dated 2015-10-21
DESCRIPTION | 12 +++++------ MD5 | 24 +++++++++++----------- NAMESPACE | 1 NEWS | 7 ++++++ R/chordDiagram.R | 5 ++++ R/genomic.R | 4 ++- build/vignette.rds |binary inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary 13 files changed, 34 insertions(+), 19 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques (Bagging and Bootstrapping) and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.0 dated 2015-09-25 and 1.1 dated 2015-10-21
DESCRIPTION | 12 ++++++------ MD5 | 6 ++++-- R/mkr.R |only man/bWGR.Rd | 6 +++--- man/mkr.Rd |only 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Interactive Graphics for Portfolio Data
Description: Creates an interactive graphics
interface to visualize backtest results of different financial
instruments, such as equities, futures, and credit default swaps.
The package does not run backtests on the given data set but
displays a graphical explanation of the backtest results. Users can
look at backtest graphics for different instruments, investment
strategies, and portfolios. Summary statistics of different
portfolio holdings are shown in the left panel, and interactive
plots of profit and loss (P\&L), net market value (NMV) and
gross market value (GMV) are displayed in the right panel.
Author: as.person(c(
"David Kane <dave.kane@gmail.com> [aut]",
"Ziqi Lu <ziqi.lu@williams.edu> [aut]",
"Fan Zhang <fan.zhang@williams.edu> [aut]",
"Miller Zijie Zhu <zijie.miller.zhu@gmail.com> [aut]"
))
Maintainer: Miller Zijie Zhu <zijie.miller.zhu@gmail.com>
Diff between backtestGraphics versions 0.1.5 dated 2015-08-13 and 0.1.6 dated 2015-10-21
backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_cumpnl_plot.R |only backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_cumpnl_plot.RData |only backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_interactive_plot.R |only backtestGraphics-0.1.5/backtestGraphics/tests/testthat/test_interactive_plot.RData |only backtestGraphics-0.1.6/backtestGraphics/DESCRIPTION | 8 backtestGraphics-0.1.6/backtestGraphics/MD5 | 22 backtestGraphics-0.1.6/backtestGraphics/R/backtestGraphics.R | 986 +++++----- backtestGraphics-0.1.6/backtestGraphics/R/cleanup_column.R | 373 +-- backtestGraphics-0.1.6/backtestGraphics/README.md | 40 backtestGraphics-0.1.6/backtestGraphics/build/vignette.rds |binary backtestGraphics-0.1.6/backtestGraphics/data/datalist | 6 backtestGraphics-0.1.6/backtestGraphics/inst/doc/backtestGraphics.R | 76 backtestGraphics-0.1.6/backtestGraphics/inst/doc/backtestGraphics.pdf |binary backtestGraphics-0.1.6/backtestGraphics/tests/testthat/test_calc_pnl.R | 20 14 files changed, 767 insertions(+), 764 deletions(-)
More information about backtestGraphics at CRAN
Permanent link
Title: Utilities for 'big.matrix' Objects from Package 'bigmemory'
Description: Extend the 'bigmemory' package with various analytics.
Functions 'bigkmeans' and 'binit' may also be used with native R objects.
For 'tapply'-like functions, the bigtabulate package may also be helpful.
For linear algebra support, see 'bigalgebra'. For mutex (locking) support
for advanced shared-memory usage, see 'synchronicity'.
Author: John W. Emerson <jayemerson@gmail.com> and Michael J. Kane <kaneplusplus@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between biganalytics versions 1.1.1 dated 2013-04-01 and 1.1.12 dated 2015-10-21
DESCRIPTION | 32 ++--- MD5 | 22 ++- NAMESPACE | 13 +- R/biglm.big.matrix.R | 2 R/kmeans.R | 28 ++-- R/zzz.R | 2 configure.win |only inst |only man/biganalytics-package.Rd | 10 - man/bigkmeans.Rd | 21 +-- man/summary.stat.Rd | 10 - src/kmeans.cpp | 264 ++++++++++++++++++++++++++++++++++++++------ src/summary_stat.cpp | 11 - 13 files changed, 298 insertions(+), 117 deletions(-)
Title: Backward Pipe Operator
Description: Provides a backward-pipe operator for 'magrittr' (%<%) or
'pipeR' (%<<%) that allows for a performing operations from right-to-left.
This is useful in instances where there is right-to-left ordering commonly
observed with nested structures such as trees/directories and markup
languages such as HTML and XML.
Author: Christopher Brown [cre, aut],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between backpipe versions 0.1.2 dated 2015-09-03 and 0.1.5 dated 2015-10-21
backpipe-0.1.2/backpipe/inst/www |only backpipe-0.1.5/backpipe/DESCRIPTION | 13 ++-- backpipe-0.1.5/backpipe/LICENSE |only backpipe-0.1.5/backpipe/MD5 | 15 ++-- backpipe-0.1.5/backpipe/NEWS |only backpipe-0.1.5/backpipe/README.md | 79 ++++++++++++++++++++++++- backpipe-0.1.5/backpipe/inst/doc/backpipe.Rmd | 53 ++++++++-------- backpipe-0.1.5/backpipe/inst/doc/backpipe.html | 36 ++++++----- backpipe-0.1.5/backpipe/vignettes/backpipe.Rmd | 53 ++++++++-------- 9 files changed, 164 insertions(+), 85 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level aroma.* packages
part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 2.13.1 dated 2015-05-26 and 2.14.0 dated 2015-10-21
aroma.core-2.13.1/aroma.core/R/whatDataType.R |only aroma.core-2.14.0/aroma.core/DESCRIPTION | 14 - aroma.core-2.14.0/aroma.core/MD5 | 48 +++-- aroma.core-2.14.0/aroma.core/NAMESPACE | 26 ++- aroma.core-2.14.0/aroma.core/NEWS | 14 + aroma.core-2.14.0/aroma.core/R/999.DEPRECATED.R | 85 ++++++++-- aroma.core-2.14.0/aroma.core/R/AromaMicroarrayDataSet.ATTRS.R | 2 aroma.core-2.14.0/aroma.core/R/AromaTabularBinarySet.ATTRS.R | 2 aroma.core-2.14.0/aroma.core/R/ChromosomeExplorer.LAYERS.R | 51 +----- aroma.core-2.14.0/aroma.core/R/ChromosomeExplorer.R | 50 ----- aroma.core-2.14.0/aroma.core/R/CopyNumberSegmentationModel.R | 5 aroma.core-2.14.0/aroma.core/R/Explorer.R | 34 ---- aroma.core-2.14.0/aroma.core/R/GladModel.R | 5 aroma.core-2.14.0/aroma.core/R/SampleAnnotationFile.R | 3 aroma.core-2.14.0/aroma.core/R/fitWHRCModel.matrix.R | 2 aroma.core-2.14.0/aroma.core/man/ChromosomeExplorer.Rd | 2 aroma.core-2.14.0/aroma.core/man/Non-documented_objects.Rd | 17 +- aroma.core-2.14.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 2 aroma.core-2.14.0/aroma.core/man/RawSequenceReads.Rd | 2 aroma.core-2.14.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 2 aroma.core-2.14.0/aroma.core/man/SegmentedCopyNumbers.Rd | 2 aroma.core-2.14.0/aroma.core/man/mergeBoxplotStats.list.Rd | 2 aroma.core-2.14.0/aroma.core/tests/binScatter.R |only aroma.core-2.14.0/aroma.core/tests/colBinnedSmoothing.R |only aroma.core-2.14.0/aroma.core/tests/colKernelSmoothing.R |only aroma.core-2.14.0/aroma.core/tests/fitGenotypeCone.R |only aroma.core-2.14.0/aroma.core/tests/fitMultiDimensionalCone.R |only aroma.core-2.14.0/aroma.core/tests/matrixBlockPolish.R |only aroma.core-2.14.0/aroma.core/tests/mergeBoxplotStats.R |only 29 files changed, 189 insertions(+), 181 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <http://www.openstreetmap.org/>,
Mapquest <http://www.mapquest.com/>, Bing Maps <http://www.bing.com/maps>
and other tiled map sources in a way that works seamlessly with plotting
from the 'sp' package. Use to create high-resolution basemaps and add hillshade
to vector based maps.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.1.1 dated 2015-10-19 and 0.1.2 dated 2015-10-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/osmtile.R | 2 +- R/projections.R | 3 +++ tests/manual/tests.R | 4 ++-- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 0.5 dated 2015-10-19 and 0.5.1 dated 2015-10-20
CHANGELOG | 10 ++++++++++ DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- NAMESPACE | 3 +++ R/ClasGenMetDef.R | 13 ++++--------- man/MAINT.Data-package.Rd | 4 ++-- 6 files changed, 29 insertions(+), 22 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-4 dated 2015-10-16 and 0.1-5 dated 2015-10-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/gimme-data.R | 10 +++++----- R/gimme.R | 2 +- man/ts1.Rd | 2 +- man/ts2.Rd | 2 +- man/ts3.Rd | 2 +- man/ts4.Rd | 2 +- man/ts5.Rd | 2 +- 10 files changed, 25 insertions(+), 24 deletions(-)
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.6 dated 2015-06-11 and 1.0.7 dated 2015-10-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ NEWS | 4 ++++ inst/CITATION | 16 ++++++++++++++++ 5 files changed, 30 insertions(+), 8 deletions(-)
Title: Quantile-Based Spectral Analysis of Time Series
Description: Methods to determine, smooth and plot quantile periodograms for
univariate and multivariate time series.
Author: Tobias Kley [aut, cre],
Stefan Birr [ctb] (Contributions to lag window estimation)
Maintainer: Tobias Kley <t.kley@lse.ac.uk>
Diff between quantspec versions 1.1-0 dated 2015-09-27 and 1.2-0 dated 2015-10-20
DESCRIPTION | 12 MD5 | 116 +- NAMESPACE | 4 NEWS | 13 R/Class-ClippedCov.R | 13 R/Class-ClippedFT.R | 61 - R/Class-FreqRep.R | 177 ++- R/Class-LagEstimator.R | 2 R/Class-LagOperator.R | 125 ++ R/Class-QRegEstimator.R | 45 - R/Class-QSpecQuantity.R | 35 R/Class-QuantilePG.R | 53 - R/Class-QuantileSD.R | 293 +++++- R/Class-SmoothedPG.R | 1529 ++++++++++++++++++++++++---------- R/RcppExports.R | 27 R/aux-functions.R | 50 + R/generics.R | 11 R/quantspec-package.R | 24 inst/doc/quantspec.pdf |binary inst/examples/QuantileSD.R | 18 inst/extdata/ref-results.rdata |binary man/ClippedCov-class.Rd | 3 man/ClippedCov-constructor.Rd | 4 man/ClippedFT-class.Rd | 9 man/ClippedFT-constructor.Rd | 13 man/FreqRep-class.Rd | 28 man/LagEstimator-class.Rd | 4 man/LagOperator-class.Rd | 3 man/QRegEstimator-constructor.Rd | 2 man/QSpecQuantity-class.Rd | 13 man/QuantilePG-constructor.Rd | 2 man/QuantileSD-class.Rd | 22 man/SmoothedPG-class.Rd | 9 man/SmoothedPG-constructor.Rd | 4 man/figures/csd-mv.pdf |only man/figures/csd-mv.png |only man/figures/main-mv.pdf |only man/figures/main-mv.png |only man/figures/main2-mv.pdf |only man/figures/main2-mv.png |only man/generics-accessors.Rd | 6 man/getCoherency-QuantileSD.Rd |only man/getCoherency-SmoothedPG.Rd |only man/getCoherencySdNaive-SmoothedPG.Rd |only man/getMeanPG-QuantileSD.Rd | 8 man/getPointwiseCIs-SmoothedPG.Rd | 54 - man/getSdBoot-SmoothedPG.Rd | 2 man/getSdNaive-SmoothedPG.Rd | 19 man/getStdError-QuantileSD.Rd | 8 man/getValues-FreqRep.Rd | 6 man/getValues-QuantilePG.Rd | 10 man/getValues-QuantileSD.Rd | 12 man/getValues-SmoothedPG.Rd | 15 man/getY-FreqRep.Rd | 5 man/lenTS.Rd |only man/plot-FreqRep.Rd | 6 man/plot-LagOperator.Rd | 31 man/plot-QuantilePG.Rd | 3 man/plot-QuantileSD.Rd | 3 man/plot-SmoothedPG.Rd | 3 man/quantspec-package.Rd | 24 man/timeSeriesValidator.Rd | 2 src/RcppExports.cpp | 13 src/computeCoherency.cpp |only tests/testthat/test-multivariate.R |only 65 files changed, 2217 insertions(+), 737 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 0.34-2 dated 2015-05-06 and 0.36-2 dated 2015-10-20
DESCRIPTION | 12 +- MD5 | 41 ++++----- NAMESPACE | 59 +++++++------ NEWS | 28 ++++++ R/EuropeanCallBE.R | 9 - R/LSopt.R | 208 ++++++++++++++++++++++++---------------------- R/TAopt.R | 5 - R/pm.R |only R/randomp.R | 14 +-- build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/unitTests/report.txt | 20 ++-- man/LS.info.Rd |only man/TA.info.Rd | 10 +- man/callMerton.Rd | 2 man/pm.Rd |only 23 files changed, 233 insertions(+), 175 deletions(-)
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.5 dated 2015-10-12 and 1.6 dated 2015-10-20
DESCRIPTION | 8 ++--- MD5 | 14 +++++---- NAMESPACE | 1 R/barnard.test.R |only R/barnardw.test.R | 74 --------------------------------------------------- man/Barnard.Rd | 2 - man/barnard.test.Rd |only man/barnardw.test.Rd | 63 ++----------------------------------------- src/Barnard.c | 36 +++++++++++++++++++++--- 9 files changed, 50 insertions(+), 148 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.8.0 dated 2015-08-07 and 2.9.0 dated 2015-10-20
DESCRIPTION | 21 ++++---- MD5 | 16 +++--- NAMESPACE | 10 +--- NEWS | 8 +++ R/999.DEPRECATED.R | 52 ---------------------- R/GenericDataFileSet.PARALLEL.R | 80 +++++++++++++++++++++++++++++++--- man/Deprecated_and_defunct_objects.Rd | 17 ------- man/dsApply.GenericDataFileSet.Rd | 6 +- tests/GenericDataFileSet,dsApply.R | 57 ++++++++++++++++++++---- 9 files changed, 159 insertions(+), 108 deletions(-)
Title: R Interface to Bloomberg
Description: An R Interface to Bloomberg is provided via the Blp API.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.0 dated 2015-08-14 and 0.3.1 dated 2015-10-20
ChangeLog | 78 ++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 19 +++++----- MD5 | 81 ++++++++++++++++++++++++++++++++------------ NAMESPACE | 1 R/RcppExports.R | 4 ++ R/bdh.R | 8 ++++ R/bdp.R | 3 + R/bds.R | 2 - R/beqs.R |only R/getTicks.R | 7 ++- README.md | 15 ++++---- build/vignette.rds |binary cleanup | 3 + configure | 23 +++++++----- inst/NEWS.Rd | 18 +++++++++ inst/doc/rblpapi-intro.R | 3 + inst/doc/rblpapi-intro.Rmd | 9 ++++ inst/doc/rblpapi-intro.html | 5 ++ inst/include |only man/bdh.Rd | 8 ++++ man/bdp.Rd | 3 + man/beqs.Rd |only src/Makevars.win | 16 +++----- src/RcppExports.cpp | 17 +++++++++ src/beqs.cpp |only src/blpapi_utils.cpp | 1 vignettes/rblpapi-intro.Rmd | 9 ++++ 27 files changed, 273 insertions(+), 60 deletions(-)
Title: Pretty Descriptive Stats
Description: Functions for conventionally formatting descriptive stats,
reshaping data frames and formatting R output as HTML.
Author: Jim Lemon <drjimlemon@gmail.com>,
Philippe Grosjean <phgrosjean@sciviews.org>
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between prettyR versions 2.1-1 dated 2015-04-29 and 2.2 dated 2015-10-20
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS | 4 ++++ man/rep_n_stack.Rd | 3 ++- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.5-12 dated 2015-05-16 and 3.6 dated 2015-10-20
DESCRIPTION | 9 +++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 14 ++++++++++++++ NEWS | 9 +++++++++ R/addtable2plot.R | 1 + R/pyramid.plot.R | 2 +- R/sizetree.R | 5 ++++- R/starPie.R | 10 +++++++++- R/twoord.plot.R | 9 ++++++--- data/soils.rda |binary man/addtable2plot.Rd | 5 +++-- man/color2D.matplot.Rd | 5 +++-- man/feather.plot.Rd | 5 +++-- man/pyramid.plot.Rd | 14 ++++++++++++++ man/sizetree.Rd | 5 ++++- man/starPie.Rd | 15 ++++++++++++++- 16 files changed, 105 insertions(+), 33 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman <Rob.Hyndman@monash.edu>.
Contributors include George Athanasopoulos, Christoph Bergmeir,
Carlos Cinelli, Yousaf Khan, Zach Mayer, Slava Razbash,
Drew Schmidt, David Shaub, Yuan Tang, Earo Wang, Zhenyu Zhou.
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 6.1 dated 2015-05-12 and 6.2 dated 2015-10-20
forecast-6.1/forecast/inst/tests |only forecast-6.1/forecast/tests/test-all.R |only forecast-6.2/forecast/ChangeLog | 16 + forecast-6.2/forecast/DESCRIPTION | 14 - forecast-6.2/forecast/MD5 | 121 +++++---- forecast-6.2/forecast/NAMESPACE | 26 + forecast-6.2/forecast/R/HoltWintersNew.R | 11 forecast-6.2/forecast/R/acf.R | 22 - forecast-6.2/forecast/R/arima.R | 23 + forecast-6.2/forecast/R/attach.R | 5 forecast-6.2/forecast/R/bootstrap.R | 83 ------ forecast-6.2/forecast/R/calendar.R | 35 +- forecast-6.2/forecast/R/checkAdmissibility.R | 2 forecast-6.2/forecast/R/clean.R | 106 ++++--- forecast-6.2/forecast/R/errors.R | 11 forecast-6.2/forecast/R/ets.R | 28 +- forecast-6.2/forecast/R/etsforecast.R | 18 - forecast-6.2/forecast/R/fitTBATS.R | 227 ++++------------- forecast-6.2/forecast/R/forecast.R | 4 forecast-6.2/forecast/R/forecast.varest.R | 4 forecast-6.2/forecast/R/forecast2.R | 5 forecast-6.2/forecast/R/forecastTBATS.R | 7 forecast-6.2/forecast/R/getResponse.R | 12 forecast-6.2/forecast/R/graph.R | 11 forecast-6.2/forecast/R/lm.R | 7 forecast-6.2/forecast/R/newarima2.R | 38 +- forecast-6.2/forecast/R/nnetar.R | 7 forecast-6.2/forecast/R/tbats.R | 35 +- forecast-6.2/forecast/README.md | 5 forecast-6.2/forecast/man/bizdays.Rd | 12 forecast-6.2/forecast/man/ets.Rd | 2 forecast-6.2/forecast/man/fitted.Arima.Rd | 2 forecast-6.2/forecast/man/forecast.Arima.Rd | 2 forecast-6.2/forecast/man/forecast.HoltWinters.Rd | 2 forecast-6.2/forecast/man/forecast.Rd | 2 forecast-6.2/forecast/man/forecast.StructTS.Rd | 2 forecast-6.2/forecast/man/forecast.bats.Rd | 2 forecast-6.2/forecast/man/forecast.ets.Rd | 2 forecast-6.2/forecast/man/forecast.lm.Rd | 2 forecast-6.2/forecast/man/forecast.stl.Rd | 2 forecast-6.2/forecast/man/meanf.Rd | 2 forecast-6.2/forecast/man/naive.Rd | 2 forecast-6.2/forecast/man/rw.f.Rd | 2 forecast-6.2/forecast/man/ses.Rd | 4 forecast-6.2/forecast/man/spline.f.Rd | 2 forecast-6.2/forecast/man/theta.Rd | 2 forecast-6.2/forecast/man/ts.display.Rd | 6 forecast-6.2/forecast/src/etsTargetFunction.cpp | 10 forecast-6.2/forecast/src/etsTargetFunction.h | 6 forecast-6.2/forecast/src/etsTargetFunctionWrapper.cpp | 2 forecast-6.2/forecast/src/etscalc.c | 15 - forecast-6.2/forecast/tests/testthat |only forecast-6.2/forecast/tests/testthat.R |only 53 files changed, 458 insertions(+), 510 deletions(-)
Title: Sequential Event Interval Analysis
Description: Functions for analysis of rate changes in sequential events.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between eventInterval versions 1.2 dated 2015-01-20 and 1.3 dated 2015-10-20
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 6 +++--- NEWS | 8 ++++++++ R/EIdist.R | 6 ++++++ 5 files changed, 27 insertions(+), 13 deletions(-)
Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 0.4.5 dated 2015-06-11 and 0.5 dated 2015-10-20
dygraphs-0.4.5/dygraphs/NEWS |only dygraphs-0.5/dygraphs/DESCRIPTION | 8 dygraphs-0.5/dygraphs/MD5 | 35 - dygraphs-0.5/dygraphs/NAMESPACE | 2 dygraphs-0.5/dygraphs/R/axis.R | 4 dygraphs-0.5/dygraphs/R/dygraph.R | 19 dygraphs-0.5/dygraphs/R/legend.R | 9 dygraphs-0.5/dygraphs/R/options.R | 33 - dygraphs-0.5/dygraphs/R/utils.R | 13 dygraphs-0.5/dygraphs/inst/NEWS |only dygraphs-0.5/dygraphs/inst/examples/examples.html | 277 ---------- dygraphs-0.5/dygraphs/inst/htmlwidgets/dygraphs.js | 229 ++++---- dygraphs-0.5/dygraphs/inst/htmlwidgets/dygraphs.yaml | 2 dygraphs-0.5/dygraphs/inst/htmlwidgets/lib/dygraphs/dygraph-combined-dev.js |only dygraphs-0.5/dygraphs/inst/htmlwidgets/lib/dygraphs/dygraph-combined.js | 8 dygraphs-0.5/dygraphs/inst/htmlwidgets/lib/dygraphs/dygraph.css | 4 dygraphs-0.5/dygraphs/man/dyLegend.Rd | 11 dygraphs-0.5/dygraphs/man/dyOptions.Rd | 25 dygraphs-0.5/dygraphs/man/dyRangeSelector.Rd | 6 dygraphs-0.5/dygraphs/man/dygraph.Rd | 7 20 files changed, 258 insertions(+), 434 deletions(-)
Title: Completing Ranks
Description: Functions for completing and recalculating rankings.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between crank versions 1.0-7 dated 2015-01-20 and 1.1 dated 2015-10-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 1 + NEWS | 4 ++++ 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson <jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles Determan Jr. <cdetermanjr@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.4.6 dated 2013-11-18 and 4.5.8 dated 2015-10-20
bigmemory-4.4.6/bigmemory/README |only bigmemory-4.4.6/bigmemory/inst/doc/vignette |only bigmemory-4.4.6/bigmemory/inst/unitTests |only bigmemory-4.4.6/bigmemory/man/flush.Rd |only bigmemory-4.5.8/bigmemory/DESCRIPTION | 33 bigmemory-4.5.8/bigmemory/MD5 | 94 bigmemory-4.5.8/bigmemory/NAMESPACE | 80 bigmemory-4.5.8/bigmemory/NEWS | 10 bigmemory-4.5.8/bigmemory/R/RcppExports.R |only bigmemory-4.5.8/bigmemory/R/bigmemory.R | 1051 ++++++--- bigmemory-4.5.8/bigmemory/R/hello-bigmemory.R |only bigmemory-4.5.8/bigmemory/R/zzz.R | 5 bigmemory-4.5.8/bigmemory/build |only bigmemory-4.5.8/bigmemory/cleanup | 2 bigmemory-4.5.8/bigmemory/configure | 2 bigmemory-4.5.8/bigmemory/configure.win |only bigmemory-4.5.8/bigmemory/inst/CITATION | 2 bigmemory-4.5.8/bigmemory/inst/doc/Overview.R |only bigmemory-4.5.8/bigmemory/inst/doc/Overview.Rnw |only bigmemory-4.5.8/bigmemory/inst/doc/Overview.pdf |only bigmemory-4.5.8/bigmemory/inst/include/bigmemory/BigMatrix.h | 14 bigmemory-4.5.8/bigmemory/inst/include/bigmemory/MatrixAccessor.hpp | 30 bigmemory-4.5.8/bigmemory/inst/include/bigmemory/bigmemoryDefines.h | 4 bigmemory-4.5.8/bigmemory/inst/include/bigmemory/util.h | 30 bigmemory-4.5.8/bigmemory/man/GetMatrixSize.Rd |only bigmemory-4.5.8/bigmemory/man/as.big.matrix-methods.Rd | 19 bigmemory-4.5.8/bigmemory/man/as.matrix-big.matrix-method.Rd |only bigmemory-4.5.8/bigmemory/man/attach.big.matrix.Rd | 68 bigmemory-4.5.8/bigmemory/man/big.matrix-class.Rd | 172 - bigmemory-4.5.8/bigmemory/man/big.matrix.Rd | 293 +- bigmemory-4.5.8/bigmemory/man/big.matrix.descriptor-class.Rd | 81 bigmemory-4.5.8/bigmemory/man/bigmemory-package.Rd | 169 - bigmemory-4.5.8/bigmemory/man/deepcopy.Rd | 81 bigmemory-4.5.8/bigmemory/man/dim-big.matrix-method.Rd |only bigmemory-4.5.8/bigmemory/man/dimnames-methods.Rd |only bigmemory-4.5.8/bigmemory/man/extract-methods.Rd |only bigmemory-4.5.8/bigmemory/man/flush-methods.Rd |only bigmemory-4.5.8/bigmemory/man/head-methods.Rd |only bigmemory-4.5.8/bigmemory/man/is.float-numeric-method.Rd |only bigmemory-4.5.8/bigmemory/man/is.float.Rd |only bigmemory-4.5.8/bigmemory/man/length-big.matrix-method.Rd |only bigmemory-4.5.8/bigmemory/man/morder.Rd | 99 bigmemory-4.5.8/bigmemory/man/mwhich-methods.Rd | 39 bigmemory-4.5.8/bigmemory/man/mwhich.Rd | 94 bigmemory-4.5.8/bigmemory/man/ncol-methods.Rd |only bigmemory-4.5.8/bigmemory/man/print-big.matrix-method.Rd |only bigmemory-4.5.8/bigmemory/man/sub.big.matrix.Rd | 73 bigmemory-4.5.8/bigmemory/man/typeof-big.matrix-method.Rd |only bigmemory-4.5.8/bigmemory/man/write.big.matrix.Rd | 136 - bigmemory-4.5.8/bigmemory/src/BigMatrix.cpp | 413 ++- bigmemory-4.5.8/bigmemory/src/RcppExports.cpp |only bigmemory-4.5.8/bigmemory/src/bigmemory.cpp | 1073 +++++++--- bigmemory-4.5.8/bigmemory/src/deepcopy.cpp | 17 bigmemory-4.5.8/bigmemory/src/util.cpp | 51 bigmemory-4.5.8/bigmemory/tests |only bigmemory-4.5.8/bigmemory/vignettes |only 56 files changed, 2803 insertions(+), 1432 deletions(-)
Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden <kieran.alden@gmail.com>
Diff between spartan versions 2.2.1 dated 2015-04-13 and 2.3 dated 2015-10-19
DESCRIPTION | 10 +-- MD5 | 26 +++++--- NAMESPACE | 4 + R/lhc_calculatePRCCForMultipleTimepoints.R |only R/lhc_countSignificantParametersOverTime.R |only R/lhc_generatePRCoEffs.R | 2 R/lhc_generateTimepointFiles.R |only R/lhc_graphPRCCForMultipleTimepoints.R |only R/oat_csv_result_file_analysis.R | 23 +++++-- R/oat_graph_Leish_ATestsMultipleTimepoints.R |only R/plotATestsFromTimepointFiles.R |only R/plotPRCCSFromTimepointFiles.R |only R/ploteFASTSiFromTimepointFiles.R |only R/prepare_parameter_value_list.R | 2 R/subset_results_by_param_value_set.R | 1 man/Technique2-oat_generate_analysis.Rd | 31 +++++++++- man/Technique3-lhc_perform_analysis.Rd | 67 +++++++++++++++++++++- man/Technique4-efast_generate_analysis_results.Rd | 10 +++ 18 files changed, 149 insertions(+), 27 deletions(-)
Title: Pacific Decadal Oscillation Index
Description: Monthly Pacific Decadal Oscillation (PDO) index
values from January 1900 to present.
Author: Joe Thorley [aut, cre],
Nathan Mantua [aut, dtc],
Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between rpdo versions 0.0.1 dated 2015-08-21 and 0.1.0 dated 2015-10-19
DESCRIPTION | 14 ++++++-------- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/data.R | 2 +- README.md | 54 ++++++++++++++++++++++++++++++++---------------------- data/pdo.rda |binary man/pdo.Rd | 2 +- 7 files changed, 51 insertions(+), 39 deletions(-)
Title: Read Tabular Data
Description: Read flat/tabular text files from disk (or a connection).
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph]
Maintainer: ORPHANED
Diff between readr versions 0.1.1 dated 2015-05-29 and 0.2.0 dated 2015-10-19
readr-0.1.1/readr/R/col_names.R |only readr-0.1.1/readr/inst/doc/design.R |only readr-0.1.1/readr/inst/doc/design.Rmd |only readr-0.1.1/readr/inst/doc/design.html |only readr-0.1.1/readr/man/col_names_standardise.Rd |only readr-0.1.1/readr/man/col_types_standardise.Rd |only readr-0.1.1/readr/man/write_csv.Rd |only readr-0.1.1/readr/src/CollectorCharacter.h |only readr-0.1.1/readr/src/CollectorDate.h |only readr-0.1.1/readr/src/CollectorDateTime.h |only readr-0.1.1/readr/src/CollectorDouble.h |only readr-0.1.1/readr/src/CollectorEuroDouble.h |only readr-0.1.1/readr/src/CollectorFactor.h |only readr-0.1.1/readr/src/CollectorInteger.h |only readr-0.1.1/readr/src/CollectorLogical.h |only readr-0.1.1/readr/src/CollectorNumeric.h |only readr-0.1.1/readr/src/CollectorSkip.h |only readr-0.1.1/readr/src/DateTimeLocale.cpp |only readr-0.1.1/readr/src/DateTimeLocale.h |only readr-0.1.1/readr/src/TzManager.h |only readr-0.1.1/readr/src/write_csv.cpp |only readr-0.1.1/readr/tests/testthat/test-datetime.R |only readr-0.1.1/readr/vignettes/design.Rmd |only readr-0.2.0/readr/DESCRIPTION | 19 readr-0.2.0/readr/LICENSE |only readr-0.2.0/readr/MD5 | 198 +++-- readr-0.2.0/readr/NAMESPACE | 40 + readr-0.2.0/readr/R/POSIXct.R |only readr-0.2.0/readr/R/RcppExports.R | 52 - readr-0.2.0/readr/R/col_types.R | 263 +++++-- readr-0.2.0/readr/R/collectors.R | 183 +++-- readr-0.2.0/readr/R/count_fields.R | 5 readr-0.2.0/readr/R/date-symbols.R |only readr-0.2.0/readr/R/encoding.R |only readr-0.2.0/readr/R/input.R | 5 readr-0.2.0/readr/R/locale.R |only readr-0.2.0/readr/R/problems.R | 68 + readr-0.2.0/readr/R/read_delim.R | 125 ++- readr-0.2.0/readr/R/read_fwf.R | 29 readr-0.2.0/readr/R/read_lines.R | 20 readr-0.2.0/readr/R/read_rds.R |only readr-0.2.0/readr/R/read_table.R | 25 readr-0.2.0/readr/R/source.R | 44 - readr-0.2.0/readr/R/sysdata.rda |only readr-0.2.0/readr/R/time.R |only readr-0.2.0/readr/R/tokenizer.R | 28 readr-0.2.0/readr/R/type_convert.R | 27 readr-0.2.0/readr/R/write.R | 150 +++- readr-0.2.0/readr/README.md | 63 - readr-0.2.0/readr/build/vignette.rds |binary readr-0.2.0/readr/inst/doc/column-types.R |only readr-0.2.0/readr/inst/doc/column-types.Rmd |only readr-0.2.0/readr/inst/doc/column-types.html |only readr-0.2.0/readr/inst/doc/locales.R |only readr-0.2.0/readr/inst/doc/locales.Rmd |only readr-0.2.0/readr/inst/doc/locales.html |only readr-0.2.0/readr/man/Tokenizers.Rd | 21 readr-0.2.0/readr/man/collector.Rd | 52 + readr-0.2.0/readr/man/cols.Rd |only readr-0.2.0/readr/man/count_fields.Rd | 9 readr-0.2.0/readr/man/datasource.Rd | 7 readr-0.2.0/readr/man/date_names.Rd |only readr-0.2.0/readr/man/encoding.Rd |only readr-0.2.0/readr/man/locale.Rd |only readr-0.2.0/readr/man/parse_datetime.Rd | 71 +- readr-0.2.0/readr/man/parse_vector.Rd | 18 readr-0.2.0/readr/man/problems.Rd | 5 readr-0.2.0/readr/man/read_delim.Rd | 67 + readr-0.2.0/readr/man/read_file.Rd | 13 readr-0.2.0/readr/man/read_fwf.Rd | 41 - readr-0.2.0/readr/man/read_lines.Rd | 27 readr-0.2.0/readr/man/read_log.Rd | 23 readr-0.2.0/readr/man/read_rds.Rd |only readr-0.2.0/readr/man/read_table.Rd | 36 - readr-0.2.0/readr/man/tokenize.Rd | 9 readr-0.2.0/readr/man/type_convert.Rd | 38 - readr-0.2.0/readr/man/write_delim.Rd |only readr-0.2.0/readr/man/write_rds.Rd |only readr-0.2.0/readr/src/Collector.cpp | 379 +++++++++-- readr-0.2.0/readr/src/Collector.h | 188 +++++ readr-0.2.0/readr/src/CollectorGuess.cpp |only readr-0.2.0/readr/src/DateTime.cpp | 7 readr-0.2.0/readr/src/DateTime.h | 166 ---- readr-0.2.0/readr/src/DateTimeParser.h | 147 ++-- readr-0.2.0/readr/src/Iconv.cpp |only readr-0.2.0/readr/src/Iconv.h | 48 - readr-0.2.0/readr/src/LocaleInfo.cpp |only readr-0.2.0/readr/src/LocaleInfo.h |only readr-0.2.0/readr/src/QiParsers.h |only readr-0.2.0/readr/src/RcppExports.cpp | 117 ++- readr-0.2.0/readr/src/Source.cpp | 10 readr-0.2.0/readr/src/Source.h | 29 readr-0.2.0/readr/src/SourceFile.h | 10 readr-0.2.0/readr/src/SourceRaw.h | 6 readr-0.2.0/readr/src/SourceString.h | 5 readr-0.2.0/readr/src/Token.h | 55 + readr-0.2.0/readr/src/Tokenizer.cpp | 12 readr-0.2.0/readr/src/Tokenizer.h | 8 readr-0.2.0/readr/src/TokenizerDelim.cpp |only readr-0.2.0/readr/src/TokenizerDelim.h | 277 -------- readr-0.2.0/readr/src/TokenizerFwf.cpp | 122 +++ readr-0.2.0/readr/src/TokenizerFwf.h | 101 -- readr-0.2.0/readr/src/TokenizerLine.h | 18 readr-0.2.0/readr/src/TokenizerLog.h | 2 readr-0.2.0/readr/src/Warnings.h | 3 readr-0.2.0/readr/src/boost.h |only readr-0.2.0/readr/src/localtime.c |only readr-0.2.0/readr/src/localtime.h |only readr-0.2.0/readr/src/parse.cpp | 53 + readr-0.2.0/readr/src/read.cpp | 172 +++- readr-0.2.0/readr/src/type_convert.cpp | 13 readr-0.2.0/readr/src/tzfile.h |only readr-0.2.0/readr/src/write_delim.cpp |only readr-0.2.0/readr/tests/testthat/enc-iso-8859-1.txt |only readr-0.2.0/readr/tests/testthat/eol-cr.txt.bz2 |only readr-0.2.0/readr/tests/testthat/eol-cr.txt.gz |only readr-0.2.0/readr/tests/testthat/eol-cr.txt.xz |only readr-0.2.0/readr/tests/testthat/eol-cr.txt.zip |only readr-0.2.0/readr/tests/testthat/raw.csv |only readr-0.2.0/readr/tests/testthat/sample_text.txt |only readr-0.2.0/readr/tests/testthat/test-col-spec.R |only readr-0.2.0/readr/tests/testthat/test-collectors.R |only readr-0.2.0/readr/tests/testthat/test-parsing-character.R |only readr-0.2.0/readr/tests/testthat/test-parsing-count-fields.R |only readr-0.2.0/readr/tests/testthat/test-parsing-datetime.R |only readr-0.2.0/readr/tests/testthat/test-parsing-factors.R |only readr-0.2.0/readr/tests/testthat/test-parsing-logical.R |only readr-0.2.0/readr/tests/testthat/test-parsing-numeric.R |only readr-0.2.0/readr/tests/testthat/test-parsing-time.R |only readr-0.2.0/readr/tests/testthat/test-parsing.R |only readr-0.2.0/readr/tests/testthat/test-read-csv.R | 169 ++++ readr-0.2.0/readr/tests/testthat/test-read-file.R |only readr-0.2.0/readr/tests/testthat/test-read-fwf.R | 24 readr-0.2.0/readr/tests/testthat/test-read-lines.R |only readr-0.2.0/readr/tests/testthat/test-tokenizer-delim.R | 6 readr-0.2.0/readr/tests/testthat/test-type-convert.R |only readr-0.2.0/readr/tests/testthat/test-write-delim.R |only readr-0.2.0/readr/vignettes/column-types.Rmd |only readr-0.2.0/readr/vignettes/locales.Rmd |only 139 files changed, 2546 insertions(+), 1382 deletions(-)
Title: Determine Optimal Clustering Algorithm and Number of Clusters
Description: Cluster analysis using statistical and biological
validation measures for both continuous and count data.
Author: Michael Sekula <michael.sekula@louisville.edu>,
Somnath Datta <somnath.datta@louisville.edu>,
and Susmita Datta <susmita.datta@louisville.edu>
Maintainer: Michael Sekula <michael.sekula@louisville.edu>
Diff between optCluster versions 1.0.0 dated 2015-06-09 and 1.0.1 dated 2015-10-19
DESCRIPTION | 14 ++-- MD5 | 16 ++--- NAMESPACE | 5 + R/optCluster-Functions.R | 13 +++- man/optCluster-class.Rd | 127 ++++++++++++++++++++++---------------------- man/optCluster.Rd | 133 +++++++++++++++++++++++------------------------ man/optHeatmap.Rd | 47 +++++++--------- man/repRankAggreg.Rd | 67 ++++++++++++----------- man/valPlot.Rd | 55 +++++++++---------- 9 files changed, 245 insertions(+), 232 deletions(-)
Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel
modeling. Includes a user-friendly interface to the 'pan' package, and
several functions for visualization, data management and the analysis
of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Diff between mitml versions 0.2-3 dated 2015-07-09 and 0.2-4 dated 2015-10-19
DESCRIPTION | 8 - MD5 | 30 ++--- NEWS | 65 +++++++----- R/clusterMeans.R | 17 ++- R/panImpute.R | 12 +- R/print.mitml.summary.R | 52 ++++++--- R/print.mitml.testEstimates.R | 18 +-- R/summary.mitml.R | 76 ++++++-------- R/testConstraints.R | 103 +++++++++++++------ R/testEstimates.R | 221 ++++++++++++++++++++++++++---------------- R/testModels.R | 1 R/zzz.R | 49 +++++++++ man/panImpute.Rd | 13 -- man/summary.mitml.Rd | 24 +++- man/testConstraints.Rd | 38 ++++--- man/testEstimates.Rd | 13 ++ 16 files changed, 469 insertions(+), 271 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
and low-temperature geochemistry. The features include calculation of the standard molal
thermodynamic properties and chemical affinities of reactions involving minerals and/or
biomolecules; a database of thermodynamic properties of aqueous, crystalline and gaseous
species; amino acid group additivity for the standard molal thermodynamic properties of
neutral and ionized proteins; use of the revised Helgeson-Kirkham-Flowers equations of state
for aqueous species; construction of equilibrium activity diagrams as a function of
temperature, pressure, and chemical activities or fugacities of basis species.
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.0.5 dated 2015-05-19 and 1.0.6 dated 2015-10-19
CHNOSZ-1.0.5/CHNOSZ/demo/cordierite.R |only CHNOSZ-1.0.5/CHNOSZ/demo/orp.R |only CHNOSZ-1.0.5/CHNOSZ/inst/tests |only CHNOSZ-1.0.5/CHNOSZ/tests/test-all.R |only CHNOSZ-1.0.6/CHNOSZ/DESCRIPTION | 13 +- CHNOSZ-1.0.6/CHNOSZ/MD5 | 130 ++++++++++++++------------- CHNOSZ-1.0.6/CHNOSZ/NAMESPACE | 12 ++ CHNOSZ-1.0.6/CHNOSZ/R/IAPWS95.R | 51 ---------- CHNOSZ-1.0.6/CHNOSZ/R/affinity.R | 6 - CHNOSZ-1.0.6/CHNOSZ/R/diagram.R | 5 - CHNOSZ-1.0.6/CHNOSZ/R/equilibrate.R | 8 - CHNOSZ-1.0.6/CHNOSZ/R/examples.R | 12 +- CHNOSZ-1.0.6/CHNOSZ/R/iprotein.R | 7 + CHNOSZ-1.0.6/CHNOSZ/R/mosaic.R | 6 - CHNOSZ-1.0.6/CHNOSZ/R/objective.R | 2 CHNOSZ-1.0.6/CHNOSZ/R/swap.basis.R | 10 +- CHNOSZ-1.0.6/CHNOSZ/R/util.fasta.R | 8 - CHNOSZ-1.0.6/CHNOSZ/R/util.list.R | 50 ++++++---- CHNOSZ-1.0.6/CHNOSZ/R/util.program.R | 19 ++- CHNOSZ-1.0.6/CHNOSZ/R/util.water.R |only CHNOSZ-1.0.6/CHNOSZ/R/water.R | 90 ------------------ CHNOSZ-1.0.6/CHNOSZ/build/vignette.rds |binary CHNOSZ-1.0.6/CHNOSZ/data/OBIGT.csv | 4 CHNOSZ-1.0.6/CHNOSZ/data/opt.csv | 4 CHNOSZ-1.0.6/CHNOSZ/demo/00Index | 4 CHNOSZ-1.0.6/CHNOSZ/demo/ORP.R |only CHNOSZ-1.0.6/CHNOSZ/demo/density.R |only CHNOSZ-1.0.6/CHNOSZ/inst/NEWS | 45 +++++++++ CHNOSZ-1.0.6/CHNOSZ/inst/doc/anintro.pdf |binary CHNOSZ-1.0.6/CHNOSZ/inst/doc/equilibrium.pdf |binary CHNOSZ-1.0.6/CHNOSZ/inst/doc/hotspring.pdf |binary CHNOSZ-1.0.6/CHNOSZ/inst/doc/wjd.pdf |binary CHNOSZ-1.0.6/CHNOSZ/man/CHNOSZ-package.Rd | 3 CHNOSZ-1.0.6/CHNOSZ/man/IAPWS95.Rd | 12 -- CHNOSZ-1.0.6/CHNOSZ/man/data.Rd | 2 CHNOSZ-1.0.6/CHNOSZ/man/examples.Rd | 12 +- CHNOSZ-1.0.6/CHNOSZ/man/swap.basis.Rd | 2 CHNOSZ-1.0.6/CHNOSZ/man/util.fasta.Rd | 2 CHNOSZ-1.0.6/CHNOSZ/man/util.program.Rd | 18 ++- CHNOSZ-1.0.6/CHNOSZ/man/util.water.Rd |only CHNOSZ-1.0.6/CHNOSZ/man/water.Rd | 35 +------ CHNOSZ-1.0.6/CHNOSZ/tests/testthat |only CHNOSZ-1.0.6/CHNOSZ/tests/testthat.R |only 43 files changed, 249 insertions(+), 323 deletions(-)
Title: Functional Clustering Algorithms
Description: Unified framework to cluster functional data according to one of seven models. All models are based on the projection of the curves onto a basis. The main function funcit() calls wrapper functions for the existing algorithms, so that input parameters are the same. A list is returned with each entry representing the same or extended output for the corresponding method. Method specific as well as general visualization tools are available.
Author: Christina Yassouridis [aut, cre],
Dominik Ernst [ctb],
Madison Giacofci [ctb],
Sophie Lambert-Lacroix [ctb],
Guillemette Marot [ctb],
Franck Picard [ctb],
Nicoleta Serban [ctb],
Huijing Jiang [ctb],
Gareth James [ctb],
Catherine Sugar [ctb],
Hans-Georg Mueller [ctb],
Jie Peng [ctb],
Chiou Jeng-Min [ctb],
Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <c_ya02@yahoo.de>
Diff between funcy versions 0.8 dated 2015-10-13 and 0.8.3 dated 2015-10-19
funcy-0.8.3/funcy/DESCRIPTION | 12 - funcy-0.8.3/funcy/MD5 | 129 +++++--------- funcy-0.8.3/funcy/NEWS.md |only funcy-0.8.3/funcy/R/distclust.R | 2 funcy-0.8.3/funcy/R/funPrinComp.R | 2 funcy-0.8.3/funcy/R/functions.R | 2 funcy-0.8.3/funcy/R/plot.R | 7 funcy-0.8.3/funcy/man/funcit.Rd | 4 funcy-0.8.3/funcy/man/funcyOutList.Rd | 2 funcy-0.8.3/funcy/man/plotFuncy.Rd | 4 funcy-0.8.3/funcy/src/Makevars | 23 +- funcy-0.8.3/funcy/src/base/ansi_colors.h | 2 funcy-0.8.3/funcy/src/base/base.h | 11 + funcy-0.8.3/funcy/src/base/cc.h | 4 funcy-0.8.3/funcy/src/base/ccmem.h | 5 funcy-0.8.3/funcy/src/base/common.c | 39 ++-- funcy-0.8.3/funcy/src/base/common.h | 61 +++--- funcy-0.8.3/funcy/src/base/debug.h | 47 +---- funcy-0.8.3/funcy/src/base/deprecated.h | 4 funcy-0.8.3/funcy/src/base/otrav.cc | 32 +-- funcy-0.8.3/funcy/src/base/otrav.h | 91 +++------- funcy-0.8.3/funcy/src/base/otrav_impl.h | 245 +++++++++++++-------------- funcy-0.8.3/funcy/src/base/test.h | 8 funcy-0.8.3/funcy/src/col/arraylist.h | 176 +++++++++---------- funcy-0.8.3/funcy/src/col/col.cc | 12 - funcy-0.8.3/funcy/src/col/col_string.h | 44 ++-- funcy-0.8.3/funcy/src/col/fastalloc.h | 2 funcy-0.8.3/funcy/src/col/heap.h | 24 +- funcy-0.8.3/funcy/src/col/intmap.h | 18 - funcy-0.8.3/funcy/src/col/rangeset.h | 10 - funcy-0.8.3/funcy/src/data/crossvalidation.h | 80 ++++---- funcy-0.8.3/funcy/src/data/dataset.cc | 110 ++++++------ funcy-0.8.3/funcy/src/data/dataset.h | 46 ++--- funcy-0.8.3/funcy/src/file/textfile.cc | 35 ++- funcy-0.8.3/funcy/src/file/textfile.h | 12 - funcy-0.8.3/funcy/src/fscm.cc | 218 ++++++++++++------------ funcy-0.8.3/funcy/src/fx/datanode.c | 10 - funcy-0.8.3/funcy/src/fx/fx.c | 122 ++++++++----- funcy-0.8.3/funcy/src/fx/stopwatch.c | 12 - funcy-0.8.3/funcy/src/la/la.h | 22 +- funcy-0.8.3/funcy/src/la/matrix.h | 124 +++++++------ funcy-0.8.3/funcy/src/la/uselapack.cc | 42 ++-- funcy-0.8.3/funcy/src/la/uselapack.h | 70 +++---- funcy-0.8.3/funcy/src/libmain.cc | 6 funcy-0.8.3/funcy/src/math/discrete.cc | 22 +- funcy-0.8.3/funcy/src/math/discrete.h | 16 - funcy-0.8.3/funcy/src/math/kernel.h | 14 - funcy-0.8.3/funcy/src/math/math_lib.h | 46 ++--- funcy-0.8.3/funcy/src/par/grain.h | 6 funcy-0.8.3/funcy/src/par/thread.h | 6 funcy-0.8/funcy/src/sparse |only funcy-0.8/funcy/src/thor |only funcy-0.8/funcy/src/tree |only 53 files changed, 1031 insertions(+), 1010 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-28 0.4.4
2014-10-06 0.4.2
2014-10-01 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-24 0.1.83
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.1 dated 2015-10-15 and 1.6.2 dated 2015-10-19
TMB-1.6.1/TMB/inst/include/Eigen |only TMB-1.6.2/TMB/DESCRIPTION | 34 + TMB-1.6.2/TMB/MD5 | 419 +---------------- TMB-1.6.2/TMB/R/TMB.R | 14 TMB-1.6.2/TMB/R/benchmark.R | 3 TMB-1.6.2/TMB/R/config.R | 3 TMB-1.6.2/TMB/R/examples.R | 9 TMB-1.6.2/TMB/R/gdbsource.R | 3 TMB-1.6.2/TMB/R/sdreport.R | 3 TMB-1.6.2/TMB/R/tmbprofile.R | 3 TMB-1.6.2/TMB/R/validation.R | 6 TMB-1.6.2/TMB/R/zzz.R | 7 TMB-1.6.2/TMB/inst/COPYRIGHTS |only TMB-1.6.2/TMB/inst/include/Rstream.hpp | 6 TMB-1.6.2/TMB/inst/include/TMB.hpp | 3 TMB-1.6.2/TMB/inst/include/Vectorize.hpp | 3 TMB-1.6.2/TMB/inst/include/atomic_macro.hpp | 3 TMB-1.6.2/TMB/inst/include/atomic_math.hpp | 13 TMB-1.6.2/TMB/inst/include/checkpoint_macro.hpp | 3 TMB-1.6.2/TMB/inst/include/config.hpp | 3 TMB-1.6.2/TMB/inst/include/convenience.hpp | 3 TMB-1.6.2/TMB/inst/include/convert.hpp | 3 TMB-1.6.2/TMB/inst/include/distributions_R.hpp | 5 TMB-1.6.2/TMB/inst/include/dnorm.hpp | 3 TMB-1.6.2/TMB/inst/include/expm.hpp | 7 TMB-1.6.2/TMB/inst/include/lgamma.hpp | 3 TMB-1.6.2/TMB/inst/include/start_parallel.hpp | 3 TMB-1.6.2/TMB/inst/include/tmb_core.hpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/R_inla.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/array.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/autodiff.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/density.cpp | 5 TMB-1.6.2/TMB/inst/include/tmbutils/kronecker.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/matexp.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/order.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/romberg.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/splines.cpp | 15 TMB-1.6.2/TMB/inst/include/tmbutils/spmat.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/tmbutils_extra.cpp | 3 TMB-1.6.2/TMB/inst/include/tmbutils/vector.cpp | 3 TMB-1.6.2/TMB/man/compile.Rd | 3 TMB-1.6.2/TMB/man/oneStepPredict.Rd | 3 TMB-1.6.2/TMB/man/precompile.Rd | 2 TMB-1.6.2/TMB/man/runExample.Rd | 4 TMB-1.6.2/TMB/man/template.Rd | 6 TMB-1.6.2/TMB/src/external_metis.c | 3 TMB-1.6.2/TMB/src/local_stubs.c | 3 TMB-1.6.2/TMB/src/solve_subset.c | 13 TMB-1.6.2/TMB/src/utils.c | 3 50 files changed, 245 insertions(+), 416 deletions(-)
Title: Fitting Separable Nonlinear Models in Spectroscopy and
Microscopy
Description: A problem-solving environment (PSE) for fitting
separable nonlinear models to measurements arising in physics
and chemistry experiments; has been extensively applied to
time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg <j.snellenburg@vu.nl>
Diff between TIMP versions 1.12.1 dated 2014-12-11 and 1.13.0 dated 2015-10-19
DESCRIPTION | 21 ++++++++----------- MD5 | 40 ++++++++++++++++++++----------------- NAMESPACE | 46 +++++++++++++++++++++++++++---------------- R/compCoh.R | 4 ++- R/displayEst.R | 38 +++++++++++++++++++---------------- R/initModelClassTest.R |only R/matlinlogplot.R | 28 +++++++++++++------------- R/plotFLIM.R | 1 R/set_plotter_kin.R | 1 R/set_plotter_spec.R | 1 data/denS4.rda |binary data/denS5.rda |binary data/donorAcceptorTagged.rda |binary data/donorTagged.rda |binary data/mea_IRF.rda |binary data/target.rda |binary man/TIMP-package.Rd | 7 ++---- man/readData.Rd | 5 ++-- man/spec-class.Rd | 2 - man/target.Rd | 2 - tests/_paramEst.txt |only tests/_selectedtraces.ps |only tests/_summary.ps |only 23 files changed, 109 insertions(+), 87 deletions(-)
Title: Constrained Single Index Model Estimation
Description: Estimation of function and index vector in single index model with and without shape constraints including different smoothness conditions.
Author: Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>,
Rohit Kumar Patra <rkp2117@columbia.edu>
Maintainer: Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>
Diff between simest versions 0.1 dated 2015-09-20 and 0.2 dated 2015-10-19
DESCRIPTION | 13 ++-- MD5 | 33 ++++++------ NAMESPACE | 3 - R/CvxLipReg.r | 4 + R/CvxLseReg.r | 22 ++++---- R/CvxPenReg.r | 137 ++++++++------------------------------------------ R/SimEst.r | 43 +++++++++------ R/SolvePenta.r | 8 +- R/merge.r | 3 - README | 5 + inst/CITATION | 5 + man/cvx.lip.reg.Rd | 2 man/cvx.lse.reg.Rd | 7 ++ man/cvx.pen.reg.Rd | 2 man/sim.est.Rd | 13 ++-- man/smooth.pen.reg.Rd | 2 src/Mfun.c | 6 +- src/pred.c |only 18 files changed, 120 insertions(+), 188 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.0.8 dated 2015-07-24 and 3.0.11 dated 2015-10-19
ChangeLog | 13 +++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- R/K1.R | 39 ++++++++++++++++++++++++++++++++++++++- R/K2.R | 39 ++++++++++++++++++++++++++++++++++++++- R/pCa.R | 2 +- R/pTA.R | 2 +- R/pmix.R | 2 +- R/ppH.R | 2 +- man/K1.Rd | 8 ++++++-- man/K2.Rd | 8 ++++++-- man/Om.Rd | 2 +- man/buffer.Rd | 2 +- man/buffesm.Rd | 2 +- man/carb.Rd | 4 +++- man/oa.Rd | 4 +++- man/pCa.Rd | 6 ++++-- man/pHinsi.Rd | 4 +++- man/pTA.Rd | 4 +++- man/pgas.Rd | 4 +++- man/pmix.Rd | 4 +++- man/ppH.Rd | 4 +++- man/psi.Rd | 4 +++- 23 files changed, 162 insertions(+), 49 deletions(-)
Title: JavaScript Charts API Tool
Description: API for using 'AmCharts' Library. Based on the 'htmlwidgets'
package, it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced
but can easily be added in the constructors. Complex properties (e.g.
'JavaScript' object) can be passed as named list. See examples at <http://
dataknowledge.github.io/rAmCharts/>. and <http://www.amcharts.com/> for
more information about the library. The package includes the free version of
'AmCharts' Library. Its only limitation is that a small link to the web site
will be displayed in your charts. If you enjoy this library, do not hesitate
to refer to this page <http://www.amcharts.com/online-store/> to purchase a
licence, and thus support its creators and get a period of Priority Support.
See also <http://www.amcharts.com/about/> for more information about
'AmCharts' company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
DataKnowledge [ctb] (See official web site at http://www.datak.fr)
Maintainer: Jeffery Petit <jeff@datak.fr>
Diff between rAmCharts versions 1.1.1 dated 2015-09-16 and 1.1.2 dated 2015-10-19
rAmCharts-1.1.1/rAmCharts/R/AmChart_getSet.R |only rAmCharts-1.1.1/rAmCharts/R/AmChart_plot.R |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amAngularGauge.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amAngularGauge.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amFunnelChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amFunnelChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amGanttChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amGanttChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amPieChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amPieChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amRadarChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amRadarChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amSerialChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amSerialChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amStockChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amStockChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amXYChart.js |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/amXYChart.yaml |only rAmCharts-1.1.1/rAmCharts/inst/htmlwidgets/lib/amcharts |only rAmCharts-1.1.1/rAmCharts/man/addArrow.Rd |only rAmCharts-1.1.1/rAmCharts/man/addAxe.Rd |only rAmCharts-1.1.1/rAmCharts/man/addGraph.Rd |only rAmCharts-1.1.1/rAmCharts/man/addGuide.Rd |only rAmCharts-1.1.1/rAmCharts/man/addLabel.Rd |only rAmCharts-1.1.1/rAmCharts/man/addSegment.Rd |only rAmCharts-1.1.1/rAmCharts/man/addSubData.Rd |only rAmCharts-1.1.1/rAmCharts/man/addTitle.Rd |only rAmCharts-1.1.1/rAmCharts/man/addTrendLine.Rd |only rAmCharts-1.1.1/rAmCharts/man/addValueAxes.Rd |only rAmCharts-1.1.1/rAmCharts/man/setAllLabels.Rd |only rAmCharts-1.1.1/rAmCharts/man/setArrows.Rd |only rAmCharts-1.1.1/rAmCharts/man/setAxes.Rd |only rAmCharts-1.1.1/rAmCharts/man/setBalloon.Rd |only rAmCharts-1.1.1/rAmCharts/man/setCategoryAxis.Rd |only rAmCharts-1.1.1/rAmCharts/man/setCategoryField.Rd |only rAmCharts-1.1.1/rAmCharts/man/setChartCursor.Rd |only rAmCharts-1.1.1/rAmCharts/man/setChartScrollbar.Rd |only rAmCharts-1.1.1/rAmCharts/man/setCreditsPosition.Rd |only rAmCharts-1.1.1/rAmCharts/man/setDataProvider.Rd |only rAmCharts-1.1.1/rAmCharts/man/setExport.Rd |only rAmCharts-1.1.1/rAmCharts/man/setGraph.Rd |only rAmCharts-1.1.1/rAmCharts/man/setGraphs.Rd |only rAmCharts-1.1.1/rAmCharts/man/setGuides.Rd |only rAmCharts-1.1.1/rAmCharts/man/setLegend.Rd |only rAmCharts-1.1.1/rAmCharts/man/setSubChartProperties.Rd |only rAmCharts-1.1.1/rAmCharts/man/setTitles.Rd |only rAmCharts-1.1.1/rAmCharts/man/setTrendLines.Rd |only rAmCharts-1.1.1/rAmCharts/man/setType.Rd |only rAmCharts-1.1.1/rAmCharts/man/setValueAxes.Rd |only rAmCharts-1.1.1/rAmCharts/man/setValueAxis.Rd |only rAmCharts-1.1.2/rAmCharts/DESCRIPTION | 52 rAmCharts-1.1.2/rAmCharts/MD5 | 697 ++++----- rAmCharts-1.1.2/rAmCharts/NAMESPACE | 19 rAmCharts-1.1.2/rAmCharts/R/AmBalloon.R | 16 rAmCharts-1.1.2/rAmCharts/R/AmChart.R | 284 ++-- rAmCharts-1.1.2/rAmCharts/R/AmChart_constructors.R | 14 rAmCharts-1.1.2/rAmCharts/R/AmChart_setters.R |only rAmCharts-1.1.2/rAmCharts/R/AmChart_shinyUtils.R | 55 rAmCharts-1.1.2/rAmCharts/R/AmCharts_plot.R |only rAmCharts-1.1.2/rAmCharts/R/AmGraph.R | 53 rAmCharts-1.1.2/rAmCharts/R/AmLegend.R | 22 rAmCharts-1.1.2/rAmCharts/R/AmObject.R | 45 rAmCharts-1.1.2/rAmCharts/R/AmStockChart.R | 706 +--------- rAmCharts-1.1.2/rAmCharts/R/AmStockChart_setters.R |only rAmCharts-1.1.2/rAmCharts/R/AxisBase.R | 48 rAmCharts-1.1.2/rAmCharts/R/AxisBase_setters.R |only rAmCharts-1.1.2/rAmCharts/R/CategoryAxis.R | 49 rAmCharts-1.1.2/rAmCharts/R/ChartCursor.R | 106 - rAmCharts-1.1.2/rAmCharts/R/ChartCursor_setters.R |only rAmCharts-1.1.2/rAmCharts/R/ChartScrollbar.R | 124 - rAmCharts-1.1.2/rAmCharts/R/ChartScrollbar_setters.R |only rAmCharts-1.1.2/rAmCharts/R/DataSet.R | 112 - rAmCharts-1.1.2/rAmCharts/R/DataSetSelector.R |only rAmCharts-1.1.2/rAmCharts/R/DataSet_setters.R |only rAmCharts-1.1.2/rAmCharts/R/GaugeArrow.R | 64 rAmCharts-1.1.2/rAmCharts/R/GaugeArrow_setters.R |only rAmCharts-1.1.2/rAmCharts/R/GaugeAxis.R | 68 rAmCharts-1.1.2/rAmCharts/R/GaugeAxis_setters.R |only rAmCharts-1.1.2/rAmCharts/R/GaugeBand.R | 21 rAmCharts-1.1.2/rAmCharts/R/Guide.R | 100 - rAmCharts-1.1.2/rAmCharts/R/Guide_setters.R |only rAmCharts-1.1.2/rAmCharts/R/Label.R | 21 rAmCharts-1.1.2/rAmCharts/R/PeriodSelector.R | 17 rAmCharts-1.1.2/rAmCharts/R/StockEvent.R | 53 rAmCharts-1.1.2/rAmCharts/R/StockEvent_setters.R |only rAmCharts-1.1.2/rAmCharts/R/StockPanel.R | 288 +--- rAmCharts-1.1.2/rAmCharts/R/StockPanel_setters.R |only rAmCharts-1.1.2/rAmCharts/R/Title.R | 22 rAmCharts-1.1.2/rAmCharts/R/TrendLine.R | 186 -- rAmCharts-1.1.2/rAmCharts/R/TrendLine_setters.R |only rAmCharts-1.1.2/rAmCharts/R/ValueAxis.R | 56 rAmCharts-1.1.2/rAmCharts/R/amBoxplot.R |only rAmCharts-1.1.2/rAmCharts/R/amHist.R | 95 - rAmCharts-1.1.2/rAmCharts/R/basicClassUnions.R |only rAmCharts-1.1.2/rAmCharts/R/classUnion.R |only rAmCharts-1.1.2/rAmCharts/R/data.R |only rAmCharts-1.1.2/rAmCharts/R/sharedGenerics.R | 14 rAmCharts-1.1.2/rAmCharts/R/shinyExamples.R | 2 rAmCharts-1.1.2/rAmCharts/data |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/amDrillChart.js | 8 rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/amDrillChart.yaml | 28 rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/amcharts.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/amstock.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/funnel.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/gantt.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/gauge.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/images |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/lang |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/patterns |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/pie.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/plugins |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/radar.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/serial.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/themes |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/lib/xy.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/ramcharts_base.js |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/ramcharts_base.yaml |only rAmCharts-1.1.2/rAmCharts/inst/htmlwidgets/style.css | 86 - rAmCharts-1.1.2/rAmCharts/inst/shiny/server.R | 6 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/drilldown/drilldown_server.R | 67 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/drilldown/drilldown_ui.R | 2 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/funnel/funnel_server.R | 110 + rAmCharts-1.1.2/rAmCharts/inst/shiny/src/funnel/funnel_ui.R | 22 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/gauge/gauge_server.R | 58 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/gauge/gauge_ui.R | 12 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/pie/pie_server.R | 160 +- rAmCharts-1.1.2/rAmCharts/inst/shiny/src/pie/pie_ui.R | 52 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/radar/radar_server.R | 94 - rAmCharts-1.1.2/rAmCharts/inst/shiny/src/radar/radar_ui.R | 2 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/serial/serial_server.R | 608 ++++++-- rAmCharts-1.1.2/rAmCharts/inst/shiny/src/serial/serial_ui.R | 49 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/stock |only rAmCharts-1.1.2/rAmCharts/inst/shiny/src/xy/xy_server.R | 50 rAmCharts-1.1.2/rAmCharts/inst/shiny/src/xy/xy_ui.R | 2 rAmCharts-1.1.2/rAmCharts/inst/shiny/ui.R | 13 rAmCharts-1.1.2/rAmCharts/man/AmBalloon-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/AmChart-class.Rd | 132 - rAmCharts-1.1.2/rAmCharts/man/AmGraph-class.Rd | 21 rAmCharts-1.1.2/rAmCharts/man/AmLegend-class.Rd | 13 rAmCharts-1.1.2/rAmCharts/man/AmObject-class.Rd | 6 rAmCharts-1.1.2/rAmCharts/man/AmStockChart-class.Rd | 153 -- rAmCharts-1.1.2/rAmCharts/man/AxisBase-class.Rd | 13 rAmCharts-1.1.2/rAmCharts/man/CategoryAxis-class.Rd | 14 rAmCharts-1.1.2/rAmCharts/man/ChartCursor-class.Rd | 16 rAmCharts-1.1.2/rAmCharts/man/ChartScrollbar-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/DataSet-class.Rd | 19 rAmCharts-1.1.2/rAmCharts/man/DataSetSelector-class.Rd |only rAmCharts-1.1.2/rAmCharts/man/GaugeArrow-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/GaugeAxis-class.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/GaugeBand-class.Rd | 17 rAmCharts-1.1.2/rAmCharts/man/Guide-class.Rd | 18 rAmCharts-1.1.2/rAmCharts/man/Label-class.Rd | 21 rAmCharts-1.1.2/rAmCharts/man/PeriodSelector-class.Rd | 6 rAmCharts-1.1.2/rAmCharts/man/StockEvent-class.Rd | 17 rAmCharts-1.1.2/rAmCharts/man/StockPanel-class.Rd | 138 + rAmCharts-1.1.2/rAmCharts/man/Title-class.Rd | 17 rAmCharts-1.1.2/rAmCharts/man/TrendLine-class.Rd | 34 rAmCharts-1.1.2/rAmCharts/man/ValueAxis-class.Rd | 18 rAmCharts-1.1.2/rAmCharts/man/amBoxplot.Rd |only rAmCharts-1.1.2/rAmCharts/man/amChartsOutput.Rd | 7 rAmCharts-1.1.2/rAmCharts/man/amHist.Rd | 37 rAmCharts-1.1.2/rAmCharts/man/controlShinyPlot.Rd |only rAmCharts-1.1.2/rAmCharts/man/data_gdp.Rd |only rAmCharts-1.1.2/rAmCharts/man/data_stock1.Rd |only rAmCharts-1.1.2/rAmCharts/man/initialize-AmChart.Rd | 566 +++++++- rAmCharts-1.1.2/rAmCharts/man/initialize-AmGraph.Rd | 12 rAmCharts-1.1.2/rAmCharts/man/initialize-AmStockChart.Rd | 202 +- rAmCharts-1.1.2/rAmCharts/man/initialize-AxisBase.Rd | 27 rAmCharts-1.1.2/rAmCharts/man/initialize-ChartCursor.Rd | 28 rAmCharts-1.1.2/rAmCharts/man/initialize-ChartScrollbar.Rd | 59 rAmCharts-1.1.2/rAmCharts/man/initialize-DataSet.Rd | 20 rAmCharts-1.1.2/rAmCharts/man/initialize-DataSetSelector.Rd |only rAmCharts-1.1.2/rAmCharts/man/initialize-GaugeArrow.Rd | 18 rAmCharts-1.1.2/rAmCharts/man/initialize-GaugeAxis.Rd | 28 rAmCharts-1.1.2/rAmCharts/man/initialize-Guide.Rd | 23 rAmCharts-1.1.2/rAmCharts/man/initialize-PeriodSelector.Rd | 4 rAmCharts-1.1.2/rAmCharts/man/initialize-StockEvent.Rd | 15 rAmCharts-1.1.2/rAmCharts/man/initialize-StockPanel.Rd | 55 rAmCharts-1.1.2/rAmCharts/man/initialize-TrendLine.Rd | 41 rAmCharts-1.1.2/rAmCharts/man/listProperties-AmChart-method.Rd | 2 rAmCharts-1.1.2/rAmCharts/man/listProperties-AmObject.Rd | 11 rAmCharts-1.1.2/rAmCharts/man/plot.AmChart.Rd | 14 rAmCharts-1.1.2/rAmCharts/man/print-AmObject-method.Rd | 13 rAmCharts-1.1.2/rAmCharts/man/renderAmCharts.Rd | 7 rAmCharts-1.1.2/rAmCharts/man/runShinyExamples.Rd | 2 rAmCharts-1.1.2/rAmCharts/man/shared-generics.Rd | 20 rAmCharts-1.1.2/rAmCharts/man/show-AmChart-method.Rd |only rAmCharts-1.1.2/rAmCharts/man/show-AmObject-method.Rd | 11 rAmCharts-1.1.2/rAmCharts/man/show-AmStockChart-method.Rd |only rAmCharts-1.1.2/rAmCharts/tests |only 190 files changed, 3544 insertions(+), 3249 deletions(-)
More information about RcmdrPlugin.Export at CRAN
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Title: Profile Analysis of Multivariate Data in R
Description: Fit profile analytic models. This includes the multivariate methods and data visualization tools
to implement profile analysis and cross-validation techniques described
in Davison & Davenport (2002) and Bulut (2013).
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins <cddesjardins@gmail.com>
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.3 dated 2015-08-26 and 0.3-1 dated 2015-10-19
DESCRIPTION | 12 ++++++------ MD5 | 44 +++++++++++++++++++++++++++++--------------- NAMESPACE | 4 ++-- NEWS | 9 ++++++++- R/anova.critpat.R | 3 ++- R/print.critpat.R | 4 ++-- README.md |only build |only data/spouse.rda |only inst |only man/EEGS.Rd | 4 ++-- man/IPMMc.Rd | 6 +++--- man/PS.Rd | 2 +- man/leisure.Rd | 5 ++--- man/mod_data.Rd | 2 +- man/nutrient.Rd | 3 +-- man/pams.Rd | 2 +- man/pbg.Rd | 3 +-- man/pr.Rd | 2 +- man/profiler-package.Rd | 2 +- man/spouse.Rd |only vignettes |only 22 files changed, 63 insertions(+), 44 deletions(-)
Title: Predictive Toxicity Assessment of Chemical Mixtures
Description: Toxicity prediction of chemical mixtures using reference models such as
'concentration addition' and 'independent action' (Backhaus, T., Faust, M., Environmental
Science and Technology. 2012, 46, 2564-2573. doi:10.1021/es2034125).
Author: Xiangwei Zhu
Maintainer: Xiangwei Zhu <xwzhunc@gmail.com>
Diff between mixtox versions 1.0 dated 2015-06-03 and 1.1 dated 2015-10-19
DESCRIPTION | 15 ++++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 5 +++++ R/curveFit.R | 10 ++++++---- R/ecaPred.R | 2 ++ R/eiaPred.R | 2 ++ man/CEx.Rd | 2 +- man/ECx.Rd | 2 +- man/NOEC.Rd | 2 +- man/caPred.Rd | 2 +- man/curveFit.Rd | 2 +- man/cytotox.Rd | 2 +- man/ecaPred.Rd | 2 +- man/eiaPred.Rd | 2 +- man/gcaPred.Rd | 2 +- man/iaPred.Rd | 2 +- man/mixtox-package.Rd | 4 ++-- 17 files changed, 51 insertions(+), 39 deletions(-)
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon, Nicolas Hengartner, Eric Matzner-Lober
Maintainer: "Pierre-Andre Cornillon" <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 1.4.5 dated 2013-09-02 and 2.0-0 dated 2015-10-19
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Title: Estimation in Dual Frame Surveys
Description: Point and interval estimation in dual frame surveys. In contrast
to classic sampling theory, where only one sampling frame is considered,
dual frame methodology assumes that there are two frames available for
sampling and that, overall, they cover the entire target population. Then,
two probability samples (one from each frame) are drawn and information
collected is suitably combined to get estimators of the parameter of
interest.
