Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search
with their old and newer search 'APIs', get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Ted Hart [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 0.3.4 dated 2015-07-10 and 0.5.0 dated 2016-01-20
DESCRIPTION | 22 +- LICENSE | 2 MD5 | 121 ++++++----- NAMESPACE | 17 + R/cr_agency.r | 4 R/cr_citation_count.r | 1 R/cr_cn.r | 114 +++++++--- R/cr_ft_links.R | 29 +- R/cr_ft_text.R | 166 +++++++++++---- R/cr_fundref.r | 189 ++++++++++++----- R/cr_journals.r | 159 ++++++++++---- R/cr_licenses.R | 49 +++- R/cr_members.r | 187 ++++++++++++----- R/cr_prefixes.r | 123 ++++++++--- R/cr_search_free.r | 5 R/cr_types.R |only R/cr_works.R | 235 ++++++++++++++++----- R/crosscite.R | 6 R/filters.R |only R/id_converter.R |only R/rcrossref-package.R | 39 +++ R/requestor.R |only R/zzz.R | 87 +++---- README.md | 177 ++++++++-------- build/vignette.rds |binary inst/doc/crossref_filters.Rmd | 8 inst/doc/crossref_filters.html | 40 +++ inst/examples/MairChamberlain2014RJournal.txt | 285 ++++++++++++++++++-------- inst/ignore |only inst/vign/crossref_filters.Rmd | 8 inst/vign/crossref_filters.md | 8 man/GET_agency_id.Rd |only man/as.tdmurl.Rd | 4 man/cr_agency.Rd | 8 man/cr_citation-defunct.Rd | 2 man/cr_citation_count.Rd | 2 man/cr_cn.Rd | 58 +++-- man/cr_ft_links.Rd | 18 - man/cr_ft_text.Rd | 71 +++++- man/cr_fundref.Rd | 95 ++++++-- man/cr_journals.Rd | 53 ++++ man/cr_licenses.Rd | 24 +- man/cr_members.Rd | 58 ++++- man/cr_prefixes.Rd | 72 ++++-- man/cr_r.Rd | 2 man/cr_search.Rd | 2 man/cr_search_free.Rd | 4 man/cr_types.Rd |only man/cr_works.Rd | 71 +++++- man/crosscite.Rd | 15 - man/extract_xpdf.Rd | 2 man/filters.Rd |only man/get_styles.Rd | 2 man/id_converter.Rd |only man/pmid2doi.Rd | 2 man/rcrossref-defunct.Rd | 6 man/rcrossref-package.Rd | 50 ++++ tests/testthat/test_cr_cn.R | 16 + tests/testthat/test_cr_ft_links.R | 6 tests/testthat/test_cr_fundref.R | 9 tests/testthat/test_cr_members.R | 11 - tests/testthat/test_cr_members_cursor.R |only tests/testthat/test_cr_prefixes.R | 12 + tests/testthat/test_cr_types.R |only tests/testthat/test_cr_works.R | 83 +++++++ tests/testthat/test_cr_works_cursor.R |only vignettes/crossref_filters.Rmd | 8 67 files changed, 2046 insertions(+), 801 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.7). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel and Romain Francois;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.5.1 dated 2015-09-24 and 0.3.2.7.0 dated 2016-01-20
ChangeLog | 28 - DESCRIPTION | 12 MD5 | 130 ++--- README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 25 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/SparseCore | 2 inst/include/Eigen/src/Cholesky/LDLT.h | 2 inst/include/Eigen/src/Cholesky/LLT.h | 2 inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 10 inst/include/Eigen/src/Core/Array.h | 15 inst/include/Eigen/src/Core/ArrayBase.h | 4 inst/include/Eigen/src/Core/CwiseBinaryOp.h | 3 inst/include/Eigen/src/Core/CwiseUnaryOp.h | 2 inst/include/Eigen/src/Core/DenseBase.h | 14 inst/include/Eigen/src/Core/DenseStorage.h | 255 ++++++---- inst/include/Eigen/src/Core/DiagonalProduct.h | 3 inst/include/Eigen/src/Core/GeneralProduct.h | 10 inst/include/Eigen/src/Core/MapBase.h | 2 inst/include/Eigen/src/Core/MathFunctions.h | 2 inst/include/Eigen/src/Core/Matrix.h | 15 inst/include/Eigen/src/Core/MatrixBase.h | 9 inst/include/Eigen/src/Core/PlainObjectBase.h | 30 + inst/include/Eigen/src/Core/Redux.h | 5 inst/include/Eigen/src/Core/Ref.h | 9 inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 10 inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 1 inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h | 8 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h | 4 inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 9 inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 3 inst/include/Eigen/src/Core/util/MKL_support.h | 32 + inst/include/Eigen/src/Core/util/Macros.h | 20 inst/include/Eigen/src/Core/util/XprHelper.h | 8 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 23 inst/include/Eigen/src/Geometry/AlignedBox.h | 2 inst/include/Eigen/src/Geometry/AngleAxis.h | 6 inst/include/Eigen/src/Geometry/Quaternion.h | 4 inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 4 inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 3 inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 3 inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h | 21 inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h | 48 + inst/include/Eigen/src/OrderingMethods/Amd.h | 5 inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h | 4 inst/include/Eigen/src/SparseCore/CompressedStorage.h | 6 inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 4 inst/include/Eigen/src/SparseCore/SparseMatrix.h | 5 inst/include/Eigen/src/SparseCore/SparseMatrixBase.h | 35 - inst/include/Eigen/src/SparseCore/SparseUtil.h | 1 inst/include/Eigen/src/SparseCore/SparseVector.h | 1 inst/include/Eigen/src/SparseLU/SparseLU.h | 4 inst/include/Eigen/src/SparseLU/SparseLUImpl.h | 2 inst/include/Eigen/src/SparseLU/SparseLU_Memory.h | 4 inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h | 8 inst/include/Eigen/src/SparseLU/SparseLU_column_bmod.h | 4 inst/include/Eigen/src/SparseLU/SparseLU_kernel_bmod.h | 4 inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h | 8 inst/include/Eigen/src/SparseLU/SparseLU_pivotL.h | 7 inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h | 2 inst/include/unsupported/Eigen/src/IterativeSolvers/DGMRES.h | 4 inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h | 3 inst/include/unsupported/Eigen/src/IterativeSolvers/MINRES.h | 3 inst/unitTests/runit.sparse.R | 5 src/fastLm.cpp | 2 66 files changed, 613 insertions(+), 308 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 2.0-1 dated 2015-12-02 and 2.0-2 dated 2016-01-20
mma-2.0-1/mma/man/data.org2.Rd |only mma-2.0-2/mma/DESCRIPTION | 8 mma-2.0-2/mma/MD5 | 24 +- mma-2.0-2/mma/NAMESPACE | 3 mma-2.0-2/mma/R/mma.r | 316 ++++++++++------------------------ mma-2.0-2/mma/man/boot.med.binx.Rd | 2 mma-2.0-2/mma/man/boot.med.contx.Rd | 4 mma-2.0-2/mma/man/data.org.Rd | 52 +++-- mma-2.0-2/mma/man/med.binx.Rd | 2 mma-2.0-2/mma/man/med.contx.Rd | 4 mma-2.0-2/mma/man/mma-package.Rd | 2 mma-2.0-2/mma/man/mma.Rd | 7 mma-2.0-2/mma/man/summary.med_iden.Rd |only mma-2.0-2/mma/man/summary.mma.Rd | 7 14 files changed, 159 insertions(+), 272 deletions(-)
Title: Joint Random Forest (JRF) for the Simultaneous Estimation of
Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre],
Pei Wang Developer [aut],
Zhidong Tu Developer [aut],
Won-min Song Developer [aut],
Adele Cutler Developer [ctb],
Leo Breiman Developer [ctb],
Andy Liaw Developer [ctb],
Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>
Diff between JRF versions 0.1-2 dated 2015-12-03 and 0.1-3 dated 2016-01-20
JRF-0.1-2/JRF/R/importance.R |only JRF-0.1-2/JRF/man/importance.Rd |only JRF-0.1-3/JRF/DESCRIPTION | 6 - JRF-0.1-3/JRF/MD5 | 14 +- JRF-0.1-3/JRF/NAMESPACE | 2 JRF-0.1-3/JRF/R/JRF.R | 183 +++++++++++++++++++++-------------- JRF-0.1-3/JRF/R/JRF_permutation.R |only JRF-0.1-3/JRF/man/JRF.Rd | 119 ++++------------------ JRF-0.1-3/JRF/man/JRF_permutation.Rd |only JRF-0.1-3/JRF/src/regTree.c | 1 10 files changed, 149 insertions(+), 176 deletions(-)
Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the OSRM API. OSRM is a routing
service based on OpenStreetMap data. See <http://project-osrm.org/> for more
information. A public API exists but one can run its own instance. This package
allows to compute distances (travel time and kilometric distance) between points
and travel time matrices.
