Wed, 25 May 2016

Package popprxl updated to version 0.1.2 with previous version 0.1.1 dated 2015-11-24

Title: Read GenAlEx Files Directly from Excel
Description: GenAlEx is a popular Excel macro for genetic analysis. The 'poppr' R package allows import of GenAlEx formatted CSV data. This package serves as a small 'poppr' add on for those who have trouble or simply do not want to export their data into CSV format.
Author: Zhian N. Kamvar [cre, aut], Niklaus J. Grünwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>

Diff between popprxl versions 0.1.1 dated 2015-11-24 and 0.1.2 dated 2016-05-25

 DESCRIPTION                       |   18 +++++++----
 MD5                               |   19 +++++++++---
 NEWS                              |   11 +++++++
 R/popprxl-package.r               |only
 R/read_genalexcel.R               |    8 +++--
 README.md                         |   58 +++++++++++++++++++++++++++++---------
 build                             |only
 inst/doc                          |only
 inst/files/num_isolates_text.xlsx |only
 inst/files/num_samp_greater.xlsx  |only
 man/popprxl.Rd                    |only
 tests/testthat/test-import.R      |    9 +++++
 vignettes                         |only
 13 files changed, 95 insertions(+), 28 deletions(-)

More information about popprxl at CRAN
Permanent link

Package openssl updated to version 0.9.4 with previous version 0.9.3 dated 2016-05-04

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [cre, aut], Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between openssl versions 0.9.3 dated 2016-05-04 and 0.9.4 dated 2016-05-25

 DESCRIPTION                         |   16 ++++----
 MD5                                 |   68 +++++++++++++++++++-----------------
 NAMESPACE                           |   12 +++++-
 NEWS                                |    7 +++
 R/aes.R                             |   62 ++++++++++++++++++++++++++++----
 R/bignum.R                          |    7 +++
 R/build.R                           |only
 R/cert.R                            |    3 +
 R/diffie.R                          |   15 ++++---
 R/hash.R                            |    7 ++-
 R/openssh.R                         |    2 -
 R/ssh2.R                            |    9 +---
 build/vignette.rds                  |binary
 inst/doc/bignum.R                   |    1 
 inst/doc/bignum.Rmd                 |    1 
 inst/doc/bignum.html                |   32 +++++++++-------
 inst/doc/crypto_hashing.html        |    4 +-
 inst/doc/keys.R                     |only
 inst/doc/keys.Rmd                   |only
 inst/doc/keys.html                  |only
 inst/doc/secure_rng.html            |   18 ++++-----
 inst/testkey.pem                    |only
 man/aes_cbc.Rd                      |   17 +++++++++
 man/bignum.Rd                       |    3 +
 man/certificates.Rd                 |    4 ++
 man/ec_dh.Rd                        |   15 ++++---
 src/aes.c                           |   35 +++++++++---------
 src/bignum.c                        |   14 +++++++
 src/keygen.c                        |   20 ++++++----
 src/openssh.c                       |   48 ++++++++++++++++++++++++-
 tests/testthat/test_keys_dsa.R      |   12 ++++++
 tests/testthat/test_keys_ecdsa.R    |    7 +++
 tests/testthat/test_keys_ecdsa384.R |    7 +++
 tests/testthat/test_keys_ecdsa521.R |    7 +++
 tests/testthat/test_keys_rsa.R      |   12 ++++++
 tests/testthat/test_my_key.R        |    3 +
 vignettes/bignum.Rmd                |    1 
 vignettes/keys.Rmd                  |only
 38 files changed, 344 insertions(+), 125 deletions(-)

More information about openssl at CRAN
Permanent link

Package treescape updated to version 1.9.16 with previous version 1.8.16 dated 2016-04-01

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 1.8.16 dated 2016-04-01 and 1.9.16 dated 2016-05-25

 treescape-1.8.16/treescape/inst/shiny/www/img/svg                               |only
 treescape-1.8.16/treescape/vignettes/figs/findgroves-with-emphasis-1.png        |only
 treescape-1.8.16/treescape/vignettes/figs/plotgroves2-1.png                     |only
 treescape-1.8.16/treescape/vignettes/figs/plotgroves2-2.png                     |only
 treescape-1.8.16/treescape/vignettes/figs/plotgroves2-3.png                     |only
 treescape-1.8.16/treescape/vignettes/figs/plotgroves3-1.png                     |only
 treescape-1.8.16/treescape/vignettes/figs/server.png                            |only
 treescape-1.8.16/treescape/vignettes/figs/treescapescatter-1.png                |only
 treescape-1.8.16/treescape/vignettes/figs/woodmice-tip-emphasis-1.png           |only
 treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-1.png                   |only
 treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-2.png                   |only
 treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-3.png                   |only
 treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-4.png                   |only
 treescape-1.8.16/treescape/vignettes/figs/woodmicePlots-5.png                   |only
 treescape-1.8.16/treescape/vignettes/treescape.md                               |only
 treescape-1.9.16/treescape/DESCRIPTION                                          |    8 
 treescape-1.9.16/treescape/MD5                                                  |   85 +-
 treescape-1.9.16/treescape/NAMESPACE                                            |    4 
 treescape-1.9.16/treescape/R/RcppExports.R                                      |   14 
 treescape-1.9.16/treescape/R/data.R                                             |   36 +
 treescape-1.9.16/treescape/R/medTree.R                                          |    4 
 treescape-1.9.16/treescape/R/plotTreeDiff.R                                     |only
 treescape-1.9.16/treescape/README.md                                            |  218 ++----
 treescape-1.9.16/treescape/build/vignette.rds                                   |binary
 treescape-1.9.16/treescape/data/DengueBEASTMCC.RData                            |only
 treescape-1.9.16/treescape/data/DengueSeqs.RData                                |only
 treescape-1.9.16/treescape/inst/doc/DengueVignette.R                            |only
 treescape-1.9.16/treescape/inst/doc/DengueVignette.Rmd                          |only
 treescape-1.9.16/treescape/inst/doc/DengueVignette.html                         |only
 treescape-1.9.16/treescape/inst/doc/treescape.R                                 |  119 +--
 treescape-1.9.16/treescape/inst/doc/treescape.Rmd                               |  235 ++++---
 treescape-1.9.16/treescape/inst/doc/treescape.html                              |  331 +++++-----
 treescape-1.9.16/treescape/inst/shiny/server.R                                  |  217 ++++++
 treescape-1.9.16/treescape/inst/shiny/ui.R                                      |  129 +++
 treescape-1.9.16/treescape/inst/shiny/www/html/help.html                        |   24 
 treescape-1.9.16/treescape/man/DengueBEASTMCC.Rd                                |only
 treescape-1.9.16/treescape/man/DengueSeqs.Rd                                    |only
 treescape-1.9.16/treescape/man/DengueTrees.Rd                                   |    2 
 treescape-1.9.16/treescape/man/medTree.Rd                                       |    4 
 treescape-1.9.16/treescape/man/plotTreeDiff.Rd                                  |only
 treescape-1.9.16/treescape/man/tipDiff.Rd                                       |only
 treescape-1.9.16/treescape/vignettes/DengueVignette.Rmd                         |only
 treescape-1.9.16/treescape/vignettes/figs/BEASTtree_diffs-1.png                 |only
 treescape-1.9.16/treescape/vignettes/figs/BEASTtree_diffs-2.png                 |only
 treescape-1.9.16/treescape/vignettes/figs/compare_BEAST_to_other_trees-1.png    |only
 treescape-1.9.16/treescape/vignettes/figs/compare_BEAST_to_other_trees-2.png    |only
 treescape-1.9.16/treescape/vignettes/figs/compare_BEAST_to_other_trees-3.png    |only
 treescape-1.9.16/treescape/vignettes/figs/compare_trees_NJ_v_ML-1.png           |only
 treescape-1.9.16/treescape/vignettes/figs/distances_readme-1.png                |only
 treescape-1.9.16/treescape/vignettes/figs/distances_readme-2.png                |only
 treescape-1.9.16/treescape/vignettes/figs/findgroves-with-emphasis_readme-1.png |only
 treescape-1.9.16/treescape/vignettes/figs/make_NJ-1.png                         |only
 treescape-1.9.16/treescape/vignettes/figs/plotgroves2_readme-1.png              |only
 treescape-1.9.16/treescape/vignettes/figs/plotgroves2_readme-2.png              |only
 treescape-1.9.16/treescape/vignettes/figs/plotgroves2_readme-3.png              |only
 treescape-1.9.16/treescape/vignettes/figs/plotgroves_readme-1.png               |only
 treescape-1.9.16/treescape/vignettes/figs/scree_plot-1.png                      |only
 treescape-1.9.16/treescape/vignettes/figs/view_ML-1.png                         |only
 treescape-1.9.16/treescape/vignettes/figs/woodmice-tip-emphasis_readme-1.png    |only
 treescape-1.9.16/treescape/vignettes/figs/woodmiceCluster1_readme-1.png         |only
 treescape-1.9.16/treescape/vignettes/figs/woodmiceMedian_readme-1.png           |only
 treescape-1.9.16/treescape/vignettes/figs/woodmicePlots_readme-1.png            |only
 treescape-1.9.16/treescape/vignettes/figs/woodmicePlots_readme-2.png            |only
 treescape-1.9.16/treescape/vignettes/figs/woodmicePlots_readme-3.png            |only
 treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff-1.png           |only
 treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff-2.png           |only
 treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff_readme-1.png    |only
 treescape-1.9.16/treescape/vignettes/figs/woodmice_plotTreeDiff_readme-2.png    |only
 treescape-1.9.16/treescape/vignettes/treescape.Rmd                              |  224 ++++--
 69 files changed, 1059 insertions(+), 595 deletions(-)

More information about treescape at CRAN
Permanent link

New package mvtboost with initial version 0.5.0
Package: mvtboost
Type: Package
Title: Tree Boosting for Multivariate Outcomes
Version: 0.5.0
Date: 2016-05-25
Author: Patrick Miller [aut, cre]
Maintainer: Patrick Miller <patrick.mil10@gmail.com>
Description: Fits a multivariate model of decision trees for multiple, continuous outcome variables. A model for each outcome variable is fit separately, selecting predictors that explain covariance in the outcomes. Built on top of 'gbm', which fits an ensemble of decision trees to univariate outcomes.
License: GPL (>= 2) | file LICENSE
URL: https://github.com/patr1ckm/mvtboost
BugReports: https://github.com/patr1ckm/mvtboost/issues
Depends: R (>= 3.0.0)
Suggests: testthat, plyr, MASS, parallel, lars, ggplot2, knitr, rmarkdown
Imports: gbm, RColorBrewer, stats, graphics, grDevices, utils,
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-25 14:41:06 UTC; pmille13
Repository: CRAN
Date/Publication: 2016-05-25 18:08:26

More information about mvtboost at CRAN
Permanent link

Package matlabr updated to version 1.1.3 with previous version 1.1 dated 2015-10-21

Title: An Interface for MATLAB using System Calls
Description: Provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to 'R.matlab', which creates a MATLAB server.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>

Diff between matlabr versions 1.1 dated 2015-10-21 and 1.1.3 dated 2016-05-25

 matlabr-1.1.3/matlabr/DESCRIPTION                |   15 +++---
 matlabr-1.1.3/matlabr/MD5                        |   23 ++++-----
 matlabr-1.1.3/matlabr/NAMESPACE                  |    2 
 matlabr-1.1.3/matlabr/R/matlab_script.R          |   57 +++++++++++++++++++----
 matlabr-1.1.3/matlabr/man/get_matlab.Rd          |    9 ++-
 matlabr-1.1.3/matlabr/man/have_matlab.Rd         |   13 ++++-
 matlabr-1.1.3/matlabr/man/rmat_to_matlab_mat.Rd  |    4 -
 matlabr-1.1.3/matlabr/man/run_matlab_code.Rd     |    2 
 matlabr-1.1.3/matlabr/man/run_matlab_script.Rd   |    4 -
 matlabr-1.1.3/matlabr/man/rvec_to_matlab.Rd      |    2 
 matlabr-1.1.3/matlabr/man/rvec_to_matlabcell.Rd  |    4 -
 matlabr-1.1.3/matlabr/man/rvec_to_matlabclist.Rd |    4 -
 matlabr-1.1/matlabr/README.md                    |only
 13 files changed, 96 insertions(+), 43 deletions(-)

More information about matlabr at CRAN
Permanent link

Package fslr updated to version 1.6.4.0 with previous version 1.5.0 dated 2015-10-21