Author: Antonio Arcos <arcos@ugr.es>, Maria del Mar Rueda <mrueda@ugr.es>,
Maria Giovanna Ranalli <giovanna.ranalli@stat.unipg.it> and David Molina
<dmolinam@ugr.es>
Maintainer: David Molina <dmolinam@ugr.es>
Diff between Frames2 versions 0.1.1 dated 2015-04-20 and 0.1.2 dated 2015-10-19
DESCRIPTION | 10 ++-- MD5 | 91 +++++++++++++++++++++--------------------- NAMESPACE | 2 R/BKA.R | 2 R/Dat.R | 9 ++-- R/JackCalDF.R | 6 +- R/JackCalSF.R | 6 +- R/JackHartley.R | 2 R/JackPEL.R | 8 +-- R/PEL.R | 12 ++--- build/vignette.rds |binary data/Dat.txt.gz |binary inst/CITATION |only inst/doc/estimation.Rnw | 2 inst/doc/estimation.pdf |binary inst/doc/formatting.data.Rnw | 2 inst/doc/formatting.data.pdf |binary man/BKA.Rd | 3 - man/CalDF.Rd | 3 - man/CalSF.Rd | 3 - man/Compare.Rd | 3 - man/CovHT.Rd | 3 - man/Dat.Rd | 9 +++- man/DatA.Rd | 3 - man/DatB.Rd | 3 - man/Domains.Rd | 3 - man/FB.Rd | 3 - man/HT.Rd | 3 - man/Hartley.Rd | 3 - man/JackBKA.Rd | 3 - man/JackCalDF.Rd | 3 - man/JackCalSF.Rd | 3 - man/JackFB.Rd | 3 - man/JackHartley.Rd | 3 - man/JackPEL.Rd | 3 - man/JackPML.Rd | 3 - man/JackSFRR.Rd | 3 - man/PEL.Rd | 5 +- man/PML.Rd | 3 - man/PiklA.Rd | 3 - man/PiklB.Rd | 3 - man/SFRR.Rd | 3 - man/VarHT.Rd | 3 - man/WeightsCalDF.Rd | 3 - man/WeightsCalSF.Rd | 3 - vignettes/estimation.Rnw | 2 vignettes/formatting.data.Rnw | 2 47 files changed, 142 insertions(+), 106 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-4 dated 2013-12-14 and 0.2-5 dated 2015-10-19
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Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design,
along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 0.0.5 dated 2015-07-28 and 1.0.0 dated 2015-10-19
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++++--------- NAMESPACE | 2 ++ NEWS | 11 +++++++++++ R/Helper.funcs.R | 15 ++++++++++++--- R/MainBar.R | 20 +++++++++----------- R/fromExpression.R |only R/fromList.R |only R/upset.R | 8 ++++---- README.md | 10 ++++++++++ man/fromExpression.Rd |only man/fromList.Rd |only man/upset.Rd | 15 +++++++++------ vignettes/basic.usage.Rmd | 17 +++++++++++++++++ 14 files changed, 90 insertions(+), 36 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides miscellaneous functions for carrying out political behaviour analysis, including measures of political fragmentation, seats allocation, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.7 dated 2015-08-13 and 1.3.8 dated 2015-10-19
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Title: R Commander
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.2-1 dated 2015-09-17 and 2.2-2 dated 2015-10-19
DESCRIPTION | 8 MD5 | 38 NEWS | 748 +-- R/commander.R | 2732 +++++------ R/data-menu.R | 28 R/distributions-sample.R | 4 R/startup.R | 32 R/statistics-models-menu.R | 12 R/utilities.R | 6204 ++++++++++++------------- inst/etc/R-logo-old.gif |only inst/etc/R-logo-old.ico |only inst/etc/R-logo.gif |binary inst/etc/R-logo.ico |binary inst/po/gl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 136 man/Rcmdr.Utilities.Rd | 1248 ++--- po/R-Rcmdr.pot | 88 po/R-fr.po | 6 po/R-gl.po | 9160 +++++++++++++++++++------------------- po/R-zh.po | 161 21 files changed, 10402 insertions(+), 10203 deletions(-)
Title: Moment-Based Estimation for Hierarchical Models
Description:
Implements methods from the paper "Fast Moment-Based Estimation
for Hierarchical Models," by Perry (2015).
Author: Patrick O. Perry
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between mbest versions 0.3 dated 2015-04-20 and 0.4 dated 2015-10-19
mbest-0.3/mbest/README.md |only mbest-0.4/mbest/DESCRIPTION | 8 ++++---- mbest-0.4/mbest/MD5 | 5 ++--- mbest-0.4/mbest/NAMESPACE | 18 ++++++++++++++---- 4 files changed, 20 insertions(+), 11 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito <mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 0.4 dated 2015-05-03 and 0.5 dated 2015-10-19
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 7 ++----- R/ClasGenMetDef.R | 4 ++-- man/MAINT.Data-package.Rd | 4 ++-- 5 files changed, 15 insertions(+), 18 deletions(-)
Title: High Dimensional Discriminant Analysis
Description: Performs linear discriminant analysis in high dimensional
problems based on reliable covariance estimators for problems
with (many) more variables than observations. Includes routines
for classifier training, prediction, cross-validation and
variable selection.
Author: Antonio Pedro Duarte Silva <psilva@porto.ucp.pt>
Maintainer: Antonio Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between HiDimDA versions 0.2-3 dated 2015-03-27 and 0.2-4 dated 2015-10-19
CHANGELOG | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 ++ man/HiDimDA-package.Rd | 4 ++-- 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Clinical Significance Functions
Description: Functions for calculating clinical significance.
Author: Jim Lemon <drjimlemon@gmail.com>,
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between clinsig versions 1.0-5 dated 2015-01-20 and 1.1 dated 2015-10-19
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 4 ++++ NEWS | 4 ++++ 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization and EM clustering. Furthermore, there are specialized
distance measures, plotting functions and some helper functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.2 dated 2015-10-16 and 1.0.3 dated 2015-10-18
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + R/svs.r | 31 +++++++++++++++++-------------- inst/extdata/Ctxt_Dut.txt | 2 +- inst/extdata/Ctxt_Eng.txt | 2 +- inst/extdata/Ctxt_Fra.txt | 2 +- man/InvT_Eng.txt.Rd | 2 +- man/InvT_Fra.txt.Rd | 2 +- man/SndT_Eng.txt.Rd | 2 +- man/SndT_Fra.txt.Rd | 2 +- man/svs-package.Rd | 2 +- 12 files changed, 42 insertions(+), 38 deletions(-)
Title: Tools for Analyzing Crossover Interference
Description: Analysis of crossover interference in experimental crosses,
particularly regarding the gamma model.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions
from Il-Youp Kwak
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between xoi versions 0.61-1 dated 2013-01-14 and 0.66-9 dated 2015-10-18
xoi-0.61-1/xoi/README.txt |only xoi-0.61-1/xoi/inst/README.txt |only xoi-0.61-1/xoi/man/xoi-internal.Rd |only xoi-0.66-9/xoi/DESCRIPTION | 24 xoi-0.66-9/xoi/MD5 | 149 ++-- xoi-0.66-9/xoi/NAMESPACE | 45 - xoi-0.66-9/xoi/R/bssbsb-data.R |only xoi-0.66-9/xoi/R/chiasma.R | 154 ++-- xoi-0.66-9/xoi/R/coi_um.R |only xoi-0.66-9/xoi/R/coincidence.R | 171 ++-- xoi-0.66-9/xoi/R/fitGamma.R | 389 ++++++---- xoi-0.66-9/xoi/R/fitStahl.R | 462 +++++++------ xoi-0.66-9/xoi/R/gammaDensities.R | 1099 +++++++++++++++++++++++-------- xoi-0.66-9/xoi/R/kfunc.R | 140 +-- xoi-0.66-9/xoi/R/kwak_coincidence.R | 132 +-- xoi-0.66-9/xoi/R/kwak_get_n_xo.R | 25 xoi-0.66-9/xoi/R/kwak_identify_xo.R | 45 - xoi-0.66-9/xoi/R/kwak_intensity.R | 124 +-- xoi-0.66-9/xoi/R/recrate.R | 281 ++++--- xoi-0.66-9/xoi/R/simStahl.R | 219 ++++-- xoi-0.66-9/xoi/R/util.R | 437 +++++++----- xoi-0.66-9/xoi/R/xoiversion.R | 26 xoi-0.66-9/xoi/data/bssbsb.RData |binary xoi-0.66-9/xoi/inst/README.md |only xoi-0.66-9/xoi/inst/STATUS.txt | 38 - xoi-0.66-9/xoi/man/bssbsb.Rd | 60 - xoi-0.66-9/xoi/man/chiasma.Rd | 98 +- xoi-0.66-9/xoi/man/coincidence.Rd | 57 - xoi-0.66-9/xoi/man/convertxoloc.Rd | 45 - xoi-0.66-9/xoi/man/countxo.Rd | 46 - xoi-0.66-9/xoi/man/distance.given.two.Rd | 134 +-- xoi-0.66-9/xoi/man/est.coi.Rd | 88 +- xoi-0.66-9/xoi/man/est.coi.um.Rd |only xoi-0.66-9/xoi/man/est.recrate.Rd | 71 +- xoi-0.66-9/xoi/man/find.breaks.Rd | 78 +- xoi-0.66-9/xoi/man/first.given.two.Rd | 133 +-- xoi-0.66-9/xoi/man/firstden.Rd | 107 +-- xoi-0.66-9/xoi/man/fitGamma.Rd | 176 ++-- xoi-0.66-9/xoi/man/fitStahl.Rd | 116 +-- xoi-0.66-9/xoi/man/gammacoi.Rd | 93 +- xoi-0.66-9/xoi/man/intensity.Rd | 57 - xoi-0.66-9/xoi/man/ioden.Rd | 98 +- xoi-0.66-9/xoi/man/joint.given.two.Rd | 122 +-- xoi-0.66-9/xoi/man/kfunc.Rd |only xoi-0.66-9/xoi/man/location.given.one.Rd | 125 +-- xoi-0.66-9/xoi/man/recrate2scanone.Rd |only xoi-0.66-9/xoi/man/simStahl.Rd | 88 +- xoi-0.66-9/xoi/man/stahlLoglik.Rd | 94 +- xoi-0.66-9/xoi/man/stahlcoi.Rd | 104 +- xoi-0.66-9/xoi/man/xoiversion.Rd | 32 xoi-0.66-9/xoi/man/xoprob.Rd | 110 +-- xoi-0.66-9/xoi/src/GammaDensities.c | 298 ++++---- xoi-0.66-9/xoi/src/GammaIntegral.c | 88 +- xoi-0.66-9/xoi/src/GammaLoglik.c | 50 - xoi-0.66-9/xoi/src/GammaS.c | 331 ++++----- xoi-0.66-9/xoi/src/GammaS.h | 102 +- xoi-0.66-9/xoi/src/GammaUtil.c | 122 +-- xoi-0.66-9/xoi/src/chiasma.c | 348 ++++----- xoi-0.66-9/xoi/src/chiasma.h | 15 xoi-0.66-9/xoi/src/coi_um.c |only xoi-0.66-9/xoi/src/coi_um.h |only xoi-0.66-9/xoi/src/coincidence.c | 300 ++++---- xoi-0.66-9/xoi/src/coincidence.h | 22 xoi-0.66-9/xoi/src/fitStahl.c | 333 ++++----- xoi-0.66-9/xoi/src/fitStahl.h | 25 xoi-0.66-9/xoi/src/kfunc.c | 146 ++-- xoi-0.66-9/xoi/src/kfunc.h | 24 xoi-0.66-9/xoi/src/kwak.h | 46 - xoi-0.66-9/xoi/src/kwak_coincidence.c | 266 +++---- xoi-0.66-9/xoi/src/kwak_get_n_xo.c | 68 - xoi-0.66-9/xoi/src/kwak_identify.c | 96 +- xoi-0.66-9/xoi/src/kwak_intensity.c | 121 +-- xoi-0.66-9/xoi/src/recrate.c | 150 ++-- xoi-0.66-9/xoi/src/recrate.h | 14 xoi-0.66-9/xoi/src/simStahl.c | 329 ++++++--- xoi-0.66-9/xoi/src/simStahl.h |only xoi-0.66-9/xoi/src/stahl_util.c | 72 +- xoi-0.66-9/xoi/src/stahl_util.h | 18 xoi-0.66-9/xoi/src/zeroin.c | 184 ++--- xoi-0.66-9/xoi/src/zeroin.h | 30 xoi-0.66-9/xoi/tests |only 81 files changed, 5380 insertions(+), 4310 deletions(-)
Title: Weighted Likelihood Estimation
Description: Approach to the robustness via Weighted Likelihood.
Author: Claudio Agostinelli <claudio.agostinelli@unitn.it>, SLATEC Common Mathematical Library <www.netlib.org/slatec>
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between wle versions 0.9-9 dated 2013-12-11 and 0.9-91 dated 2015-10-18
wle-0.9-9/wle/R/mle.cv.robust.bootstrap.R |only wle-0.9-9/wle/R/wle.normal.high.R |only wle-0.9-9/wle/R/wle.normal.high.chisq.R |only wle-0.9-9/wle/R/wle.normal.high.r.R |only wle-0.9-9/wle/man/wle.lm.control.Rd |only wle-0.9-9/wle/src/wleaicls.f |only wle-0.9-91/wle/DESCRIPTION | 14 +-- wle-0.9-91/wle/MD5 | 100 ++++++++++++------------- wle-0.9-91/wle/NAMESPACE | 115 ++++++++++++++++++++++++++++ wle-0.9-91/wle/R/densitynormalmulti.R |only wle-0.9-91/wle/R/wle.control.R | 119 +++++++++++++++++++++++++++++- wle-0.9-91/wle/R/wle.weights2.R |only wle-0.9-91/wle/README | 4 - wle-0.9-91/wle/data/artificial.rda |binary wle-0.9-91/wle/data/cavendish.rda |binary wle-0.9-91/wle/data/hald.rda |binary wle-0.9-91/wle/data/rocky.rda |binary wle-0.9-91/wle/data/selection.rda |binary wle-0.9-91/wle/man/wle.aic.ar.Rd | 16 ++-- wle-0.9-91/wle/man/wle.fracdiff.Rd | 46 ++++++----- wle-0.9-91/wle/man/wle.glm.Rd | 2 wle-0.9-91/wle/man/wle.glm.weights.Rd | 8 +- wle-0.9-91/wle/man/wle.weights.Rd | 4 - wle-0.9-91/wle/src/dbetawrapper.c | 2 wle-0.9-91/wle/src/densitynormalmulti.f |only wle-0.9-91/wle/src/dqagie.f | 6 + wle-0.9-91/wle/src/dqagpe.f | 3 wle-0.9-91/wle/src/genprm.f | 4 - wle-0.9-91/wle/src/initds.f | 4 + wle-0.9-91/wle/src/mleaic.f | 5 - wle-0.9-91/wle/src/mlecp.f | 26 ------ wle-0.9-91/wle/src/mlecv.f | 2 wle-0.9-91/wle/src/mlestepwise.f | 3 wle-0.9-91/wle/src/weights.f | 2 wle-0.9-91/wle/src/weights2.f |only wle-0.9-91/wle/src/wleaic.f | 2 wle-0.9-91/wle/src/wlecp.f | 22 ----- wle-0.9-91/wle/src/wlecv.f | 2 wle-0.9-91/wle/src/wlecvone.f | 6 - wle-0.9-91/wle/src/wlecvonem.f | 5 - wle-0.9-91/wle/src/wlecvonemc.f | 5 - wle-0.9-91/wle/src/wlegamma.f | 12 +-- wle-0.9-91/wle/src/wleinvga.f | 2 wle-0.9-91/wle/src/wlenmix.f | 2 wle-0.9-91/wle/src/wlenorm.f | 8 +- wle-0.9-91/wle/src/wlenormalhigh.f | 8 +- wle-0.9-91/wle/src/wlenormalmulti.f | 8 +- wle-0.9-91/wle/src/wleonestepfix.f | 43 +--------- wle-0.9-91/wle/src/wleregfix.f | 6 - wle-0.9-91/wle/src/wlestepwise.f | 1 wle-0.9-91/wle/src/wwlecv.f | 2 wle-0.9-91/wle/src/xercnt.f | 6 + wle-0.9-91/wle/src/xerhlt.f | 1 wle-0.9-91/wle/src/xermsg.f | 2 wle-0.9-91/wle/src/xerprn.f | 4 - wle-0.9-91/wle/src/xersve.f | 14 +-- 56 files changed, 416 insertions(+), 230 deletions(-)
Title: A Modern and Easy-to-Use Crypto Library
Description: Bindings to libsodium: a modern, easy-to-use software library for
encryption, decryption, signatures, password hashing and more. Sodium uses
curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein,
which has become very popular after it was discovered that the NSA had
backdoored Dual EC DRBG.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between sodium versions 0.1 dated 2015-10-11 and 0.2 dated 2015-10-18
DESCRIPTION | 8 +++++--- MD5 | 12 +++++++++++- NEWS |only build |only inst |only vignettes |only 6 files changed, 16 insertions(+), 4 deletions(-)
Title: Functions for Calculating Daily Solar Radiation and
Evapotranspiration
Description: Calculating daily global solar radiation at horizontal surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith equation to calculate evapotranspiration is also included.
Author: Jedrzej S. Bojanowski
Maintainer: Jedrzej S. Bojanowski <jedrzej.bojanowski@gmail.com>
Diff between sirad versions 2.0-7 dated 2013-01-23 and 2.3-0 dated 2015-10-18
sirad-2.0-7/sirad/data/CFC.rda |only sirad-2.0-7/sirad/data/CSTmap.rda |only sirad-2.0-7/sirad/man/CFC.Rd |only sirad-2.0-7/sirad/man/CSTmap.Rd |only sirad-2.3-0/sirad/DESCRIPTION | 23 ++---- sirad-2.3-0/sirad/MD5 | 105 +++++++++++++++---------------- sirad-2.3-0/sirad/NAMESPACE | 5 + sirad-2.3-0/sirad/R/ap.R | 20 +++-- sirad-2.3-0/sirad/R/apcal.R | 32 ++++----- sirad-2.3-0/sirad/R/bc.R | 10 +- sirad-2.3-0/sirad/R/bcauto.R | 35 +++++----- sirad-2.3-0/sirad/R/bccal.R | 14 ++-- sirad-2.3-0/sirad/R/corrEarthSunDist.R | 4 - sirad-2.3-0/sirad/R/cst.R | 38 +++++------ sirad-2.3-0/sirad/R/cstRead.r | 7 -- sirad-2.3-0/sirad/R/dayLength.R | 12 +-- sirad-2.3-0/sirad/R/dayOfYear.R | 8 +- sirad-2.3-0/sirad/R/daylightTimeFactor.R | 8 +- sirad-2.3-0/sirad/R/degrees.R | 8 +- sirad-2.3-0/sirad/R/deltaVP.r | 4 - sirad-2.3-0/sirad/R/es.r | 4 - sirad-2.3-0/sirad/R/et0.r | 18 ++--- sirad-2.3-0/sirad/R/exd.R | 14 ++-- sirad-2.3-0/sirad/R/exh.R | 16 ++-- sirad-2.3-0/sirad/R/extrat.R | 18 ++--- sirad-2.3-0/sirad/R/ha.R | 20 +++-- sirad-2.3-0/sirad/R/hacal.R | 18 ++--- sirad-2.3-0/sirad/R/hauto.r | 23 +++--- sirad-2.3-0/sirad/R/hourAngle.R | 4 - sirad-2.3-0/sirad/R/mh.R | 22 +++--- sirad-2.3-0/sirad/R/modeval.r | 38 +++++------ sirad-2.3-0/sirad/R/opticalAirMass.R | 8 +- sirad-2.3-0/sirad/R/psychC.r | 4 - sirad-2.3-0/sirad/R/radians.R | 8 +- sirad-2.3-0/sirad/R/rnl.r | 4 - sirad-2.3-0/sirad/R/rns.r | 4 - sirad-2.3-0/sirad/R/solarDecl.R | 4 - sirad-2.3-0/sirad/R/solarZenithAngle.R | 4 - sirad-2.3-0/sirad/R/su.R | 22 ++++-- sirad-2.3-0/sirad/R/sucal.R | 26 +++---- sirad-2.3-0/sirad/R/sunElevationAngle.R | 8 +- sirad-2.3-0/sirad/R/sysdata.rda |only sirad-2.3-0/sirad/R/timeOfSunrise.R | 4 - sirad-2.3-0/sirad/R/timeOfSunset.R | 4 - sirad-2.3-0/sirad/R/ts.CMSAF.R | 64 ++++++++++++------ sirad-2.3-0/sirad/R/wind2.r | 8 +- sirad-2.3-0/sirad/man/ap.Rd | 24 ++++--- sirad-2.3-0/sirad/man/bcauto.Rd | 11 ++- sirad-2.3-0/sirad/man/bccal.Rd | 7 +- sirad-2.3-0/sirad/man/et0.Rd | 11 +-- sirad-2.3-0/sirad/man/ha.Rd | 16 +++- sirad-2.3-0/sirad/man/hauto.Rd | 6 + sirad-2.3-0/sirad/man/modeval.Rd | 8 +- sirad-2.3-0/sirad/man/sirad-package.Rd | 10 +- sirad-2.3-0/sirad/man/su.Rd | 19 +++-- sirad-2.3-0/sirad/man/ts.CMSAF.Rd | 6 - 56 files changed, 443 insertions(+), 375 deletions(-)
Title: Fits the FastRCS Robust Multivariable Linear Regression Model
Description: The FastRCS algorithm of Vakili and Schmitt (2014) for robust fit of the multivariable linear regression model and outliers detection.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili <vakili.kaveh.email@gmail.com>
Diff between FastRCS versions 0.0.6 dated 2015-01-09 and 0.0.7 dated 2015-10-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 3 +++ R/FastRCS.R | 8 ++++++-- man/FRCSnumStarts.Rd | 2 +- man/FastRCS-package.Rd | 1 + man/FastRCS.Rd | 8 +++++--- man/plot.FastRCS.Rd | 2 +- man/quanf.Rd | 2 +- src/FastRCS.cpp | 10 +++++----- 10 files changed, 37 insertions(+), 27 deletions(-)
Title: Average and Conditional Effects
Description: Use structural equation modeling to estimate average and conditional effects of a treatment variable
on an outcome variable, taking into account multiple continuous and categorical covariates.
Author: Axel Mayer [aut, cre],
Lisa Dietzfelbinger [ctb]
Maintainer: Axel Mayer <amayer2010@gmail.com>
Diff between EffectLiteR versions 0.3-3 dated 2015-04-30 and 0.4-1 dated 2015-10-18
DESCRIPTION | 12 - MD5 | 13 - NAMESPACE | 13 + R/effectliter.R | 417 ++++++++++++++++++++++++++++++++++++++----------- inst/elrshiny/server.R | 271 ++++++++++++++++++++++++------- inst/elrshiny/ui.R | 46 ++++- man/effectLite.Rd | 4 man/elrReadData.Rd |only 8 files changed, 606 insertions(+), 170 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.8 dated 2015-09-05 and 0.9 dated 2015-10-18
V8-0.8/V8/man/new_context.Rd |only V8-0.9/V8/DESCRIPTION | 6 +-- V8-0.9/V8/MD5 | 17 +++++----- V8-0.9/V8/NAMESPACE | 1 V8-0.9/V8/NEWS | 9 +++++ V8-0.9/V8/R/V8.R | 72 ++++++++++++++++++++++++++++--------------- V8-0.9/V8/configure | 8 ++-- V8-0.9/V8/man/V8.Rd |only V8-0.9/V8/src/Makevars.win | 10 ++--- V8-0.9/V8/src/tests |only V8-0.9/V8/tools/winlibs.R | 25 +++++++------- 11 files changed, 89 insertions(+), 59 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.2-0 dated 2015-09-08 and 1.2-1 dated 2015-10-18
sp-1.2-0/sp/tests/mp.R |only sp-1.2-0/sp/tests/over.R |only sp-1.2-1/sp/ChangeLog | 91 ++++++ sp-1.2-1/sp/DESCRIPTION | 10 sp-1.2-1/sp/MD5 | 64 ++-- sp-1.2-1/sp/R/CRS-methods.R | 8 sp-1.2-1/sp/R/SpatialLines-methods.R | 16 - sp-1.2-1/sp/R/SpatialLinesDataFrame-methods.R | 4 sp-1.2-1/sp/R/SpatialMultiPoints-methods.R | 9 sp-1.2-1/sp/R/SpatialMultiPointsDataFrame-methods.R | 2 sp-1.2-1/sp/R/merge.R | 65 ++-- sp-1.2-1/sp/R/over.R | 4 sp-1.2-1/sp/R/spsample.R | 4 sp-1.2-1/sp/demo/depend.R | 45 --- sp-1.2-1/sp/demo/mp.R | 2 sp-1.2-1/sp/inst/ChangeLog | 91 ++++++ sp-1.2-1/sp/inst/NEWS.Rd | 19 + sp-1.2-1/sp/inst/doc/csdacm.pdf |binary sp-1.2-1/sp/inst/doc/intro_sp.R | 52 +-- sp-1.2-1/sp/inst/doc/intro_sp.Rnw | 276 ++++++++++---------- sp-1.2-1/sp/inst/doc/intro_sp.pdf |binary sp-1.2-1/sp/inst/doc/over.R | 54 +++ sp-1.2-1/sp/inst/doc/over.Rnw | 67 ++++ sp-1.2-1/sp/inst/doc/over.pdf |binary sp-1.2-1/sp/inst/include/sp.h | 2 sp-1.2-1/sp/man/CRS-class.Rd | 7 sp-1.2-1/sp/man/SpatialLines-class.Rd | 2 sp-1.2-1/sp/man/SpatialLinesDataFrame-class.Rd | 1 sp-1.2-1/sp/man/aggregate.Rd | 5 sp-1.2-1/sp/src/sp.h | 2 sp-1.2-1/sp/tests/agg.R |only sp-1.2-1/sp/tests/agg.Rout.save |only sp-1.2-1/sp/tests/pass1.Rout.save | 33 +- sp-1.2-1/sp/vignettes/intro_sp.Rnw | 276 ++++++++++---------- sp-1.2-1/sp/vignettes/over.Rnw | 67 ++++ 35 files changed, 837 insertions(+), 441 deletions(-)
Title: Basic Wireless Communications Simulation
Description: A communications simulation package supporting common wireless modulation
formats including BPSK, QPSK, 8-PSK, 16-PSK, 16-QAM and 64-QAM. The package includes AWGN
noise generation, and raised cosine and square root raised cosine pulse shaping. It also
includes convenience functions for plotting constellation diagrams, density plots, stem
plots and eye diagrams. Together these functions enable the evaluation of bit error and
symbol error rates, evaluation of pulse shaping and inter-symbol interference and support
visualization of the respective signals and noise in a variety of formats.
Author: Alberto Gutierrez [aut, cre]
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Diff between rwirelesscom versions 1.4.2 dated 2015-10-15 and 1.4.3 dated 2015-10-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/rwirelesscom.cpp | 26 +++++++++++++++++--------- 3 files changed, 22 insertions(+), 14 deletions(-)
Title: Access and Plot CanVec and CanVec+ Data for Rapid Basemap
Creation in Canada
Description: Provides an interface to the National Topographic System (NTS), which is
the way in which a number of freely available Canadian datasets
are organized. CanVec and CanVec+ datasets, which include all data used
to create Canadian topographic maps, are two such datasets that are useful
in creating vector-based maps for locations across Canada. This packages searches
CanVec data by location, plots it using pretty defaults, and exports it to
human-readable shapefiles for use in another GIS.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rcanvec versions 0.1.2 dated 2015-10-06 and 0.1.3 dated 2015-10-18
rcanvec-0.1.2/rcanvec/R/bboxtools.R |only rcanvec-0.1.2/rcanvec/R/geocode.R |only rcanvec-0.1.2/rcanvec/man/makebbox.Rd |only rcanvec-0.1.2/rcanvec/man/searchbbox.Rd |only rcanvec-0.1.2/rcanvec/man/zoom.Rd |only rcanvec-0.1.3/rcanvec/DESCRIPTION | 14 +- rcanvec-0.1.3/rcanvec/MD5 | 31 ++---- rcanvec-0.1.3/rcanvec/NAMESPACE | 3 rcanvec-0.1.3/rcanvec/R/canvec.R | 115 ++++++++++++++++++------ rcanvec-0.1.3/rcanvec/R/canvec.qplot.R | 65 +++++++++++-- rcanvec-0.1.3/rcanvec/R/nts.R | 4 rcanvec-0.1.3/rcanvec/data/canvec_layers.rda |binary rcanvec-0.1.3/rcanvec/man/canvec.export.Rd | 25 +++-- rcanvec-0.1.3/rcanvec/man/canvec.plot.Rd | 4 rcanvec-0.1.3/rcanvec/man/canvec.qplot.Rd | 36 +++++-- rcanvec-0.1.3/rcanvec/man/nts.Rd | 2 rcanvec-0.1.3/rcanvec/man/ntsstring.Rd | 2 rcanvec-0.1.3/rcanvec/man/rcanvec-package.Rd | 34 ++----- rcanvec-0.1.3/rcanvec/tests/testthat/test_nts.R | 6 - 19 files changed, 232 insertions(+), 109 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for
multi-label data sets along with an interactive Shiny application to ease their
use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@outlook.com>
Diff between mldr versions 0.2.51 dated 2015-09-16 and 0.2.82 dated 2015-10-18
DESCRIPTION | 10 +++++----- MD5 | 33 ++++++++++++++++++++------------- NAMESPACE | 4 ++++ R/concurrence.R |only R/measures.R | 13 +++++++++++-- R/mldr.R | 5 ++--- R/read.arff.R | 4 ++-- data/birds.rda |binary data/emotions.rda |binary data/genbase.rda |binary demo/00Index | 1 + demo/decouple.R | 2 +- demo/rebuild_datasets.R |only inst/CITATION |only inst/doc/mldr.pdf |binary inst/shiny/rsconnect |only inst/shiny/server.R | 41 ++++++++++++++++++++++++++++++++--------- inst/shiny/ui.R | 15 ++++++++++----- man/concurrenceReport.Rd |only man/labelInteractions.Rd |only man/remedial.Rd |only 21 files changed, 88 insertions(+), 40 deletions(-)
Title: Hydrologic Indices for Daily Time Series Data
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Author: Nick Bond
Maintainer: Nick Bond <n.bond@griffith.edu.au>
Diff between hydrostats versions 0.2.3 dated 2014-12-21 and 0.2.4 dated 2015-10-18
hydrostats-0.2.3/hydrostats/data/Acheron.txt |only hydrostats-0.2.3/hydrostats/data/Cooper.txt |only hydrostats-0.2.4/hydrostats/DESCRIPTION | 13 - hydrostats-0.2.4/hydrostats/MD5 | 30 +-- hydrostats-0.2.4/hydrostats/NAMESPACE | 3 hydrostats-0.2.4/hydrostats/NEWS | 11 + hydrostats-0.2.4/hydrostats/R/baseflows.R | 172 +++++++++--------- hydrostats-0.2.4/hydrostats/R/flood.length.max.R | 2 hydrostats-0.2.4/hydrostats/R/high.spell.lengths.R | 3 hydrostats-0.2.4/hydrostats/R/high.spells.R | 4 hydrostats-0.2.4/hydrostats/README.md | 2 hydrostats-0.2.4/hydrostats/data/Acheron.txt.gz |only hydrostats-0.2.4/hydrostats/data/Cooper.txt.gz |only hydrostats-0.2.4/hydrostats/man/baseflows.Rd | 7 hydrostats-0.2.4/hydrostats/man/daily.cv.Rd | 2 hydrostats-0.2.4/hydrostats/man/flood.length.max.Rd | 12 - hydrostats-0.2.4/hydrostats/man/high.spell.lengths.Rd | 2 hydrostats-0.2.4/hydrostats/man/hydrostats-package.Rd | 4 18 files changed, 152 insertions(+), 115 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-26 dated 2015-08-26 and 1.1-0 dated 2015-10-18
gstat-1.0-26/gstat/LICENCE |only gstat-1.0-26/gstat/configure |only gstat-1.0-26/gstat/configure.in |only gstat-1.0-26/gstat/configure.win |only gstat-1.0-26/gstat/src/chfactor.c |only gstat-1.0-26/gstat/src/config.hin |only gstat-1.0-26/gstat/src/config.w32 |only gstat-1.0-26/gstat/src/copy.c |only gstat-1.0-26/gstat/src/err.c |only gstat-1.0-26/gstat/src/err.h |only gstat-1.0-26/gstat/src/ext_dbase.h |only gstat-1.0-26/gstat/src/hsehldr.c |only gstat-1.0-26/gstat/src/init.c |only gstat-1.0-26/gstat/src/ivecop.c |only gstat-1.0-26/gstat/src/lex.l |only gstat-1.0-26/gstat/src/lufactor.c |only gstat-1.0-26/gstat/src/machine.c |only gstat-1.0-26/gstat/src/machine.hin |only gstat-1.0-26/gstat/src/machine.w32 |only gstat-1.0-26/gstat/src/matop.c |only gstat-1.0-26/gstat/src/matrix.h |only gstat-1.0-26/gstat/src/matrix2.h |only gstat-1.0-26/gstat/src/meminfo.c |only gstat-1.0-26/gstat/src/meminfo.h |only gstat-1.0-26/gstat/src/memory.c |only gstat-1.0-26/gstat/src/meschach |only gstat-1.0-26/gstat/src/norm.c |only gstat-1.0-26/gstat/src/polygon.c |only gstat-1.0-26/gstat/src/polygon.h |only gstat-1.0-26/gstat/src/pxop.c |only gstat-1.0-26/gstat/src/qrfactor.c |only gstat-1.0-26/gstat/src/solve.c |only gstat-1.0-26/gstat/src/sparse.c |only gstat-1.0-26/gstat/src/sparse.h |only gstat-1.0-26/gstat/src/sparse2.h |only gstat-1.0-26/gstat/src/sprow.c |only gstat-1.0-26/gstat/src/submat.c |only gstat-1.0-26/gstat/src/vecop.c |only gstat-1.0-26/gstat/src/version.c |only gstat-1.0-26/gstat/src/zmatrix.h |only gstat-1.0-26/gstat/src/zmatrix2.h |only gstat-1.1-0/gstat/DESCRIPTION | 10 gstat-1.1-0/gstat/MD5 | 193 - gstat-1.1-0/gstat/R/gstat.cv.R | 8 gstat-1.1-0/gstat/R/krige0.R | 41 gstat-1.1-0/gstat/R/load.variogram.model.R | 18 gstat-1.1-0/gstat/R/predict.gstat.R | 19 gstat-1.1-0/gstat/R/stVariogramModels.R | 33 gstat-1.1-0/gstat/R/vgm.R | 2 gstat-1.1-0/gstat/R/zzz.R | 1 gstat-1.1-0/gstat/build/vignette.rds |binary gstat-1.1-0/gstat/cleanup | 3 gstat-1.1-0/gstat/data/coalash.rda |binary gstat-1.1-0/gstat/data/fulmar.rda |binary gstat-1.1-0/gstat/data/jura.rda |binary gstat-1.1-0/gstat/data/meuse.all.rda |binary gstat-1.1-0/gstat/data/meuse.alt.rda |binary gstat-1.1-0/gstat/data/ncp.grid.rda |binary gstat-1.1-0/gstat/data/oxford.rda |binary gstat-1.1-0/gstat/data/pcb.rda |binary gstat-1.1-0/gstat/data/sic2004.rda |binary gstat-1.1-0/gstat/data/sic97.rda |binary gstat-1.1-0/gstat/data/tull.rda |binary gstat-1.1-0/gstat/data/vv.rda |binary gstat-1.1-0/gstat/data/walker.rda |binary gstat-1.1-0/gstat/data/wind.rda |binary gstat-1.1-0/gstat/inst/ChangeLog | 276 + gstat-1.1-0/gstat/inst/NEWS.Rd |only gstat-1.1-0/gstat/inst/doc/gstat.pdf |binary gstat-1.1-0/gstat/inst/doc/prs.pdf |binary gstat-1.1-0/gstat/inst/doc/spatio-temporal-kriging.pdf |binary gstat-1.1-0/gstat/inst/doc/st.R | 6 gstat-1.1-0/gstat/inst/doc/st.Rnw | 6 gstat-1.1-0/gstat/inst/doc/st.pdf |binary gstat-1.1-0/gstat/man/fit.StVariogram.Rd | 11 gstat-1.1-0/gstat/man/krigeST.Rd | 12 gstat-1.1-0/gstat/man/predict.gstat.Rd | 4 gstat-1.1-0/gstat/man/sic2004.Rd | 4 gstat-1.1-0/gstat/man/sic97.Rd | 6 gstat-1.1-0/gstat/man/vgmST.Rd | 3 gstat-1.1-0/gstat/man/walker.Rd | 5 gstat-1.1-0/gstat/src/Makevars |only gstat-1.1-0/gstat/src/chol.c |only gstat-1.1-0/gstat/src/config.h |only gstat-1.1-0/gstat/src/data.c | 1353 -------- gstat-1.1-0/gstat/src/data.h | 5 gstat-1.1-0/gstat/src/defs.h | 59 gstat-1.1-0/gstat/src/fit.c | 198 - gstat-1.1-0/gstat/src/gcdist.c | 12 gstat-1.1-0/gstat/src/getest.c | 55 gstat-1.1-0/gstat/src/gls.c | 279 - gstat-1.1-0/gstat/src/glvars.c | 152 gstat-1.1-0/gstat/src/glvars.h | 14 gstat-1.1-0/gstat/src/lex.c | 247 - gstat-1.1-0/gstat/src/lm.c | 73 gstat-1.1-0/gstat/src/mapio.c | 2847 ----------------- gstat-1.1-0/gstat/src/msim.c | 414 -- gstat-1.1-0/gstat/src/mtrx.c |only gstat-1.1-0/gstat/src/mtrx.h |only gstat-1.1-0/gstat/src/nsearch.c | 2 gstat-1.1-0/gstat/src/parse.c | 107 gstat-1.1-0/gstat/src/predict.c | 539 --- gstat-1.1-0/gstat/src/random.c | 75 gstat-1.1-0/gstat/src/reml.c | 46 gstat-1.1-0/gstat/src/s.c | 94 gstat-1.1-0/gstat/src/select.c | 49 gstat-1.1-0/gstat/src/sem.c | 216 - gstat-1.1-0/gstat/src/sem.h | 2 gstat-1.1-0/gstat/src/sim.c | 17 gstat-1.1-0/gstat/src/stat.c | 51 gstat-1.1-0/gstat/src/userio.c | 107 gstat-1.1-0/gstat/src/utils.c | 136 gstat-1.1-0/gstat/src/vario.c | 73 gstat-1.1-0/gstat/src/vario.h | 2 gstat-1.1-0/gstat/src/vario_fn.c | 6 gstat-1.1-0/gstat/tests/fit.Rout.save | 18 gstat-1.1-0/gstat/tests/merge.Rout.save | 44 gstat-1.1-0/gstat/tests/unproj.Rout.save | 68 gstat-1.1-0/gstat/tests/windst.Rout.save | 16 gstat-1.1-0/gstat/vignettes/st.Rnw | 6 120 files changed, 817 insertions(+), 7226 deletions(-)
Title: A Multi-Platform GUI for Drawing Customizable Graphs in R
Diff between GrapheR versions 1.9-84 dated 2014-07-27 and 1.9-85 dated 2015-10-18
Description: A multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Hervé
Maintainer: Maxime Hervé
GrapheR-1.9-84/GrapheR/man/Env.Rd |only
GrapheR-1.9-84/GrapheR/man/active.erreur.Rd |only
GrapheR-1.9-85/GrapheR/DESCRIPTION | 12 -
GrapheR-1.9-85/GrapheR/MD5 | 16 +-
GrapheR-1.9-85/GrapheR/NAMESPACE | 11 +
GrapheR-1.9-85/GrapheR/NEWS | 29 ----
GrapheR-1.9-85/GrapheR/R/Sources.R | 179 +++++++-------------------
GrapheR-1.9-85/GrapheR/R/zzzz.R | 2
GrapheR-1.9-85/GrapheR/build/vignette.rds |binary
GrapheR-1.9-85/GrapheR/man/GrapheR-package.Rd | 8 -
10 files changed, 86 insertions(+), 171 deletions(-)
Title: Comparing Correlations
Description: Statistical tests for the comparison between two
correlations based on either independent or dependent groups.
Dependent correlations can either be overlapping or
nonoverlapping. A web interface is available at
http://comparingcorrelations.org. A plugin for the R GUI and
IDE RKWard is included. Please install RKWard from
https://rkward.kde.org to use this feature. The respective R
package 'rkward' cannot be installed directly from a
repository, as it is a part of RKWard.
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen <mail@birkdiedenhofen.de>
Diff between cocor versions 1.1-1 dated 2015-04-10 and 1.1-2 dated 2015-10-18
ChangeLog | 6 ++++ DESCRIPTION | 27 ++++++++++++--------- MD5 | 35 ++++++++++++++-------------- NAMESPACE | 3 +- R/0helper.r | 4 +-- R/cocor-package.R | 8 +++--- R/cocor.dep.groups.nonoverlap.r | 8 +++--- inst/CITATION | 7 +++-- inst/doc |only inst/rkward/rkwarddev.cocor.plugin.script.R | 4 +-- inst/tests/test.r | 5 ++++ man/as.htest.Rd | 3 +- man/cocor-package.Rd | 12 +++++---- man/cocor.Rd | 3 +- man/cocor.dep.groups.nonoverlap.Rd | 11 ++++---- man/cocor.dep.groups.overlap.Rd | 3 +- man/cocor.indep.groups.Rd | 3 +- man/get.cocor.input.Rd | 3 +- man/get.cocor.results.Rd | 3 +- 19 files changed, 88 insertions(+), 60 deletions(-)
Title: Robust Linear Regression with Compositional Data as Covariates
Description: Provides functionality to perform robust regression
on compositional data. To get information on the distribution of the
estimates, various bootstrapping methods are implemented for the
compositional as well as for standard robust regression models, to provide
a direct comparison between them.
Author: David Kepplinger <david.kepplinger@gmail.com>
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between complmrob versions 0.5.8 dated 2014-12-09 and 0.6.1 dated 2015-10-18
ChangeLog | 5 ++++ DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++--------------- NAMESPACE | 21 +++++++++++++++++- R/complmrob.R | 4 +++ R/plot-methods.R | 46 ++++++++++++++++++++++++++++------------ man/bootStat-methods.Rd | 17 +++++++------- man/bootcoefs.Rd | 3 +- man/complmrob.Rd | 3 +- man/confint.Rd | 3 +- man/format.perc.Rd | 3 +- man/isomLR.Rd | 5 ++-- man/plot.bootcoefs.Rd | 3 +- man/plot.complmrob.Rd | 3 +- man/predictdf.complmrob.part.Rd | 13 ++++++----- man/print-methods.Rd | 7 +++--- man/print.summary.complmrob.Rd | 3 +- man/summary-methods.Rd | 7 +++--- 18 files changed, 124 insertions(+), 64 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 3.0.1 dated 2015-08-28 and 3.0.3 dated 2015-10-18
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NAMESPACE | 2 - R/CMplot.r | 65 ++++++++++++++++++++++++++++++++++++++++++-------- man/CMplot-package.Rd | 9 ++++-- 5 files changed, 70 insertions(+), 22 deletions(-)
Title: Prepare Species Distributions for the Use in Phylogenetic
Analyses
Description: Preparation of species occurrences and distribution data for the use in phylogenetic analyses. SpeciesgeocodeR is built for data cleaning, data exploration and data analysis and especially suited for biogeographical and ecological questions on large datasets. The package includes the easy creation of summary-tables and -graphs and geographical maps, the automatic cleaning of geographic occurrence data, the calculating of coexistence matrices and species ranges (EOO) as well as mapping diversity in geographic areas.
Author: Alexander Zizka [aut, cre]
Maintainer: Alexander Zizka <alexander.zizka@bioenv.gu.se>
Diff between speciesgeocodeR versions 1.0-3 dated 2015-07-14 and 1.0-4 dated 2015-10-17
speciesgeocodeR-1.0-3/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.Rmd |only speciesgeocodeR-1.0-3/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.html |only speciesgeocodeR-1.0-4/speciesgeocodeR/DESCRIPTION | 15 - speciesgeocodeR-1.0-4/speciesgeocodeR/MD5 | 70 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/NAMESPACE | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/R/GeoClean.R | 35 ++- speciesgeocodeR-1.0-4/speciesgeocodeR/R/ReadPoints.R | 80 +++++-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpGeoCod.R | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpGeoCodH.R | 4 speciesgeocodeR-1.0-4/speciesgeocodeR/R/SpeciesGeoCoder.R | 38 +-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/Spgc2BioGeoBEARS.R |only speciesgeocodeR-1.0-4/speciesgeocodeR/R/WriteOut.R | 62 +++-- speciesgeocodeR-1.0-4/speciesgeocodeR/R/speciesgeocodeR-internal.R | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/inst/doc/data_cleaning_and_exploration.pdf |binary speciesgeocodeR-1.0-4/speciesgeocodeR/man/CoExClass.Rd | 62 ++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/GeoClean.Rd | 43 +-- speciesgeocodeR-1.0-4/speciesgeocodeR/man/GetElevation.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/MapGrid.Rd | 74 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/MapRichness.Rd | 112 +++++----- speciesgeocodeR-1.0-4/speciesgeocodeR/man/PlotHull.Rd | 4 speciesgeocodeR-1.0-4/speciesgeocodeR/man/ReadPoints.Rd | 18 + speciesgeocodeR-1.0-4/speciesgeocodeR/man/RichnessGrid.Rd | 3 speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpGeoCod.Rd | 21 + speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpGeoCodH.Rd | 23 -- speciesgeocodeR-1.0-4/speciesgeocodeR/man/SpeciesGeoCoder.Rd | 23 +- speciesgeocodeR-1.0-4/speciesgeocodeR/man/Spgc2Biogeobears.Rd |only speciesgeocodeR-1.0-4/speciesgeocodeR/man/WriteOut.Rd | 11 speciesgeocodeR-1.0-4/speciesgeocodeR/man/WwfLoad.Rd | 71 +++--- speciesgeocodeR-1.0-4/speciesgeocodeR/man/countryref.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs_in.Rd | 6 speciesgeocodeR-1.0-4/speciesgeocodeR/man/lemurs_test.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/mdg_biomes.Rd | 6 speciesgeocodeR-1.0-4/speciesgeocodeR/man/mdg_poly.Rd | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/man/plot.spgeoOUT.Rd | 8 speciesgeocodeR-1.0-4/speciesgeocodeR/man/speciesgeocodeR-package.Rd | 99 ++++---- speciesgeocodeR-1.0-4/speciesgeocodeR/man/summary.spgeoIN.Rd | 2 speciesgeocodeR-1.0-4/speciesgeocodeR/man/summary.spgeoOUT.Rd | 6 38 files changed, 504 insertions(+), 420 deletions(-)
More information about speciesgeocodeR at CRAN
Permanent link
Title: Diverse Basic Statistical and Graphical Functions
Diff between RVAideMemoire versions 0.9-50 dated 2015-08-08 and 0.9-51 dated 2015-10-17
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 -
MD5 | 22 ++--
NEWS | 7 +
R/MVA.biplot.R | 56 +++++++++--
R/MVA.load.R | 2
R/MVA.scores.R | 2
R/byf.hist.R | 16 +--
R/plotresid.R | 215 +++++++++++++++++++++++--------------------
R/zzz.R | 2
man/RVAideMemoire-package.Rd | 4
man/byf.hist.Rd | 8 +
man/plotresid.Rd | 8 -
12 files changed, 212 insertions(+), 138 deletions(-)
Title: Discrete Weibull Distributions (Type 1 and 3)
Description: Probability mass function, distribution function, quantile function, random generation and parameter estimation for the type I and III discrete Weibull distributions.
Author: Alessandro Barbiero
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between DiscreteWeibull versions 1.0.1 dated 2015-07-08 and 1.1 dated 2015-10-17
DESCRIPTION | 8 +-- MD5 | 28 ++++++------- R/Edweibull.R | 75 ++++++++++++++++++++++-------------- man/DiscreteWeibull-package.Rd | 9 ++-- man/Edweibull.Rd | 19 ++++++--- man/Edweibull3.Rd | 40 +++++++++---------- man/ddweibull.Rd | 22 +++++----- man/ddweibull3.Rd | 84 ++++++++++++++++++++--------------------- man/estdweibull.Rd | 23 +++++------ man/estdweibull3.Rd | 72 +++++++++++++++++------------------ man/loglikedw.Rd | 10 ++-- man/loglikedw3.Rd | 12 ++--- man/lossdw.Rd | 8 +-- man/lossdw3.Rd | 12 ++--- man/varFisher.Rd | 7 +-- 15 files changed, 228 insertions(+), 201 deletions(-)
More information about DiscreteWeibull at CRAN
Permanent link
Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.6 dated 2015-07-21 and 0.8 dated 2015-10-17
DESCRIPTION | 14 +++++++------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- R/model.R | 17 +++++++---------- R/plot.R | 4 +++- inst/itemModelExplorer/server.R | 16 +++++++++++++++- inst/itemModelExplorer/ui.R | 3 ++- inst/modelBuilder/www/sort.css | 2 ++ man/SitemPlot.Rd | 3 ++- man/addExploratoryFactors.Rd | 3 ++- man/iccPlot.Rd | 3 ++- man/itemModelExplorer.Rd | 3 ++- man/itemResponseMap.Rd | 7 ++++++- man/modelBuilder.Rd | 3 ++- man/plotInformation.Rd | 3 ++- man/replicateModelBy.Rd | 3 ++- man/uniquenessPrior.Rd | 3 ++- man/univariatePrior.Rd | 3 ++- 18 files changed, 78 insertions(+), 48 deletions(-)
Title: Creates a Model Matrix via Feature Hashing with a Formula
Interface
Description: Feature hashing, also called as the hashing trick, is a method to transform
features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix.
Without looking up the indices in an associative array,
it applies a hash function to the features and uses their hash values as indices directly.
The method of feature hashing in this package was proposed in Weinberger et al. (2009).
The hashing algorithm is the murmurhash3 from the digest package.
Please see the README in https://github.com/wush978/FeatureHashing for more information.
Author: Wush Wu [aut, cre],
Michael Benesty [aut, ctb]
Maintainer: Wush Wu <wush978@gmail.com>
Diff between FeatureHashing versions 0.9.1 dated 2015-09-22 and 0.9.1.1 dated 2015-10-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/FeatureHashing.html | 4 ++-- src/hash_function.h | 1 + src/hash_internal.cpp | 3 ++- tests/test-progress_bar.R | 4 ++-- 6 files changed, 15 insertions(+), 13 deletions(-)
More information about FeatureHashing at CRAN
Permanent link
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 2.0.0 dated 2015-07-24 and 2.0.1 dated 2015-10-17
DESCRIPTION | 8 MD5 | 8 NAMESPACE | 1 R/cjoint.R | 889 +++++++++++++++++++++++++++++++++++++------------------ man/plot.amce.Rd | 6 5 files changed, 625 insertions(+), 287 deletions(-)
Title: Search and Download Papers from the bioRxiv Preprint Server
Description: The bioRxiv preprint server (http://www.biorxiv.org) is a website where scientists can post preprints of scholarly texts in biology. Users can search and download PDFs in bulk from the preprint server. The text of abstracts are stored as raw text within R, and PDFs can easily be saved and imported for text mining with packages such as 'tm'.
Author: Edmund Hart [aut, cre]
Maintainer: Edmund Hart <edmund.m.hart@gmail.com>
Diff between biorxivr versions 0.1.1 dated 2015-05-28 and 0.1.2 dated 2015-10-17
DESCRIPTION | 8 +-- MD5 | 32 ++++++------ NAMESPACE | 6 +- R/bx_download.R | 1 R/bx_extract.R | 1 R/bx_search.R | 1 inst/doc/vignette.R | 3 + inst/doc/vignette.Rmd | 4 + inst/doc/vignette.html | 94 ++++++++++++++++++------------------ man/bx_download.Rd | 2 man/bx_extract.Rd | 2 man/bx_extract_single.Rd | 2 man/bx_search.Rd | 2 man/plot.biorxiv_paper.Rd | 2 man/print.summary.biorxiv_search.Rd | 2 man/summary.biorxiv_search.Rd | 2 vignettes/vignette.Rmd | 4 + 17 files changed, 95 insertions(+), 73 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.3.2 dated 2015-09-03 and 0.4.1 dated 2015-10-17
DESCRIPTION | 11 +-- MD5 | 19 +++-- NAMESPACE | 7 +- NEWS | 12 +++ R/qic.R | 196 +++++++++++++++++++++++++++++++++++++++++--------------- R/tcc.R |only R/trc.R | 54 ++++++++++----- README.md | 3 man/plot.tcc.Rd |only man/qic.Rd | 26 ++++--- man/tcc.Rd |only man/trc.Rd | 7 +- 12 files changed, 240 insertions(+), 95 deletions(-)
Title: Diagnostics Plots for Bicluster Data
Description: Diagnostic tools based on two-way
anova and median-polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non-bicluster rows- or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding two bicluster methods from the fabia and isa2 R
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
Diff between BcDiag versions 1.0.9 dated 2015-10-10 and 1.0.10 dated 2015-10-17
DESCRIPTION | 12 +-- MD5 | 6 - R/profileBic.R | 209 ++++++++++++++++++++++++++++++++++++++++++++++-------- man/profileBic.Rd | 5 + 4 files changed, 192 insertions(+), 40 deletions(-)
Title: Tools for Semantic Vector Spaces
Description: Various tools for semantic vector spaces, such as
correspondence analysis (simple, multiple and discriminant), latent
semantic analysis, probabilistic latent semantic analysis, non-negative
matrix factorization and EM clustering. Furthermore, there are specialized
distance measures, plotting functions and some helper functions.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between svs versions 1.0.1 dated 2015-10-15 and 1.0.2 dated 2015-10-16
svs-1.0.1/svs/inst/extdata/Ctxt_Dut.csv |only svs-1.0.1/svs/inst/extdata/Ctxt_Eng.csv |only svs-1.0.1/svs/inst/extdata/Ctxt_Fra.csv |only svs-1.0.1/svs/inst/extdata/InvT_Eng.csv |only svs-1.0.1/svs/inst/extdata/InvT_Fra.csv |only svs-1.0.1/svs/inst/extdata/SndT_Eng.csv |only svs-1.0.1/svs/inst/extdata/SndT_Fra.csv |only svs-1.0.1/svs/man/Ctxt_Dut.csv.Rd |only svs-1.0.1/svs/man/Ctxt_Eng.csv.Rd |only svs-1.0.1/svs/man/Ctxt_Fra.csv.Rd |only svs-1.0.1/svs/man/InvT_Eng.csv.Rd |only svs-1.0.1/svs/man/InvT_Fra.csv.Rd |only svs-1.0.1/svs/man/SndT_Eng.csv.Rd |only svs-1.0.1/svs/man/SndT_Fra.csv.Rd |only svs-1.0.2/svs/DESCRIPTION | 8 +-- svs-1.0.2/svs/MD5 | 48 ++++++++++---------- svs-1.0.2/svs/R/svs.r | 74 +++++++++++++++++++------------- svs-1.0.2/svs/inst/extdata/Ctxt_Dut.txt |only svs-1.0.2/svs/inst/extdata/Ctxt_Eng.txt |only svs-1.0.2/svs/inst/extdata/Ctxt_Fra.txt |only svs-1.0.2/svs/inst/extdata/InvT_Eng.txt |only svs-1.0.2/svs/inst/extdata/InvT_Fra.txt |only svs-1.0.2/svs/inst/extdata/SndT_Eng.txt |only svs-1.0.2/svs/inst/extdata/SndT_Fra.txt |only svs-1.0.2/svs/man/Ctxt_Dut.txt.Rd |only svs-1.0.2/svs/man/Ctxt_Eng.txt.Rd |only svs-1.0.2/svs/man/Ctxt_Fra.txt.Rd |only svs-1.0.2/svs/man/InvT_Eng.txt.Rd |only svs-1.0.2/svs/man/InvT_Fra.txt.Rd |only svs-1.0.2/svs/man/SndT_Eng.txt.Rd |only svs-1.0.2/svs/man/SndT_Fra.txt.Rd |only svs-1.0.2/svs/man/fast_E_M.Rd | 3 - svs-1.0.2/svs/man/fast_dca.Rd | 3 - svs-1.0.2/svs/man/fast_lsa.Rd | 3 - svs-1.0.2/svs/man/fast_mca.Rd | 3 - svs-1.0.2/svs/man/fast_nmf.Rd | 3 - svs-1.0.2/svs/man/fast_psa.Rd | 3 - svs-1.0.2/svs/man/fast_sca.Rd | 3 - svs-1.0.2/svs/man/svs-package.Rd | 18 ++++--- 39 files changed, 97 insertions(+), 72 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.0.1 dated 2015-09-22 and 2.1.0 dated 2015-10-16
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS | 9 +++++++++ R/xform.R | 34 ++++++++++++++++++++++++++++------ man/xform.Rd | 26 ++++++++++++++++++++------ src/DeformationField.cpp | 2 +- src/main.cpp | 35 +++++++++++++++++++++++++++++++++++ src/reg-lib/_reg_aladin.h | 22 +++++++++++----------- tests/testthat/test-10-xform.R | 7 +++++++ tests/testthat/test-20-niftyreg.R | 4 ++-- tests/testthat/test-25-transform.R | 3 +++ 12 files changed, 134 insertions(+), 42 deletions(-)
Title: Interactive Dendrograms
Description: Interactive dendrogram that enables the user to select and
color clusters, to zoom and pan the dendrogram, and to visualize
the clustered data not only in a built-in heat map, but also in
'GGobi' interactive plots and user-supplied plots.
This is a backport of Qt-based 'idendro'
(https://github.com/tsieger/idendro) to base R graphics and Tcl/Tk GUI.
Author: Tomas Sieger
Maintainer: Tomas Sieger <tomas.sieger@seznam.cz>
Diff between idendr0 versions 1.5.1 dated 2015-10-14 and 1.5.2 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/idendro.R | 9 +++++---- man/hca5000.Rd | 8 ++++---- man/idendr0-package.Rd | 4 ++-- man/idendro.Rd | 8 ++++---- 7 files changed, 31 insertions(+), 24 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-3 dated 2015-10-05 and 0.1-4 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/gimme.R | 12 ++++++------ man/gimmeSEM.Rd | 2 +- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.1 dated 2015-10-12 and 6.1.1 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 7 ++++--- NEWS | 4 ++++ R/FormatNests.R | 2 +- R/STSRE_TSD.R | 8 ++++---- R/TRN_MHmcmc_p.R | 4 ++-- R/embryogrowth-package.R | 4 ++-- R/hist.NestsResult.R | 4 ++-- R/info.nests.R | 18 +++++++++--------- R/likelihoodR.R | 10 +++++----- R/nest.R | 2 +- R/plot.NestsResult.R | 10 +++++----- R/plotR.R | 8 ++++---- R/plotR_hist.R | 2 +- R/searchR.R | 10 +++++----- R/tsd_MHmcmc_p.R | 2 +- R/weightmaxentropy.R | 2 +- man/STSRE_TSD.Rd | 8 ++++---- man/embryogrowth-package.Rd | 4 ++-- man/nest.Rd | 2 +- 21 files changed, 82 insertions(+), 77 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between coda versions 0.17-1 dated 2015-03-03 and 0.18-1 dated 2015-10-16
CHANGELOG | 15 ++++++++++ DESCRIPTION | 16 ++++++----- MD5 | 20 +++++++------- NAMESPACE | 17 ++++++++--- R/codamenu.R | 16 ----------- R/mcextractor.R | 8 ++++- R/mcmclist.R | 80 +++++++++++++++++++++++++++++++++++--------------------- R/util.R | 3 -- data/line.rda |binary inst/AUTHORS | 15 +++++++++- man/cumuplot.Rd | 4 -- 11 files changed, 118 insertions(+), 76 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks.
Author: David Moriña (Centre for Research in Environmental Epidemiology, CREAL) and Albert Navarro (Universitat Autònoma de Barcelona)
Maintainer: David Moriña Soler <david.morina@uab.cat>
Diff between survsim versions 1.1.3 dated 2015-03-26 and 1.1.4 dated 2015-10-16
survsim-1.1.3/survsim/R/survsim-internal.R |only survsim-1.1.3/survsim/README.md |only survsim-1.1.4/survsim/DESCRIPTION | 11 +-- survsim-1.1.4/survsim/MD5 | 16 ++--- survsim-1.1.4/survsim/NAMESPACE | 8 +- survsim-1.1.4/survsim/R/crisk.ncens.sim.R | 85 +++++++++++++++++---------- survsim-1.1.4/survsim/man/crisk.sim.Rd | 4 - survsim-1.1.4/survsim/man/mult.ev.sim.Rd | 2 survsim-1.1.4/survsim/man/rec.ev.sim.Rd | 2 survsim-1.1.4/survsim/man/simple.surv.sim.Rd | 4 - 10 files changed, 79 insertions(+), 53 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.3 dated 2015-09-12 and 1.2.4 dated 2015-10-16
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/likelihood.R | 5 +++-- R/mnlogit.R | 2 ++ 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The HistData package provides a collection of small data sets
that are interesting and important in the history of statistics and data visualization.
The goal of the package is to make these available, both for instructional use
and for historical research. Some of these present interesting challenges for graphics
or analysis in R.
Author: Michael Friendly [aut, cre],
Stephane Dray [ctb],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.7-5 dated 2014-04-26 and 0.7-6 dated 2015-10-16
DESCRIPTION | 16 ++++---- MD5 | 92 +++++++++++++++++++++++----------------------- NEWS | 4 ++ data/Arbuthnot.RData |binary data/Armada.RData |only data/Bowley.RData |binary data/Cavendish.RData |binary data/ChestSizes.RData |binary data/CushnyPeebles.RData |binary data/CushnyPeeblesN.RData |binary data/Dactyl.RData |binary data/DrinksWages.RData |binary data/Fingerprints.RData |binary data/Galton.RData |binary data/GaltonFamilies.RData |binary data/Guerry.RData |binary data/Jevons.RData |binary data/Langren.all.RData |binary data/Langren1644.RData |binary data/Macdonell.RData |binary data/MacdonellDF.RData |binary data/Michelson.RData |binary data/MichelsonSets.RData |binary data/Minard.cities.RData |binary data/Minard.temp.RData |binary data/Minard.troops.RData |binary data/Nightingale.RData |binary data/OldMaps.RData |binary data/PearsonLee.RData |binary data/PolioTrials.RData |binary data/Prostitutes.RData |binary data/Pyx.RData |binary data/Quarrels.RData |binary data/Snow.deaths.RData |binary data/Snow.polygons.RData |binary data/Snow.pumps.RData |binary data/Snow.streets.RData |binary data/Wheat.RData |binary data/Wheat.monarchs.RData |binary data/Yeast.RData |binary data/YeastD.mat.RData |binary data/ZeaMays.RData |binary man/Armada.Rd |only man/Cavendish.Rd | 2 - man/HistData-package.Rd | 9 ++-- man/Michelson.Rd | 2 - man/PolioTrials.Rd | 2 - man/Snow.Rd | 7 ++- 48 files changed, 71 insertions(+), 63 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel hydraulics.
Provides functions for computing normal and critical depths, steady-state
water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 1.0 dated 2015-10-11 and 1.1 dated 2015-10-16
DESCRIPTION | 8 +-- MD5 | 26 +++++----- NAMESPACE | 2 R/graduallyvariedflow_v2.r | 7 ++ R/route_wave_v4.r | 1 inst/doc/quickstart.R | 2 inst/doc/quickstart.Rmd | 6 +- inst/doc/quickstart.html | 91 ++++++-------------------------------- inst/doc/technical-vignette.Rmd | 6 ++ inst/doc/technical-vignette.html | 6 ++ man/compute_profile.Rd | 4 + src/rivmech_characteristic_v7.cpp | 21 ++++++-- vignettes/quickstart.Rmd | 6 +- vignettes/technical-vignette.Rmd | 6 ++ 14 files changed, 83 insertions(+), 109 deletions(-)
Title: CAlibrating Penalities Using Slope HEuristics
Description: Calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics.
Author: Sylvain Arlot, Vincent Brault, Jean-Patrick Baudry, Cathy Maugis and Bertrand Michel
Maintainer: Vincent Brault <vincent.brault@agroparistech.fr>
Diff between capushe versions 1.0 dated 2012-02-17 and 1.1 dated 2015-10-16
capushe-1.0/capushe/main.R |only capushe-1.0/capushe/testsDev |only capushe-1.1/capushe/DESCRIPTION | 20 ++--- capushe-1.1/capushe/MD5 | 29 +++---- capushe-1.1/capushe/NAMESPACE | 43 ++++++----- capushe-1.1/capushe/R/DDSE.R | 6 - capushe-1.1/capushe/R/Djump.R | 109 ++++++++++++++++++++++++----- capushe-1.1/capushe/R/capushe.R | 99 ++++++++++++++++++++++---- capushe-1.1/capushe/R/prog.R | 4 - capushe-1.1/capushe/man/BICAICcapushe.Rd | 2 capushe-1.1/capushe/man/DDSE.Rd | 2 capushe-1.1/capushe/man/Djump.Rd | 32 +++++++- capushe-1.1/capushe/man/capushe-package.Rd | 4 - capushe-1.1/capushe/man/capushe.Rd | 15 +++ capushe-1.1/capushe/man/validation.Rd | 2 15 files changed, 276 insertions(+), 91 deletions(-)
Title: R Wrapper for the Bit.ly, Ow.ly and Goo.gl API
Description: Allows users accessing 'Bit.ly API' http://dev.bitly.com/ and retrieve many useful statistics. Additionally provides an experimental support of 'Ow.ly' http://ow.ly/api-docs and 'Goo.gl' http://goo.gl.
Author: John Malc [aut, cre] (@dmpe)
Maintainer: John Malc <cincenko@outlook.com>
Diff between RBitly versions 0.6.1 dated 2015-07-04 and 0.7.3 dated 2015-10-16
DESCRIPTION | 20 - MD5 | 92 ++++---- NAMESPACE | 9 NEWS | 20 + R/ApiKey.R | 113 ++++++++-- R/Domains.R | 4 R/Links.R | 210 +++++++++++++++++-- R/LinksMetrics.R | 67 ++++-- R/UserInfo.R | 22 -- R/UserMetrics.R | 24 +- README.md | 97 ++++----- build/vignette.rds |binary inst/doc/Tutorial.R | 53 +++- inst/doc/Tutorial.Rmd | 64 +++-- inst/doc/Tutorial.html | 134 ++++++++---- man/bitly_pro_domain.Rd | 2 man/link_Metrics_Clicks.Rd | 4 man/link_Metrics_Countries.Rd | 2 man/link_Metrics_Encoders.Rd | 2 man/link_Metrics_EncodersByCount.Rd | 2 man/link_Metrics_EncodersCount.Rd | 2 man/link_Metrics_Owly.Rd |only man/link_Metrics_Referrers.Rd | 2 man/link_Metrics_ReferrersByDomain.Rd | 2 man/link_Metrics_ReferringDomains.Rd | 2 man/links_Expand.Rd | 2 man/links_ExpandGoogl.Rd |only man/links_ExpandOwly.Rd |only man/links_Info.Rd | 2 man/links_InfoOwly.Rd |only man/links_Lookup.Rd | 2 man/links_Shorten.Rd | 9 man/links_ShortenGoogl.Rd |only man/links_ShortenOwly.Rd |only man/rbitlyApi.Rd | 24 +- man/rbitlyApi_up.Rd | 2 man/user_Info.Rd | 2 man/user_LinkHistory.Rd | 2 man/user_Metrics_Clicks.Rd | 2 man/user_Metrics_Countries.Rd | 2 man/user_Metrics_PopularLinks.Rd | 2 man/user_Metrics_Referrers.Rd | 2 man/user_Metrics_ReferringDomains.Rd | 2 man/user_Metrics_ShortenCounts.Rd | 2 man/user_TrackingDomains.Rd | 2 tests/testthat/test-Domains.R | 2 tests/testthat/test-Links.R | 39 +++ tests/testthat/test-UserInfo_LinkMetrics.R | 7 tests/testthat/test-UserMetrics.R | 4 vignettes/Tutorial.Rmd | 312 +++++++++++++++-------------- 50 files changed, 918 insertions(+), 454 deletions(-)
Title: Preprocessing of Aligned Sequences from HTS Analyses
Description: Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil@mssm.edu>
Diff between Pasha versions 0.99.16 dated 2015-08-01 and 0.99.18 dated 2015-10-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pipelineChipSeq.R | 30 ++++++++++++++---------------- inst/doc/Pasha.pdf |binary src/MultireadCSEMBcTree.h | 2 +- tests/test_Pasha.Rout.save | 25 ++++++++++++++++--------- 6 files changed, 40 insertions(+), 35 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.4 dated 2015-09-02 and 1.4.1 dated 2015-10-16
DESCRIPTION | 14 ++++--- MD5 | 42 +++++++++++++-------- R/Fst.R | 24 +++++++++--- R/GenDist.R |only R/MCreml.R | 59 +++++++++++++++++++++++++++++- R/RcppExports.R | 4 ++ R/gibbs.R | 26 +++++++++++++ R/gwas.R | 49 ++++++++++++++++--------- R/gwas2.R | 57 ++++++++++++++--------------- R/manhattan.R | 4 +- R/reml.R | 100 ++++++++++++++++++++++++++-------------------------- R/wgr.R |only build |only inst/doc |only man/Internals.Rd | 28 +++++++++++++- man/NAM-package.Rd | 6 +-- man/gibbs.Rd | 1 man/reference.Rd | 66 +++++++++++++++++----------------- man/reml.Rd | 9 ++++ man/snpQC.Rd | 2 - man/tpod.Rd | 41 ++++++++++----------- man/wgr.Rd |only src/KMUP.cpp |only src/RcppExports.cpp | 18 +++++++++ vignettes |only 25 files changed, 360 insertions(+), 190 deletions(-)
Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB), pre-formatted for general analysis and genome-wide association analysis using the NAM package.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between SoyNAM versions 1.0 dated 2015-07-29 and 1.1 dated 2015-10-15
SoyNAM-1.0/SoyNAM/R/BLUP.R |only SoyNAM-1.0/SoyNAM/man/BLUP.Rd |only SoyNAM-1.0/SoyNAM/man/ENV.Rd |only SoyNAM-1.1/SoyNAM/DESCRIPTION | 10 +++++----- SoyNAM-1.1/SoyNAM/MD5 | 17 +++++++++-------- SoyNAM-1.1/SoyNAM/R/BLUPs.R |only SoyNAM-1.1/SoyNAM/data/datalist | 1 + SoyNAM-1.1/SoyNAM/data/soybase.RData |only SoyNAM-1.1/SoyNAM/data/soynam.RData |binary SoyNAM-1.1/SoyNAM/man/BLUP1.Rd |only SoyNAM-1.1/SoyNAM/man/BLUP2.Rd |only SoyNAM-1.1/SoyNAM/man/SoyNAM-package.Rd | 8 ++++---- SoyNAM-1.1/SoyNAM/man/soynam.Rd | 20 ++++++++++++++++---- 13 files changed, 35 insertions(+), 21 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function
fitting with an emphasis on splines, spatial data and spatial
statistics. The major methods include cubic, and thin plate splines,
Kriging and compact covariances for large data sets. The splines and
Kriging methods are supporting by functions that can determine the
smoothing parameter (nugget and sill variance) by cross validation
and also by restricted maximum likelihood. For Kriging there is
an easy to function that also estimates the correlation scale (range).
A major feature is that
any covariance function implemented in R and following a simple fields
format can be used for spatial prediction. There are also many useful
functions for plotting and
working with spatial data as images. This package also contains an
implementation of sparse matrix methods for large spatial data sets and
currently requires the sparse matrix (spam) package.