Author: Timothée Giraud [cre, aut]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between osrm versions 1.1 dated 2015-11-06 and 2.0.0 dated 2016-01-20
osrm-1.1/osrm/NEWS |only osrm-1.1/osrm/R/osrmTableErrors.R |only osrm-1.1/osrm/R/osrmTableOD.R |only osrm-1.1/osrm/inst |only osrm-1.1/osrm/man/osrmTableErrors.Rd |only osrm-1.1/osrm/man/osrmTableOD.Rd |only osrm-2.0.0/osrm/DESCRIPTION | 14 - osrm-2.0.0/osrm/MD5 | 30 +-- osrm-2.0.0/osrm/NAMESPACE | 2 osrm-2.0.0/osrm/R/osrmTable.R | 255 +++++++++++++++++++++++++------- osrm-2.0.0/osrm/R/osrmViaroute.R | 33 +--- osrm-2.0.0/osrm/R/osrmViarouteGeom.R | 73 ++++----- osrm-2.0.0/osrm/R/package.R | 17 +- osrm-2.0.0/osrm/R/zzz.R | 2 osrm-2.0.0/osrm/README.md | 11 - osrm-2.0.0/osrm/man/osrm.Rd | 17 +- osrm-2.0.0/osrm/man/osrmTable.Rd | 60 +++++-- osrm-2.0.0/osrm/man/osrmViaroute.Rd | 16 -- osrm-2.0.0/osrm/man/osrmViarouteGeom.Rd | 34 +--- 19 files changed, 363 insertions(+), 201 deletions(-)
Title: Access to the Gitlab API
Description: Provides R functions to access the API of the project and
repository management web application gitlab. For many common tasks (repository
file access, issue assignment and status, commenting) convenience wrappers
are provided, and in addition the full API can be used by specifying request
locations. Gitlab is open-source software and can be self-hosted or used on
gitlab.com.
Author: Jirka Lewandowski [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between gitlabr versions 0.5.1 dated 2015-10-27 and 0.6.2 dated 2016-01-20
DESCRIPTION | 24 ++++---- MD5 | 22 ++++--- NAMESPACE | 8 ++ R/gitlab_api.R | 11 ++- R/gitlabr-package.R | 2 R/magrittr_extensions.R | 19 ++++++ R/projects_and_repos.R | 109 ++++++++++++++++++++++++++++++++++++++ man/branches.Rd |only man/create_merge_request.Rd |only man/get_file.Rd | 13 +++- man/gitlab.Rd | 6 +- man/pipe_into.Rd |only man/push_file.Rd |only vignettes/quick-start-gitlabr.Rmd | 10 ++- 14 files changed, 193 insertions(+), 31 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 0.1.1 dated 2015-10-13 and 0.1.2 dated 2016-01-20
DiffusionRgqd-0.1.1/DiffusionRgqd/man/figures/desktop.ini |only DiffusionRgqd-0.1.2/DiffusionRgqd/DESCRIPTION | 11 DiffusionRgqd-0.1.2/DiffusionRgqd/MD5 | 106 ++++++--- DiffusionRgqd-0.1.2/DiffusionRgqd/NAMESPACE | 3 DiffusionRgqd-0.1.2/DiffusionRgqd/NEWS.md | 26 +- DiffusionRgqd-0.1.2/DiffusionRgqd/R/BiGQD.density.R | 85 ++++--- DiffusionRgqd-0.1.2/DiffusionRgqd/R/BiGQD.mcmc.R | 46 ++-- DiffusionRgqd-0.1.2/DiffusionRgqd/R/BiGQD.mle.R | 26 +- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.density.R | 111 ++++++---- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.dic.R | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.estimates.R | 65 +++-- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.mcmc.R | 51 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.mle.R | 35 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/R/GQD.plot.R | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/README.md | 35 +++ DiffusionRgqd-0.1.2/DiffusionRgqd/build |only DiffusionRgqd-0.1.2/DiffusionRgqd/data/SDEsim5.txt |only DiffusionRgqd-0.1.2/DiffusionRgqd/demo |only DiffusionRgqd-0.1.2/DiffusionRgqd/inst |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/BiGQD.density.Rd | 51 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/BiGQD.mcmc.Rd | 45 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/BiGQD.mle.Rd | 45 +++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/DiffusionRgqd-package.Rd | 6 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.TIpassage.Rd | 6 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.aic.Rd | 2 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.density.Rd | 40 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.dic.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.estimates.Rd | 15 + DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.mcmc.Rd | 38 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.mle.Rd | 42 ++- DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.passage.Rd | 6 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.plot.