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 1.5.0 dated 2015-10-21 and 1.6.4.0 dated 2016-05-25

 fslr-1.5.0/fslr/README.md                           |only
 fslr-1.6.4.0/fslr/DESCRIPTION                       |   21 
 fslr-1.6.4.0/fslr/MD5                               |  554 ++++++++--------
 fslr-1.6.4.0/fslr/NAMESPACE                         |   35 +
 fslr-1.6.4.0/fslr/R/applyEmptyImageDimensions.R     |only
 fslr-1.6.4.0/fslr/R/applywarp.R                     |    8 
 fslr-1.6.4.0/fslr/R/aux_file.R                      |    3 
 fslr-1.6.4.0/fslr/R/bitpix.R                        |    3 
 fslr-1.6.4.0/fslr/R/breaker.R                       |only
 fslr-1.6.4.0/fslr/R/cal_max.R                       |    3 
 fslr-1.6.4.0/fslr/R/cal_min.R                       |    3 
 fslr-1.6.4.0/fslr/R/check_nifti.R                   |   14 
 fslr-1.6.4.0/fslr/R/checkimg.R                      |    5 
 fslr-1.6.4.0/fslr/R/checknii.R                      |    3 
 fslr-1.6.4.0/fslr/R/copyNIfTIHeader.R               |   14 
 fslr-1.6.4.0/fslr/R/data_type.R                     |    3 
 fslr-1.6.4.0/fslr/R/datatype.R                      |    3 
 fslr-1.6.4.0/fslr/R/descrip.R                       |    3 
 fslr-1.6.4.0/fslr/R/dim_.R                          |    3 
 fslr-1.6.4.0/fslr/R/double_ortho.R                  |    3 
 fslr-1.6.4.0/fslr/R/dropEmptyImageDimensions.R      |   88 +-
 fslr-1.6.4.0/fslr/R/fast.R                          |   16 
 fslr-1.6.4.0/fslr/R/finite_img.R                    |only
 fslr-1.6.4.0/fslr/R/flirt_apply.R                   |    8 
 fslr-1.6.4.0/fslr/R/fnirt.R                         |   16 
 fslr-1.6.4.0/fslr/R/fsl_anat.R                      |    2 
 fslr-1.6.4.0/fslr/R/fsl_data_dir.R                  |only
 fslr-1.6.4.0/fslr/R/fsl_slicetimer.R                |only
 fslr-1.6.4.0/fslr/R/fslabs.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslacos.R                       |    4 
 fslr-1.6.4.0/fslr/R/fsladd.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslasin.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslatan.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslbinv.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslchfiletype.R                 |    4 
 fslr-1.6.4.0/fslr/R/fslcos.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslcpgeom.R                     |    4 
 fslr-1.6.4.0/fslr/R/fsldilate.R                     |   13 
 fslr-1.6.4.0/fslr/R/fsldiv.R                        |    4 
 fslr-1.6.4.0/fslr/R/fsledge.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslentropy.R                    |only
 fslr-1.6.4.0/fslr/R/fslexp.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslfill2.R                      |    6 
 fslr-1.6.4.0/fslr/R/fslgetorient.R                  |only
 fslr-1.6.4.0/fslr/R/fslhd.R                         |  667 +++++++++++---------
 fslr-1.6.4.0/fslr/R/fslindex.R                      |    4 
 fslr-1.6.4.0/fslr/R/fsllog.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslmean.R                       |only
 fslr-1.6.4.0/fslr/R/fslmul.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslnan.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslnanm.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslrand.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslrandn.R                      |    4 
 fslr-1.6.4.0/fslr/R/fslrecip.R                      |    4 
 fslr-1.6.4.0/fslr/R/fslrem.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslroi.R                        |only
 fslr-1.6.4.0/fslr/R/fslsd.R                         |only
 fslr-1.6.4.0/fslr/R/fslsin.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslsqr.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslsqrt.R                       |    4 
 fslr-1.6.4.0/fslr/R/fslsub.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslsum.R                        |   17 
 fslr-1.6.4.0/fslr/R/fsltan.R                        |    4 
 fslr-1.6.4.0/fslr/R/fslvolume.R                     |only
 fslr-1.6.4.0/fslr/R/getEmptyImageDimensions.R       |only
 fslr-1.6.4.0/fslr/R/intent_code.R                   |    3 
 fslr-1.6.4.0/fslr/R/intent_name.R                   |    3 
 fslr-1.6.4.0/fslr/R/intent_p1.R                     |    3 
 fslr-1.6.4.0/fslr/R/intent_p2.R                     |    3 
 fslr-1.6.4.0/fslr/R/intent_p3.R                     |    3 
 fslr-1.6.4.0/fslr/R/magic.R                         |    3 
 fslr-1.6.4.0/fslr/R/maskEmptyImageDimensions.R      |only
 fslr-1.6.4.0/fslr/R/mcflirt.R                       |only
 fslr-1.6.4.0/fslr/R/mni_fname.R                     |only
 fslr-1.6.4.0/fslr/R/ortho2.R                        |    2 
 fslr-1.6.4.0/fslr/R/ortho_diff.R                    |   13 
 fslr-1.6.4.0/fslr/R/overlay2.R                      |only
 fslr-1.6.4.0/fslr/R/pixdim.R                        |    1 
 fslr-1.6.4.0/fslr/R/qform.R                         |    1 
 fslr-1.6.4.0/fslr/R/qform_code.R                    |    3 
 fslr-1.6.4.0/fslr/R/readNIfTI2.R                    |   26 
 fslr-1.6.4.0/fslr/R/replace_dropped_dimensions.R    |only
 fslr-1.6.4.0/fslr/R/rescale_img.R                   |   98 +-
 fslr-1.6.4.0/fslr/R/scl_inter.R                     |    3 
 fslr-1.6.4.0/fslr/R/scl_slope.R                     |    3 
 fslr-1.6.4.0/fslr/R/sform_code.R                    |    3 
 fslr-1.6.4.0/fslr/R/sizeof_hdr.R                    |    3 
 fslr-1.6.4.0/fslr/R/slice_code.R                    |    3 
 fslr-1.6.4.0/fslr/R/slice_duration.R                |    3 
 fslr-1.6.4.0/fslr/R/slice_end.R                     |    3 
 fslr-1.6.4.0/fslr/R/slice_start.R                   |    3 
 fslr-1.6.4.0/fslr/R/susan.R                         |    2 
 fslr-1.6.4.0/fslr/R/tempimg.R                       |   24 
 fslr-1.6.4.0/fslr/R/toffset.R                       |    1 
 fslr-1.6.4.0/fslr/R/vox_offset.R                    |    3 
 fslr-1.6.4.0/fslr/R/window_img.R                    |    4 
 fslr-1.6.4.0/fslr/R/writenii.R                      |   32 
 fslr-1.6.4.0/fslr/R/zero_pad.R                      |only
 fslr-1.6.4.0/fslr/R/zlimmer.R                       |only
 fslr-1.6.4.0/fslr/build/vignette.rds                |binary
 fslr-1.6.4.0/fslr/inst/doc/fslr.Rmd                 |    2 
 fslr-1.6.4.0/fslr/inst/doc/fslr.html                |    2 
 fslr-1.6.4.0/fslr/man/applyEmptyImageDimensions.Rd  |only
 fslr-1.6.4.0/fslr/man/aux_file-methods.Rd           |    4 
 fslr-1.6.4.0/fslr/man/bitpix-methods.Rd             |    4 
 fslr-1.6.4.0/fslr/man/breaker.Rd                    |only
 fslr-1.6.4.0/fslr/man/cal_max-methods.Rd            |    4 
 fslr-1.6.4.0/fslr/man/cal_min-methods.Rd            |    4 
 fslr-1.6.4.0/fslr/man/check_file.Rd                 |    8 
 fslr-1.6.4.0/fslr/man/check_nifti-methods.Rd        |   10 
 fslr-1.6.4.0/fslr/man/check_outfile.Rd              |    4 
 fslr-1.6.4.0/fslr/man/checkimg-methods.Rd           |    9 
 fslr-1.6.4.0/fslr/man/checknii-methods.Rd           |    7 
 fslr-1.6.4.0/fslr/man/checkout.Rd                   |    6 
 fslr-1.6.4.0/fslr/man/cog.Rd                        |    8 
 fslr-1.6.4.0/fslr/man/colorbar.Rd                   |    4 
 fslr-1.6.4.0/fslr/man/copyNIfTIHeader.Rd            |   17 
 fslr-1.6.4.0/fslr/man/data_type-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/datatype-methods.Rd           |    4 
 fslr-1.6.4.0/fslr/man/datatype.Rd                   |   16 
 fslr-1.6.4.0/fslr/man/descrip-methods.Rd            |    4 
 fslr-1.6.4.0/fslr/man/dim_-methods.Rd               |    4 
 fslr-1.6.4.0/fslr/man/double_ortho.Rd               |   10 
 fslr-1.6.4.0/fslr/man/dropEmptyImageDimensions.Rd   |   31 
 fslr-1.6.4.0/fslr/man/fast.Rd                       |    8 
 fslr-1.6.4.0/fslr/man/fast.help.Rd                  |    2 
 fslr-1.6.4.0/fslr/man/file_imgext.Rd                |    4 
 fslr-1.6.4.0/fslr/man/finite_img-methods.Rd         |only
 fslr-1.6.4.0/fslr/man/flirt.Rd                      |    6 
 fslr-1.6.4.0/fslr/man/flirt.help.Rd                 |    4 
 fslr-1.6.4.0/fslr/man/flirt_apply.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fnirt.Rd                      |    6 
 fslr-1.6.4.0/fslr/man/fnirt.help.Rd                 |    2 
 fslr-1.6.4.0/fslr/man/fnirt_with_affine.Rd          |    6 
 fslr-1.6.4.0/fslr/man/fnirt_with_affine_apply.Rd    |    8 
 fslr-1.6.4.0/fslr/man/fsl_anat.Rd                   |    4 
 fslr-1.6.4.0/fslr/man/fsl_anat.help.Rd              |    2 
 fslr-1.6.4.0/fslr/man/fsl_applywarp.Rd              |    6 
 fslr-1.6.4.0/fslr/man/fsl_applywarp.help.Rd         |    2 
 fslr-1.6.4.0/fslr/man/fsl_atlas_dir.Rd              |only
 fslr-1.6.4.0/fslr/man/fsl_biascorrect.Rd            |    6 
 fslr-1.6.4.0/fslr/man/fsl_data_dir.Rd               |only
 fslr-1.6.4.0/fslr/man/fsl_slicetimer.Rd             |only
 fslr-1.6.4.0/fslr/man/fsl_std_dir.Rd                |only
 fslr-1.6.4.0/fslr/man/fslabs.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslabs.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslacos.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslacos.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fsladd.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fsladd.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslasin.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslasin.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslatan.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslatan.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslbet.Rd                     |    8 
 fslr-1.6.4.0/fslr/man/fslbet.help.Rd                |    4 
 fslr-1.6.4.0/fslr/man/fslbin.Rd                     |    6 
 fslr-1.6.4.0/fslr/man/fslbin.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslbinv.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslbinv.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslchfiletype.Rd              |    6 
 fslr-1.6.4.0/fslr/man/fslchfiletype.help.Rd         |    4 
 fslr-1.6.4.0/fslr/man/fslcmd.Rd                     |   14 
 fslr-1.6.4.0/fslr/man/fslcog.Rd                     |   17 
 fslr-1.6.4.0/fslr/man/fslcos.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslcos.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslcpgeom.Rd                  |    6 
 fslr-1.6.4.0/fslr/man/fslcpgeom.help.Rd             |    4 
 fslr-1.6.4.0/fslr/man/fsldilate.Rd                  |   19 
 fslr-1.6.4.0/fslr/man/fsldir.Rd                     |    5 
 fslr-1.6.4.0/fslr/man/fsldiv.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fsldiv.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fsledge.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fsledge.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslentropy.Rd                 |only
 fslr-1.6.4.0/fslr/man/fslerode.Rd                   |   19 
 fslr-1.6.4.0/fslr/man/fslerode.help.Rd              |    6 
 fslr-1.6.4.0/fslr/man/fslexp.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslexp.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslfill.Rd                    |   15 
 fslr-1.6.4.0/fslr/man/fslfill.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslfill2.Rd                   |    6 
 fslr-1.6.4.0/fslr/man/fslhd.Rd                      |    6 
 fslr-1.6.4.0/fslr/man/fslhd.help.Rd                 |    4 
 fslr-1.6.4.0/fslr/man/fslhd.parse.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslhelp.Rd                    |    4 
 fslr-1.6.4.0/fslr/man/fslindex.Rd                   |   10 
 fslr-1.6.4.0/fslr/man/fslindex.help.Rd              |    6 
 fslr-1.6.4.0/fslr/man/fsllog.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fsllog.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslmask.Rd                    |   12 
 fslr-1.6.4.0/fslr/man/fslmask.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslmaths.Rd                   |    6 
 fslr-1.6.4.0/fslr/man/fslmaths.help.Rd              |    4 
 fslr-1.6.4.0/fslr/man/fslmean.Rd                    |only
 fslr-1.6.4.0/fslr/man/fslmerge.Rd                   |    8 
 fslr-1.6.4.0/fslr/man/fslmerge.help.Rd              |    4 
 fslr-1.6.4.0/fslr/man/fslmul.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslmul.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslnan.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslnan.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslnanm.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslnanm.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslorient.Rd                  |    6 
 fslr-1.6.4.0/fslr/man/fslorient.help.Rd             |    4 
 fslr-1.6.4.0/fslr/man/fslorient_wrap.Rd             |only
 fslr-1.6.4.0/fslr/man/fslorienter.Rd                |only
 fslr-1.6.4.0/fslr/man/fslrand.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslrand.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslrandn.Rd                   |   10 
 fslr-1.6.4.0/fslr/man/fslrandn.help.Rd              |    6 
 fslr-1.6.4.0/fslr/man/fslrange.Rd                   |   16 
 fslr-1.6.4.0/fslr/man/fslrecip.Rd                   |   10 
 fslr-1.6.4.0/fslr/man/fslrecip.help.Rd              |    6 
 fslr-1.6.4.0/fslr/man/fslrem.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslrem.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslreorient2std.Rd            |    6 
 fslr-1.6.4.0/fslr/man/fslreorient2std.help.Rd       |    4 
 fslr-1.6.4.0/fslr/man/fslroi.Rd                     |only
 fslr-1.6.4.0/fslr/man/fslsd.Rd                      |only
 fslr-1.6.4.0/fslr/man/fslsin.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslsin.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslsmooth.Rd                  |   15 
 fslr-1.6.4.0/fslr/man/fslsmooth.help.Rd             |    6 
 fslr-1.6.4.0/fslr/man/fslsqr.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslsqr.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslsqrt.Rd                    |   10 
 fslr-1.6.4.0/fslr/man/fslsqrt.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslstats.Rd                   |   13 
 fslr-1.6.4.0/fslr/man/fslstats.help.Rd              |    7 
 fslr-1.6.4.0/fslr/man/fslsub.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fslsub.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslsub2.Rd                    |   12 
 fslr-1.6.4.0/fslr/man/fslsub2.help.Rd               |    6 
 fslr-1.6.4.0/fslr/man/fslsum.Rd                     |    9 
 fslr-1.6.4.0/fslr/man/fslswapdim.Rd                 |    6 
 fslr-1.6.4.0/fslr/man/fslswapdim.help.Rd            |    4 
 fslr-1.6.4.0/fslr/man/fsltan.Rd                     |   10 
 fslr-1.6.4.0/fslr/man/fsltan.help.Rd                |    6 
 fslr-1.6.4.0/fslr/man/fslthresh.Rd                  |   12 
 fslr-1.6.4.0/fslr/man/fslthresh.help.Rd             |    6 
 fslr-1.6.4.0/fslr/man/fslval.Rd                     |    6 
 fslr-1.6.4.0/fslr/man/fslval.help.Rd                |    4 
 fslr-1.6.4.0/fslr/man/fslview.Rd                    |    4 
 fslr-1.6.4.0/fslr/man/fslview.help.Rd               |    4 
 fslr-1.6.4.0/fslr/man/fslvol.Rd                     |    4 
 fslr-1.6.4.0/fslr/man/fslvolume.Rd                  |only
 fslr-1.6.4.0/fslr/man/get.fsl.Rd                    |    7 
 fslr-1.6.4.0/fslr/man/get.fsloutput.Rd              |    4 
 fslr-1.6.4.0/fslr/man/get.imgext.Rd                 |    4 
 fslr-1.6.4.0/fslr/man/getEmptyImageDimensions.Rd    |only
 fslr-1.6.4.0/fslr/man/getForms.Rd                   |    8 
 fslr-1.6.4.0/fslr/man/have.fsl.Rd                   |    2 
 fslr-1.6.4.0/fslr/man/intent_code-methods.Rd        |    4 
 fslr-1.6.4.0/fslr/man/intent_name-methods.Rd        |    4 
 fslr-1.6.4.0/fslr/man/intent_p1-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/intent_p2-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/intent_p3-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/magic-methods.Rd              |    4 
 fslr-1.6.4.0/fslr/man/maskEmptyImageDimensions.Rd   |only
 fslr-1.6.4.0/fslr/man/mask_img.Rd                   |    4 
 fslr-1.6.4.0/fslr/man/mcflirt.Rd                    |only
 fslr-1.6.4.0/fslr/man/mcflirt.help.Rd               |only
 fslr-1.6.4.0/fslr/man/melodic.Rd                    |    4 
 fslr-1.6.4.0/fslr/man/melodic.help.Rd               |    4 
 fslr-1.6.4.0/fslr/man/mni_fname.Rd                  |only
 fslr-1.6.4.0/fslr/man/mni_img.Rd                    |only
 fslr-1.6.4.0/fslr/man/multi_overlay.Rd              |only
 fslr-1.6.4.0/fslr/man/newnii.Rd                     |    4 
 fslr-1.6.4.0/fslr/man/niftiarr.Rd                   |    2 
 fslr-1.6.4.0/fslr/man/nii.stub.Rd                   |    4 
 fslr-1.6.4.0/fslr/man/orientation-methods.Rd        |    6 
 fslr-1.6.4.0/fslr/man/ortho2.Rd                     |   16 
 fslr-1.6.4.0/fslr/man/ortho_diff.Rd                 |   11 
 fslr-1.6.4.0/fslr/man/pixdim-methods.Rd             |    4 
 fslr-1.6.4.0/fslr/man/qform_code-methods.Rd         |    4 
 fslr-1.6.4.0/fslr/man/readNIfTI2.Rd                 |   15 
 fslr-1.6.4.0/fslr/man/replace_dropped_dimensions.Rd |only
 fslr-1.6.4.0/fslr/man/rescale_img.Rd                |   14 
 fslr-1.6.4.0/fslr/man/robust_window.Rd              |    6 
 fslr-1.6.4.0/fslr/man/scl_inter-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/scl_slope-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/sform_code-methods.Rd         |    4 
 fslr-1.6.4.0/fslr/man/sizeof_hdr-methods.Rd         |    4 
 fslr-1.6.4.0/fslr/man/slice_code-methods.Rd         |    4 
 fslr-1.6.4.0/fslr/man/slice_duration-methods.Rd     |    4 
 fslr-1.6.4.0/fslr/man/slice_end-methods.Rd          |    4 
 fslr-1.6.4.0/fslr/man/slice_start-methods.Rd        |    4 
 fslr-1.6.4.0/fslr/man/susan.Rd                      |   12 
 fslr-1.6.4.0/fslr/man/susan.help.Rd                 |    4 
 fslr-1.6.4.0/fslr/man/tempimg.Rd                    |   16 
 fslr-1.6.4.0/fslr/man/toffset-methods.Rd            |    4 
 fslr-1.6.4.0/fslr/man/vox_offset-methods.Rd         |    4 
 fslr-1.6.4.0/fslr/man/window_img.Rd                 |    6 
 fslr-1.6.4.0/fslr/man/writeNIfTI2.Rd                |   19 
 fslr-1.6.4.0/fslr/man/xyz.Rd                        |    2 
 fslr-1.6.4.0/fslr/man/zero_pad.Rd                   |only
 fslr-1.6.4.0/fslr/man/zlimmer.Rd                    |only
 fslr-1.6.4.0/fslr/man/zscore_img.Rd                 |   14 
 fslr-1.6.4.0/fslr/vignettes/fslr.Rmd                |    2 
 300 files changed, 1762 insertions(+), 1357 deletions(-)