Use help(fields) to get started and for an
overview. The fields source code is deliberately commented and
provides useful explanations of numerical details in addition to the
manual pages. The commented source code can be viewed by expanding the
source code .tar.gz file and looking in R subdirectory.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between fields versions 8.2-1 dated 2015-02-28 and 8.3-5 dated 2015-10-15
fields-8.2-1/fields/R/ozone.R |only fields-8.2-1/fields/R/vgram.R |only fields-8.2-1/fields/man/predict.surface.Rd |only fields-8.3-5/fields/DESCRIPTION | 14 fields-8.3-5/fields/MD5 | 196 ++++--- fields-8.3-5/fields/NAMESPACE | 16 fields-8.3-5/fields/R/ChicagoO3.R |only fields-8.3-5/fields/R/ExponentialUpper.R |only fields-8.3-5/fields/R/Krig.family.R | 10 fields-8.3-5/fields/R/MLESpatialProcess.R | 356 +++++++++----- fields-8.3-5/fields/R/as.image.R | 17 fields-8.3-5/fields/R/compactToMat.R |only fields-8.3-5/fields/R/cubic.cov.R | 9 fields-8.3-5/fields/R/exp.cov.R | 123 +++- fields-8.3-5/fields/R/exp.simple.cov.R | 7 fields-8.3-5/fields/R/image.family.R | 7 fields-8.3-5/fields/R/mKrig.MLE.R | 235 +++++---- fields-8.3-5/fields/R/mKrig.MLE.joint.R |only fields-8.3-5/fields/R/mKrig.R |only fields-8.3-5/fields/R/mKrig.family.R | 180 ------- fields-8.3-5/fields/R/predict.Krig.R | 24 fields-8.3-5/fields/R/predictSurface.Krig.R |only fields-8.3-5/fields/R/predictSurface.family.R | 5 fields-8.3-5/fields/R/quilt.plot.R | 15 fields-8.3-5/fields/R/rad.cov.R | 5 fields-8.3-5/fields/R/rdist.R | 40 - fields-8.3-5/fields/R/rdist.earth.R | 4 fields-8.3-5/fields/R/rdist.earth.vec.R |only fields-8.3-5/fields/R/rdist.vec.R |only fields-8.3-5/fields/R/spatialProcess.R | 8 fields-8.3-5/fields/R/stationary.cov.R | 205 ++++---- fields-8.3-5/fields/R/stationary.taper.cov.R | 4 fields-8.3-5/fields/R/supportsArg.R |only fields-8.3-5/fields/R/unrollZGrid.R |only fields-8.3-5/fields/R/vgram.family.R |only fields-8.3-5/fields/R/vgram.matrix.R | 36 - fields-8.3-5/fields/R/wendland.family.R | 12 fields-8.3-5/fields/README |only fields-8.3-5/fields/data/COmonthlyMet.rda |binary fields-8.3-5/fields/man/CO.Rd | 14 fields-8.3-5/fields/man/CovarianceUpper.Rd |only fields-8.3-5/fields/man/Krig.Amatrix.Rd | 6 fields-8.3-5/fields/man/Krig.Rd | 12 fields-8.3-5/fields/man/Krig.engine.default.Rd | 4 fields-8.3-5/fields/man/MLESpatialProcess.Rd | 204 +++++--- fields-8.3-5/fields/man/Tps.Rd | 61 +- fields-8.3-5/fields/man/as.image.Rd | 6 fields-8.3-5/fields/man/compactToMat.Rd |only fields-8.3-5/fields/man/exp.cov.Rd | 44 + fields-8.3-5/fields/man/fields-internal.Rd | 10 fields-8.3-5/fields/man/gcv.Krig.Rd | 2 fields-8.3-5/fields/man/grid.list.Rd | 20 fields-8.3-5/fields/man/image.plot.Rd | 18 fields-8.3-5/fields/man/mKrig.MLE.Rd | 222 ++++++-- fields-8.3-5/fields/man/mKrig.Rd | 193 ++++--- fields-8.3-5/fields/man/ozone.Rd | 13 fields-8.3-5/fields/man/plot.Krig.Rd | 4 fields-8.3-5/fields/man/predict.Krig.Rd | 4 fields-8.3-5/fields/man/predictSE.Krig.Rd | 2 fields-8.3-5/fields/man/predictSurface.Rd | 51 +- fields-8.3-5/fields/man/print.Krig.Rd | 2 fields-8.3-5/fields/man/quilt.plot.Rd | 5 fields-8.3-5/fields/man/rdist.Rd | 35 + fields-8.3-5/fields/man/rdist.earth.Rd | 24 fields-8.3-5/fields/man/spatialProcess.Rd | 7 fields-8.3-5/fields/man/summary.Krig.Rd | 2 fields-8.3-5/fields/man/supportsArg.Rd |only fields-8.3-5/fields/man/surface.Krig.Rd | 2 fields-8.3-5/fields/man/transformx.Rd | 2 fields-8.3-5/fields/man/vgram.Rd | 95 +++ fields-8.3-5/fields/src/ExponentialUpperC.c |only fields-8.3-5/fields/src/addToDiagC.c |only fields-8.3-5/fields/src/compactToMatC.c |only fields-8.3-5/fields/src/expfnC.c |only fields-8.3-5/fields/src/multebC.c |only fields-8.3-5/fields/src/rdist.f |only fields-8.3-5/fields/src/rdistC.c |only fields-8.3-5/fields/tests/Krig.Z.test.R | 4 fields-8.3-5/fields/tests/Krig.Z.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.se.W.Rout.save | 14 fields-8.3-5/fields/tests/Krig.se.grid.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.se.test.R | 8 fields-8.3-5/fields/tests/Krig.se.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.test.R | 26 - fields-8.3-5/fields/tests/Krig.test.Rout.save | 14 fields-8.3-5/fields/tests/Krig.test.W.Rout.save | 14 fields-8.3-5/fields/tests/KrigGCVREML.test.R | 25 fields-8.3-5/fields/tests/KrigGCVREML.test.Rout.save | 21 fields-8.3-5/fields/tests/Likelihood.test.Rout.save | 14 fields-8.3-5/fields/tests/REMLest.test.Rout.save | 14 fields-8.3-5/fields/tests/Tps.test.R | 6 fields-8.3-5/fields/tests/Tps.test.Rout.save | 14 fields-8.3-5/fields/tests/Wend.test.Rout.save | 14 fields-8.3-5/fields/tests/cov.test.Rout.save | 14 fields-8.3-5/fields/tests/derivative.test.Rout.save | 14 fields-8.3-5/fields/tests/diag.multiply.test.Rout.save | 14 fields-8.3-5/fields/tests/diagonal2.test.Rout.save | 14 fields-8.3-5/fields/tests/evlpoly.test.Rout.save | 14 fields-8.3-5/fields/tests/fastTpsPredict.test.Rout.save |only fields-8.3-5/fields/tests/mKrig.MLE.test.R |only fields-8.3-5/fields/tests/mKrig.MLE.test.Rout.save |only fields-8.3-5/fields/tests/mKrig.Z.Rout.save | 14 fields-8.3-5/fields/tests/mKrig.parameters.test.Rout.save | 14 fields-8.3-5/fields/tests/mKrig.se.test.R | 18 fields-8.3-5/fields/tests/mKrig.se.test.Rout.save | 14 fields-8.3-5/fields/tests/mKrig.test.R | 157 ++++-- fields-8.3-5/fields/tests/mKrig.test.Rout.save | 33 + fields-8.3-5/fields/tests/misc.test.Rout.save | 14 fields-8.3-5/fields/tests/spam.test.Rout.save | 14 fields-8.3-5/fields/tests/sreg.test.Rout.save | 14 fields-8.3-5/fields/tests/test.cov.R |only fields-8.3-5/fields/tests/test.cov.Rout.save |only fields-8.3-5/fields/tests/vgram.test.R | 15 fields-8.3-5/fields/tests/vgram.test.Rout.save | 14 114 files changed, 2059 insertions(+), 1154 deletions(-)
Title: Sparse and Non-Sparse Partial Robust M Regression and
Classification
Description: Robust dimension reduction methods for regression and discriminant analysis are implemented that yield estimates with a partial least squares alike interpretability. Partial robust M regression (PRM) is robust to both vertical outliers and leverage points. Sparse partial robust M regression (SPRM) is a related robust method with sparse coefficient estimate, and therefore with intrinsic variable selection. For bianry classification related discriminant methods are PRM-DA and SPRM-DA.
Author: Sven Serneels, BASF Corp and Irene Hoffmann
Maintainer: Irene Hoffmann <irene.hoffmann@tuwien.ac.at>
Diff between sprm versions 1.1 dated 2014-12-10 and 1.2 dated 2015-10-15
DESCRIPTION | 16 ++-- MD5 | 89 +++++++++++++++++--------- NAMESPACE | 36 ++++++++++ R/balancedfolds.R |only R/biplot.prm.R | 10 +- R/biplot.prmda.R |only R/biplot.sprm.R | 6 - R/biplot.sprmda.R |only R/biweight.R |only R/daprpr.R | 4 - R/dbshdy.R | 2 R/int_weight.R |only R/intervals.prm.R | 2 R/intervals.sprm.R | 2 R/ldafitfun.R |only R/nipls.R | 5 - R/plot.prm.R | 25 ++++++- R/plot.sprm.R | 19 +++++ R/predict.prm.R | 4 - R/predict.prmda.R |only R/predict.sprm.R | 3 R/predict.sprmda.R |only R/print.prmda.R |only R/print.sprmda.R |only R/prmda.R |only R/prmdaCV.R |only R/prms.R | 89 ++++++++++---------------- R/prmsCV.R | 34 ++++++---- R/snipls.R | 22 +++--- R/sprmda.R |only R/sprmdaCV.R |only R/sprms.R | 167 +++++++++++++++++++++++--------------------------- R/sprmsCV.R | 13 ++- R/summary.prmda.R |only R/summary.sprmda.R |only R/weig.R |only man/biplot.prm.Rd | 9 +- man/biplot.prmda.Rd |only man/biplot.sprm.Rd | 11 ++- man/biplot.sprmda.Rd |only man/plot.prm.Rd | 8 +- man/plot.sprm.Rd | 6 - man/predict.prm.Rd | 10 -- man/predict.prmda.Rd |only man/predict.sprm.Rd | 2 man/predict.sprmda.Rd |only man/prmda.Rd |only man/prmdaCV.Rd |only man/prms.Rd | 5 - man/prmsCV.Rd | 6 - man/sprm-package.Rd | 12 ++- man/sprmda.Rd |only man/sprmdaCV.Rd |only man/sprms.Rd | 5 - man/sprmsCV.Rd | 14 ++-- man/summary.prm.Rd | 2 man/summary.prmda.Rd |only man/summary.sprm.Rd | 2 man/summary.sprmda.Rd |only 59 files changed, 369 insertions(+), 271 deletions(-)
Title: Choi and Hall Style Data Sharpening
Description: Functions for use in perturbing data prior to use of nonparametric smoothers
and clustering.
Author: Douglas Woolford and John Braun
Maintainer: John Braun <braun@stats.uwo.ca>
Diff between CHsharp versions 0.3 dated 2012-11-05 and 0.4 dated 2015-10-15
DESCRIPTION | 23 ++++++++++++----------- MD5 | 20 +++++++++++++++++--- NAMESPACE | 9 ++++----- R/MISE.R |only R/SecondDerivativePenalty.R |only R/lambda.R |only R/numericalDerivative.R |only R/penlocreg.R |only R/pllr.R |only R/sharpen.R |only data/d.rda |binary man/MISE.Rd |only man/SecondDerivativePenalty.Rd |only man/lambda.Rd |only man/numericalDerivative.Rd |only man/penlocreg.Rd |only man/pllr.Rd |only man/sharpen.Rd |only 18 files changed, 33 insertions(+), 19 deletions(-)
More information about easyVerification at CRAN
Permanent link
Title: World Population Prospects 2015
Description: Provides data from the United Nation's World Population Prospects 2015.
Author: Population Division, Department of Economic and Social Affairs, United Nations.
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wpp2015 versions 1.0-0 dated 2015-08-08 and 1.0-1 dated 2015-10-15
ChangeLog | 4 DESCRIPTION | 8 MD5 | 8 data/UNlocations.txt | 550 ++++++++++++++++++++++++------------------------- man/wpp2015-package.Rd | 4 5 files changed, 289 insertions(+), 285 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@isped.u-bordeaux2.fr>
Diff between VSURF versions 1.0.1 dated 2015-10-12 and 1.0.2 dated 2015-10-15
DESCRIPTION | 10 +++--- MD5 | 10 ++++-- NEWS | 7 ++++ tests/testthat/case_win32_test_iris.R |only tests/testthat/case_win32b_test_orange.R |only tests/testthat/test_iris.R | 46 +++++++------------------------ tests/testthat/test_orange.R | 39 +++++--------------------- 7 files changed, 36 insertions(+), 76 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.13-0 dated 2015-08-29 and 1.14-0 dated 2015-10-15
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- R/designMatrices_aux2.R | 6 ++++-- R/stud_prior.R | 2 +- R/tam.pv.R | 7 ++++--- inst/NEWS | 24 ++++++++++++++++++++++++ man/TAM-package.Rd | 3 +-- man/tam.pv.Rd | 2 +- 8 files changed, 47 insertions(+), 22 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized ML estimators for the
precision matrix as well as supporting functions to employ these estimators
in a graphical modeling setting.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 1.4 dated 2014-11-27 and 2.0 dated 2015-10-15
DESCRIPTION | 22 MD5 | 96 NAMESPACE | 32 R/RcppExports.R |only R/rags2ridges.R | 6392 +++++++++++++++++++++------------------ R/rags2ridgesFused.R |only R/rags2ridgesMisc.R |only README.md |only inst/CITATION | 74 inst/NEWS.Rd |only man/GGMblockNullPenalty.Rd | 34 man/GGMblockTest.Rd | 41 man/GGMmutualInfo.Rd |only man/GGMnetworkStats.Rd | 16 man/GGMnetworkStats.fused.Rd |only man/GGMpathStats.Rd | 54 man/GGMpathStats.fused.Rd |only man/KLdiv.Rd | 20 man/KLdiv.fused.Rd |only man/NLL.Rd |only man/Ugraph.Rd | 41 man/adjacentMat.Rd | 9 man/armaRidgeP.Rd |only man/conditionNumberPlot.Rd | 36 man/covML.Rd | 10 man/covMLknown.Rd |only man/createS.Rd |only man/default.penalty.Rd |only man/default.target.Rd | 20 man/default.target.fused.Rd |only man/edgeHeat.Rd | 14 man/evaluateS.Rd | 12 man/evaluateSfit.Rd | 24 man/fullMontyS.Rd | 20 man/fused.test.Rd |only man/getKEGGPathway.Rd |only man/is.Xlist.Rd |only man/isSymmetricPD.Rd |only man/kegg.target.Rd |only man/loss.Rd | 26 man/optPenalty.LOOCV.Rd | 31 man/optPenalty.LOOCVauto.Rd | 18 man/optPenalty.aLOOCV.Rd | 41 man/optPenalty.fused.Rd |only man/pcor.Rd | 8 man/plot.ptest.Rd |only man/pooledS.Rd |only man/print.optPenaltyFusedGrid.Rd |only man/print.ptest.Rd |only man/rags2ridges-package.Rd | 94 man/ridgeP.Rd |only man/ridgeP.fused.Rd |only man/ridgePathS.Rd | 35 man/ridgeS.Rd | 43 man/rmvnormal.Rd |only man/sparsify.Rd | 20 man/sparsify.fused.Rd |only src |only tests |only 59 files changed, 4006 insertions(+), 3277 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Pablo Barberá [ctb],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.8.4-2 dated 2015-09-09 and 0.8.6-0 dated 2015-10-15
DESCRIPTION | 11 MD5 | 63 - NAMESPACE | 5 NEWS | 30 R/corpus.R | 21 R/dfm-classes.R | 137 ++ R/dfm-main.R | 123 +- R/dfm-methods.R | 32 R/dictionaries.R | 51 + R/kwic.R | 244 ++++- R/ngrams.R | 131 -- R/settings.R | 2 R/stopwords.R | 242 ++++- R/textfile.R | 15 R/toLower.R | 2 R/tokenize.R | 80 - R/tokenize_outtakes.R |only R/wordstem.R | 24 inst/doc/development-plans.html | 842 ++++++++++-------- inst/doc/quickstart.Rmd | 1 inst/doc/quickstart.html | 1833 ++++++++++++++++++++++------------------ man/corpus.Rd | 8 man/dfm.Rd | 59 - man/dictionary.Rd | 2 man/head.dfm.Rd |only man/kwic.Rd | 49 - man/ngrams.Rd | 9 man/print.dfm.Rd | 19 man/print.tokenizedTexts.Rd |only man/selectFeatures.Rd | 34 man/textfile.Rd | 2 man/tokenize.Rd | 9 man/weight.Rd | 17 vignettes/quickstart.Rmd | 1 34 files changed, 2508 insertions(+), 1590 deletions(-)
Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala <teelaa@utu.fi>
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.4 dated 2015-08-04 and 0.9.4-2 dated 2015-10-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/introduction.Rnw | 4 ++-- man/hamlet-package.Rd | 4 ++-- vignettes/introduction.Rnw | 4 ++-- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Tools for Cycling Data Analysis
Description: A suite of functions for analysing cycling data.
Author: Jordan Mackie [aut, cre]
Maintainer: Jordan Mackie <jmackie@protonmail.com>
Diff between cycleRtools versions 1.0.2 dated 2015-10-14 and 1.0.3 dated 2015-10-15
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++----------- NAMESPACE | 3 +- NEWS | 4 +++ R/Wbal.R | 8 ------- R/convert_time.R | 48 ++++++++++++++++++++++++++++------------------ R/download_elev_data.R | 7 ------ R/elevation_correct.R | 3 +- man/Wbal.Rd | 8 ------- man/convert_time.Rd | 20 +++++++++---------- man/download_elev_data.Rd | 7 ------ man/elevation_correct.Rd | 2 + 12 files changed, 66 insertions(+), 72 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.5-0 dated 2015-10-08 and 1.6-0 dated 2015-10-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/BIFIE.data.jack.R | 19 +++++++++---------- R/BIFIE.univar.R | 2 +- R/BIFIE.univar.test.R | 28 +++++++++++++++++++++++++++- R/BIFIE_table_multiple_groupings.R | 2 +- inst/NEWS | 14 ++++++++++++++ man/BIFIE.univar.test.Rd | 32 +++++++++++++++++++++++++++++++- man/BIFIEsurvey-package.Rd | 7 ++++++- 9 files changed, 101 insertions(+), 27 deletions(-)
Title: Basic Wireless Communications Simulation
Description: A communications simulation package supporting common wireless modulation
formats including BPSK, QPSK, 8-PSK, 16-PSK, 16-QAM and 64-QAM. The package includes AWGN
noise generation, and raised cosine and square root raised cosine pulse shaping. It also
includes convenience functions for plotting constellation diagrams, density plots, stem
plots and eye diagrams. Together these functions enable the evaluation of bit error and
symbol error rates, evaluation of pulse shaping and inter-symbol interference and support
visualization of the respective signals and noise in a variety of formats.
Author: Alberto Gutierrez [aut, cre]
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Diff between rwirelesscom versions 1.3 dated 2015-09-11 and 1.4.2 dated 2015-10-15
DESCRIPTION | 26 +++-- MD5 | 50 ++++++----- NAMESPACE | 15 +++ R/RcppExports.R |only R/rwirelesscom.R | 216 +++++++++++++++++++++++++++++++++++++++---------- man/eyediagram.Rd |only man/f16pskdemod.Rd | 16 +-- man/f16pskmod.Rd | 25 +++-- man/f16qamdemod.Rd | 16 +-- man/f16qammod.Rd | 25 +++-- man/f64qamdemod.Rd | 16 +-- man/f64qammod.Rd | 25 +++-- man/f8pskdemod.Rd | 16 +-- man/f8pskmod.Rd | 25 +++-- man/fNo.Rd | 16 +-- man/fbpskdemod.Rd | 16 +-- man/fbpskmod.Rd | 25 +++-- man/fqpskdemod.Rd | 16 +-- man/fqpskmod.Rd | 19 +--- man/iqdensityplot.Rd | 18 ++-- man/iqscatterplot.Rd | 16 +-- man/rcosine.Rd |only man/rwirelesscom.Rd | 17 ++- man/sinc.Rd |only man/sqrtrcosine.Rd |only man/stemplot.Rd |only src |only tests/testthat.R | 2 tests/testthat/test1.R | 104 ++++++++++++++++++++--- 29 files changed, 491 insertions(+), 229 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between PSCBS versions 0.45.1 dated 2015-09-17 and 0.50.0 dated 2015-10-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 9 +++++++++ R/segmentByPairedPSCBS.R | 15 +++++---------- inst/doc/CBS.pdf |binary inst/doc/PairedPSCBS.pdf |binary man/segmentByPairedPSCBS.Rd | 8 ++------ 7 files changed, 27 insertions(+), 27 deletions(-)
Title: Tables so Beautifully Fine-Tuned You Will Believe It's Magic
Description: The introduction of the broom package has made converting model objects into data
frames as simple as a single function. While the broom package focuses on providing tidy
data frames that can be used in advanced analysis, it deliberately stops short of providing
functionality for reporting models in publication-ready tables. pixiedust provides this
functionality with a programming interface intended to be similar to ggplot2's system of
layers with fine tuned control over each cell of the table. Options for output include
printing to the console and to the common markdown formats (markdown, HTML, and LaTeX).
With a little pixiedust (and happy thoughts) tables can really fly.
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <nutter@battelle.org>
Diff between pixiedust versions 0.1.1 dated 2015-08-03 and 0.5.0 dated 2015-10-15
pixiedust-0.1.1/pixiedust/R/add_sprinkles.R |only pixiedust-0.1.1/pixiedust/R/sprinkles.R |only pixiedust-0.1.1/pixiedust/man/add_sprinkles.Rd |only pixiedust-0.1.1/pixiedust/man/sprinkles.Rd |only pixiedust-0.5.0/pixiedust/DESCRIPTION | 13 pixiedust-0.5.0/pixiedust/LICENSE | 6 pixiedust-0.5.0/pixiedust/MD5 | 107 pixiedust-0.5.0/pixiedust/NAMESPACE | 69 pixiedust-0.5.0/pixiedust/NEWS | 252 pixiedust-0.5.0/pixiedust/R/as.data.frame.dust.R |only pixiedust-0.5.0/pixiedust/R/chain.R | 28 pixiedust-0.5.0/pixiedust/R/dust.R | 414 - pixiedust-0.5.0/pixiedust/R/glance_foot.R |only pixiedust-0.5.0/pixiedust/R/medley.R |only pixiedust-0.5.0/pixiedust/R/perform_function.R | 62 pixiedust-0.5.0/pixiedust/R/pixiedust-pkg.R |only pixiedust-0.5.0/pixiedust/R/print.dust.R | 70 pixiedust-0.5.0/pixiedust/R/print_dust_console.R | 153 pixiedust-0.5.0/pixiedust/R/print_dust_html.R | 322 - pixiedust-0.5.0/pixiedust/R/print_dust_latex.R |only pixiedust-0.5.0/pixiedust/R/print_dust_markdown.R | 190 pixiedust-0.5.0/pixiedust/R/pvalString.R | 84 pixiedust-0.5.0/pixiedust/R/redust.R |only pixiedust-0.5.0/pixiedust/R/sprinkle.R |only pixiedust-0.5.0/pixiedust/R/sprinkle_colnames.R | 175 pixiedust-0.5.0/pixiedust/R/sprinkle_print_method.R |only pixiedust-0.5.0/pixiedust/R/sprinkle_table.R |only pixiedust-0.5.0/pixiedust/R/tidy_levels_labels.R |only pixiedust-0.5.0/pixiedust/R/zzz.R | 16 pixiedust-0.5.0/pixiedust/README.md | 432 - pixiedust-0.5.0/pixiedust/build/vignette.rds |binary pixiedust-0.5.0/pixiedust/inst/doc/advancedMagic.R |only pixiedust-0.5.0/pixiedust/inst/doc/advancedMagic.Rmd |only pixiedust-0.5.0/pixiedust/inst/doc/advancedMagic.html |only pixiedust-0.5.0/pixiedust/inst/doc/pixiedust.R | 114 pixiedust-0.5.0/pixiedust/inst/doc/pixiedust.Rmd | 556 +- pixiedust-0.5.0/pixiedust/inst/doc/pixiedust.html | 2736 ++-------- pixiedust-0.5.0/pixiedust/inst/doc/sprinkles.R | 10 pixiedust-0.5.0/pixiedust/inst/doc/sprinkles.Rmd | 108 pixiedust-0.5.0/pixiedust/inst/doc/sprinkles.html | 525 - pixiedust-0.5.0/pixiedust/inst/sprinkles.csv | 57 pixiedust-0.5.0/pixiedust/man/as.data.frame.dust.Rd |only pixiedust-0.5.0/pixiedust/man/chain.Rd | 36 pixiedust-0.5.0/pixiedust/man/dust.Rd | 214 pixiedust-0.5.0/pixiedust/man/glance_foot.Rd |only pixiedust-0.5.0/pixiedust/man/medley.Rd |only pixiedust-0.5.0/pixiedust/man/pixiedust.Rd |only pixiedust-0.5.0/pixiedust/man/print.dust.Rd | 52 pixiedust-0.5.0/pixiedust/man/pvalString.Rd | 100 pixiedust-0.5.0/pixiedust/man/sprinkle.Rd |only pixiedust-0.5.0/pixiedust/man/sprinkle_colnames.Rd | 89 pixiedust-0.5.0/pixiedust/man/tidy_levels_labels.Rd |only pixiedust-0.5.0/pixiedust/tests/testthat.R | 6 pixiedust-0.5.0/pixiedust/tests/testthat/test-as.data.frame.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-dust.R | 124 pixiedust-0.5.0/pixiedust/tests/testthat/test-glance_foot.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-medley.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-perform_function.R | 48 pixiedust-0.5.0/pixiedust/tests/testthat/test-print.dust.R | 212 pixiedust-0.5.0/pixiedust/tests/testthat/test-print_dust_methods.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-pvalString.R | 26 pixiedust-0.5.0/pixiedust/tests/testthat/test-redust.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-roundSafe.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-sprinkle_colnames.R | 56 pixiedust-0.5.0/pixiedust/tests/testthat/test-sprinkle_table.R |only pixiedust-0.5.0/pixiedust/tests/testthat/test-sprinkles.R | 944 +-- pixiedust-0.5.0/pixiedust/tests/testthat/test-tidy_label_level.R |only pixiedust-0.5.0/pixiedust/vignettes/advancedMagic.Rmd |only pixiedust-0.5.0/pixiedust/vignettes/pixiedust.Rmd | 556 +- pixiedust-0.5.0/pixiedust/vignettes/pixiedust_in_latex.Rmd |only pixiedust-0.5.0/pixiedust/vignettes/sprinkles.Rmd | 108 71 files changed, 4256 insertions(+), 4814 deletions(-)
Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between ndtv versions 0.6.1 dated 2015-04-30 and 0.7.0 dated 2015-10-15
ChangeLog | 11 ++ DESCRIPTION | 17 +-- MD5 | 59 +++++++----- NAMESPACE | 14 ++ R/export.movie.R | 54 ++++++++--- R/layout_centering.R | 10 +- R/ndtvAnimationWidget.R |only R/render.d3_animation.R | 125 ++++++++++++++++---------- R/specialEffects.R |only R/tea_utils.R | 4 R/timecube.R |only R/transmissionTimeline.R |only build/vignette.rds |binary inst/doc/ndtv.R | 80 +++++++++++----- inst/doc/ndtv.Rnw | 44 +++++++-- inst/doc/ndtv.pdf |binary inst/htmlwidgets |only inst/javascript/ndtv-d3/src/css/styles.css | 1 inst/javascript/ndtv-d3/src/js/ndtv-d3.js | 16 +-- inst/javascript/ndtv-d3/src/lib/d3.slider.css | 1 man/effectFun.Rd |only man/install.ffmpeg.Rd | 4 man/ndtv-package.Rd | 2 man/render.animation.Rd | 11 +- man/render.d3movie.Rd | 16 ++- man/timePrism.Rd |only man/timeline.Rd | 4 man/toy_epi_sim.Rd | 2 man/transmissionTimeline.Rd |only tests/d3_animation_tests.R | 6 + tests/effects_tests.R |only tests/networkAnimationTest.R | 2 tests/timeline_test.R | 7 + tests/transmissionTimelineTests.R |only vignettes/ndtv.Rnw | 44 +++++++-- 35 files changed, 369 insertions(+), 165 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [cre, aut],
Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.6 dated 2015-07-16 and 1.7 dated 2015-10-15
geigen-1.6/geigen/inst/CITATION |only geigen-1.7/geigen/DESCRIPTION | 20 ++++++++++++-------- geigen-1.7/geigen/MD5 | 13 ++++++------- geigen-1.7/geigen/NEWS | 6 ++++++ geigen-1.7/geigen/R/gsvd.R | 2 ++ geigen-1.7/geigen/man/geigen-package.Rd | 2 +- geigen-1.7/geigen/man/geigen.Rd | 2 +- geigen-1.7/geigen/man/gsvd.Rd | 8 ++++---- 8 files changed, 32 insertions(+), 21 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.1 dated 2015-10-05 and 0.8.2 dated 2015-10-14
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS | 11 ++- R/MulticoreFuture.R | 2 R/futureAssign.R | 2 R/globals.R | 62 ++++++++++++++--- demo/mandelbrot.R | 4 - man/eager.Rd | 136 +++++++++++++++++++-------------------- man/multicore.Rd | 166 ++++++++++++++++++++++++------------------------ tests/demo.R |only tests/dotdotdot.R | 6 + tests/futureAssign_OP.R | 6 - tests/globals,tricky.R |only 13 files changed, 240 insertions(+), 185 deletions(-)
Title: Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>
Diff between ClusterStability versions 1.0.1 dated 2015-09-15 and 1.0.2 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/ClusterStability.R | 4 ++-- man/ClusterStability-package.Rd | 4 ++-- man/ClusterStability.Rd | 4 ++-- man/ClusterStability_exact.Rd | 4 ++-- 7 files changed, 24 insertions(+), 18 deletions(-)
More information about ClusterStability at CRAN
Permanent link
Title: Applies Multiclass AdaBoost.M1, SAMME and Bagging
Description: It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging
algorithm using classification trees as individual classifiers. Once these classifiers have been
trained, they can be used to predict on new data. Also, cross validation estimation of the error can
be done. Since version 2.0 the function margins() is available to calculate the margins for these
classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument
of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu
et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as
a function of the number of iterations. In addition, the ensembles can be pruned using the option
'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probability of
each class for observations can be obtained. Version 3.1 modifies the relative importance measure
to take into account the gain of the Gini index given by a variable in each tree and the weights of
these trees. Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo
and Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover, three new plots are also
available importanceplot(), plot.errorevol() and plot.margins(). Version 4.1 allows to predict on
unlabeled data.
Author: Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from Li Guo
Maintainer: Esteban Alfaro <Esteban.Alfaro@uclm.es>
Diff between adabag versions 4.0 dated 2014-12-21 and 4.1 dated 2015-10-14
DESCRIPTION | 23 ++++++++++---------- MD5 | 38 ++++++++++++++++----------------- NAMESPACE | 4 +++ R/adaboost.M1.R | 28 ++++++++++++++++++------ R/bagging.R | 29 +++++++++++++++++++++---- R/errorevol.R | 8 ++++--- R/predict.bagging.R | 41 +++++++++++++++++++++--------------- R/predict.boosting.R | 30 ++++++++++++++++++++------ R/select.R | 8 +++---- man/MarginOrderedPruning.Bagging.rd | 3 +- man/adabag-internal.Rd | 2 - man/adabag-package.Rd | 39 ++++++++++++++++++++-------------- man/bagging.Rd | 5 ++-- man/boosting.Rd | 5 ++-- man/errorevol.rd | 2 - man/margins.Rd | 2 - man/plot.errorevol.rd | 2 - man/plot.margins.rd | 2 - man/predict.bagging.Rd | 4 +-- man/predict.boosting.Rd | 4 +-- 20 files changed, 176 insertions(+), 103 deletions(-)
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.3 dated 2015-06-26 and 2.4 dated 2015-10-14
DESCRIPTION | 12 ++- MD5 | 31 +++++---- NAMESPACE | 9 ++ NEWS | 7 ++ R/itreemap.R | 9 +- R/pkg.R | 4 - R/tmAggregate.R | 32 +++++++-- R/tmColorsLegend.R | 6 - R/tmGenerateRect.R | 6 - R/treemap.R | 160 ++++++++++++++++++++++++++++++++++++------------- R/value2col.R | 71 +++++++++++++-------- build |only inst |only man/itreemap.Rd | 5 + man/treemap-package.Rd | 4 - man/treemap.Rd | 41 +++++++++--- vignettes |only 17 files changed, 277 insertions(+), 120 deletions(-)
Title: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Description: Interface to the API for 'TreeBASE' (http://treebase.org)
from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic
trees (of species, population, or genes) and the data used to create
them.
Author: Carl Boettiger [aut, cre],
Duncan Temple Lang [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between treebase versions 0.1.1 dated 2015-06-16 and 0.1.2 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 4 +--- NEWS | 6 ++++++ R/metadata.R | 4 +++- man/cache_treebase.Rd | 2 +- man/clean_data.Rd | 2 +- man/download_metadata.Rd | 2 +- man/drop_nonascii.Rd | 2 +- man/drop_nontrees.Rd | 2 +- man/dryad_metadata.Rd | 2 +- man/get_nex.Rd | 2 +- man/get_study.Rd | 2 +- man/get_study_id.Rd | 2 +- man/have_branchlength.Rd | 2 +- man/metadata.Rd | 3 ++- man/metadata_from_oai.Rd | 2 +- man/oai_metadata.Rd | 2 +- man/phylo_metadata.Rd | 2 +- man/search_treebase.Rd | 2 +- man/show_metadata.Rd | 2 +- man/treebase.Rd | 2 +- tests/testthat/test_basic.R | 4 ++-- 23 files changed, 56 insertions(+), 49 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.5 dated 2014-12-09 and 0.6 dated 2015-10-14
GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetOptimizerMTK.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetOptimizerPIC.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetterCombinedMTK.R |only GeneticSubsetter-0.5/GeneticSubsetter/R/SubsetterCombinedPIC.R |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetOptimizerMTK.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetOptimizerPIC.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetterCombinedMTK.Rd |only GeneticSubsetter-0.5/GeneticSubsetter/man/SubsetterCombinedPIC.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/DESCRIPTION | 10 +- GeneticSubsetter-0.6/GeneticSubsetter/MD5 | 34 +++++----- GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetOptimizer.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetter.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/CoreSetterCombined.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/HET.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/MTK.R |only GeneticSubsetter-0.6/GeneticSubsetter/R/SubsetterMTK.R | 2 GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetOptimizer.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetter.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/CoreSetterCombined.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/GeneticSubsetter.Rd | 10 +- GeneticSubsetter-0.6/GeneticSubsetter/man/MTK.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/MtkCalc.Rd | 6 - GeneticSubsetter-0.6/GeneticSubsetter/man/PIC.Rd |only GeneticSubsetter-0.6/GeneticSubsetter/man/PicCalc.Rd | 12 +-- GeneticSubsetter-0.6/GeneticSubsetter/man/SubsetterMTK.Rd | 8 -- GeneticSubsetter-0.6/GeneticSubsetter/man/SubsetterPIC.Rd | 5 - GeneticSubsetter-0.6/GeneticSubsetter/man/genotypes.Rd | 2 27 files changed, 40 insertions(+), 49 deletions(-)
More information about GeneticSubsetter at CRAN
Permanent link
Title: Statistical Comparisons with Distance-Function Based Permutation
Tests
Description: Provides tools for making statistical comparisons with distance-function based permutation tests developed by P. W. Mielke, Jr. and colleagues at Colorado State University (Mielke, P. W. & Berry, K. J. Permutation Methods: A Distance Function Approach (Springer, New York, 2001)) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U. S. Geological Survey.
Author: Marian Talbert, Jon Richards, Paul Mielke, and Brian Cade
Maintainer: Marian Talbert <mtalbert@usgs.gov>
Diff between Blossom versions 1.2 dated 2015-10-14 and 1.3 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/InternalFcts.f90 | 11 ++++++----- 3 files changed, 13 insertions(+), 12 deletions(-)
Title: Easier cluster computing (based on snow).
Description: Usability wrapper around snow for easier development of
parallel R programs. This package offers e.g. extended error
checks, and additional functions. All functions work in
sequential mode, too, if no cluster is present or wished.
Package is also designed as connector to the cluster management
tool sfCluster, but can also used without it.
Author: Jochen Knaus
Maintainer: Jochen Knaus <jo@imbi.uni-freiburg.de>
Diff between snowfall versions 1.84-6 dated 2013-12-18 and 1.84-6.1 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/init.R | 10 +++++----- R/sysdata.rda |binary data/test.rda |binary 5 files changed, 13 insertions(+), 13 deletions(-)
Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between reportr versions 1.1.2 dated 2014-03-12 and 1.2.0 dated 2015-10-14
reportr-1.1.2/reportr/R/infix.R |only reportr-1.1.2/reportr/R/substitute.R |only reportr-1.1.2/reportr/man/infix.Rd |only reportr-1.1.2/reportr/man/substitute.Rd |only reportr-1.2.0/reportr/DESCRIPTION | 15 +- reportr-1.2.0/reportr/MD5 | 17 +- reportr-1.2.0/reportr/NAMESPACE | 13 + reportr-1.2.0/reportr/R/00_constants.R | 13 + reportr-1.2.0/reportr/R/reportr.R | 227 ++++++++++++++++++++++++++------ reportr-1.2.0/reportr/README.md |only reportr-1.2.0/reportr/man/reportr.Rd | 164 +++++++++++++++++------ reportr-1.2.0/reportr/tests |only 12 files changed, 348 insertions(+), 101 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.4.1 dated 2015-10-06 and 0.5.0 dated 2015-10-14
DESCRIPTION | 6 +- MD5 | 20 +++--- NEWS | 8 ++ R/Globals-class.R | 2 R/cleanup.R | 30 ++++++---- R/globalsOf.R | 20 +++++- R/utils.R | 20 ++++++ man/cleanup.Globals.Rd | 41 ++++++------- man/globalsOf.Rd | 144 ++++++++++++++++++++++++------------------------- tests/globalsOf.R | 69 +++++++++++++++++++++++ tests/utils.R | 57 +++++++++++++++++++ 11 files changed, 295 insertions(+), 122 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.3 dated 2015-10-06 and 1.1.4 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/GDM_Table_Funcs.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Optimal Designs for Copula Models
Description: A direct approach to optimal designs for copula models based on the Fisher information. Provides flexible functions for building joint PDFs, evaluating the Fisher information and finding optimal designs. It includes an extensible solution to summation and integration called 'nint', functions for transforming, plotting and comparing designs, as well as a set of tools for common low-level tasks.
Author: Andreas Rappold [aut, cre]
Maintainer: Andreas Rappold <arappold@gmx.at>
Diff between docopulae versions 0.3.1 dated 2015-09-30 and 0.3.2 dated 2015-10-14
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- R/examples/main.R | 17 +++++++----- R/main.R | 71 ++++++++++++++++++++++++++++++++-------------------- man/Defficiency.Rd | 6 ++-- man/Dsensitivity.Rd | 16 ++++++++--- man/FedorovWynn.Rd | 5 ++- man/design.Rd | 3 +- man/numDerivLogf.Rd | 16 +++++------ man/param.Rd | 17 +++++++----- man/plot.desigh.Rd | 10 +++++-- 11 files changed, 113 insertions(+), 74 deletions(-)
Title: Item Focused Trees for the Identification of Items in
Differential Item Functioning
Description: Item focused recursive partitioning for simultaneous selection of
items and variables that induce Differential Item Functioning (DIF) in Item Response models.
Author: Moritz Berger
Maintainer: Moritz Berger <moritz.berger@stat.uni-muenchen.de>
Diff between DIFtree versions 1.0.0 dated 2015-04-28 and 1.1.0 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/DIFtree.R | 52 +++++++++++++++++++++++++++++++++++++++++----------- R/plot.DIFtree.R | 8 +++----- man/DIFtree.Rd | 3 ++- 5 files changed, 54 insertions(+), 25 deletions(-)
Title: Tools for Structural Reliability Analysis
Description: A variety of tools useful for performing structural
reliability analysis, such as with structure function and
system signatures. Plans to expand more widely.
Author: Louis Aslett <aslett@stats.ox.ac.uk>
Maintainer: Louis Aslett <aslett@stats.ox.ac.uk>
Diff between ReliabilityTheory versions 0.1.4 dated 2014-06-12 and 0.1.5 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS | 5 +++++ R/MinimalVertexPairCutSets.R | 2 +- README.md |only man/ReliabilityTheory-package.Rd | 4 ++-- 7 files changed, 20 insertions(+), 13 deletions(-)
More information about ReliabilityTheory at CRAN
Permanent link
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test.
Author: Michael Thrun, Onno Hansen-Goos, Rabea Griese, Catharina Lippmann, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between AdaptGauss versions 1.0 dated 2015-10-09 and 1.1.0 dated 2015-10-14
DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 2 +- R/AdaptGauss.R | 6 +++--- R/Chi2testMixtures.R | 3 +++ R/KStestMixtures.R |only man/AdaptGauss-package.Rd | 4 ++-- man/AdaptGauss.Rd | 19 ++++++++++--------- man/BayesDecisionBoundaries.Rd | 2 +- man/BayesForMixes.Rd | 1 + man/CDFMixtures.Rd | 2 +- man/Chi2testMixtures.Rd | 9 +++++++-- man/EMGauss.Rd | 1 + man/KStestMixtures.Rd |only man/paretoDensityEstimationForGMM.Rd | 6 +++--- man/paretoRadiusForGMM.Rd | 4 ++-- man/qqplotGMM.Rd | 2 +- 17 files changed, 57 insertions(+), 44 deletions(-)
Title: Unit Testing for R
Description: A unit testing system designed to be fun, flexible and easy to
set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 0.10.0 dated 2015-05-22 and 0.11.0 dated 2015-10-14
DESCRIPTION | 13 ++-- MD5 | 103 ++++++++++++++++++------------------ NAMESPACE | 8 ++ R/auto-test.r | 27 +++++---- R/compare.r | 41 ++++++++------ R/expect-that.r | 17 +++-- R/expectation.r | 7 +- R/expectations-equality.R | 4 - R/expectations-matches.R | 48 ++++++++++++---- R/expectations-silent.R |only R/expectations.r | 67 ++++++++++++++++++++++- R/mock.r | 5 + R/praise.R |only R/reporter-stop.r | 2 R/reporter-summary.r | 24 +++----- R/reporter-tap.r | 2 R/reporter.r | 2 R/test-example.R | 2 R/test-files.r | 21 +++++-- R/test-package.r | 28 +++++---- R/test-results.r | 2 R/test-that.r | 15 ++--- R/utils.r | 38 ++++++++++++- R/watcher.r | 9 +-- README.md | 23 ++------ man/StopReporter-class.Rd | 2 man/compare.Rd | 2 man/equivalence.Rd | 10 ++- man/expect-compare.Rd | 15 ++++- man/expect_equal_to_reference.Rd | 8 +- man/expect_is.Rd | 6 +- man/expect_named.Rd | 6 +- man/expect_null.Rd | 6 +- man/expect_silent.Rd |only man/expect_true.Rd | 8 +- man/expectation.Rd | 6 +- man/find_test_scripts.Rd | 4 + man/matching-expectations.Rd | 21 ++++--- man/not.Rd | 4 + man/skip.Rd | 12 ++++ man/takes_less_than.Rd | 7 +- man/test_examples.Rd | 2 man/test_package.Rd | 21 +++---- man/test_that.Rd | 10 +-- man/with_mock.Rd | 3 + tests/testthat/test-bare.r | 4 + tests/testthat/test-compare.r | 26 +++++++++ tests/testthat/test-expectations.r | 13 ++++ tests/testthat/test-mock.r | 2 tests/testthat/test-reporter-list.r | 10 ++- tests/testthat/test-reporter-tap.r |only tests/testthat/test-silence.R | 2 tests/testthat/test-test_dir.r | 16 +++-- tests/testthat/test-watcher.r | 8 ++ tests/testthat/test_dir/test-skip.r |only 55 files changed, 500 insertions(+), 242 deletions(-)
Title: R Unit Test Framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools.
Author: Matthias Burger <burgerm@users.sourceforge.net>, Klaus
Juenemann <k.junemann@gmx.net>, Thomas Koenig
<thomas.koenig@epigenomics.com>
Maintainer: Roman Zenka <zenka.roman@mayo.edu>
Diff between RUnit versions 0.4.29 dated 2015-08-11 and 0.4.30 dated 2015-10-14
DESCRIPTION | 9 +++++---- MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS | 3 +++ R/junitProtocol.r |only build/RUnit.pdf |binary inst/doc/RUnit.pdf |binary inst/unitTests/runitJUnitProtocol.r |only man/textProtocol.Rd | 22 ++++++++++++++++++---- 9 files changed, 35 insertions(+), 14 deletions(-)
Title: Tools for Working with Rotation Data
Description: Tools for working with rotational data, including
simulation from the most commonly used distributions on SO(3),
methods for different Bayes, mean and median type estimators for
the central orientation of a sample, confidence/credible
regions for the central orientation based on those estimators and
a novel visualization technique for rotation data. Most recently,
functions to identify potentially discordant (outlying) values
have been added.
Author: Bryan Stanfill <bstanfill2003@gmail.com>, Heike Hofmann
<hofmann@iastate.edu>, Ulrike Genschel <ulrike@iastate.edu>
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between rotations versions 1.3 dated 2014-12-16 and 1.4 dated 2015-10-14
DESCRIPTION | 12 LICENSE | 2 MD5 | 164 +-- NAMESPACE | 234 ++-- NEWS | 270 ++--- R/RcppExports.R | 362 +++--- R/bayes.R | 534 ++++----- R/distributions.R | 1131 +++++++++++---------- R/estimators.R | 592 +++++------ R/grid-search.R | 200 +-- R/help.R | 20 R/kappa.R | 233 ++-- R/parameterizations.R | 1002 +++++++++--------- R/plot.R | 1060 ++++++++++--------- R/preliminary.R | 1423 +++++++++++++------------- R/primatives.R | 670 ++++++------ R/regions.R | 1076 ++++++++++---------- R/robust.R | 188 +-- build/vignette.rds |binary data/datalist | 4 inst/CITATION | 32 inst/REFERENCES.bib | 367 +++--- inst/doc/rotations-intro.R | 156 +- inst/doc/rotations-intro.Rnw | 732 ++++++------- inst/doc/rotations-intro.pdf |binary inst/include/rotations.h | 18 inst/include/rotations_RcppExports.h | 1713 ++++++++++++++++---------------- man/Angular-distributions.Rd | 40 man/Arithmetic.Rd | 155 +- man/Cayley.Rd | 164 +-- man/Fisher.Rd | 154 +- man/Haar.Rd | 142 +- man/MCMCSO3.Rd | 166 +-- man/Maxwell.Rd |only man/Mises.Rd | 142 +- man/Q4-class.Rd | 20 man/Q4.Rd | 212 +-- man/SO3-class.Rd | 22 man/SO3.Rd | 218 ++-- man/UARS.Rd | 172 +-- man/bayes.mean.Rd | 188 +-- man/bayesCR.Rd | 186 +-- man/cayley.kappa.Rd | 84 - man/center.Rd | 88 - man/chang.Rd | 122 +- man/discord.Rd | 104 - man/drill.Rd | 114 +- man/fisher.kappa.Rd | 85 - man/fisheretal.Rd | 134 +- man/genR.Rd | 92 - man/gradient.search.Rd | 98 - man/log.SO3.Rd | 86 - man/maxwell.kappa.Rd |only man/mean.SO3.Rd | 166 +-- man/median.SO3.Rd | 152 +- man/mis.angle.Rd | 108 +- man/mis.axis.Rd | 116 +- man/nickel.Rd | 120 +- man/plot.SO3.Rd | 182 +-- man/pointsXYZ.Rd | 68 - man/prentice.Rd | 118 +- man/project.SO3.Rd | 88 - man/region.Rd | 140 +- man/rot.dist.Rd | 132 +- man/rotations.Rd | 30 man/rotdist.sum.Rd | 130 +- man/skew.exp.Rd | 68 - man/vmises.kappa.Rd | 85 - man/weighted.mean.SO3.Rd | 168 +-- man/zhang.Rd | 122 +- src/CppBayesFunctions.cpp | 106 + src/Makevars.win | 12 src/RcppExports.cpp | 649 ++++-------- src/basics.cpp | 1 tests/test-all.R | 2 tests/testthat/test_arithmetic.R | 78 - tests/testthat/test_basics.R | 90 - tests/testthat/test_conversions.R | 40 tests/testthat/test_discord.R | 28 tests/testthat/test_estimators.R | 60 - tests/testthat/test_metrics.R | 24 vignettes/RJournal_edited.sty | 670 ++++++------ vignettes/rotations-intro.Rnw | 732 ++++++------- vignettes/stanfill-hofmann-genschel.bib | 754 +++++++------- 84 files changed, 10304 insertions(+), 10118 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in NeXML format. The
package should add new functionality to R such as the possibility to
manipulate NeXML objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.0.3 dated 2015-05-26 and 2.0.4 dated 2015-10-14
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++++ NEWS | 5 +++++ R/add_basic_meta.R | 2 ++ R/classes.R | 3 ++- R/get_characters.R | 11 ++++++----- R/simmap.R | 4 ++++ build/vignette.rds |binary tests/testthat/test_publish.R | 7 ++++++- tests/testthat/test_rdf.R | 2 ++ 11 files changed, 44 insertions(+), 20 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.4 dated 2015-10-01 and 0.0.5 dated 2015-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Aggregate.R | 2 +- R/create_infotables.R | 1 + inst/doc/Information-vignette.html | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Interactive Dendrograms
Description: Interactive dendrogram that enables the user to select and
color clusters, to zoom and pan the dendrogram, and to visualize
the clustered data not only in a built-in heat map, but also in
'GGobi' interactive plots and user-supplied plots.
This is a backport of Qt-based 'idendro'
(https://github.com/tsieger/idendro) to base R graphics and Tcl/Tk GUI.
Author: Tomas Sieger
Maintainer: Tomas Sieger <tomas.sieger@seznam.cz>
Diff between idendr0 versions 1.5.0 dated 2015-10-07 and 1.5.1 dated 2015-10-14
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS | 11 +++++++++-- R/idendro.R | 40 ++++++++++++++++++++++++++++++---------- README.md | 4 ++-- demo/idendroWithGgobi.R | 1 - man/idendr0-package.Rd | 7 ++++--- man/idendro.Rd | 3 +-- 8 files changed, 59 insertions(+), 32 deletions(-)
Title: Study Design and Data Analysis in the Presence of Error-Prone
Diagnostic Tests and Self-Reported Outcomes
Description: We consider studies in which information from error-prone
diagnostic tests or self-reports are gathered sequentially to determine the
occurrence of a silent event. Using a likelihood-based approach
incorporating the proportional hazards assumption, we provide functions to
estimate the survival distribution and covariate effects. We also provide
functions for power and sample size calculations for this setting.
Author: Xiangdong Gu and Raji Balasubramanian
Maintainer: Xiangdong Gu <ustcgxd@gmail.com>
Diff between icensmis versions 1.2.1 dated 2014-06-27 and 1.3.0 dated 2015-10-14
DESCRIPTION | 15 MD5 | 30 + NAMESPACE | 11 R/HighDimCR.R | 20 - R/RcppExports.R | 16 R/datasim.R | 27 + R/icpower.R | 221 +++++-------- README.md |only man/datasim.Rd | 11 man/icmis.Rd | 3 man/icpower.Rd | 10 man/icpower.val.Rd | 3 man/icpowerpf.Rd | 3 src/HighDimCR.cpp | 24 - src/RcppExports.cpp | 878 +++++++++++++++++++++++----------------------------- src/powerfuncs.cpp |only tests |only 17 files changed, 594 insertions(+), 678 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
Author: John Wambaugh and Robert Pearce, Schmitt method implementation by Jimena Davis, dynamic model adapted from code by R. Woodrow Setzer, Rabbit parameters from Nisha Sipes
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.2 dated 2015-05-11 and 1.3 dated 2015-10-14
DESCRIPTION | 9 ++-- MD5 | 74 +++++++++++++++++----------------- NAMESPACE | 6 ++ R/Calc_Hepatic_Clearance.r | 2 R/Calc_ratioblood2plasma.R | 2 R/Calc_volume_of_distribution.R | 59 ++++++++++++++++++++------- R/Export_PBTK_Jarnac.R | 26 +++++------ R/Export_PBTK_SBML.R | 24 +++++------ R/Get_lumped_tissues.R | 32 +++++++++----- R/Parameterize_PBTK.r | 44 ++++++-------------- R/Predict_partitioning_Schmitt.R | 17 +++---- R/add_chemtable.R | 6 +- R/calc_analytic_css.R | 14 +++--- R/calc_css.R | 47 +++++++++++++-------- R/get_Wetmore_Css.R | 17 +++++-- R/get_Wetmore_Oral_Equiv.R | 5 +- R/get_chem_id.R | 1 R/get_cheminfo.R | 1 R/in.list.R |only R/ionization_functions.R | 17 +++++-- R/solve_3comp.R | 7 +-- R/solve_pbtk.R | 5 +- data/Tables.RData |binary man/Parameterize_PBTK.Rd | 12 ++--- man/Wetmore.data.Rd | 2 man/Wetmore_Css.Rd | 2 man/Wetmore_Oral_Equiv.Rd | 9 ++++ man/calc_analytic_css.Rd | 2 man/calc_css.Rd | 10 ++-- man/calc_ionization.Rd |only man/chem.lists.Rd |only man/chem_physical_and_invitro_data.Rd | 3 + man/get_cheminfo.Rd | 29 +++++++++++++ man/get_wetmore_cheminfo.Rd | 7 +++ man/in_list.Rd |only man/parameterize_3comp.Rd | 8 +-- man/solve_3comp_pbpk.Rd | 2 man/solve_pbtk.Rd | 2 tests/cheminfo_test.Rout.save | 22 +++++----- tests/other_tests.Rout.save | 64 ++++++++++++++--------------- 40 files changed, 352 insertions(+), 237 deletions(-)
Title: Foreach Parallel Adaptor for the 'snow' Package
Description: Provides a parallel backend for the %dopar% function using
Luke Tierney's snow package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Stephen Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doSNOW versions 1.0.12 dated 2014-03-13 and 1.0.14 dated 2015-10-14
DESCRIPTION | 22 ++++++---- MD5 | 8 +-- NAMESPACE | 1 R/doSNOW.R | 102 +++++++++++++++++++++++++++++++++++++++++++++----- man/registerDoSNOW.Rd | 1 5 files changed, 113 insertions(+), 21 deletions(-)
Title: Foreach Parallel Adaptor for the 'parallel' Package
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut],
Dan Tenenbaum [ctb]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doParallel versions 1.0.8 dated 2014-02-28 and 1.0.10 dated 2015-10-14
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 4 +++- R/doParallel.R | 9 ++++++--- build/vignette.rds |binary inst/doc/gettingstartedParallel.pdf |binary 7 files changed, 31 insertions(+), 18 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Chris H. Fleming and J. M. Calabrese
Maintainer: C. H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.2.8 dated 2015-08-26 and 0.2.9 dated 2015-10-14
DESCRIPTION | 12 - MD5 | 68 +++++---- NAMESPACE | 1 NEWS | 20 ++ R/generic.R | 72 ++++++++++ R/kde.R | 331 +++++++++++++++++++++++++++++++++++------------- R/krige.R | 151 +++++++++++++++++++++ R/likelihood.R | 95 +++++++++---- R/periodogram.R | 186 ++++++++++++++++++++++++-- R/telemetry.R | 116 ++++++++++++---- R/variogram.R | 124 ++++++++++++----- TODO | 27 ++- build/vignette.rds |binary data/gazelle.rda |only inst/doc/akde.html | 14 +- inst/doc/variogram.R | 50 +++++-- inst/doc/variogram.Rmd | 63 ++++++--- inst/doc/variogram.html | 83 +++++++----- man/akde.Rd | 20 +- man/akde.bandwidth.Rd | 7 - man/as.telemetry.Rd | 3 man/buffalo.Rd | 4 man/ctmm-package.Rd | 4 man/ctmm.fit.Rd | 7 - man/ctmm.loglike.Rd | 2 man/export.Rd | 6 man/gazelle.Rd |only man/mean.variogram.Rd | 6 man/periodogram.Rd | 25 ++- man/plot.variogram.Rd | 4 man/simulate.ctmm.Rd | 2 man/summary.akde.Rd | 8 - man/summary.ctmm.Rd | 2 man/variogram.Rd | 14 +- man/variogram.fit.Rd | 6 vignettes/variogram.Rmd | 63 ++++++--- 36 files changed, 1196 insertions(+), 400 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-02-24 1.54
2012-04-24 1.53
2012-04-19 1.52
2011-11-23 1.50
2011-09-24 1.49
2011-09-02 1.48
2011-08-12 1.47
2011-08-10 1.46
2011-07-23 1.45
2011-06-01 1.44
2011-05-16 1.43
2011-03-31 1.42
2011-02-28 1.41
2011-02-18 1.31.1
2010-12-12 1.31
2010-11-08 1.3
2010-09-22 1.2
2010-08-17 1.01
2010-06-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-28 1.3
2014-01-11 1.2
2013-12-08 1.1
2013-10-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-14 1.1
2013-06-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-19 1.1
2015-02-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-25 0.94
2014-03-07 0.93
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-15 0.5-4
2014-05-19 0.5-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-23 0.7-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-31 1.0
Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Lord & Barton's four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2015).
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between fourPNO versions 1.0 dated 2015-10-12 and 1.0.1 dated 2015-10-13
fourPNO-1.0.1/fourPNO/DESCRIPTION | 6 +++--- fourPNO-1.0.1/fourPNO/MD5 | 18 +++++++++--------- fourPNO-1.0.1/fourPNO/R/RcppExports.R | 18 +++++++++--------- fourPNO-1.0.1/fourPNO/man/Gibbs_2PNO.Rd | 6 +++--- fourPNO-1.0.1/fourPNO/man/Gibbs_4PNO.Rd | 8 ++++---- fourPNO-1.0.1/fourPNO/man/Y_4pno_simulate.Rd | 4 ++-- fourPNO-1.0.1/fourPNO/man/min2LL_4pno.Rd | 4 ++-- fourPNO-1.0.1/fourPNO/man/update_WKappaZ_NA.Rd | 4 ++-- fourPNO-1.0.1/fourPNO/src/RcppExports.cpp | 24 ++++++++++++------------ fourPNO-1.0.1/fourPNO/src/fourpno_101315.cpp |only fourPNO-1.0/fourPNO/src/fourpno_012915.cpp |only 11 files changed, 46 insertions(+), 46 deletions(-)
Title: Learning Causal Cyclic Graphs from Unknown Shift Interventions
Description: Code for 'backShift', an algorithm to estimate the connectivity
matrix of a directed (possibly cyclic) graph with hidden variables. The
underlying system is required to be linear and we assume that observations
under different shift interventions are available. For more details,
see <http://arxiv.org/abs/1506.02494>.
Author: Christina Heinze <heinze@stat.math.ethz.ch>
Maintainer: Christina Heinze <heinze@stat.math.ethz.ch>
Diff between backShift versions 0.1.2 dated 2015-08-19 and 0.1.3 dated 2015-10-13
DESCRIPTION | 10 +- MD5 | 16 ++-- R/checkDiagonalization.R | 14 ++- R/computeVarEnv.R | 3 R/plotGraph.R | 146 ++++++++++++++++++++--------------------- R/simulate.R | 2 inst/doc/exampleBackShift.html | 2 man/plotDiagonalization.Rd | 4 - tests |only 9 files changed, 103 insertions(+), 94 deletions(-)
Title: Analysis of Means
Description: Analysis of means (ANOM) as used in technometrical computing. The package takes results from multiple comparisons with the grand mean (obtained with 'multcomp', 'SimComp', 'nparcomp', or 'MCPAN') or corresponding simultaneous confidence intervals as input and produces ANOM decision charts that illustrate which group means deviate significantly from the grand mean.
Author: Philip Pallmann
Maintainer: Philip Pallmann <p.pallmann@lancaster.ac.uk>
Diff between ANOM versions 0.4 dated 2015-08-14 and 0.4.2 dated 2015-10-13
ANOM-0.4.2/ANOM/DESCRIPTION | 10 +++++----- ANOM-0.4.2/ANOM/MD5 | 11 +++++------ ANOM-0.4.2/ANOM/R/ANOM.R | 2 ++ ANOM-0.4.2/ANOM/R/ANOMgen.R | 1 + ANOM-0.4.2/ANOM/inst/NEWS | 12 ++++++++++++ ANOM-0.4.2/ANOM/inst/doc/ANOM.pdf |binary ANOM-0.4/ANOM/inst/CITATION |only 7 files changed, 25 insertions(+), 11 deletions(-)
Title: Sparse Learning Algorithms Using a LASSO-Type Penalty for
Coefficient Estimation and Model Prediction
Description: Coefficient estimation and model prediction based on
the LASSO sparse learning algorithm and its improved versions
such as Bolasso, bootstrap ranking LASSO, two-stage hybrid LASSO
and others. These estimation procedures are applied in the fields
of variable selection, graphical modeling and forecasting.
Author: Pi Guo, Yuantao Hao
Maintainer: Pi Guo <guopi.01@163.com>
Diff between SparseLearner versions 1.0 dated 2015-10-10 and 1.0.1 dated 2015-10-13
SparseLearner-1.0.1/SparseLearner/DESCRIPTION | 17 ++-- SparseLearner-1.0.1/SparseLearner/MD5 | 20 ++--- SparseLearner-1.0.1/SparseLearner/NAMESPACE | 2 SparseLearner-1.0.1/SparseLearner/R/BRLasso.R | 18 ++--- SparseLearner-1.0.1/SparseLearner/R/Bolasso.R | 16 ++-- SparseLearner-1.0.1/SparseLearner/R/Sparse.graph.R |only SparseLearner-1.0.1/SparseLearner/R/TSLasso.R | 20 +++-- SparseLearner-1.0.1/SparseLearner/man/BRLasso.Rd | 57 ++++++++++++---- SparseLearner-1.0.1/SparseLearner/man/Bolasso.Rd | 45 ++++++++---- SparseLearner-1.0.1/SparseLearner/man/Sparse.graph.Rd |only SparseLearner-1.0.1/SparseLearner/man/TSLasso.Rd | 64 ++++++++++++------ SparseLearner-1.0/SparseLearner/R/SGraph.R |only SparseLearner-1.0/SparseLearner/man/SGraph.Rd |only 13 files changed, 172 insertions(+), 87 deletions(-)
Title: Inference and Analysis for Generalized Quadratic Diffusions
Description: Tools for performing inference and analysis on a class of quadratic diffusion processes for both scalar and bivariate diffusion systems. For scalar diffusions, a module is provided for solving first passage time problems for both time-homogeneous and time-inhomogeneous GQDs.
Author: Etienne A.D. Pienaar [aut, cre],
Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>
Diff between DiffusionRgqd versions 0.1.0 dated 2015-10-12 and 0.1.1 dated 2015-10-13
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 5 data/SDEsim1.txt | 800 +++++++++++++++++++++---------------------- man/DiffusionRgqd-package.Rd | 10 man/GQD.aic.Rd | 2 man/GQD.dic.Rd | 21 - man/GQD.estimates.Rd | 10 man/GQD.mcmc.Rd | 10 man/GQD.mle.Rd | 8 man/SDEsim1.Rd | 6 11 files changed, 441 insertions(+), 457 deletions(-)
Title: Functions and Methods for Correspondence Regression
Description: A collection of tools for correspondence regression, i.e. the
correspondence analysis of the crosstabulation of a categorical variable Y
in function of another one X, where X can in turn be made up of the
combination of various categorical variables. Consequently, correspondence
regression can be used to analyze the effects for a polytomous or
multinomial outcome variable.
Author: Koen Plevoets [aut, cre]
Maintainer: Koen Plevoets <koen.plevoets@ugent.be>
Diff between corregp versions 0.1.3 dated 2015-09-07 and 0.1.4 dated 2015-10-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/corregp.r | 1 - inst/CITATION | 4 ++-- man/plot3d.corregp.Rd | 1 - 5 files changed, 10 insertions(+), 12 deletions(-)
Title: Methods to Analyse Ring Re-Encounter Data
Description: R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to http://www.tandfonline.com/doi/full/10.1080/03078698.2014.933053.
Author: Fraenzi Korner-Nievergelt, Rob Robinson
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@vogelwarte.ch>
Diff between birdring versions 1.2 dated 2014-09-24 and 1.3 dated 2015-10-13
DESCRIPTION | 14 +++++++------- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 7 +++++++ R/bootci.dc.r | 9 +-------- R/critical.check.ringing.event.r |only R/dayofyear.R | 1 - R/dc.r | 8 +------- R/decimal.coord.r | 2 +- R/loxodrom.dir.r | 6 +++--- R/loxodrom.dist.r | 2 +- R/mercatorlat.R | 2 +- R/overlap.r | 36 ++++++++++++++++++++++++++++-------- R/read.euring2000.r | 2 +- R/read.euring2000plus.r | 2 +- man/birdring-package.Rd | 3 ++- man/critical.check.ringing.event.Rd |only man/loxodrom.dir.Rd | 8 ++++---- man/orthodrom.dist.Rd | 8 ++++---- man/overlap.Rd | 28 +++++++++++++++++++++++++--- man/read.euring2000plus.rd | 4 ++-- 20 files changed, 108 insertions(+), 70 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.1 dated 2015-08-05 and 0.3.3 dated 2015-10-13
DESCRIPTION | 15 +-- MD5 | 63 ++++++------ R/convertDVH.R | 228 +++++++++++++++++++++++++++++----------------- R/dvhDistance.R | 3 R/getDMEAN.R | 74 ++++++++------ R/getMetric.R | 37 +++---- R/parseCadplan.R | 64 +++++++++--- R/parseEclipse.R | 55 ++++++++--- R/parseHiArt.R | 4 R/parseMasterplan.R | 9 - R/parseMonaco.R | 7 - R/parsePinnacleDVH.R | 28 +++-- R/parseRayStation.R |only R/readDVH.R | 7 - R/showDVH.R | 15 --- R/smoothDVH.R | 69 ++++++++++--- R/unix/parseDVH.R | 6 + R/windows/parseDVH.R | 6 + inst/ChangeLog | 20 +++- inst/DVHshiny/ABOUT.md | 4 inst/DVHshiny/server.R | 3 inst/DVHshiny/ui.R | 3 inst/doc/DVHmetrics.Rnw | 4 inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.Rnw | 2 inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 4 man/convertDVH.Rd | 6 - man/getDMEAN.Rd | 13 +- man/readDVH.Rd | 8 + man/showDVH.Rd | 2 vignettes/DVHmetrics.Rnw | 4 vignettes/DVHshiny.Rnw | 2 33 files changed, 485 insertions(+), 280 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-24 1.0.1
2015-09-22 1.0.0
Title: Stochastic Mortality Modelling
Description: Implementation of the family of generalised age-period-cohort
stochastic mortality models. This family of models encompasses many models
proposed in the actuarial and demographic literature including the Lee-Carter model
and the Cairns-Blake-Dowd model. It includes functions for fitting mortality models,
analysing their goodness-of-fit and performing mortality projections and
simulations.
Author: Andres Villegas <andresmauriciovillegas@gmail.com>,
Pietro Millossovich <Pietro.Millossovich.1@city.ac.uk>,
Vladimir Kaishev <Vladimir.Kaishev.1@city.ac.uk>
Maintainer: Andres Villegas <andresmauriciovillegas@gmail.com>
Diff between StMoMo versions 0.2.0 dated 2015-06-10 and 0.3.0 dated 2015-10-13
DESCRIPTION | 6 MD5 | 37 NAMESPACE | 29 R/docStMoMo.R | 5 R/fitStMoMo.R | 8 R/forecastfitStMoMo.R | 53 + R/simulatebootStMoMo.R | 9 R/simulatefitStMoMo.R | 13 README.md | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/StMoMoVignette.R | 5 inst/doc/StMoMoVignette.Rnw | 88 +- inst/doc/StMoMoVignette.pdf |binary man/fit.StMoMo.Rd | 8 man/forecast.fitStMoMo.Rd | 40 + man/simulate.bootStMoMo.Rd | 15 man/simulate.fitStMoMo.Rd | 15 vignettes/StMoMoVignette.Rnw | 88 +- vignettes/elsarticle.cls | 1618 +++++++++++++++++++++---------------------- 20 files changed, 1108 insertions(+), 931 deletions(-)
Title: Tools for Harnessing MLBAM Gameday Data and Visualizing PITCHf/x
Description: With pitchRx, one can easily obtain Major League Baseball Advanced
Media's Gameday data (as well as store it in a remote database). The
Gameday website hosts a wealth of data in XML format, but perhaps most
interesting is PITCHf/x. Among other things, PITCHf/x data can be used to
recreate a baseball's flight path from a pitcher's hand to home plate. With
pitchRx, one can easily create animations and interactive 3D scatterplots
of the baseball's flight path. PITCHf/x data is also commonly used to
generate a static plot of baseball locations at the moment they cross home
plate. These plots, sometimes called strike-zone plots, can also refer to a
plot of event probabilities over the same region. pitchRx provides an easy
and robust way to generate strike-zone plots using the ggplot2 package.
Author: Carson Sievert <sievert@iastate.edu>
Maintainer: Carson Sievert <sievert@iastate.edu>
Diff between pitchRx versions 1.7 dated 2015-04-04 and 1.8 dated 2015-10-13
DESCRIPTION | 7 +- MD5 | 46 ++++++++--------- NAMESPACE | 11 +++- NEWS | 6 ++ R/animateFX.R | 38 +++++++------- R/help.R | 5 + R/scrape.R | 132 +++++++++++++++++++++++++------------------------ data/gids.rda |binary man/animateFX.Rd | 42 ++++++--------- man/export.Rd | 27 +++------- man/fields.Rd | 9 +-- man/getSnapshots.Rd | 13 +--- man/gids.Rd | 5 - man/interactiveFX.Rd | 21 +++---- man/makeUrls.Rd | 19 ++----- man/nonMLBgids.Rd | 5 - man/pitchRx.Rd | 2 man/pitches.Rd | 5 - man/players.Rd | 11 +--- man/scrape.Rd | 72 ++++++++------------------ man/scrapeFX.Rd | 10 +-- man/strikeFX.Rd | 67 ++++++++---------------- man/update_db.Rd | 16 ++--- man/urlsToDataFrame.Rd | 15 +---- 24 files changed, 259 insertions(+), 325 deletions(-)
Title: Compute the Top Decile Lift and Plot the Lift Curve
Description: Compute the top decile lift and plot the lift curve. Cumulative lift curves are also supported.
Author: Steven Hoornaert, Michel Ballings, Dirk Van den Poel
Maintainer: Steven Hoornaert <Steven.Hoornaert@UGent.be>
Diff between lift versions 0.0.1 dated 2015-10-01 and 0.0.2 dated 2015-10-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plotLift.R | 2 +- inst/NEWS | 5 ++++- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Provides Iterator Construct for R
Description: Support for iterators, which allow a programmer to traverse
through all the elements of a vector, list, or other collection
of data.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between iterators versions 1.0.7 dated 2014-04-11 and 1.0.8 dated 2015-10-13
DESCRIPTION | 21 +++++++++++++-------- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/iterators.pdf |binary inst/doc/writing.pdf |binary 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Provides Foreach Looping Construct for R
Description: Support for the foreach looping construct. Foreach is an
idiom that allows for iterating over elements in a collection,
without the use of an explicit loop counter. This package in
particular is intended to be used for its return value, rather
than for its side effects. In that sense, it is similar to the
standard lapply function, but doesn't require the evaluation
of a function. Using foreach without side effects also
facilitates executing the loop in parallel.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between foreach versions 1.4.2 dated 2014-04-11 and 1.4.3 dated 2015-10-13
DESCRIPTION | 21 +++++++++++++-------- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/foreach.pdf |binary inst/doc/nested.pdf |binary 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Foreach Parallel Adaptor for 'parallel'
Description: Provides a parallel backend for the %dopar% function using
the multicore functionality of the parallel package.