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/GQD.remove.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim1.Rd | 2 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim2.Rd | 4 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim4.Rd | 5 DiffusionRgqd-0.1.2/DiffusionRgqd/man/SDEsim5.Rd |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/BivEqn1.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/BivEqn2.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/BivEqn3.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/SDEsim5.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/ScalarEqn1.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/ScalarEqn2.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/ScalarEqn3.png |only DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/TransDens1.png |binary DiffusionRgqd-0.1.2/DiffusionRgqd/man/figures/TransDens2.png |binary DiffusionRgqd-0.1.2/DiffusionRgqd/vignettes |only 47 files changed, 665 insertions(+), 262 deletions(-)
Title: Bindings to the CommonMark Reference Implementation
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the libcmark reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.6 dated 2016-01-03 and 0.7 dated 2016-01-20
DESCRIPTION | 6 MD5 | 22 NEWS | 7 src/cmark/blocks.c | 6 src/cmark/cmark.h | 20 src/cmark/cmark_version.h | 4 src/cmark/commonmark.c | 57 src/cmark/html.c | 2 src/cmark/iterator.c | 3 src/cmark/node.c | 16 src/cmark/render.c | 20 src/cmark/scanners.c |26864 +++++++++++++++++----------------------------- 12 files changed, 10561 insertions(+), 16466 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.3.0 dated 2016-01-19 and 1.3.1 dated 2016-01-20
DESCRIPTION | 8 ++--- MD5 | 16 +++++------ NEWS | 3 ++ build/vignette.rds |binary inst/doc/discreteBPCP.R | 6 ++-- inst/doc/discreteBPCP.Rnw | 63 ++++++++++++++++++++++++++++++++------------- inst/doc/discreteBPCP.pdf |binary man/bpcp-package.Rd | 4 +- vignettes/discreteBPCP.Rnw | 63 ++++++++++++++++++++++++++++++++------------- 9 files changed, 110 insertions(+), 53 deletions(-)
Title: Univariate Outlier Detection
Description: Detect outliers in one-dimensional data.
Author: Mark van der Loo <mark.vanderloo@gmail.com>
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between extremevalues versions 2.3.1 dated 2015-07-14 and 2.3.2 dated 2016-01-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 4 ++++ inst/CITATION | 6 +++--- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools inspired by Stata to explore data.frames (summarize,
tabulate, xtile, pctile, binscatter, elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.5.0 dated 2016-01-01 and 0.6.0 dated 2016-01-20
statar-0.5.0/statar/R/tag.R |only statar-0.5.0/statar/man/tag.Rd |only statar-0.6.0/statar/DESCRIPTION | 6 +-- statar-0.6.0/statar/MD5 | 31 ++++++++++--------- statar-0.6.0/statar/NAMESPACE | 4 +- statar-0.6.0/statar/R/fill_gap.R |only statar-0.6.0/statar/R/is.panel.R | 39 ++++++++++++++----------- statar-0.6.0/statar/R/statar.R | 1 statar-0.6.0/statar/R/sum_up.R | 20 ++++++------ statar-0.6.0/statar/R/tab.R | 13 ++++---- statar-0.6.0/statar/README.md | 4 +- statar-0.6.0/statar/inst/doc/panel-data.Rmd | 29 +++++++++++++----- statar-0.6.0/statar/inst/doc/panel-data.html | 33 +++++++++++++++------ statar-0.6.0/statar/man/fill_gap.Rd |only statar-0.6.0/statar/man/is.panel.Rd | 19 ++++++------ statar-0.6.0/statar/man/sum_up.Rd | 4 +- statar-0.6.0/statar/man/tab.Rd | 4 +- statar-0.6.0/statar/tests/testthat/test_fill.R |only statar-0.6.0/statar/vignettes/panel-data.Rmd | 29 +++++++++++++----- 19 files changed, 144 insertions(+), 92 deletions(-)
Title: Using Percolation and Conductance to Find Information Flow
Certainty in a Direct Network
Description: To find the certainty of dominance interactions with indirect interactions being considered.