More information about fslr at CRAN
Permanent link

Package blackbox updated to version 1.0.8 with previous version 1.0 dated 2016-04-14

Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph], Leblois Raphaël [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between blackbox versions 1.0 dated 2016-04-14 and 1.0.8 dated 2016-05-25

 DESCRIPTION                  |   16 +++++-----
 MD5                          |   63 ++++++++++++++++++++++---------------------
 NAMESPACE                    |    2 -
 R/Cpredict.R                 |   24 ++++++++++------
 R/LRTfn.R                    |    4 +-
 R/OKrig.R                    |    3 --
 R/blackbox.R                 |    2 -
 R/buildFONKgpointls.R        |    2 -
 R/calcPredictorOK.R          |    2 -
 R/calcProfileOK.R            |    2 -
 R/calcgridRelProfile.R       |   21 ++++++++------
 R/canonize.R                 |   57 ++++++++++++++++++++++++++++++--------
 R/findReplicates.R           |    2 -
 R/findglobalMLE.R            |    2 -
 R/fromFONKtoanyspace.R       |    4 +-
 R/generateNewPoints.R        |   46 ++++++++-----------------------
 R/generateNextpointsfromCI.R |   38 +++++++++++++++----------
 R/overmessage.R              |    7 ----
 R/profileFn.R                |    4 +-
 R/providefullhull.R          |    4 +-
 R/prune_by_dist.R            |only
 R/rhull.R                    |    4 +-
 R/sampleByResp.R             |    9 ++----
 R/savePredictor.R            |   23 ++++++++++++---
 R/subHullWrapper.R           |   35 +++++++++--------------
 R/zoomProfile.R              |    2 -
 inst                         |only
 man/blackbox-internal.Rd     |    5 +--
 src/Krigmain.cpp             |    5 ++-
 src/Makevars.win             |only
 src/Matern.h                 |    2 -
 src/pointls.cpp              |    3 +-
 src/qr.h                     |    6 ++--
 src/smoothFriends.h          |    6 ++--
 34 files changed, 218 insertions(+), 187 deletions(-)

More information about blackbox at CRAN
Permanent link

Package Rlabkey updated to version 2.1.130 with previous version 2.1.129 dated 2015-12-15

Title: Data Exchange Between R and LabKey Server
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

Diff between Rlabkey versions 2.1.129 dated 2015-12-15 and 2.1.130 dated 2016-05-25

 DESCRIPTION                         |   10 -
 MD5                                 |   96 +++++++-------
 NAMESPACE                           |   44 +++---
 NEWS                                |  208 ++++++++++++++++---------------
 R/labkey.defaults.R                 |only
 R/labkey.deleteRows.R               |  162 ++++++++----------------
 R/labkey.executeSql.R               |   72 ++--------
 R/labkey.getFolders.R               |   48 -------
 R/labkey.getQueryInfo.R             |   40 ------
 R/labkey.getQueryLists.R            |   51 +------
 R/labkey.getSchemas.R               |   40 ------
 R/labkey.importRows.R               |   53 --------
 R/labkey.insertRows.R               |  162 +++++++++---------------
 R/labkey.saveBatch.R                |  224 +++++++++++++--------------------
 R/labkey.selectRows.R               |   66 +--------
 R/labkey.updateRows.R               |  164 ++++++++----------------
 R/makeDF.R                          |   30 +++-
 R/makeFilter.R                      |  238 ++++++++++++++++++------------------
 R/schemaObjects.R                   |    2 
 build/vignette.rds                  |binary
 inst/doc/RlabkeyExample.Rnw         |   12 -
 inst/doc/usersguide.pdf             |binary
 man/Rlabkey-package.Rd              |  143 ++++++++++-----------
 man/RlabkeyUsersGuide.Rd            |   48 +++----
 man/getFolderPath.Rd                |   62 ++++-----
 man/getLookups.Rd                   |  102 +++++++--------
 man/getRows.Rd                      |   98 +++++++-------
 man/getSchema.Rd                    |  100 +++++++--------
 man/getSession.Rd                   |  186 ++++++++++++++--------------
 man/labkey.deleteRows.Rd            |  208 +++++++++++++++----------------
 man/labkey.executeSql.Rd            |  162 ++++++++++++------------
 man/labkey.getDefaultViewDetails.Rd |   96 +++++++-------
 man/labkey.getFolders.Rd            |  106 ++++++++--------
 man/labkey.getLookupDetails.Rd      |  150 +++++++++++-----------
 man/labkey.getQueries.Rd            |  104 +++++++--------
 man/labkey.getQueryDetails.Rd       |  170 ++++++++++++-------------
 man/labkey.getQueryViews.Rd         |  108 ++++++++--------
 man/labkey.getSchemas.Rd            |   98 +++++++-------
 man/labkey.insertRows.Rd            |  182 +++++++++++++--------------
 man/labkey.makeRemotePath.Rd        |   90 ++++++-------
 man/labkey.saveBatch.Rd             |  150 +++++++++++-----------
 man/labkey.selectRows.Rd            |  224 ++++++++++++++++-----------------
 man/labkey.setDefaults.Rd           |only
 man/labkey.updateRows.Rd            |  188 ++++++++++++++--------------
 man/lsFolders.Rd                    |   78 +++++------
 man/lsProjects.Rd                   |   70 +++++-----
 man/lsSchemas.Rd                    |   70 +++++-----
 man/makeFilter.Rd                   |  222 ++++++++++++++++-----------------
 man/saveResults.Rd                  |  124 +++++++++---------
 vignettes/RlabkeyExample.Rnw        |   12 -
 50 files changed, 2317 insertions(+), 2756 deletions(-)