Author: Rich Calaway [cre],
Revolution Analytics [aut, cph],
Steve Weston [aut]
Maintainer: Rich Calaway <richcala@microsoft.com>
Diff between doMC versions 1.3.3 dated 2014-02-28 and 1.3.4 dated 2015-10-13
DESCRIPTION | 23 ++++++++++++++--------- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/gettingstartedMC.pdf |binary 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Create Graph Diagrams and Flowcharts Using R
Description: Create graph diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Andrei Kashcha [aut, cph] (vivagraphjs library in htmlwidgets/lib,
https://github.com/anvaka/VivaGraphJS),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.8 dated 2015-10-08 and 0.8.1 dated 2015-10-13
DiagrammeR-0.8.1/DiagrammeR/DESCRIPTION | 10 +-- DiagrammeR-0.8.1/DiagrammeR/MD5 | 31 +++------ DiagrammeR-0.8.1/DiagrammeR/NAMESPACE | 6 - DiagrammeR-0.8.1/DiagrammeR/R/combine_graphs.R | 3 DiagrammeR-0.8.1/DiagrammeR/R/grViz.R | 32 ---------- DiagrammeR-0.8.1/DiagrammeR/R/render_graph.R | 14 ---- DiagrammeR-0.8.1/DiagrammeR/R/visnetwork.R | 5 + DiagrammeR-0.8.1/DiagrammeR/README.md | 2 DiagrammeR-0.8.1/DiagrammeR/man/combine_graphs.Rd | 3 DiagrammeR-0.8.1/DiagrammeR/man/grViz.Rd | 32 ---------- DiagrammeR-0.8.1/DiagrammeR/man/render_graph.Rd | 5 - DiagrammeR-0.8/DiagrammeR/R/graphviz_export.R |only DiagrammeR-0.8/DiagrammeR/R/roll_palette.R |only DiagrammeR-0.8/DiagrammeR/R/scale_edges.R |only DiagrammeR-0.8/DiagrammeR/R/scale_nodes.R |only DiagrammeR-0.8/DiagrammeR/man/exportSVG.Rd |only DiagrammeR-0.8/DiagrammeR/man/roll_palette.Rd |only DiagrammeR-0.8/DiagrammeR/man/scale_edges.Rd |only DiagrammeR-0.8/DiagrammeR/man/scale_nodes.Rd |only DiagrammeR-0.8/DiagrammeR/tests/testthat/test-export_SVG.R |only DiagrammeR-0.8/DiagrammeR/tests/testthat/test-roll_palette.R |only DiagrammeR-0.8/DiagrammeR/tests/testthat/test-scale_nodes_edges.R |only 22 files changed, 33 insertions(+), 110 deletions(-)
Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9.3 dated 2015-08-11 and 0.9.4 dated 2015-10-12
DESCRIPTION | 16 +-- MD5 | 47 ++++---- NAMESPACE | 2 R/CommonFG.R | 28 +++++ R/H5File.R | 99 +++++++++++++++--- R/H5Group.R | 6 - R/H5Location-Attribute.R | 14 +- R/RcppExports.R | 12 +- inst/NEWS.Rd | 13 ++ inst/test-f32.h5 |only inst/test-f32.py |only man/CommonFG.Rd | 8 + man/H5File.Rd | 96 +++++++++++++++--- src/Attribute.cpp | 56 +++++++++- src/Attribute.h | 4 src/Dataset.cpp | 9 - src/Group.cpp | 29 +---- src/Group.h | 3 src/Helpers.cpp | 192 +++++++++++++++++++----------------- src/RcppExports.cpp | 31 +++++ tests/testthat/test-Attribute.R | 44 ++++++++ tests/testthat/test-DataSet-IO-NA.R |only tests/testthat/test-DataSet.R | 17 +++ tests/testthat/test-H5File.R | 16 +++ tests/testthat/test-H5Group.R | 69 ++++++++++++ tests/testthat/test-vlen.R | 47 ++++++++ 26 files changed, 660 insertions(+), 198 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton <nick@ggtern.com>
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 1.0.6.0 dated 2015-08-03 and 1.0.6.1 dated 2015-10-12
DESCRIPTION | 10 +- MD5 | 53 ++++++------ NEWS | 10 ++ R/coord-tern.R | 39 ++------- R/data.R | 8 + R/geom-confidence.R | 59 +++++++------- R/gg-internal.R | 1 R/ggtern-build.R | 1 R/onLoad.R | 4 R/scales.R | 26 ++++-- R/stat-interpolate-tern.R | 10 ++ R/tern-render.R | 59 ++++++++------ R/theme-defaults.R | 180 +++++++++++++++++++++++++------------------- R/theme-elements.R | 5 - R/theme-noarrows.R | 4 R/utilities.R | 37 ++++++++- README.md | 3 build/partial.rdb |binary data/Feldspar.RData |binary man/coord_tern.Rd | 5 - man/data_Feldspar.Rd | 11 +- man/getBreaks.Rd |only man/scale_TLR_continuous.Rd | 26 +++--- man/theme_custom.Rd | 9 +- man/theme_elements.Rd | 1 man/theme_gray.Rd | 1 man/theme_rgbw.Rd | 4 man/themeshowhidearrows.Rd | 4 28 files changed, 335 insertions(+), 235 deletions(-)
Title: Modified Variance Estimators for Generalized Estimating
Equations
Description: Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance.
Author: Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between geesmv versions 1.2 dated 2015-08-28 and 1.3 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GEE.var.mbn.R | 2 +- man/GEE.var.mbn.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate. The analysis of paired
receiver operating curves is supported as well, so that a comparison of two predictors is possible.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.3.0 dated 2015-10-08 and 0.3.1 dated 2015-10-12
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/fbroc.methods.R | 6 ++++-- man/plot.fbroc.roc.Rd | 2 ++ 4 files changed, 14 insertions(+), 10 deletions(-)
Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) testing and correcting of publication bias in multivariate meta-analysis settings.
Author: Yong Chen, Chuan Hong, Haitao Chu
Maintainer: Yong Chen <ychen.upenn@gmail.com>
Diff between xmeta versions 1.0 dated 2015-10-02 and 1.0-1 dated 2015-10-12
DESCRIPTION | 16 ++++++++-------- MD5 | 8 +++++--- NAMESPACE | 2 +- R/galaxy.R |only man/galaxy.Rd |only man/xmeta-package.Rd | 3 ++- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between gemtc versions 0.7 dated 2015-09-09 and 0.7-1 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 +++++++ inst/gemtc.randomeffects.txt | 2 +- 4 files changed, 15 insertions(+), 8 deletions(-)
More information about batteryreduction at CRAN
Permanent link
Title: Barnard's Unconditional Test
Description: Barnard's unconditional test for 2x2 contingency tables.
Author: Kamil Erguler
Maintainer: Kamil Erguler <k.erguler@cyi.ac.cy>
Diff between Barnard versions 1.4 dated 2015-10-09 and 1.5 dated 2015-10-12
DESCRIPTION | 9 ++++---- MD5 | 6 ++--- R/barnardw.test.R | 57 ++++++++++++++++++++++++++++++--------------------- man/barnardw.test.Rd | 26 +++++++++++------------ 4 files changed, 55 insertions(+), 43 deletions(-)
Title: Bayesian Network Feature Finder
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan <zlan6@gatech.edu>
Diff between BANFF versions 0.3 dated 2015-02-16 and 1.0 dated 2015-10-12
BANFF-0.3/BANFF/R/All_functions.R |only BANFF-0.3/BANFF/R/main.R |only BANFF-1.0/BANFF/DESCRIPTION | 9 +-- BANFF-1.0/BANFF/MD5 | 43 ++++++++++++++- BANFF-1.0/BANFF/NAMESPACE | 74 ++++++++++++++------------- BANFF-1.0/BANFF/R/DPM.HODC.R |only BANFF-1.0/BANFF/R/DPdensitycluster.R |only BANFF-1.0/BANFF/R/EM.HODC.R |only BANFF-1.0/BANFF/R/Generating_Zi.R |only BANFF-1.0/BANFF/R/Gibbsfortheta.R |only BANFF-1.0/BANFF/R/Grid.Adjmatrix.Transfer.R |only BANFF-1.0/BANFF/R/HODCMclust.R |only BANFF-1.0/BANFF/R/HyperPara.Select.R |only BANFF-1.0/BANFF/R/Initial_mu_var.R |only BANFF-1.0/BANFF/R/Innerfunc.R |only BANFF-1.0/BANFF/R/Inte_Distance.R |only BANFF-1.0/BANFF/R/Iteration3_DPdensity.R |only BANFF-1.0/BANFF/R/Iteration3_DPdensity_Par.R |only BANFF-1.0/BANFF/R/Iteration3_Mclust.R |only BANFF-1.0/BANFF/R/Kmeans.R |only BANFF-1.0/BANFF/R/LikelihoodHistory.R |only BANFF-1.0/BANFF/R/Mixture.R |only BANFF-1.0/BANFF/R/Model.R |only BANFF-1.0/BANFF/R/Networks.Fast.R |only BANFF-1.0/BANFF/R/Networks.STD.R |only BANFF-1.0/BANFF/R/Parameter_Define.R |only BANFF-1.0/BANFF/R/Pi_rho_gen.R |only BANFF-1.0/BANFF/R/Pi_rho_selecting.R |only BANFF-1.0/BANFF/R/Plot.Subnetwork.R |only BANFF-1.0/BANFF/R/Step1_1_Update_gi_zi.R |only BANFF-1.0/BANFF/R/Step1_2_Check.R |only BANFF-1.0/BANFF/R/Step_2_Update_mu_var.R |only BANFF-1.0/BANFF/R/Step_3_switch_the_label.R |only BANFF-1.0/BANFF/R/Subnetwork.Select.R |only BANFF-1.0/BANFF/R/SummaryAccuracy.R |only BANFF-1.0/BANFF/R/TPR.R |only BANFF-1.0/BANFF/R/Transfer.R |only BANFF-1.0/BANFF/R/biGaussian.R |only BANFF-1.0/BANFF/R/plot.Networks.Fast.R |only BANFF-1.0/BANFF/R/plot.Networks.STD.R |only BANFF-1.0/BANFF/R/summary.Networks.Fast.R |only BANFF-1.0/BANFF/R/summary.Networks.STD.R |only 42 files changed, 83 insertions(+), 43 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@isped.u-bordeaux2.fr>
Diff between VSURF versions 1.0.0 dated 2015-05-15 and 1.0.1 dated 2015-10-12
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 14 +++++++++++++- NEWS | 9 ++++++++- R/VSURF.R | 16 ++++++++-------- R/VSURF_interp.R | 18 +++++++----------- R/VSURF_pred.R | 2 +- R/VSURF_thres.R | 27 ++++++++++++--------------- R/plot.VSURF.R | 1 + man/VSURF.Rd | 6 +++--- man/VSURF_interp.Rd | 4 ++-- man/VSURF_thres.Rd | 5 +++-- tests |only 13 files changed, 78 insertions(+), 59 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, PCA and correlation matrices, cluster analyses, scatter plots, Likert scales, effects plots of regression models (including interaction terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.8.3 dated 2015-08-26 and 1.8.4 dated 2015-10-12
DESCRIPTION | 8 MD5 | 58 NAMESPACE | 1 NEWS | 1290 +++++++------- R/helpfunctions.R | 1555 ++++++++--------- R/sjPlotAnova.R | 2 R/sjPlotFrequencies.R | 14 R/sjPlotGLME.R | 4231 +++++++++++++++++++++++------------------------ R/sjPlotInteractions.R | 2967 ++++++++++++++++---------------- R/sjPlotLinreg.R | 9 R/sjPlotLinregMultiple.R | 6 R/sjPlotPCA.R | 2 R/sjTabCorr.R | 1020 +++++------ R/sjTabDataFrame.R | 3 R/sjTabFrequencies.R | 2 R/sjTabItemAnalysis.R | 13 R/sjTabLinReg.R | 3062 +++++++++++++++++----------------- R/sjTabOdds.R | 2720 +++++++++++++++--------------- R/sjTabPCA.R | 1188 ++++++------- R/sjTabSPSS.R | 792 ++++---- R/sjTabStackFrq.R | 1038 +++++------ README.md | 36 man/sjPlot-package.Rd | 102 - man/sjp.glmer.Rd | 7 man/sjp.int.Rd | 783 ++++---- man/sjp.lm.Rd | 496 ++--- man/sjp.lmer.Rd | 7 man/sjt.glmer.Rd | 17 man/sjt.lmer.Rd | 17 man/view_df.Rd | 26 30 files changed, 10817 insertions(+), 10655 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended for people coming from other statistical software packages like 'SPSS', and/or who are new to R), supporting following common tasks:
1) Reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this includes easy ways to get and set label attributes, to convert labelled vectors into factors (and vice versa), or to deal with multiple declared missing values etc.
2) Data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values.
3) Convenient functions to perform frequently used statistical tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.1 dated 2015-08-26 and 1.2 dated 2015-10-12
DESCRIPTION | 11 - MD5 | 34 +-- NAMESPACE | 1 NEWS | 12 + R/as_labelled.R | 2 R/converge_ok.R |only R/reliab_test.R | 8 R/set_na.R | 461 ++++++++++++++++++++++++-------------------------- R/to_na.R | 136 +++++++------- R/weight.R | 8 README.md | 136 +++++--------- man/as_labelled.Rd | 2 man/converge_ok.Rd |only man/mean_n.Rd | 144 +++++++-------- man/sjmisc-package.Rd | 4 man/std_beta.Rd | 128 ++++++------- man/to_na.Rd | 2 man/weight.Rd | 10 - man/weight2.Rd | 4 19 files changed, 549 insertions(+), 554 deletions(-)
Title: Interface Between GRASS 7 Geographical Information System and R
Description: Interpreted interface between GRASS 7 geographical
information system and R, based on starting R from within the GRASS GIS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 6, for which
spgrass6 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb],
Sebastian Jeworutzki [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.1-2 dated 2015-08-23 and 0.1-3 dated 2015-10-12
ChangeLog | 1066 ---------------------------------------------------------- DESCRIPTION | 8 MD5 | 6 R/vect_link.R | 91 ++-- 4 files changed, 52 insertions(+), 1119 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 0.11 dated 2015-09-10 and 0.12 dated 2015-10-12
DESCRIPTION | 8 MD5 | 146 ++- NAMESPACE | 31 R/Clustering.R | 3 R/aggregatingAux.R | 10 R/aggregatingMeta.R | 21 R/cdist.R | 70 + R/do.R | 370 ++++++---- R/dotPlot.R | 5 R/dpqrdist.R | 32 R/favstats.R | 5 R/frequencyPolygon.R | 2 R/groupwiseModels.R |only R/integrateODE.R | 1 R/makeFun.R | 6 R/maps2.R | 9 R/mm.R | 148 ---- R/mosaic-package.R | 2 R/mplot.R | 44 - R/plotModel.R | 195 +++-- R/resample.R | 57 - R/statTally.R | 4 R/xpnorm.R | 38 - build/vignette.rds |binary inst/doc/GraphicsWithMosaic.html | 38 - inst/doc/LessVolume-MoreCreativity.Rmd | 6 inst/doc/LessVolume-MoreCreativity.html | 14 inst/doc/MinimalR.pdf |binary inst/doc/Resampling.R | 2 inst/doc/Resampling.Rnw | 2 inst/doc/Resampling.pdf |binary inst/doc/mosaic-resources.html | 4 inst/doc/plotModel-vignette.R |only inst/doc/plotModel-vignette.Rmd |only inst/doc/plotModel-vignette.html |only man/MSPE.Rd |only man/aggregating.Rd | 3 man/cdist.Rd | 23 man/cull_for_do.Rd |only man/do.Rd | 5 man/dotPlot.Rd | 2 man/freqpolygon.Rd | 2 man/gwm.Rd |only man/makeFun.Rd | 4 man/mm.Rd | 51 - man/mosaic-internal.Rd | 7 man/mplot.Rd | 12 man/nicenames.Rd | 4 man/plotModel.Rd | 9 man/pqrdata2.Rd | 15 man/qdist.Rd | 16 man/resample.Rd | 2 tests/testthat/test-aggregating.R | 11 tests/testthat/test-do.R |only tests/testthat/test-groupwiseModels.R | 34 vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-14-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-2.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-17-3.png |binary vignettes/GraphicsWithMosaic_files/figure-html/unnamed-chunk-8-2.png |binary vignettes/LessVolume-MoreCreativity.Rmd | 6 vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-50-1.png |binary vignettes/LessVolume-MoreCreativity_files/figure-html/unnamed-chunk-51-1.png |binary vignettes/Resampling.Rnw | 2 vignettes/plotModel-vignette.Rmd |only vignettes/plotModel-vignette_files |only 68 files changed, 785 insertions(+), 696 deletions(-)
Title: Preference Rating for Visual Stimuli Based on Elo Ratings
Description: Allows calculating global scores for characteristics of visual stimuli. Stimuli are presented as sequence of pairwise comparisons ('contests'), during each of which a rater expresses preference for one stimulus over the other. The algorithm for calculating global scores is based on Elo rating, which updates individual scores after each single pairwise contest. Elo rating is widely used to rank chess players according to their performance. Its core feature is that dyadic contests with expected outcomes lead to smaller changes of participants' scores than outcomes that were unexpected. As such, Elo rating is an efficient tool to rate individual stimuli when a large number of such stimuli are paired against each other in the context of experiments where the goal is to rank stimuli according to some characteristic of interest.
Author: Christof Neumann
Maintainer: Christof Neumann <christofneumann1@gmail.com>
Diff between EloChoice versions 0.28 dated 2015-10-11 and 0.29 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/NEWS.Rd | 6 ++++++ inst/doc/tutorial.Rnw | 2 +- inst/doc/tutorial.pdf |binary man/EloChoice-package.Rd | 4 ++-- src/eloint.cpp | 41 +++++++++++++++++------------------------ vignettes/tutorial.Rnw | 2 +- 8 files changed, 38 insertions(+), 39 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between embryogrowth versions 6.0 dated 2015-04-15 and 6.1 dated 2015-10-12
embryogrowth-6.0/embryogrowth/R/fonctionfit.R |only embryogrowth-6.1/embryogrowth/DESCRIPTION | 12 embryogrowth-6.1/embryogrowth/MD5 | 202 - embryogrowth-6.1/embryogrowth/NAMESPACE | 9 embryogrowth-6.1/embryogrowth/NEWS | 32 embryogrowth-6.1/embryogrowth/R/ChangeSSM.R | 8 embryogrowth-6.1/embryogrowth/R/Exponential.R | 2 embryogrowth-6.1/embryogrowth/R/FormatNests.R | 40 embryogrowth-6.1/embryogrowth/R/GRTRN_MHmcmc.R | 32 embryogrowth-6.1/embryogrowth/R/GenerateTest.R | 3 embryogrowth-6.1/embryogrowth/R/Gompertz.R | 2 embryogrowth-6.1/embryogrowth/R/Linear.R | 2 embryogrowth-6.1/embryogrowth/R/MovingIncubation.R | 337 -- embryogrowth-6.1/embryogrowth/R/SSM.R | 6 embryogrowth-6.1/embryogrowth/R/STRN_MHmcmc.R | 19 embryogrowth-6.1/embryogrowth/R/STRN_fit.R | 2 embryogrowth-6.1/embryogrowth/R/TRN_MHmcmc_p.R | 22 embryogrowth-6.1/embryogrowth/R/TSP.list.R |only embryogrowth-6.1/embryogrowth/R/embryogrowth-package.R | 12 embryogrowth-6.1/embryogrowth/R/fonctionMCMC.R | 6 embryogrowth-6.1/embryogrowth/R/gradientRichardson.R | 2 embryogrowth-6.1/embryogrowth/R/hessianRichardson.R | 2 embryogrowth-6.1/embryogrowth/R/hist.Nests.R | 6 embryogrowth-6.1/embryogrowth/R/hist.NestsResult.R | 7 embryogrowth-6.1/embryogrowth/R/info.nests.R | 952 +++++-- embryogrowth-6.1/embryogrowth/R/likelihoodR.R | 10 embryogrowth-6.1/embryogrowth/R/modelTSD.R | 5 embryogrowth-6.1/embryogrowth/R/plot.NestsResult.R | 1275 +--------- embryogrowth-6.1/embryogrowth/R/plot.tsd.R | 4 embryogrowth-6.1/embryogrowth/R/plotR.R | 14 embryogrowth-6.1/embryogrowth/R/plotR_hist.R | 36 embryogrowth-6.1/embryogrowth/R/plot_transition.R | 4 embryogrowth-6.1/embryogrowth/R/resultNest_4p.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_4p_weight.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_6p.R | 2 embryogrowth-6.1/embryogrowth/R/resultNest_newp.R | 8 embryogrowth-6.1/embryogrowth/R/result_mcmc_4p.R | 4 embryogrowth-6.1/embryogrowth/R/result_mcmc_4p_weight.R | 9 embryogrowth-6.1/embryogrowth/R/result_mcmc_6p.R | 2 embryogrowth-6.1/embryogrowth/R/result_mcmc_newp.R | 21 embryogrowth-6.1/embryogrowth/R/searchR.R | 138 - embryogrowth-6.1/embryogrowth/R/summary.Nests.R | 4 embryogrowth-6.1/embryogrowth/R/tempConst.R | 2 embryogrowth-6.1/embryogrowth/R/tsd.R | 47 embryogrowth-6.1/embryogrowth/R/tsd_MHmcmc.R | 12 embryogrowth-6.1/embryogrowth/R/tsd_MHmcmc_p.R | 11 embryogrowth-6.1/embryogrowth/R/weightmaxentropy.R | 10 embryogrowth-6.1/embryogrowth/data/STSRE_TSD.rda |binary embryogrowth-6.1/embryogrowth/data/TSP.list.rda |only embryogrowth-6.1/embryogrowth/data/resultNest_4p.rda |binary embryogrowth-6.1/embryogrowth/data/resultNest_6p.rda |binary embryogrowth-6.1/embryogrowth/data/resultNest_newp.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_4p.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_4p_weight.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_6p.rda |binary embryogrowth-6.1/embryogrowth/data/result_mcmc_newp.rda |binary embryogrowth-6.1/embryogrowth/man/ChangeSSM.Rd | 10 embryogrowth-6.1/embryogrowth/man/FormatNests.Rd | 2 embryogrowth-6.1/embryogrowth/man/GRTRN_MHmcmc.Rd | 32 embryogrowth-6.1/embryogrowth/man/GenerateAnchor.Rd | 2 embryogrowth-6.1/embryogrowth/man/GenerateConstInc.Rd | 2 embryogrowth-6.1/embryogrowth/man/GenerateTest.Rd | 2 embryogrowth-6.1/embryogrowth/man/MovingIncubation.Rd | 43 embryogrowth-6.1/embryogrowth/man/STRN.Rd | 2 embryogrowth-6.1/embryogrowth/man/STRN_MHmcmc.Rd | 9 embryogrowth-6.1/embryogrowth/man/STSRE_NestingArea.Rd | 2 embryogrowth-6.1/embryogrowth/man/STSRE_TSD.Rd | 8 embryogrowth-6.1/embryogrowth/man/TRN_MHmcmc_p.Rd | 8 embryogrowth-6.1/embryogrowth/man/TSP.list.Rd |only embryogrowth-6.1/embryogrowth/man/TestParallel.Rd | 2 embryogrowth-6.1/embryogrowth/man/dydt.Gompertz.Rd | 4 embryogrowth-6.1/embryogrowth/man/dydt.exponential.Rd | 4 embryogrowth-6.1/embryogrowth/man/dydt.linear.Rd | 4 embryogrowth-6.1/embryogrowth/man/embryogrowth-package.Rd | 14 embryogrowth-6.1/embryogrowth/man/hist.Nests.Rd | 2 embryogrowth-6.1/embryogrowth/man/hist.NestsResult.Rd | 2 embryogrowth-6.1/embryogrowth/man/info.nests.Rd | 86 embryogrowth-6.1/embryogrowth/man/likelihoodR.Rd | 2 embryogrowth-6.1/embryogrowth/man/logLik.NestsResult.Rd | 2 embryogrowth-6.1/embryogrowth/man/logLik.tsd.Rd | 2 embryogrowth-6.1/embryogrowth/man/nest.Rd | 2 embryogrowth-6.1/embryogrowth/man/plot.NestsResult.Rd | 105 embryogrowth-6.1/embryogrowth/man/plot.tsd.Rd | 2 embryogrowth-6.1/embryogrowth/man/plotR.Rd | 6 embryogrowth-6.1/embryogrowth/man/plotR_hist.Rd | 2 embryogrowth-6.1/embryogrowth/man/plot_transition.Rd | 4 embryogrowth-6.1/embryogrowth/man/predict.tsd.Rd | 6 embryogrowth-6.1/embryogrowth/man/resultNest_4p.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_4p_transition.Rd | 2 embryogrowth-6.1/embryogrowth/man/resultNest_4p_weight.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_6p.Rd | 4 embryogrowth-6.1/embryogrowth/man/resultNest_newp.Rd | 10 embryogrowth-6.1/embryogrowth/man/result_mcmc_4p.Rd | 6 embryogrowth-6.1/embryogrowth/man/result_mcmc_4p_weight.Rd | 11 embryogrowth-6.1/embryogrowth/man/result_mcmc_6p.Rd | 4 embryogrowth-6.1/embryogrowth/man/result_mcmc_newp.Rd | 23 embryogrowth-6.1/embryogrowth/man/searchR.Rd | 47 embryogrowth-6.1/embryogrowth/man/summary.Nests.Rd | 6 embryogrowth-6.1/embryogrowth/man/switch.transition.Rd | 2 embryogrowth-6.1/embryogrowth/man/tempConst.Rd | 4 embryogrowth-6.1/embryogrowth/man/tsd.Rd | 16 embryogrowth-6.1/embryogrowth/man/tsd_MHmcmc.Rd | 6 embryogrowth-6.1/embryogrowth/man/tsd_MHmcmc_p.Rd | 6 embryogrowth-6.1/embryogrowth/man/weightmaxentropy.Rd | 4 104 files changed, 1694 insertions(+), 2177 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.2 dated 2015-10-03 and 1.0.3 dated 2015-10-12
DESCRIPTION | 10 +++++----- INSTALL | 2 +- MD5 | 12 ++++++------ inst/doc/compendiumdb.pdf |binary man/compendiumdb-package.Rd | 4 ++-- man/downloadGEOdata.Rd | 2 +- man/loadDatabaseSchema.Rd | 2 +- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: IP Address Geolocation
Description: Connectors to online and offline sources for taking IP addresses and geolocating them to country, city, timezone and other geographic ranges. For individual connectors, see the package index.
Author: Oliver Keyes [aut, cre], Drew Schmidt [aut], David Robinson [ctb], Maxmind, Inc. [cph], Pascal Gloor [cph]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between rgeolocate versions 0.4.1 dated 2015-07-25 and 0.5.0 dated 2015-10-12
rgeolocate-0.4.1/rgeolocate/R/freegeoip.R |only rgeolocate-0.4.1/rgeolocate/man/freegeoip.Rd |only rgeolocate-0.4.1/rgeolocate/tests/testthat/test_freegeoip.R |only rgeolocate-0.5.0/rgeolocate/DESCRIPTION | 12 rgeolocate-0.5.0/rgeolocate/MD5 | 49 - rgeolocate-0.5.0/rgeolocate/NAMESPACE | 1 rgeolocate-0.5.0/rgeolocate/NEWS | 13 rgeolocate-0.5.0/rgeolocate/R/maxmind.R | 17 rgeolocate-0.5.0/rgeolocate/R/telize.R | 2 rgeolocate-0.5.0/rgeolocate/README.md | 5 rgeolocate-0.5.0/rgeolocate/build/vignette.rds |binary rgeolocate-0.5.0/rgeolocate/configure | 29 - rgeolocate-0.5.0/rgeolocate/configure.ac | 14 rgeolocate-0.5.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.Rmd | 2 rgeolocate-0.5.0/rgeolocate/inst/doc/Introduction_to_rgeolocate.html | 276 ++-------- rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-Anonymous-IP-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-City-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/inst/extdata/GeoIP2-Precision-City-Test.mmdb |only rgeolocate-0.5.0/rgeolocate/man/maxmind.Rd | 15 rgeolocate-0.5.0/rgeolocate/man/telize.Rd | 2 rgeolocate-0.5.0/rgeolocate/src/Makevars.win | 2 rgeolocate-0.5.0/rgeolocate/src/config.h.in | 6 rgeolocate-0.5.0/rgeolocate/src/maxmind.cpp | 71 ++ rgeolocate-0.5.0/rgeolocate/src/maxmind.h | 4 rgeolocate-0.5.0/rgeolocate/src/maxminddb_config.h | 25 rgeolocate-0.5.0/rgeolocate/tests/testthat/test_ip_api.R | 13 rgeolocate-0.5.0/rgeolocate/tests/testthat/test_maxmind.R | 35 + rgeolocate-0.5.0/rgeolocate/vignettes/Introduction_to_rgeolocate.Rmd | 2 rgeolocate-0.5.0/rgeolocate/vignettes/Introduction_to_rgeolocate.md |only 29 files changed, 239 insertions(+), 356 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network
representation that offers unmatched efficiency, modularity,
and extensibility. FCNN4R provides standard teaching
(backpropagation, Rprop, simulated annealing) and pruning algorithms
(minimum magnitude, Optimal Brain Surgeon), but it is first
and foremost an efficient computational engine. Users can easily
implement their algorithms by taking advantage of fast gradient
computing routines, as well as network reconstruction functionality
(removing weights and redundant neurons).
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.4.1 dated 2015-08-26 and 0.5.0 dated 2015-10-12
DESCRIPTION | 29 ++++------ MD5 | 39 +++++++------ NAMESPACE | 3 + R/mlp_gteach.R |only R/mlp_net.R | 97 +++++++++++++++++++++------------- R/mlp_plot.R | 41 ++++++++------ R/mlp_teach.R | 6 +- man/FCNN4R-package.Rd | 50 ++++++++++------- man/mlp_export_C.Rd | 10 +-- man/mlp_net-combining-two-networks.Rd | 6 +- man/mlp_net-export-import.Rd | 8 +- man/mlp_net.Rd | 6 +- man/mlp_teach_bp.Rd | 2 man/mlp_teach_grprop.Rd |only man/mlp_teach_rprop.Rd | 4 - man/mlp_teach_sa.Rd |only src/fcnn/export.cpp | 6 +- src/fcnn/level1.h | 42 ++++++++------ src/fcnn/level3.cpp | 3 - src/fcnn/struct.cpp | 48 ++++++++++++---- src/fcnn/utils.cpp | 12 ++++ src/fcnn/utils.h | 4 + 22 files changed, 253 insertions(+), 163 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: An easily accessible continuous (and discrete) time dynamic
modelling package for panel and time series data, reliant upon the OpenMx.
package (http://openmx.psyc.virginia.edu/) for computation. Most
dynamic modelling approaches to longitudinal data rely on the assumption
that time intervals between observations are consistent. When this
assumption is adhered to, the data gathering process is necessarily limited
to a specific schedule, and when broken, the resulting parameter estimates
may be biased and reduced in power. Continuous time models are
conceptually similar to vector autoregressive models (thus also the latent
change models popularised in a structural equation modelling context),
however by explicitly including the length of time between observations,
continuous time models are freed from the assumption that measurement
intervals are consistent. This allows: data to be gathered irregularly;
the elimination of noise and bias due to varying measurement intervals;
parsimonious structures for complex dynamics.
The application of such a model in this SEM framework allows full-information
maximum-likelihood estimates for both N = 1 and N > 1 cases, multiple
measured indicators per latent process, and the flexibility to incorporate
additional elements, including individual heterogeneity in the latent
process and manifest intercepts, and time dependent and independent
exogenous covariates. Furthermore, due to the SEM implementation we are
able to estimate a random effects model where the impact of time dependent
and time independent predictors can be assessed simultaneously, but without
the classic problems of random effects models assuming no covariance
between unit level effects and predictors.
Author: Manuel Voelkle [aut, cph] (Original development of continuous time
model specification within OpenMx, advisor for further development),
Han Oud [aut, cph] (Original development of continuous time model
specification within OpenMx),
Charles Driver [aut, cre, cph] (Further development of continuous time
model specification within OpenMx, package development,
documentation and maintenance)
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 1.1.1 dated 2015-08-10 and 1.1.3 dated 2015-10-12
DESCRIPTION | 12 MD5 | 63 - NAMESPACE | 4 R/ctCI.R |only R/ctDeintervalise.R | 12 R/ctFit.R | 807 ++++++++++++------ R/ctGenerate.R | 30 R/ctLabel.R | 1 R/ctModel.R | 4 R/ctMultigroupFit.R | 31 R/ctPSMfit.R |only R/ctsem.R | 5 R/plot.ctsemFit.R | 247 ++++- R/summary.ctsemFit.R | 424 ++++++--- build/vignette.rds |binary data/ctExample1.rda |binary data/ctExample1TIpred.rda |binary inst/doc/ctsem.R | 296 ++++-- inst/doc/ctsem.pdf |binary inst/doc/ctsem.rnw | 640 +++++++++----- man/ctCI.Rd |only man/ctFit.Rd | 75 + man/ctGenerate.Rd | 22 man/ctModel.Rd | 3 man/ctMultigroupFit.Rd | 14 man/ctPSMfit.Rd |only man/ctsem.Rd | 5 man/plot.ctsemFit.Rd | 17 man/plot.ctsemMultigroupFit.Rd |only man/summary.ctsemFit.Rd | 16 man/summary.ctsemMultigroupFit.Rd |only vignettes/ctsem.rnw | 640 +++++++++----- vignettes/ctsem_paper_source.zip |only vignettes/pathdiagramtwoprocessbasic.pdf |binary vignettes/pathdiagramtwoprocessfull2.pdf |binary vignettes/references.bib | 1343 +++++++++++++++++-------------- 36 files changed, 2996 insertions(+), 1715 deletions(-)
Title: Get Hourly Meteorological Data from Global Stations
Description: Selectively acquire hourly meteorological data from stations located all over the world.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between stationaRy versions 0.3 dated 2015-06-23 and 0.4 dated 2015-10-12
DESCRIPTION | 14 MD5 | 32 NAMESPACE | 13 R/get_isd_station_data.R | 2211 ++++++++++++++++++++++++++++++++++++++++++-- R/get_isd_stations.R | 79 + R/map_isd_stations.R |only R/select_isd_station.R | 45 README.md | 246 +++- inst/000000-00000-2015.gz |only inst/999999-63897-2013.gz |only inst/999999-63897-2014.gz |only inst/999999-63897-2015.gz |only inst/stations.rda |binary inst/stations_map.png |only man/get_isd_station_data.Rd | 104 +- man/get_isd_stations.Rd | 37 man/map_isd_stations.Rd |only man/select_isd_station.Rd | 11 tests |only 19 files changed, 2569 insertions(+), 223 deletions(-)
Title: Integration of One-Dimensional Functions with Double Exponential
Formulas
Description: Numerical quadrature of functions of one variable over a finite or infinite interval
with double exponential formulas.
Author: Hiroyuki Okamura
Maintainer: Hiroyuki Okamura <okamu@rel.hiroshima-u.ac.jp>
Diff between deformula versions 0.1.0 dated 2015-10-09 and 0.1.1 dated 2015-10-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/deformula-package.Rd | 4 ++-- src/R_deformula.cpp | 4 ++-- src/deformula.cpp | 3 ++- src/include/deformula.hpp | 7 +++++-- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Edit, Run and Evaluate APSIM Simulations Easily Using R
Description: The Agricultural Production Systems sIMulator (APSIM) is a widely
used simulator of agricultural systems. This package includes
functions to create, edit and run APSIM simulations from R. It
also includes functions to visualize the results of an APSIM simulation
and perform sensitivity/uncertainty analysis of APSIM either via functions
in the sensitivity package or by novel emulator-based functions.
For more on APSIM including download instructions go to
\url{www.apsim.info}.
Author: Bryan Stanfill
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between apsimr versions 1.1 dated 2015-07-29 and 1.2 dated 2015-10-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 9 +++++++++ R/runAPSIM.R | 6 +++--- R/visualize.R | 9 +++++++-- build/vignette.rds |binary inst/doc/apsimr-basics.pdf |binary man/apsimr-package.Rd | 6 +++--- 8 files changed, 34 insertions(+), 20 deletions(-)
Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel hydraulics.
Provides functions for computing normal and critical depths, steady-state
water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 0.9.2 dated 2015-04-01 and 1.0 dated 2015-10-11
DESCRIPTION | 14 ++--- MD5 | 45 +++++++++------- NAMESPACE | 15 ++++- R/graduallyvariedflow_v2.r | 94 +++++++++++++++++++---------------- R/rivr-methods.r |only R/route_wave_v4.r | 36 +++++++++---- R/zzz.r |only build/vignette.rds |binary inst/doc/quickstart.R | 4 + inst/doc/quickstart.Rmd | 24 ++++++++ inst/doc/quickstart.html | 102 +++++++++++++++++++++++++++++++++----- inst/doc/technical-vignette.R |only inst/doc/technical-vignette.Rmd |only inst/doc/technical-vignette.html |only man/channel_geom.Rd | 2 man/compute_profile.Rd | 2 man/conveyance.Rd | 2 man/critical_depth.Rd | 2 man/froude.Rd | 2 man/normal_depth.Rd | 2 man/rivr-package.Rd | 9 --- man/route_wave.Rd | 2 man/waterolympics.Rd | 2 src/rivmech_characteristic_v7.cpp | 20 ++++++- vignettes/channeldiagram.png |only vignettes/quickstart.Rmd | 24 ++++++++ vignettes/technical-vignette.Rmd |only 27 files changed, 292 insertions(+), 111 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.6.1 dated 2015-10-11 and 0.6.2 dated 2015-10-11
PRIMsrc-0.6.1/PRIMsrc/inst/doc/PRIMsrc_0.6.1.pdf |only PRIMsrc-0.6.2/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.2/PRIMsrc/MD5 | 8 PRIMsrc-0.6.2/PRIMsrc/R/PRIMsrc.r | 22 - PRIMsrc-0.6.2/PRIMsrc/inst/NEWS | 268 +++++++++++------------ PRIMsrc-0.6.2/PRIMsrc/inst/doc/PRIMsrc_0.6.2.pdf |only 6 files changed, 153 insertions(+), 153 deletions(-)
Title: Hybrid Bayesian Networks Using R and JAGS
Description: Facilities for easy implementation of hybrid Bayesian networks
using R. Bayesian networks are directed acyclic graphs representing joint
probability distributions, where each node represents a random variable and
each edge represents conditionality. The full joint distribution is
therefore factorized as a product of conditional densities, where each node
is assumed to be independent of its non-descendents given information on its
parent nodes. Since exact, closed-form algorithms are computationally
burdensome for inference within hybrid networks that contain a combination
of continuous and discrete nodes, particle-based approximation techniques
like Markov Chain Monte Carlo are popular. We provide a user-friendly
interface to constructing these networks and running inference using the 'rjags' package.
Econometric analyses (maximum expected utility under competing policies,
value of information) involving decision and utility nodes are also
supported.
Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between HydeNet versions 0.9.0 dated 2015-07-02 and 0.10.0 dated 2015-10-11
DESCRIPTION | 16 MD5 | 120 ++- NEWS | 27 R/HydeNetwork.R | 181 ++-- R/HydePosterior.R | 9 R/HydeUtilities.R | 53 + R/PolicyMatrix.R | 21 R/bindPosterior.R | 43 - R/compileDecisionModel.R | 157 +++- R/compileJagsModel.R | 84 -- R/cpt.R | 155 +--- R/inputCPT.R | 46 - R/modelToNode.R | 15 R/plot.HydeNetwork.R | 16 R/rToJags.R | 2 R/setNode.R | 150 ++-- R/setNodeModels.R | 51 - R/writeJagsModel.R | 8 README.md | 7 build/vignette.rds |binary data/jagsFunctions.RData |binary inst/doc/DecisionNetworks.R | 11 inst/doc/DecisionNetworks.Rmd | 30 inst/doc/DecisionNetworks.html | 981 +++++++++++--------------- inst/doc/GettingStartedWithHydeNet.R | 12 inst/doc/GettingStartedWithHydeNet.Rmd | 29 inst/doc/GettingStartedWithHydeNet.html | 723 ++++++------------- inst/doc/HydeNetPlots.R | 76 +- inst/doc/HydeNetPlots.Rmd | 42 - inst/doc/HydeNetPlots.html | 501 ++++--------- inst/doc/WorkingWithHydeNetObjects.R | 8 inst/doc/WorkingWithHydeNetObjects.Rmd | 32 inst/doc/WorkingWithHydeNetObjects.html | 1187 ++++++++++++-------------------- inst/img |only man/HydeNetwork.Rd | 6 man/HydePosterior.Rd | 14 man/compileDecisionModel.Rd | 11 man/setNode.Rd | 18 man/setNodeModels.Rd | 2 tests |only vignettes/DecisionNetworks.Rmd | 30 vignettes/GettingStartedWithHydeNet.Rmd | 29 vignettes/HydeNetPlots.Rmd | 42 - vignettes/WorkingWithHydeNetObjects.Rmd | 32 vignettes/vignette_images |only 45 files changed, 2198 insertions(+), 2779 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de> and Alexander Ristig <alexander.ristig@univie.ac.at>
Maintainer: Alexander Ristig <alexander.ristig@univie.ac.at>
Diff between HAC versions 1.0-3 dated 2015-05-12 and 1.0-4 dated 2015-10-11
DESCRIPTION | 14 - MD5 | 24 +-- NAMESPACE | 5 R/estimate.r | 2 build/vignette.rds |binary inst/ChangeLog | 12 - inst/doc/HAC.R | 333 +++++++++++++++++++++++------------------------ inst/doc/HAC.Rnw | 86 +++++------- inst/doc/HAC.pdf |binary man/estimate.copula.Rd | 4 vignettes/HAC-speed2.pdf |binary vignettes/HAC.Rnw | 86 +++++------- vignettes/ref.bib | 34 ++++ 13 files changed, 307 insertions(+), 293 deletions(-)
Title: Selecting Variables in Regression Models
Description: A simple method
to select the best model or best subset of variables using
different types of data (binary, Gaussian or Poisson) and
applying it in different contexts (parametric or non-parametric).
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between FWDselect versions 2.0 dated 2015-05-17 and 2.0.1 dated 2015-10-11
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 12 +++++++++++- NEWS | 16 +++++++++++++--- R/FWDselect.R | 2 +- R/plot.qselection.R | 2 ++ R/qselection.R | 8 +++++++- R/selection.R | 31 ++++++++++++++++++++++--------- R/test.R | 40 ++++++++++++++++++++++++++++++---------- man/FWDselect.Rd | 2 +- man/qselection.Rd | 8 +++++++- man/selection.Rd | 8 +++++++- man/test.Rd | 14 +++++++++++--- 13 files changed, 129 insertions(+), 48 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.13 dated 2015-08-24 and 0.99.14 dated 2015-10-11
DESCRIPTION | 8 MD5 | 73 - NAMESPACE | 13 NEWS | 37 R/DescTools.r | 2879 +++------------------------------------- R/FastDesc.R | 389 +++++ R/SpecialPlots.r |only R/Tables.r |only data/d.whisky.rda |only demo/plots.R | 16 inst/doc/DescToolsCompanion.pdf |binary inst/doc/TablesInR.pdf |binary man/Assocs.Rd | 4 man/Canvas.Rd | 9 man/ColToRgb.Rd | 10 man/CramerV.Rd | 10 man/Desc.table.Rd | 26 man/DescTools-package.Rd | 5 man/GCD.Rd | 2 man/Gini.Rd | 3 man/HotellingsT.Rd | 2 man/PDFManual.Rd | 6 man/PercTable.Rd | 18 man/Permn.Rd | 18 man/PlotBubble.Rd | 24 man/PlotDesc.Rd | 10 man/PlotFdist.Rd | 3 man/PlotHorizBar.Rd | 2 man/PlotMiss.Rd |only man/PlotQQ.Rd | 18 man/PlotRCol.Rd | 6 man/RgbToCol.Rd | 11 man/SmoothSpline.Rd |only man/Stamp.Rd | 18 man/TOne.Rd | 9 man/d.whisky.Rd |only man/identify.formula.Rd | 12 man/like.Rd | 3 man/lines.loess.Rd | 18 src/aux_fct.cpp | 7 tests |only 41 files changed, 907 insertions(+), 2762 deletions(-)
Title: Robust Selection of Cluster Number K
Description: Facilitates optimal clustering of a data set. Provides a framework to run a wide range of clustering algorithms to determine the optimal number (k) of clusters in the data. Then analyzes the cluster assignments from each clustering algorithm to identify samples that repeatedly classify to the same group. We call these 'core clusters', providing a basis for later class discovery.
Author: Albert Chen [aut, cre], Timothy E Sweeney [aut], Olivier Gevaert [ths]
Maintainer: Albert Chen <acc2015@stanford.edu>
Diff between COMMUNAL versions 1.0 dated 2015-02-11 and 1.1.0 dated 2015-10-11
COMMUNAL-1.0/COMMUNAL/vignettes/COMMUNAL-001.pdf |only COMMUNAL-1.1.0/COMMUNAL/DESCRIPTION | 14 COMMUNAL-1.1.0/COMMUNAL/MD5 | 51 COMMUNAL-1.1.0/COMMUNAL/NAMESPACE | 8 COMMUNAL-1.1.0/COMMUNAL/R/communal.R | 738 ++++++++----- COMMUNAL-1.1.0/COMMUNAL/R/extract_core.R | 9 COMMUNAL-1.1.0/COMMUNAL/R/plot_range_3d.R | 418 +++++-- COMMUNAL-1.1.0/COMMUNAL/R/test_range.R | 106 + COMMUNAL-1.1.0/COMMUNAL/build/vignette.rds |binary COMMUNAL-1.1.0/COMMUNAL/data/BRCA.100.RData |binary COMMUNAL-1.1.0/COMMUNAL/data/BRCA.results.RData |binary COMMUNAL-1.1.0/COMMUNAL/inst/CITATION |only COMMUNAL-1.1.0/COMMUNAL/inst/doc/COMMUNAL.R | 227 +-- COMMUNAL-1.1.0/COMMUNAL/inst/doc/COMMUNAL.Rnw | 302 ++--- COMMUNAL-1.1.0/COMMUNAL/inst/doc/COMMUNAL.pdf |binary COMMUNAL-1.1.0/COMMUNAL/man/BRCA.results.Rd | 7 COMMUNAL-1.1.0/COMMUNAL/man/COMMUNAL-class.Rd | 2 COMMUNAL-1.1.0/COMMUNAL/man/COMMUNAL-package.Rd | 31 COMMUNAL-1.1.0/COMMUNAL/man/COMMUNAL.Rd | 212 ++- COMMUNAL-1.1.0/COMMUNAL/man/clusterKeys.Rd | 13 COMMUNAL-1.1.0/COMMUNAL/man/clusterRange.Rd | 118 +- COMMUNAL-1.1.0/COMMUNAL/man/examineCounts.Rd | 6 COMMUNAL-1.1.0/COMMUNAL/man/measureMonotonic.Rd |only COMMUNAL-1.1.0/COMMUNAL/man/plotRange3D.Rd | 51 COMMUNAL-1.1.0/COMMUNAL/man/returnCore.Rd | 6 COMMUNAL-1.1.0/COMMUNAL/man/testAlgsMinSize.Rd |only COMMUNAL-1.1.0/COMMUNAL/vignettes/COMMUNAL-concordance.tex |only COMMUNAL-1.1.0/COMMUNAL/vignettes/COMMUNAL.Rnw | 302 ++--- COMMUNAL-1.1.0/COMMUNAL/vignettes/framed.sty |only COMMUNAL-1.1.0/COMMUNAL/vignettes/snapshot.png |only 30 files changed, 1511 insertions(+), 1110 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where blocks
can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each set of
nested blocks optimized within the levels of any existing higher-level blocks.
Block sizes are equal if the number of blocks exactly divides the number of plots,
otherwise they differ by at most one plot. The design output is a data
table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.7 dated 2015-08-21 and 1.8 dated 2015-10-11
DESCRIPTION | 8 MD5 | 8 R/blocks.r | 503 +++++++++++++++++++++++++------------------------------ R/upper_bounds.r | 25 +- man/blocks.Rd | 33 +-- 5 files changed, 267 insertions(+), 310 deletions(-)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and
fuzzy multisets, customizable sets, and intervals.
Author: David Meyer [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between sets versions 1.0-15 dated 2015-07-08 and 1.0-16 dated 2015-10-11
sets-1.0-15/sets/inst/doc/sets.bib |only sets-1.0-16/sets/DESCRIPTION | 6 +++--- sets-1.0-16/sets/MD5 | 18 +++++++++--------- sets-1.0-16/sets/NAMESPACE | 10 ++++++++++ sets-1.0-16/sets/build/vignette.rds |binary sets-1.0-16/sets/data/fuzzy_docs.rda |binary sets-1.0-16/sets/inst/NEWS.Rd | 13 ++++++++++--- sets-1.0-16/sets/inst/doc/sets.Rnw | 2 +- sets-1.0-16/sets/inst/doc/sets.pdf |binary sets-1.0-16/sets/man/sets-internal.Rd |only sets-1.0-16/sets/vignettes/sets.Rnw | 2 +- 11 files changed, 34 insertions(+), 17 deletions(-)
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre],
Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between relations versions 0.6-5 dated 2015-04-30 and 0.6-6 dated 2015-10-11
DESCRIPTION | 8 ++-- MD5 | 36 ++++++++++----------- R/algebra.R | 2 - R/charfun.R | 4 +- R/domain.R | 2 - R/dual.R | 2 - R/getters.R | 2 - R/graph.R | 14 ++++---- R/relation.R | 8 ++-- R/utilities.R | 2 - build/vignette.rds |binary data/Cetacea.rda |binary data/Felines.rda |binary data/SVM_Benchmarking_Classification.rda |binary data/SVM_Benchmarking_Classification_Consensus.rda |binary data/SVM_Benchmarking_Regression.rda |binary data/SVM_Benchmarking_Regression_Consensus.rda |binary inst/NEWS.Rd | 27 +++++++++++++++ inst/doc/relations.pdf |binary 19 files changed, 66 insertions(+), 41 deletions(-)
Title: Matplotlib Default Color Map
Description: Port of the new 'matplotlib' color maps ('viridis' - the default -,
'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/>
is a popular plotting library for 'python'. These color maps are designed in
such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3 dated 2015-10-11 and 0.3.1 dated 2015-10-11
DESCRIPTION | 22 ++++++++++++---------- MD5 | 6 +++--- README.md | 3 +++ inst/doc/intro-to-viridis.html | 6 +++--- 4 files changed, 21 insertions(+), 16 deletions(-)
Title: Quantification of Pinned Microbial Cultures
Description: The goal of this package is to allow users to robustly
and quickly grid and quantify sizes of pinned colonies in plate images.
gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately.
It includes several image pre-processing techniques, such
as autorotation of plates, noise removal, contrast adjustment and image
resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih <wagih@ebi.ac.uk>
Diff between gitter versions 1.1 dated 2015-10-09 and 1.1.1 dated 2015-10-11
gitter-1.1.1/gitter/CHANGES | 6 ++++++ gitter-1.1.1/gitter/DESCRIPTION | 15 +++++++-------- gitter-1.1.1/gitter/MD5 | 18 +++++++++--------- gitter-1.1.1/gitter/R/Help.R |only gitter-1.1.1/gitter/R/Main.R |only gitter-1.1.1/gitter/R/Peaks.R |only gitter-1.1.1/gitter/build/BUILD.R | 2 +- gitter-1.1.1/gitter/man/gitter.Rd | 2 +- gitter-1.1.1/gitter/man/gitter.batch.Rd | 2 +- gitter-1.1.1/gitter/man/gitter.demo.Rd | 2 +- gitter-1.1/gitter/R/help.r |only gitter-1.1/gitter/R/main.r |only gitter-1.1/gitter/R/peaks.r |only 13 files changed, 26 insertions(+), 21 deletions(-)
Title: Another Object Orientation System
Description: Another implementation of object-orientation in R. It provides
syntactic sugar for the S4 class system and two alternative new
implementations. One is an experimental version built around S4
and the other one makes it more convenient to work with lists as objects.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between aoos versions 0.3.0 dated 2015-08-06 and 0.4.0 dated 2015-10-11
aoos-0.3.0/aoos/R/Accessor.R |only aoos-0.3.0/aoos/R/Binary.R |only aoos-0.3.0/aoos/R/Infix.R |only aoos-0.3.0/aoos/R/Private.R |only aoos-0.3.0/aoos/R/Show.R |only aoos-0.3.0/aoos/R/aoos.R |only aoos-0.3.0/aoos/R/defineClass.R |only aoos-0.3.0/aoos/R/defineRefClass.R |only aoos-0.3.0/aoos/R/helper.R |only aoos-0.3.0/aoos/R/packageStartupMessage.R |only aoos-0.3.0/aoos/R/public-interfaces.R |only aoos-0.3.0/aoos/R/retList.R |only aoos-0.3.0/aoos/tests/testthat/test-Accessor.R |only aoos-0.3.0/aoos/tests/testthat/test-Binary.R |only aoos-0.3.0/aoos/tests/testthat/test-Class.R |only aoos-0.3.0/aoos/tests/testthat/test-Infix.R |only aoos-0.3.0/aoos/tests/testthat/test-basics.R |only aoos-0.3.0/aoos/tests/testthat/test-inheritance.R |only aoos-0.3.0/aoos/tests/testthat/test-publicInterface.R |only aoos-0.3.0/aoos/tests/testthat/test-retList.R |only aoos-0.3.0/aoos/tests/testthat/test-self.R |only aoos-0.3.0/aoos/tests/testthat/test-summary.R |only aoos-0.4.0/aoos/DESCRIPTION | 25 +- aoos-0.4.0/aoos/MD5 | 106 ++++++----- aoos-0.4.0/aoos/NAMESPACE | 16 + aoos-0.4.0/aoos/NEWS | 63 +++++- aoos-0.4.0/aoos/R/DC-Binary.R |only aoos-0.4.0/aoos/R/DC-Show.R |only aoos-0.4.0/aoos/R/DC-aoos.R |only aoos-0.4.0/aoos/R/DC-defineClass.R |only aoos-0.4.0/aoos/R/DC-public-interfaces.R |only aoos-0.4.0/aoos/R/NAMESPACE.R | 7 aoos-0.4.0/aoos/R/RL-Infix.R |only aoos-0.4.0/aoos/R/RL-envHelper.R |only aoos-0.4.0/aoos/R/RL-retList.R |only aoos-0.4.0/aoos/R/S4-expressions.R |only aoos-0.4.0/aoos/R/S4-generics-test.R |only aoos-0.4.0/aoos/R/S4-generics.R |only aoos-0.4.0/aoos/R/S4-roxygen-parser.R |only aoos-0.4.0/aoos/R/S4-types.R |only aoos-0.4.0/aoos/R/S4RC-Accessor.R |only aoos-0.4.0/aoos/R/S4RC-Private.R |only aoos-0.4.0/aoos/R/S4RC-defineRefClass.R |only aoos-0.4.0/aoos/build/vignette.rds |binary aoos-0.4.0/aoos/inst/doc/Introduction.R | 3 aoos-0.4.0/aoos/inst/doc/Introduction.Rmd | 51 ++++- aoos-0.4.0/aoos/inst/doc/Introduction.html | 6 aoos-0.4.0/aoos/inst/doc/S4SyntacticSugar.R |only aoos-0.4.0/aoos/inst/doc/S4SyntacticSugar.Rmd |only aoos-0.4.0/aoos/inst/doc/S4SyntacticSugar.html |only aoos-0.4.0/aoos/inst/doc/aoosClasses.html | 4 aoos-0.4.0/aoos/inst/doc/performance.html | 26 +- aoos-0.4.0/aoos/inst/doc/referenceClasses.html | 4 aoos-0.4.0/aoos/inst/doc/retListClasses.html | 8 aoos-0.4.0/aoos/man/Accessor.Rd | 2 aoos-0.4.0/aoos/man/Binary.Rd | 2 aoos-0.4.0/aoos/man/Infix.Rd | 2 aoos-0.4.0/aoos/man/Private.Rd | 2 aoos-0.4.0/aoos/man/S4generics.Rd |only aoos-0.4.0/aoos/man/Show.Rd | 2 aoos-0.4.0/aoos/man/aoos.Rd | 6 aoos-0.4.0/aoos/man/defineClass.Rd | 2 aoos-0.4.0/aoos/man/defineRefClass.Rd | 2 aoos-0.4.0/aoos/man/envHelper.Rd | 2 aoos-0.4.0/aoos/man/genericTest.Rd |only aoos-0.4.0/aoos/man/grapes-type-grapes.Rd |only aoos-0.4.0/aoos/man/parser.Rd |only aoos-0.4.0/aoos/man/publicInterface.Rd | 2 aoos-0.4.0/aoos/man/retList.Rd | 24 +- aoos-0.4.0/aoos/tests/testthat/test-00-S4RC-defineRefClass.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-Binary.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-basics.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-inheritance.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-publicInterface.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-self.R |only aoos-0.4.0/aoos/tests/testthat/test-DC-summary.R |only aoos-0.4.0/aoos/tests/testthat/test-RL-Infix.R |only aoos-0.4.0/aoos/tests/testthat/test-RL-retList.R |only aoos-0.4.0/aoos/tests/testthat/test-S4-generics.R |only aoos-0.4.0/aoos/tests/testthat/test-S4-types.R |only aoos-0.4.0/aoos/tests/testthat/test-S4RC-Accessor.R |only aoos-0.4.0/aoos/vignettes/Introduction.Rmd | 51 ++++- aoos-0.4.0/aoos/vignettes/S4SyntacticSugar.Rmd |only 83 files changed, 301 insertions(+), 117 deletions(-)
Title: Regular Expression Removal, Extraction, and Replacement Tools
Description: A collection of regular expression tools associated with
the 'qdap' package that may be useful outside of the context of
discourse analysis. Tools include
removal/extraction/replacement of abbreviations, dates, dollar
amounts, email addresses, hash tags, numbers, percentages,
citations, person tags, phone numbers, times, and zip codes.
Author: Jason Gray [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapRegex versions 0.5.0 dated 2015-08-16 and 0.5.1 dated 2015-10-11
DESCRIPTION | 18 +- MD5 | 16 +- NEWS | 10 + README.md | 246 ++++++++++++++++++++-------------------- data/regex_cheat.rda |binary data/regex_supplement.rda |binary data/regex_usa.rda |binary inst/CITATION | 4 tests/testthat/test-rm_number.R | 10 - 9 files changed, 162 insertions(+), 142 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to correct for
the sample selection bias from observed outcomes in matching
markets. This includes one-sided matching of agents into
groups as well as two-sided matching of students to schools.
The package also contains R code for three matching algorithms:
the deferred-acceptance (or Gale-Shapley) algorithm for
stable marriage and college admissions problems, the
top-trading-cycles algorithm for house allocation and a
partitioning linear programme for the roommates problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 0.1-6 dated 2015-10-06 and 0.1-7 dated 2015-10-11
matchingMarkets-0.1-6/matchingMarkets/NEWS |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/1_Introduction.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/2_Example.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/3_StructuralModel.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/AppendixA.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/AppendixC.Rnw |only matchingMarkets-0.1-6/matchingMarkets/vignettes/Sections/AppendixD.Rnw |only matchingMarkets-0.1-7/matchingMarkets/DESCRIPTION | 31 ++-- matchingMarkets-0.1-7/matchingMarkets/MD5 | 34 ++--- matchingMarkets-0.1-7/matchingMarkets/NEWS.md |only matchingMarkets-0.1-7/matchingMarkets/README.md |only matchingMarkets-0.1-7/matchingMarkets/inst/doc/matching.Rnw | 43 +----- matchingMarkets-0.1-7/matchingMarkets/inst/doc/matching.pdf |binary matchingMarkets-0.1-7/matchingMarkets/man/matchingMarkets-package.Rd | 3 matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/1_Introduction.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/2_Example.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/3_StructuralModel.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/4_MonteCarloResults.Rnw | 35 ++--- matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/5_Application.Rnw | 6 matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/6_Conclusion.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixA.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixB.Rnw | 66 +++++----- matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixC.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/Sections/AppendixD.tex |only matchingMarkets-0.1-7/matchingMarkets/vignettes/matching.Rnw | 43 +----- matchingMarkets-0.1-7/matchingMarkets/vignettes/matching.bib | 39 +++++ 26 files changed, 158 insertions(+), 142 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb],
Tengfei Yin [ctb],
Nan Xiao [aut, cre]
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between liftr versions 0.2 dated 2015-07-31 and 0.3 dated 2015-10-11
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NEWS.md | 11 +++++++++++ R/drender.R | 10 +++++++--- R/lift.R | 18 +++++++++++------- build/vignette.rds |binary inst/Dockerfile.Rmd | 4 +++- inst/cranpkg.Rmd |only inst/doc/liftr-intro.Rmd | 6 +++--- inst/doc/liftr-intro.html | 12 ++++++------ man/drender.Rd | 8 +++++--- man/lift.Rd | 4 ++-- vignettes/liftr-intro.Rmd | 6 +++--- 13 files changed, 67 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-03 1.0.3
Title: Matplotlib Default Color Map
Description: Port of the new Matplotlib default color map ('viridis') to R.
This color map is designed in such a way that it will analytically be
perfectly perceptually-uniform, both in regular form and also when
converted to black-and-white. It is also designed to be perceived by
readers with the most common form of color blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.2.5 dated 2015-09-14 and 0.3 dated 2015-10-11
DESCRIPTION | 14 - MD5 | 31 +- NAMESPACE | 4 R/scales.R | 192 +++++++++-------- R/viridis.R | 71 +++++- README.md | 35 +-- build/vignette.rds |binary data/viridis.map.rda |binary inst/doc/intro-to-viridis.R | 145 +++++++++---- inst/doc/intro-to-viridis.Rmd | 276 +++++++++++++++++++------ inst/doc/intro-to-viridis.html | 213 ++++++++++++------- man/scale_viridis.Rd | 25 +- man/viridis.Rd | 29 ++ man/viridis.map.Rd | 3 man/viridis_pal.Rd | 6 vignettes/intro-to-viridis.Rmd | 276 +++++++++++++++++++------ vignettes/us.tmax_nohads_ll_20150219_float.tif |only 17 files changed, 933 insertions(+), 387 deletions(-)
Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>
Diff between RNeo4j versions 1.5.1 dated 2015-09-11 and 1.6.0 dated 2015-10-11
DESCRIPTION | 8 +-- MD5 | 20 +++---- R/allShortestPaths.R | 2 R/cypherToList.R | 2 R/internal.R | 12 ++-- R/shortestPath.R | 2 man/allShortestPaths.Rd | 2 man/shortestPath.Rd | 2 tests/testthat/test-cypherToList.R | 39 +++++++++++++++ tests/testthat/test-nodes.R | 96 +++++++++++++++++++++++++++++++++---- tests/testthat/test-paths.R | 26 ++++++++-- 11 files changed, 176 insertions(+), 35 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jxd101@case.edu>
Diff between PRIMsrc versions 0.6.0 dated 2015-09-16 and 0.6.1 dated 2015-10-11
PRIMsrc-0.6.0/PRIMsrc/data/Synthetic.5.rda |only PRIMsrc-0.6.0/PRIMsrc/inst/doc/PRIMsrc_0.6.0.pdf |only PRIMsrc-0.6.0/PRIMsrc/man/Synthetic.5-data.Rd |only PRIMsrc-0.6.1/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.6.1/PRIMsrc/MD5 | 52 PRIMsrc-0.6.1/PRIMsrc/R/PRIMsrc.internal.r | 1 PRIMsrc-0.6.1/PRIMsrc/R/PRIMsrc.r | 3036 ++++++++++---------- PRIMsrc-0.6.1/PRIMsrc/data/Synthetic.1b.rda |only PRIMsrc-0.6.1/PRIMsrc/data/Synthetic.4.rda |binary PRIMsrc-0.6.1/PRIMsrc/data/datalist | 2 PRIMsrc-0.6.1/PRIMsrc/inst/NEWS | 18 PRIMsrc-0.6.1/PRIMsrc/inst/doc/Abstract.JCB2016.pdf |binary PRIMsrc-0.6.1/PRIMsrc/inst/doc/PRIMsrc_0.6.1.pdf |only PRIMsrc-0.6.1/PRIMsrc/man/PrimSRC-package.Rd | 44 PRIMsrc-0.6.1/PRIMsrc/man/Real.1-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Real.2-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.1-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.1b-data.Rd |only PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.2-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.3-data.Rd | 2 PRIMsrc-0.6.1/PRIMsrc/man/Synthetic.4-data.Rd | 16 PRIMsrc-0.6.1/PRIMsrc/man/plot.Rd | 69 PRIMsrc-0.6.1/PRIMsrc/man/plot_boxkm.Rd | 3 PRIMsrc-0.6.1/PRIMsrc/man/plot_boxtrace.Rd | 7 PRIMsrc-0.6.1/PRIMsrc/man/plot_boxtraj.Rd | 7 PRIMsrc-0.6.1/PRIMsrc/man/plot_profile.Rd | 5 PRIMsrc-0.6.1/PRIMsrc/man/predict.Rd | 35 PRIMsrc-0.6.1/PRIMsrc/man/print.Rd | 34 PRIMsrc-0.6.1/PRIMsrc/man/sbh.Rd | 39 PRIMsrc-0.6.1/PRIMsrc/man/summary.Rd | 31 30 files changed, 1765 insertions(+), 1652 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb],
Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.4 dated 2015-10-02 and 0.2.6 dated 2015-10-11
DESCRIPTION | 14 ++-- MD5 | 28 +++++---- NAMESPACE | 3 + NEWS | 12 ++++ R/chordNetwork.R |only R/diagonalNetwork.R | 4 - R/sankeyNetwork.R | 25 ++++++-- README.md | 2 inst/examples/examples.R | 42 ++++++++++++-- inst/htmlwidgets/chordNetwork.js |only inst/htmlwidgets/chordNetwork.yaml |only inst/htmlwidgets/lib/sankey.js | 107 +++++++++++++++++++++++++++++++------ inst/htmlwidgets/sankeyNetwork.js | 90 +++++++++++++++++++++++++++---- man/chordNetwork.Rd |only man/diagonalNetwork.Rd | 4 - man/networkD3-shiny.Rd | 10 ++- man/sankeyNetwork.Rd | 22 +++++-- 17 files changed, 294 insertions(+), 69 deletions(-)
Title: Fast Truncated SVD, PCA and Symmetric Eigendecomposition for
Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular and eigenvalue decompositions and principal component analysis of large sparse or dense matrices.
Author: Jim Baglama and Lothar Reichel
Maintainer: Bryan W. Lewis <blewis@illposed.net>
Diff between irlba versions 1.0.3 dated 2014-01-25 and 2.0.0 dated 2015-10-11
irlba-1.0.3/irlba/NEWS |only irlba-1.0.3/irlba/inst/doc/irlba.R |only irlba-2.0.0/irlba/DESCRIPTION | 19 - irlba-2.0.0/irlba/MD5 | 23 - irlba-2.0.0/irlba/NAMESPACE | 8 irlba-2.0.0/irlba/R/eigen.R |only irlba-2.0.0/irlba/R/irlba.R | 626 ++++++++++++++++++--------------- irlba-2.0.0/irlba/R/utility.R |only irlba-2.0.0/irlba/README.md |only irlba-2.0.0/irlba/build |only irlba-2.0.0/irlba/inst/doc/irlba.Rnw | 194 ++++++---- irlba-2.0.0/irlba/inst/doc/irlba.pdf |binary irlba-2.0.0/irlba/man/irlba.Rd | 191 +++++++--- irlba-2.0.0/irlba/man/partial_eigen.Rd |only irlba-2.0.0/irlba/tests/test.R | 86 ++-- irlba-2.0.0/irlba/vignettes/irlba.Rnw | 194 ++++++---- 16 files changed, 850 insertions(+), 491 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-52 dated 2015-07-17 and 6.0-57 dated 2015-10-11
DESCRIPTION | 23 - MD5 | 73 +-- NAMESPACE | 5 R/aaa.R | 417 ++++++++++-------- R/adaptive.R | 14 R/confusionMatrix.R | 4 R/createDataPartition.R | 1 R/createFolds.R | 3 R/createResample.R | 4 R/ggplot.R | 99 ++++ R/lift.R | 1 R/misc.R | 101 +--- R/modelLookup.R | 40 + R/preProcess.R | 817 ++++++++++++++++++++++++------------ R/print.train.R | 75 ++- R/reg_sims.R | 15 R/rfe.R | 42 - R/train.default.R | 44 + R/trainControl.R | 4 R/updates.R | 4 R/varImp.R | 129 +---- R/workflows.R | 7 build/vignette.rds |binary inst/NEWS.Rd | 28 + inst/doc/caret.pdf |binary inst/models/models.RData |binary man/confusionMatrix.Rd | 2 man/extractPrediction.Rd | 2 man/plot.rfe.Rd | 2 man/plot.train.Rd | 2 man/postResample.Rd | 9 man/preProcess.Rd | 19 man/sensitivity.Rd | 2 man/train.Rd | 7 man/trainControl.Rd | 11 man/twoClassSim.Rd | 24 - tests/testthat/preProcess_methods.R |only vignettes/caret.Rnw | 2 38 files changed, 1248 insertions(+), 784 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb],
Bob Rudis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.3.1 dated 2015-10-07 and 1.3.2 dated 2015-10-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ README.md | 2 +- src/parsing.cpp | 3 ++- tests/testthat/test_parsing.R | 6 ++++++ 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Model Checking and Variable Selection in Nonparametric
Regression
Description: Provides tests of significance for covariates (or groups of covariates) in a fully nonparametric regression model and a variable (or group) selection procedure based on False Discovery Rate. In addition, it provides a function for local polynomial regression for any number of dimensions, using a bandwidth specified by the user or automatically chosen by cross validation or an adaptive procedure.
Author: Adriano Zanin Zambom
Maintainer: Adriano Zanin Zambom <adriano.zambom@gmail.com>
Diff between NonpModelCheck versions 1.0 dated 2012-09-22 and 2.0 dated 2015-10-10
DESCRIPTION | 20 MD5 | 29 - NAMESPACE | 5 R/group.npvarselec.R | 935 +++++++++++++++++++++----------------------- R/localpoly.reg.R | 481 +++++++++++----------- R/npmodelcheck.R | 485 +++++++++++----------- R/npvarselec.R | 595 +++++++++++++--------------- R/plot3d.localpoly.reg.R | 131 +++--- man/group.npvarselec.Rd | 27 - man/localpoly.reg.Rd | 48 +- man/npmodelcheck.Rd | 37 - man/npvarselec.Rd | 25 - man/plot3d.localpoly.reg.Rd | 25 - src/Makevars | 2 src/Makevars.win |only src/local_poly_estimator.c | 54 -- 16 files changed, 1435 insertions(+), 1464 deletions(-)
More information about NonpModelCheck at CRAN
Permanent link
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scatterpoints by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, use the unit hydrograph in a linear storage cascade, convert lists to data.frames, fit multiple functions by regression (power, reciprocal, exponential, logarithmic, polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.8.1 dated 2015-06-03 and 1.9.0 dated 2015-10-10
berryFunctions-1.8.1/berryFunctions/ChangeLog |only berryFunctions-1.9.0/berryFunctions/DESCRIPTION | 11 berryFunctions-1.9.0/berryFunctions/MD5 | 64 - berryFunctions-1.9.0/berryFunctions/NAMESPACE | 5 berryFunctions-1.9.0/berryFunctions/NEWS |only berryFunctions-1.9.0/berryFunctions/R/approx2.R |only berryFunctions-1.9.0/berryFunctions/R/ciBand.R |only berryFunctions-1.9.0/berryFunctions/R/climateGraph.r | 5 berryFunctions-1.9.0/berryFunctions/R/combineFiles.r | 9 berryFunctions-1.9.0/berryFunctions/R/createDoc.r | 6 berryFunctions-1.9.0/berryFunctions/R/exp4p.r | 20 berryFunctions-1.9.0/berryFunctions/R/linLogHist.R | 3 berryFunctions-1.9.0/berryFunctions/R/linLogTrans.R | 353 +++---- berryFunctions-1.9.0/berryFunctions/R/linReg.R | 24 berryFunctions-1.9.0/berryFunctions/R/logSpaced.R | 2 berryFunctions-1.9.0/berryFunctions/R/mReg.r | 473 +++++----- berryFunctions-1.9.0/berryFunctions/R/movAv.R | 35 berryFunctions-1.9.0/berryFunctions/R/pastec.R | 14 berryFunctions-1.9.0/berryFunctions/R/pointZoom.R | 21 berryFunctions-1.9.0/berryFunctions/R/sortDF.R |only berryFunctions-1.9.0/berryFunctions/R/timer.R |only berryFunctions-1.9.0/berryFunctions/inst/extdata/solitaire.txt | 2 berryFunctions-1.9.0/berryFunctions/man/approx2.Rd |only berryFunctions-1.9.0/berryFunctions/man/berryFunctions-package.Rd | 31 berryFunctions-1.9.0/berryFunctions/man/ci.Rd | 2 berryFunctions-1.9.0/berryFunctions/man/ciBand.Rd |only berryFunctions-1.9.0/berryFunctions/man/combineFiles.Rd | 3 berryFunctions-1.9.0/berryFunctions/man/expReg.Rd | 2 berryFunctions-1.9.0/berryFunctions/man/linLogHist.Rd | 6 berryFunctions-1.9.0/berryFunctions/man/linLogTrans.Rd | 5 berryFunctions-1.9.0/berryFunctions/man/linReg.Rd | 99 +- berryFunctions-1.9.0/berryFunctions/man/logSpaced.Rd | 4 berryFunctions-1.9.0/berryFunctions/man/mReg.Rd | 405 ++++---- berryFunctions-1.9.0/berryFunctions/man/movAv.Rd | 10 berryFunctions-1.9.0/berryFunctions/man/pointZoom.Rd | 11 berryFunctions-1.9.0/berryFunctions/man/quantileBands.Rd | 2 berryFunctions-1.9.0/berryFunctions/man/sortDF.Rd |only berryFunctions-1.9.0/berryFunctions/man/timer.Rd |only 38 files changed, 875 insertions(+), 752 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Diagnostics Plots for Bicluster Data
Description: Diagnostic tools based on two-way
anova and median-polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non-bicluster rows- or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding two bicluster methods from the fabia and isa2 R
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
Diff between BcDiag versions 1.0.8 dated 2015-01-22 and 1.0.9 dated 2015-10-10
DESCRIPTION | 16 +++++++-------- MD5 | 8 +++---- NAMESPACE | 4 +++ R/profileBic.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++---- man/profileBic.Rd | 4 ++- 5 files changed, 72 insertions(+), 17 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2015. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods)
NCA identifies necessary (but not sufficient) conditions in datasets. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or input) is necessary but not sufficient for a (desired) level of y (e.g. good performance or output).