Author: Kevin Fujii [aut],
Jian Jin [aut, cre],
Aaron Shev [aut],
Brianne Beisner [aut],
Brenda McCowan [aut, cph],
Hsieh Fushing [aut, cph]
Maintainer: Jian Jin <jinjian.pku@gmail.com>
Diff between Perc versions 0.1.0 dated 2015-10-22 and 0.1.1 dated 2016-01-20
DESCRIPTION | 8 ++--- MD5 | 18 +++++++----- R/as.conflictmat.R | 11 ++++--- R/conductance.R | 5 ++- R/findAllRankOrder.R | 70 ++++++++++++++++++++++++++++++++++-------------- R/sim.rank.order.R | 61 +++++++---------------------------------- build/vignette.rds |binary man/getAllCosts.Rd |only man/getAllRankOrder.Rd |only man/getBestRankOrder.Rd |only man/getSimOutput.Rd |only vignettes/Perc.Rmd | 20 ++++++------- 12 files changed, 96 insertions(+), 97 deletions(-)
Title: Parametric Bootstrap and Kenward Roger Based Methods for Mixed
Model Comparison
Diff between pbkrtest versions 0.4-4 dated 2015-12-12 and 0.4-5 dated 2016-01-20
Description: Test in mixed effects models.
Attention is on mixed effects models as implemented in the
lme4 package.
The package implements a parametric bootstrap test and a Kenward-Roger
modification of F-tests for linear mixed effects models and a parametric bootstrap
test for generalized linear mixed models.
Author: Ulrich Halekoh
Maintainer: Søren Højsgaard
ChangeLog | 19
DESCRIPTION | 12
MD5 | 46 +-
R/KR-Sigma-G.R | 346 ++++++++--------
R/KR-Sigma-G2.R | 306 +++++++-------
R/KR-across-versions.R | 40 -
R/KR-init-modcomp.R | 128 +++---
R/KR-linearAlgebra.R | 120 ++---
R/KR-modcomp.R | 540 +++++++++++++-------------
R/KR-vcovAdj.R | 155 -------
R/KR-vcovAdj0.R | 232 +++++------
R/KR-vcovAdj15.R |only
R/KR-vcovAdj16.R |only
R/PB-anova.R | 110 ++---
R/PB-modcomp.R | 764 ++++++++++++++++++-------------------
R/PB-refdist.R | 281 +++++--------
R/PB-utils.R | 76 +--
R/getKR.R | 24 -
R/get_ddf_Lb.R | 338 ++++++++--------
R/modelCoercion.R | 344 ++++++++--------
build/vignette.rds |binary
inst/doc/pbkrtest-introduction.pdf |binary
man/KRmodcomp.Rd | 2
man/pbkrtest-internal.Rd | 2
man/vcovAdj.Rd | 53 +-
25 files changed, 1893 insertions(+), 2045 deletions(-)
Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation
of matrix- and multidimensional-valued functions with
respect to multidimensional independent variables.
Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between madness versions 0.1.0 dated 2015-12-15 and 0.2.0 dated 2016-01-20
DESCRIPTION | 27 +++++---- MD5 | 42 ++++++++++----- NAMESPACE | 3 + R/diag.r |only R/eigen.r |only R/madness_pkg.r | 15 +++++ R/matwise.r | 79 +---------------------------- R/max.r |only R/norm.r |only R/reshape.r | 36 ------------- R/theta.r | 1 R/to_objective.r |only R/twomoments.r | 82 ++++++++++++++++++++++-------- README.md | 70 ++++++++++++++++++++++--- build |only inst/doc |only man/NEWS.Rd | 21 +++++++ man/eigen.Rd |only man/matwise.Rd | 38 +------------- man/max.Rd |only man/norm.Rd |only man/reshapes.Rd | 11 ---- man/to_objective.Rd |only man/todiag.Rd |only man/twomoments.Rd | 22 ++++++-- tests/testthat/test-basic.r | 103 ++++++++++++++++++++++++++++++++++---- tests/testthat/test-correctness.r | 46 ++++++++++++++++ vignettes |only 28 files changed, 367 insertions(+), 229 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.0.0 dated 2015-10-04 and 1.1.3 dated 2016-01-20
geoknife-1.0.0/geoknife/R/loadOutput.R |only geoknife-1.1.3/geoknife/DESCRIPTION | 20 - geoknife-1.1.3/geoknife/MD5 | 177 +++++----- geoknife-1.1.3/geoknife/NAMESPACE | 3 geoknife-1.1.3/geoknife/R/01-webdata-obj.R | 18 - geoknife-1.1.3/geoknife/R/02-webgeom-obj.R | 28 + geoknife-1.1.3/geoknife/R/03-geojob-obj.R | 6 geoknife-1.1.3/geoknife/R/04-webprocess-obj.R | 42 +- geoknife-1.1.3/geoknife/R/06-simplegeom-obj.R | 38 +- geoknife-1.1.3/geoknife/R/07-datagroup-obj.R | 6 geoknife-1.1.3/geoknife/R/algorithm-webprocess.R | 13 geoknife-1.1.3/geoknife/R/attribute-webgeom.R | 5 geoknife-1.1.3/geoknife/R/check.R | 2 geoknife-1.1.3/geoknife/R/download-geojob.R | 5 geoknife-1.1.3/geoknife/R/email-geojob.R | 5 geoknife-1.1.3/geoknife/R/gcontent.R |only geoknife-1.1.3/geoknife/R/geoknife-generic.R | 7 geoknife-1.1.3/geoknife/R/geom-webgeom.R | 36 +- geoknife-1.1.3/geoknife/R/inputs-webprocess.R | 27 + geoknife-1.1.3/geoknife/R/parseTimeseries.R | 28 - geoknife-1.1.3/geoknife/R/processInputsToXML.R | 17 geoknife-1.1.3/geoknife/R/query-webdata-times.R | 18 - geoknife-1.1.3/geoknife/R/query-webdata-variables.R | 8 geoknife-1.1.3/geoknife/R/query-webdata.R | 42 +- geoknife-1.1.3/geoknife/R/query-webgeom.R | 2 geoknife-1.1.3/geoknife/R/query-webprocess.R | 2 geoknife-1.1.3/geoknife/R/result.R |only geoknife-1.1.3/geoknife/R/setJobState.R | 6 geoknife-1.1.3/geoknife/R/setProcessInputs.R | 6 geoknife-1.1.3/geoknife/R/show-webdata.R | 4 geoknife-1.1.3/geoknife/R/start-geojob.R | 48 +- geoknife-1.1.3/geoknife/R/times-webdata.R | 77 +++- geoknife-1.1.3/geoknife/R/url-generic.R | 60 ++- geoknife-1.1.3/geoknife/R/values-webgeom.R | 39 +- geoknife-1.1.3/geoknife/R/variables-webdata.R | 27 - geoknife-1.1.3/geoknife/R/version-generic.R | 33 + geoknife-1.1.3/geoknife/README.md | 18 - geoknife-1.1.3/geoknife/build/vignette.rds |binary geoknife-1.1.3/geoknife/demo/prism_subset.R | 8 geoknife-1.1.3/geoknife/inst/CITATION | 2 geoknife-1.1.3/geoknife/inst/doc/geoknife.html | 69 +-- geoknife-1.1.3/geoknife/man/XML-method.Rd | 4 geoknife-1.1.3/geoknife/man/abstract-datagroup.Rd | 2 geoknife-1.1.3/geoknife/man/algorithm-webprocess.Rd | 7 geoknife-1.1.3/geoknife/man/attribute.Rd | 4 geoknife-1.1.3/geoknife/man/bufferPoint.Rd | 2 geoknife-1.1.3/geoknife/man/canStart.Rd | 8 geoknife-1.1.3/geoknife/man/cancel-methods.Rd | 2 geoknife-1.1.3/geoknife/man/check-geojob.Rd | 2 geoknife-1.1.3/geoknife/man/datagroup-class.Rd | 5 geoknife-1.1.3/geoknife/man/datagroup-methods.Rd | 2 geoknife-1.1.3/geoknife/man/download.Rd | 4 geoknife-1.1.3/geoknife/man/email-method.Rd | 4 geoknife-1.1.3/geoknife/man/fetchGML_IDs.Rd | 2 geoknife-1.1.3/geoknife/man/gcontent.Rd |only geoknife-1.1.3/geoknife/man/geojob-class.Rd | 5 geoknife-1.1.3/geoknife/man/geojob-methods.Rd | 4 geoknife-1.1.3/geoknife/man/geoknife-methods.Rd | 32 - geoknife-1.1.3/geoknife/man/geom.Rd | 9 geoknife-1.1.3/geoknife/man/getJobState.Rd | 2 geoknife-1.1.3/geoknife/man/inputs-webprocess.Rd | 14 geoknife-1.1.3/geoknife/man/parseTimeseries.Rd | 5 geoknife-1.1.3/geoknife/man/query.Rd | 5 geoknife-1.1.3/geoknife/man/result-methods.Rd | 10 geoknife-1.1.3/geoknife/man/setJobState.Rd | 8 geoknife-1.1.3/geoknife/man/simplegeom-class.Rd | 20 - geoknife-1.1.3/geoknife/man/simplegeom-methods.Rd | 7 geoknife-1.1.3/geoknife/man/start-methods.Rd | 11 geoknife-1.1.3/geoknife/man/successful-methods.Rd | 3 geoknife-1.1.3/geoknife/man/times-webdata.Rd | 2 geoknife-1.1.3/geoknife/man/times_query-method.Rd | 4 geoknife-1.1.3/geoknife/man/url.Rd | 26 - geoknife-1.1.3/geoknife/man/values.Rd | 14 geoknife-1.1.3/geoknife/man/variables-webdata.Rd | 4 geoknife-1.1.3/geoknife/man/variables_query-method.Rd | 4 geoknife-1.1.3/geoknife/man/version.Rd | 4 geoknife-1.1.3/geoknife/man/waitUntilFinished.Rd | 4 geoknife-1.1.3/geoknife/man/webdata-class.Rd | 5 geoknife-1.1.3/geoknife/man/webdata-methods.Rd | 4 geoknife-1.1.3/geoknife/man/webgeom-class.Rd | 10 geoknife-1.1.3/geoknife/man/webgeom-methods.Rd | 24 + geoknife-1.1.3/geoknife/man/webprocess-class.Rd | 12 geoknife-1.1.3/geoknife/man/webprocess-methods.Rd | 2 geoknife-1.1.3/geoknife/tests/testthat/test-geoknife_com.R | 4 geoknife-1.1.3/geoknife/tests/testthat/test-geoknife_setters.R | 4 geoknife-1.1.3/geoknife/tests/testthat/test-geoknife_xml_parser.R | 1 geoknife-1.1.3/geoknife/tests/testthat/test-processErrors.R | 15 geoknife-1.1.3/geoknife/tests/testthat/test-times_webdata.R |only geoknife-1.1.3/geoknife/tests/testthat/test-waitUntilFinished.R | 4 geoknife-1.1.3/geoknife/tests/testthat/test-webdata_object.R | 3 geoknife-1.1.3/geoknife/tests/testthat/test-webprocess_input.R | 27 + geoknife-1.1.3/geoknife/tests/testthat/test-webprocess_object.R | 14 92 files changed, 788 insertions(+), 538 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. 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, e.g.
'f <- future({ mandelbrot(c(0.28,0), side=2) })' and 'v <- value(f)'.
The 'resolve()' function can be used to check if a future is resolved or not.
An infix assignment operator '%<=%' exists for creating futures whose values
are accessible by the assigned variables (as promises), e.g.
'v %<=% { mandelbrot(c(0.28,0), side=2) }'.