More information about Rlabkey at CRAN
Permanent link

Package mlt.docreg updated to version 0.0-32 with previous version 0.0-30 dated 2016-02-24

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt.docreg versions 0.0-30 dated 2016-02-24 and 0.0-32 dated 2016-05-25

 DESCRIPTION        |   18 +++----
 MD5                |   16 +++---
 build/vignette.rds |binary
 inst/NEWS.Rd       |    7 ++
 inst/doc/mlt.R     |   72 +++++++++++++++++++++++++----
 inst/doc/mlt.Rnw   |  129 ++++++++++++++++++++++++++++++++++++++++++++---------
 inst/doc/mlt.pdf   |binary
 vignettes/mlt.Rnw  |  129 ++++++++++++++++++++++++++++++++++++++++++++---------
 vignettes/mlt.bib  |   27 +++++------
 9 files changed, 316 insertions(+), 82 deletions(-)

More information about mlt.docreg at CRAN
Permanent link

Package mlt updated to version 0.0-33 with previous version 0.0-32 dated 2016-05-25

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt versions 0.0-32 dated 2016-05-25 and 0.0-33 dated 2016-05-25

 DESCRIPTION  |    8 ++++----
 MD5          |    6 +++---
 R/R.R        |    2 +-
 inst/NEWS.Rd |    7 +++++++
 4 files changed, 15 insertions(+), 8 deletions(-)

More information about mlt at CRAN
Permanent link

Package mcPAFit updated to version 0.1.3 with previous version 0.1.2 dated 2016-05-17

Title: Estimating Preferential Attachment from a Single Network Snapshot by Markov Chain Monte Carlo
Description: A Markov chain Monte Carlo method is provided to estimate the preferential attachment function from a single network snapshot. Conventional methods require the complete information about the appearance order of all nodes and edges in the network. This package incorporates the appearance order into the state space and estimates it together with the preferential attachment function. Auxiliary variables are introduced to facilitate fast Gibbs sampling.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>

Diff between mcPAFit versions 0.1.2 dated 2016-05-17 and 0.1.3 dated 2016-05-25

 DESCRIPTION            |   14 
 MD5                    |   16 
 NAMESPACE              |    1 
 R/create_sim_data.R    |    7 
 R/mcPAFit.R            |   11 
 man/create_sim_data.Rd |   24 -
 man/mcPAFit-package.Rd |   22 -
 man/mcPAFit.Rd         |   87 +---
 src/Cpp_code.cpp       |  861 ++++++++++++++++++++++---------------------------
 9 files changed, 481 insertions(+), 562 deletions(-)

More information about mcPAFit at CRAN
Permanent link

Package genie updated to version 1.0.2 with previous version 1.0.0 dated 2016-03-07

Title: A New, Fast, and Outlier Resistant Hierarchical Clustering Algorithm
Description: A new hierarchical clustering linkage criterion: the Genie algorithm links two clusters in such a way that a chosen economic inequity measure (e.g., the Gini index) of the cluster sizes does not increase drastically above a given threshold. Benchmarks indicate a high practical usefulness of the introduced method: it most often outperforms the Ward or average linkage in terms of the clustering quality while retaining the single linkage speed, see (Gagolewski et al. 2016 <DOI:10.1016/j.ins.2016.05.003>) for more details.
Author: Marek Gagolewski [aut, cre], Maciej Bartoszuk [aut], Anna Cena [aut]
Maintainer: Marek Gagolewski <gagolews@rexamine.com>

Diff between genie versions 1.0.0 dated 2016-03-07 and 1.0.2 dated 2016-05-25

 DESCRIPTION                  |   14 +++++++++-----
 MD5                          |   15 ++++++++-------
 NEWS                         |   11 +++++++++++
 R/genie-package.R            |   13 +++++--------
 R/hclust2.R                  |    2 +-
 inst                         |only
 man/genie-package.Rd         |    7 +++++--
 man/hclust2.Rd               |    2 +-
 tests/testthat/test-single.R |    2 ++
 9 files changed, 42 insertions(+), 24 deletions(-)

More information about genie at CRAN
Permanent link

Package BigVAR updated to version 1.0.1 with previous version 1.0 dated 2016-05-17

Title: Dimension Reduction Methods for Multivariate Time Series
Description: Estimates VAR and VARX models with structured Lasso Penalties.
Author: Will Nicholson [cre, aut], David Matteson [aut], Jacob Bien [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>

Diff between BigVAR versions 1.0 dated 2016-05-17 and 1.0.1 dated 2016-05-25

 DESCRIPTION                                |    6 
 MD5                                        |   53 ++--
 NAMESPACE                                  |    2 
 NEWS                                       |only
 R/BigVAR.R                                 |    2 
 R/BigVARAlgorithms.R                       |   96 ++++---
 R/BigVARObjectClass.R                      |  192 ++++++++-------
 R/BigVARSupportFunctions.R                 |  161 +++++++-----
 man/A.Rd                                   |    2 
 man/BigVAR-class.Rd                        |    4 
 man/BigVAR.Rd                              |    4 
 man/BigVAR.est-methods.Rd                  |    2 
 man/BigVAR.results-plot-methods.Rd         |    2 
 man/BigVAR.results.Rd                      |    2 
 man/MultVarSim.Rd                          |    2 
 man/SparsityPlot.BigVAR.results-methods.Rd |    2 
 man/VARXFit.Rd                             |    5 
 man/VARXForecastEval.Rd                    |    3 
 man/VarptoVar1MC.Rd                        |    2 
 man/Y.Rd                                   |    2 
 man/constructModel.Rd                      |   27 +-
 man/cv.BigVAR-methods.Rd                   |    4 
 man/plot.BigVAR-methods.Rd                 |    2 
 man/predict-methods-BigVAR.results.Rd      |    2 
 man/show-methods-BigVAR.results.Rd         |    2 
 man/show-methods.Rd                        |    4 
 src/DataCons.cpp                           |  365 +++++++++++++++++++++++------
 src/ExperimentalBigVARFunctionsX.cpp       |   30 +-
 28 files changed, 647 insertions(+), 333 deletions(-)

More information about BigVAR at CRAN
Permanent link

Package SeqFeatR updated to version 0.2.3 with previous version 0.2.2 dated 2016-03-24

Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>

Diff between SeqFeatR versions 0.2.2 dated 2016-03-24 and 0.2.3 dated 2016-05-25

 DESCRIPTION                           |   12 +-
 MD5                                   |   13 +-
 NAMESPACE                             |   13 ++
 NEWS                                  |    6 +
 R/comparewithancestral.R              |    8 -
 inst/doc/SeqFeatR_tutorial.pdf        |binary
 inst/extdata/Example_aa_for_cwa.fasta |only
 man/comparewithancestral.Rd           |  156 +++++++++++++++++-----------------
 8 files changed, 112 insertions(+), 96 deletions(-)

More information about SeqFeatR at CRAN
Permanent link

Package kantorovich updated to version 2.0.0 with previous version 1.1.0 dated 2016-02-04

Title: Kantorovich Distance Between Probability Measures
Description: Computes the Kantorovich distance between two probability measures on a finite set.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>

Diff between kantorovich versions 1.1.0 dated 2016-02-04 and 2.0.0 dated 2016-05-25

 DESCRIPTION                      |   10 +-
 MD5                              |   32 ++++----
 NAMESPACE                        |    9 +-
 R/kantorovich.R                  |    8 --
 R/kantorovich_glpk.R             |only
 R/kantorovich_lpsolve.R          |only
 build/vignette.rds               |binary
 inst/doc/kantorovich.R           |   18 ++++
 inst/doc/kantorovich.Rmd         |   39 +++++++++
 inst/doc/kantorovich.html        |  155 +++++++++++++++++++++++++--------------
 man/kantorovich-package.Rd       |    4 -
 man/kantorovich_glpk.Rd          |only
 man/kantorovich_lp.Rd            |only
 tests/testthat/test-Pascal.R     |   66 +++++++++++++++-
 tests/testthat/test-edistances.R |    2 
 tests/testthat/test-ejoinings.R  |    4 -
 tests/testthat/test-glpk.R       |only
 tests/testthat/test-lpSolve.R    |only
 tests/testthat/test-rotation.R   |   32 +++++++-
 vignettes/kantorovich.Rmd        |   39 +++++++++
 20 files changed, 327 insertions(+), 91 deletions(-)