Author: Jan Dul <jdul@rsm.nl>
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 1.0 dated 2015-07-02 and 1.1 dated 2015-10-10
NCA-1.0/NCA/R/p_bottleneck_fdh.R |only NCA-1.1/NCA/DESCRIPTION | 11 ++--- NCA-1.1/NCA/MD5 | 63 ++++++++++++++++-------------- NCA-1.1/NCA/NAMESPACE | 4 - NCA-1.1/NCA/R/nca.R | 72 ++++++++++++++++++++++++----------- NCA-1.1/NCA/R/nca_ce_fdh.R | 31 ++++++++------- NCA-1.1/NCA/R/nca_ce_vrs.R | 42 +++++++++++--------- NCA-1.1/NCA/R/nca_cols.R | 7 +-- NCA-1.1/NCA/R/nca_cr_fdh.R | 32 +++++++++------ NCA-1.1/NCA/R/nca_cr_vrs.R | 34 +++++++++------- NCA-1.1/NCA/R/nca_lh.R | 2 NCA-1.1/NCA/R/nca_ols.R | 2 NCA-1.1/NCA/R/nca_qr.R | 9 ++-- NCA-1.1/NCA/R/nca_sfa.R | 26 ++++++++++-- NCA-1.1/NCA/R/onAttach.R | 2 NCA-1.1/NCA/R/p_above.R | 4 + NCA-1.1/NCA/R/p_bottleneck_ce.R |only NCA-1.1/NCA/R/p_ceiling.R | 49 ++++++++++++++++++----- NCA-1.1/NCA/R/p_display_bottleneck.R | 10 ++-- NCA-1.1/NCA/R/p_display_graphs.R | 32 ++++++++------- NCA-1.1/NCA/R/p_display_tables.R | 6 +- NCA-1.1/NCA/R/p_fast_peers.R |only NCA-1.1/NCA/R/p_ineffs.R | 40 ++++++++++--------- NCA-1.1/NCA/R/p_optimal_peers.R | 6 +- NCA-1.1/NCA/R/p_utils.R | 9 ++-- NCA-1.1/NCA/man/NCA-package.Rd | 2 NCA-1.1/NCA/man/nca.Rd | 21 +++++++--- NCA-1.1/NCA/man/nca.example.Rd | 20 ++++----- NCA-1.1/NCA/man/nca_ce_fdh.Rd | 4 + NCA-1.1/NCA/man/nca_ce_vrs.Rd | 9 +++- NCA-1.1/NCA/man/nca_cr_fdh.Rd | 3 - NCA-1.1/NCA/man/nca_cr_vrs.Rd | 3 - NCA-1.1/NCA/man/nca_qr.Rd | 8 ++- NCA-1.1/NCA/tests |only 34 files changed, 351 insertions(+), 212 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.20-2 dated 2015-09-02 and 2.20-23 dated 2015-10-10
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++------------- NAMESPACE | 4 ++- R/helpers.R | 19 ++++++++++++-- R/lsmip.R | 2 - R/plot.lsm.R | 5 +++ R/ref.grid.R | 30 +++++++++++++++------- R/summary.R | 23 ++--------------- inst/NEWS | 11 ++++++++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 58 ++++++++++++++++++++++++-------------------- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 8 ++++-- man/models.Rd | 4 ++- man/ref.grid.Rd | 2 - man/summary.Rd | 5 ++- man/update.Rd | 14 ++++++++-- vignettes/using-lsmeans.rnw | 8 ++++-- 18 files changed, 144 insertions(+), 91 deletions(-)
Title: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>
Diff between gdalUtils versions 2.0.1.5 dated 2015-10-04 and 2.0.1.7 dated 2015-10-10
DESCRIPTION | 13 ++++++++----- MD5 | 6 +++--- R/gdal_chooseInstallation.R | 12 ++++++++++-- R/gdal_setInstallation.R | 8 +++++--- 4 files changed, 26 insertions(+), 13 deletions(-)
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.0 dated 2015-10-08 and 0.8.1 dated 2015-10-10
DESCRIPTION | 10 ++-- MD5 | 39 +++++++++-------- NAMESPACE | 5 ++ R/FSA-internals.R | 16 +++---- R/FSAUtils.R | 37 +++++++++++++++- R/comparisonsDVR.R |only man/col2rgbt.Rd |only man/compIntercepts.Rd |only man/compSlopes.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test_AgeLengthKey.R | 57 ++++++++++++------------- tests/testthat/test_CatchCurve_ChapmanRobson.R | 5 -- tests/testthat/test_FSAUtils.R | 15 ++++++ tests/testthat/test_PSD.R | 47 ++++++++++++-------- tests/testthat/test_StockRecruit.R | 6 -- tests/testthat/test_VonBertalanffy.R | 4 - tests/testthat/test_WSWR.R | 4 - tests/testthat/test_capHistConvert.R | 9 --- tests/testthat/test_comparisonsDVR.R |only tests/testthat/test_depletion.R | 4 - tests/testthat/test_mrClosed.R | 4 - tests/testthat/test_mrOpen.R | 4 - tests/testthat/test_removal.R | 4 - 23 files changed, 148 insertions(+), 122 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random
Forest. The Weighted Subspace Random Forest algorithm was
proposed in the International Journal of Data Warehousing and
Mining, 8(2):44-63, 2012, proposed by Baoxun Xu, Joshua Zhexue
Huang, Graham Williams, Qiang Wang, and Yunming Ye. The algorithm
can classify very high-dimensional data with random forests built
using small subspaces. A novel variable weighting method is used
for variable subspace selection in place of the traditional random
variable sampling.This new approach is particularly useful in
building models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre],
Graham Williams [aut],
Junchao Lv [ctb],
Baoxun Xu [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.5.24 dated 2015-07-07 and 1.5.29 dated 2015-10-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS.Rd | 13 +++++++++++++ inst/doc/wsrf-guide.html | 6 +++--- src/dataset.cpp | 2 +- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero <favero@cbs.dtu.dk>
Diff between sequenza versions 2.1.1 dated 2015-01-27 and 2.1.2 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 46 +++++++++++++++++++++++++++++++++++++++++++++- NEWS | 4 ++++ R/next.R | 12 +++++++++++- build/vignette.rds |binary data/CP.example.RData |binary data/example.seqz.rda |binary inst/doc/sequenza.pdf |binary 9 files changed, 72 insertions(+), 14 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.8 dated 2015-08-30 and 0.8.1 dated 2015-10-09
rmarkdown-0.8.1/rmarkdown/DESCRIPTION | 8 - rmarkdown-0.8.1/rmarkdown/MD5 | 32 +++-- rmarkdown-0.8.1/rmarkdown/R/html_dependencies.R | 55 ++-------- rmarkdown-0.8.1/rmarkdown/R/html_resources.R | 24 ++-- rmarkdown-0.8.1/rmarkdown/R/output_format.R | 12 +- rmarkdown-0.8.1/rmarkdown/R/render.R | 3 rmarkdown-0.8.1/rmarkdown/R/word_document.R | 12 +- rmarkdown-0.8.1/rmarkdown/inst/NEWS |only rmarkdown-0.8.1/rmarkdown/inst/rmd/ioslides/default.html | 2 rmarkdown-0.8.1/rmarkdown/inst/rmd/ioslides/ioslides-13.5.1/js/slide-deck.js | 2 rmarkdown-0.8.1/rmarkdown/man/knitr_options.Rd | 8 + rmarkdown-0.8.1/rmarkdown/man/word_document.Rd | 10 + rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/csvs |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/directory-refs.Rmd |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/empty |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/nonempty |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/resource-files.Rmd |only rmarkdown-0.8.1/rmarkdown/tests/testthat/test-resources.R | 45 ++++++++ rmarkdown-0.8/rmarkdown/NEWS |only 19 files changed, 132 insertions(+), 81 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between paco versions 0.2.1 dated 2015-07-18 and 0.2.2 dated 2015-10-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/PACo.r | 8 +++++--- R/add_pcoord.r | 16 ++++++++-------- R/paco_links.r | 1 + man/PACo.Rd | 4 +++- man/add_pcoord.Rd | 4 +++- 7 files changed, 29 insertions(+), 22 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-62 dated 2015-08-24 and 0.1-63 dated 2015-10-09
Surrogate-0.1-62/Surrogate/R/SummaryTrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/R/TrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/R/plot.TrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/man/TrialLevelContCont.Rd |only Surrogate-0.1-62/Surrogate/man/plot.TrialLevelContCont.Rd |only Surrogate-0.1-63/Surrogate/DESCRIPTION | 8 Surrogate-0.1-63/Surrogate/MD5 | 80 +++-- Surrogate-0.1-63/Surrogate/NAMESPACE | 27 + Surrogate-0.1-63/Surrogate/NEWS | 6 Surrogate-0.1-63/Surrogate/R/FixedBinBinIT.r |only Surrogate-0.1-63/Surrogate/R/FixedBinContIT.r |only Surrogate-0.1-63/Surrogate/R/FixedContBinIT.r |only Surrogate-0.1-63/Surrogate/R/FixedContContIT.r | 27 - Surrogate-0.1-63/Surrogate/R/ICABinBin.R | 142 ++++------ Surrogate-0.1-63/Surrogate/R/MarginalProbs.R | 2 Surrogate-0.1-63/Surrogate/R/Pred.TrialT.ContCont.R |only Surrogate-0.1-63/Surrogate/R/Prentice.R |only Surrogate-0.1-63/Surrogate/R/SummaryITContCont.R | 4 Surrogate-0.1-63/Surrogate/R/SummaryTrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/TrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/TwoStageSurvSurv.R | 14 Surrogate-0.1-63/Surrogate/R/UnifixedContCont.R | 4 Surrogate-0.1-63/Surrogate/R/UnimixedContCont.R | 7 Surrogate-0.1-63/Surrogate/R/plot.BinContCombnIT.R |only Surrogate-0.1-63/Surrogate/R/plot.InfoTheoretic.R | 1 Surrogate-0.1-63/Surrogate/R/plot.SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/plot.TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/plot.TrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/summary.SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/summary.TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/summary.TwoStageSurvSurv.R | 6 Surrogate-0.1-63/Surrogate/R/summaryBinContCombnIT.R |only Surrogate-0.1-63/Surrogate/data/Schizo.rda |binary Surrogate-0.1-63/Surrogate/man/FixedBinBinIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedBinContIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedContBinIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedContContIT.Rd | 13 Surrogate-0.1-63/Surrogate/man/ICABinBin.Rd | 32 +- Surrogate-0.1-63/Surrogate/man/MixedContContIT.Rd | 5 Surrogate-0.1-63/Surrogate/man/Plot.PredTrialTContCont.Rd |only Surrogate-0.1-63/Surrogate/man/Pred.TrialT.ContCont.Rd |only Surrogate-0.1-63/Surrogate/man/Prentice.Rd |only Surrogate-0.1-63/Surrogate/man/Schizo.Rd | 7 Surrogate-0.1-63/Surrogate/man/SurvSurv.Rd |only Surrogate-0.1-63/Surrogate/man/TrialLevelIT.Rd |only Surrogate-0.1-63/Surrogate/man/TrialLevelMA.Rd |only Surrogate-0.1-63/Surrogate/man/TwoStageSurvSurv.Rd | 6 Surrogate-0.1-63/Surrogate/man/UnifixedContCont.Rd | 5 Surrogate-0.1-63/Surrogate/man/UnimixedContCont.Rd | 3 Surrogate-0.1-63/Surrogate/man/plot.InformationTheoreticBinCombn.Rd |only Surrogate-0.1-63/Surrogate/man/plot.InformationTheoreticSurvSurv.Rd |only Surrogate-0.1-63/Surrogate/man/plot.MetaAnalytic.Rd | 3 Surrogate-0.1-63/Surrogate/man/plot.TrialLevelIT.Rd |only Surrogate-0.1-63/Surrogate/man/plot.TrialLevelMA.Rd |only Surrogate-0.1-63/Surrogate/man/plot.TwoStageSurvSurv.Rd | 12 Surrogate-0.1-63/Surrogate/man/summary.gen.Rd | 20 + 58 files changed, 261 insertions(+), 173 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.2.0 dated 2015-07-01 and 0.3.0 dated 2015-10-09
rerddap-0.2.0/rerddap/R/cache.R |only rerddap-0.2.0/rerddap/tests/testthat/test-griddap.R |only rerddap-0.3.0/rerddap/DESCRIPTION | 6 rerddap-0.3.0/rerddap/MD5 | 62 ++++--- rerddap-0.3.0/rerddap/NAMESPACE | 20 ++ rerddap-0.3.0/rerddap/NEWS | 20 ++ rerddap-0.3.0/rerddap/R/cache_delete.R |only rerddap-0.3.0/rerddap/R/cache_details.R |only rerddap-0.3.0/rerddap/R/cache_list.R |only rerddap-0.3.0/rerddap/R/convert_time.R | 2 rerddap-0.3.0/rerddap/R/convert_units.R | 2 rerddap-0.3.0/rerddap/R/fipscounty.R | 2 rerddap-0.3.0/rerddap/R/grid.R | 19 +- rerddap-0.3.0/rerddap/R/info.R | 3 rerddap-0.3.0/rerddap/R/keywords.R | 2 rerddap-0.3.0/rerddap/R/ncdf_helpers.R | 20 ++ rerddap-0.3.0/rerddap/R/rerddap-package.r | 6 rerddap-0.3.0/rerddap/R/search_adv.R | 1 rerddap-0.3.0/rerddap/R/table.R | 8 - rerddap-0.3.0/rerddap/README.md | 2 rerddap-0.3.0/rerddap/build/vignette.rds |binary rerddap-0.3.0/rerddap/inst/doc/rerddap_vignette.Rmd | 148 +++++++++---------- rerddap-0.3.0/rerddap/inst/doc/rerddap_vignette.html | 148 +++++++++---------- rerddap-0.3.0/rerddap/inst/vign/rerddap_vignette.Rmd | 15 + rerddap-0.3.0/rerddap/inst/vign/rerddap_vignette.md | 148 +++++++++---------- rerddap-0.3.0/rerddap/man/cache_delete.Rd |only rerddap-0.3.0/rerddap/man/cache_details.Rd |only rerddap-0.3.0/rerddap/man/cache_list.Rd | 29 +-- rerddap-0.3.0/rerddap/man/convert_time.Rd | 2 rerddap-0.3.0/rerddap/man/convert_units.Rd | 2 rerddap-0.3.0/rerddap/man/fipscounty.Rd | 2 rerddap-0.3.0/rerddap/man/griddap.Rd | 10 + rerddap-0.3.0/rerddap/man/key_words.Rd | 2 rerddap-0.3.0/rerddap/man/tabledap.Rd | 5 rerddap-0.3.0/rerddap/tests/testthat/test-griddap.r |only rerddap-0.3.0/rerddap/vignettes/rerddap_vignette.Rmd | 148 +++++++++---------- 36 files changed, 456 insertions(+), 378 deletions(-)
Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 2.7 dated 2015-08-03 and 2.9 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/pedgene.R | 25 ++++++++++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ tests/test.pedgene.expanded.R | 5 +++++ tests/test.pedgene.expanded.Rout.save | 25 +++++++++++++++++-------- 7 files changed, 53 insertions(+), 27 deletions(-)
Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g.,
http://en.wikipedia.org/wiki/GitHub#Gist,
https://help.github.com/articles/about-gists/). A 'gist' is simply one or
more files with code/text/images/etc. This package allows the user to
create new 'gists', update 'gists' with new files, rename files, delete files,
get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in
your default browser, get embed code for a 'gist', list 'gist' 'commits', and
get rate limit information when 'authenticated'. Some requests require
authentication and some do not. 'Gists' website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut],
Karthik Ram [aut],
Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between gistr versions 0.3.0 dated 2015-07-03 and 0.3.4 dated 2015-10-09
gistr-0.3.0/gistr/tests/localtests/figure |only gistr-0.3.0/gistr/tests/testthat/figure |only gistr-0.3.4/gistr/DESCRIPTION | 8 - gistr-0.3.4/gistr/MD5 | 34 ++---- gistr-0.3.4/gistr/NAMESPACE | 2 gistr-0.3.4/gistr/R/gist_create.R | 19 ++- gistr-0.3.4/gistr/R/gist_create_git.R |only gistr-0.3.4/gistr/R/gist_create_obj.R | 2 gistr-0.3.4/gistr/R/gistr-package.R | 45 ++++++-- gistr-0.3.4/gistr/R/tabl.R | 90 ++++++++++++---- gistr-0.3.4/gistr/README.md | 2 gistr-0.3.4/gistr/build/vignette.rds |binary gistr-0.3.4/gistr/inst/ignore/gist_create_git.R | 21 +++ gistr-0.3.4/gistr/man/create_gists.Rd |only gistr-0.3.4/gistr/man/gist_create.Rd | 2 gistr-0.3.4/gistr/man/gist_create_git.Rd |only gistr-0.3.4/gistr/man/gist_create_obj.Rd | 2 gistr-0.3.4/gistr/man/tabl.Rd | 33 +++++ gistr-0.3.4/gistr/tests/testthat/test-gist_create_git.R |only 19 files changed, 198 insertions(+), 62 deletions(-)
Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from published literature and contributions from colleagues.
Author: Gary A. Nelson <gary.nelson@state.ma.us>
Maintainer: Gary A. Nelson <gary.nelson@state.ma.us>
Diff between fishmethods versions 1.8-0 dated 2015-05-28 and 1.9-0 dated 2015-10-09
DESCRIPTION | 10 - MD5 | 20 ++- NAMESPACE | 14 ++ R/agesurv.R | 25 ++++ R/astrocalc4r.R |only R/bhnoneq.R | 271 +++++++++++++++++++++++++++++------------------------ R/cpuekapp.R |only data/kappenman.rda |only man/agesurv.Rd | 12 +- man/astrocalc4r.Rd |only man/bheq2.Rd | 2 man/bhnoneq.Rd | 27 ++--- man/cpuekapp.Rd |only man/kappenman.Rd |only 14 files changed, 231 insertions(+), 150 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.31.3 dated 2015-07-09 and 1.31.4 dated 2015-10-09
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++--------- R/CA.R | 9 +++--- R/FAMD.R | 3 +- R/HCPC.R | 4 +-- R/MCA.R | 7 +++-- R/MFA.R | 5 ++- R/PCA.R | 4 +-- R/plot.HCPC.R | 2 - R/plotellipses.r | 9 ++++-- inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary 12 files changed, 40 insertions(+), 33 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare and David Loris
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-09
ChannelAttribution-1.1/ChannelAttribution/man/Dy.Rd |only ChannelAttribution-1.1/ChannelAttribution/vignettes |only ChannelAttribution-1.2/ChannelAttribution/DESCRIPTION | 10 ChannelAttribution-1.2/ChannelAttribution/MD5 | 21 ChannelAttribution-1.2/ChannelAttribution/R/ChannelAttribution.R | 21 ChannelAttribution-1.2/ChannelAttribution/data/PathData.rda |binary ChannelAttribution-1.2/ChannelAttribution/man/ChannelAttribution-package.Rd | 33 ChannelAttribution-1.2/ChannelAttribution/man/Data.Rd |only ChannelAttribution-1.2/ChannelAttribution/man/heuristic_models.Rd | 16 ChannelAttribution-1.2/ChannelAttribution/man/markov_model.Rd | 33 ChannelAttribution-1.2/ChannelAttribution/src/ChannelAttribution.cpp | 1026 ++++++---- ChannelAttribution-1.2/ChannelAttribution/src/ChannelAttribution.h | 8 12 files changed, 741 insertions(+), 427 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and
where to focus code optimization, using Amdahl's law and visual aids
based on line profiling. Amdahl's profiler organises profiling output
files (including memory profiling) in a visually appealing way.
It is meant to help to balance development
vs. execution time by helping to identify the most promising sections
of code to optimize and projecting potential gains. The package is
an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>
Diff between aprof versions 0.2.5 dated 2015-07-20 and 0.3.1 dated 2015-10-09
DESCRIPTION | 12 - MD5 | 12 - R/aprof.R | 416 +++++++++++++++++++++++++++---------------------- man/aprof.Rd | 50 +++-- man/plot.Rd | 10 - man/print.Rd | 2 man/readLineDensity.Rd | 4 7 files changed, 283 insertions(+), 223 deletions(-)
Title: An R Package for Quantification of Pinned Microbial Culture
Description: The goal of this package is to allow users to robustly
and quickly grid and quantify sizes of pinned colonies in plate images.
gitter works by first finding the grid of colonies from a preprocessed image
and then locating the bounds of each colony separately.
It includes several image pre-processing techniques, such
as autorotation of plates, noise removal, contrast adjustment and image
resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih <wagih@ebi.ac.uk>
Diff between gitter versions 1.0.4 dated 2014-01-23 and 1.1 dated 2015-10-09
gitter-1.0.4/gitter/R/Help.R |only gitter-1.0.4/gitter/R/Main.R |only gitter-1.0.4/gitter/R/Peaks.R |only gitter-1.0.4/gitter/man/gitter-package.Rd |only gitter-1.1/gitter/DESCRIPTION | 20 ++-- gitter-1.1/gitter/MD5 | 29 +++--- gitter-1.1/gitter/NAMESPACE | 27 +++++- gitter-1.1/gitter/R/help.r |only gitter-1.1/gitter/R/io.r |only gitter-1.1/gitter/R/main.r |only gitter-1.1/gitter/R/peaks.r |only gitter-1.1/gitter/R/plot.r |only gitter-1.1/gitter/build/BUILD.R | 21 +++- gitter-1.1/gitter/man/gitter.Rd | 131 +++++++++--------------------- gitter-1.1/gitter/man/gitter.batch.Rd | 68 ++++----------- gitter-1.1/gitter/man/gitter.demo.Rd | 45 +--------- gitter-1.1/gitter/man/gitter.read.Rd | 46 ++-------- gitter-1.1/gitter/man/plate.warnings.Rd | 43 ++------- gitter-1.1/gitter/man/plot.gitter.Rd | 106 ++++++++---------------- gitter-1.1/gitter/man/summary.gitter.Rd | 47 ++-------- 20 files changed, 205 insertions(+), 378 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description:
We provide a set of functions to retrieve information about GIMMS NDVI3g
files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native
binary (ENVI) format directly into R based on the widely applied 'raster'
package; and calculate monthly value composites (e.g. maximum value
composites, MVC) from the bi-monthly input data.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.1 dated 2015-10-08 and 0.1.1 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/createHdr.R | 2 ++ man/createHdr.Rd | 2 ++ 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Utility Sparse Matrix Functions for Quantitative Language
Comparison
Description: Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw <cysouw@mac.com>
Diff between qlcMatrix versions 0.9.4 dated 2015-04-27 and 0.9.5 dated 2015-10-09
DESCRIPTION | 9 +- MD5 | 28 ++++---- NAMESPACE | 5 + NEWS.md |only R/array.R |only R/assoc.R | 4 - R/base.R | 84 +++++++++++++----------- R/split.R | 7 +- R/utils.R | 42 ++++++++---- build/vignette.rds |binary inst/doc/transformingDataSparse.html | 19 ++++- man/array.Rd |only man/bibles.Rd | 6 - man/qlcMatrix-package.Rd | 6 - man/rowMax.Rd | 2 man/unfold.Rd | 118 ++++++++++++++++++++--------------- man/unfoldBlockMatrix.Rd |only 17 files changed, 196 insertions(+), 134 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative
discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences,
turns of talk, syllables and other assorted analysis tasks. The
package provides parsing tools for preparing transcript data.
Many functions enable the user to aggregate data by any number
of grouping variables, providing analysis and seamless
integration with other R packages that undertake higher level
analysis and visualization of text. This affords the user a
more efficient and targeted analysis. 'qdap' is designed for
transcript analysis, however, many functions are applicable to
other areas of Text Mining/Natural Language Processing.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.2.2 dated 2015-07-05 and 2.2.4 dated 2015-10-09
DESCRIPTION | 12 - MD5 | 44 ++--- NAMESPACE | 1 NEWS | 30 +++ R/add_s.R |only R/as.tdm.R | 2 R/automated_readability_index.R | 2 R/common.R | 3 R/formality.R | 3 R/lexical_classification.R | 28 ++- R/name2sex.R | 64 ++++++-- R/pos.R | 22 +- R/question_type.R | 4 R/word_cor.R | 15 + README.md | 3 inst/CITATION | 6 inst/Rmd_vignette/qdap_vignette.Rmd | 265 +++++++++++++++++----------------- inst/doc/cleaning_and_debugging.pdf |binary inst/doc/tm_package_compatibility.pdf |binary man/add_s.Rd |only man/as.tdm.Rd | 2 man/lexical_classification.Rd | 4 man/pos.Rd | 7 man/word_cor.Rd | 16 +- 24 files changed, 313 insertions(+), 220 deletions(-)
Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite,
and topographic map servers are directly supported, including CloudMade,
Mapnik, Bing, stamen, and MapQuest. Maps can be plotted using either base
graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.
Author: Ian Fellows, using the JMapViewer library by Jan Peter Stotz
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between OpenStreetMap versions 0.3.1 dated 2013-04-14 and 0.3.2 dated 2015-10-09
OpenStreetMap-0.3.1/OpenStreetMap/javasrc |only OpenStreetMap-0.3.1/OpenStreetMap/man/raster.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/DESCRIPTION | 24 - OpenStreetMap-0.3.2/OpenStreetMap/MD5 | 123 +++++----- OpenStreetMap-0.3.2/OpenStreetMap/NAMESPACE | 13 - OpenStreetMap-0.3.2/OpenStreetMap/R/OpenStreetMap-package.R | 4 OpenStreetMap-0.3.2/OpenStreetMap/R/autoplot.R | 23 - OpenStreetMap-0.3.2/OpenStreetMap/R/osm.R | 20 - OpenStreetMap-0.3.2/OpenStreetMap/R/zzz.R | 13 - OpenStreetMap-0.3.2/OpenStreetMap/inst/java/RTileController.jar |binary OpenStreetMap-0.3.2/OpenStreetMap/java |only OpenStreetMap-0.3.2/OpenStreetMap/man/LA_places.Rd | 5 OpenStreetMap-0.3.2/OpenStreetMap/man/autoplot.OpenStreetMap.Rd | 15 - OpenStreetMap-0.3.2/OpenStreetMap/man/autoplot.osmtile.Rd | 13 - OpenStreetMap-0.3.2/OpenStreetMap/man/getMapInfo.Rd | 7 OpenStreetMap-0.3.2/OpenStreetMap/man/launchMapHelper.Rd | 10 OpenStreetMap-0.3.2/OpenStreetMap/man/longlat.Rd | 6 OpenStreetMap-0.3.2/OpenStreetMap/man/openmap.Rd | 42 +-- OpenStreetMap-0.3.2/OpenStreetMap/man/openproj.Rd | 16 - OpenStreetMap-0.3.2/OpenStreetMap/man/osm.Rd | 6 OpenStreetMap-0.3.2/OpenStreetMap/man/osmtile.Rd | 16 - OpenStreetMap-0.3.2/OpenStreetMap/man/plot.OpenStreetMap.Rd | 19 - OpenStreetMap-0.3.2/OpenStreetMap/man/plot.osmtile.Rd | 18 - OpenStreetMap-0.3.2/OpenStreetMap/man/print.OpenStreetMap.Rd | 10 OpenStreetMap-0.3.2/OpenStreetMap/man/projectMercator.Rd | 13 - OpenStreetMap-0.3.2/OpenStreetMap/man/raster-OpenStreetMap-method.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/man/raster-osmtile-method.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/man/setCloudMadeKey.Rd | 9 OpenStreetMap-0.3.2/OpenStreetMap/man/states.Rd | 5 29 files changed, 224 insertions(+), 206 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.2 dated 2015-06-29 and 1.2.3 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 1 + NEWS | 7 +++++++ R/HelpersMG-package.R | 4 ++-- R/LD50.R | 4 ++-- R/MHalgoGen.R | 20 +++++++++----------- R/sun.info.R | 18 ++++++++---------- R/wget.R |only man/HelpersMG-package.Rd | 4 ++-- man/sun.info.Rd | 14 +++++++------- man/wget.Rd |only 12 files changed, 53 insertions(+), 47 deletions(-)
Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>
Diff between FIACH versions 0.1.1 dated 2015-10-01 and 0.1.2 dated 2015-10-09
DESCRIPTION | 6 MD5 | 61 ++--- NAMESPACE | 22 - R/GUI.R | 11 R/RcppExports.R | 272 ++++++++++++------------ R/arrMat.R | 10 R/basisFunctions.R | 42 +-- R/boldContrast.R | 148 ++++++------- R/fd.R | 34 +-- R/fiach.R | 18 + R/gaussKernel.R | 20 - R/highBasis.R | 18 - R/highPass.R | 34 +-- R/kaiserWin.R | 48 ++-- R/kmeansMask.R | 14 - R/lowBasis.R | 22 - R/matArr.R | 6 R/naSpline.R | 82 +++---- R/quantMask.r | 18 - R/rawPeriodogram.R | 64 ++--- R/sinc.R | 30 +- R/spmHrf.R | 18 - R/spmOrth.R | 24 +- R/t2Grey.R | 12 - R/t2sGrey.R | 26 +- R/viewR.R | 531 +++++++++++------------------------------------- inst/extdata/mni.nii.gz |only man/GUI.Rd | 42 +-- man/rawPeriodogram.Rd | 108 ++++----- man/rp.Rd | 68 +++--- man/sinc.Rd | 86 +++---- man/viewR.Rd | 5 32 files changed, 827 insertions(+), 1073 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.0 dated 2015-09-23 and 0.6.1 dated 2015-10-08
DESCRIPTION | 8 - INDEX | 1 MD5 | 27 ++--- NAMESPACE | 6 + R/nhanes.R | 204 ++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/Introducing_nhanesA.R | 9 - inst/doc/Introducing_nhanesA.Rmd | 22 ++-- inst/doc/Introducing_nhanesA.html | 47 ++++---- man/browseNHANES.Rd |only man/nhanes.Rd | 4 man/nhanesAttr.Rd | 2 man/nhanesTables.Rd | 10 + man/nhanesTranslate.Rd | 1 vignettes/Introducing_nhanesA.Rmd | 22 ++-- 15 files changed, 218 insertions(+), 145 deletions(-)
Title: Create Graph Diagrams and Flowcharts Using R
Description: Create graph diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Andrei Kashcha [aut, cph] (vivagraphjs library in htmlwidgets/lib,
https://github.com/anvaka/VivaGraphJS),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.7 dated 2015-06-11 and 0.8 dated 2015-10-08
DiagrammeR-0.7/DiagrammeR/R/edge_relationship.R |only DiagrammeR-0.7/DiagrammeR/build |only DiagrammeR-0.7/DiagrammeR/inst/doc |only DiagrammeR-0.7/DiagrammeR/man/edge_relationship.Rd |only DiagrammeR-0.7/DiagrammeR/vignettes |only DiagrammeR-0.8/DiagrammeR/DESCRIPTION | 61 DiagrammeR-0.8/DiagrammeR/LICENSE | 2 DiagrammeR-0.8/DiagrammeR/MD5 | 250 + DiagrammeR-0.8/DiagrammeR/NAMESPACE | 24 DiagrammeR-0.8/DiagrammeR/R/DiagrammeR.R | 46 DiagrammeR-0.8/DiagrammeR/R/add_edges.R | 217 + DiagrammeR-0.8/DiagrammeR/R/add_node.R | 295 +- DiagrammeR-0.8/DiagrammeR/R/add_to_series.R | 45 DiagrammeR-0.8/DiagrammeR/R/combine_edges.R | 15 DiagrammeR-0.8/DiagrammeR/R/combine_graphs.R |only DiagrammeR-0.8/DiagrammeR/R/combine_nodes.R | 11 DiagrammeR-0.8/DiagrammeR/R/country_graph.R |only DiagrammeR-0.8/DiagrammeR/R/create_edges.R | 13 DiagrammeR-0.8/DiagrammeR/R/create_graph.R | 863 +++--- DiagrammeR-0.8/DiagrammeR/R/create_nodes.R | 26 DiagrammeR-0.8/DiagrammeR/R/create_random_graph.R |only DiagrammeR-0.8/DiagrammeR/R/create_series.R | 24 DiagrammeR-0.8/DiagrammeR/R/create_subgraph.R | 19 DiagrammeR-0.8/DiagrammeR/R/delete_edge.R | 17 DiagrammeR-0.8/DiagrammeR/R/delete_node.R | 10 DiagrammeR-0.8/DiagrammeR/R/display_graph_object.R | 9 DiagrammeR-0.8/DiagrammeR/R/edge_count.R | 80 DiagrammeR-0.8/DiagrammeR/R/edge_info.R | 52 DiagrammeR-0.8/DiagrammeR/R/edge_present.R | 15 DiagrammeR-0.8/DiagrammeR/R/edge_rel.R |only DiagrammeR-0.8/DiagrammeR/R/get_edges.R | 18 DiagrammeR-0.8/DiagrammeR/R/get_nodes.R | 11 DiagrammeR-0.8/DiagrammeR/R/get_predecessors.R | 5 DiagrammeR-0.8/DiagrammeR/R/get_successors.R | 7 DiagrammeR-0.8/DiagrammeR/R/grViz.R | 69 DiagrammeR-0.8/DiagrammeR/R/graph_count.R | 25 DiagrammeR-0.8/DiagrammeR/R/graphviz_export.R | 39 DiagrammeR-0.8/DiagrammeR/R/import_graph.R |only DiagrammeR-0.8/DiagrammeR/R/is_graph_directed.R | 3 DiagrammeR-0.8/DiagrammeR/R/is_graph_empty.R | 4 DiagrammeR-0.8/DiagrammeR/R/mermaid.R | 4 DiagrammeR-0.8/DiagrammeR/R/node_count.R | 81 DiagrammeR-0.8/DiagrammeR/R/node_info.R | 20 DiagrammeR-0.8/DiagrammeR/R/node_present.R | 8 DiagrammeR-0.8/DiagrammeR/R/node_type.R | 18 DiagrammeR-0.8/DiagrammeR/R/remove_from_series.R | 31 DiagrammeR-0.8/DiagrammeR/R/render_graph.R | 251 - DiagrammeR-0.8/DiagrammeR/R/render_graph_from_series.R | 42 DiagrammeR-0.8/DiagrammeR/R/roll_palette.R | 41 DiagrammeR-0.8/DiagrammeR/R/scale_edges.R | 27 DiagrammeR-0.8/DiagrammeR/R/scale_nodes.R | 26 DiagrammeR-0.8/DiagrammeR/R/select_graph_from_series.R |only DiagrammeR-0.8/DiagrammeR/R/series_info.R | 6 DiagrammeR-0.8/DiagrammeR/R/spectools.R | 3 DiagrammeR-0.8/DiagrammeR/R/subset_series.R | 36 DiagrammeR-0.8/DiagrammeR/R/trigger_script.R | 6 DiagrammeR-0.8/DiagrammeR/R/visnetwork.R |only DiagrammeR-0.8/DiagrammeR/R/vivagraph.R |only DiagrammeR-0.8/DiagrammeR/R/x11_hex.R | 3 DiagrammeR-0.8/DiagrammeR/README.md | 36 DiagrammeR-0.8/DiagrammeR/inst/examples |only DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/VivaGraphJS |only DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.css | 284 +- DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.slim.min.js | 23 DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/lib/viz/viz.js | 1337 ---------- DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/vivagraph.js |only DiagrammeR-0.8/DiagrammeR/inst/htmlwidgets/vivagraph.yaml |only DiagrammeR-0.8/DiagrammeR/man/DiagrammeR.Rd | 13 DiagrammeR-0.8/DiagrammeR/man/DiagrammeROutput.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/add_edges.Rd | 40 DiagrammeR-0.8/DiagrammeR/man/add_node.Rd | 19 DiagrammeR-0.8/DiagrammeR/man/add_to_series.Rd | 27 DiagrammeR-0.8/DiagrammeR/man/combine_edges.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/combine_graphs.Rd |only DiagrammeR-0.8/DiagrammeR/man/combine_nodes.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/country_graph.Rd |only DiagrammeR-0.8/DiagrammeR/man/create_edges.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/create_graph.Rd | 71 DiagrammeR-0.8/DiagrammeR/man/create_nodes.Rd | 8 DiagrammeR-0.8/DiagrammeR/man/create_random_graph.Rd |only DiagrammeR-0.8/DiagrammeR/man/create_series.Rd | 23 DiagrammeR-0.8/DiagrammeR/man/create_subgraph.Rd | 19 DiagrammeR-0.8/DiagrammeR/man/delete_edge.Rd | 7 DiagrammeR-0.8/DiagrammeR/man/display_graph_object.Rd | 9 DiagrammeR-0.8/DiagrammeR/man/edge_count.Rd | 18 DiagrammeR-0.8/DiagrammeR/man/edge_info.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/edge_present.Rd | 9 DiagrammeR-0.8/DiagrammeR/man/edge_rel.Rd |only DiagrammeR-0.8/DiagrammeR/man/exportSVG.Rd | 11 DiagrammeR-0.8/DiagrammeR/man/get_edges.Rd | 14 DiagrammeR-0.8/DiagrammeR/man/get_nodes.Rd | 8 DiagrammeR-0.8/DiagrammeR/man/get_predecessors.Rd | 5 DiagrammeR-0.8/DiagrammeR/man/get_successors.Rd | 5 DiagrammeR-0.8/DiagrammeR/man/grViz.Rd | 17 DiagrammeR-0.8/DiagrammeR/man/grVizOutput.Rd | 10 DiagrammeR-0.8/DiagrammeR/man/graph_count.Rd | 25 DiagrammeR-0.8/DiagrammeR/man/import_graph.Rd |only DiagrammeR-0.8/DiagrammeR/man/is_graph_directed.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/is_graph_empty.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/mermaid.Rd | 4 DiagrammeR-0.8/DiagrammeR/man/node_count.Rd | 11 DiagrammeR-0.8/DiagrammeR/man/node_info.Rd | 20 DiagrammeR-0.8/DiagrammeR/man/node_present.Rd | 8 DiagrammeR-0.8/DiagrammeR/man/node_type.Rd | 18 DiagrammeR-0.8/DiagrammeR/man/remove_from_series.Rd | 31 DiagrammeR-0.8/DiagrammeR/man/renderDiagrammeR.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/renderGrViz.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/render_graph.Rd | 41 DiagrammeR-0.8/DiagrammeR/man/render_graph_from_series.Rd | 36 DiagrammeR-0.8/DiagrammeR/man/replace_in_spec.Rd | 3 DiagrammeR-0.8/DiagrammeR/man/roll_palette.Rd | 19 DiagrammeR-0.8/DiagrammeR/man/scale_edges.Rd | 24 DiagrammeR-0.8/DiagrammeR/man/scale_nodes.Rd | 23 DiagrammeR-0.8/DiagrammeR/man/select_graph_from_series.Rd |only DiagrammeR-0.8/DiagrammeR/man/series_info.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/subset_series.Rd | 38 DiagrammeR-0.8/DiagrammeR/man/trigger_script.Rd | 6 DiagrammeR-0.8/DiagrammeR/man/visnetwork.Rd |only DiagrammeR-0.8/DiagrammeR/man/vivagraph.Rd |only DiagrammeR-0.8/DiagrammeR/man/x11_hex.Rd | 3 DiagrammeR-0.8/DiagrammeR/tests |only 121 files changed, 2277 insertions(+), 2984 deletions(-)
More information about SurvRegCensCov at CRAN
Permanent link
Title: Path Manipulation Utilities
Description: Utilities for paths, files and directories.
Author: Richard Cotton [aut, cre], Janko Thyson [ctb]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between pathological versions 0.0-6 dated 2015-05-10 and 0.0-7 dated 2015-10-08
pathological-0.0-6/pathological/inst |only pathological-0.0-6/pathological/tests/run-all.R |only pathological-0.0-7/pathological/DESCRIPTION | 12 pathological-0.0-7/pathological/MD5 | 35 +- pathological-0.0-7/pathological/NAMESPACE | 99 +++--- pathological-0.0-7/pathological/NEWS | 7 pathological-0.0-7/pathological/R/paths.R | 247 +++++++++++++--- pathological-0.0-7/pathological/README.md | 3 pathological-0.0-7/pathological/man/choose_files.Rd |only pathological-0.0-7/pathological/man/r_profile.Rd | 23 + pathological-0.0-7/pathological/man/standardize_path.Rd | 7 pathological-0.0-7/pathological/tests/testthat |only pathological-0.0-7/pathological/tests/testthat.R |only 13 files changed, 310 insertions(+), 123 deletions(-)
Title: NeuroAnatomy Toolbox (nat) Extension for Handling Template
Brains
Description: Extends package nat (NeuroAnatomy Toolbox) by providing objects
and functions for handling template brains.
Author: James Manton and Gregory Jefferis
Maintainer: James Manton <ajd.manton@googlemail.com>
Diff between nat.templatebrains versions 0.6 dated 2015-07-01 and 0.6.1 dated 2015-10-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 4 ++++ R/reg_repos.R | 4 ++-- R/transformation.R | 2 +- README.md | 2 ++ man/add_reg_folders.Rd | 2 +- 7 files changed, 20 insertions(+), 14 deletions(-)
More information about nat.templatebrains at CRAN
Permanent link
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate. The analysis of paired
receiver operating curves is supported as well, so that a comparison of two predictors is possible.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.2.1 dated 2015-06-07 and 0.3.0 dated 2015-10-08
fbroc-0.2.1/fbroc/man/conf.roc.Rd |only fbroc-0.2.1/fbroc/man/perf.roc.Rd |only fbroc-0.3.0/fbroc/DESCRIPTION | 13 + fbroc-0.3.0/fbroc/MD5 | 61 +++++---- fbroc-0.3.0/fbroc/NAMESPACE | 21 ++- fbroc-0.3.0/fbroc/R/RcppExports.R | 44 +++++- fbroc-0.3.0/fbroc/R/fbroc.R | 72 ++++++++-- fbroc-0.3.0/fbroc/R/fbroc.helper.functions.R |only fbroc-0.3.0/fbroc/R/fbroc.methods.R | 115 +++++++++++------ fbroc-0.3.0/fbroc/R/fbroc.paired.R |only fbroc-0.3.0/fbroc/R/fbroc.paired.methods.R |only fbroc-0.3.0/fbroc/R/fbroc.perf.R | 19 +- fbroc-0.3.0/fbroc/R/fbroc.roc.R | 76 +++++++---- fbroc-0.3.0/fbroc/R/perf.paired.roc.R |only fbroc-0.3.0/fbroc/README.md | 6 fbroc-0.3.0/fbroc/man/boot.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/boot.roc.Rd | 1 fbroc-0.3.0/fbroc/man/conf.Rd |only fbroc-0.3.0/fbroc/man/conf.fbroc.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/conf.fbroc.roc.Rd |only fbroc-0.3.0/fbroc/man/extract.roc.Rd |only fbroc-0.3.0/fbroc/man/fbroc.Rd | 42 ++++-- fbroc-0.3.0/fbroc/man/perf.Rd |only fbroc-0.3.0/fbroc/man/perf.fbroc.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/perf.fbroc.roc.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.conf.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.conf.paired.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.paired.roc.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.perf.Rd | 12 - fbroc-0.3.0/fbroc/man/plot.fbroc.perf.paired.Rd |only fbroc-0.3.0/fbroc/man/plot.fbroc.roc.Rd | 12 + fbroc-0.3.0/fbroc/man/print.fbroc.perf.Rd | 2 fbroc-0.3.0/fbroc/man/print.fbroc.perf.paired.Rd |only fbroc-0.3.0/fbroc/src/RcppExports.cpp | 147 ++++++++++++++++++++-- fbroc-0.3.0/fbroc/src/interface.common.cpp | 16 ++ fbroc-0.3.0/fbroc/src/interface.common.h | 5 fbroc-0.3.0/fbroc/src/interface.paired.cpp | 151 +++++++++++++++++++++++ fbroc-0.3.0/fbroc/src/interface.single.cpp | 49 ++++--- fbroc-0.3.0/fbroc/src/performance.h | 3 fbroc-0.3.0/fbroc/src/roc.cpp | 133 +++++++++++++------- fbroc-0.3.0/fbroc/src/roc.h | 2 41 files changed, 766 insertions(+), 236 deletions(-)
Title: Fast, Low Memory-Footprint Digests of R Objects
Description: Provides an R interface to Bob Jenkin's streaming,
non-cryptographic 'SpookyHash' hash algorithm for use in digest-based
comparisons of R objects. 'fastdigest' plugs directly into R's internal
serialization machinery, allowing digests of all R objects the serialize()
function supports, including reference-style objects via custom hooks. Speed is
high and scales linearly by object size; memory usage is constant and
negligible.
Author: Gabriel Becker, Bob Jenkins (SpookyHash algorithm and C++ implementation)
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between fastdigest versions 0.6-2 dated 2015-10-07 and 0.6-3 dated 2015-10-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 5 ++++- src/SpookyV2.cpp | 3 ++- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.3.0 dated 2015-09-24 and 1.3.1 dated 2015-10-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/dunn.test.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply imputed datasets and
nested multiply imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between BIFIEsurvey versions 1.4-0 dated 2015-09-08 and 1.5-0 dated 2015-10-08
DESCRIPTION | 11 +++++------ MD5 | 7 ++++--- inst/CITATION |only inst/NEWS | 12 +++++++++--- man/BIFIEsurvey-package.Rd | 4 ++-- 5 files changed, 20 insertions(+), 14 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.4 dated 2015-09-10 and 0.4.6 dated 2015-10-08
DESCRIPTION | 12 MD5 | 100 ++-- NAMESPACE | 1 R/incPercentile.R | 37 - R/linarpr.R | 43 -- R/linarpt.R | 40 - R/linarr.R | 65 +-- R/lingini.R | 41 - R/lingini2.R | 40 - R/lingpg.R | 50 +- R/linpoormed.R | 41 - R/linqsr.R | 39 - R/linrmir.R | 47 +- R/linrmpg.R | 45 -- R/residual_est.R | 2 R/var_srs.R | 10 R/vardchanges.R | 58 -- R/vardchangespoor.R | 84 +-- R/vardcros.R | 1030 +++++++++++++++++++++++------------------------- R/vardcrospoor.R | 80 +-- R/vardom.R | 89 +--- R/vardom_othstr.R | 94 +--- R/vardomh.R | 97 +--- R/variance_est.R | 52 -- R/variance_othstr.R | 80 +-- R/varpoord.R | 101 ++-- inst/CITATION | 4 inst/NEWS | 10 man/domain.Rd | 10 man/incPercentile.Rd | 12 man/linarpr.Rd | 20 man/linarpt.Rd | 14 man/linarr.Rd | 32 - man/lingini.Rd | 14 man/lingini2.Rd | 14 man/lingpg.Rd | 19 man/linpoormed.Rd | 16 man/linqsr.Rd | 14 man/linrmir.Rd | 24 - man/linrmpg.Rd | 26 - man/vardchanges.Rd | 21 man/vardchangespoor.Rd | 32 - man/vardcros.Rd | 20 man/vardcrospoor.Rd | 34 - man/vardom.Rd | 42 - man/vardom_othstr.Rd | 49 -- man/vardomh.Rd | 47 -- man/vardpoor-package.Rd | 6 man/variance_est.Rd | 61 -- man/variance_othstr.Rd | 19 man/varpoord.Rd | 58 +- 51 files changed, 1351 insertions(+), 1645 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm, dppm similar to glm. Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm. The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.42-2 dated 2015-06-29 and 1.43-0 dated 2015-10-08
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spatstat-1.43-0/spatstat/man/as.owin.Rd | 9 spatstat-1.43-0/spatstat/man/as.ppm.Rd | 15 spatstat-1.43-0/spatstat/man/austates.Rd |only spatstat-1.43-0/spatstat/man/bdspots.Rd | 3 spatstat-1.43-0/spatstat/man/branchlabelfun.Rd | 4 spatstat-1.43-0/spatstat/man/bw.ppl.Rd | 6 spatstat-1.43-0/spatstat/man/cdf.test.mppm.Rd | 36 spatstat-1.43-0/spatstat/man/coef.mppm.Rd | 19 spatstat-1.43-0/spatstat/man/collapse.fv.Rd | 22 spatstat-1.43-0/spatstat/man/colourtools.Rd | 82 + spatstat-1.43-0/spatstat/man/contour.im.Rd | 26 spatstat-1.43-0/spatstat/man/dclf.progress.Rd | 40 spatstat-1.43-0/spatstat/man/dclf.sigtrace.Rd |only spatstat-1.43-0/spatstat/man/dclf.test.Rd | 53 - spatstat-1.43-0/spatstat/man/default.expand.Rd | 6 spatstat-1.43-0/spatstat/man/default.rmhcontrol.Rd | 8 spatstat-1.43-0/spatstat/man/density.lpp.Rd | 33 spatstat-1.43-0/spatstat/man/detpointprocfamilyfun.Rd |only spatstat-1.43-0/spatstat/man/dg.envelope.Rd |only spatstat-1.43-0/spatstat/man/dg.progress.Rd |only spatstat-1.43-0/spatstat/man/dg.sigtrace.Rd |only spatstat-1.43-0/spatstat/man/dg.test.Rd |only spatstat-1.43-0/spatstat/man/diagnose.ppm.Rd | 3 spatstat-1.43-0/spatstat/man/dim.detpointprocfamily.Rd |only spatstat-1.43-0/spatstat/man/distfun.lpp.Rd | 2 spatstat-1.43-0/spatstat/man/dkernel.Rd |only spatstat-1.43-0/spatstat/man/domain.Rd | 5 spatstat-1.43-0/spatstat/man/dppBessel.Rd |only spatstat-1.43-0/spatstat/man/dppCauchy.Rd |only spatstat-1.43-0/spatstat/man/dppGauss.Rd |only spatstat-1.43-0/spatstat/man/dppMatern.Rd |only spatstat-1.43-0/spatstat/man/dppPowerExp.Rd |only spatstat-1.43-0/spatstat/man/dppapproxkernel.Rd |only spatstat-1.43-0/spatstat/man/dppapproxpcf.Rd |only spatstat-1.43-0/spatstat/man/dppeigen.Rd |only spatstat-1.43-0/spatstat/man/dppkernel.Rd |only spatstat-1.43-0/spatstat/man/dppm.Rd |only spatstat-1.43-0/spatstat/man/dppparbounds.Rd |only spatstat-1.43-0/spatstat/man/dppspecden.Rd |only spatstat-1.43-0/spatstat/man/dppspecdenrange.Rd |only spatstat-1.43-0/spatstat/man/emend.Rd |only spatstat-1.43-0/spatstat/man/emend.ppm.Rd |only spatstat-1.43-0/spatstat/man/envelope.Rd | 35 spatstat-1.43-0/spatstat/man/envelope.lpp.Rd | 15 spatstat-1.43-0/spatstat/man/envelope.pp3.Rd | 13 spatstat-1.43-0/spatstat/man/fitted.mppm.Rd | 19 spatstat-1.43-0/spatstat/man/fixef.mppm.Rd |only spatstat-1.43-0/spatstat/man/fourierbasis.Rd |only spatstat-1.43-0/spatstat/man/gordon.Rd | 5 spatstat-1.43-0/spatstat/man/hierpair.family.Rd | 8 spatstat-1.43-0/spatstat/man/intensity.dppm.Rd |only spatstat-1.43-0/spatstat/man/intensity.lpp.Rd | 2 spatstat-1.43-0/spatstat/man/intensity.ppx.Rd |only spatstat-1.43-0/spatstat/man/is.stationary.Rd | 23 spatstat-1.43-0/spatstat/man/kernel.factor.Rd |only spatstat-1.43-0/spatstat/man/kppm.Rd | 5 spatstat-1.43-0/spatstat/man/lgcp.estK.Rd | 13 spatstat-1.43-0/spatstat/man/linearKcross.Rd | 4 spatstat-1.43-0/spatstat/man/linearKcross.inhom.Rd | 4 spatstat-1.43-0/spatstat/man/linearKdot.Rd | 6 spatstat-1.43-0/spatstat/man/linearKdot.inhom.Rd | 4 spatstat-1.43-0/spatstat/man/linearmarkconnect.Rd | 4 spatstat-1.43-0/spatstat/man/linearmarkequal.Rd | 2 spatstat-1.43-0/spatstat/man/linearpcfcross.Rd | 6 spatstat-1.43-0/spatstat/man/linearpcfcross.inhom.Rd | 6 spatstat-1.43-0/spatstat/man/linearpcfdot.Rd | 6 spatstat-1.43-0/spatstat/man/linearpcfdot.inhom.Rd | 4 spatstat-1.43-0/spatstat/man/logLik.dppm.Rd |only spatstat-1.43-0/spatstat/man/logLik.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/logLik.mppm.Rd | 19 spatstat-1.43-0/spatstat/man/lpp.Rd | 7 spatstat-1.43-0/spatstat/man/markcorr.Rd | 13 spatstat-1.43-0/spatstat/man/markcrosscorr.Rd |only spatstat-1.43-0/spatstat/man/mergeLevels.Rd | 12 spatstat-1.43-0/spatstat/man/methods.dppm.Rd |only spatstat-1.43-0/spatstat/man/methods.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/methods.linfun.Rd | 6 spatstat-1.43-0/spatstat/man/methods.lppm.Rd | 18 spatstat-1.43-0/spatstat/man/model.frame.ppm.Rd | 16 spatstat-1.43-0/spatstat/man/model.images.Rd | 18 spatstat-1.43-0/spatstat/man/model.matrix.ppm.Rd | 19 spatstat-1.43-0/spatstat/man/mppm.Rd | 68 + spatstat-1.43-0/spatstat/man/nnfun.lpp.Rd | 7 spatstat-1.43-0/spatstat/man/objsurf.Rd | 11 spatstat-1.43-0/spatstat/man/parameters.Rd | 5 spatstat-1.43-0/spatstat/man/plot.bermantest.Rd | 6 spatstat-1.43-0/spatstat/man/plot.dppm.Rd |only spatstat-1.43-0/spatstat/man/plot.influence.ppm.Rd | 2 spatstat-1.43-0/spatstat/man/plot.linim.Rd | 6 spatstat-1.43-0/spatstat/man/plot.mppm.Rd | 61 - spatstat-1.43-0/spatstat/man/plot.ppp.Rd | 5 spatstat-1.43-0/spatstat/man/plot.slrm.Rd | 4 spatstat-1.43-0/spatstat/man/pool.envelope.Rd | 1 spatstat-1.43-0/spatstat/man/ppm.Rd | 2 spatstat-1.43-0/spatstat/man/ppm.ppp.Rd | 18 spatstat-1.43-0/spatstat/man/predict.dppm.Rd |only spatstat-1.43-0/spatstat/man/predict.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/predict.lppm.Rd | 2 spatstat-1.43-0/spatstat/man/predict.mppm.Rd | 24 spatstat-1.43-0/spatstat/man/predict.slrm.Rd | 2 spatstat-1.43-0/spatstat/man/progressreport.Rd | 41 spatstat-1.43-0/spatstat/man/quadrat.test.mppm.Rd | 25 spatstat-1.43-0/spatstat/man/quantile.density.Rd |only spatstat-1.43-0/spatstat/man/rCauchy.Rd | 4 spatstat-1.43-0/spatstat/man/rLGCP.Rd | 5 spatstat-1.43-0/spatstat/man/rMatClust.Rd | 4 spatstat-1.43-0/spatstat/man/rVarGamma.Rd | 4 spatstat-1.43-0/spatstat/man/ranef.mppm.Rd |only spatstat-1.43-0/spatstat/man/rdpp.Rd |only spatstat-1.43-0/spatstat/man/reach.dppm.Rd |only spatstat-1.43-0/spatstat/man/relrisk.ppm.Rd | 1 spatstat-1.43-0/spatstat/man/residuals.dppm.Rd |only spatstat-1.43-0/spatstat/man/residuals.kppm.Rd | 2 spatstat-1.43-0/spatstat/man/residuals.mppm.Rd | 27 spatstat-1.43-0/spatstat/man/rgbim.Rd | 12 spatstat-1.43-0/spatstat/man/rmh.ppm.Rd | 2 spatstat-1.43-0/spatstat/man/rmpoispp.Rd | 7 spatstat-1.43-0/spatstat/man/rpoispp.Rd | 15 spatstat-1.43-0/spatstat/man/rtemper.Rd |only spatstat-1.43-0/spatstat/man/rthin.Rd | 6 spatstat-1.43-0/spatstat/man/simulate.dppm.Rd |only spatstat-1.43-0/spatstat/man/simulate.ppm.Rd | 7 spatstat-1.43-0/spatstat/man/slrm.Rd | 2 spatstat-1.43-0/spatstat/man/spatdim.Rd |only spatstat-1.43-0/spatstat/man/spatstat-internal.Rd | 91 +- spatstat-1.43-0/spatstat/man/spatstat-package.Rd | 70 + spatstat-1.43-0/spatstat/man/spatstat.options.Rd | 27 spatstat-1.43-0/spatstat/man/split.ppp.Rd | 3 spatstat-1.43-0/spatstat/man/studpermu.test.Rd | 6 spatstat-1.43-0/spatstat/man/subfits.Rd | 21 spatstat-1.43-0/spatstat/man/subset.ppp.Rd | 29 spatstat-1.43-0/spatstat/man/suffstat.Rd | 9 spatstat-1.43-0/spatstat/man/superimpose.Rd | 6 spatstat-1.43-0/spatstat/man/unitname.Rd | 6 spatstat-1.43-0/spatstat/man/update.detpointprocfamily.Rd |only spatstat-1.43-0/spatstat/man/valid.Rd |only spatstat-1.43-0/spatstat/man/valid.detpointprocfamily.Rd |only spatstat-1.43-0/spatstat/man/valid.ppm.Rd | 10 spatstat-1.43-0/spatstat/man/vcov.mppm.Rd | 29 spatstat-1.43-0/spatstat/man/waterstriders.Rd | 2 spatstat-1.43-0/spatstat/src/methas.c | 18 spatstat-1.43-0/spatstat/src/methas.h | 2 spatstat-1.43-0/spatstat/src/mhloop.h | 74 + spatstat-1.43-0/spatstat/src/mhv4.h | 4 spatstat-1.43-0/spatstat/src/mhv5.h |only spatstat-1.43-0/spatstat/src/rthin.c |only spatstat-1.43-0/spatstat/tests/alltests.R | 121 +- spatstat-1.43-0/spatstat/vignettes/datasets.Rnw | 20 spatstat-1.43-0/spatstat/vignettes/packagesizes.txt | 3 spatstat-1.43-0/spatstat/vignettes/replicated.Rnw | 151 +++ spatstat-1.43-0/spatstat/vignettes/updates.Rnw | 359 +++++++- 341 files changed, 6319 insertions(+), 2301 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 1.0.0 dated 2015-08-14 and 1.1.0 dated 2015-10-08
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 17 +++++++++++++++-- R/diagnostics.R | 4 ++-- R/extractors.R | 4 ++-- R/out.R | 4 ++-- R/parse_spc.R | 3 +++ R/plot.R | 4 ++-- R/read_series.R | 3 +++ R/seas.R | 5 ++--- R/series.R | 11 +++++++++-- R/static.R | 4 ++-- README.md | 27 ++++++++++++--------------- inst/doc/seas.pdf |binary man/final.Rd | 4 ++-- man/out.Rd | 4 ++-- man/plot.seas.Rd | 4 ++-- man/qs.Rd | 4 ++-- man/seas.Rd | 5 ++--- man/series.Rd | 11 +++++++++-- man/static.Rd | 4 ++-- vignettes/README.tex | 24 ++++++++++++------------ 22 files changed, 113 insertions(+), 85 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.1.0 dated 2015-06-14 and 1.1.1 dated 2015-10-08
nodiv-1.1.0/nodiv/tests/testthat/test_initial.R |only nodiv-1.1.1/nodiv/DESCRIPTION | 6 nodiv-1.1.1/nodiv/MD5 | 16 + nodiv-1.1.1/nodiv/NAMESPACE | 7 nodiv-1.1.1/nodiv/R/Add_to_data_object.R | 102 ++++++++---- nodiv-1.1.1/nodiv/R/Methods_for_data_objects.R | 60 ++++++- nodiv-1.1.1/nodiv/R/Node_based_analysis.R | 13 - nodiv-1.1.1/nodiv/R/Prepare_data.R | 132 ++++++++++++---- nodiv-1.1.1/nodiv/man/gridData.Rd |only nodiv-1.1.1/nodiv/tests/testthat/test_access.R |only nodiv-1.1.1/nodiv/tests/testthat/test_basic_functions.R |only 11 files changed, 258 insertions(+), 78 deletions(-)
Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currenty it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between meteoForecast versions 0.45 dated 2015-05-21 and 0.47 dated 2015-10-08
meteoForecast-0.45/meteoForecast/data |only meteoForecast-0.47/meteoForecast/DESCRIPTION | 10 - meteoForecast-0.47/meteoForecast/MD5 | 23 +-- meteoForecast-0.47/meteoForecast/NAMESPACE | 50 ++++++-- meteoForecast-0.47/meteoForecast/R/composeURL.R | 89 ++++++++++----- meteoForecast-0.47/meteoForecast/R/grepVar.R | 25 ++-- meteoForecast-0.47/meteoForecast/R/pointNCDC.R | 12 +- meteoForecast-0.47/meteoForecast/R/rasterMeteoGalicia.R | 2 meteoForecast-0.47/meteoForecast/man/getPoint.Rd | 10 - meteoForecast-0.47/meteoForecast/man/getRaster.Rd | 2 meteoForecast-0.47/meteoForecast/man/vars.Rd | 94 ++-------------- 11 files changed, 152 insertions(+), 165 deletions(-)
Title: Lightweight Logging for R Scripts
Description: Provides flexible but lightweight logging facilities for R scripts. Supports priority levels for logs and messages, flagging messages, capturing script output, switching logs, and logging to files or connections.
Author: Ben Bond-Lamberty [aut, cre]
Maintainer: Ben Bond-Lamberty <bondlamberty@pnnl.gov>
Diff between luzlogr versions 0.1.0 dated 2015-10-05 and 0.1.1 dated 2015-10-08
luzlogr-0.1.0/luzlogr/vignettes/Introduction.Rmd |only luzlogr-0.1.1/luzlogr/DESCRIPTION | 9 +++++---- luzlogr-0.1.1/luzlogr/MD5 | 14 +++++++++----- luzlogr-0.1.1/luzlogr/NEWS | 6 ++++++ luzlogr-0.1.1/luzlogr/README.md | 10 +++++----- luzlogr-0.1.1/luzlogr/build |only luzlogr-0.1.1/luzlogr/inst |only luzlogr-0.1.1/luzlogr/tests/testthat/test_logging.R | 12 ++++++++++++ luzlogr-0.1.1/luzlogr/vignettes/intro-luzlogr.Rmd |only 9 files changed, 37 insertions(+), 14 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 0.1-1 dated 2015-05-20 and 0.1-2 dated 2015-10-08
lamW-0.1-1/lamW/inst/NEWS.Rd |only lamW-0.1-2/lamW/DESCRIPTION | 8 ++++---- lamW-0.1-2/lamW/MD5 | 14 +++++++------- lamW-0.1-2/lamW/build/partial.rdb |binary lamW-0.1-2/lamW/inst/News.Rd |only lamW-0.1-2/lamW/man/lamW-package.Rd | 9 +++------ lamW-0.1-2/lamW/man/lamW.Rd | 4 ++-- lamW-0.1-2/lamW/src/lambertW.cpp | 8 ++++++-- lamW-0.1-2/lamW/tests/testthat/test-lamW.R | 10 +++++----- 9 files changed, 27 insertions(+), 26 deletions(-)
Title: Calibration Plot for Proteomics
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
Author: Quentin Giai Gianetto, Florence Combes, Yohann Couté, Christophe Bruley, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>
Diff between cp4p versions 0.3.1 dated 2015-08-17 and 0.3.2 dated 2015-10-08
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 2 +- R/calibration_plot.R | 25 ++++++++++--------------- inst |only man/LFQRatio2.Rd | 4 ++-- man/LFQRatio25.Rd | 4 ++-- man/adjust.p.Rd | 2 +- man/calibration.plot.Rd | 2 +- man/cp4p-package.Rd | 2 +- man/estim.pi0.Rd | 2 +- 11 files changed, 33 insertions(+), 37 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: Implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma DB et al. - 2013).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1.1 dated 2015-10-01 and 1.1.2 dated 2015-10-08
clere-1.1.1/clere/vignettes/RJpaper-vignette.ltx |only clere-1.1.1/clere/vignettes/biblio.bib |only clere-1.1.1/clere/vignettes/images |only clere-1.1.2/clere/DESCRIPTION | 10 +++---- clere-1.1.2/clere/MD5 | 31 +++++++++++------------ clere-1.1.2/clere/R/fitPacs.R | 6 ++++ clere-1.1.2/clere/build/vignette.rds |binary clere-1.1.2/clere/data/algoComp.RData |binary clere-1.1.2/clere/data/numExpRealData.RData |binary clere-1.1.2/clere/data/numExpSimData.RData |binary clere-1.1.2/clere/inst/doc/RJpaper-vignette.pdf |binary clere-1.1.2/clere/inst/doc/Vignette.pdf |only clere-1.1.2/clere/inst/doc/Vignette.pdf.asis |only clere-1.1.2/clere/man/clere-package.Rd | 4 +- clere-1.1.2/clere/man/fitPacs.Rd | 21 ++++++++------- clere-1.1.2/clere/man/numExpRealData.Rd | 2 - clere-1.1.2/clere/src/Model.cpp | 5 +-- clere-1.1.2/clere/src/pacs.cpp | 29 ++++++++++++--------- clere-1.1.2/clere/vignettes/Vignette.pdf.asis |only 19 files changed, 60 insertions(+), 48 deletions(-)
Title: Calibration Functions for Analytical Chemistry
Description: Simple functions for plotting linear
calibration functions and estimating standard errors for measurements
according to the Handbook of Chemometrics and Qualimetrics: Part A
by Massart et al. There are also functions estimating the limit
of detection (LOD) and limit of quantification (LOQ).
The functions work on model objects from - optionally weighted - linear
regression (lm) or robust linear regression ('rlm' from the 'MASS' package).
Author: Johannes Ranke [aut, cre, cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between chemCal versions 0.1-34 dated 2014-04-25 and 0.1-37 dated 2015-10-08
DESCRIPTION | 24 +++++++++++++----------- MD5 | 35 +++++++++++++++++++++++++++++------ NAMESPACE | 8 ++++++++ build/vignette.rds |binary data/din32645.rda |binary inst/doc/chemCal.pdf |binary inst/staticdocs |only inst/web |only man/din32645.Rd | 4 ++-- 9 files changed, 52 insertions(+), 19 deletions(-)
Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive
package. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre],
Sunkyu Choi [trl],
Ivanka Skakun [trl],
Gergely Dar<c3><b3>czi [trl],
Anton Antonov [trl],
Hisham Ben Hamidane [trl],
Anja Billing [trl],
Aditya Bhagwat [trl],
Rasmus B<c3><a5><c3><a5>th [trl],
Mine Cetinkaya-Rundel [trl],
Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.base versions 0.0-2 dated 2015-10-06 and 0.0-3 dated 2015-10-08
DESCRIPTION | 8 +- MD5 | 14 ++-- NEWS | 1 R/assert-identical-to-true-false-na.R | 19 +++-- R/assert-is-true-false-na.R | 107 +++++++++++++++++++++++++++++---- R/is-true-false-na.R | 44 +++++++------ man/Truth.Rd | 34 +++++----- tests/testthat/test-is-true-false-na.R | 92 ++++++++++++++++++++++++++++ 8 files changed, 251 insertions(+), 68 deletions(-)
More information about assertive.base at CRAN
Permanent link
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.3-0 dated 2015-07-15 and 0.3-1 dated 2015-10-08
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Title: Ternary Search Tree for Auto-Completion and Spell Checking
Description: A ternary search tree is a type of prefix tree with up to three children and the ability for incremental string search. The package uses this ability for word auto-completion and spell checking. Includes a dataset with the 10001 most frequent English words.