This package implements synchronous "lazy" and "eager" futures, and asynchronous
"multicore", "multisession" and ad hoc "cluster" futures. 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 0.10.0 dated 2015-12-30 and 0.11.0 dated 2016-01-20
future-0.10.0/future/R/MulticoreFuture.R |only future-0.11.0/future/DESCRIPTION | 31 - future-0.11.0/future/MD5 | 113 ++- future-0.11.0/future/NAMESPACE | 115 ++- future-0.11.0/future/NEWS | 28 future-0.11.0/future/R/ClusterFuture-class.R |only future-0.11.0/future/R/Future-class.R | 71 ++ future-0.11.0/future/R/FutureRegistry.R | 17 future-0.11.0/future/R/LazyFuture-class.R | 5 future-0.11.0/future/R/MulticoreFuture-class.R |only future-0.11.0/future/R/MultisessionFuture-class.R |only future-0.11.0/future/R/availableCores.R | 240 ++++---- future-0.11.0/future/R/cluster.R |only future-0.11.0/future/R/eager.R | 8 future-0.11.0/future/R/flapply.R |only future-0.11.0/future/R/future.R | 5 future-0.11.0/future/R/futureAssign_OP.R | 4 future-0.11.0/future/R/futureCall.R |only future-0.11.0/future/R/futureOf.R | 10 future-0.11.0/future/R/globals.R | 210 ++++--- future-0.11.0/future/R/multicore.R | 138 +++- future-0.11.0/future/R/multisession.R |only future-0.11.0/future/R/plan.R | 64 +- future-0.11.0/future/R/utils.R | 46 + future-0.11.0/future/demo/mandelbrot.R | 44 + future-0.11.0/future/inst/doc/future-issues.html | 10 future-0.11.0/future/inst/doc/future-issues.md.rsp | 385 ++++++------ future-0.11.0/future/inst/doc/future.html | 70 +- future-0.11.0/future/inst/doc/future.md.rsp | 596 ++++++++++---------- future-0.11.0/future/man/ClusterFuture-class.Rd |only future-0.11.0/future/man/MulticoreFuture-class.Rd | 12 future-0.11.0/future/man/availableCores.Rd | 123 ++-- future-0.11.0/future/man/cluster.Rd |only future-0.11.0/future/man/eager.Rd | 139 ++-- future-0.11.0/future/man/future.Rd | 116 +-- future-0.11.0/future/man/futureAssign.Rd | 10 future-0.11.0/future/man/injectNextStrategy.Rd |only future-0.11.0/future/man/lazy.Rd | 12 future-0.11.0/future/man/multicore.Rd | 175 +++-- future-0.11.0/future/man/multisession.Rd |only future-0.11.0/future/man/plan.Rd | 21 future-0.11.0/future/man/requestCore.Rd | 66 +- future-0.11.0/future/man/resolve.Rd | 80 +- future-0.11.0/future/man/supportsMulticore.Rd | 40 - future-0.11.0/future/man/usedCores.Rd | 40 - future-0.11.0/future/tests/FutureRegistry.R | 17 future-0.11.0/future/tests/availableCores.R | 28 future-0.11.0/future/tests/cluster.R |only future-0.11.0/future/tests/demo.R | 39 - future-0.11.0/future/tests/dotdotdot.R | 92 +-- future-0.11.0/future/tests/flapply.R |only future-0.11.0/future/tests/future.R | 3 future-0.11.0/future/tests/futureAssign_OP.R | 207 +++--- future-0.11.0/future/tests/futureCall.R |only future-0.11.0/future/tests/futures.R | 132 ++-- future-0.11.0/future/tests/globals,tricky.R | 177 +---- future-0.11.0/future/tests/lazy.R | 4 future-0.11.0/future/tests/multicore.R | 154 ++--- future-0.11.0/future/tests/multisession.R |only future-0.11.0/future/tests/plan.R | 2 future-0.11.0/future/tests/resolve.R | 11 future-0.11.0/future/tests/rng.R | 61 +- future-0.11.0/future/tests/sessions.R |only future-0.11.0/future/tests/utils.R | 81 ++ future-0.11.0/future/vignettes/future-issues.md.rsp | 385 ++++++------ future-0.11.0/future/vignettes/future.md.rsp | 596 ++++++++++---------- 66 files changed, 2802 insertions(+), 2231 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com>
Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.2 dated 2015-12-03 and 2.0.3 dated 2016-01-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/GHCN_FUNCTIONS.R | 4 ++-- R/SSURGO_FUNCTIONS.R | 2 ++ README.md | 2 +- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Correlational Class Analysis
Description: Perform a correlational class analysis of the data, resulting in a partition of the data into separate modules.
Author: Andrei Boutyline
Maintainer: Andrei Boutyline <andrei.boutyline@gmail.com>
Diff between corclass versions 0.1 dated 2013-12-10 and 0.1.1 dated 2016-01-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 8 ++++++++ R/cca.R | 24 ++++++++++++++---------- man/corclass-package.Rd | 6 +++--- man/plot.cca.Rd | 2 +- 6 files changed, 35 insertions(+), 23 deletions(-)