More information about kantorovich at CRAN
Permanent link

Package Haplin updated to version 6.0 with previous version 5.5 dated 2015-05-15

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@fhi.no>

Diff between Haplin versions 5.5 dated 2015-05-15 and 6.0 dated 2016-05-25

 Haplin-5.5/Haplin/R/f.make.design.R               |only
 Haplin-6.0/Haplin/DESCRIPTION                     |   15 
 Haplin-6.0/Haplin/MD5                             |  147 +++++----
 Haplin-6.0/Haplin/NAMESPACE                       |   55 +--
 Haplin-6.0/Haplin/R/coef.tri.glm.R                |    4 
 Haplin-6.0/Haplin/R/f.EM.missing.R                |   31 +-
 Haplin-6.0/Haplin/R/f.Rplot.R                     |   31 +-
 Haplin-6.0/Haplin/R/f.catch.R                     |    3 
 Haplin-6.0/Haplin/R/f.check.pars.R                |  110 +++----
 Haplin-6.0/Haplin/R/f.compute.effects.R           |    6 
 Haplin-6.0/Haplin/R/f.data.R                      |   38 +-
 Haplin-6.0/Haplin/R/f.debug.pvalues.R             |   18 -
 Haplin-6.0/Haplin/R/f.design.make.R               |only
 Haplin-6.0/Haplin/R/f.final.loglike.R             |    4 
 Haplin-6.0/Haplin/R/f.hapArg.R                    |only
 Haplin-6.0/Haplin/R/f.hapSim.R                    |only
 Haplin-6.0/Haplin/R/f.hapTests.R                  |only
 Haplin-6.0/Haplin/R/f.jackknife.R                 |   14 
 Haplin-6.0/Haplin/R/f.make.index.R                |   26 +
 Haplin-6.0/Haplin/R/f.plot.effects.R              |   59 +--
 Haplin-6.0/Haplin/R/f.pos.match.R                 |    2 
 Haplin-6.0/Haplin/R/f.preliminary.freq.R          |   55 +--
 Haplin-6.0/Haplin/R/f.prep.dataout.R              |    8 
 Haplin-6.0/Haplin/R/f.prob.R                      |   95 +++---
 Haplin-6.0/Haplin/R/f.rand.geno.R                 |    7 
 Haplin-6.0/Haplin/R/f.redistribute.R              |   23 -
 Haplin-6.0/Haplin/R/f.repl.thin.R                 |    2 
 Haplin-6.0/Haplin/R/f.sel.haplos.R                |   59 ++-
 Haplin-6.0/Haplin/R/f.sel.markers.R               |    5 
 Haplin-6.0/Haplin/R/f.sim.R                       |   35 +-
 Haplin-6.0/Haplin/R/f.var.covar.R                 |    6 
 Haplin-6.0/Haplin/R/gxe.R                         |only
 Haplin-6.0/Haplin/R/hapPower.R                    |only
 Haplin-6.0/Haplin/R/hapRun.R                      |only
 Haplin-6.0/Haplin/R/hapSim.R                      |only
 Haplin-6.0/Haplin/R/haplin.R                      |  237 ++++++++-------
 Haplin-6.0/Haplin/R/haplinSlide.R                 |   97 ++----
 Haplin-6.0/Haplin/R/haplinStrat.R                 |   11 
 Haplin-6.0/Haplin/R/haptable.gxe.R                |only
 Haplin-6.0/Haplin/R/haptable.haplin.R             |   11 
 Haplin-6.0/Haplin/R/haptable.haplinSlide.R        |    4 
 Haplin-6.0/Haplin/R/haptable.haplinStrat.R        |    4 
 Haplin-6.0/Haplin/R/plot.haplin.R                 |   30 -
 Haplin-6.0/Haplin/R/print.gxe.R                   |only
 Haplin-6.0/Haplin/R/print.haplin.R                |    2 
 Haplin-6.0/Haplin/R/print.summary.haplin.R        |    2 
 Haplin-6.0/Haplin/R/print.summary.tri.glm.R       |   20 -
 Haplin-6.0/Haplin/R/suest.R                       |   22 -
 Haplin-6.0/Haplin/R/summary.haplin.R              |   41 +-
 Haplin-6.0/Haplin/R/summary.tri.glm.R             |   19 -
 Haplin-6.0/Haplin/inst/doc/Haplin_data_format.pdf |binary
 Haplin-6.0/Haplin/inst/doc/Haplin_power.pdf       |only
 Haplin-6.0/Haplin/inst/doc/index.html             |    3 
 Haplin-6.0/Haplin/man/cbindFiles.Rd               |   98 +++---
 Haplin-6.0/Haplin/man/convertPed.Rd               |  204 ++++++-------
 Haplin-6.0/Haplin/man/gwaaToHaplin.Rd             |  118 +++----
 Haplin-6.0/Haplin/man/gxe.Rd                      |only
 Haplin-6.0/Haplin/man/hapPower.Rd                 |only
 Haplin-6.0/Haplin/man/hapRun.Rd                   |only
 Haplin-6.0/Haplin/man/hapSim.Rd                   |only
 Haplin-6.0/Haplin/man/haplin.Rd                   |  296 +++++++++----------
 Haplin-6.0/Haplin/man/haplinSlide.Rd              |  146 ++++-----
 Haplin-6.0/Haplin/man/haplinStrat.Rd              |only
 Haplin-6.0/Haplin/man/haplinTDT.Rd                |  336 +++++++++++-----------
 Haplin-6.0/Haplin/man/haptable.Rd                 |  148 ++++-----
 Haplin-6.0/Haplin/man/lineByLine.Rd               |  166 +++++-----
 Haplin-6.0/Haplin/man/output.Rd                   |   86 ++---
 Haplin-6.0/Haplin/man/pQQ.Rd                      |   66 ++--
 Haplin-6.0/Haplin/man/pedToHaplin.Rd              |  110 +++----
 Haplin-6.0/Haplin/man/plot.haplin.Rd              |   94 +++---
 Haplin-6.0/Haplin/man/plot.haplinTDT.Rd           |   90 ++---
 Haplin-6.0/Haplin/man/plot.haptable.Rd            |  116 +++----
 Haplin-6.0/Haplin/man/prepPed.Rd                  |  120 +++----
 Haplin-6.0/Haplin/man/print.haplin.Rd             |   64 ++--
 Haplin-6.0/Haplin/man/print.summary.haplin.Rd     |   88 ++---
 Haplin-6.0/Haplin/man/rbindFiles.Rd               |  122 +++----
 Haplin-6.0/Haplin/man/snpPos.Rd                   |    2 
 Haplin-6.0/Haplin/man/snpPower.Rd                 |  144 ++++-----
 Haplin-6.0/Haplin/man/snpSampleSize.Rd            |  137 ++++----
 Haplin-6.0/Haplin/man/suest.Rd                    |  142 ++++-----
 Haplin-6.0/Haplin/man/summary.haplin.Rd           |   80 ++---
 Haplin-6.0/Haplin/man/summary.haplinTDT.Rd        |   68 ++--
 Haplin-6.0/Haplin/man/toDataFrame.Rd              |   58 +--
 83 files changed, 2286 insertions(+), 2174 deletions(-)

More information about Haplin at CRAN
Permanent link

Package Directional updated to version 2.0 with previous version 1.9 dated 2016-04-21

Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

Diff between Directional versions 1.9 dated 2016-04-21 and 2.0 dated 2016-05-25

 DESCRIPTION                |   10 +-
 MD5                        |   90 ++++++++++++++-----------
 NAMESPACE                  |    8 +-
 R/acg.R                    |   18 +++--
 R/circ.cor1.R              |   19 +++--
 R/circ.cor2.R              |   25 ++++---
 R/circlin.cor.R            |   13 ++-
 R/conc.test.R              |   13 ++-
 R/dirknn.tune.R            |    6 -
 R/euclid.R                 |    3 
 R/f.rbing.R                |    1 
 R/group.gof.R              |only
 R/group.vm.R               |only
 R/hcf.aov.R                |   10 ++
 R/hcf.circaov.R            |    9 ++
 R/kent.contour.R           |   12 +--
 R/kent.logcon.R            |only
 R/kent.mle.R               |   42 ++++++++---
 R/lambert.inv.R            |    9 +-
 R/matrixfisher.mle.R       |only
 R/meandir.test.R           |   36 +++++-----
 R/mediandir.R              |   13 +--
 R/mediandir_2.R            |   14 +--
 R/mix.vmf.R                |  159 ++++++++++++++++++++++++++-------------------
 R/pvm.R                    |only
 R/rbingham.R               |   54 ++++++++++++---
 R/rfb.R                    |    4 -
 R/rkent.R                  |    5 -
 R/rmatrixfisher.R          |only
 R/rvmf.R                   |   16 ++--
 R/spher.reg.R              |    7 +
 R/spml.reg.R               |   47 ++++++++-----
 R/vmf.contour.R            |   14 ++-
 R/vmf.kde.R                |    2 
 R/vmfkde.tune.R            |   10 +-
 R/wood.mle.R               |   40 +++++++----
 man/Directional-package.Rd |   14 +--
 man/fb.saddle.Rd           |   28 +++++--
 man/group.gof.Rd           |only
 man/group.vm.Rd            |only
 man/kent.logcon.Rd         |only
 man/kent.mle.Rd            |   16 ++++
 man/kuiper.Rd              |    2 
 man/lambert.Rd             |   10 ++
 man/matrixfisher.mle.Rd    |only
 man/pvm.Rd                 |only
 man/rfb.Rd                 |    6 -
 man/rkent.Rd               |    4 -
 man/rmatrixfisher.Rd       |only
 man/rvmf.Rd                |    2 
 man/spml.reg.Rd            |    3 
 man/wood.mle.Rd            |   11 +++
 52 files changed, 512 insertions(+), 293 deletions(-)

More information about Directional at CRAN
Permanent link

New package condSURV with initial version 0.1.0
Package: condSURV
Type: Package
Title: Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data
Version: 0.1.0
Date: 2016-05-25
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Luis Meira-Machado <lmachado@math.uminho.pt>
Description: Method to implement some newly developed methods for the estimation of the conditional survival function.
Depends: R (>= 3.0.1)
License: GPL (>= 2)
LazyData: TRUE
Imports: KernSmooth, doParallel, parallel, doRNG, foreach
NeedsCompilation: yes
Packaged: 2016-05-25 09:43:25 UTC; Sestelo
Repository: CRAN
Date/Publication: 2016-05-25 11:56:42

More information about condSURV at CRAN
Permanent link

Package mlt updated to version 0.0-32 with previous version 0.0-30 dated 2016-02-20

Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation models via the most likely transformation approach.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt versions 0.0-30 dated 2016-02-20 and 0.0-32 dated 2016-05-25

 mlt-0.0-30/mlt/tests/AFT-Ex.Rout.save   |only
 mlt-0.0-30/mlt/tests/GBSG2.Rout.save    |only
 mlt-0.0-32/mlt/DESCRIPTION              |    8 ++---
 mlt-0.0-32/mlt/MD5                      |   39 +++++++++++++--------------
 mlt-0.0-32/mlt/NAMESPACE                |   11 ++++++-
 mlt-0.0-32/mlt/R/confband.R             |    2 -
 mlt-0.0-32/mlt/R/ctm.R                  |   45 ++++++++++++++++++++++++++++++--
 mlt-0.0-32/mlt/R/distr.R                |   26 +++++++++++-------
 mlt-0.0-32/mlt/R/dpq_etc.R              |   45 ++++++++++++++++----------------
 mlt-0.0-32/mlt/R/loglik.R               |   19 ++++++++-----
 mlt-0.0-32/mlt/R/methods.R              |   15 +++++++++-
 mlt-0.0-32/mlt/R/mlt.R                  |   35 ++++++++++++++----------
 mlt-0.0-32/mlt/R/plot.R                 |   14 +++++++--
 mlt-0.0-32/mlt/R/predict.R              |   16 ++++++++---
 mlt-0.0-32/mlt/R/sample.R               |   22 ++++++++++-----
 mlt-0.0-32/mlt/inst/NEWS.Rd             |   23 ++++++++++++++++
 mlt-0.0-32/mlt/man/ctm-methods.Rd       |only
 mlt-0.0-32/mlt/man/mlt-methods.Rd       |    9 +++++-
 mlt-0.0-32/mlt/man/predict.Rd           |   17 +++++++++---
 mlt-0.0-32/mlt/tests/Cox-Ex.Rout.save   |    8 ++---
 mlt-0.0-32/mlt/tests/bugfixes.Rout.save |   14 ++++-----
 mlt-0.0-32/mlt/tests/lm-Ex.Rout.save    |   10 +++----
 22 files changed, 257 insertions(+), 121 deletions(-)

More information about mlt at CRAN
Permanent link

Package treethresh updated to version 0.1-9 with previous version 0.1-8 dated 2014-11-20

Title: Methods for Tree-Based Local Adaptive Thresholding
Description: An implementation of TreeThresh, a locally adaptive version of EbayesThresh.
Author: Ludger Evers <ludger.evers@glasgow.ac.uk> and Tim Heaton <t.heaton@sheffield.ac.uk>
Maintainer: Ludger Evers <ludger.evers@glasgow.ac.uk>

Diff between treethresh versions 0.1-8 dated 2014-11-20 and 0.1-9 dated 2016-05-25

 DESCRIPTION              |   13 ++++++-------
 MD5                      |   11 +++++++----
 NAMESPACE                |   34 ++++++++++++++++++----------------
 build/vignette.rds       |binary
 inst/doc/onedwavillu.pdf |only
 inst/doc/prune.pdf       |only
 inst/doc/twodwavillu.pdf |only
 man/coefficients.Rd      |    2 +-
 8 files changed, 32 insertions(+), 28 deletions(-)

More information about treethresh at CRAN
Permanent link

Package simcausal updated to version 0.5.1 with previous version 0.5.0 dated 2016-02-20

Title: Simulating Longitudinal Data with Causal Inference Applications
Description: A flexible tool for simulating complex longitudinal data using structural equations, with emphasis on problems in causal inference. Specify interventions and simulate from intervened data generating distributions. Define and evaluate treatment-specific means, the average treatment effects and coefficients from working marginal structural models. User interface designed to facilitate the conduct of transparent and reproducible simulation studies, and allows concise expression of complex functional dependencies for a large number of time-varying nodes. See the package vignette for more information, documentation and examples.
Author: Oleg Sofrygin [aut, cre], Mark J. van der Laan [aut], Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>