Author: Ricardo Merino [aut, cre],
Samantha Fernandez [ctb]
Maintainer: Ricardo Merino <ricardo.merino.raldua@gmail.com>
Diff between TSTr versions 1.0 dated 2015-09-06 and 1.1 dated 2015-10-07
TSTr-1.0/TSTr/R/updateTree.R |only TSTr-1.0/TSTr/R/updateTree.default.R |only TSTr-1.0/TSTr/R/updateTree.tstTree.R |only TSTr-1.0/TSTr/inst/doc/index.html |only TSTr-1.0/TSTr/man/updateTree.Rd |only TSTr-1.1/TSTr/DESCRIPTION | 14 +- TSTr-1.1/TSTr/MD5 | 73 ++++++++--- TSTr-1.1/TSTr/NAMESPACE | 24 +++ TSTr-1.1/TSTr/R/Add.R | 2 TSTr-1.1/TSTr/R/Addlist.R |only TSTr-1.1/TSTr/R/PNcheck.R |only TSTr-1.1/TSTr/R/PNcheck.default.R |only TSTr-1.1/TSTr/R/PNcheck.tstTree.R |only TSTr-1.1/TSTr/R/SDcheck.R |only TSTr-1.1/TSTr/R/SDcheck.default.R |only TSTr-1.1/TSTr/R/SDcheck.dist1_DT.R |only TSTr-1.1/TSTr/R/SDcheck.dist2_DT.R |only TSTr-1.1/TSTr/R/SDcheck.dist3_DT.R |only TSTr-1.1/TSTr/R/SDcheck.spellTree_1.R |only TSTr-1.1/TSTr/R/SDcheck.spellTree_2.R |only TSTr-1.1/TSTr/R/SDcheck.spellTree_3.R |only TSTr-1.1/TSTr/R/SDkeeper.R |only TSTr-1.1/TSTr/R/SDkeeper.default.R |only TSTr-1.1/TSTr/R/addToTree.R |only TSTr-1.1/TSTr/R/addToTree.default.R |only TSTr-1.1/TSTr/R/addToTree.tstTree.R |only TSTr-1.1/TSTr/R/crearDT.R |only TSTr-1.1/TSTr/R/crearFullDT.R |only TSTr-1.1/TSTr/R/crearFullTree.R |only TSTr-1.1/TSTr/R/delList.R |only TSTr-1.1/TSTr/R/delete.R |only TSTr-1.1/TSTr/R/deletion1.R |only TSTr-1.1/TSTr/R/deletion2.R |only TSTr-1.1/TSTr/R/deletion3.R |only TSTr-1.1/TSTr/R/insertion.R |only TSTr-1.1/TSTr/R/matricear.R |only TSTr-1.1/TSTr/R/newTree.R | 1 TSTr-1.1/TSTr/R/replace.R |only TSTr-1.1/TSTr/R/searchTreeSD.R |only TSTr-1.1/TSTr/R/searchWordSD.R |only TSTr-1.1/TSTr/R/spellSD.R |only TSTr-1.1/TSTr/R/spellTree_1.R |only TSTr-1.1/TSTr/R/spellTree_2.R |only TSTr-1.1/TSTr/R/spellTree_3.R |only TSTr-1.1/TSTr/R/suggestions.R |only TSTr-1.1/TSTr/R/transpose.R |only TSTr-1.1/TSTr/R/variations.R |only TSTr-1.1/TSTr/build/TSTr.pdf |only TSTr-1.1/TSTr/build/vignette.rds |binary TSTr-1.1/TSTr/inst/doc/TSTr.R | 19 ++- TSTr-1.1/TSTr/inst/doc/TSTr.Rmd | 113 +++++++++++++++--- TSTr-1.1/TSTr/inst/doc/TSTr.html | 213 ++++++++++++++++++++++++++-------- TSTr-1.1/TSTr/man/PNcheck.Rd |only TSTr-1.1/TSTr/man/SDcheck.Rd |only TSTr-1.1/TSTr/man/SDkeeper.Rd |only TSTr-1.1/TSTr/man/TSTr-package.Rd | 20 +-- TSTr-1.1/TSTr/man/addToTree.Rd |only TSTr-1.1/TSTr/man/newTree.Rd | 2 TSTr-1.1/TSTr/vignettes/TSTr.Rmd | 113 +++++++++++++++--- TSTr-1.1/TSTr/vignettes/Thumbs.db |binary TSTr-1.1/TSTr/vignettes/banner.jpg |only TSTr-1.1/TSTr/vignettes/bannera.html |only 62 files changed, 482 insertions(+), 112 deletions(-)
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System. These tools address common challenges
associated with continuous time series data for environmental decision
making.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between SWMPr versions 2.1.0 dated 2015-08-10 and 2.1.4 dated 2015-10-07
DESCRIPTION | 8 +- MD5 | 24 +++---- NAMESPACE | 2 R/swmpr_analyze.R | 166 +++++++++++++++++++++++++++++++------------------ R/swmpr_misc.R | 4 - R/swmpr_organize.R | 20 +++-- R/swmpr_retrieval.R | 6 - man/aggremetab.Rd | 10 ++ man/comb.Rd | 2 man/na.approx.swmpr.Rd | 1 man/plot_metab.Rd | 3 man/setstep.Rd | 8 +- man/smoother.Rd | 12 +-- 13 files changed, 161 insertions(+), 105 deletions(-)
Title: Dynamic Extensions for Network Objects
Description: Simple interface routines to facilitate the handling of network objects with complex intertemporal data. This is a part of the "statnet" suite of packages for network analysis.
Author: Carter T. Butts [aut],
Ayn Leslie-Cook [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut, cre],
Zack Almquist [ctb],
David R. Hunter [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Steven M. Goodreau [ctb],
Jeffrey Horner [ctb],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamic versions 0.8.0 dated 2015-09-21 and 0.8.1 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/networkDynamic.pdf |binary tests/utils_tests.R | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
More information about networkDynamic at CRAN
Permanent link
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.2 dated 2015-10-05 and 1.2.1 dated 2015-10-07
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- R/symscorestat.R | 2 +- inst/Makefile |only inst/testperm.f90 | 4 +++- src/signtestperm.f90 | 12 +++++++++--- 6 files changed, 21 insertions(+), 12 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.9.4 dated 2015-03-06 and 1.9.5 dated 2015-10-07
CHANGELOG | 9 ++++- DESCRIPTION | 10 +++--- MD5 | 66 +++++++++++++++++++++---------------------- NAMESPACE | 10 +++++- R/kcde.R | 29 +++++++++---------- R/kcopula.R | 12 ++++++- R/kda.R | 73 +++++++++++++++++++++--------------------------- R/kdde.R | 20 ++----------- R/kde.R | 44 +++++++++++++--------------- R/normal.R | 2 - build/vignette.rds |binary inst/doc/kde.pdf |binary man/Hlscv.Rd | 3 - man/Hns.Rd | 3 - man/Hpi.Rd | 21 ++++++------- man/Hscv.Rd | 5 +-- man/binning.Rd | 1 man/contour.Rd | 3 + man/ise.mixt.Rd | 1 man/kcde.Rd | 16 +++++----- man/kcopula.Rd | 4 +- man/kda.Rd | 8 ++--- man/kdde.Rd | 3 - man/kde.Rd | 14 ++++----- man/kfe.Rd | 7 +--- man/kroc.Rd | 9 +++-- man/ks-package.Rd | 8 ++--- man/mixt.Rd | 2 - man/plot.kcde.Rd | 10 +++--- man/plot.kda.Rd | 17 +++++------ man/plot.kdde.Rd | 9 ++--- man/plot.kde.Rd | 31 ++++++++++---------- man/plot.kde.loctest.Rd | 6 +-- man/pre.transform.Rd | 4 -- 34 files changed, 222 insertions(+), 238 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.4-0 dated 2015-10-01 and 0.4-1 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ICP.R | 3 ++- R/hiddenICP.R | 4 ++-- R/print.InvariantCausalPrediction.R | 8 ++++---- R/print.hiddenInvariantCausalPrediction.R | 6 +++--- 6 files changed, 20 insertions(+), 19 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Dose-Response Data Evaluation
Description: A somewhat outdated package of basic and easy-to-use functions for
fitting dose-response curves to continuous dose-response data, calculating some
(eco)toxicological parameters and plotting the results. Please consider using
the more powerful and actively developed 'drc' package. Functions that are
fitted are the cumulative density function of the lognormal distribution
(probit fit), of the logistic distribution (logit fit), of the weibull
distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
derived from the latter, which is used to describe data showing stimulation at
low doses (hormesis). In addition, functions checking, plotting and retrieving
dose-response data retrieved from a database accessed via RODBC are included.
As an alternative to the original fitting methods, the algorithms from the drc
package can be used.
Author: Johannes Ranke [aut, cre]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between drfit versions 0.6.3 dated 2014-07-28 and 0.6.4 dated 2015-10-07
DESCRIPTION | 40 +++++++++++++++++++++------------------- MD5 | 14 +++++++------- NAMESPACE | 10 +++------- R/checkexperiment.R | 14 +++++++++----- R/checksubstance.R | 10 +++++++--- R/drdata.R | 16 ++++++++++------ data/XY.rda |binary inst/doc/drfit-Rnews.pdf |binary 8 files changed, 57 insertions(+), 47 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.16 dated 2015-09-13 and 0.5.18 dated 2015-10-07
DESCRIPTION | 8 MD5 | 37 +-- NAMESPACE | 1 R/vtreat.R | 232 ++++++++++++++--------- README.md | 27 +- build/vignette.rds |binary inst/doc/vtreat.R | 16 + inst/doc/vtreat.Rmd | 66 ++++-- inst/doc/vtreat.html | 393 +++++++++++++++++++++++----------------- inst/doc/vtreatOverfit.R | 4 inst/doc/vtreatOverfit.Rmd | 20 +- inst/doc/vtreatOverfit.html | 123 ++++++------ man/designTreatmentsC.Rd | 22 +- man/designTreatmentsN.Rd | 14 - man/prepare.Rd | 6 man/vtreat-package.Rd | 4 tests/testthat/testRareCases.R |only tests/testthat/testWeirdTypes.R | 30 +-- vignettes/vtreat.Rmd | 50 ++--- vignettes/vtreatOverfit.Rmd | 20 +- 20 files changed, 609 insertions(+), 464 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Description: Implementation of the vine graphical model for building
high-dimensional probability distributions as a factorization of
bivariate copulas and marginal density functions. This package
provides S4 classes for vines (C-vines and D-vines) and methods
for inference, goodness-of-fit tests, density/distribution
function evaluation, and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut],
Joris Meys [ctb]
Maintainer: Yasser Gonzalez-Fernandez <ygonzalezfernandez@gmail.com>
Diff between vines versions 1.1.3 dated 2015-03-25 and 1.1.4 dated 2015-10-07
vines-1.1.3/vines/tests/hfunctions.R |only vines-1.1.4/vines/DESCRIPTION | 33 ++++++++------ vines-1.1.4/vines/MD5 | 57 +++++++++++++------------ vines-1.1.4/vines/NAMESPACE | 5 -- vines-1.1.4/vines/NEWS | 8 +++ vines-1.1.4/vines/R/Vine.R | 24 +++++----- vines-1.1.4/vines/R/dimnames.R | 24 +++++----- vines-1.1.4/vines/R/dvine.R | 24 +++++----- vines-1.1.4/vines/R/h.R | 67 ++++++++++++++---------------- vines-1.1.4/vines/R/hinverse.R | 54 +++++++++++------------- vines-1.1.4/vines/R/pvine.R | 24 +++++----- vines-1.1.4/vines/R/rvine.R | 24 +++++----- vines-1.1.4/vines/R/show.R | 24 +++++----- vines-1.1.4/vines/R/vineFit.R | 24 +++++----- vines-1.1.4/vines/R/vineFitML.R | 24 +++++----- vines-1.1.4/vines/R/vineGoF.R | 24 +++++----- vines-1.1.4/vines/R/vineIter.R | 24 +++++----- vines-1.1.4/vines/R/vineOrder.R | 24 +++++----- vines-1.1.4/vines/R/vinePIT.R | 24 +++++----- vines-1.1.4/vines/R/vineParameters.R | 24 +++++----- vines-1.1.4/vines/inst/CITATION | 2 vines-1.1.4/vines/man/h-methods.Rd | 31 ++++++++----- vines-1.1.4/vines/man/hinverse-methods.Rd | 25 ++++++----- vines-1.1.4/vines/src/h.c | 61 +++++++++++++-------------- vines-1.1.4/vines/src/h.h | 47 ++++++++++----------- vines-1.1.4/vines/src/hinverse.c | 49 ++++++++++----------- vines-1.1.4/vines/src/hinverse.h | 41 ++++++++---------- vines-1.1.4/vines/src/register.c | 55 ++++++++++++------------ vines-1.1.4/vines/tests/testthat |only vines-1.1.4/vines/tests/testthat.R |only 30 files changed, 431 insertions(+), 416 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for handling URLs that so far includes functions for URL
encoding and decoding, parsing, and parameter extraction. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Mark Greenaway [ctb],
Bob Rudis [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.2.1 dated 2015-08-31 and 1.3.1 dated 2015-10-07
urltools-1.2.1/urltools/man/suffix_refresh.Rd |only urltools-1.2.1/urltools/man/url_parameters.Rd |only urltools-1.3.1/urltools/DESCRIPTION | 8 - urltools-1.3.1/urltools/MD5 | 45 +++--- urltools-1.3.1/urltools/NAMESPACE | 4 urltools-1.3.1/urltools/NEWS | 24 +++ urltools-1.3.1/urltools/R/RcppExports.R | 109 +++++++++++---- urltools-1.3.1/urltools/R/suffix.R | 48 ------ urltools-1.3.1/urltools/R/urltools.R | 8 - urltools-1.3.1/urltools/README.md | 2 urltools-1.3.1/urltools/inst/doc/urltools.R | 32 +++- urltools-1.3.1/urltools/inst/doc/urltools.Rmd | 56 +++++-- urltools-1.3.1/urltools/inst/doc/urltools.html | 54 +++++-- urltools-1.3.1/urltools/man/param_get.Rd |only urltools-1.3.1/urltools/man/param_remove.Rd |only urltools-1.3.1/urltools/man/param_set.Rd |only urltools-1.3.1/urltools/man/suffix_dataset.Rd | 1 urltools-1.3.1/urltools/man/suffix_extract.Rd | 3 urltools-1.3.1/urltools/src/RcppExports.cpp | 49 +++++- urltools-1.3.1/urltools/src/param.cpp |only urltools-1.3.1/urltools/src/parameter.cpp |only urltools-1.3.1/urltools/src/parameter.h |only urltools-1.3.1/urltools/src/parsing.cpp | 76 +++++----- urltools-1.3.1/urltools/src/parsing.h | 42 ++--- urltools-1.3.1/urltools/src/urltools.cpp | 42 ----- urltools-1.3.1/urltools/tests/testthat/test_parameters.R |only urltools-1.3.1/urltools/tests/testthat/test_parsing.R | 31 ++-- urltools-1.3.1/urltools/vignettes/urltools.Rmd | 56 +++++-- 28 files changed, 411 insertions(+), 279 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.8 dated 2015-07-24 and 0.8.9 dated 2015-10-07
DESCRIPTION | 6 MD5 | 72 ++-- R/dataset_metrics.r | 20 - R/downloads.R | 40 +- R/elevation.r | 67 ++-- R/name_lookup.r | 4 R/name_usage.r | 59 +-- R/occ_count.r | 2 R/occ_download.R | 14 R/occ_download_import.R | 1 R/occ_search.r | 10 R/rgbif-package.r | 1 R/zzz.r | 26 - README.md | 99 +++-- build/vignette.rds |binary inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 153 ++++----- inst/doc/issues_vignette.html | 153 ++++----- inst/doc/rgbif_vignette.html | 563 +++++++++++++++++----------------- inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 153 ++++----- inst/vign/rgbif_vignette.Rmd | 2 inst/vign/rgbif_vignette.md | 561 +++++++++++++++++---------------- man/dataset_metrics.Rd | 4 man/downloads.Rd | 12 man/name_usage.Rd | 4 man/occ_count.Rd | 2 man/occ_download.Rd | 11 tests/testthat/test-dataset_metrics.r | 11 tests/testthat/test-dataset_suggest.r | 4 tests/testthat/test-elevation.R | 22 + tests/testthat/test-gbifmap.r | 3 tests/testthat/test-name_lookup.r | 7 tests/testthat/test-name_usage.r | 168 +++++++++- tests/testthat/test-occ_search.r | 82 +++- vignettes/issues_vignette.Rmd | 153 ++++----- vignettes/rgbif_vignette.Rmd | 561 +++++++++++++++++---------------- 37 files changed, 1686 insertions(+), 1364 deletions(-)
Title: Visualisation of Sequential Probability Distributions Using Fan
Charts
Description: Visualise sequential distributions using a range of plotting
styles. Sequential distribution data can be input as either simulations or
values corresponding to percentiles over time. Plots are added to
existing graphic devices using the fan function. Users can choose from four
different styles, including fan chart type plots, where a set of coloured
polygon, with shadings corresponding to the percentile values are layered
to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel" <g.j.abel@gmail.com>
Diff between fanplot versions 3.4.0 dated 2015-01-28 and 3.4.1 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ R/fan.R | 3 ++- R/fan0.R | 10 ++++------ inst/CITATION |only man/fan.Rd | 9 +++++++-- man/fanplot-pacakge.Rd |only 8 files changed, 29 insertions(+), 18 deletions(-)
Title: Benford Analysis for Data Validation and Forensic Analytics
Description: The Benford Analysis package provides tools that make it easier to
validate data using Benford's Law.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between benford.analysis versions 0.1.1 dated 2014-05-01 and 0.1.2.1 dated 2015-10-07
DESCRIPTION | 10 +- MD5 | 68 +++++++------- NAMESPACE | 51 ++++++----- R/data.documentation.R | 174 +++++++++++++++++++------------------- R/functions-new.R | 10 +- R/get.functions.R | 18 +-- R/internal.functions-new-code-2.R | 12 -- README.md |only man/MAD.Rd | 9 + man/benford.Rd | 143 ++++++++++++++----------------- man/benford.analysis.Rd | 45 +++------ man/census.2000_2010.Rd | 9 - man/census.2009.Rd | 6 - man/chisq.Rd | 12 +- man/corporate.payment.Rd | 10 +- man/dfactor.Rd | 9 + man/duplicatesTable.Rd | 8 - man/extract.digits.Rd | 53 ++++------- man/getBfd.Rd | 10 +- man/getData.Rd | 13 +- man/getDigits.Rd | 15 +-- man/getDuplicates.Rd | 10 +- man/getSuspects.Rd | 20 +--- man/lakes.perimeter.Rd | 10 +- man/mantissa.Rd | 10 +- man/marc.Rd | 12 +- man/p.these.digits.Rd | 4 man/p.this.digit.at.n.Rd | 10 +- man/plot.Benford.Rd | 20 +--- man/print.Benford.Rd | 10 +- man/sino.forest.Rd | 9 - man/suspectsTable.Rd | 18 +-- man/taxable.incomes.1978.Rd | 9 - tests/testthat/test-benford.R | 33 ++++++- tests/testthat/test-extract.R | 108 ++++++++++++----------- tests/testthat/test-get.R |only 36 files changed, 488 insertions(+), 480 deletions(-)
More information about benford.analysis at CRAN
Permanent link
Title: Matrix Exponential
Description: Computation of the matrix exponential, logarithm, and related quantities.
Author: Vincent Goulet, Christophe Dutang, Martin Maechler,
David Firth, Marina Shapira, Michael Stadelmann,
expm-developers@lists.R-forge.R-project.org
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between expm versions 0.99-1.1 dated 2014-02-12 and 0.999-0 dated 2015-10-07
ChangeLog | 17 + DESCRIPTION | 16 - MD5 | 84 ++++---- NAMESPACE | 10 R/balance.R | 2 R/expm.R | 29 +- R/expm2.R | 287 ++++++++++++++-------------- R/expmCond-all.R | 24 -- R/expm_vec.R | 2 R/logm.Higham08.R | 28 ++ R/logm.R | 2 R/sqrtm.R | 2 build/vignette.rds |binary demo/balanceTst.R | 8 demo/exact-fn.R | 4 demo/expm.R | 2 inst/doc/expm.R | 1 inst/doc/expm.pdf |binary inst/po/en@quot |only inst/po/fr/LC_MESSAGES/expm.mo |only inst/test-tools.R | 2 man/balance.Rd | 5 man/expAtv.Rd | 2 man/expm.Rd | 26 +- man/expmCond.Rd | 4 man/expmFrechet.Rd | 2 man/logm.Rd | 11 - po/R-expm.pot |only po/expm.pot | 78 ++++++- po/fr.po | 88 +++++++- src/R_dgebal.c | 19 + src/expm.h | 5 src/init.c | 3 src/matexp_MH09.c |only src/matpow.c | 13 - src/matrexp.f | 12 - src/matrexpO.f | 420 +++++++++++++++++++++-------------------- src/mexp-common.f | 23 +- tests/bal-ex.R | 15 + tests/ex.R | 68 +++--- tests/ex2.R | 21 +- tests/exact-ex.R | 83 +++++--- tests/expm-Cond.R | 16 - tests/log+sqrt.R | 23 +- tests/matpow-ex.R |only 45 files changed, 870 insertions(+), 587 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2 dated 2015-03-10 and 2.2.1 dated 2015-10-07
DESCRIPTION | 12 - MD5 | 18 - NAMESPACE | 6 R/autoevenn.R | 22 -- R/evenn.R | 502 +++++++++++++++++++++++++++++++-------------------- R/man.evenn.R | 56 +++-- man/autoevenn.Rd | 5 man/eVenn-package.Rd | 7 man/evenn.Rd | 14 - man/man.evenn.Rd | 2 10 files changed, 385 insertions(+), 259 deletions(-)
Title: Response-Surface Analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth <russell-lenth@uiowa.edu>
Diff between rsm versions 2.7-3 dated 2015-09-03 and 2.7-4 dated 2015-10-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/rsm.R | 7 +++++-- inst/NEWS | 4 ++++ inst/doc/rs-illus.pdf |binary inst/doc/rsm-plots.pdf |binary inst/doc/rsm.pdf |binary 7 files changed, 19 insertions(+), 12 deletions(-)
Title: Import Stata Data Files
Description: Function to read and write the Stata file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.7.1 dated 2015-08-07 and 0.8 dated 2015-10-07
readstata13-0.7.1/readstata13/src/statadefines.h |only readstata13-0.7.1/readstata13/src/swap_endian.h |only readstata13-0.8/readstata13/DESCRIPTION | 10 readstata13-0.8/readstata13/MD5 | 45 readstata13-0.8/readstata13/NAMESPACE | 1 readstata13-0.8/readstata13/NEWS | 8 readstata13-0.8/readstata13/R/RcppExports.R | 17 readstata13-0.8/readstata13/R/dbcal.R | 1 readstata13-0.8/readstata13/R/read.R | 246 +++-- readstata13-0.8/readstata13/R/readstata13.R | 8 readstata13-0.8/readstata13/R/save.R | 205 +++- readstata13-0.8/readstata13/R/tools.R | 2 readstata13-0.8/readstata13/README.md | 26 readstata13-0.8/readstata13/inst/include |only readstata13-0.8/readstata13/man/read.dta13.Rd | 110 +- readstata13-0.8/readstata13/man/readstata13.Rd | 4 readstata13-0.8/readstata13/man/save.dta13.Rd | 49 - readstata13-0.8/readstata13/man/stata_pre13_save.Rd |only readstata13-0.8/readstata13/src/Makevars |only readstata13-0.8/readstata13/src/Makevars.win |only readstata13-0.8/readstata13/src/RcppExports.cpp | 28 readstata13-0.8/readstata13/src/rcpp_pre13_savestata.cpp |only readstata13-0.8/readstata13/src/rcpp_readstata.cpp | 718 --------------- readstata13-0.8/readstata13/src/rcpp_savestata.cpp | 160 ++- readstata13-0.8/readstata13/src/read_dta.cpp |only readstata13-0.8/readstata13/src/read_pre13_dta.cpp |only 26 files changed, 639 insertions(+), 999 deletions(-)
Title: Paternity Exclusion in Autopolyploid Species
Description: Functions to perform paternity exclusion via allele
matching, in autopolyploid species having ploidy 4, 6, or 8. The
marker data data used can be genotypic (copy numbers known) or
'phenotypic' (copy numbers not known).
Author: Alexander Zwart
Maintainer: Alexander Zwart <Alec.Zwart@csiro.au>
Diff between PolyPatEx versions 0.9 dated 2014-07-02 and 0.9.1 dated 2015-10-07
DESCRIPTION | 12 +++--- LICENSE | 4 +- MD5 | 54 +++++++++++++-------------- NAMESPACE | 5 ++ R/PolyPatEx-package.R | 76 +++++++++++++++++++-------------------- R/convertToPhenot.R | 8 ++-- R/genotPPE.R | 5 +- R/inputData.R | 3 + R/multilocusTypes.R | 9 ++-- R/phenotPPE.R | 5 +- R/potentialFatherIDs.R | 3 + build/vignette.rds |binary inst/doc/PolyPatEx-vignette.Rnw | 20 +++++----- inst/doc/PolyPatEx-vignette.pdf |binary man/FR_Genotype.Rd | 3 + man/GF_Phenotype.Rd | 3 + man/PolyPatEx-package.Rd | 3 + man/convertToPhenot.Rd | 3 + man/fixCSV.Rd | 3 + man/foreignAlleles.Rd | 3 + man/genotPPE.Rd | 3 + man/inputData.Rd | 3 + man/multilocusTypes.Rd | 3 + man/phenotPPE.Rd | 3 + man/potentialFatherCounts.Rd | 3 + man/potentialFatherIDs.Rd | 3 + man/preprocessData.Rd | 3 + vignettes/PolyPatEx-vignette.Rnw | 20 +++++----- 28 files changed, 144 insertions(+), 119 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.2.6 dated 2015-07-17 and 2.3.1 dated 2015-10-07
DESCRIPTION | 10 MD5 | 415 ++++++++-------- NAMESPACE | 1 R/MxAlgebra.R | 5 R/MxCompute.R | 8 R/MxDataWLS.R | 2 R/MxExpectation.R | 15 R/MxExpectationGREML.R | 18 R/MxExpectationLISREL.R | 207 +++---- R/MxExpectationNormal.R | 169 +++--- R/MxExpectationRAM.R | 73 +- R/MxExpectationStateSpace.R | 4 R/MxFactorScores.R | 91 +++ R/MxFitFunctionGREML.R | 9 R/MxFitFunctionWLS.R | 87 ++- R/MxMatrix.R | 8 R/MxModelFunctions.R | 13 R/MxRestore.R | 36 + R/MxRun.R | 406 ++++++++------- R/MxRunHelperFunctions.R | 1 R/MxSummary.R | 19 R/MxVersion.R | 2 R/sysdata.rda |binary data/LongitudinalOverdispersedCounts.rda |only data/datalist | 1 inst/CITATION | 2 inst/models/enormous/lib/stderrlib.R | 5 inst/models/nightly/FactorScores.R | 46 + inst/models/nightly/GREML_monophenotype_1GRM.R |only inst/models/nightly/GREML_monophenotype_1GRM_GradDesc.R |only inst/models/passing/ContinuousOnlyWLSTest.R | 2 inst/models/passing/GeneralizedEstimatingEquations.R |only inst/models/passing/IntroSEM-BivariateStd.R | 7 inst/models/passing/IntroSEM-ThreeFactorScale2Test.R | 3 inst/models/passing/MatrixCreation.R | 19 inst/models/passing/MatrixErrorDetection.R | 7 inst/models/passing/MultilevelUniRandomSlopeInt.R | 25 inst/models/passing/MultipleGroupWLS.R |only inst/models/passing/RemoveEntriesTest.R | 19 inst/models/passing/SimpleConfidenceIntervals.R | 5 inst/models/passing/SimpleMLAlgebraCIs.R | 5 inst/models/passing/StateSpaceInputs.R | 47 + inst/models/passing/UnivariateRandomInterceptWide.R | 49 + inst/models/passing/rfitfunc.R | 9 man/BaseCompute-class.Rd | 3 man/LongitudinalOverdispersedCounts.Rd |only man/MxAlgebraFormula-class.Rd | 3 man/MxBaseExpectation-class.Rd | 3 man/MxBaseFitFunction-class.Rd | 3 man/MxBaseNamed-class.Rd | 3 man/MxBaseObjectiveMetaData-class.Rd | 3 man/MxCharOrList-class.Rd | 3 man/MxCharOrNumber-class.Rd | 3 man/MxCompute-class.Rd | 3 man/MxDataFrameOrMatrix-class.Rd | 3 man/MxDataStatic-class.Rd | 3 man/MxDirectedGraph-class.Rd | 3 man/MxExpectationXclass.Rd | 3 man/MxFitFunction-class.Rd | 3 man/MxFlatModel-class.Rd | 3 man/MxInterval-class.Rd | 3 man/MxLISRELModel-class.Rd | 3 man/MxListOrNull-class.Rd | 3 man/MxOptionalChar-class.Rd | 3 man/MxOptionalCharOrNumber-class.Rd | 3 man/MxOptionalLogical-class.Rd | 3 man/MxOptionalMatrix-class.Rd | 3 man/MxOptionalNumeric-class.Rd | 3 man/MxRAMGraph-class.Rd | 3 man/MxRAMMetaData-class.Rd | 3 man/MxRAMModel-class.Rd | 3 man/OpenMx.Rd | 3 man/expm.Rd | 3 man/genericFitDependencies-MxBaseFitFunction-method.Rd | 3 man/imxAddDependency.Rd | 3 man/imxCheckMatrices.Rd | 3 man/imxCheckVariables.Rd | 3 man/imxConDecMatrixSlots.Rd | 3 man/imxConstraintRelations.Rd | 3 man/imxConvertIdentifier.Rd | 3 man/imxConvertLabel.Rd | 3 man/imxConvertSubstitution.Rd | 3 man/imxCreateMatrix.Rd | 3 man/imxDataTypes.Rd | 3 man/imxDefaultGetSlotDisplayNames.Rd | 3 man/imxDeparse.Rd | 3 man/imxDependentModels.Rd | 3 man/imxDetermineDefaultOptimizer.Rd | 3 man/imxDiff.Rd | 3 man/imxDmvnorm.Rd | 3 man/imxEvalByName.Rd | 3 man/imxExtractMethod.Rd | 3 man/imxExtractNames.Rd | 3 man/imxExtractReferences.Rd | 3 man/imxExtractSlot.Rd | 3 man/imxFlattenModel.Rd | 3 man/imxFreezeModel.Rd | 3 man/imxGenSwift.Rd | 3 man/imxGenerateLabels.Rd | 3 man/imxGenerateNamespace.Rd | 3 man/imxGenericModelBuilder.Rd | 3 man/imxGetSlotDisplayNames.Rd | 3 man/imxHasNPSOL.Rd | 3 man/imxHasOpenMP.Rd | 3 man/imxIdentifier.Rd | 3 man/imxIndependentModels.Rd | 3 man/imxInitModel.Rd | 3 man/imxIsDefinitionVariable.Rd | 3 man/imxIsPath.Rd | 3 man/imxLocateFunction.Rd | 3 man/imxLocateIndex.Rd | 3 man/imxLocateLabel.Rd | 3 man/imxLog.Rd | 3 man/imxLookupSymbolTable.Rd | 3 man/imxModelBuilder.Rd | 3 man/imxModelTypes.Rd | 3 man/imxMpiWrap.Rd | 3 man/imxOriginalMx.Rd | 3 man/imxPPML.Rd | 3 man/imxPPML.Test.Battery.Rd | 3 man/imxPPML.Test.Test.Rd | 3 man/imxPreprocessModel.Rd | 3 man/imxReplaceMethod.Rd | 3 man/imxReplaceModels.Rd | 3 man/imxReplaceSlot.Rd | 3 man/imxReservedNames.Rd | 3 man/imxReverseIdentifier.Rd | 3 man/imxSameType.Rd | 3 man/imxSeparatorChar.Rd | 3 man/imxSfClient.Rd | 3 man/imxSimpleRAMPredicate.Rd | 3 man/imxSparseInvert.Rd | 3 man/imxSquareMatrix.Rd | 3 man/imxSymmetricMatrix.Rd | 3 man/imxTypeName.Rd | 3 man/imxUntitledName.Rd | 3 man/imxUntitledNumber.Rd | 3 man/imxUntitledNumberReset.Rd | 3 man/imxUpdateModelValues.Rd | 3 man/imxVariableTypes.Rd | 3 man/imxVerifyMatrix.Rd | 3 man/imxVerifyModel.Rd | 3 man/imxVerifyName.Rd | 3 man/imxVerifyReference.Rd | 3 man/logm.Rd | 3 man/mxAlgebraFromString.Rd | 3 man/mxAvailableOptimizers.Rd | 3 man/mxComputeConfidenceInterval.Rd | 3 man/mxComputeDefault.Rd | 3 man/mxComputeEM.Rd | 3 man/mxComputeGradientDescent.Rd | 11 man/mxComputeHessianQuality.Rd | 3 man/mxComputeIterate.Rd | 3 man/mxComputeNewtonRaphson.Rd | 3 man/mxComputeNothing.Rd | 3 man/mxComputeNumericDeriv.Rd | 3 man/mxComputeOnce.Rd | 3 man/mxComputeReportDeriv.Rd | 3 man/mxComputeSequence.Rd | 3 man/mxComputeStandardError.Rd | 3 man/mxDataDynamic.Rd | 3 man/mxExpectationBA81.Rd | 3 man/mxFactorScores.Rd | 14 man/mxFitFunctionMultigroup.Rd | 10 man/mxGenerateData.Rd | 5 man/mxGetExpected.Rd | 15 man/mxMI.Rd | 3 man/mxMakeNames.Rd | 3 man/mxMatrix.Rd | 17 man/mxOption.Rd | 3 man/mxRestore.Rd | 10 man/mxSetDefaultOptions.Rd | 3 man/mxSimplify2Array.Rd | 3 man/mxTryHard.Rd | 6 man/omxCheckCloseEnough.Rd | 3 man/omxCheckError.Rd | 3 man/omxCheckNamespace.Rd | 3 man/omxCheckWarning.Rd | 3 man/omxConstrainMLThresholds.Rd | 3 man/omxDetectCores.Rd | 3 man/omxGetNPSOL.Rd | 3 man/omxGetRAMDepth.Rd | 3 man/omxManifestModelByParameterJacobian.Rd |only man/omxNameAnonymousParameters.Rd | 3 man/omxNormalQuantiles.Rd | 3 man/omxParallelCI.Rd | 3 man/omxQuotes.Rd | 3 man/omxRAMtoML.Rd | 3 man/omxSaturatedModel.Rd | 2 man/summary-MxModel.Rd | 13 src/Compute.cpp | 11 src/Compute.h | 2 src/ComputeGD.cpp | 31 + src/glue.cpp | 2 src/nloptcpp.cpp | 2 src/omxAlgebra.cpp | 5 src/omxData.cpp | 43 - src/omxData.h | 11 src/omxDefines.h | 1 src/omxFIMLSingleIteration.cpp | 19 src/omxGREMLExpectation.cpp | 7 src/omxGREMLfitfunction.cpp | 125 ++-- src/omxHessianCalculation.cpp | 9 src/omxImportFrontendState.cpp | 4 src/omxMatrix.cpp | 8 src/omxMatrix.h | 11 src/omxRowFitFunction.cpp | 3 src/omxSadmvnWrapper.cpp | 2 src/omxState.cpp | 52 +- src/omxState.h | 7 src/omxStateSpaceExpectation.cpp | 14 src/omxWLSFitFunction.cpp | 19 212 files changed, 1681 insertions(+), 1062 deletions(-)
Title: Solving Least Squares Problems under Equality/Inequality
Constraints
Description: It contains functions that solve least squares linear
regression problems under linear equality/inequality
constraints. It is developed based on the 'Fortran' program of
Lawson and Hanson (1974, 1995), which is public domain and
available at http://www.netlib.org/lawson-hanson.
Author: Yong Wang [aut, cre],
Charles L. Lawson [aut],
Richard J. Hanson [aut]
Maintainer: Yong Wang <yongwang@auckland.ac.nz>
Diff between lsei versions 1.1-0 dated 2015-09-27 and 1.1-1 dated 2015-10-07
Changes | 7 +++++ DESCRIPTION | 11 ++++---- MD5 | 14 +++++----- NAMESPACE | 2 - R/lsei.R | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++--------- man/hfti.Rd | 12 ++++----- man/lsei.Rd | 78 ++++++++++++++++++++++++++++++++++++++++++++++-------------- man/nnls.Rd | 75 +++++++++++++++++++++++++++++++++++++++++++++------------ 8 files changed, 211 insertions(+), 65 deletions(-)
Title: Empirical Bayesian Elastic Net
Description: Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models. As a special case of the 'EBglmnet'
package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.
Author: Anhui Huang
Maintainer: Anhui Huang <a.huang1@umiami.edu>
Diff between EBEN versions 4.1 dated 2015-06-26 and 4.6 dated 2015-10-07
DESCRIPTION | 8 MD5 | 26 NAMESPACE | 3 R/EBelasticNet.Binomial.R | 2 R/EBelasticNet.BinomialCV.R | 44 + R/EBelasticNet.Gaussian.R | 22 R/EBelasticNet.GaussianCV.R | 13 man/EBEN-package.Rd | 5 man/EBelasticNet.Binomial.Rd | 8 man/EBelasticNet.BinomialCV.Rd | 11 src/ElasticNetBinaryNEmainEff.c | 605 ++++++++++++++++--- src/ElasticNetBinaryNeFull.c | 1211 ++++++++++++++++++++++++++++++++++------ src/elasticNetLinearNeFull2.c | 140 +++- src/elasticNetLinearNeMainEff.c | 330 +++++++--- 14 files changed, 1924 insertions(+), 504 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks,
including the methods 'backShift' (from package 'backShift'),
'bivariateANM' (bivariate additive noise model),
'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'),
'hiddenICP' (invariant causal prediction with hidden variables),
'ICP' (invariant causal prediction) (from package 'InvariantCausalPrediction'),
'GES' (greedy equivalence search),
'GIES' (greedy interventional equivalence search),
'LINGAM', 'PC' (PC Algorithm),
'RFCI' (really fast causal inference)
(all from package 'pcalg') and regression.
Author: Christina Heinze <heinze@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze <heinze@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.1.1 dated 2015-06-23 and 0.1.4 dated 2015-10-07
DESCRIPTION | 10 ++++----- MD5 | 10 ++++----- NAMESPACE | 3 ++ R/runHiddenICP.R | 14 +++++++------ R/runICP.R | 19 +++++++++--------- tests/testthat/test_getParents_defaults_all_methods.R | 3 -- 6 files changed, 32 insertions(+), 27 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Breiman and Cutler's Random Forests for Classification and
Regression
Description: Classification and regression based on a forest of trees
using random inputs.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by
Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between randomForest versions 4.6-10 dated 2014-07-17 and 4.6-12 dated 2015-10-07
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 9 +++++++++ R/MDSplot.R | 4 ++-- R/combine.R | 33 ++++++++++++++++++--------------- R/margin.R | 4 ++-- R/randomForest.default.R | 4 +++- inst/NEWS | 13 +++++++++++++ man/randomForest.Rd | 2 +- man/rfImpute.Rd | 2 +- src/regrf.c | 6 +++--- src/rf.c | 14 +++++++------- src/rfutils.c | 2 +- 13 files changed, 79 insertions(+), 52 deletions(-)
Title: Statistical Methods for Regional Counts
Description: Provides statistical methods for the analysis of data aggregated spatially over regions (areal data).
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 0.1.5 dated 2015-10-01 and 0.1.6 dated 2015-10-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/scan.test.R | 2 +- man/scan.test.Rd | 2 +- tests/testthat/test-scan.test.R | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.5 dated 2015-09-25 and 1.6 dated 2015-10-06
DESCRIPTION | 8 +++---- MD5 | 30 +++++++++++++------------- R/Biplot.R | 26 ++++++++++++++-------- R/CA.R | 20 ++++++++--------- R/GSVD.R | 21 ++++++++++++++---- R/IM.R | 2 - R/MFA.R | 12 +++++----- R/NormData.R | 2 - R/PCA.R | 13 ++++++----- R/Plot.CA.R | 56 ++++++++++++++++++++++++------------------------- R/Plot.MFA.R | 10 ++++---- R/Plot.PCA.R | 6 ++--- man/CA.Rd | 4 +-- man/DataQuali.Rd | 2 - man/MFA.Rd | 4 +-- man/MVar.pt-package.Rd | 4 +-- 16 files changed, 121 insertions(+), 99 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.2.0.0 dated 2015-08-30 and 0.2.0.1 dated 2015-10-06
DESCRIPTION | 8 - MD5 | 10 +- inst/doc/dotwhisker-vignette.html | 180 ++++++++++++++++---------------------- inst/doc/dwplot-vignette.R |only inst/doc/kl2007_examples.html | 90 +++++++------------ inst/doc/vignette.bib |only inst/doc/vignette_dwplot.bib |only vignettes/vignette_dwplot.bib |only 8 files changed, 123 insertions(+), 165 deletions(-)
Title: Statistical Procedures for Agricultural Research
Description: Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu <f.mendiburu@cgiar.org>
Diff between agricolae versions 1.2-2 dated 2015-08-13 and 1.2-3 dated 2015-10-06
DESCRIPTION | 12 - MD5 | 110 +++++----- NAMESPACE | 3 NEWS | 10 R/BIB.test.R | 10 R/DAU.test.R | 6 R/HSD.test.R | 5 R/LSD.test.R | 7 R/PBIB.test.r | 480 +++++++++++++++++++++++------------------------ R/REGW.test.R |only R/SNK.test.R | 4 R/design.ab.R | 8 R/design.alpha.R | 11 - R/design.bib.R | 8 R/design.crd.R | 7 R/design.cyclic.R | 8 R/design.dau.R | 13 - R/design.graeco.R | 16 - R/design.lattice.R | 14 - R/design.lsd.R | 10 R/design.rcbd.R | 13 - R/design.split.R | 14 - R/design.strip.R | 10 R/design.youden.r | 11 - R/diffograph.R |only R/duncan.test.r | 4 R/durbin.test.R | 4 R/friedman.R | 5 R/kruskal.R | 10 R/median.test.r | 3 R/order.group.R | 9 R/scheffe.test.R | 4 R/waerden.test.R | 5 R/waller.test.R | 2 build/vignette.rds |binary inst/doc/tutorial.R | 274 ++++++++++++++------------ inst/doc/tutorial.Rnw | 81 +++++-- inst/doc/tutorial.pdf |binary man/HSD.test.Rd | 9 man/REGW.test.Rd |only man/SNK.test.Rd | 9 man/agricolae-package.Rd | 7 man/design.ab.Rd | 3 man/design.alpha.Rd | 3 man/design.bib.Rd | 4 man/design.crd.Rd | 3 man/design.cyclic.Rd | 4 man/design.dau.Rd | 4 man/design.graeco.Rd | 3 man/design.lattice.Rd | 3 man/design.lsd.Rd | 3 man/design.rcbd.Rd | 3 man/design.split.Rd | 3 man/design.strip.Rd | 3 man/design.youden.rd | 4 man/diffograph.Rd |only man/duncan.test.Rd | 9 vignettes/tutorial.Rnw | 81 +++++-- 58 files changed, 765 insertions(+), 584 deletions(-)
Title: Structural Estimators and Algorithms for the Analysis of Stable
Matchings
Description: Implements structural estimators to correct for the
sample selection bias from observed outcomes in matching markets. Also
contains R code for matching algorithms such as the deferred-acceptance
algorithm for college admissions, the top-trading-cycles algorithm for
house allocation and a partitioning linear program for the roommates
problem.
Author: Thilo Klein
Maintainer: Thilo Klein <thilo@klein.co.uk>
Diff between matchingMarkets versions 0.1-5 dated 2015-07-08 and 0.1-6 dated 2015-10-06
DESCRIPTION | 12 +++++---- MD5 | 54 +++++++++++++++++++++++++++++------------ NEWS |only R/khb.R | 12 ++++----- R/mfx.R | 3 ++ R/stabit.R | 30 ++++++++++++++++++---- build |only data/baac00.RData |binary data/klein15a.RData |binary data/klein15b.RData |binary inst |only man/baac00.Rd | 22 ++++++++-------- man/khb.Rd | 2 - man/klein15a.Rd | 2 - man/klein15b.Rd | 29 +++++++++++----------- man/matchingMarkets-package.Rd | 2 - man/mfx.Rd | 4 +++ man/stabit.Rd | 6 +++- src/stabitCpp.cpp | 20 +++++++++++---- tests |only vignettes |only 21 files changed, 131 insertions(+), 67 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Indirect methods for estimating bilateral migration flows in the presence of partial or missing data. Methods might be relevant to other categorical data situations on non-migration data, where for example, marginal totals are known and only auxiliary bilateral data is available.
Author: Guy J. Abel
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between migest versions 1.7 dated 2015-06-18 and 1.7.1 dated 2015-10-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- demo/cfplot_nat.R | 4 ++-- demo/cfplot_reg.R | 2 +- man/migest-package.Rd | 10 +++++++--- man/rc9.Rd | 2 +- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Analysing Inbreeding Based on Genetic Markers
Description: A framework for analysing inbreeding and heterozygosity-fitness correlations (HFCs) from
microsatellite and SNP markers.
Author: Martin A. Stoffel [aut, cre],
Mareike Esser [aut]
Maintainer: Martin A. Stoffel <martin.adam.stoffel@gmail.com>
Diff between inbreedR versions 0.1.0 dated 2015-09-05 and 0.2.0 dated 2015-10-06
DESCRIPTION | 9 +- MD5 | 32 ++++---- R/g2_microsats.R | 2 R/plot.inbreed.R | 85 ++++++++++++++++++++++- R/print.inbreed.R | 12 ++- R/r2_Wf.R | 78 +++++++++++++++++---- R/r2_hf.R | 130 ++++++++++++++++++++++++------------ README.md | 8 +- inst/doc/inbreedR_step_by_step.R | 7 + inst/doc/inbreedR_step_by_step.Rmd | 13 +++ inst/doc/inbreedR_step_by_step.html | 44 ++++++------ man/plot.inbreed.Rd | 6 + man/r2_Wf.Rd | 20 ++++- man/r2_hf.Rd | 30 +++++--- tests/testthat/test-r2_Wf.R | 11 +++ tests/testthat/test-r2_hf.R | 28 +++++-- vignettes/inbreedR_step_by_step.Rmd | 13 +++ 17 files changed, 394 insertions(+), 134 deletions(-)
Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut],
Hanna Meyer [aut],
Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>
Diff between hsdar versions 0.3.0 dated 2015-07-28 and 0.3.1 dated 2015-10-06
ChangeLog | 9 DESCRIPTION | 8 MD5 | 28 +- R/nri_methods.R | 31 ++ R/rastermeta.R | 2 R/spectral_resampling_response.R | 37 ++ inst/doc/References.pdf |binary inst/doc/hsdar-intro.pdf |binary man/Clman-methods.Rd | 2 man/derivative_speclib.Rd | 2 man/normalized.ratio.index-methods.Rd | 3 man/subset_speclib.Rd | 2 src/apply_response.f90 | 2 src/dataSpec_P5B_PROSAIL.f90 | 422 +++++++++++++++++----------------- src/dataSpec_P5B_PROSPECT.f90 | 2 15 files changed, 303 insertions(+), 247 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.2 dated 2015-09-12 and 1.1.3 dated 2015-10-06
DESCRIPTION | 8 +- MD5 | 6 - R/GDM_Table_Funcs.R | 165 ++++++++++++++++++++++++++++++++++----------------- man/gdm.transform.Rd | 4 - 4 files changed, 118 insertions(+), 65 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.95.1337 dated 2015-09-19 and 0.95.1367 dated 2015-10-06
rgl-0.95.1337/rgl/R/interpSetter.R |only rgl-0.95.1337/rgl/inst/doc/WebGL.R |only rgl-0.95.1337/rgl/inst/doc/rgl.R |only rgl-0.95.1337/rgl/po |only rgl-0.95.1337/rgl/vignettes/WebGL.md |only rgl-0.95.1337/rgl/vignettes/plotsnapshot.png |only rgl-0.95.1337/rgl/vignettes/rgl.md |only rgl-0.95.1337/rgl/vignettes/test.Rmd |only rgl-0.95.1337/rgl/vignettes/unnamed_chunk_1snapshot.png |only rgl-0.95.1337/rgl/vignettes/unnamed_chunk_2snapshot.png |only rgl-0.95.1367/rgl/DESCRIPTION | 11 rgl-0.95.1367/rgl/MD5 | 45 rgl-0.95.1367/rgl/NAMESPACE | 4 rgl-0.95.1367/rgl/R/bgplot3d.R | 89 rgl-0.95.1367/rgl/R/scene.R | 4 rgl-0.95.1367/rgl/R/webGL.R | 150 rgl-0.95.1367/rgl/build/vignette.rds |binary rgl-0.95.1367/rgl/configure | 9 rgl-0.95.1367/rgl/configure.ac | 8 rgl-0.95.1367/rgl/configure.win | 1 rgl-0.95.1367/rgl/inst/NEWS | 9 rgl-0.95.1367/rgl/inst/doc/WebGL.html | 1412 ++-- rgl-0.95.1367/rgl/inst/doc/rgl.Rmd | 4 rgl-0.95.1367/rgl/inst/doc/rgl.html | 4664 +++++++--------- rgl-0.95.1367/rgl/man/show2d.Rd |only rgl-0.95.1367/rgl/src/build/autoconf/config.guess | 384 - rgl-0.95.1367/rgl/src/build/autoconf/config.sub | 148 rgl-0.95.1367/rgl/src/glgui.cpp | 4 rgl-0.95.1367/rgl/vignettes/rgl.Rmd | 4 29 files changed, 3423 insertions(+), 3527 deletions(-)
Title: Seamless Interface to Octave -- And Matlab
Description: Direct interface to Octave. The primary goal is to facilitate the
port of Matlab/Octave scripts to R. The package enables to call any Octave
functions from R and as well as browsing their documentation, passing
variables between R and Octave, using R core RNGs in Octave, which ensures
that stochastic computations are also reproducible.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux <renaud@tx.technion.ac.il>
Diff between RcppOctave versions 0.14.5 dated 2014-09-20 and 0.18.1 dated 2015-10-06
RcppOctave-0.14.5/RcppOctave/configure.win |only RcppOctave-0.14.5/RcppOctave/man/dot-DollarNames-commaOctave-method.Rd |only RcppOctave-0.14.5/RcppOctave/man/show-commaOctave-method.Rd |only RcppOctave-0.14.5/RcppOctave/src/Makevars.win.in |only RcppOctave-0.18.1/RcppOctave/DESCRIPTION | 14 RcppOctave-0.18.1/RcppOctave/MD5 | 144 +- RcppOctave-0.18.1/RcppOctave/NAMESPACE | 39 RcppOctave-0.18.1/RcppOctave/NEWS | 18 RcppOctave-0.18.1/RcppOctave/R/Octave-class.R | 39 RcppOctave-0.18.1/RcppOctave/R/OctaveFunction-class.R | 4 RcppOctave-0.18.1/RcppOctave/R/base-functions.R | 42 RcppOctave-0.18.1/RcppOctave/R/config-vars.R.in | 28 RcppOctave-0.18.1/RcppOctave/R/config.R | 69 - RcppOctave-0.18.1/RcppOctave/R/eval.R | 1 RcppOctave-0.18.1/RcppOctave/R/interface.R | 5 RcppOctave-0.18.1/RcppOctave/R/package.R | 125 ++ RcppOctave-0.18.1/RcppOctave/R/random.R | 42 RcppOctave-0.18.1/RcppOctave/R/utils.R | 16 RcppOctave-0.18.1/RcppOctave/README | 4 RcppOctave-0.18.1/RcppOctave/build/RcppOctave.pdf |binary RcppOctave-0.18.1/RcppOctave/build/vignette.rds |binary RcppOctave-0.18.1/RcppOctave/cleanup | 9 RcppOctave-0.18.1/RcppOctave/configure | 484 ++++++---- RcppOctave-0.18.1/RcppOctave/configure.ac | 207 ++-- RcppOctave-0.18.1/RcppOctave/exec/configure-win |only RcppOctave-0.18.1/RcppOctave/exec/m4.R |only RcppOctave-0.18.1/RcppOctave/exec/m4.win | 113 ++ RcppOctave-0.18.1/RcppOctave/exec/octave.m4 |only RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave-unitTests.R | 2 RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave-unitTests.Rnw | 44 RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave-unitTests.pdf |binary RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave.R | 30 RcppOctave-0.18.1/RcppOctave/inst/doc/RcppOctave.pdf |binary RcppOctave-0.18.1/RcppOctave/inst/unitTests/runit.stats.R | 7 RcppOctave-0.18.1/RcppOctave/man/Octave-class.Rd | 36 RcppOctave-0.18.1/RcppOctave/man/Octave.config.Rd | 66 - RcppOctave-0.18.1/RcppOctave/man/Octave.home.Rd | 38 RcppOctave-0.18.1/RcppOctave/man/OctaveFunction-class.Rd | 26 RcppOctave-0.18.1/RcppOctave/man/OctaveInterface.Rd | 83 - RcppOctave-0.18.1/RcppOctave/man/RcppOctave-package.Rd | 57 - RcppOctave-0.18.1/RcppOctave/man/autocomplete.Rd |only RcppOctave-0.18.1/RcppOctave/man/check.equal.Rd | 7 RcppOctave-0.18.1/RcppOctave/man/dot-CallOctave.Rd | 9 RcppOctave-0.18.1/RcppOctave/man/dot-isPlatformCompatible.Rd |only RcppOctave-0.18.1/RcppOctave/man/mfiles.Rd | 14 RcppOctave-0.18.1/RcppOctave/man/o_addpath.Rd | 24 RcppOctave-0.18.1/RcppOctave/man/o_assign.Rd | 43 RcppOctave-0.18.1/RcppOctave/man/o_clear.Rd | 9 RcppOctave-0.18.1/RcppOctave/man/o_config_info.Rd | 20 RcppOctave-0.18.1/RcppOctave/man/o_eval.Rd | 11 RcppOctave-0.18.1/RcppOctave/man/o_exist.Rd | 9 RcppOctave-0.18.1/RcppOctave/man/o_help.Rd | 35 RcppOctave-0.18.1/RcppOctave/man/o_identity.Rd | 10 RcppOctave-0.18.1/RcppOctave/man/o_load.Rd | 5 RcppOctave-0.18.1/RcppOctave/man/o_ls.Rd | 26 RcppOctave-0.18.1/RcppOctave/man/o_rexp.Rd | 22 RcppOctave-0.18.1/RcppOctave/man/o_rgamma.Rd | 29 RcppOctave-0.18.1/RcppOctave/man/o_rnorm.Rd | 22 RcppOctave-0.18.1/RcppOctave/man/o_rpois.Rd |only RcppOctave-0.18.1/RcppOctave/man/o_runif.Rd | 20 RcppOctave-0.18.1/RcppOctave/man/o_source.Rd | 14 RcppOctave-0.18.1/RcppOctave/man/o_version.Rd | 6 RcppOctave-0.18.1/RcppOctave/man/o_who.Rd | 16 RcppOctave-0.18.1/RcppOctave/man/o_whos.Rd | 11 RcppOctave-0.18.1/RcppOctave/man/octave-ll.Rd | 24 RcppOctave-0.18.1/RcppOctave/man/octave_config.Rd | 27 RcppOctave-0.18.1/RcppOctave/man/sourceExamples.Rd | 7 RcppOctave-0.18.1/RcppOctave/man/system.mfile.Rd | 15 RcppOctave-0.18.1/RcppOctave/src/Makevars.in | 31 RcppOctave-0.18.1/RcppOctave/src/Makevars.win |only RcppOctave-0.18.1/RcppOctave/src/compatibility.h |only RcppOctave-0.18.1/RcppOctave/src/conversion.cpp | 32 RcppOctave-0.18.1/RcppOctave/src/modules/Makefile.in | 34 RcppOctave-0.18.1/RcppOctave/src/modules/PKG_ADD | 1 RcppOctave-0.18.1/RcppOctave/src/modules/Rrng.cc | 21 RcppOctave-0.18.1/RcppOctave/src/rcpp_octave.cpp | 27 RcppOctave-0.18.1/RcppOctave/src/rcpp_octave.h | 26 RcppOctave-0.18.1/RcppOctave/tests/doRUnit.R | 3 RcppOctave-0.18.1/RcppOctave/vignettes/RcppOctave-unitTests.Rnw | 44 79 files changed, 1502 insertions(+), 944 deletions(-)
Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MFAg versions 1.2 dated 2015-09-16 and 1.3 dated 2015-10-06
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/GSVD.R | 25 +++++++++++++++++++------ R/IM.R | 23 ++++++++++++++--------- R/MFA.R | 12 ++++++------ R/NormData.R | 2 +- R/Plot.MFA.R | 8 ++++---- man/DataQuali.Rd | 2 +- man/GSVD.Rd | 8 ++++---- man/MFA.Rd | 8 ++++---- man/MFAg-package.Rd | 4 ++-- man/NormData.Rd | 2 +- man/Plot.MFA.Rd | 5 +++-- 13 files changed, 75 insertions(+), 56 deletions(-)
Title: Combinatorial Efficient Global Optimization
Description: Model building, surrogate model
based optimization and Efficient Global Optimization in combinatorial
or mixed search spaces.
Author: Martin Zaefferer <mzaefferer@gmail.com>
Maintainer: Martin Zaefferer <mzaefferer@gmail.com>
Diff between CEGO versions 1.0.1108 dated 2015-01-06 and 2.0.0 dated 2015-10-06
CEGO-1.0.1108/CEGO/R/optimizer.R |only CEGO-1.0.1108/CEGO/man/combinatorialKrigingLikelihood.Rd |only CEGO-1.0.1108/CEGO/man/initializeDesign.Rd |only CEGO-1.0.1108/CEGO/man/longestIncreasingSubsequence.Rd |only CEGO-1.0.1108/CEGO/man/predict.CKriging.Rd |only CEGO-1.0.1108/CEGO/man/predict.CLM.Rd |only CEGO-1.0.1108/CEGO/man/predict.CRBFN.Rd |only CEGO-2.0.0/CEGO/DESCRIPTION | 10 CEGO-2.0.0/CEGO/MD5 | 170 ++-- CEGO-2.0.0/CEGO/NAMESPACE | 20 CEGO-2.0.0/CEGO/NEWS | 33 CEGO-2.0.0/CEGO/R/DoE.R |only CEGO-2.0.0/CEGO/R/binaryBenchmarkFunctions.R | 2 CEGO-2.0.0/CEGO/R/cegoPackage.R | 11 CEGO-2.0.0/CEGO/R/distanceBasedLandscapeGenerators.R | 53 - CEGO-2.0.0/CEGO/R/distanceCalculation.R | 67 + CEGO-2.0.0/CEGO/R/misc.R | 46 - CEGO-2.0.0/CEGO/R/modelKriging.R | 369 ++++++---- CEGO-2.0.0/CEGO/R/modelLm.R | 49 - CEGO-2.0.0/CEGO/R/modelRBFN.R | 83 +- CEGO-2.0.0/CEGO/R/optim2opt.R |only CEGO-2.0.0/CEGO/R/optimCEGO.R |only CEGO-2.0.0/CEGO/R/optimEA.R |only CEGO-2.0.0/CEGO/R/optimInterface.R | 61 - CEGO-2.0.0/CEGO/R/optimRS.R |only CEGO-2.0.0/CEGO/R/permutationBenchmarkFunctions.R | 26 CEGO-2.0.0/CEGO/R/permutationDistances.r | 169 ++-- CEGO-2.0.0/CEGO/R/permutationOperators.R | 135 +++ CEGO-2.0.0/CEGO/man/CEGO-package.Rd | 12 CEGO-2.0.0/CEGO/man/benchmarkGeneratorFSP.Rd | 2 CEGO-2.0.0/CEGO/man/benchmarkGeneratorNKL.Rd | 2 CEGO-2.0.0/CEGO/man/benchmarkGeneratorQAP.Rd | 6 CEGO-2.0.0/CEGO/man/benchmarkGeneratorTSP.Rd | 2 CEGO-2.0.0/CEGO/man/benchmarkGeneratorWT.Rd | 2 CEGO-2.0.0/CEGO/man/buildModel.Rd | 16 CEGO-2.0.0/CEGO/man/combinatorialKriging.Rd | 90 -- CEGO-2.0.0/CEGO/man/combinatorialLM.Rd | 50 - CEGO-2.0.0/CEGO/man/combinatorialRBFN.Rd | 61 - CEGO-2.0.0/CEGO/man/designRandom.Rd |only CEGO-2.0.0/CEGO/man/distanceMatrix.Rd | 3 CEGO-2.0.0/CEGO/man/distanceMatrixUpdate.Rd |only CEGO-2.0.0/CEGO/man/distanceMatrixWrapper.Rd |only CEGO-2.0.0/CEGO/man/distancePermutationAdjacency.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationChebyshev.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationCos.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationEuclidean.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationHamming.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationInsert.Rd | 14 CEGO-2.0.0/CEGO/man/distancePermutationInterchange.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLCSeq.Rd | 20 CEGO-2.0.0/CEGO/man/distancePermutationLCStr.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLee.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLevenshtein.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationLex.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationManhattan.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationPosition.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationPosition2.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationR.Rd | 2 CEGO-2.0.0/CEGO/man/distancePermutationSwap.Rd | 2 CEGO-2.0.0/CEGO/man/distanceVector.Rd | 3 CEGO-2.0.0/CEGO/man/fcorrCubic.Rd | 4 CEGO-2.0.0/CEGO/man/fcorrGauss.Rd | 4 CEGO-2.0.0/CEGO/man/fcorrLinear.Rd | 4 CEGO-2.0.0/CEGO/man/fcorrSphere.Rd | 4 CEGO-2.0.0/CEGO/man/infillExpectedImprovement.Rd | 2 CEGO-2.0.0/CEGO/man/landscapeGeneratorGaussian.Rd | 9 CEGO-2.0.0/CEGO/man/landscapeGeneratorGaussianBuild.Rd | 2 CEGO-2.0.0/CEGO/man/landscapeGeneratorGaussianEval.Rd | 2 CEGO-2.0.0/CEGO/man/landscapeGeneratorMUL.Rd | 24 CEGO-2.0.0/CEGO/man/landscapeGeneratorUNI.Rd | 16 CEGO-2.0.0/CEGO/man/lexicographicPermutationOrderNumber.Rd | 2 CEGO-2.0.0/CEGO/man/modelKriging.Rd |only CEGO-2.0.0/CEGO/man/modelKrigingLikelihood.Rd |only CEGO-2.0.0/CEGO/man/modelLinear.Rd |only CEGO-2.0.0/CEGO/man/modelRBFN.Rd |only CEGO-2.0.0/CEGO/man/mutationBinary.Rd | 2 CEGO-2.0.0/CEGO/man/mutationBinaryFast.Rd | 2 CEGO-2.0.0/CEGO/man/mutationPermutationInterchange.Rd | 9 CEGO-2.0.0/CEGO/man/mutationPermutationReversal.Rd |only CEGO-2.0.0/CEGO/man/mutationPermutationSwap.Rd | 9 CEGO-2.0.0/CEGO/man/optim2Opt.Rd | 21 CEGO-2.0.0/CEGO/man/optimCEGO.Rd | 56 - CEGO-2.0.0/CEGO/man/optimEA.Rd | 35 CEGO-2.0.0/CEGO/man/optimInterface.Rd | 28 CEGO-2.0.0/CEGO/man/optimRS.Rd | 23 CEGO-2.0.0/CEGO/man/optimizeModel.Rd |only CEGO-2.0.0/CEGO/man/predict.modelKriging.Rd |only CEGO-2.0.0/CEGO/man/predict.modelLinear.Rd |only CEGO-2.0.0/CEGO/man/predict.modelRBFN.Rd |only CEGO-2.0.0/CEGO/man/recombinationBinaryUniformCrossoverFast.Rd | 2 CEGO-2.0.0/CEGO/man/recombinationPermutationCycleCrossover.Rd | 2 CEGO-2.0.0/CEGO/man/removeDuplicates.Rd | 2 CEGO-2.0.0/CEGO/man/removeDuplicatesOffspring.Rd | 6 CEGO-2.0.0/CEGO/man/solutionFunctionGeneratorBinary.Rd | 2 CEGO-2.0.0/CEGO/man/solutionFunctionGeneratorPermutation.Rd | 2 CEGO-2.0.0/CEGO/man/step2Opt.Rd | 4 CEGO-2.0.0/CEGO/man/tournamentSelection.Rd | 4 CEGO-2.0.0/CEGO/src/permutationDistance.c | 341 ++++++--- 98 files changed, 1259 insertions(+), 981 deletions(-)
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Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.11-10 dated 2015-06-16 and 0.11-22 dated 2015-10-06
DESCRIPTION | 19 ++++--- MD5 | 25 +++++----- NAMESPACE | 27 ++++++----- R/codeGeno.r | 110 ++++++++++++++++++++------------------------- R/kinship.r | 4 - R/plot.pedigree.r | 30 ++++++------ R/read.write.vcf.r | 15 +++--- man/add.individuals.Rd | 32 +++++++++++-- man/codeGeno.Rd | 2 man/create.gpData.Rd | 18 ++++--- man/discard.individuals.Rd |only man/discard.markers.Rd | 29 +++++------ man/kinship.Rd | 4 - man/write.vcf.Rd | 11 ++++ 14 files changed, 182 insertions(+), 144 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante <pante.eric@gmail.com>
Diff between marmap versions 0.9.2 dated 2015-01-28 and 0.9.3 dated 2015-10-06
marmap-0.9.2/marmap/data/datalist |only marmap-0.9.3/marmap/DESCRIPTION | 10 ++--- marmap-0.9.3/marmap/MD5 | 37 ++++++++++--------- marmap-0.9.3/marmap/NAMESPACE | 18 ++++++--- marmap-0.9.3/marmap/R/griddify.R |only marmap-0.9.3/marmap/R/plot.bathy.R | 4 +- marmap-0.9.3/marmap/build/vignette.rds |binary marmap-0.9.3/marmap/data/aleutians.rda |binary marmap-0.9.3/marmap/data/celt.rda |binary marmap-0.9.3/marmap/data/florida.rda |binary marmap-0.9.3/marmap/data/hawaii.rda |binary marmap-0.9.3/marmap/data/hawaii.sites.rda |binary marmap-0.9.3/marmap/data/irregular.rda |only marmap-0.9.3/marmap/data/metallo.rda |binary marmap-0.9.3/marmap/data/nw.atlantic.coast.rda |binary marmap-0.9.3/marmap/data/nw.atlantic.rda |binary marmap-0.9.3/marmap/inst/doc/marmap-DataAnalysis.pdf |binary marmap-0.9.3/marmap/inst/doc/marmap-ImportExport.pdf |binary marmap-0.9.3/marmap/inst/doc/marmap.pdf |binary marmap-0.9.3/marmap/man/griddify.Rd |only marmap-0.9.3/marmap/man/irregular.Rd |only marmap-0.9.3/marmap/man/marmap.Rd | 4 +- 22 files changed, 41 insertions(+), 32 deletions(-)
Title: Flow Selection and Analysis
Description: Selections on flow matrices, statistics on selected flows, map and graph visualisations.
Author: Timothée Giraud [cre, aut],
Laurent Beauguitte [aut],
Marianne Guérois [ctb]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between flows versions 1.0 dated 2015-07-17 and 1.1 dated 2015-10-06
DESCRIPTION | 8 +- MD5 | 27 ++++---- NEWS |only R/flows.R | 151 +++++-------------------------------------------- build/vignette.rds |binary inst/doc/flows.R | 4 - inst/doc/flows.Rmd | 6 - inst/doc/flows.html | 16 ++--- man/compmat.Rd | 3 man/domflows.Rd | 9 -- man/flows.Rd | 3 man/plotDomFlows.Rd | 3 man/plotMapDomFlows.Rd | 3 man/statmat.Rd | 8 +- vignettes/flows.Rmd | 6 - 15 files changed, 64 insertions(+), 183 deletions(-)
Title: Enhanced Least Absolute Shrinkage and Selection Operator
Regression Model
Description: Performs some enhanced variable selection algorithms
based on the least absolute shrinkage and selection operator for regression model.
Author: Pi Guo
Maintainer: Pi Guo <guopi.01@163.com>
Diff between elasso versions 1.0 dated 2015-09-17 and 1.1 dated 2015-10-06
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/BRLasso.R | 18 +++++++++++------- man/BRLasso.Rd | 17 +++++++++++------ 4 files changed, 31 insertions(+), 21 deletions(-)
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Title: An Interface for MIXMOD
Description: A collection of functions designed to run supervised and
unsupervised classification with MIXture MODelling.
Author: Remi Lebret [aut, cre],
Serge Iovleff [aut],
Florent Langrognet [aut],
Benjamin Auder [ctb],
C. Biernacki [ctb],
G. Celeux [ctb],
G. Govaert [ctb]
Maintainer: Remi Lebret <remi@lebret.ch>
Diff between Rmixmod versions 2.0.2 dated 2014-03-21 and 2.0.3 dated 2015-10-06
DESCRIPTION | 46 +++++++++++++++++----------------- MD5 | 40 +++++++++++++++-------------- NAMESPACE | 15 +++++++++++ R/CompositeModel.R | 3 +- R/CompositeParameter.R | 7 +++-- R/GaussianModel.R | 3 +- R/GaussianParameter.R | 8 ++--- R/MixmodCluster.R | 2 + R/MixmodLearn.R | 2 + R/MixmodPredict.R | 2 + R/MixmodResults.R | 6 ++++ R/MultinomialModel.R | 3 +- R/Rmixmod.R | 7 ++--- R/Strategy.R | 4 ++ R/global.R | 1 R/zzz.R | 2 - README |only inst/CITATION |only man/Rmixmod-package.Rd | 4 +- src/mixmod/Kernel/Model/ModelType.cpp | 5 --- src/mixmod/Matrix/GeneralMatrix.cpp | 5 --- tests/test.R | 2 - 22 files changed, 99 insertions(+), 68 deletions(-)
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the LZ77
algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip) but
offers more dense compression.
Author: Jeroen Ooms [aut, cre],
Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between brotli versions 0.2 dated 2015-10-03 and 0.3 dated 2015-10-06
DESCRIPTION | 18 ++++++++---------- MD5 | 5 +++-- src/Makevars | 5 +++-- src/config.h |only 4 files changed, 14 insertions(+), 14 deletions(-)
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Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive
package. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre],
Sunkyu Choi [trl],
Ivanka Skakun [trl],
Gergely Dar<c3><b3>czi [trl],
Anton Antonov [trl],
Hisham Ben Hamidane [trl],
Anja Billing [trl],
Aditya Bhagwat [trl],
Rasmus B<c3><a5><c3><a5>th [trl],
Mine Cetinkaya-Rundel [trl],
Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.base versions 0.0-1 dated 2015-07-14 and 0.0-2 dated 2015-10-06
assertive.base-0.0-1/assertive.base/man/DIM.Rd |only assertive.base-0.0-1/assertive.base/man/n_elements.Rd |only assertive.base-0.0-2/assertive.base/DESCRIPTION | 49 ++ assertive.base-0.0-2/assertive.base/MD5 | 66 ++- assertive.base-0.0-2/assertive.base/NAMESPACE | 110 ++--- assertive.base-0.0-2/assertive.base/NEWS | 4 assertive.base-0.0-2/assertive.base/R/are-identical.R |only assertive.base-0.0-2/assertive.base/R/assert-are-identical.R |only assertive.base-0.0-2/assertive.base/R/assert-identical-to-true-false-na.R | 52 +- assertive.base-0.0-2/assertive.base/R/assert-is-true-false-na.R | 132 ++++-- assertive.base-0.0-2/assertive.base/R/cause.R | 29 - assertive.base-0.0-2/assertive.base/R/coercion.R | 2 assertive.base-0.0-2/assertive.base/R/conditions.R |only assertive.base-0.0-2/assertive.base/R/engine.R | 19 assertive.base-0.0-2/assertive.base/R/internal.R | 4 assertive.base-0.0-2/assertive.base/R/is-identical-to-true-false-na.R | 23 - assertive.base-0.0-2/assertive.base/R/is-true-false-na.R | 20 assertive.base-0.0-2/assertive.base/R/utils.R | 81 ---- assertive.base-0.0-2/assertive.base/README.md | 121 ++++-- assertive.base-0.0-2/assertive.base/inst |only assertive.base-0.0-2/assertive.base/man/Truth.Rd | 64 ++- assertive.base-0.0-2/assertive.base/man/are_identical.Rd |only assertive.base-0.0-2/assertive.base/man/assert_engine.Rd | 5 assertive.base-0.0-2/assertive.base/man/assertionError.Rd |only assertive.base-0.0-2/assertive.base/man/call_and_name.Rd | 4 assertive.base-0.0-2/assertive.base/man/is2.Rd | 2 assertive.base-0.0-2/assertive.base/man/merge.list.Rd | 9 assertive.base-0.0-2/assertive.base/po/R-assertive.base.pot | 201 ++++------ assertive.base-0.0-2/assertive.base/po/R-de.po |only assertive.base-0.0-2/assertive.base/po/R-el.po |only assertive.base-0.0-2/assertive.base/po/R-fr.po |only assertive.base-0.0-2/assertive.base/po/R-hu.po |only assertive.base-0.0-2/assertive.base/po/R-ko.po |only assertive.base-0.0-2/assertive.base/po/R-nl.po |only assertive.base-0.0-2/assertive.base/po/R-ru.po |only assertive.base-0.0-2/assertive.base/po/R-sv.po |only assertive.base-0.0-2/assertive.base/po/R-tr.po |only assertive.base-0.0-2/assertive.base/po/R-uk.po |only assertive.base-0.0-2/assertive.base/tests/testthat/test-are-identical.R |only 39 files changed, 619 insertions(+), 378 deletions(-)
More information about assertive.base at CRAN
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Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.4-7 dated 2015-07-14 and 0.5-0 dated 2015-10-06
DESCRIPTION | 41 +++-- MD5 | 47 ++++-- NAMESPACE | 15 +- R/Class-SDMXComponents.R | 2 R/Class-SDMXDataStructure.R | 2 R/Class-SDMXRESTRequestBuilder.R |only R/Class-SDMXRequestBuilder.R |only R/Class-SDMXServiceProvider.R |only R/Class-SDMXStructureType.R | 1 R/SDMXDataStructure-methods.R | 13 + R/SDMXDataStructures-methods.R | 49 +++++++ R/SDMXRESTRequestBuilder-methods.R |only R/SDMXRequestBuilder-methods.R |only R/SDMXServiceProvider-methods.R |only R/profile.R |only R/readSDMX.R | 238 ++++++++++++++++++++-------------- README.md | 166 +++++++++++++++++++++-- build |only inst/doc |only man/SDMXRESTRequestBuilder-class.Rd |only man/SDMXRequestBuilder-class.Rd |only man/SDMXServiceProvider-class.Rd |only man/addSDMXServiceProvider.Rd |only man/findSDMXServiceProvider.Rd |only man/getSDMXServiceProviders.Rd |only man/readSDMX.Rd | 24 +++ man/rsdmx-package.Rd | 4 man/setSDMXServiceProviders.Rd |only tests/testthat/test_DataStructures.R | 25 +++ tests/testthat/test_Main_Helpers.R |only tests/testthat/test_RequestBuilder.R |only tests/testthat/test_ServiceProvider.R |only vignettes/quickstart.Rmd | 42 ++++-- 33 files changed, 511 insertions(+), 158 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut], Martin Maechler [aut],
Ben Bolker [aut, cre], Steven Walker [aut],
Rune Haubo Bojesen Christensen [ctb],
Henrik Singmann [ctb], Bin Dai [ctb],
Gabor Grothendieck [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-9 dated 2015-08-20 and 1.1-10 dated 2015-10-06
lme4-1.1-10/lme4/DESCRIPTION | 6 +- lme4-1.1-10/lme4/MD5 | 36 ++++++------ lme4-1.1-10/lme4/NAMESPACE | 25 ++++++-- lme4-1.1-10/lme4/R/AllClass.R | 6 +- lme4-1.1-10/lme4/R/bootMer.R | 14 ++++ lme4-1.1-10/lme4/R/lmer.R | 85 +++++++++++++++-------------- lme4-1.1-10/lme4/R/predict.R | 28 ++++++--- lme4-1.1-10/lme4/R/profile.R | 8 +- lme4-1.1-10/lme4/R/utilities.R | 53 +++++++++--------- lme4-1.1-10/lme4/README.md | 9 +-- lme4-1.1-10/lme4/inst/CITATION | 48 ++++++++-------- lme4-1.1-10/lme4/inst/NEWS.Rd | 57 +++++++++++++++---- lme4-1.1-10/lme4/inst/tests/test-lmer.R | 18 ++++++ lme4-1.1-10/lme4/inst/tests/test-methods.R | 25 ++++++-- lme4-1.1-10/lme4/man/bootMer.Rd | 7 ++ lme4-1.1-10/lme4/man/devcomp.Rd | 4 - lme4-1.1-10/lme4/man/golden-class.Rd | 23 ++++++- lme4-1.1-10/lme4/man/lmerControl.Rd | 50 ++++++++--------- lme4-1.1-10/lme4/man/utilities.Rd |only lme4-1.1-9/lme4/man/golden.Rd |only 20 files changed, 317 insertions(+), 185 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.2.0 dated 2015-09-25 and 0.3.0 dated 2015-10-06
DESCRIPTION | 6 - MD5 | 33 ++++--- NAMESPACE | 4 NEWS.md | 19 ++++ R/generics.R | 161 +++++++++++++++++++++++++++++-------- R/helpers.R | 2 R/kdecop.R | 9 ++ R/plot.kdecopula.R | 33 ++++--- README.md | 128 +++++++++++++++++++---------- inst/README-unnamed-chunk-10-1.png |only inst/README-unnamed-chunk-12-1.png |only inst/README-unnamed-chunk-3-1.png |binary inst/README-unnamed-chunk-6-1.png |binary inst/README-unnamed-chunk-7-1.png |binary inst/README-unnamed-chunk-8-1.png |binary inst/README-unnamed-chunk-9-1.png |binary man/logLik.kdecopula.Rd |only src/interp.cpp | 3 src/renorm.cpp | 6 - 19 files changed, 292 insertions(+), 112 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is to make it as simple as possible to identify global objects for the purpose of exporting them in distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.4.0 dated 2015-09-18 and 0.4.1 dated 2015-10-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 28 ++++++++++++++-------------- NEWS | 5 +++++ R/globalsOf.R | 7 ++++++- tests/globalsOf.R | 42 ++++++++++++++++++++++++++++-------------- 6 files changed, 61 insertions(+), 37 deletions(-)
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to the system
clipboards of Windows, OS X, and Linux.
Author: Matthew Lincoln [aut, cre],
Louis Maddox [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.1.1 dated 2015-09-03 and 0.2.0 dated 2015-10-06
DESCRIPTION | 7 ++--- MD5 | 25 ++++++++++-------- NAMESPACE | 1 NEWS.md | 23 ++++++++++++++++- R/clipboard.R | 70 +++++++++++++++++++++++++++++++++++++++------------- R/flat_str.R | 37 +++++++++++++++++++++++++-- R/linux_clipboard.R | 27 ++++++++++++-------- R/osx_clipboard.R | 32 ++++++++++++++--------- R/win_clipboard.R | 24 ++++++++++++----- README.md | 32 +++++++++++++++++++---- man/clear_clip.Rd |only man/read_clip.Rd | 7 +++++ man/write_clip.Rd | 44 +++++++++++++++++++++++++------- tests |only 14 files changed, 248 insertions(+), 81 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa & Stephane Jankowski
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++++-- NAMESPACE | 2 +- R/symscorestat.R |only inst |only man/symscorestat.Rd |only src/signtestperm.f90 |only 7 files changed, 11 insertions(+), 7 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.7.0 dated 2015-10-01 and 0.7.1 dated 2015-10-05
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Allele Imputation and Haplotype Reconstruction from Pedigree
Databases
Description: Simulation of alphanumeric alleles, imputation of genetic missing data and reconstruction of non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many different factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used either simulated datasets or loaded databases (in .ped file biallelic format). Haplotype reconstruction can be performed even with missing data because of alleHap, firstly imputes the genotypes. All this considering that each member (due to meiosis) should unequivocally have two alleles, one inherited from each parent.
Author: Nathan Medina-Rodriguez and Angelo Santana
Maintainer: Nathan Medina-Rodriguez <nathan.medina@ulpgc.es>
Diff between alleHap versions 0.7.2 dated 2014-08-10 and 0.9.2 dated 2015-10-05
alleHap-0.7.2/alleHap/R/buildFunctions.R |only alleHap-0.7.2/alleHap/R/buildHaps.R |only alleHap-0.7.2/alleHap/R/simFams.R |only alleHap-0.7.2/alleHap/R/simFunctions.R |only alleHap-0.7.2/alleHap/man/buildHaps.Rd |only alleHap-0.7.2/alleHap/man/simFams.Rd |only alleHap-0.9.2/alleHap/DESCRIPTION | 26 ++++------ alleHap-0.9.2/alleHap/MD5 | 33 +++++++++---- alleHap-0.9.2/alleHap/NAMESPACE | 13 +++-- alleHap-0.9.2/alleHap/R/alleImputer.R |only alleHap-0.9.2/alleHap/R/alleLoader.R |only alleHap-0.9.2/alleHap/R/alleSimulator.R |only alleHap-0.9.2/alleHap/R/hapPhaser.R |only alleHap-0.9.2/alleHap/build |only alleHap-0.9.2/alleHap/inst |only alleHap-0.9.2/alleHap/man/alleHap-package.Rd | 65 ++++++++++++++++++--------- alleHap-0.9.2/alleHap/man/alleImputer.Rd |only alleHap-0.9.2/alleHap/man/alleLoader.Rd |only alleHap-0.9.2/alleHap/man/alleSimulator.Rd |only alleHap-0.9.2/alleHap/man/hapPhaser.Rd |only alleHap-0.9.2/alleHap/vignettes |only 21 files changed, 88 insertions(+), 49 deletions(-)
Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes and multivariate extreme value distributions for various parametric models.
Author: Leo Belzile [aut, cre]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>
Diff between mev versions 1.2 dated 2015-08-24 and 1.3 dated 2015-10-05
DESCRIPTION | 8 MD5 | 18 - NAMESPACE | 2 NEWS | 21 ++ R/RcppExports.R | 93 ++++++++-- R/rmev_wrapper.R | 263 +++++++++++++++++++++++----- man/rmev.Rd | 22 +- man/rmevspec.Rd | 2 src/RcppExports.cpp | 78 +++++++- src/ev_sampling.cpp | 472 +++++++++++++++++++++++++++++++++++----------------- 10 files changed, 736 insertions(+), 243 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-2 dated 2015-09-11 and 0.1-3 dated 2015-10-05
gimme-0.1-2/gimme/man/gimme.Rd |only gimme-0.1-3/gimme/DESCRIPTION | 20 - gimme-0.1-3/gimme/MD5 | 34 + gimme-0.1-3/gimme/NAMESPACE | 25 + gimme-0.1-3/gimme/R/aggSEM.R | 41 +- gimme-0.1-3/gimme/R/deconvolve_funcs.R |only gimme-0.1-3/gimme/R/gimme-pkg.R | 21 - gimme-0.1-3/gimme/R/gimme.R | 529 +++++++++++++++--------------- gimme-0.1-3/gimme/R/gimmeInteractive.R |only gimme-0.1-3/gimme/R/indSEM.R | 40 +- gimme-0.1-3/gimme/R/spm_funcs.R |only gimme-0.1-3/gimme/man/aggSEM.Rd | 28 - gimme-0.1-3/gimme/man/gimme-package.Rd | 14 gimme-0.1-3/gimme/man/gimmeInteractive.Rd |only gimme-0.1-3/gimme/man/gimmeSEM.Rd |only gimme-0.1-3/gimme/man/indSEM.Rd | 33 - gimme-0.1-3/gimme/man/ts1.Rd | 3 gimme-0.1-3/gimme/man/ts2.Rd | 3 gimme-0.1-3/gimme/man/ts3.Rd | 3 gimme-0.1-3/gimme/man/ts4.Rd | 3 gimme-0.1-3/gimme/man/ts5.Rd | 3 21 files changed, 435 insertions(+), 365 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.8.0 dated 2015-09-07 and 0.8.1 dated 2015-10-05
future-0.8.0/future/R/tweakExpression.R |only future-0.8.0/future/tests/MulticoreFutureRegistry.R |only future-0.8.1/future/DESCRIPTION | 8 future-0.8.1/future/MD5 | 43 ++-- future-0.8.1/future/NEWS | 14 + future-0.8.1/future/R/FutureRegistry.R |only future-0.8.1/future/R/MulticoreFuture.R | 48 ---- future-0.8.1/future/R/availableCores.R | 2 future-0.8.1/future/R/eager.R | 13 + future-0.8.1/future/R/globals.R |only future-0.8.1/future/R/lazy.R | 32 --- future-0.8.1/future/R/multicore.R | 14 + future-0.8.1/future/build/vignette.rds |binary future-0.8.1/future/inst/doc/future.html | 10 future-0.8.1/future/inst/doc/future.md.rsp | 10 future-0.8.1/future/inst/doc/issues.html |only future-0.8.1/future/inst/doc/issues.md.rsp |only future-0.8.1/future/man/eager.Rd | 130 ++++++------ future-0.8.1/future/man/lazy.Rd | 212 ++++++++++---------- future-0.8.1/future/man/multicore.Rd | 161 +++++++-------- future-0.8.1/future/man/plan.Rd | 190 ++++++++--------- future-0.8.1/future/tests/FutureRegistry.R |only future-0.8.1/future/tests/dotdotdot.R |only future-0.8.1/future/tests/eager.R | 15 - future-0.8.1/future/tests/multicore.R | 29 +- future-0.8.1/future/vignettes/future.md.rsp | 10 future-0.8.1/future/vignettes/issues.md.rsp |only 27 files changed, 475 insertions(+), 466 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfmta versions 1.3-2 dated 2015-04-29 and 1.3-3 dated 2015-10-05
DESCRIPTION | 8 MD5 | 12 - configure | 18 - src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 2 src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 2 src/CppBugs/cppbugs/mcmc.math.hpp | 106 +++------- src/CppBugs/cppbugs/mcmc.model.hpp | 4 7 files changed, 63 insertions(+), 89 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfcomb versions 2.1-4 dated 2015-09-11 and 2.1-5 dated 2015-10-05
DESCRIPTION | 8 MD5 | 14 - configure | 18 - src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 2 src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 2 src/CppBugs/cppbugs/mcmc.math.hpp | 106 +++------- src/CppBugs/cppbugs/mcmc.model.hpp | 4 src/plateau.cpp | 4 8 files changed, 66 insertions(+), 92 deletions(-)
Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements t-tests (independent and dependent samples), ANOVA (including between-within subject designs) and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut],
Rand Wilcox [aut],
Felix Schoenbrodt [ctr]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.3-2 dated 2015-07-23 and 0.4-0 dated 2015-10-05
WRS2-0.3-2/WRS2/R/tsplit.R |only WRS2-0.3-2/WRS2/man/tsplit.Rd |only WRS2-0.4-0/WRS2/DESCRIPTION | 29 +++++------ WRS2-0.4-0/WRS2/MD5 | 92 +++++++++++++++++++++++------------- WRS2-0.4-0/WRS2/NAMESPACE | 12 ++++ WRS2-0.4-0/WRS2/R/ancboot.R | 8 ++- WRS2-0.4-0/WRS2/R/ancova.R | 22 +++++++- WRS2-0.4-0/WRS2/R/bwtrim.R |only WRS2-0.4-0/WRS2/R/mest.R |only WRS2-0.4-0/WRS2/R/msmedse.R | 2 WRS2-0.4-0/WRS2/R/pairdepb.R | 3 - WRS2-0.4-0/WRS2/R/pb2gen.R | 2 WRS2-0.4-0/WRS2/R/pbad2way.R | 34 +++++++------ WRS2-0.4-0/WRS2/R/print.mcp2.R |only WRS2-0.4-0/WRS2/R/print.pb2.R |only WRS2-0.4-0/WRS2/R/print.rmanovab.R | 2 WRS2-0.4-0/WRS2/R/print.yuen.R | 3 - WRS2-0.4-0/WRS2/R/rmmcp.R | 2 WRS2-0.4-0/WRS2/R/rungen.R |only WRS2-0.4-0/WRS2/R/runhat.R |only WRS2-0.4-0/WRS2/R/runmbo.R |only WRS2-0.4-0/WRS2/R/runmean.R |only WRS2-0.4-0/WRS2/R/sppba.R | 66 ++++++++++++------------- WRS2-0.4-0/WRS2/R/sppbb.R | 52 +++++++++++--------- WRS2-0.4-0/WRS2/R/sppbi.R | 52 +++++++++++--------- WRS2-0.4-0/WRS2/R/t2way.R | 9 ++- WRS2-0.4-0/WRS2/R/trimse.R | 2 WRS2-0.4-0/WRS2/R/tsub.R | 2 WRS2-0.4-0/WRS2/R/winmean.R |only WRS2-0.4-0/WRS2/R/winse.R |only WRS2-0.4-0/WRS2/R/yuen.R | 3 - WRS2-0.4-0/WRS2/R/yuenbt.R | 7 +- WRS2-0.4-0/WRS2/R/yuend.R | 43 +++++++++------- WRS2-0.4-0/WRS2/build |only WRS2-0.4-0/WRS2/data/Pygmalion.rda |only WRS2-0.4-0/WRS2/data/chile.rda |only WRS2-0.4-0/WRS2/data/electric.rda |only WRS2-0.4-0/WRS2/data/eurosoccer.rda |only WRS2-0.4-0/WRS2/data/goggles.rda |binary WRS2-0.4-0/WRS2/data/hangover.rda |only WRS2-0.4-0/WRS2/data/swimming.rda |only WRS2-0.4-0/WRS2/inst/NEWS.Rd | 12 ++++ WRS2-0.4-0/WRS2/inst/doc |only WRS2-0.4-0/WRS2/man/Pygmalion.Rd |only WRS2-0.4-0/WRS2/man/WineTasting.Rd | 2 WRS2-0.4-0/WRS2/man/ancova.Rd | 16 +----- WRS2-0.4-0/WRS2/man/bwtrim.Rd |only WRS2-0.4-0/WRS2/man/chile.Rd |only WRS2-0.4-0/WRS2/man/electric.Rd |only WRS2-0.4-0/WRS2/man/eurosoccer.Rd |only WRS2-0.4-0/WRS2/man/goggles.Rd | 8 ++- WRS2-0.4-0/WRS2/man/hangover.Rd |only WRS2-0.4-0/WRS2/man/rmanova.Rd | 2 WRS2-0.4-0/WRS2/man/rmanovab.Rd | 2 WRS2-0.4-0/WRS2/man/runmean.Rd |only WRS2-0.4-0/WRS2/man/swimming.Rd |only WRS2-0.4-0/WRS2/man/t3way.Rd | 2 WRS2-0.4-0/WRS2/man/trimse.Rd |only WRS2-0.4-0/WRS2/man/yuen.Rd | 21 +++----- WRS2-0.4-0/WRS2/man/yuend.Rd |only WRS2-0.4-0/WRS2/vignettes |only 61 files changed, 310 insertions(+), 202 deletions(-)
Title: Simulating Phylogenetic Trees
Description: Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@bsse.ethz.ch>
Diff between TreeSim versions 2.1 dated 2014-09-18 and 2.2 dated 2015-10-05
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NAMESPACE | 4 +++- R/LTT.plot.gen.R | 35 ++++++++++++++++++++++------------- R/collapse.singles.R |only man/LTT.plot.Rd | 13 +++++++++++++ man/LTT.plot.gen.Rd | 40 +++++++++++++++++++++------------------- man/TreeSim-package.Rd | 8 ++++---- 8 files changed, 77 insertions(+), 50 deletions(-)
Title: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of
Ordinary Differential Equations
Description: Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE).
Includes routines that: (1) generate gradient and Jacobian matrices (full and banded),
(2) find roots of non-linear equations by the Newton-Raphson method,
(3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running,
(4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ODEs
by numerical differencing (using the method-of-lines approach).
Includes fortran code.
Author: Karline Soetaert [aut, cre],
yale sparse matrix package authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between rootSolve versions 1.6.5.1 dated 2014-11-06 and 1.6.6 dated 2015-10-05
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NAMESPACE | 6 ++++-- R/stode.R | 5 ++++- R/stodes.R | 3 +++ build/vignette.rds |binary 6 files changed, 24 insertions(+), 15 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.5 dated 2015-07-17 and 0.1.6 dated 2015-10-05
RcppRedis-0.1.5/RcppRedis/R/RcppExports.R |only RcppRedis-0.1.5/RcppRedis/src/RcppExports.cpp |only RcppRedis-0.1.6/RcppRedis/ChangeLog | 27 +++ RcppRedis-0.1.6/RcppRedis/DESCRIPTION | 8 - RcppRedis-0.1.6/RcppRedis/MD5 | 15 - RcppRedis-0.1.6/RcppRedis/README.md | 4 RcppRedis-0.1.6/RcppRedis/inst/NEWS.Rd | 23 ++ RcppRedis-0.1.6/RcppRedis/inst/tests/runit.basicRtests.R | 7 RcppRedis-0.1.6/RcppRedis/inst/tests/runit.listTests.R |only RcppRedis-0.1.6/RcppRedis/src/Redis.cpp | 117 +++++++++++++-- 10 files changed, 174 insertions(+), 27 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.2.0 dated 2015-03-31 and 0.5.0 dated 2015-10-05
gvc-0.2.0/gvc/R/block_matrix.R |only gvc-0.2.0/gvc/R/minus_block_matrix.R |only gvc-0.2.0/gvc/man/block_matrix.Rd |only gvc-0.2.0/gvc/man/minus_block_matrix.Rd |only gvc-0.2.0/gvc/tests/testthat/test_block_matrix.R |only gvc-0.2.0/gvc/tests/testthat/test_minus_block_matrix.R |only gvc-0.5.0/gvc/DESCRIPTION | 18 +-- gvc-0.5.0/gvc/MD5 | 47 +++++--- gvc-0.5.0/gvc/NAMESPACE | 9 + gvc-0.5.0/gvc/NEWS | 32 +++++ gvc-0.5.0/gvc/R/dfddva.R |only gvc-0.5.0/gvc/R/dfdfva.R |only gvc-0.5.0/gvc/R/downstream.R |only gvc-0.5.0/gvc/R/e2r.R | 18 +++ gvc-0.5.0/gvc/R/ffddva.R |only gvc-0.5.0/gvc/R/gvc.R |only gvc-0.5.0/gvc/R/i2e.R | 19 +++ gvc-0.5.0/gvc/R/nrca.R | 36 +----- gvc-0.5.0/gvc/R/upstream.R |only gvc-0.5.0/gvc/README.md | 96 ++++++++++++++--- gvc-0.5.0/gvc/build |only gvc-0.5.0/gvc/inst |only gvc-0.5.0/gvc/man/dfddva.Rd |only gvc-0.5.0/gvc/man/dfdfva.Rd |only gvc-0.5.0/gvc/man/downstream.Rd |only gvc-0.5.0/gvc/man/e2r.Rd | 19 +++ gvc-0.5.0/gvc/man/ffddva.Rd |only gvc-0.5.0/gvc/man/gvc.Rd |only gvc-0.5.0/gvc/man/i2e.Rd | 19 +++ gvc-0.5.0/gvc/man/nrca.Rd | 8 - gvc-0.5.0/gvc/man/upstream.Rd |only gvc-0.5.0/gvc/tests/testthat/test_e2r.R |only gvc-0.5.0/gvc/tests/testthat/test_i2e.R |only gvc-0.5.0/gvc/tests/testthat/test_nrca.R |only gvc-0.5.0/gvc/vignettes |only 35 files changed, 240 insertions(+), 81 deletions(-)
Title: Risk Regression Models for Survival Analysis with Competing
Risks
Description: Risk regression models for survival analysis with and without
competing risks.
Author: Thomas Alexander Gerds, Thomas Harder Scheike
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 1.1.1 dated 2014-12-10 and 1.1.7 dated 2015-10-05
riskRegression-1.1.1/riskRegression/src/matrix.h |only riskRegression-1.1.7/riskRegression/DESCRIPTION | 17 riskRegression-1.1.7/riskRegression/MD5 | 71 +-- riskRegression-1.1.7/riskRegression/NAMESPACE | 23 + riskRegression-1.1.7/riskRegression/R/CSC.R | 180 ++++++---- riskRegression-1.1.7/riskRegression/R/FGR.R | 8 riskRegression-1.1.7/riskRegression/R/coef.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/R/plot.CauseSpecificCox.R | 34 + riskRegression-1.1.7/riskRegression/R/plot.predictedRisk.R | 2 riskRegression-1.1.7/riskRegression/R/plot.riskRegression.R | 9 riskRegression-1.1.7/riskRegression/R/plotEffects.R | 9 riskRegression-1.1.7/riskRegression/R/predict.CauseSpecificCox.R | 2 riskRegression-1.1.7/riskRegression/R/predict.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/predict.riskRegression.R | 5 riskRegression-1.1.7/riskRegression/R/print.CauseSpecificCox.R | 12 riskRegression-1.1.7/riskRegression/R/print.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/print.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/R/print.subjectWeights.R | 2 riskRegression-1.1.7/riskRegression/R/print.timevarCoefList.R | 2 riskRegression-1.1.7/riskRegression/R/riskRegression-package.R | 4 riskRegression-1.1.7/riskRegression/R/riskRegression.R | 11 riskRegression-1.1.7/riskRegression/R/subjectWeights.R | 14 riskRegression-1.1.7/riskRegression/R/summary.FGR.R | 2 riskRegression-1.1.7/riskRegression/R/summary.riskRegression.R | 2 riskRegression-1.1.7/riskRegression/man/CSC.Rd | 78 ++-- riskRegression-1.1.7/riskRegression/man/FGR.Rd | 44 +- riskRegression-1.1.7/riskRegression/man/Melanoma.Rd | 21 - riskRegression-1.1.7/riskRegression/man/plot.riskRegression.Rd | 52 +- riskRegression-1.1.7/riskRegression/man/plotEffects.Rd | 58 +-- riskRegression-1.1.7/riskRegression/man/predict.riskRegression.Rd | 21 - riskRegression-1.1.7/riskRegression/man/riskRegression.Rd | 100 ++--- riskRegression-1.1.7/riskRegression/man/subjectWeights.Rd | 61 +-- riskRegression-1.1.7/riskRegression/src/matrix.c | 2 riskRegression-1.1.7/riskRegression/src/riskregression.h | 50 ++ riskRegression-1.1.7/riskRegression/tests/test-FGR.R | 21 + riskRegression-1.1.7/riskRegression/tests/testthat/CauseSpecificCoxRegression.R | 7 riskRegression-1.1.7/riskRegression/tests/testthat/brier.R | 4 37 files changed, 547 insertions(+), 389 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 1.5.1 dated 2014-12-10 and 1.5.5 dated 2015-10-05
prodlim-1.5.1/prodlim/R/contrastMethods.R |only prodlim-1.5.1/prodlim/R/modelMatrix.R |only prodlim-1.5.1/prodlim/R/readFormula.R |only prodlim-1.5.5/prodlim/DESCRIPTION | 11 prodlim-1.5.5/prodlim/MD5 | 132 ++++----- prodlim-1.5.5/prodlim/NAMESPACE | 34 ++ prodlim-1.5.5/prodlim/R/EventHistory.frame.R | 3 prodlim-1.5.5/prodlim/R/Hist.R | 4 prodlim-1.5.5/prodlim/R/List2Matrix.R |only prodlim-1.5.5/prodlim/R/atRisk.R | 113 ++++---- prodlim-1.5.5/prodlim/R/backGround.R | 63 ++-- prodlim-1.5.5/prodlim/R/checkCauses.R |only prodlim-1.5.5/prodlim/R/dimColor.R | 4 prodlim-1.5.5/prodlim/R/followup.R |only prodlim-1.5.5/prodlim/R/getStates.R | 6 prodlim-1.5.5/prodlim/R/jackknife.R | 4 prodlim-1.5.5/prodlim/R/lifeTab.competing.risks.R | 275 ++++++++++---------- prodlim-1.5.5/prodlim/R/lifeTab.survival.R | 4 prodlim-1.5.5/prodlim/R/plot.Hist.R | 3 prodlim-1.5.5/prodlim/R/plot.prodlim.R | 161 ++++++++--- prodlim-1.5.5/prodlim/R/predict.prodlim.R | 77 ++--- prodlim-1.5.5/prodlim/R/print.Hist.R | 3 prodlim-1.5.5/prodlim/R/print.IntIndex.R | 3 prodlim-1.5.5/prodlim/R/print.neighborhood.R | 3 prodlim-1.5.5/prodlim/R/print.prodlim.R | 3 prodlim-1.5.5/prodlim/R/print.quantile.prodlim.R | 31 +- prodlim-1.5.5/prodlim/R/print.summary.prodlim.R | 39 +- prodlim-1.5.5/prodlim/R/prodlim-package.R |only prodlim-1.5.5/prodlim/R/prodlim.R | 90 +++--- prodlim-1.5.5/prodlim/R/prodlimIcensSurv.R | 158 +++++------ prodlim-1.5.5/prodlim/R/quantile.prodlim.R | 50 ++- prodlim-1.5.5/prodlim/R/strip.terms.R | 4 prodlim-1.5.5/prodlim/R/summary.Hist.R | 3 prodlim-1.5.5/prodlim/R/summary.prodlim.R | 154 ++++++----- prodlim-1.5.5/prodlim/man/EventHistory.frame.Rd | 71 ++--- prodlim-1.5.5/prodlim/man/Hist.Rd | 159 +++++------ prodlim-1.5.5/prodlim/man/List2Matrix.Rd |only prodlim-1.5.5/prodlim/man/PercentAxis.Rd | 13 prodlim-1.5.5/prodlim/man/SimCompRisk.Rd | 14 - prodlim-1.5.5/prodlim/man/SimSurv.Rd | 17 - prodlim-1.5.5/prodlim/man/SmartControl.Rd | 47 +-- prodlim-1.5.5/prodlim/man/atRisk.Rd | 61 +--- prodlim-1.5.5/prodlim/man/backGround.Rd | 31 +- prodlim-1.5.5/prodlim/man/confInt.Rd | 47 +-- prodlim-1.5.5/prodlim/man/crModel.Rd | 13 prodlim-1.5.5/prodlim/man/dimColor.Rd | 17 - prodlim-1.5.5/prodlim/man/getEvent.Rd | 22 - prodlim-1.5.5/prodlim/man/getStates.Rd | 7 prodlim-1.5.5/prodlim/man/jackknife.Rd | 35 +- prodlim-1.5.5/prodlim/man/leaveOneOut.Rd | 16 - prodlim-1.5.5/prodlim/man/markTime.Rd | 24 - prodlim-1.5.5/prodlim/man/meanNeighbors.Rd | 11 prodlim-1.5.5/prodlim/man/model.design.Rd | 91 ++---- prodlim-1.5.5/prodlim/man/neighborhood.Rd | 49 +-- prodlim-1.5.5/prodlim/man/parseSpecialNames.Rd | 21 - prodlim-1.5.5/prodlim/man/plot.Hist.Rd | 85 ++---- prodlim-1.5.5/prodlim/man/plot.prodlim.Rd | 275 ++++++++++---------- prodlim-1.5.5/prodlim/man/plotCompetingRiskModel.Rd | 12 prodlim-1.5.5/prodlim/man/plotIllnessDeathModel.Rd | 18 - prodlim-1.5.5/prodlim/man/predict.prodlim.Rd | 94 +++--- prodlim-1.5.5/prodlim/man/predictSurvIndividual.Rd | 14 - prodlim-1.5.5/prodlim/man/print.prodlim.Rd | 15 - prodlim-1.5.5/prodlim/man/prodlim.Rd | 266 ++++++++----------- prodlim-1.5.5/prodlim/man/quantile.prodlim.Rd | 32 +- prodlim-1.5.5/prodlim/man/row.match.Rd | 21 - prodlim-1.5.5/prodlim/man/sindex.Rd | 42 +-- prodlim-1.5.5/prodlim/man/strip.terms.Rd | 35 +- prodlim-1.5.5/prodlim/man/summary.Hist.Rd | 21 - prodlim-1.5.5/prodlim/man/summary.prodlim.Rd | 90 +++--- prodlim-1.5.5/prodlim/man/survModel.Rd | 12 prodlim-1.5.5/prodlim/tests/testthat/prodlim.R | 29 +- 71 files changed, 1708 insertions(+), 1554 deletions(-)
Title: Prediction Error Curves for Risk Prediction Models in Survival
Analysis
Description: Validation of risk predictions obtained from survival models and
competing risk models based on censored data using inverse weighting and
cross-validation.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between pec versions 2.4.4 dated 2014-12-05 and 2.4.7 dated 2015-10-05
pec-2.4.4/pec/data/GBSG2.RData |only pec-2.4.7/pec/DESCRIPTION | 15 pec-2.4.7/pec/MD5 | 152 +++-- pec-2.4.7/pec/NAMESPACE | 63 ++ pec-2.4.7/pec/R/R2.R | 2 pec-2.4.7/pec/R/calPlot.R | 625 +++++++++++++++-------- pec-2.4.7/pec/R/cindex.R | 92 +-- pec-2.4.7/pec/R/crps.R | 2 pec-2.4.7/pec/R/ibs.R | 2 pec-2.4.7/pec/R/ipcw.R | 16 pec-2.4.7/pec/R/marginal.prodlim.R | 6 pec-2.4.7/pec/R/pec-package.R | 5 pec-2.4.7/pec/R/pec.R | 78 +- pec-2.4.7/pec/R/plot.Cindex.R | 2 pec-2.4.7/pec/R/plot.calibrationPlot.R |only pec-2.4.7/pec/R/plot.confScoreSurv.R | 2 pec-2.4.7/pec/R/plot.pec.R | 94 ++- pec-2.4.7/pec/R/plot.riskReclassification.R |only pec-2.4.7/pec/R/plotPredictEventProb.R | 2 pec-2.4.7/pec/R/plotPredictSurvProb.R | 2 pec-2.4.7/pec/R/predictEventProb.R | 32 - pec-2.4.7/pec/R/predictEventProb.coxboost.R | 8 pec-2.4.7/pec/R/predictEventProb.pseudoForest.R | 4 pec-2.4.7/pec/R/predictEventProb.selectFGR.R | 6 pec-2.4.7/pec/R/predictLifeYearsLost.R | 19 pec-2.4.7/pec/R/predictRestrictedMeanTime.R |only pec-2.4.7/pec/R/predictSurvProb.FastBw.R | 35 - pec-2.4.7/pec/R/predictSurvProb.R | 60 +- pec-2.4.7/pec/R/predictSurvProb.cforest.R | 6 pec-2.4.7/pec/R/predictSurvProb.ctree.R | 4 pec-2.4.7/pec/R/predictSurvProb.penfitS3.R | 2 pec-2.4.7/pec/R/predictSurvProb.pseudoForest.R | 4 pec-2.4.7/pec/R/print.Cindex.R | 2 pec-2.4.7/pec/R/print.ConfScoreSurv.R | 2 pec-2.4.7/pec/R/print.IPCW.R | 2 pec-2.4.7/pec/R/print.R2.R | 2 pec-2.4.7/pec/R/print.calibrationPlot.R |only pec-2.4.7/pec/R/print.crps.R | 2 pec-2.4.7/pec/R/print.method.R | 2 pec-2.4.7/pec/R/print.multiSplitTest.R | 2 pec-2.4.7/pec/R/print.pec.R | 19 pec-2.4.7/pec/R/print.reclassification.R |only pec-2.4.7/pec/R/print.splitMethod.R | 2 pec-2.4.7/pec/R/print.vandeWielTest.R | 2 pec-2.4.7/pec/R/pseudoPecMethods.R | 41 - pec-2.4.7/pec/R/reclass.R |only pec-2.4.7/pec/R/resolveSplitMethod.R | 2 pec-2.4.7/pec/R/selectCox.R | 7 pec-2.4.7/pec/R/simCost.R | 4 pec-2.4.7/pec/R/summary.Cindex.R | 2 pec-2.4.7/pec/R/summary.confScoreSurv.R | 2 pec-2.4.7/pec/R/summary.pec.R | 2 pec-2.4.7/pec/R/wallyPlot.R |only pec-2.4.7/pec/data/GBSG2.csv.gz |only pec-2.4.7/pec/man/GBSG2.Rd | 21 pec-2.4.7/pec/man/Pbc3.Rd | 35 - pec-2.4.7/pec/man/R2.Rd | 58 +- pec-2.4.7/pec/man/Special.Rd | 48 - pec-2.4.7/pec/man/calPlot.Rd | 248 +++++---- pec-2.4.7/pec/man/cindex.Rd | 395 ++++++-------- pec-2.4.7/pec/man/cost.Rd | 19 pec-2.4.7/pec/man/coxboost.Rd | 42 - pec-2.4.7/pec/man/crps.Rd | 49 - pec-2.4.7/pec/man/ipcw.Rd | 100 +-- pec-2.4.7/pec/man/pec.Rd | 635 ++++++++++-------------- pec-2.4.7/pec/man/pecCforest.Rd | 17 pec-2.4.7/pec/man/pecCtree.Rd | 4 pec-2.4.7/pec/man/pecRpart.Rd | 11 pec-2.4.7/pec/man/plot.calibrationPlot.Rd |only pec-2.4.7/pec/man/plot.pec.Rd | 118 ++-- pec-2.4.7/pec/man/plotPredictEventProb.Rd | 85 +-- pec-2.4.7/pec/man/plotPredictSurvProb.Rd | 84 +-- pec-2.4.7/pec/man/predictEventProb.Rd | 43 - pec-2.4.7/pec/man/predictLifeYearsLost.Rd | 49 - pec-2.4.7/pec/man/predictRestrictedMeanTime.Rd |only pec-2.4.7/pec/man/predictSurvProb.Rd | 103 ++- pec-2.4.7/pec/man/print.pec.Rd | 24 pec-2.4.7/pec/man/reclass.Rd |only pec-2.4.7/pec/man/resolvesplitMethod.Rd | 39 - pec-2.4.7/pec/man/selectCox.Rd | 31 - pec-2.4.7/pec/man/selectFGR.Rd | 35 - pec-2.4.7/pec/man/simCost.Rd | 7 pec-2.4.7/pec/man/wallyPlot.Rd |only pec-2.4.7/pec/src/auc.c |only 84 files changed, 1949 insertions(+), 1788 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar constructs are implemented. Block-diagonal matrices can be extracted or removed using two small functions implemented here. In addition, non-square matrices are supported. Block diagonal matrices occur when two dimensions of a data set are combined along one edge of a matrix. For example, trade-flow data in the 'decompr' and 'gvc' packages have each country-industry combination occur along both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 0.3.0 dated 2015-06-15 and 0.4.0 dated 2015-10-05
diagonals-0.3.0/diagonals/R/diag.R |only diagonals-0.3.0/diagonals/man/diag-set.Rd |only diagonals-0.4.0/diagonals/DESCRIPTION | 6 diagonals-0.4.0/diagonals/MD5 | 20 - diagonals-0.4.0/diagonals/NEWS | 6 diagonals-0.4.0/diagonals/R/fatdiag.R | 139 ++++++---- diagonals-0.4.0/diagonals/R/matricise.R |only diagonals-0.4.0/diagonals/README.md | 1 diagonals-0.4.0/diagonals/build/vignette.rds |binary diagonals-0.4.0/diagonals/inst/doc/fatdiag.html | 323 +++++++++++++++++------- diagonals-0.4.0/diagonals/man/fatdiag.Rd | 12 diagonals-0.4.0/diagonals/man/matricise.Rd |only diagonals-0.4.0/diagonals/tests |only 13 files changed, 357 insertions(+), 150 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial clustering of applications with noise) and OPTICS (ordering points to identify the clustering structure) clustering algorithms and the LOF (local outlier factor) algorithm. The implementations uses the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-4 dated 2015-09-17 and 0.9-5 dated 2015-10-05
DESCRIPTION | 14 ++++----- MD5 | 41 ++++++++++++++-------------- NAMESPACE | 1 R/optics.R | 66 +++++++++++++++++++++++----------------------- README.md |only inst/NEWS | 8 ++++- inst/tests/test-lof.R | 11 +++++-- inst/tests/test-optics.R | 26 +++++++++++++++--- man/dbscan.Rd | 2 + man/lof.Rd | 1 man/optics.Rd | 17 +++++++++-- src/ANN.cpp | 6 ++-- src/R_kNN.cpp | 7 ++-- src/R_optics.cpp | 44 ++++++++++++++++++------------ src/R_regionQuery.cpp | 2 - src/kd_dump.cpp | 2 - src/kd_fix_rad_search.cpp | 10 +++--- src/kd_pr_search.cpp | 12 ++++---- src/kd_search.cpp | 12 ++++---- src/kd_util.cpp | 10 +++--- src/pr_queue.h | 10 +++--- src/pr_queue_k.h | 2 - 22 files changed, 177 insertions(+), 127 deletions(-)
Title: High Dimensional Factor Analysis and Confounder Adjusted Testing
and Estimation
Description: Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
Author: Jingshu Wang [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@stanford.edu>
Diff between cate versions 1.0.3 dated 2015-09-09 and 1.0.4 dated 2015-10-05
DESCRIPTION | 10 - MD5 | 37 +++---- NAMESPACE | 1 R/adjust_functions.R | 21 ++-- R/cate.R | 225 +++++++++++++++++++++++++++++++------------- R/factor_functions.R | 1 R/other_methods.R | 81 +++++++++------ R/simulate_functions.R | 5 build/vignette.rds |binary inst/doc/cate-vignette.R | 21 ++-- inst/doc/cate-vignette.Rnw | 43 +++++--- inst/doc/cate-vignette.pdf |binary man/adjust.latent.Rd | 8 - man/cate.Rd | 54 +++++++--- man/est.confounder.num.Rd | 15 +- man/gen.sim.data.Rd | 4 man/gender.sm.Rd | 1 man/parse.cate.formula.Rd |only man/wrapper.Rd | 32 +++--- vignettes/cate-vignette.Rnw | 43 +++++--- 20 files changed, 397 insertions(+), 205 deletions(-)
Title: Graphing Nonlinear Relations Among Latent Variables from
Structural Equation Mixture Models
Description: Contains a graphical user interface to generate the
diagnostic plots proposed by Bauer (2005) and Pek & Chalmers (2015) to investigate
nonlinear bivariate relationships in latent regression models using
structural equation mixture models (SEMMs).
Author: Bethany Kok [ctb],
Jolynn Pek [ctb],
Sonya Sterba [ctb],
Dan Bauer [ctb],
Phil Chalmers [cre, ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between plotSEMM versions 2.0 dated 2014-07-07 and 2.1 dated 2015-10-04
DESCRIPTION | 24 ++-- MD5 | 67 +++++++++-- NAMESPACE | 6 - R/plotSEMM-package.R | 35 +----- R/plotSEMM_GUI.R | 252 ++++++++++++++++++++++++-------------------- R/plotSEMM_ci.R | 58 +++++----- R/plotSEMM_contour.R | 5 R/plotSEMM_probability.R | 100 ++++++++--------- R/plotSEMM_setup.R | 118 ++++++++++---------- R/plotSEMM_setup2.R | 5 R/read.plotSEMM_wACOV.R | 2 inst |only man/plotSEMM.Rd | 28 +--- man/plotSEMM_GUI.Rd | 30 +++-- man/plotSEMM_contour.Rd | 8 + man/plotSEMM_probability.Rd | 11 + man/plotSEMM_setup.Rd | 5 17 files changed, 410 insertions(+), 344 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.5 dated 2015-05-09 and 0.6 dated 2015-10-04
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 7 +++++++ NEWS | 5 +++++ R/ShinyGUIClass.R | 7 ++++--- R/mirtCAT-package.R | 1 + R/mirtCAT.R | 11 +++++++---- R/server.R | 2 +- R/zzz-methods.R | 18 +++++++++++++----- README.md | 5 +++++ build/vignette.rds |binary man/mirtCAT.Rd | 21 +++++++++++++++------ tests/GUI-tests/GUI-tests.R | 14 ++++++++++++-- 13 files changed, 87 insertions(+), 38 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.3.0 dated 2015-10-03 and 0.3.1 dated 2015-10-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 ++++- src/Makevars | 13 +++++++------ 4 files changed, 18 insertions(+), 14 deletions(-)
Title: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities
Description: Wrappers for the Geospatial Data Abstraction Library (GDAL)
Utilities.
Author: Jonathan Asher Greenberg and Matteo Mattiuzzi
Maintainer: Jonathan Asher Greenberg <gdalUtils@estarcion.net>
Diff between gdalUtils versions 0.3.1 dated 2014-01-30 and 2.0.1.5 dated 2015-10-04
DESCRIPTION | 13 - MD5 | 94 +++++--- NAMESPACE | 17 + R/align_rasters.R |only R/gdal_contour.R |only R/gdal_grid.R |only R/gdal_rasterize.R | 13 - R/gdal_setInstallation.R | 34 ++- R/gdal_translate.R | 42 ++- R/gdaladdo.R | 15 - R/gdalbuildvrt.R | 16 - R/gdaldem.R | 7 R/gdalinfo.R | 70 ++++-- R/gdallocationinfo.R |only R/gdalmanage.R |only R/gdalsrsinfo.R | 6 R/gdaltindex.R |only R/gdaltransform.R |only R/gdalwarp.R | 53 +++- R/get_subdatasets.R | 3 R/mosaic_rasters.R | 73 ++++++ R/nearblack.R |only R/ogr2ogr.R | 145 +++++++++---- R/ogrinfo.R | 22 +- R/ogrlineref.R |only R/ogrtindex.R |only man/align_rasters.Rd |only man/batch_gdal_translate.Rd | 48 +--- man/gdal_chooseInstallation.Rd | 22 -- man/gdal_cmd_builder.Rd | 63 ++--- man/gdal_contour.Rd |only man/gdal_grid.Rd |only man/gdal_rasterize.Rd | 209 ++++++------------- man/gdal_setInstallation.Rd | 73 ++---- man/gdal_translate.Rd | 252 ++++++++--------------- man/gdaladdo.Rd | 69 ++---- man/gdalbuildvrt.Rd | 204 +++++------------- man/gdaldem.Rd | 183 +++++----------- man/gdalinfo.Rd | 192 +++++------------ man/gdallocationinfo.Rd |only man/gdalmanage.Rd |only man/gdalsrsinfo.Rd | 72 ++---- man/gdaltindex.Rd |only man/gdaltransform.Rd |only man/gdalwarp.Rd | 327 +++++++++++------------------- man/get_subdatasets.Rd | 38 +-- man/mosaic_rasters.Rd | 39 +-- man/nearblack.Rd |only man/ogr2ogr.Rd | 412 ++++++++++++++------------------------ man/ogrinfo.Rd | 155 +++++--------- man/ogrlineref.Rd |only man/ogrtindex.Rd |only man/qm.Rd | 7 man/remove_file_extension.Rd | 7 man/tahoe_highrez_training.Rd | 2 man/tahoe_lidar_bareearth.tif.Rd | 5 man/tahoe_lidar_highesthit.tif.Rd | 5 man/test_modis.hdf.Rd | 2 58 files changed, 1301 insertions(+), 1708 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.600.2.0 dated 2015-09-19 and 0.6.100.0.0 dated 2015-10-04
ChangeLog | 16 DESCRIPTION | 8 MD5 | 144 +- inst/NEWS.Rd | 22 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 6 inst/include/armadillo_bits/Col_bones.hpp | 2 inst/include/armadillo_bits/Cube_bones.hpp | 33 inst/include/armadillo_bits/Cube_meat.hpp | 216 ++-- inst/include/armadillo_bits/Glue_bones.hpp | 15 inst/include/armadillo_bits/Mat_bones.hpp | 27 inst/include/armadillo_bits/Mat_meat.hpp | 205 +--- inst/include/armadillo_bits/Op_bones.hpp | 20 inst/include/armadillo_bits/Row_bones.hpp | 2 inst/include/armadillo_bits/SpMat_bones.hpp | 201 +-- inst/include/armadillo_bits/arma_forward.hpp |only inst/include/armadillo_bits/arma_ostream_meat.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 8 inst/include/armadillo_bits/arrayops_bones.hpp | 31 inst/include/armadillo_bits/arrayops_meat.hpp | 198 --- inst/include/armadillo_bits/atlas_bones.hpp | 10 inst/include/armadillo_bits/atlas_wrapper.hpp | 58 + inst/include/armadillo_bits/auxlib_bones.hpp | 20 inst/include/armadillo_bits/auxlib_meat.hpp | 110 +- inst/include/armadillo_bits/blas_bones.hpp | 28 inst/include/armadillo_bits/blas_wrapper.hpp | 68 + inst/include/armadillo_bits/compiler_setup.hpp | 4 inst/include/armadillo_bits/field_bones.hpp | 12 inst/include/armadillo_bits/field_meat.hpp | 1 inst/include/armadillo_bits/fn_conv.hpp | 15 inst/include/armadillo_bits/fn_cumprod.hpp | 6 inst/include/armadillo_bits/fn_cumsum.hpp | 6 inst/include/armadillo_bits/fn_diff.hpp | 6 inst/include/armadillo_bits/fn_hist.hpp | 62 - inst/include/armadillo_bits/fn_histc.hpp | 30 inst/include/armadillo_bits/fn_join.hpp | 111 +- inst/include/armadillo_bits/fn_norm.hpp | 861 ++--------------- inst/include/armadillo_bits/fn_reshape.hpp | 2 inst/include/armadillo_bits/fn_schur.hpp |only inst/include/armadillo_bits/fn_shuffle.hpp | 56 - inst/include/armadillo_bits/fn_sort.hpp | 54 - inst/include/armadillo_bits/glue_conv_bones.hpp | 6 inst/include/armadillo_bits/glue_conv_meat.hpp | 69 - inst/include/armadillo_bits/glue_hist_bones.hpp | 20 inst/include/armadillo_bits/glue_hist_meat.hpp | 291 ++--- inst/include/armadillo_bits/glue_histc_bones.hpp | 17 inst/include/armadillo_bits/glue_histc_meat.hpp | 193 +-- inst/include/armadillo_bits/glue_join_bones.hpp | 28 inst/include/armadillo_bits/glue_join_meat.hpp | 147 +- inst/include/armadillo_bits/mtGlue_bones.hpp | 21 inst/include/armadillo_bits/mtOp_bones.hpp | 41 inst/include/armadillo_bits/mul_gemm.hpp | 6 inst/include/armadillo_bits/mul_gemv.hpp | 6 inst/include/armadillo_bits/mul_herk.hpp | 4 inst/include/armadillo_bits/mul_syrk.hpp | 4 inst/include/armadillo_bits/op_cumprod_bones.hpp | 4 inst/include/armadillo_bits/op_cumprod_meat.hpp | 21 inst/include/armadillo_bits/op_cumsum_bones.hpp | 4 inst/include/armadillo_bits/op_cumsum_meat.hpp | 21 inst/include/armadillo_bits/op_diff_bones.hpp | 4 inst/include/armadillo_bits/op_diff_meat.hpp | 25 inst/include/armadillo_bits/op_dot_meat.hpp | 4 inst/include/armadillo_bits/op_hist_bones.hpp | 7 inst/include/armadillo_bits/op_hist_meat.hpp | 60 - inst/include/armadillo_bits/op_norm_bones.hpp |only inst/include/armadillo_bits/op_norm_meat.hpp |only inst/include/armadillo_bits/op_prod_bones.hpp | 9 inst/include/armadillo_bits/op_prod_meat.hpp | 73 - inst/include/armadillo_bits/op_shuffle_bones.hpp | 15 inst/include/armadillo_bits/op_shuffle_meat.hpp | 52 - inst/include/armadillo_bits/op_sort_bones.hpp | 12 inst/include/armadillo_bits/op_sort_meat.hpp | 44 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 176 ++- inst/include/armadillo_bits/subview_meat.hpp | 14 75 files changed, 1870 insertions(+), 2206 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xzhu20@crimson.ua.edu>
Diff between ManlyMix versions 0.1.1 dated 2015-10-02 and 0.1.2 dated 2015-10-04
DESCRIPTION | 25 +++++++++++++++++-------- MD5 | 8 ++++---- NEWS | 4 ++++ man/ManlyMix-package.Rd | 48 ++++++++++++++++++++++++++++++------------------ src/crosen.c | 32 ++++++++++++++++++++++++++++---- 5 files changed, 83 insertions(+), 34 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.5-18 dated 2015-04-04 and 0.5-19 dated 2015-10-03
DESCRIPTION | 13 - MD5 | 97 +++++------ NAMESPACE | 56 ++++-- R/00class.R | 14 + R/00generic.R | 9 + R/ctr_estfun.R | 16 + R/ctr_pml_plrt.R | 148 ++++++++-------- R/ctr_pml_plrt2.R |only R/ctr_pml_plrt_nested.R | 12 - R/lav_fit.R | 60 ------ R/lav_fit_measures.R | 16 + R/lav_matrix.R | 4 R/lav_model.R | 12 + R/lav_model_compute.R | 15 + R/lav_model_estimate.R | 16 + R/lav_model_gradient.R | 19 +- R/lav_model_implied.R |only R/lav_model_information.R | 14 + R/lav_model_objective.R | 5 R/lav_model_vcov.R | 83 ++++++++- R/lav_modification.R | 322 ++++++++++++------------------------ R/lav_object_generate.R | 92 ++++++++++ R/lav_object_inspect.R | 243 ++++++++++++++++++++++++--- R/lav_object_methods.R | 246 ++++++++++++++++++++------- R/lav_object_post_check.R |only R/lav_partable.R | 45 +++-- R/lav_partable_complete.R | 101 ++++++----- R/lav_partable_constraints.R | 212 ++++++------------------ R/lav_partable_vnames.R | 66 ++++--- R/lav_predict.R | 113 ++++++++++-- R/lav_print.R | 361 +++++++++++++++++++++++++++++++++++++++++ R/lav_representation_lisrel.R | 183 ++++++++++++++++++-- R/lav_residuals.R | 14 + R/lav_standardize.R | 12 - R/lav_start.R | 7 R/lav_syntax.R | 122 +++++++------ R/lav_test.R | 19 ++ R/lav_test_LRT.R | 18 +- R/lav_test_diff.R | 198 ++++++++++++++-------- R/lav_test_score.R | 316 ++++++++++++++++++++++++++--------- R/lavaan.R | 110 +++++++----- man/fitMeasures.Rd | 2 man/lavInspect.Rd | 11 + man/lavMatrixRepresentation.Rd | 8 man/lavPredict.Rd | 17 + man/lavTestScore.Rd |only man/lav_model.Rd |only man/lav_partable.Rd | 22 ++ man/lavaan-class.Rd | 6 man/modificationIndices.Rd | 8 man/parameterEstimates.Rd | 41 +++- man/standardizedSolution.Rd | 9 - 52 files changed, 2396 insertions(+), 1137 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>, Vivekananda
Roy <vroy@iastate.edu>
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.2.150402 dated 2015-04-02 and 0.3.0 dated 2015-10-03
geoBayes-0.2.150402/geoBayes/src/skelpnts.f90 |only geoBayes-0.3.0/geoBayes/DESCRIPTION | 18 - geoBayes-0.3.0/geoBayes/MD5 | 68 ++-- geoBayes-0.3.0/geoBayes/NAMESPACE | 19 + geoBayes-0.3.0/geoBayes/NEWS | 5 geoBayes-0.3.0/geoBayes/R/bf.R | 75 ++-- geoBayes-0.3.0/geoBayes/R/calcbf.R | 3 geoBayes-0.3.0/geoBayes/R/comparebinlinks.R | 2 geoBayes-0.3.0/geoBayes/R/geoesteb.R | 17 - geoBayes-0.3.0/geoBayes/R/linkfcn.R | 44 ++ geoBayes-0.3.0/geoBayes/R/mcsp2.R | 16 geoBayes-0.3.0/geoBayes/man/bf1skel.Rd | 8 geoBayes-0.3.0/geoBayes/man/bf2new.Rd | 3 geoBayes-0.3.0/geoBayes/man/bf2optim.Rd | 3 geoBayes-0.3.0/geoBayes/man/bfse.Rd | 3 geoBayes-0.3.0/geoBayes/man/comparebinlinks.Rd | 3 geoBayes-0.3.0/geoBayes/man/ebsglmm.Rd | 16 geoBayes-0.3.0/geoBayes/man/ebstrga.Rd | 3 geoBayes-0.3.0/geoBayes/man/geoBayes.Rd | 3 geoBayes-0.3.0/geoBayes/man/linkfcn.Rd | 17 - geoBayes-0.3.0/geoBayes/man/mcmcmake.Rd | 3 geoBayes-0.3.0/geoBayes/man/mcsglmm.Rd | 13 geoBayes-0.3.0/geoBayes/man/mcstrga.Rd | 3 geoBayes-0.3.0/geoBayes/man/mkpredgrid2d.Rd | 3 geoBayes-0.3.0/geoBayes/man/plotbf2.Rd | 3 geoBayes-0.3.0/geoBayes/man/rhizoctonia.Rd | 3 geoBayes-0.3.0/geoBayes/man/stackdata.Rd | 3 geoBayes-0.3.0/geoBayes/src/Makevars | 7 geoBayes-0.3.0/geoBayes/src/auxfcns.c | 12 geoBayes-0.3.0/geoBayes/src/bfsp.f90 | 107 ++++-- geoBayes-0.3.0/geoBayes/src/calcb2.f90 | 416 ++++++++++++++----------- geoBayes-0.3.0/geoBayes/src/linkfcn.f90 | 33 + geoBayes-0.3.0/geoBayes/src/llik.f90 | 92 +++++ geoBayes-0.3.0/geoBayes/src/mcsp2.f90 | 150 ++++++++- geoBayes-0.3.0/geoBayes/src/pdfw.f90 |only geoBayes-0.3.0/geoBayes/src/pdfy.f90 | 104 ++++++ 36 files changed, 925 insertions(+), 353 deletions(-)
Title: An Enhanced Chart for Simple and Truthful Representation of
Single Observations over Multiple Classes
Description: The sinaplot is a data visualization chart suitable for plotting
any single variable in a multiclass dataset. It is an enhanced jitter strip
chart, where the width of the jitter is controlled by the density
distribution of the data within each class.
Author: Nikos Sidiropoulos [aut, cre],
Sina Hadi Sohi [aut],
Nicolas Rapin [aut],
Frederik Otzen Bagger [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>
Diff between sinaplot versions 0.1.1 dated 2015-10-01 and 0.1.2 dated 2015-10-03
sinaplot-0.1.1/sinaplot/inst/temp.Rmd |only sinaplot-0.1.2/sinaplot/DESCRIPTION | 15 ++++++++------- sinaplot-0.1.2/sinaplot/MD5 | 14 +++++++++----- sinaplot-0.1.2/sinaplot/NEWS |only sinaplot-0.1.2/sinaplot/R/sinaplot.R | 8 ++------ sinaplot-0.1.2/sinaplot/build |only sinaplot-0.1.2/sinaplot/inst/doc |only sinaplot-0.1.2/sinaplot/man/sinaplot.Rd | 8 ++++---- sinaplot-0.1.2/sinaplot/vignettes/SinaPlot.Rmd | 11 +++++++---- 9 files changed, 30 insertions(+), 26 deletions(-)
Title: Nonparametric Methods for Cognitive Diagnosis
Description: An array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.
Author: Yi Zheng [aut, cre],
Chia-Yi Chiu [aut],
Jeffrey A. Douglas [ctb]
Maintainer: Yi Zheng <yi.isabel.zheng@asu.edu>
Diff between NPCD versions 1.0-8 dated 2015-05-02 and 1.0-9 dated 2015-10-03
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 5 ++++- R/AlphaMLE.R | 2 +- R/AlphaNP.R | 2 +- R/CDL.R | 4 ++-- R/CDP.R |only R/ItemFit.R |only R/JMLE.R | 2 +- R/ParMLE.R | 4 ++-- man/AlphaMLE.Rd | 3 ++- man/AlphaNP.Rd | 3 +++ man/CDL.Rd | 2 +- man/CDP.Rd |only man/ItemFit.Rd |only man/JMLE.Rd | 3 ++- man/NPCD.Rd | 4 ++-- man/ParMLE.Rd | 4 ++-- 18 files changed, 44 insertions(+), 32 deletions(-)
Title: Generalized Linear Autoregressive Moving Average Models
Description: Functions are provided for estimation, testing, diagnostic checking and forecasting of generalized linear autoregressive moving average (GLARMA) models for discrete valued time series with regression variables. These are a class of observation driven non-linear non-Gaussian state space models. The state vector consists of a linear regression component plus an observation driven component consisting of an autoregressive-moving average (ARMA) filter of past predictive residuals. Currently three distributions (Poisson, negative binomial and binomial) can be used for the response series. Three options (Pearson, score-type and unscaled) for the residuals in the observation driven component are available. Estimation is via maximum likelihood (conditional on initializing values for the ARMA process) optimized using Fisher scoring or Newton Raphson iterative methods. Likelihood ratio and Wald tests for the observation driven component allow testing for serial dependence in generalized linear model settings. Graphical diagnostics including model fits, autocorrelation functions and probability integral transform residuals are included in the package. Several standard data sets are included in the package.
Author: William T.M. Dunsmuir <w.dunsmuir@unsw.edu.au>, Cenanning Li
<cli113@aucklanduni.ac.nz>, and David J. Scott
<d.scott@auckland.ac.nz>
Maintainer: "William T.M. Dunsmuir" <w.dunsmuir@unsw.edu.au>
Diff between glarma versions 1.3-0 dated 2014-09-25 and 1.4-0 dated 2015-10-03
ChangeLog | 9 ++++++++- DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- build/vignette.rds |binary inst/CITATION | 36 +++++++++++++++++++----------------- inst/doc/glarma.pdf |binary inst/unitTests/Makefile | 44 ++++++++++++++++++++++---------------------- man/glarma.Rd | 20 ++++++++++++++------ 9 files changed, 83 insertions(+), 60 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between coneproj versions 1.7 dated 2015-09-02 and 1.8 dated 2015-10-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/coneproj.R | 2 +- man/qprog.Rd | 1 + src/coneproj.cpp | 7 +++++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland
<p.d.moerland@amc.uva.nl>
Maintainer: Umesh Nandal <u.k.nandal@amc.uva.nl>
Diff between compendiumdb versions 1.0.1 dated 2015-06-15 and 1.0.2 dated 2015-10-03
DESCRIPTION | 11 INSTALL | 9 MD5 | 22 NAMESPACE | 33 - R/checkUpdates.R |only R/createESET.R | 236 ++++---- inst/doc/compendiumdb.pdf |binary inst/extdata/compendiumSchema.sql | 4 inst/scripts/Perl/loadAllforGSEeset.pl | 915 ++++++++++++++++----------------- inst/scripts/README | 2 man/checkUpdates.Rd |only man/compendiumdb-package.Rd | 4 man/createESET.Rd | 2 13 files changed, 631 insertions(+), 607 deletions(-)
Title: Tools for Sotkanet Open Data Portal
Description: Tools to download data from the Sotkanet open data portal.
Author: Leo Lahti, Einari Happonen, Juuso Parkkinen, Joona Lehtomaki
Maintainer: Leo Lahti <louhos@googlegroups.com>
Diff between sotkanet versions 0.9.14 dated 2015-06-24 and 0.9.21 dated 2015-10-03
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 1 R/base_url.R | 2 R/csv.R | 10 -- inst/doc/tutorial.R | 107 +++++++++++----------- inst/doc/tutorial.Rmd | 11 +- inst/doc/tutorial.html | 217 +++++++++++++++++++++++++++++++++++++++++++++- man/sotkanet.csv_query.Rd | 9 - vignettes/tutorial.Rmd | 11 +- 10 files changed, 300 insertions(+), 94 deletions(-)
Title: Penalized Likelihood Estimation and Prediction under the Joint
Cox Models Between Tumour Progression and Death for
Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.1 dated 2015-09-25 and 2.2 dated 2015-10-03
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NAMESPACE | 3 + R/F.window.R | 45 ++++++++++++++++++++++++++--- man/F.window.Rd | 70 ++++++++++++++++++++++++++++------------------ man/joint.Cox-package.Rd | 4 +- man/jointCox.indep.reg.Rd | 2 - man/jointCox.reg.Rd | 2 - 8 files changed, 101 insertions(+), 47 deletions(-)
Title: Command Line Option Parser
Description: A command line parser inspired by Python's 'optparse' library to
be used with Rscript to write "#!" shebang scripts that accept short and
long flag/options.
Author: Trevor L Davis. Some documentation and examples ported from Allen Day's
getopt package. Some documentation from the optparse Python module by the
Python Software Foundation. Contributions from Steve Lianoglou, Jim
Nikelski, Kirill Müller, Peter Humburg, and Rich FitzJohn.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between optparse versions 1.3.0 dated 2014-12-11 and 1.3.2 dated 2015-10-03
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- NAMESPACE | 3 ++- NEWS | 5 ++++- R/optparse.R | 24 +++++++++++++++--------- build/vignette.rds |binary inst/COPYRIGHTS | 4 +++- inst/doc/optparse.pdf |binary man/OptionParser-class.Rd | 2 +- man/OptionParser.Rd | 2 +- man/OptionParserOption-class.Rd | 2 +- man/add_make_option.Rd | 4 +++- man/optparse-package.Rd | 2 +- man/parse_args.Rd | 2 +- man/print_help.Rd | 2 +- tests/testthat/test-optparse.R | 36 +++++++++++++++++++++++++++++++----- 16 files changed, 85 insertions(+), 45 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-0 dated 2015-06-26 and 1.2-1 dated 2015-10-03
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/jomo1.MCMCchain.R | 4 +++- R/jomo1.R | 4 +++- R/jomo1cat.MCMCchain.R | 15 +++++++++------ R/jomo1cat.R | 16 ++++++++++------ R/jomo1mix.MCMCchain.R | 15 +++++++++------ R/jomo1mix.R | 15 +++++++++------ R/jomo1ran.MCMCchain.R | 4 +++- R/jomo1ran.R | 4 +++- R/jomo1rancat.MCMCchain.R | 15 +++++++++------ R/jomo1rancat.R | 15 +++++++++------ R/jomo1rancathr.MCMCchain.R | 15 +++++++++------ R/jomo1rancathr.R | 15 +++++++++------ R/jomo1rancon.MCMCchain.R | 1 - R/jomo1rancon.R | 1 - R/jomo1ranconhr.MCMCchain.R | 1 - R/jomo1ranconhr.R | 1 - R/jomo1ranmix.MCMCchain.R | 15 +++++++++------ R/jomo1ranmix.R | 16 ++++++++++------ R/jomo1ranmixhr.MCMCchain.R | 16 ++++++++++------ R/jomo1ranmixhr.R | 16 ++++++++++------ 22 files changed, 149 insertions(+), 105 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.2 dated 2015-09-25 and 1.3 dated 2015-10-03
DESCRIPTION | 8 MD5 | 14 R/supportRegion.R | 46 ++ build/vignette.rds |binary inst/doc/hisse-vignette.Rmd | 18 - inst/doc/hisse-vignette.html | 693 +++++++++++++------------------------------ man/supportRegion.Rd | 3 vignettes/hisse-vignette.Rmd | 18 - 8 files changed, 288 insertions(+), 512 deletions(-)
Title: Streamlining Design and Deployment of Complex Workflows
Description:
This framework allows you to design and implement complex pipelines, and
deploy them on your institution's computing cluster. This has been built
keeping in mind the needs of bioinformatics workflows. However, it is
easily extendable to any field where a series of steps (shell commands)
are to be executed in a (work)flow.
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Diff between flowr versions 0.9.7.10 dated 2015-08-22 and 0.9.8.2 dated 2015-10-03
flowr-0.9.7.10/flowr/inst/doc/build-pipes.R |only flowr-0.9.7.10/flowr/inst/doc/build-pipes.Rmd |only flowr-0.9.7.10/flowr/inst/doc/build-pipes.html |only flowr-0.9.7.10/flowr/inst/doc/example_sleep.R |only flowr-0.9.7.10/flowr/inst/doc/example_sleep.Rmd |only flowr-0.9.7.10/flowr/inst/doc/example_sleep.html |only flowr-0.9.7.10/flowr/inst/doc/hpcc-support.R |only flowr-0.9.7.10/flowr/inst/doc/hpcc-support.Rmd |only flowr-0.9.7.10/flowr/inst/doc/hpcc-support.html |only flowr-0.9.7.10/flowr/inst/doc/quick-start.R |only flowr-0.9.7.10/flowr/inst/doc/quick-start.Rmd |only flowr-0.9.7.10/flowr/inst/doc/quick-start.html |only flowr-0.9.7.10/flowr/man/as.flowdef.Rd |only flowr-0.9.7.10/flowr/man/as.flowmat.Rd |only flowr-0.9.7.10/flowr/man/calc_boxdim.Rd |only flowr-0.9.7.10/flowr/man/cmds_to_flow.Rd |only flowr-0.9.7.10/flowr/man/detect_dep_type.Rd |only flowr-0.9.7.10/flowr/man/flow-class.Rd |only flowr-0.9.7.10/flowr/man/get_resources.Rd |only flowr-0.9.7.10/flowr/man/get_resources_lsf.Rd |only flowr-0.9.7.10/flowr/man/parse_jobids.Rd |only flowr-0.9.7.10/flowr/man/parse_lsf_out.Rd |only flowr-0.9.7.10/flowr/man/queue-class.Rd |only flowr-0.9.7.10/flowr/man/read_fobj.Rd |only flowr-0.9.7.10/flowr/man/render_dependency.Rd |only flowr-0.9.7.10/flowr/man/render_queue_cmd.Rd |only flowr-0.9.7.10/flowr/man/split_multi_dep.Rd |only flowr-0.9.7.10/flowr/man/subset_fdef.Rd |only flowr-0.9.7.10/flowr/man/subset_fmat.Rd |only flowr-0.9.7.10/flowr/man/update_flow_det.Rd |only flowr-0.9.7.10/flowr/tests/testthat/test-rerun.R |only flowr-0.9.7.10/flowr/tests/testthat/test_plots.R |only flowr-0.9.7.10/flowr/vignettes/build-pipes.Rmd |only flowr-0.9.7.10/flowr/vignettes/example_sleep.Rmd |only flowr-0.9.7.10/flowr/vignettes/hpcc-support.Rmd |only flowr-0.9.7.10/flowr/vignettes/imgs |only flowr-0.9.7.10/flowr/vignettes/quick-start.Rmd |only flowr-0.9.8.2/flowr/DESCRIPTION | 25 - 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flowr-0.9.8.2/flowr/man/job.Rd | 4 flowr-0.9.8.2/flowr/man/kill.Rd | 35 + flowr-0.9.8.2/flowr/man/opts_flow.Rd | 23 flowr-0.9.8.2/flowr/man/plot_flow.Rd | 16 flowr-0.9.8.2/flowr/man/queue.Rd | 17 flowr-0.9.8.2/flowr/man/rerun.Rd | 47 +- flowr-0.9.8.2/flowr/man/run.Rd | 46 + flowr-0.9.8.2/flowr/man/setup.Rd | 21 flowr-0.9.8.2/flowr/man/status.Rd | 40 + flowr-0.9.8.2/flowr/man/submit_flow.Rd | 10 flowr-0.9.8.2/flowr/man/submit_job.Rd | 4 flowr-0.9.8.2/flowr/man/submit_run.Rd |only flowr-0.9.8.2/flowr/man/test_queue.Rd | 5 flowr-0.9.8.2/flowr/man/to_flow.Rd | 72 ++- flowr-0.9.8.2/flowr/man/to_flowdef.Rd | 103 ++++ flowr-0.9.8.2/flowr/man/to_flowdet.Rd | 11 flowr-0.9.8.2/flowr/man/to_flowmat.Rd | 49 +- flowr-0.9.8.2/flowr/man/verbose.Rd |only flowr-0.9.8.2/flowr/man/whisker_render.Rd | 5 flowr-0.9.8.2/flowr/tests/README.md |only flowr-0.9.8.2/flowr/tests/fastq_mutect_err1.def |only flowr-0.9.8.2/flowr/tests/testthat.R | 11 flowr-0.9.8.2/flowr/tests/testthat/test-plots.R |only flowr-0.9.8.2/flowr/tests/testthat/test-toflow.R |only flowr-0.9.8.2/flowr/vignettes/files |only flowr-0.9.8.2/flowr/vignettes/flowr_install.Rmd |only flowr-0.9.8.2/flowr/vignettes/flowr_overview.Rmd |only flowr-0.9.8.2/flowr/vignettes/flowr_overview_files |only flowr-0.9.8.2/flowr/vignettes/flowr_tutorial.Rmd |only flowr-0.9.8.2/flowr/vignettes/flowr_tutorial_files |only 124 files changed, 3123 insertions(+), 1448 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-10 dated 2015-09-16 and 0.2-11 dated 2015-10-03
CHANGELOG | 12 + DESCRIPTION | 8 - MD5 | 43 +++--- NAMESPACE | 5 R/02sequences.R | 50 ++++++- R/03rules.R | 159 +++++++++++++++++++----- R/20support.R | 278 +++++++++++++++++++++++++++---------------- man/cspade.Rd | 9 + man/itemFrequency-methods.Rd | 2 man/ruleInduction-methods.Rd | 34 +++-- man/sequences-class.Rd | 4 man/support-methods.Rd | 9 + man/times-methods.Rd | 2 src/ptree.c |only tests/arules.Rout.save | 8 - tests/idlists.R | 13 +- tests/idlists.Rout.save | 20 ++- tests/makebin.Rout.save | 12 - tests/native.Rout.save | 12 - tests/ptree.R |only tests/ptree.Rout.save |only tests/similarity.Rout.save | 12 - tests/zaki.R | 17 ++ tests/zaki.Rout.save | 36 ++++- 24 files changed, 519 insertions(+), 226 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.0 dated 2015-10-01 and 1.1 dated 2015-10-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ inst/doc/gaston.pdf |binary src/diago.h | 2 +- src/diago_full.h | 2 +- src/diago_full_nocovar.h | 2 +- src/diago_nocovar.h | 2 +- 7 files changed, 13 insertions(+), 13 deletions(-)
Title: Paralellised Versions of Constraint Based Causal Discovery
Algorithms
Description: Parallelise constraint based causality discovery and causal inference methods. The parallelised algorithms in the package will generate the same results as that of the pcalg package but will be much more efficient.
Author: Thuc Duy Le, Tao Hoang, Shu Hu, and Liang Zhang
Maintainer: Thuc Duy Le <Thuc.Le@unisa.edu.au>
Diff between ParallelPC versions 1.0 dated 2015-10-01 and 1.1 dated 2015-10-02
DESCRIPTION | 6 ++-- MD5 | 4 +-- R/ParallelPC.R | 71 ++++++++++++++++++++++++++++++++++++++++++++------------- 3 files changed, 60 insertions(+), 21 deletions(-)
Title: Spherical K-Function
Description: Spherical K-function for point-pattern analysis on the sphere.