Diff between simcausal versions 0.5.0 dated 2016-02-20 and 0.5.1 dated 2016-05-25

 simcausal-0.5.0/simcausal/R/estimatetarget.r                     |only
 simcausal-0.5.0/simcausal/R/parserfunctions.r                    |only
 simcausal-0.5.0/simcausal/man/DAG_Class.Rd                       |only
 simcausal-0.5.0/simcausal/man/Node_Class.Rd                      |only
 simcausal-0.5.0/simcausal/man/rcategor.Rd                        |only
 simcausal-0.5.0/simcausal/man/rcategor.int.Rd                    |only
 simcausal-0.5.1/simcausal/DESCRIPTION                            |    9 
 simcausal-0.5.1/simcausal/MD5                                    |  146 -
 simcausal-0.5.1/simcausal/NAMESPACE                              |   10 
 simcausal-0.5.1/simcausal/NEWS                                   |    9 
 simcausal-0.5.1/simcausal/R/DAG_node_R6.R                        |   33 
 simcausal-0.5.1/simcausal/R/distributions.R                      |  135 -
 simcausal-0.5.1/simcausal/R/network.R                            |   70 
 simcausal-0.5.1/simcausal/R/network_distributions.R              |only
 simcausal-0.5.1/simcausal/R/node.R                               |  126 -
 simcausal-0.5.1/simcausal/R/parserfunctions_R6.r                 |   91 -
 simcausal-0.5.1/simcausal/R/simcausal-package.r                  |   53 
 simcausal-0.5.1/simcausal/R/simcausal.r                          |   49 
 simcausal-0.5.1/simcausal/R/simulation.r                         |  102 -
 simcausal-0.5.1/simcausal/R/targetparam.r                        |  198 --
 simcausal-0.5.1/simcausal/README.md                              |   90 -
 simcausal-0.5.1/simcausal/build/vignette.rds                     |binary
 simcausal-0.5.1/simcausal/inst/doc/simcausal_vignette.R          |  339 +--
 simcausal-0.5.1/simcausal/inst/doc/simcausal_vignette.Rnw        |  592 +++---
 simcausal-0.5.1/simcausal/inst/doc/simcausal_vignette.pdf        |binary
 simcausal-0.5.1/simcausal/man/A.Rd                               |    3 
 simcausal-0.5.1/simcausal/man/DAG.empty.Rd                       |    2 
 simcausal-0.5.1/simcausal/man/DF.to.long.Rd                      |    4 
 simcausal-0.5.1/simcausal/man/DF.to.longDT.Rd                    |    4 
 simcausal-0.5.1/simcausal/man/Define_sVar.Rd                     |    6 
 simcausal-0.5.1/simcausal/man/N.Rd                               |    3 
 simcausal-0.5.1/simcausal/man/NetInd.to.sparseAdjMat.Rd          |    2 
 simcausal-0.5.1/simcausal/man/NetIndClass.Rd                     |    2 
 simcausal-0.5.1/simcausal/man/add.action.Rd                      |   34 
 simcausal-0.5.1/simcausal/man/add.nodes.Rd                       |    2 
 simcausal-0.5.1/simcausal/man/distr.list.Rd                      |    2 
 simcausal-0.5.1/simcausal/man/doLTCF.Rd                          |    6 
 simcausal-0.5.1/simcausal/man/eval.target.Rd                     |    6 
 simcausal-0.5.1/simcausal/man/igraph.to.sparseAdjMat.Rd          |    2 
 simcausal-0.5.1/simcausal/man/net.list.Rd                        |only
 simcausal-0.5.1/simcausal/man/network.Rd                         |   21 
 simcausal-0.5.1/simcausal/man/node.Rd                            |  311 ++-
 simcausal-0.5.1/simcausal/man/parents.Rd                         |    3 
 simcausal-0.5.1/simcausal/man/plotDAG.Rd                         |    2 
 simcausal-0.5.1/simcausal/man/plotSurvEst.Rd                     |    2 
 simcausal-0.5.1/simcausal/man/print.DAG.Rd                       |    2 
 simcausal-0.5.1/simcausal/man/print.DAG.action.Rd                |    2 
 simcausal-0.5.1/simcausal/man/print.DAG.node.Rd                  |    2 
 simcausal-0.5.1/simcausal/man/rbern.Rd                           |    7 
 simcausal-0.5.1/simcausal/man/rcat.b1.Rd                         |only
 simcausal-0.5.1/simcausal/man/rcat.factor.Rd                     |only
 simcausal-0.5.1/simcausal/man/rconst.Rd                          |   24 
 simcausal-0.5.1/simcausal/man/rdistr.template.Rd                 |   13 
 simcausal-0.5.1/simcausal/man/rnet.SmWorld.Rd                    |only
 simcausal-0.5.1/simcausal/man/rnet.gnm.Rd                        |only
 simcausal-0.5.1/simcausal/man/rnet.gnp.Rd                        |only
 simcausal-0.5.1/simcausal/man/set.DAG.Rd                         |  240 +-
 simcausal-0.5.1/simcausal/man/set.targetE.Rd                     |    2 
 simcausal-0.5.1/simcausal/man/set.targetMSM.Rd                   |    2 
 simcausal-0.5.1/simcausal/man/sim.Rd                             |   12 
 simcausal-0.5.1/simcausal/man/simcausal.Rd                       |    2 
 simcausal-0.5.1/simcausal/man/simfull.Rd                         |   10 
 simcausal-0.5.1/simcausal/man/simobs.Rd                          |   10 
 simcausal-0.5.1/simcausal/man/sparseAdjMat.to.NetInd.Rd          |    2 
 simcausal-0.5.1/simcausal/man/sparseAdjMat.to.igraph.Rd          |    2 
 simcausal-0.5.1/simcausal/man/vecfun.add.Rd                      |    2 
 simcausal-0.5.1/simcausal/man/vecfun.all.print.Rd                |    2 
 simcausal-0.5.1/simcausal/man/vecfun.print.Rd                    |    2 
 simcausal-0.5.1/simcausal/man/vecfun.remove.Rd                   |    2 
 simcausal-0.5.1/simcausal/man/vecfun.reset.Rd                    |    2 
 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_00.R           |  872 +++++-----
 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_01_nets.R      |    9 
 simcausal-0.5.1/simcausal/tests/RUnit/RUnit_tests_02_MV.R        |   38 
 simcausal-0.5.1/simcausal/tests/examples/MSM.examples.R          |only
 simcausal-0.5.1/simcausal/tests/examples/add.action.R            |   30 
 simcausal-0.5.1/simcausal/tests/examples/example.simnets.R       |   17 
 simcausal-0.5.1/simcausal/tests/examples/set.DAG.R               |  238 +-
 simcausal-0.5.1/simcausal/tests/examples/set.targetE.examples.R  |only
 simcausal-0.5.1/simcausal/tests/examples/sim.impute.examples12.R |    2 
 simcausal-0.5.1/simcausal/vignettes/SimCausal_Networks_2016.bib  |only
 simcausal-0.5.1/simcausal/vignettes/mystyles.sty                 |only
 simcausal-0.5.1/simcausal/vignettes/psi.n.mat.rda                |only
 simcausal-0.5.1/simcausal/vignettes/simcausal_vignette.Rnw       |  592 +++---
 83 files changed, 2392 insertions(+), 2217 deletions(-)

More information about simcausal at CRAN
Permanent link

New package rSARP with initial version 1.0.0
Package: rSARP
Title: Functions to Create and Evaluate Search and Rescue Plans
Version: 1.0.0
Author: John Hutcheson [aut, cre]
Maintainer: John Hutcheson <jacknx8a@gmail.com>
Description: Tools to create, evaluate, critique, revise, track progress, and communicate a detailed wilderness or urban search plan to management. This package uses and creates csv files in the R working directory to document inputs and results. It also creates a series of PDF and PNG files to accomplish communication of the plan. The program creates and revises search plans using Bayesian models. The package includes functions bestsearch(), searchstatus() and searchme() to model the number of searchers and hours required to search an area, calculate the probability of detection, probability of success, and project the best plan given limited resources.
Depends: R (>= 3.2.4)
Imports: ggplot2, lattice, qcc, grid, methods, grDevices, graphics, stats
License: GPL (>= 3)
LazyData: TRUE
BuildVignettes: TRUE
Packaged: 2016-05-24 16:10:22 UTC; NX8A
Suggests: R.rsp
VignetteBuilder: R.rsp
RoxygenNote: 5.0.1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-05-25 06:09:17

More information about rSARP at CRAN
Permanent link

Package PoisNonNor updated to version 1.1 with previous version 1.0 dated 2015-02-06

Title: Simultaneous Generation of Count and Continuous Data
Description: Generation of count (assuming Poisson distribution) and continuous data (using Fleishman polynomials) simultaneously.
Author: Hakan Demirtas, Yaru Shi, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>

Diff between PoisNonNor versions 1.0 dated 2015-02-06 and 1.1 dated 2016-05-25

 DESCRIPTION               |   16 ++---
 MD5                       |   14 ++--
 man/Param.fleishman.Rd    |   58 +++++++++---------
 man/PoisNonNor-package.Rd |   74 +++++++++++------------
 man/RNG_P_NN.Rd           |  144 +++++++++++++++++++++++-----------------------
 man/fleishman.roots.Rd    |   52 ++++++++--------
 man/intercor.NNP.Rd       |  106 ++++++++++++++++-----------------
 man/intercor.PP.Rd        |   78 ++++++++++++------------
 8 files changed, 271 insertions(+), 271 deletions(-)

More information about PoisNonNor at CRAN
Permanent link

Package MST updated to version 1.3 with previous version 1.2 dated 2015-12-01

Title: Multivariate Survival Trees
Description: Constructs trees for multivariate survival data using marginal and frailty models.
Author: Xiaogang Su [aut], Peter Calhoun [aut, cre], Juanjuan Fan [aut]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>

Diff between MST versions 1.2 dated 2015-12-01 and 1.3 dated 2016-05-25

 MST-1.2/MST/man/MST.plot.Rd              |only
 MST-1.2/MST/man/MST.plot.latex.Rd        |only
 MST-1.2/MST/man/bootstrap.grow.prune.Rd  |only
 MST-1.2/MST/man/bootstrap.size.Rd        |only
 MST-1.2/MST/man/grow.MST.Rd              |only
 MST-1.2/MST/man/prune.size.testsample.Rd |only
 MST-1.2/MST/man/send.down.Rd             |only
 MST-1.3/MST/DESCRIPTION                  |   10 ++--
 MST-1.3/MST/MD5                          |   37 ++++++++----------
 MST-1.3/MST/NAMESPACE                    |   12 +----
 MST-1.3/MST/R/MST.R                      |   63 +++++++++++++++++++++++--------
 MST-1.3/MST/R/MST.plot.R                 |    2 
 MST-1.3/MST/R/bootstrap.grow.prune.R     |    4 -
 MST-1.3/MST/R/grow.MST.R                 |    4 -
 MST-1.3/MST/R/listIntoParty.R            |only
 MST-1.3/MST/R/listIntoTree.R             |only
 MST-1.3/MST/R/partition.MST.R            |   43 +++++++++++++--------
 MST-1.3/MST/R/prune.size.testsample.R    |    2 
 MST-1.3/MST/R/sortTree.R                 |    3 -
 MST-1.3/MST/R/splitting.stat.MST2.R      |    9 ++--
 MST-1.3/MST/R/splitting.stat.MST3.R      |only
 MST-1.3/MST/R/splitting.stat.MST4.R      |only
 MST-1.3/MST/man/MST-package.Rd           |   31 ++++++++++-----
 MST-1.3/MST/man/MST.Rd                   |   48 ++++++++++++-----------
 MST-1.3/MST/man/rmultime.Rd              |    6 +-
 25 files changed, 163 insertions(+), 111 deletions(-)

More information about MST at CRAN
Permanent link

Package BinOrdNonNor updated to version 1.1 with previous version 1.0 dated 2015-02-03

Title: Concurrent Generation of Binary, Ordinal and Continuous Data
Description: Generation of samples from a mix of binary, ordinal and continuous random variables with a pre-specified correlation matrix and marginal distributions.
Author: Hakan Demirtas, Yue Wang, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>

Diff between BinOrdNonNor versions 1.0 dated 2015-02-03 and 1.1 dated 2016-05-25

 DESCRIPTION                 |   14 ++---
 MD5                         |   10 +--
 NAMESPACE                   |    4 +
 man/BinOrdNonNor-package.Rd |   68 ++++++++++++------------
 man/IntermediateONN.Rd      |   72 ++++++++++++-------------
 man/genBinOrdNN.Rd          |  122 ++++++++++++++++++++++----------------------
 6 files changed, 146 insertions(+), 144 deletions(-)

More information about BinOrdNonNor at CRAN
Permanent link

Tue, 24 May 2016

Package shinystan updated to version 2.2.0 with previous version 2.1.0 dated 2016-01-06

Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
Description: A graphical user interface for interactive Markov chain Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by RStudio's Shiny web application framework and works with the output of MCMC programs written in any programming language (and has extended functionality for Stan models fit using the rstan and rstanarm packages).
Author: Jonah Gabry [aut, cre], Stan Development Team [ctb], Michael Andreae [ctb], Michael Betancourt [ctb], Bob Carpenter [ctb], Yuanjun Gao [ctb], Andrew Gelman [ctb], Ben Goodrich [ctb], Daniel Lee [ctb], Dongying Song [ctb], Rob Trangucci [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between shinystan versions 2.1.0 dated 2016-01-06 and 2.2.0 dated 2016-05-24

 shinystan-2.1.0/shinystan/R/array2shinystan.R                                                               |only
 shinystan-2.1.0/shinystan/R/as.shinystan.R                                                                  |only
 shinystan-2.1.0/shinystan/R/chains2shinystan.R                                                              |only
 shinystan-2.1.0/shinystan/R/convenience.R                                                                   |only
 shinystan-2.1.0/shinystan/R/eight_schools.R                                                                 |only
 shinystan-2.1.0/shinystan/R/launch_shinystan_demo.R                                                         |only
 shinystan-2.1.0/shinystan/R/mcmc2shinystan.R                                                                |only
 shinystan-2.1.0/shinystan/R/model_code.R                                                                    |only
 shinystan-2.1.0/shinystan/R/notes.R                                                                         |only
 shinystan-2.1.0/shinystan/R/rename_model.R                                                                  |only
 shinystan-2.1.0/shinystan/R/shinystan-class.R                                                               |only
 shinystan-2.1.0/shinystan/R/sso_info.R                                                                      |only
 shinystan-2.1.0/shinystan/R/stan2shinystan.R                                                                |only
 shinystan-2.1.0/shinystan/R/stanreg2shinystan.R                                                             |only
 shinystan-2.1.0/shinystan/inst/ShinyStan/ggplot_fns_old.rda                                                 |only
 shinystan-2.1.0/shinystan/inst/ShinyStan/server_files/utilities/ppcheck_names_descriptions.R                |only
 shinystan-2.1.0/shinystan/man/eight_schools.Rd                                                              |only
 shinystan-2.1.0/shinystan/man/model_code.Rd                                                                 |only
 shinystan-2.1.0/shinystan/man/notes.Rd                                                                      |only
 shinystan-2.1.0/shinystan/man/sso_info.Rd                                                                   |only
 shinystan-2.1.0/shinystan/tests/testthat/data_for_tests.R                                                   |only
 shinystan-2.1.0/shinystan/tests/testthat/test_manipulating_sso.R                                            |only
 shinystan-2.1.0/shinystan/tests/testthat/test_options.R                                                     |only
 shinystan-2.2.0/shinystan/DESCRIPTION                                                                       |   31 
 shinystan-2.2.0/shinystan/MD5                                                                               |  254 +++---
 shinystan-2.2.0/shinystan/NAMESPACE                                                                         |    7 
 shinystan-2.2.0/shinystan/NEWS.md                                                                           |only
 shinystan-2.2.0/shinystan/R/deploy_shinystan.R                                                              |  164 +++-
 shinystan-2.2.0/shinystan/R/drop_parameters.R                                                               |only
 shinystan-2.2.0/shinystan/R/generate_quantity.R                                                             |  120 +--
 shinystan-2.2.0/shinystan/R/launch_shinystan.R                                                              |  113 ++
 shinystan-2.2.0/shinystan/R/misc.R                                                                          |  174 ----
 shinystan-2.2.0/shinystan/R/retrieve.R                                                                      |  176 +++-
 shinystan-2.2.0/shinystan/R/shinystan-objects.R                                                             |only
 shinystan-2.2.0/shinystan/R/shinystan-package.R                                                             |   66 -
 shinystan-2.2.0/shinystan/R/sso-metadata.R                                                                  |only
 shinystan-2.2.0/shinystan/R/update_sso.R                                                                    |   84 +-
 shinystan-2.2.0/shinystan/R/zzz.R                                                                           |    5 
 shinystan-2.2.0/shinystan/build/vignette.rds                                                                |binary
 shinystan-2.2.0/shinystan/data/eight_schools.rda                                                            |binary
 shinystan-2.2.0/shinystan/inst/ShinyStan/css/ShinyStan.css                                                  |    8 
 shinystan-2.2.0/shinystan/inst/ShinyStan/global.R                                                           |   17 
 shinystan-2.2.0/shinystan/inst/ShinyStan/global_utils.R                                                     |  260 +-----
 shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/gg_theme_elements.R                               |   97 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/hmc_diagnostics_helpers.R                         |   88 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/shinystan_helpers.R                               |   34 
 shinystan-2.2.0/shinystan/inst/ShinyStan/helper_functions/summary_stats_helpers.R                           |   54 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/accept_stat.html                                              |    4 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/citation.html                                                 |    4 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/home_page_links.html                                          |   31 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/mcse.html                                                     |    2 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/ndivergent.html                                               |   56 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/neff.html                                                     |   18 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/nleapfrog.html                                                |    2 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/rhat.html                                                     |    6 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/stepsize.html                                                 |    6 
 shinystan-2.2.0/shinystan/inst/ShinyStan/html/treedepth.html                                                |   15 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server.R                                                           |  131 ++-
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/debounce.R                                            |   11 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ppcheck_helpers.R              |   15 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_rep_vs_obs.R      |   15 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_resids.R          |   24 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_test_statistics.R |   16 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/pp_utils.R              |   73 +
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rep_vs_resid_rep.R      |   16 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rstanarm.R              |   18 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/y_vs_avg_rep.R          |   16 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ppcheck/ui/pp_get_y_and_yrep.R         |   69 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/autocorr.R                      |   54 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/diagnostics.R                   |  392 +++++-----
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/multitrace.R                    |   16 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/rhat_neff_mcse.R                |   96 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/server/summary_stats_sampler.R         |   44 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/diagnose/ui/multitrace_customize.R              |   16 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/server/multiparameter_plot.R           |   75 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/server/summary_stats.R                 |   18 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/server/summary_stats_latex.R           |   50 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/estimate/ui/multiparam_selectize.R              |   59 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/bivariate.R                      |  102 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/density.R                        |  144 ++-
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/histogram.R                      |   62 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/multiview.R                      |  100 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/summary_stats_param.R            |   35 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/server/trivariate.R                     |   76 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/pages/explore/ui/ui_trivariate_select_x.R             |   10 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/utilities/extract_sso.R                               |  109 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/utilities/make_param_list_with_groups_sort.R          |   18 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_files/utilities/par_samps_reactive.R                        |   23 
 shinystan-2.2.0/shinystan/inst/ShinyStan/server_utils.R                                                     |only
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui.R                                                               |  274 +-----
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_diagnose.R                                           |only
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_estimate.R                                           |only
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_explore.R                                            |only
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_home.R                                               |only
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/PAGE_more_menu.R                                          |only
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/about.R                                                   |  111 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/autocorr_customize.R                                      |   75 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/bivariate_customize.R                                     |  197 +++--
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/density_customize.R                                       |  367 ++++++---
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_by_parameter.R                                |   28 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_customize.R                                   |   55 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_help.R                                        |   93 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_ndivergent.R                                  |   16 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_sample.R                                      |   40 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_stepsize.R                                    |   15 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/diagnostics_treedepth.R                                   |   34 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/dynamic_trace_helptext.R                                  |   30 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/glossary.R                                                |   92 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/help.R                                                    |  161 ++--
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/hist_customize.R                                          |   81 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/model_code.R                                              |   52 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/multiparam_customize.R                                    |  152 ++-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/notepad.R                                                 |   50 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/pp_about.R                                                |   68 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/pp_navlist.R                                              |  216 +++--
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/pp_navlist_rstanarm.R                                     |  151 ++-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/rhat_neff_mcse_layout.R                                   |  133 ++-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/sampler_stats_customize.R                                 |   57 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/table_customize.R                                         |   47 -
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/table_latex_main.R                                        |   14 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/table_latex_sidebar.R                                     |   71 +
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/trivariate_customize.R                                    |  110 +-
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_files/trivariate_select.R                                       |   31 
 shinystan-2.2.0/shinystan/inst/ShinyStan/ui_utils.R                                                         |only
 shinystan-2.2.0/shinystan/inst/doc/deploy_shinystan.Rmd                                                     |   19 
 shinystan-2.2.0/shinystan/inst/doc/deploy_shinystan.html                                                    |   75 +
 shinystan-2.2.0/shinystan/inst/doc/shinystan-package.Rmd                                                    |    4 
 shinystan-2.2.0/shinystan/inst/doc/shinystan-package.html                                                   |   88 +-
 shinystan-2.2.0/shinystan/man/as.shinystan.Rd                                                               |  205 +++--
 shinystan-2.2.0/shinystan/man/deploy_shinystan.Rd                                                           |   31 
 shinystan-2.2.0/shinystan/man/drop_parameters.Rd                                                            |only
 shinystan-2.2.0/shinystan/man/generate_quantity.Rd                                                          |   49 -
 shinystan-2.2.0/shinystan/man/launch_shinystan.Rd                                                           |   35 
 shinystan-2.2.0/shinystan/man/launch_shinystan_demo.Rd                                                      |   32 
 shinystan-2.2.0/shinystan/man/rename_model.Rd                                                               |   24 
 shinystan-2.2.0/shinystan/man/retrieve.Rd                                                                   |   46 -
 shinystan-2.2.0/shinystan/man/shinystan-class.Rd                                                            |   50 -
 shinystan-2.2.0/shinystan/man/shinystan-metadata.Rd                                                         |only
 shinystan-2.2.0/shinystan/man/shinystan-package.Rd                                                          |   57 -
 shinystan-2.2.0/shinystan/man/update_sso.Rd                                                                 |   27 
 shinystan-2.2.0/shinystan/tests/testthat/data_for_retrieve_tests.R                                          |only
 shinystan-2.2.0/shinystan/tests/testthat/old_sso_for_tests.rda                                              |only
 shinystan-2.2.0/shinystan/tests/testthat/stanfit2_for_tests.rda                                             |only
 shinystan-2.2.0/shinystan/tests/testthat/test_creating_sso.R                                                |  164 +++-
 shinystan-2.2.0/shinystan/tests/testthat/test_deploy_shinystan.R                                            |only
 shinystan-2.2.0/shinystan/tests/testthat/test_misc.R                                                        |only
 shinystan-2.2.0/shinystan/tests/testthat/test_using_sso.R                                                   |only
 shinystan-2.2.0/shinystan/vignettes/deploy_shinystan.Rmd                                                    |   19 
 shinystan-2.2.0/shinystan/vignettes/shinystan-package.Rmd                                                   |    4 
 149 files changed, 4144 insertions(+), 3405 deletions(-)

More information about shinystan at CRAN
Permanent link

Package plotSEMM updated to version 2.2 with previous version 2.1 dated 2015-10-04

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 [aut], Jolynn Pek [aut], Sonya Sterba [ctb], Dan Bauer [ctb], Phil Chalmers [cre, aut]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

Diff between plotSEMM versions 2.1 dated 2015-10-04 and 2.2 dated 2016-05-24

 DESCRIPTION                 |   29 +++++++++++++++--------------
 MD5                         |   14 +++++++-------
 NAMESPACE                   |    2 +-
 man/plotSEMM.Rd             |    2 +-
 man/plotSEMM_GUI.Rd         |    4 ++--
 man/plotSEMM_contour.Rd     |   18 +++++++++---------
 man/plotSEMM_probability.Rd |    2 +-
 man/plotSEMM_setup.Rd       |    2 +-
 8 files changed, 37 insertions(+), 36 deletions(-)

More information about plotSEMM at CRAN
Permanent link

Package IsoplotR updated to version 0.3 with previous version 0.2 dated 2016-05-05

Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using the 'York' approach. Future versions will include functionality for the Ar-Ar, Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, including isochrons, age spectra, ternary diagrams, kernel density estimates, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 0.2 dated 2016-05-05 and 0.3 dated 2016-05-24

 IsoplotR-0.2/IsoplotR/man/I.A.Rd            |only
 IsoplotR-0.2/IsoplotR/man/get.covmat.Rd     |only
 IsoplotR-0.2/IsoplotR/man/get.ellipse.Rd    |only
 IsoplotR-0.2/IsoplotR/man/get.ratios.Rd     |only
 IsoplotR-0.3/IsoplotR/DESCRIPTION           |    8 -
 IsoplotR-0.3/IsoplotR/MD5                   |   37 ++++--
 IsoplotR-0.3/IsoplotR/NAMESPACE             |   19 ++-
 IsoplotR-0.3/IsoplotR/R/UPb.R               |  130 ++++++++++++-----------
 IsoplotR-0.3/IsoplotR/R/concordia.R         |  142 +++++++++++++++++--------
 IsoplotR-0.3/IsoplotR/R/constants.R         |  153 ++++++++++++++--------------
 IsoplotR-0.3/IsoplotR/R/discordia.R         |only
 IsoplotR-0.3/IsoplotR/R/errorellipse.R      |    4 
 IsoplotR-0.3/IsoplotR/R/io.R                |   15 ++
 IsoplotR-0.3/IsoplotR/R/json.R              |only
 IsoplotR-0.3/IsoplotR/R/regression.R        |only
 IsoplotR-0.3/IsoplotR/R/toolbox.R           |   49 +-------
 IsoplotR-0.3/IsoplotR/R/zzz.R               |only
 IsoplotR-0.3/IsoplotR/data/UPb.rda          |binary
 IsoplotR-0.3/IsoplotR/inst/constants.json   |only
 IsoplotR-0.3/IsoplotR/man/I.R.Rd            |only
 IsoplotR-0.3/IsoplotR/man/concordia.age.Rd  |only
 IsoplotR-0.3/IsoplotR/man/concordia.plot.Rd |   10 +
 IsoplotR-0.3/IsoplotR/man/discordia.age.Rd  |only
 IsoplotR-0.3/IsoplotR/man/ellipse.Rd        |only
 IsoplotR-0.3/IsoplotR/man/lambda.Rd         |   20 ++-
 IsoplotR-0.3/IsoplotR/man/settings.Rd       |only
 IsoplotR-0.3/IsoplotR/man/yorkfit.Rd        |only
 27 files changed, 327 insertions(+), 260 deletions(-)