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li<liao@umail.iu.edu>
Diff between SphericalK versions 1.1 dated 2015-02-12 and 1.2 dated 2015-10-02
SphericalK-1.1/SphericalK/man/SphericalK-package.Rd |only SphericalK-1.2/SphericalK/DESCRIPTION | 8 - SphericalK-1.2/SphericalK/MD5 | 9 -- SphericalK-1.2/SphericalK/NAMESPACE | 1 SphericalK-1.2/SphericalK/R/SphericalK.R | 88 +++++++++----------- SphericalK-1.2/SphericalK/man/sphere_grid.Rd | 8 - 6 files changed, 55 insertions(+), 59 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <daniel.bowman@unc.edu>
Diff between rNOMADS versions 2.1.4 dated 2015-06-03 and 2.1.5 dated 2015-10-02
DESCRIPTION | 15 ++++++++------- MD5 | 17 +++++++++-------- NAMESPACE | 5 ++++- NEWS | 3 +++ R/GetArchiveGrib.R | 25 +++++++++---------------- R/GetDODS.R | 14 ++++---------- R/GetRealTimeGrib.R | 6 ++---- R/Models.R | 13 +++++-------- R/RNomadsTools.R | 25 ++++++++++++++++++++++++- man/LinkExtractor.Rd |only 10 files changed, 68 insertions(+), 55 deletions(-)
Title: Multidimensional Numerical Integration
Description: It is a wrapper around the Cuba-1.6 library by Thomas Hahn available from the URL http://www.feynarts.de/cuba/. Implement four general-purpose multidimensional integration algorithms: Vegas, Suave, Divonne and Cuhre.
Author: The Cuba library has been written by Thomas Hahn (http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was written by Annie Bouvier and Kiên Kiêu
Maintainer: Annie Bouvier <Annie.Bouvier@jouy.inra.fr>
Diff between R2Cuba versions 1.0-11 dated 2013-04-15 and 1.1-0 dated 2015-10-02
R2Cuba-1.0-11/R2Cuba/ChangeLog |only R2Cuba-1.0-11/R2Cuba/tests/essaiArgu.R |only R2Cuba-1.0-11/R2Cuba/tests/essaiArgu.Rout.save |only R2Cuba-1.0-11/R2Cuba/tests/kk.R |only R2Cuba-1.0-11/R2Cuba/tests/kk.Rout.save |only R2Cuba-1.0-11/R2Cuba/tests/vegas.Rout.save.sv |only R2Cuba-1.1-0/R2Cuba/DESCRIPTION | 20 ++--- R2Cuba-1.1-0/R2Cuba/MD5 | 94 ++++++++++++------------ R2Cuba-1.1-0/R2Cuba/NAMESPACE | 5 - R2Cuba-1.1-0/R2Cuba/NEWS |only R2Cuba-1.1-0/R2Cuba/R/commoncuba.R | 33 ++++++++ R2Cuba-1.1-0/R2Cuba/R/cuhre.R | 38 ++++++++- R2Cuba-1.1-0/R2Cuba/R/divonne.R | 28 +++++++ R2Cuba-1.1-0/R2Cuba/R/suave.R | 26 ++++++ R2Cuba-1.1-0/R2Cuba/R/vegas.R | 28 +++++++ R2Cuba-1.1-0/R2Cuba/build |only R2Cuba-1.1-0/R2Cuba/demo/00Index | 2 R2Cuba-1.1-0/R2Cuba/man/R2Cuba-package.Rd | 24 +----- R2Cuba-1.1-0/R2Cuba/man/cuhre.Rd | 6 - R2Cuba-1.1-0/R2Cuba/man/divonne.Rd | 2 R2Cuba-1.1-0/R2Cuba/man/suave.Rd | 4 - R2Cuba-1.1-0/R2Cuba/man/vegas.Rd | 2 R2Cuba-1.1-0/R2Cuba/src/common_stddecl.h | 60 +++++++-------- R2Cuba-1.1-0/R2Cuba/src/cuhre_Cuhre.c | 96 ++++++++----------------- R2Cuba-1.1-0/R2Cuba/src/cuhre_DoSample.c | 59 ++++++++++++++- R2Cuba-1.1-0/R2Cuba/src/cuhre_Integrate.c | 87 ++++++++++++---------- R2Cuba-1.1-0/R2Cuba/src/cuhre_Rule.c | 23 ++++- R2Cuba-1.1-0/R2Cuba/src/cuhre_Rule.h | 20 ++--- R2Cuba-1.1-0/R2Cuba/src/cuhre_common.c | 2 R2Cuba-1.1-0/R2Cuba/src/cuhre_decl.h | 5 - R2Cuba-1.1-0/R2Cuba/src/cuhre_util.h | 8 +- R2Cuba-1.1-0/R2Cuba/src/divonne_Divonne.c | 10 +- R2Cuba-1.1-0/R2Cuba/src/divonne_Explore.c | 3 R2Cuba-1.1-0/R2Cuba/src/divonne_FindMinimum.c | 1 R2Cuba-1.1-0/R2Cuba/src/divonne_Integrate.c | 3 R2Cuba-1.1-0/R2Cuba/src/divonne_Rule.h | 9 +- R2Cuba-1.1-0/R2Cuba/src/divonne_Sample.c | 2 R2Cuba-1.1-0/R2Cuba/src/divonne_Split.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_Fluct.h | 1 R2Cuba-1.1-0/R2Cuba/src/suave_Integrate.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_Sample.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_Suave.c | 3 R2Cuba-1.1-0/R2Cuba/src/suave_util.h | 3 R2Cuba-1.1-0/R2Cuba/src/vegas_Grid.c | 3 R2Cuba-1.1-0/R2Cuba/src/vegas_Vegas.c | 3 R2Cuba-1.1-0/R2Cuba/tests/Gtilde2.R |only R2Cuba-1.1-0/R2Cuba/tests/Gtilde2.Rout.save |only R2Cuba-1.1-0/R2Cuba/tests/MWE.R |only R2Cuba-1.1-0/R2Cuba/tests/MWE.Rout.save |only R2Cuba-1.1-0/R2Cuba/tests/cuhre.R | 8 -- R2Cuba-1.1-0/R2Cuba/tests/cuhre.Rout.save | 17 +--- R2Cuba-1.1-0/R2Cuba/tests/divonne.Rout.save | 7 - R2Cuba-1.1-0/R2Cuba/tests/peak.Rout.save | 7 - R2Cuba-1.1-0/R2Cuba/tests/suave.Rout.save | 7 - 54 files changed, 464 insertions(+), 304 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.1 dated 2015-08-25 and 0.2.4 dated 2015-10-02
networkD3-0.2.1/networkD3/man/JSONtoDF.Rd |only networkD3-0.2.4/networkD3/DESCRIPTION | 16 +- networkD3-0.2.4/networkD3/MD5 | 45 ++--- networkD3-0.2.4/networkD3/NAMESPACE | 4 networkD3-0.2.4/networkD3/NEWS | 33 ++++ networkD3-0.2.4/networkD3/R/dendroNetwork.R | 7 networkD3-0.2.4/networkD3/R/diagonalNetwork.R | 25 +-- networkD3-0.2.4/networkD3/R/forceNetwork.R | 19 +- networkD3-0.2.4/networkD3/R/radialNetwork.R | 25 +-- networkD3-0.2.4/networkD3/R/sankeyNetwork.R | 35 ++-- networkD3-0.2.4/networkD3/R/utils.R | 78 ++++----- networkD3-0.2.4/networkD3/README.md | 19 +- networkD3-0.2.4/networkD3/inst/examples/examples.R | 18 +- networkD3-0.2.4/networkD3/inst/examples/shiny/server.R | 20 +- networkD3-0.2.4/networkD3/inst/examples/shiny/ui.R | 2 networkD3-0.2.4/networkD3/inst/htmlwidgets/dendroNetwork.js | 2 networkD3-0.2.4/networkD3/inst/htmlwidgets/diagonalNetwork.js | 69 +++++++- networkD3-0.2.4/networkD3/inst/htmlwidgets/lib/sankey.js | 48 ++++-- networkD3-0.2.4/networkD3/inst/htmlwidgets/radialNetwork.js | 80 +++++++++- networkD3-0.2.4/networkD3/inst/htmlwidgets/sankeyNetwork.js | 14 + networkD3-0.2.4/networkD3/man/diagonalNetwork.Rd | 18 +- networkD3-0.2.4/networkD3/man/forceNetwork.Rd | 17 -- networkD3-0.2.4/networkD3/man/radialNetwork.Rd | 18 +- networkD3-0.2.4/networkD3/man/sankeyNetwork.Rd | 23 +- 24 files changed, 403 insertions(+), 232 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.0-1 dated 2015-09-28 and 3.0.0-2 dated 2015-10-02
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- src/Makefile | 34 ++++++++++++++++------------------ src/Makefile.win | 20 +++++++++++++++----- src/legacy_convert.awk |only src/world.name | 2 +- 6 files changed, 41 insertions(+), 32 deletions(-)
More information about imputeMissings at CRAN
Permanent link
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and `iDigBio`. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.3.2 dated 2015-09-12 and 0.4.0 dated 2015-10-02
DESCRIPTION | 17 +- MD5 | 44 ++--- NAMESPACE | 7 R/as.vertnet.R |only R/inat.R | 148 +++++++---------- R/methods.r | 53 ++++-- R/occ.r | 108 +++++++++---- R/occ2df.R | 20 ++ R/plugins.r | 55 +++--- R/tbldf.R | 6 R/wkt_bbox.R | 20 ++ R/wkt_vis.r | 88 +++++++--- R/zzz.r | 9 + README.md | 126 ++++----------- inst/doc/spocc_vignette.Rmd | 343 +++++++++++++++++++---------------------- inst/doc/spocc_vignette.html | 346 +++++++++++++++++++----------------------- man/as.vertnet.Rd |only man/occ.Rd | 131 ++++++++++++++- man/spocc_objects.Rd | 9 + man/wkt_vis.Rd | 14 + tests/testthat/test-occ.R | 149 +++++++++++++++--- tests/testthat/test-occ2df.R |only tests/testthat/test-options.R | 5 tests/testthat/test-wkt_vis.R |only vignettes/spocc_vignette.Rmd | 343 +++++++++++++++++++---------------------- 25 files changed, 1156 insertions(+), 885 deletions(-)
Title: R Interface to EPP-Lab, a Java Program for Exploratory
Projection Pursuit
Description: An R Interface to EPP-lab v1.0. EPP-lab is a Java program for projection pursuit using genetic algorithms written by Alain Berro and S. Larabi Marie-Sainte and is included in the package.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between REPPlab versions 0.9.1 dated 2015-02-05 and 0.9.2 dated 2015-10-02
DESCRIPTION | 13 +- MD5 | 69 +++++++------- NAMESPACE | 39 ++++---- R/EPPlabAgg.R |only R/REPPlab-package.R |only R/REPPlab.R | 131 +++++++++++++++++++++++++++ R/coef.epplab.R | 22 ++++ R/fitted.epplab.R | 31 ++++++ R/outlier.R | 56 +++++++++++ R/pairs.epplab.R | 23 ++++ R/plot.epplab.R | 49 ++++++++++ R/plot.epplabOutlier.R | 43 ++++++++- R/predict.epplab.R | 39 ++++++++ R/print.epplab.R | 22 ++++ R/print.epplabOutlier.R | 33 ++++++ R/screeplot.epplab.R | 35 +++++++ R/summary.epplab.R | 23 ++++ R/summary.epplabOutlier.R | 39 +++++++- R/whitenSVD.R | 96 ++++++++++++++------ inst/ChangeLog | 7 + man/EPPlab.Rd | 204 ++++++++++++++++++++++++------------------- man/EPPlabAgg.Rd |only man/EPPlabOutlier.Rd | 101 +++++++++------------ man/REPPlab-package.Rd | 67 ++++++-------- man/ReliabilityData.Rd | 47 ++++----- man/WhitenSVD.Rd | 117 ++++++++++++------------ man/coef.epplab.Rd | 37 +++---- man/fitted.epplab.Rd | 43 ++++----- man/pairs.epplab.Rd | 41 ++++---- man/plot.epplab.Rd | 70 ++++++++------ man/plot.epplabOutlier.Rd | 57 ++++++------ man/predict.epplab.Rd | 49 +++++----- man/print.epplab.Rd | 37 +++---- man/print.epplabOutlier.Rd | 39 ++++---- man/screeplot.epplab.Rd | 57 ++++++------ man/summary.epplab.Rd | 40 ++++---- man/summary.epplabOutlier.Rd | 42 ++++---- 37 files changed, 1221 insertions(+), 597 deletions(-)
Title: Fungible Coefficients and Monte Carlo Functions
Description: Functions for computing fungible coefficients and Monte Carlo data.
Author: Niels G. Waller <nwaller@umn.edu> and Jeff Jones <jeff.jones@kornferry.com>
Maintainer: Niels G. Waller <nwaller@umn.edu>
Diff between fungible versions 1.0 dated 2015-08-18 and 1.1 dated 2015-10-02
DESCRIPTION | 8 MD5 | 24 +- R/corSmooth.R | 22 +- R/fungible.R | 16 - R/fungibleR.R | 105 +++++++++--- R/seBeta.R | 136 ++++++++------- R/seBetaCor.R | 366 ++++++++++++++++++++++--------------------- inst/CITATION | 4 inst/doc/fungible-manual.pdf |binary man/corSmooth.Rd | 6 man/fungibleR.Rd | 5 man/seBeta.Rd | 101 ++++++----- man/seBetaCor.Rd | 95 +++++------ 13 files changed, 485 insertions(+), 403 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats used in and outside of R.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 0.1.0 dated 2015-08-06 and 0.1.4 dated 2015-10-02
fulltext-0.1.0/fulltext/tests/test-all.R |only fulltext-0.1.4/fulltext/DESCRIPTION | 19 - fulltext-0.1.4/fulltext/MD5 | 60 ++- fulltext-0.1.4/fulltext/NAMESPACE | 11 fulltext-0.1.4/fulltext/R/europe_pmc_utils.R |only fulltext-0.1.4/fulltext/R/extract_tools.R |only fulltext-0.1.4/fulltext/R/ft_extract.R | 15 fulltext-0.1.4/fulltext/R/ft_get.R | 75 ++-- fulltext-0.1.4/fulltext/R/ft_get_si.R |only fulltext-0.1.4/fulltext/R/ft_links.R |only fulltext-0.1.4/fulltext/R/fulltext-package.R | 4 fulltext-0.1.4/fulltext/R/pdfx.R | 16 fulltext-0.1.4/fulltext/R/plugins_get.R | 266 +++------------ fulltext-0.1.4/fulltext/R/plugins_get_old.R |only fulltext-0.1.4/fulltext/R/plugins_links.R |only fulltext-0.1.4/fulltext/R/plugins_search.R | 46 +- fulltext-0.1.4/fulltext/R/zzz.R | 21 + fulltext-0.1.4/fulltext/README.md | 131 +++++-- fulltext-0.1.4/fulltext/build/vignette.rds |binary fulltext-0.1.4/fulltext/inst/doc/fulltext_vignette.Rmd | 88 +++- fulltext-0.1.4/fulltext/inst/doc/fulltext_vignette.html | 92 +++-- fulltext-0.1.4/fulltext/inst/vign/formats.md | 4 fulltext-0.1.4/fulltext/inst/vign/fulltext_vignette.md | 88 +++- fulltext-0.1.4/fulltext/man/eupmc.Rd |only fulltext-0.1.4/fulltext/man/extract_tools.Rd |only fulltext-0.1.4/fulltext/man/ft_extract.Rd | 7 fulltext-0.1.4/fulltext/man/ft_get.Rd | 3 fulltext-0.1.4/fulltext/man/ft_get_si.Rd |only fulltext-0.1.4/fulltext/man/ft_links.Rd |only fulltext-0.1.4/fulltext/man/fulltext-package.Rd | 1 fulltext-0.1.4/fulltext/man/pdfx.Rd | 3 fulltext-0.1.4/fulltext/tests/longtests |only fulltext-0.1.4/fulltext/tests/testthat/test-ft_extract.R | 18 - fulltext-0.1.4/fulltext/tests/testthat/test-ft_get.R | 44 ++ fulltext-0.1.4/fulltext/tests/testthat/test-ft_get_si.r |only fulltext-0.1.4/fulltext/tests/testthat/test-ft_search.R | 30 + fulltext-0.1.4/fulltext/vignettes/fulltext_vignette.Rmd | 88 +++- 37 files changed, 651 insertions(+), 479 deletions(-)
Title: SNPs Enrichment Analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil <mickael.canouil@cnrs.fr>
Diff between snpEnrichment versions 1.6.3 dated 2015-02-09 and 1.7.0 dated 2015-10-01
snpEnrichment-1.6.3/snpEnrichment/README.md |only snpEnrichment-1.7.0/snpEnrichment/ChangeLog | 18 ++++++++++ snpEnrichment-1.7.0/snpEnrichment/DESCRIPTION | 14 +++---- snpEnrichment-1.7.0/snpEnrichment/MD5 | 16 ++++---- snpEnrichment-1.7.0/snpEnrichment/NAMESPACE | 10 ++++- snpEnrichment-1.7.0/snpEnrichment/R/Global.R | 2 - snpEnrichment-1.7.0/snpEnrichment/R/enrichment.R | 15 +++++++- snpEnrichment-1.7.0/snpEnrichment/data/toyEnrichment.RData |binary snpEnrichment-1.7.0/snpEnrichment/man/snpEnrichment-package.Rd | 4 +- snpEnrichment-1.7.0/snpEnrichment/tests |only 10 files changed, 56 insertions(+), 23 deletions(-)
Title: Statistical Comparison of Multiple Algorithms in Multiple
Problems
Description: Given a matrix with results of different algorithms for different problems, the package uses statistical tests and corrections to assess the differences between algorithms.
Author: Borja Calvo [aut, cre],
Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>
Diff between scmamp versions 0.2.1 dated 2015-09-23 and 0.2.3 dated 2015-10-01
DESCRIPTION | 10 +- MD5 | 33 ++++----- NAMESPACE | 1 R/plotting.R | 159 ++++++++++++++++++++++++++++++++++++++++++++-- R/post_hoc.R | 16 ++-- R/scmamp.R | 106 ++++++++++++++++++++++++++---- R/sysdata.rda |binary build/vignette.rds |binary data/data_blum_2015.RData |binary data/data_gh_2008.RData |binary data/data_gh_2010.RData |binary man/adjustFinner.Rd | 4 - man/adjustHolland.Rd | 4 - man/adjustLi.Rd | 4 - man/adjustRom.Rd | 4 - man/drawAlgorithmGraph.Rd | 2 man/plotCD.Rd | 2 man/plotRanking.Rd |only 18 files changed, 289 insertions(+), 56 deletions(-)
Title: Distance Weighted Discrimination (DWD) and Kernel Methods
Description: A novel implementation that solves the DWD and the kernel DWD which can be hundred times faster than the existing implementation of DWD based on the second-order-cone programming (SOCP). The package also handles some other general loss functions including large-margin unified machines (LUM).
Author: Boxiang Wang <boxiang@umn.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Boxiang Wang <boxiang@umn.edu>
Diff between kerndwd versions 1.1.1 dated 2015-09-06 and 1.1.2 dated 2015-10-01
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/cv.kerndwd.R | 10 +++++++--- R/kerndwd.R | 3 ++- R/predict.kerndwd.R | 8 ++++++-- R/utilities.R | 4 ++-- man/cv.kerndwd.Rd | 2 +- man/dots.Rd | 8 ++++---- man/kerndwd.Rd | 4 ++-- 9 files changed, 37 insertions(+), 28 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Testing
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace and GraceR tests to perform graph-guided hypothesis test on the association between the response and the predictor.
Author: Sen Zhao
Maintainer: Sen Zhao <senz@uw.edu>
Diff between Grace versions 0.1 dated 2015-08-18 and 0.1.1 dated 2015-10-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/grace.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Cleaning Geometries from Spatial Objects
Description:
Provides a set of utility tools to inspect spatial objects, facilitate
handling and reporting of topology errors and geometry validity issues.
Finally, it provides a geometry cleaner that will fix all geometry problems,
and eliminate (at least reduce) the likelihood of having issues when doing
spatial data processing.
Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between cleangeo versions 0.1-0 dated 2015-09-27 and 0.1-1 dated 2015-10-01
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++++------- R/cleangeo.R | 4 ++-- R/clgeo_Clean.R | 39 ++++++++++++++++++++------------------- README.md | 5 +++-- build |only inst/doc |only man/cleangeo.Rd | 4 ++-- tests/testthat/test_Clean.R | 9 ++++++++- vignettes/quickstart.Rmd | 12 +++++------- 10 files changed, 57 insertions(+), 45 deletions(-)
Title: Species Richness Estimation and Modeling
Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa.
Author: Amy Willis and John Bunge
Maintainer: Amy Willis <adw96@cornell.edu>
Diff between breakaway versions 1.0 dated 2014-08-04 and 2.0 dated 2015-10-01
breakaway-1.0/breakaway/R/betta_basic.R |only breakaway-1.0/breakaway/man/betta_basic.Rd |only breakaway-2.0/breakaway/DESCRIPTION | 12 +-- breakaway-2.0/breakaway/MD5 | 19 +++-- breakaway-2.0/breakaway/NAMESPACE | 9 ++ breakaway-2.0/breakaway/R/betta.R |only breakaway-2.0/breakaway/R/breakaway_nof1.R | 78 ++++++++++++++--------- breakaway-2.0/breakaway/R/hawaii.R |only breakaway-2.0/breakaway/man/betta.Rd |only breakaway-2.0/breakaway/man/betta_pic.Rd |only breakaway-2.0/breakaway/man/breakaway-package.Rd | 17 ++--- breakaway-2.0/breakaway/man/breakaway.Rd | 11 +-- breakaway-2.0/breakaway/man/breakaway_nof1.Rd | 11 +-- breakaway-2.0/breakaway/man/hawaii.Rd |only 14 files changed, 94 insertions(+), 63 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Taxonomic information from around the web. This package
interacts with a suite of web 'APIs' for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.6.2 dated 2015-08-07 and 0.6.6 dated 2015-10-01
taxize-0.6.2/taxize/man/get_ubioid.Rd |only taxize-0.6.2/taxize/man/ubio_classification.Rd |only taxize-0.6.2/taxize/man/ubio_classification_search.Rd |only taxize-0.6.2/taxize/man/ubio_id.Rd |only taxize-0.6.2/taxize/man/ubio_search.Rd |only taxize-0.6.2/taxize/man/ubio_synonyms.Rd |only taxize-0.6.2/taxize/tests/testthat/test-ubio_classification.R |only taxize-0.6.6/taxize/DESCRIPTION | 10 taxize-0.6.6/taxize/MD5 | 225 +++++----- taxize-0.6.6/taxize/NAMESPACE | 4 taxize-0.6.6/taxize/R/children.R | 23 - taxize-0.6.6/taxize/R/classification.R | 4 taxize-0.6.6/taxize/R/comm2sci.R | 7 taxize-0.6.6/taxize/R/eol_dataobjects.R | 22 taxize-0.6.6/taxize/R/gbif_parse.R | 2 taxize-0.6.6/taxize/R/get_eolid.R | 16 taxize-0.6.6/taxize/R/get_gbifid.R | 24 - taxize-0.6.6/taxize/R/get_ids.R | 18 taxize-0.6.6/taxize/R/get_nbnid.R | 51 -- taxize-0.6.6/taxize/R/get_tsn.R | 2 taxize-0.6.6/taxize/R/get_ubioid.R | 125 +---- taxize-0.6.6/taxize/R/get_uid.R | 20 taxize-0.6.6/taxize/R/gni_parse.R | 30 - taxize-0.6.6/taxize/R/gnr_resolve.R | 157 +++--- taxize-0.6.6/taxize/R/iplant_resolve.R | 3 taxize-0.6.6/taxize/R/ipni_search.R | 34 - taxize-0.6.6/taxize/R/itis.R | 89 ++- taxize-0.6.6/taxize/R/itis_downstream.R | 62 +- taxize-0.6.6/taxize/R/itis_getrecord.R | 26 - taxize-0.6.6/taxize/R/itis_hierarchy.R | 19 taxize-0.6.6/taxize/R/itis_kingdomnames.R | 18 taxize-0.6.6/taxize/R/itis_lsid.R | 16 taxize-0.6.6/taxize/R/itis_native.R | 22 taxize-0.6.6/taxize/R/itis_refs.R | 7 taxize-0.6.6/taxize/R/itis_taxrank.R | 12 taxize-0.6.6/taxize/R/iucn_getname.R | 3 taxize-0.6.6/taxize/R/iucn_id.R |only taxize-0.6.6/taxize/R/iucn_summary.R | 3 taxize-0.6.6/taxize/R/names_list.r | 3 taxize-0.6.6/taxize/R/nbn_classification.R | 7 taxize-0.6.6/taxize/R/nbn_search.R | 13 taxize-0.6.6/taxize/R/nbn_synonyms.R | 3 taxize-0.6.6/taxize/R/ncbi_children.R | 10 taxize-0.6.6/taxize/R/ncbi_get_taxon_summary.R | 13 taxize-0.6.6/taxize/R/phylomatic_format.R | 2 taxize-0.6.6/taxize/R/ping.R | 19 taxize-0.6.6/taxize/R/plantminer.R | 56 +- taxize-0.6.6/taxize/R/scrapenames.r | 2 taxize-0.6.6/taxize/R/synonyms.R | 31 - taxize-0.6.6/taxize/R/tax_name.R | 34 - taxize-0.6.6/taxize/R/tax_rank.R | 10 taxize-0.6.6/taxize/R/taxize-package.R | 16 taxize-0.6.6/taxize/R/taxize_cite.R | 17 taxize-0.6.6/taxize/R/tnrs.R | 8 taxize-0.6.6/taxize/R/tnrs_sources.r | 4 taxize-0.6.6/taxize/R/tp_refs.R | 3 taxize-0.6.6/taxize/R/ubio_classification.R | 75 --- taxize-0.6.6/taxize/R/ubio_classification_search.R | 35 - taxize-0.6.6/taxize/R/ubio_id.R | 91 ---- taxize-0.6.6/taxize/R/ubio_search.R | 67 -- taxize-0.6.6/taxize/R/ubio_synonyms.R | 59 -- taxize-0.6.6/taxize/R/upstream.R | 6 taxize-0.6.6/taxize/R/vascan_search.r | 49 +- taxize-0.6.6/taxize/R/zzz.R | 3 taxize-0.6.6/taxize/README.md | 63 -- taxize-0.6.6/taxize/build/vignette.rds |binary taxize-0.6.6/taxize/data/rank_ref.RData |binary taxize-0.6.6/taxize/inst/doc/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/inst/doc/taxize_infotable.html | 126 +---- taxize-0.6.6/taxize/inst/doc/taxize_vignette.Rmd | 80 --- taxize-0.6.6/taxize/inst/doc/taxize_vignette.html | 79 --- taxize-0.6.6/taxize/inst/vign/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/inst/vign/taxize_infotable.md | 40 - taxize-0.6.6/taxize/inst/vign/taxize_vignette.Rmd | 7 taxize-0.6.6/taxize/inst/vign/taxize_vignette.md | 80 --- taxize-0.6.6/taxize/man/eol_dataobjects.Rd | 10 taxize-0.6.6/taxize/man/get_eolid.Rd | 2 taxize-0.6.6/taxize/man/get_ids.Rd | 12 taxize-0.6.6/taxize/man/get_ubioid-defunct.Rd |only taxize-0.6.6/taxize/man/get_uid.Rd | 14 taxize-0.6.6/taxize/man/getitistermsfromcommonname.Rd | 4 taxize-0.6.6/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.6.6/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.6.6/taxize/man/gnr_resolve.Rd | 41 + taxize-0.6.6/taxize/man/ipni_search.Rd | 4 taxize-0.6.6/taxize/man/itis_getrecord.Rd | 7 taxize-0.6.6/taxize/man/itis_hierarchy.Rd | 7 taxize-0.6.6/taxize/man/itis_kingdomnames.Rd | 7 taxize-0.6.6/taxize/man/itis_lsid.Rd | 4 taxize-0.6.6/taxize/man/itis_native.Rd | 3 taxize-0.6.6/taxize/man/itis_refs.Rd | 5 taxize-0.6.6/taxize/man/itis_taxrank.Rd | 2 taxize-0.6.6/taxize/man/iucn_id.Rd |only taxize-0.6.6/taxize/man/ncbi_children.Rd | 7 taxize-0.6.6/taxize/man/ncbi_get_taxon_summary.Rd | 4 taxize-0.6.6/taxize/man/ping.Rd | 4 taxize-0.6.6/taxize/man/plantminer.Rd | 24 - taxize-0.6.6/taxize/man/searchforanymatchpaged.Rd | 4 taxize-0.6.6/taxize/man/synonyms.Rd | 16 taxize-0.6.6/taxize/man/tax_rank.Rd | 4 taxize-0.6.6/taxize/man/taxize-defunct.Rd | 7 taxize-0.6.6/taxize/man/taxize-package.Rd | 6 taxize-0.6.6/taxize/man/taxize_cite.Rd | 1 taxize-0.6.6/taxize/man/tnrs.Rd | 6 taxize-0.6.6/taxize/man/ubio_classification-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_classification_search-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_id-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_ping-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_search-defunct.Rd |only taxize-0.6.6/taxize/man/ubio_synonyms-defunct.Rd |only taxize-0.6.6/taxize/man/vascan_search.Rd | 12 taxize-0.6.6/taxize/tests/testthat/Rplots.pdf |only taxize-0.6.6/taxize/tests/testthat/test-eol_dataobjects.R | 2 taxize-0.6.6/taxize/tests/testthat/test-gbif_parse.R | 11 taxize-0.6.6/taxize/tests/testthat/test-gnr_resolve.R | 36 - taxize-0.6.6/taxize/tests/testthat/test-ipni_search.R |only taxize-0.6.6/taxize/tests/testthat/test-itis_lsid.R | 2 taxize-0.6.6/taxize/tests/testthat/test-iucn_id.R |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_tree.R | 1 taxize-0.6.6/taxize/tests/testthat/test-ping.R | 6 taxize-0.6.6/taxize/tests/testthat/test-plantminer.R | 18 taxize-0.6.6/taxize/vignettes/taxize_infotable.Rmd | 40 - taxize-0.6.6/taxize/vignettes/taxize_vignette.Rmd | 80 --- 123 files changed, 1026 insertions(+), 1636 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling and modelling.
Functions include models for species population density, download utilities for
climate and global deforestation spatial products, spatial smoothing,
multivariate separability, point process model for creating pseudo-absences
and sub-sampling, polygon and point-distance landscape metrics, auto-logistic
model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-1 dated 2015-02-24 and 0.1-2 dated 2015-10-01
DESCRIPTION | 24 ++++--- MD5 | 146 +++++++++++++++++++++++++-------------------- NAMESPACE | 14 ++++ R/bearing.distance.R |only R/breeding.density.R | 35 +++++----- R/concordance.R |only R/conf.interval.R |only R/correlogram.R | 18 ++--- R/csi.R | 7 +- R/download.daymet.R | 5 - R/download.hansen.R | 5 - R/download.prism.R | 7 +- R/group.pdf.R | 10 +-- R/hexagons.R | 7 +- R/idw.smoothing.R | 4 - R/kl.divergence.R | 4 - R/land.metrics.R | 20 +++--- R/local.min.max.R | 25 +++---- R/loess.boot.R |only R/loess.ci.R |only R/logistic.regression.R | 20 +++--- R/moments.R | 52 ++++++++-------- R/nni.R | 2 R/o.ring.R | 27 ++++---- R/optimal.k.R | 9 +- R/outliers.R | 11 +-- R/parea.sample.R | 7 +- R/plot.loess.boot.R |only R/point.in.poly.R | 4 - R/pp.subsample.R | 13 ++-- R/print.loess.boot.R |only R/pseudo.absence.R | 27 ++++---- R/raster.entropy.R | 6 - R/raster.vol.R |only R/sample.line.R |only R/separability.R | 36 +++++------ R/sp.na.omit.R | 3 R/stratified.random.R | 3 R/summary.loess.boot.R |only R/tpi.R |only R/trend.line.R | 24 +++---- R/wt.centroids.R | 5 - R/zonal.stats.R | 12 +-- inst/CITATION | 4 - inst/NEWS | 10 +++ man/bearing.distance.Rd |only man/breeding.density.Rd | 2 man/concordance.Rd |only man/conf.interval.Rd |only man/correlogram.Rd | 2 man/csi.Rd | 2 man/download.daymet.Rd | 2 man/download.hansen.Rd | 2 man/download.prism.Rd | 2 man/group.pdf.Rd | 84 ++++++++++++------------- man/hexagons.Rd | 76 +++++++++++------------ man/idw.smoothing.Rd | 2 man/kl.divergence.Rd | 74 +++++++++++----------- man/land.metrics.Rd | 11 +-- man/local.min.max.Rd | 2 man/loess.boot.Rd |only man/loess.ci.Rd |only man/logistic.regression.Rd | 10 +-- man/moments.Rd | 2 man/nni.Rd | 2 man/o.ring.Rd | 14 ++-- man/optimal.k.Rd | 2 man/outliers.Rd | 2 man/parea.sample.Rd | 2 man/plot.loess.boot.Rd |only man/point.in.poly.Rd | 104 ++++++++++++++++---------------- man/pp.subsample.Rd | 2 man/print.loess.boot.Rd |only man/pseudo.absence.Rd | 2 man/raster.entropy.Rd | 102 +++++++++++++++---------------- man/raster.vol.Rd |only man/sample.line.Rd |only man/separability.Rd | 2 man/sp.na.omit.Rd | 90 +++++++++++++-------------- man/stratified.random.Rd | 2 man/summary.loess.boot.Rd |only man/tpi.Rd |only man/trend.line.Rd | 2 man/wt.centroid.Rd | 86 +++++++++++++------------- man/zonal.stats.Rd | 132 ++++++++++++++++++++-------------------- 85 files changed, 743 insertions(+), 682 deletions(-)
Title: Sparse Bayesian Models for Regression, Subgroup Analysis, and
Panel Data
Description: Sparse modeling provides a mean selecting a small number of non-zero effects from a large possible number of candidate effects. This package includes a suite of methods for sparse modeling: estimation via EM or MCMC, approximate confidence intervals with nominal coverage, and diagnostic and summary plots. Beyond regression analyses, applications include subgroup analysis, particularly for conjoint experiments, and panel data. Future versions will include extensions to limited dependent variables, models with truncated outcomes, and propensity score and instrumental variable analysis.
Author: Marc Ratkovic and Dustin Tingley
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Diff between sparsereg versions 1.0 dated 2015-07-21 and 1.1 dated 2015-10-01
sparsereg-1.0/sparsereg/R/type2tobit.R |only sparsereg-1.0/sparsereg/man/type2tobit.Rd |only sparsereg-1.0/sparsereg/man/volcanoplot.Rd |only sparsereg-1.1/sparsereg/ChangeLog |only sparsereg-1.1/sparsereg/DESCRIPTION | 12 - sparsereg-1.1/sparsereg/MD5 | 29 +- sparsereg-1.1/sparsereg/NAMESPACE | 7 sparsereg-1.1/sparsereg/R/subgroup.R | 248 +++++++++++++++++++---- sparsereg-1.1/sparsereg/R/updateREs.R | 16 + sparsereg-1.1/sparsereg/R/utility.R | 2 sparsereg-1.1/sparsereg/man/difference.Rd | 2 sparsereg-1.1/sparsereg/man/plot.sparsereg.Rd | 6 sparsereg-1.1/sparsereg/man/print.sparsereg.Rd | 5 sparsereg-1.1/sparsereg/man/sparsereg-package.Rd | 2 sparsereg-1.1/sparsereg/man/sparsereg.Rd | 52 ++-- sparsereg-1.1/sparsereg/man/summary.sparsereg.Rd | 4 sparsereg-1.1/sparsereg/man/violinplot.Rd |only sparsereg-1.1/sparsereg/src/subgroup.cpp | 15 - 18 files changed, 288 insertions(+), 112 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
In addition, various risk estimation methods are included.
Note that the package 'sdcMicroGUI' includes a graphical user interface for various methods
in this package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 4.5.0 dated 2015-05-04 and 4.6.0 dated 2015-10-01
sdcMicro-4.5.0/sdcMicro/R/localSupp2.R |only sdcMicro-4.5.0/sdcMicro/R/localSupp2Wrapper.R |only sdcMicro-4.5.0/sdcMicro/R/plot.localSuppression.R |only sdcMicro-4.5.0/sdcMicro/R/print.freqCalc.R |only sdcMicro-4.5.0/sdcMicro/R/print.indivRisk.R |only sdcMicro-4.5.0/sdcMicro/R/print.localSuppression.R |only sdcMicro-4.5.0/sdcMicro/R/print.micro.R |only sdcMicro-4.5.0/sdcMicro/R/summary.freqCalc.R |only sdcMicro-4.5.0/sdcMicro/R/summary.micro.R |only sdcMicro-4.5.0/sdcMicro/R/summary.pram.r |only sdcMicro-4.5.0/sdcMicro/R/swappNum.R |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-html.brew |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-latex.brew |only sdcMicro-4.5.0/sdcMicro/inst/templates/template-report-text.brew |only sdcMicro-4.5.0/sdcMicro/man/extractManipData-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/groupVars-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/localSupp2.Rd |only sdcMicro-4.5.0/sdcMicro/man/localSupp2Wrapper.Rd |only sdcMicro-4.5.0/sdcMicro/man/removeDirectID-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/renameVars-methods.Rd |only sdcMicro-4.5.0/sdcMicro/man/sdcMicro-deprecated.Rd |only sdcMicro-4.5.0/sdcMicro/man/swappNum-deprecated.Rd |only sdcMicro-4.5.0/sdcMicro/man/swappNum.Rd |only sdcMicro-4.5.0/sdcMicro/man/varToFactor-methods.Rd |only sdcMicro-4.6.0/sdcMicro/DESCRIPTION | 47 sdcMicro-4.6.0/sdcMicro/MD5 | 238 - sdcMicro-4.6.0/sdcMicro/NAMESPACE | 236 - sdcMicro-4.6.0/sdcMicro/R/0classes.r | 304 + sdcMicro-4.6.0/sdcMicro/R/GUIfunctions.R | 319 + sdcMicro-4.6.0/sdcMicro/R/LLmodGlobalRisk.R | 371 - sdcMicro-4.6.0/sdcMicro/R/LocalRecProg.R | 261 - sdcMicro-4.6.0/sdcMicro/R/RcppExports.R |only sdcMicro-4.6.0/sdcMicro/R/addNoise.r | 245 - sdcMicro-4.6.0/sdcMicro/R/aux_functions.r | 523 +- sdcMicro-4.6.0/sdcMicro/R/dRisk.R | 114 sdcMicro-4.6.0/sdcMicro/R/dRiskRMD.R | 237 - sdcMicro-4.6.0/sdcMicro/R/dUtility.R | 161 sdcMicro-4.6.0/sdcMicro/R/dataGen.r | 125 sdcMicro-4.6.0/sdcMicro/R/dataSets.R |only sdcMicro-4.6.0/sdcMicro/R/freqCalc.r | 968 ++--- sdcMicro-4.6.0/sdcMicro/R/globalRecode.R | 120 sdcMicro-4.6.0/sdcMicro/R/indivRisk.R | 246 - sdcMicro-4.6.0/sdcMicro/R/localSupp.R | 144 sdcMicro-4.6.0/sdcMicro/R/localSuppression.R | 814 +++- sdcMicro-4.6.0/sdcMicro/R/maG.R | 478 +- sdcMicro-4.6.0/sdcMicro/R/mafast.R | 234 - sdcMicro-4.6.0/sdcMicro/R/mdav.R | 53 sdcMicro-4.6.0/sdcMicro/R/measure_risk.R | 723 ++- sdcMicro-4.6.0/sdcMicro/R/methods.r | 224 - sdcMicro-4.6.0/sdcMicro/R/microaggregation.R | 1883 +++++----- sdcMicro-4.6.0/sdcMicro/R/modRisk.R |only sdcMicro-4.6.0/sdcMicro/R/plotFunctions.R |only sdcMicro-4.6.0/sdcMicro/R/plotMicro.R | 271 - sdcMicro-4.6.0/sdcMicro/R/pram.R | 749 ++- sdcMicro-4.6.0/sdcMicro/R/printFunctions.R | 467 +- sdcMicro-4.6.0/sdcMicro/R/rankSwap.R | 194 - sdcMicro-4.6.0/sdcMicro/R/report.R | 811 +--- sdcMicro-4.6.0/sdcMicro/R/sdcMicro-package.R |only sdcMicro-4.6.0/sdcMicro/R/show_sdcMicroObj.R | 57 sdcMicro-4.6.0/sdcMicro/R/shuffle.R | 721 +-- sdcMicro-4.6.0/sdcMicro/R/suda2.R | 220 - sdcMicro-4.6.0/sdcMicro/R/timeEstimation.R | 82 sdcMicro-4.6.0/sdcMicro/R/topBotCoding.R | 171 sdcMicro-4.6.0/sdcMicro/R/valTable.R | 246 - sdcMicro-4.6.0/sdcMicro/R/zzz.R | 20 sdcMicro-4.6.0/sdcMicro/build/vignette.rds |binary sdcMicro-4.6.0/sdcMicro/data/CASCrefmicrodata.rda |binary sdcMicro-4.6.0/sdcMicro/data/EIA.rda |binary sdcMicro-4.6.0/sdcMicro/data/Tarragona.rda |binary sdcMicro-4.6.0/sdcMicro/data/casc1.rda |binary sdcMicro-4.6.0/sdcMicro/data/francdat.rda |binary sdcMicro-4.6.0/sdcMicro/data/free1.rda |binary sdcMicro-4.6.0/sdcMicro/data/microData.rda |binary sdcMicro-4.6.0/sdcMicro/data/testdata.RData |binary sdcMicro-4.6.0/sdcMicro/data/testdata2.RData |binary sdcMicro-4.6.0/sdcMicro/inst/CITATION |only sdcMicro-4.6.0/sdcMicro/inst/doc/sdc_guidelines.R | 208 - sdcMicro-4.6.0/sdcMicro/inst/doc/sdc_guidelines.pdf |binary sdcMicro-4.6.0/sdcMicro/inst/templates/report-template.rmd |only sdcMicro-4.6.0/sdcMicro/inst/templates/report.css | 34 sdcMicro-4.6.0/sdcMicro/man/CASCrefmicrodata.Rd | 82 sdcMicro-4.6.0/sdcMicro/man/EIA.Rd | 203 - sdcMicro-4.6.0/sdcMicro/man/LLmodGlobalRisk.Rd | 127 sdcMicro-4.6.0/sdcMicro/man/LocalRecProg.Rd | 193 - sdcMicro-4.6.0/sdcMicro/man/Tarragona.Rd | 81 sdcMicro-4.6.0/sdcMicro/man/addNoise.Rd | 236 - sdcMicro-4.6.0/sdcMicro/man/calcRisks.Rd | 42 sdcMicro-4.6.0/sdcMicro/man/casc1.Rd | 38 sdcMicro-4.6.0/sdcMicro/man/dRisk.Rd | 133 sdcMicro-4.6.0/sdcMicro/man/dRiskRMD.Rd | 166 sdcMicro-4.6.0/sdcMicro/man/dUtility.Rd | 165 sdcMicro-4.6.0/sdcMicro/man/dataGen.Rd | 132 sdcMicro-4.6.0/sdcMicro/man/extractManipData.Rd |only sdcMicro-4.6.0/sdcMicro/man/francdat.Rd | 67 sdcMicro-4.6.0/sdcMicro/man/free1.Rd | 55 sdcMicro-4.6.0/sdcMicro/man/freqCalc.Rd | 161 sdcMicro-4.6.0/sdcMicro/man/generateStrata.Rd | 65 sdcMicro-4.6.0/sdcMicro/man/globalRecode.Rd | 133 sdcMicro-4.6.0/sdcMicro/man/groupVars.Rd |only sdcMicro-4.6.0/sdcMicro/man/indivRisk.Rd | 87 sdcMicro-4.6.0/sdcMicro/man/localSupp.Rd | 153 sdcMicro-4.6.0/sdcMicro/man/localSuppression.Rd | 194 - sdcMicro-4.6.0/sdcMicro/man/mafast.Rd | 166 sdcMicro-4.6.0/sdcMicro/man/measure_risk.Rd | 254 - sdcMicro-4.6.0/sdcMicro/man/microData.Rd | 40 sdcMicro-4.6.0/sdcMicro/man/microaggrGower.Rd | 161 sdcMicro-4.6.0/sdcMicro/man/microaggregation.Rd | 353 - sdcMicro-4.6.0/sdcMicro/man/modRisk.Rd |only sdcMicro-4.6.0/sdcMicro/man/plot.localSuppression.Rd | 75 sdcMicro-4.6.0/sdcMicro/man/plot.sdcMicroObj.Rd |only sdcMicro-4.6.0/sdcMicro/man/plotMicro.Rd | 80 sdcMicro-4.6.0/sdcMicro/man/pram.Rd | 194 - sdcMicro-4.6.0/sdcMicro/man/print.freqCalc.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/print.indivRisk.Rd | 68 sdcMicro-4.6.0/sdcMicro/man/print.localSuppression.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/print.micro.Rd | 58 sdcMicro-4.6.0/sdcMicro/man/print.modrisk.Rd |only sdcMicro-4.6.0/sdcMicro/man/print.pram.Rd |only sdcMicro-4.6.0/sdcMicro/man/print.sdcMicroObj.Rd | 75 sdcMicro-4.6.0/sdcMicro/man/print.suda2.Rd | 60 sdcMicro-4.6.0/sdcMicro/man/rankSwap.Rd | 220 - sdcMicro-4.6.0/sdcMicro/man/removeDirectID.Rd |only sdcMicro-4.6.0/sdcMicro/man/renameVars.Rd |only sdcMicro-4.6.0/sdcMicro/man/report.Rd | 66 sdcMicro-4.6.0/sdcMicro/man/sdcMicro-package.Rd | 517 +- sdcMicro-4.6.0/sdcMicro/man/sdcMicroObj-class.Rd | 211 - sdcMicro-4.6.0/sdcMicro/man/shuffle.Rd | 248 - sdcMicro-4.6.0/sdcMicro/man/suda2.Rd | 191 - sdcMicro-4.6.0/sdcMicro/man/summary.freqCalc.Rd | 87 sdcMicro-4.6.0/sdcMicro/man/summary.micro.Rd | 110 sdcMicro-4.6.0/sdcMicro/man/summary.pram.Rd | 80 sdcMicro-4.6.0/sdcMicro/man/testdata.Rd | 119 sdcMicro-4.6.0/sdcMicro/man/topBotCoding.Rd | 111 sdcMicro-4.6.0/sdcMicro/man/valTable.Rd | 130 sdcMicro-4.6.0/sdcMicro/man/varToFactor.Rd |only sdcMicro-4.6.0/sdcMicro/src/RcppExports.cpp |only sdcMicro-4.6.0/sdcMicro/src/calcSuppInds.cpp |only sdcMicro-4.6.0/sdcMicro/tests/globalRecoding_test.R | 18 sdcMicro-4.6.0/sdcMicro/tests/microaggregation_test.R | 28 sdcMicro-4.6.0/sdcMicro/tests/reporting_test.R | 41 sdcMicro-4.6.0/sdcMicro/tests/testhat.R |only sdcMicro-4.6.0/sdcMicro/tests/testthat |only 142 files changed, 11288 insertions(+), 8425 deletions(-)
Title: Stratified Analysis with Nonparametric Covariable Adjustment
Description: There are several functions to implement the method for analysis in a randomized clinical trial with strata with following key features. A stratified Mann-Whitney estimator addresses the comparison between two randomized groups for a strictly ordinal response variable. The multivariate vector of such stratified Mann-Whitney estimators for multivariate response variables can be considered for one or more response variables such as in repeated measurements and these can have missing completely at random (MCAR) data. Non-parametric covariance adjustment is also considered with the minimal assumption of randomization. The p-value for hypothesis test and confidence interval are provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between sanon versions 1.4 dated 2014-09-04 and 1.5 dated 2015-10-01
DESCRIPTION | 12 +-- MD5 | 49 +++++++------- NAMESPACE | 32 ++++++++- R/sanon.r | 29 +++++++- data/cpain.rda |binary data/heartburn.rda |binary data/resp.rda |binary data/sebor.rda |binary data/skin.rda |binary inst |only man/catecovar.Rd | 18 ++--- man/coef.sanon.Rd | 20 ++--- man/confint.sanon.Rd | 39 +++-------- man/contrast.Rd | 55 ++++++--------- man/covar.Rd | 10 +- man/cpain.Rd | 30 +++----- man/grp.Rd | 13 +-- man/heartburn.Rd | 44 +++++------- man/resp.Rd | 53 +++++---------- man/sanon-package.Rd | 17 ++-- man/sanon.Rd | 176 ++++++++++++++++++--------------------------------- man/sebor.Rd | 47 +++++-------- man/skin.Rd | 43 ++++-------- man/strt.Rd | 11 +-- man/summary.sanon.Rd | 27 +++---- man/vcov.sanon.Rd | 17 ++-- 26 files changed, 331 insertions(+), 411 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 1.5.2 dated 2015-02-04 and 1.5.3 dated 2015-10-01
DESCRIPTION | 13 +- MD5 | 26 ++-- NAMESPACE | 4 NEWS | 6 + R/branches.R | 3 R/lib.R | 45 ++++++- R/node.labs.R | 2 R/prp.R | 6 - inst/doc/prp.pdf |binary inst/slowtests/make.bat | 2 inst/slowtests/test.prp.R | 168 +++++++++++++++++----------- inst/slowtests/test.prp.Rout.save | 223 ++++++++++++++++++++++---------------- inst/slowtests/user-manual-figs.R | 20 +++ inst/slowtests/webpage-figs.R | 4 14 files changed, 334 insertions(+), 188 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 1.0-9102 dated 2014-12-11 and 3.3.1 dated 2015-10-01
DESCRIPTION | 24 - MD5 | 242 +++++++------- NAMESPACE | 2 R/phreeqc.R | 2 data/databases.rda |binary data/examples.rda |binary man/Amm.dat.Rd | 19 - man/ex1.Rd | 33 + man/ex10.Rd | 45 +- man/ex11.Rd | 43 +- man/ex12.Rd | 59 +-- man/ex13.Rd | 42 +- man/ex14.Rd | 52 +-- man/ex15.Rd | 47 +- man/ex15.dat.Rd | 16 man/ex16.Rd | 53 +-- man/ex17.Rd | 52 +-- man/ex18.Rd | 72 ++-- man/ex19.Rd | 38 +- man/ex2.Rd | 29 - man/ex20.Rd | 57 +-- man/ex21.Rd | 52 +-- man/ex22.Rd | 46 +- man/ex3.Rd | 51 +-- man/ex4.Rd | 54 +-- man/ex5.Rd | 41 +- man/ex6.Rd | 36 +- man/ex7.Rd | 61 +-- man/ex8.Rd | 38 +- man/ex9.Rd | 62 +-- man/iso.dat.Rd | 18 - man/llnl.dat.Rd | 17 - man/minteq.dat.Rd | 14 man/minteq.v4.dat.Rd | 14 man/phrAccumulateLine.Rd | 12 man/phrClearAccumulatedLines.Rd | 11 man/phrGetAccumulatedLines.Rd | 6 man/phrGetComponentList.Rd | 5 man/phrGetDumpFileName.Rd | 17 - man/phrGetDumpFileOn.Rd | 12 man/phrGetDumpStrings.Rd | 16 man/phrGetDumpStringsOn.Rd | 12 man/phrGetErrorFileName.Rd | 18 - man/phrGetErrorFileOn.Rd | 12 man/phrGetErrorStrings.Rd | 28 - man/phrGetErrorStringsOn.Rd | 12 man/phrGetLogFileName.Rd | 15 man/phrGetLogFileOn.Rd | 12 man/phrGetLogStrings.Rd | 12 man/phrGetLogStringsOn.Rd | 12 man/phrGetOutputFileName.Rd | 15 man/phrGetOutputFileOn.Rd | 12 man/phrGetOutputStrings.Rd | 12 man/phrGetOutputStringsOn.Rd | 12 man/phrGetSelectedOutput.Rd | 30 - man/phrGetSelectedOutputFileName.Rd | 15 man/phrGetWarningStrings.Rd | 14 man/phrLoadDatabase.Rd | 7 man/phrLoadDatabaseString.Rd | 9 man/phrRunAccumulated.Rd | 27 - man/phrRunFile.Rd | 6 man/phrRunString.Rd | 18 - man/phrSetDumpFileName.Rd | 19 - man/phrSetDumpFileOn.Rd | 20 - man/phrSetDumpStringsOn.Rd | 22 - man/phrSetErrorFileName.Rd | 17 - man/phrSetErrorFileOn.Rd | 23 - man/phrSetErrorStringsOn.Rd | 25 - man/phrSetLogFileName.Rd | 21 - man/phrSetLogFileOn.Rd | 24 - man/phrSetLogStringsOn.Rd | 22 - man/phrSetOutputFileName.Rd | 20 - man/phrSetOutputFileOn.Rd | 22 - man/phrSetOutputStringsOn.Rd | 22 - man/phrSetSelectedOutputFileName.Rd | 20 - man/phrSetSelectedOutputFileOn.Rd | 22 - man/phreeqc-package.Rd | 26 - man/phreeqc.dat.Rd | 17 - man/pitzer.dat.Rd | 17 - man/sit.dat.Rd | 17 - man/wateq4f.dat.Rd | 15 src/IPhreeqc.cpp | 118 +++++-- src/IPhreeqc.h | 30 + src/IPhreeqcLib.cpp | 16 src/IPhreeqchpp.h | 9 src/phreeqcpp/ChartHandler.cpp | 2 src/phreeqcpp/ChartObject.cpp | 20 - src/phreeqcpp/GasPhase.cpp | 18 - src/phreeqcpp/NameDouble.cpp | 1 src/phreeqcpp/PBasic.cpp | 326 ++++++++++++++++++- src/phreeqcpp/PBasic.h | 4 src/phreeqcpp/PPassemblage.cpp | 1 src/phreeqcpp/Phreeqc.cpp | 6 src/phreeqcpp/Phreeqc.h | 43 ++ src/phreeqcpp/Solution.cpp | 61 +++ src/phreeqcpp/Solution.h | 2 src/phreeqcpp/StorageBinList.cpp | 29 + src/phreeqcpp/SurfaceCharge.cpp | 44 ++ src/phreeqcpp/SurfaceCharge.h | 2 src/phreeqcpp/basicsubs.cpp | 444 +++++++++++++++++++++++++- src/phreeqcpp/cvdense.cpp | 5 src/phreeqcpp/cvode.cpp | 9 src/phreeqcpp/dumper.cpp | 4 src/phreeqcpp/dw.cpp | 3 src/phreeqcpp/gases.cpp | 23 + src/phreeqcpp/integrate.cpp | 9 src/phreeqcpp/inverse.cpp | 19 - src/phreeqcpp/isotopes.cpp | 22 + src/phreeqcpp/kinetics.cpp | 4 src/phreeqcpp/mainsubs.cpp | 53 +++ src/phreeqcpp/model.cpp | 170 ++++++++-- src/phreeqcpp/pitzer.cpp | 604 +++++++++++++++++++++++++++++------- src/phreeqcpp/pitzer_structures.cpp | 15 src/phreeqcpp/prep.cpp | 39 +- src/phreeqcpp/print.cpp | 41 ++ src/phreeqcpp/read.cpp | 15 src/phreeqcpp/sit.cpp | 387 +++++++++++++++++++++-- src/phreeqcpp/step.cpp | 4 src/phreeqcpp/structures.cpp | 48 +- src/phreeqcpp/tally.cpp | 8 src/phreeqcpp/tidy.cpp | 67 +++ src/phreeqcpp/utilities.cpp | 5 122 files changed, 3494 insertions(+), 1447 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J. Owens [ctb], Christophe Dutang [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.1.9 dated 2015-07-10 and 1.1.10 dated 2015-10-01
ChangeLog | 4 DESCRIPTION | 10 MD5 | 34 NEWS | 10 R/3_demographicFunctions.R | 4 R/5_actuarialFunctions.R | 904 ++++++++------ R/8_mdtFunctions.R | 8 README.md | 3 build/vignette.rds |binary data/demoGermany.rda |only inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary inst/doc/introToLifecontingencies.Rmd | 2 inst/doc/introToLifecontingencies.pdf |binary man/demoGermany.Rd |only man/demoIta.Rd | 2 man/lifecontingencies-package.Rd | 4 vignettes/introToLifecontingencies.Rmd | 2 vignettes/introToLifecontingencies_files |only 18 files changed, 585 insertions(+), 402 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of
CppJieba
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>
Diff between jiebaR versions 0.5 dated 2015-04-29 and 0.6 dated 2015-10-01
DESCRIPTION | 10 - MD5 | 102 +++++++++------ NAMESPACE | 5 NEWS | 10 + R/RcppExports.R | 24 ++- R/filter.R | 41 +++++- R/jiebar.R | 48 +++++-- R/print.R | 11 + R/quick.R | 2 R/segment.R | 21 ++- R/tagger.R | 17 +- R/words_freq.R |only R/zzz.R | 3 README.md | 3 build/vignette.rds |binary inst/include/jiebaRAPI.h |only inst/include/lib/DictTrie.hpp | 7 - inst/include/lib/HMMSegment.hpp | 2 inst/include/segtype.hpp | 253 ++++++++++++++++++++------------------ man/DICTPATH.Rd | 2 man/distance.Rd | 2 man/edit_dict.Rd | 2 man/filecoding.Rd | 2 man/filter_segment.Rd | 6 man/freq.Rd |only man/jiebaR.Rd | 2 man/keywords.Rd | 2 man/less-than-equals-.keywords.Rd | 2 man/less-than-equals-.qseg.Rd | 2 man/less-than-equals-.segment.Rd | 2 man/less-than-equals-.simhash.Rd | 2 man/less-than-equals-.tagger.Rd | 2 man/print.hmmseg.Rd | 5 man/segment.Rd | 2 man/set_qsegmodel.Rd | 2 man/show_dictpath.Rd | 2 man/simhash.Rd | 2 man/tagging.Rd | 2 man/worker.Rd | 8 - src/RcppExports.cpp | 146 ++++++++++++--------- src/detect.cpp | 3 src/init.c |only src/segtype.cpp | 99 ++++++++++---- src/word_freq.cpp |only tests/testthat/CPP_API |only tests/testthat/C_API |only tests/testthat/test-api.R |only tests/testthat/test-cut.R | 39 +++++ 48 files changed, 571 insertions(+), 326 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
'Springer', 2009.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.6.0 dated 2015-03-31 and 0.7.0 dated 2015-10-01
DESCRIPTION | 17 +- MD5 | 58 ++++--- NAMESPACE | 37 ++++ R/confounders.R | 96 +++++++++++- R/confounders.emm.R | 119 +++++++++++++-- R/confounders.limit.R | 27 +++ R/confounders.poly.R | 114 +++++++++++++-- R/mbias.R |only R/misclassification.R | 79 +++++++++- R/multidimBias.R | 62 ++++++++ R/plot.mbias.R |only R/print.mbias.R |only R/probsens.R | 311 +++++++++++++++++++++++++++++++++++------ R/probsens.conf.R | 245 ++++++++++++++++++++++++++++---- R/probsens.irr.R |only R/probsens.irr.conf.R |only R/probsens.sel.R | 101 +++++++++++-- R/selection.R | 40 +++++ README.md | 105 +++++++++++++ man/confounders.Rd | 128 +++++++++------- man/confounders.emm.Rd | 161 +++++++++++---------- man/confounders.limit.Rd | 54 ++++--- man/confounders.poly.Rd | 170 +++++++++++----------- man/mbias.Rd |only man/misclassification.Rd | 121 ++++++++------- man/multidimBias.Rd | 128 +++++++++------- man/plot.mbias.Rd |only man/print.mbias.Rd |only man/probsens.Rd | 145 ++++++++++--------- man/probsens.conf.Rd | 114 ++++++++------- man/probsens.irr.Rd |only man/probsens.irr.conf.Rd |only man/probsens.sel.Rd | 88 ++++++----- man/selection.Rd | 74 +++++---- tests/testthat/test-probsens.R | 154 ++++++++++++++++++++ 35 files changed, 2064 insertions(+), 684 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.2 dated 2015-09-01 and 0.0.3 dated 2015-10-01
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 1 NEWS | 7 ++ R/epifit-package.R | 7 +- R/epifit.R | 75 ++++++++++++++------- R/modules.R | 172 +++++++++++++++++++++++++++++++------------------- R/pytable.R |only man/epifit-package.Rd | 7 +- man/epifit.Rd | 42 +++++++++--- man/pytable.Rd |only 11 files changed, 223 insertions(+), 114 deletions(-)
Title: Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution
Description: Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.
Author: Mathias Borritz Milfeldt [aut, cre]
Maintainer: Mathias Borritz Milfeldt <mathias@milfeldt.dk>
Diff between epandist versions 1.0.0 dated 2015-09-27 and 1.0.1 dated 2015-10-01
DESCRIPTION | 6 ++-- MD5 | 34 +++++++++++++------------- R/cepan.R | 2 - R/depan.R | 2 - R/evepan.R | 4 +-- R/pepan.R | 2 - R/qepan.R | 2 - R/repan.R | 2 - inst/doc/Vignette_epandist.R | 15 ++++++++++- inst/doc/Vignette_epandist.Rmd | 44 +++++++++++++++++++++++++++++++--- inst/doc/Vignette_epandist.html | 51 +++++++++++++++++++++++++++++++--------- man/cepan.Rd | 2 - man/depan.Rd | 2 - man/evepan.Rd | 4 +-- man/pepan.Rd | 2 - man/qepan.Rd | 2 - man/repan.Rd | 2 - vignettes/Vignette_epandist.Rmd | 44 +++++++++++++++++++++++++++++++--- 18 files changed, 168 insertions(+), 54 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.2 dated 2015-09-17 and 2.2.3 dated 2015-10-01
DESCRIPTION | 8 MD5 | 18 - NEWS | 9 inst/CITATION | 37 +- inst/doc/dbmss.R | 2 inst/doc/dbmss.Rnw | 18 - inst/doc/dbmss.pdf |binary man/dbmss-package.Rd | 4 vignettes/dbmss.Rnw | 18 - vignettes/dbmss.bib | 816 +++++++++++++++++++++++++-------------------------- 10 files changed, 474 insertions(+), 456 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: The R package clere implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma DB et al. - 2013).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1 dated 2014-02-21 and 1.1.1 dated 2015-10-01
clere-1.1.1/clere/DESCRIPTION | 22 ++-- clere-1.1.1/clere/MD5 | 46 ++++++---- clere-1.1.1/clere/NAMESPACE | 5 + clere-1.1.1/clere/R/Clere.R | 91 ------------------- clere-1.1.1/clere/R/fitClere.R |only clere-1.1.1/clere/R/fitPacs.R |only clere-1.1.1/clere/build |only clere-1.1.1/clere/data |only clere-1.1.1/clere/inst |only clere-1.1.1/clere/man/Clere-class.Rd | 138 ++++++++++++++---------------- clere-1.1.1/clere/man/Pacs-class.Rd |only clere-1.1.1/clere/man/algoComp.Rd |only clere-1.1.1/clere/man/clere-package.Rd | 35 +++---- clere-1.1.1/clere/man/clusters-methods.Rd | 18 +-- clere-1.1.1/clere/man/fitClere.Rd |only clere-1.1.1/clere/man/fitPacs.Rd |only clere-1.1.1/clere/man/is.clere.Rd | 16 +-- clere-1.1.1/clere/man/numExpRealData.Rd |only clere-1.1.1/clere/man/numExpSimData.Rd |only clere-1.1.1/clere/man/plot-methods.Rd | 16 +-- clere-1.1.1/clere/man/predict-methods.Rd | 18 +-- clere-1.1.1/clere/man/summary-methods.Rd | 16 +-- clere-1.1.1/clere/src/Model.cpp | 26 +++-- clere-1.1.1/clere/src/clere.cpp | 8 - clere-1.1.1/clere/src/pacs.cpp |only clere-1.1.1/clere/vignettes |only clere-1.1/clere/R/fit.clere.R |only clere-1.1/clere/man/fit.clere.Rd |only clere-1.1/clere/man/ggPlot-methods.Rd |only 29 files changed, 190 insertions(+), 265 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors with or without shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The cone information criterion (CIC) may be used to select the best combination of variables and shapes. This package depends on the R package coneproj.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between cgam versions 1.2 dated 2014-09-10 and 1.3 dated 2015-10-01
DESCRIPTION | 13 +-- MD5 | 10 +- NAMESPACE | 5 + R/cgam.R | 193 +++++++++++++++++++++++++++++++++++++++++++------------ man/cgam.Rd | 4 - man/plotpersp.Rd | 26 +++++-- 6 files changed, 189 insertions(+), 62 deletions(-)
Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between SpatialTools versions 0.5.8 dated 2014-07-02 and 1.0.0 dated 2015-10-01
SpatialTools-0.5.8/SpatialTools/R/old_code.R |only SpatialTools-0.5.8/SpatialTools/man/mspe.uk.Rd |only SpatialTools-0.5.8/SpatialTools/man/pweights.uk.Rd |only SpatialTools-1.0.0/SpatialTools/DESCRIPTION | 10 - SpatialTools-1.0.0/SpatialTools/MD5 | 25 +- SpatialTools-1.0.0/SpatialTools/NAMESPACE | 10 - SpatialTools-1.0.0/SpatialTools/NEWS | 2 SpatialTools-1.0.0/SpatialTools/R/arg_check.R | 110 ----------- SpatialTools-1.0.0/SpatialTools/R/contour_tools.R | 4 SpatialTools-1.0.0/SpatialTools/R/cov.R | 4 SpatialTools-1.0.0/SpatialTools/R/generate_norm.R | 2 SpatialTools-1.0.0/SpatialTools/R/krige_tools.R | 194 +-------------------- SpatialTools-1.0.0/SpatialTools/man/krige.ok.Rd | 11 - SpatialTools-1.0.0/SpatialTools/man/krige.sk.Rd | 10 - SpatialTools-1.0.0/SpatialTools/man/krige.uk.Rd | 10 - 15 files changed, 61 insertions(+), 331 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.4.1 dated 2014-09-07 and 1.5 dated 2015-10-01
Rsomoclu-1.4.1/Rsomoclu/src/somocluWrap.h |only Rsomoclu-1.4.1/Rsomoclu/src/trainOneEpoch.cpp |only Rsomoclu-1.5/Rsomoclu/DESCRIPTION | 12 - Rsomoclu-1.5/Rsomoclu/MD5 | 32 +- Rsomoclu-1.5/Rsomoclu/R/Rsomoclu.R | 19 + Rsomoclu-1.5/Rsomoclu/configure |only Rsomoclu-1.5/Rsomoclu/data/rgbs.txt.gz |binary Rsomoclu-1.5/Rsomoclu/man/Rsomoclu.train.Rd | 46 ++-- Rsomoclu-1.5/Rsomoclu/src/Makefile.in |only Rsomoclu-1.5/Rsomoclu/src/Makefile.root.in |only Rsomoclu-1.5/Rsomoclu/src/Rsomoclu.cpp | 238 +++++++-------------- Rsomoclu-1.5/Rsomoclu/src/config.h.in |only Rsomoclu-1.5/Rsomoclu/src/configure |only Rsomoclu-1.5/Rsomoclu/src/denseCpuKernels.cpp | 88 ++++--- Rsomoclu-1.5/Rsomoclu/src/denseGpuKernels.cu |only Rsomoclu-1.5/Rsomoclu/src/install-sh |only Rsomoclu-1.5/Rsomoclu/src/mapDistanceFunctions.cpp | 62 +++-- Rsomoclu-1.5/Rsomoclu/src/somoclu.h | 152 +++++++------ Rsomoclu-1.5/Rsomoclu/src/sparseCpuKernels.cpp | 101 ++++---- Rsomoclu-1.5/Rsomoclu/src/training.cpp |only Rsomoclu-1.5/Rsomoclu/src/uMatrix.cpp | 35 +-- Rsomoclu-1.5/Rsomoclu/tests/R_interface_test.R | 8 22 files changed, 398 insertions(+), 395 deletions(-)
Title: Rcmdr Evidence Based Medicine Plug-in Package
Description: Rcmdr plug-in GUI extension for Evidence Based Medicine medical indicators calculations (Sensitivity, specificity, absolute risk reduction, relative risk, ...).
Author: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Maintainer: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Diff between RcmdrPlugin.EBM versions 1.0-8 dated 2014-09-08 and 1.0-10 dated 2015-10-01
DESCRIPTION | 12 - MD5 | 8 - NAMESPACE | 2 R/CrossTab.R | 429 ++++++++++++++++++++++++++++++----------------------------- inst/CHANGES | 4 5 files changed, 240 insertions(+), 215 deletions(-)
More information about RcmdrPlugin.EBM at CRAN
Permanent link
Title: A Tool for Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.4 dated 2015-08-04 and 0.4.1 dated 2015-10-01
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 4 ++-- R/manage_expansion_sim.R | 12 +----------- R/range_raster.R | 3 +-- build/vignette.rds |binary data/cabrera.rda |binary data/landscape_change.rda |binary data/mc_df.rda |binary data/occ.landscape.rda |binary data/occ.landscape2.rda |binary data/param1.rda |binary data/rg_exp.rda |binary data/rland.rda |binary inst/doc/MetaLandSim.pdf |binary inst/logo/logo.gif |binary inst/logo/logo2.gif |binary man/MetaLandSim-package.Rd | 4 ++-- 18 files changed, 27 insertions(+), 38 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-4 dated 2015-09-17 and 0.4-0 dated 2015-10-01
DESCRIPTION | 8 +-- MD5 | 25 ++++++----- NAMESPACE | 3 - R/ICP.R | 64 +++++++++++++++++------------- R/getpval.R | 13 ++++-- R/getpvalClassif.R | 29 +++++++------ R/hiddenICP.R | 34 +++++++++++++-- R/plot.InvariantCausalPrediction.R | 2 R/print.InvariantCausalPrediction.R | 31 +++++++------- R/print.hiddenInvariantCausalPrediction.R |only R/pvalfunc.R | 19 +++++++- R/summary.InvariantCausalPrediction.R | 25 +---------- man/ICP.Rd | 61 +++++++++++++++------------- man/hiddenICP.Rd | 45 +++++++++++---------- 14 files changed, 206 insertions(+), 153 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for binary classification models using weight-of-evidence (WOE) and information value (IV). In order to make the package as efficient as possible, aggregations are done in data.table and creation of WOE vectors can be distributed across multiple cores. The package also supports exploration for uplift models (NWOE and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.3 dated 2015-09-16 and 0.0.4 dated 2015-10-01
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- R/CheckInputs.R | 2 + R/Information.R | 39 ++++++++++++++++++++++++------------- R/create_infotables.R | 7 +++++- R/plot_infotables.R | 21 ++++++++++++++----- build/vignette.rds |binary inst/doc/Information-vignette.Rmd | 2 - inst/doc/Information-vignette.html | 4 +-- man/Information.Rd | 37 +++++++++++++++++++++++------------ man/create_infotables.Rd | 4 +-- man/plot_infotables.Rd | 21 ++++++++++++++----- vignettes/Information-vignette.Rmd | 2 - 13 files changed, 111 insertions(+), 60 deletions(-)
Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>
Diff between FIACH versions 0.1.0 dated 2015-09-30 and 0.1.1 dated 2015-10-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include productivity evaluation using distance measures, benchmarking,
risk analysis, technology adoption model, inverse optimization, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 1.0 dated 2015-09-27 and 1.5 dated 2015-10-01
DESCRIPTION | 8 - MD5 | 40 ++++---- NAMESPACE | 1 R/DJL-internal.R | 251 ++++++++++++++++++++++++++--------------------------- R/dm.ddf.R | 7 - R/dm.sf.R | 7 - R/map.soa.ddf.R | 43 +++++---- R/map.soa.dea.R | 43 +++++---- R/map.soa.sbm.R | 41 +++++--- R/map.soa.sf.R | 43 +++++---- R/roc.dea.R | 7 - R/roc.sf.R |only man/dm.ddf.Rd | 11 +- man/dm.dea.Rd | 7 - man/dm.sbm.Rd | 8 - man/dm.sf.Rd | 9 - man/map.soa.ddf.Rd | 10 +- man/map.soa.dea.Rd | 11 +- man/map.soa.sbm.Rd | 10 +- man/map.soa.sf.Rd | 39 +++++--- man/roc.dea.Rd | 1 man/roc.sf.Rd |only 22 files changed, 338 insertions(+), 259 deletions(-)