More information about IsoplotR at CRAN
Permanent link

Package googleAnalyticsR updated to version 0.1.1 with previous version 0.1.0 dated 2016-05-12

Title: Google Analytics API into R
Description: R library for interacting with the Google Analytics Reporting API v3 and v4.
Author: Mark Edmondson [aut, cre], Artem Klevtsov [ctb], Johann deBoer [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

Diff between googleAnalyticsR versions 0.1.0 dated 2016-05-12 and 0.1.1 dated 2016-05-24

 DESCRIPTION                    |    6 +++---
 MD5                            |   10 +++++-----
 NEWS.md                        |    6 +++++-
 R/ga_v4_get.R                  |    4 ++--
 README.md                      |   10 +++++-----
 inst/doc/googleAnalyticsR.html |    4 ++--
 6 files changed, 22 insertions(+), 18 deletions(-)

More information about googleAnalyticsR at CRAN
Permanent link

Package ecoengine updated to version 1.10.0 with previous version 1.9.1 dated 2015-03-30

Title: Programmatic Interface to the API Serving UC Berkeley's Natural History Data
Description: The ecoengine provides access to more than 5 million georeferenced specimen records from the University of California, Berkeley's Natural History Museums.
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram <karthik.ram@gmail.com>

Diff between ecoengine versions 1.9.1 dated 2015-03-30 and 1.10.0 dated 2016-05-24

 ecoengine-1.10.0/ecoengine/DESCRIPTION                |   21 +--
 ecoengine-1.10.0/ecoengine/LICENSE                    |only
 ecoengine-1.10.0/ecoengine/MD5                        |   59 ++++-----
 ecoengine-1.10.0/ecoengine/NAMESPACE                  |    6 
 ecoengine-1.10.0/ecoengine/NEWS                       |    6 
 ecoengine-1.10.0/ecoengine/R/ecoengine_package.R      |    1 
 ecoengine-1.10.0/ecoengine/R/ee_browse_photos.R       |    9 -
 ecoengine-1.10.0/ecoengine/R/ee_checklists.R          |  104 ++++++++++------
 ecoengine-1.10.0/ecoengine/R/ee_observations.R        |   23 +--
 ecoengine-1.10.0/ecoengine/R/ee_photos.R              |  115 ++++++++++--------
 ecoengine-1.10.0/ecoengine/R/ee_search.R              |    7 -
 ecoengine-1.10.0/ecoengine/R/ee_sources.R             |    1 
 ecoengine-1.10.0/ecoengine/R/ee_utils.R               |   14 +-
 ecoengine-1.10.0/ecoengine/man/california_counties.Rd |    2 
 ecoengine-1.10.0/ecoengine/man/checklist_details.Rd   |    2 
 ecoengine-1.10.0/ecoengine/man/ecoengine.Rd           |    4 
 ecoengine-1.10.0/ecoengine/man/ee_about.Rd            |    3 
 ecoengine-1.10.0/ecoengine/man/ee_cbind.Rd            |    2 
 ecoengine-1.10.0/ecoengine/man/ee_checklists.Rd       |    2 
 ecoengine-1.10.0/ecoengine/man/ee_footprints.Rd       |    2 
 ecoengine-1.10.0/ecoengine/man/ee_observations.Rd     |    4 
 ecoengine-1.10.0/ecoengine/man/ee_pages.Rd            |    2 
 ecoengine-1.10.0/ecoengine/man/ee_paginator.Rd        |    2 
 ecoengine-1.10.0/ecoengine/man/ee_photos.Rd           |    4 
 ecoengine-1.10.0/ecoengine/man/ee_search.Rd           |    2 
 ecoengine-1.10.0/ecoengine/man/ee_search_obs.Rd       |    2 
 ecoengine-1.10.0/ecoengine/man/ee_sources.Rd          |    2 
 ecoengine-1.10.0/ecoengine/man/full_sensor_list.Rd    |    2 
 ecoengine-1.10.0/ecoengine/man/print.ecoengine.Rd     |    2 
 ecoengine-1.10.0/ecoengine/man/view_photos.Rd         |    2 
 ecoengine-1.9.1/ecoengine/R/ee_map.R                  |only
 ecoengine-1.9.1/ecoengine/man/ee_map.Rd               |only
 32 files changed, 230 insertions(+), 177 deletions(-)

More information about ecoengine at CRAN
Permanent link

New package bitrugs with initial version 0.1
Package: bitrugs
Type: Package
Title: Bayesian Inference of Transmission Routes Using Genome Sequences
Version: 0.1
Date: 2016-05-24
Author: Colin Worby
Maintainer: Colin Worby <cworby@hsph.harvard.edu>
Description: MCMC methods to estimate transmission dynamics and infection routes in hospitals using genomic sampling data.
License: GPL-3
NeedsCompilation: yes
Packaged: 2016-05-24 17:38:46 UTC; colin
Repository: CRAN
Date/Publication: 2016-05-24 23:30:13

More information about bitrugs at CRAN
Permanent link

Package HSAR updated to version 0.4.0 with previous version 0.3.6 dated 2015-12-22

Title: Hierarchical Spatial Autoregressive Model (HSAR)
Description: A library of the Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm.
Author: Guanpeng Dong, Richard Harris, Angelos Mimis
Maintainer: Angelos Mimis <mimis@panteion.gr>

Diff between HSAR versions 0.3.6 dated 2015-12-22 and 0.4.0 dated 2016-05-24

 HSAR-0.3.6/HSAR/data/land_prices.RData            |only
 HSAR-0.3.6/HSAR/man/land_prices.Rd                |only
 HSAR-0.4.0/HSAR/DESCRIPTION                       |   10 -
 HSAR-0.4.0/HSAR/MD5                               |   54 ++++---
 HSAR-0.4.0/HSAR/NAMESPACE                         |    9 +
 HSAR-0.4.0/HSAR/R/RcppExports.R                   |   16 +-
 HSAR-0.4.0/HSAR/R/data_checks.R                   |only
 HSAR-0.4.0/HSAR/R/hsar.R                          |   58 ++++++-
 HSAR-0.4.0/HSAR/R/print.hsar.R                    |only
 HSAR-0.4.0/HSAR/R/sar.R                           |   42 +++++
 HSAR-0.4.0/HSAR/R/summary.hsar.R                  |  103 +++++++------
 HSAR-0.4.0/HSAR/R/utils.R                         |only
 HSAR-0.4.0/HSAR/build                             |only
 HSAR-0.4.0/HSAR/data/Beijingdistricts.RData       |only
 HSAR-0.4.0/HSAR/data/datalist                     |    4 
 HSAR-0.4.0/HSAR/data/landSPDF.RData               |only
 HSAR-0.4.0/HSAR/data/landprice.RData              |only
 HSAR-0.4.0/HSAR/inst                              |only
 HSAR-0.4.0/HSAR/man/Beijingdistricts.Rd           |only
 HSAR-0.4.0/HSAR/man/HSAR-package.Rd               |   19 +-
 HSAR-0.4.0/HSAR/man/hsar.Rd                       |  164 +++++++++++++++++-----
 HSAR-0.4.0/HSAR/man/landSPDF.Rd                   |only
 HSAR-0.4.0/HSAR/man/landprice.Rd                  |only
 HSAR-0.4.0/HSAR/man/sar.Rd                        |   90 +++++++-----
 HSAR-0.4.0/HSAR/man/summary.mcmc_hsar.Rd          |   23 +--
 HSAR-0.4.0/HSAR/man/summary.mcmc_hsar_lambda_0.Rd |only
 HSAR-0.4.0/HSAR/man/summary.mcmc_hsar_rho_0.Rd    |only
 HSAR-0.4.0/HSAR/man/summary.mcmc_sar.Rd           |   16 --
 HSAR-0.4.0/HSAR/src/RcppExports.cpp               |   48 ++++--
 HSAR-0.4.0/HSAR/src/hsar.cpp                      |  129 +++++++++--------
 HSAR-0.4.0/HSAR/src/hsar_lambda_0.cpp             |  115 ++++++++-------
 HSAR-0.4.0/HSAR/src/hsar_rho_0.cpp                |  106 ++++++++------
 HSAR-0.4.0/HSAR/src/sar.cpp                       |   80 ++++++----
 HSAR-0.4.0/HSAR/vignettes                         |only
 34 files changed, 699 insertions(+), 387 deletions(-)

More information about HSAR at CRAN
Permanent link

Package GiniWegNeg updated to version 1.0.1 with previous version 1.0 dated 2016-01-13

Title: Computing the Gini-Based Coefficients for Weighted and Negative Attributes
Description: Gini-based coefficients and plot of the ordinary and generalized curve of maximum inequality in the presence of weighted and negative attributes.
Author: Emanuela Raffinetti, Fabio Aimar
Maintainer: Emanuela Raffinetti <emanuela.raffinetti@unimi.it>

Diff between GiniWegNeg versions 1.0 dated 2016-01-13 and 1.0.1 dated 2016-05-24

 GiniWegNeg-1.0.1/GiniWegNeg/DESCRIPTION               |   14 ++--
 GiniWegNeg-1.0.1/GiniWegNeg/MD5                       |   28 ++++-----
 GiniWegNeg-1.0.1/GiniWegNeg/R/GRSVc.R                 |   12 ++--
 GiniWegNeg-1.0.1/GiniWegNeg/R/Gini_CTR_BS.R           |   44 +++++++--------
 GiniWegNeg-1.0.1/GiniWegNeg/R/Gini_RSV.R              |   22 +++----
 GiniWegNeg-1.0.1/GiniWegNeg/R/PGini_RSV.R             |only
 GiniWegNeg-1.0.1/GiniWegNeg/R/RSVc.R                  |   12 ++--
 GiniWegNeg-1.0.1/GiniWegNeg/data/BI2012.rda           |binary
 GiniWegNeg-1.0.1/GiniWegNeg/man/BI2012.Rd             |   26 ++++-----
 GiniWegNeg-1.0.1/GiniWegNeg/man/GRSVc.Rd              |   48 ++++++++--------
 GiniWegNeg-1.0.1/GiniWegNeg/man/GiniWegNeg-package.Rd |   37 ++++++-------
 GiniWegNeg-1.0.1/GiniWegNeg/man/Gini_CTR_BS.Rd        |   41 ++++++++------
 GiniWegNeg-1.0.1/GiniWegNeg/man/Gini_RSV.Rd           |   43 +++++++++------
 GiniWegNeg-1.0.1/GiniWegNeg/man/PGini_RSV.Rd          |only
 GiniWegNeg-1.0.1/GiniWegNeg/man/RSVc.Rd               |   51 +++++++++---------
 GiniWegNeg-1.0/GiniWegNeg/R/Gini.R                    |only
 GiniWegNeg-1.0/GiniWegNeg/man/Gini.Rd                 |only
 17 files changed, 200 insertions(+), 178 deletions(-)

More information about GiniWegNeg at CRAN
Permanent link

Package GGIR updated to version 1.2-8 with previous version 1.2-7 dated 2016-05-13

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 1.2-7 dated 2016-05-13 and 1.2-8 dated 2016-05-24

 DESCRIPTION         |    8 
 MD5                 |   22 
 R/g.analyse.R       | 1878 ++++++++++++++++++++++++++--------------------------
 R/g.getbout.R       |    9 
 R/g.getmeta.R       |   25 
 R/g.inspectfile.R   |  412 +++++------
 R/g.part2.R         |  308 ++++----
 R/g.shell.GGIR.R    |    6 
 R/g.wavread.R       |    4 
 inst/NEWS.Rd        |    9 
 man/GGIR-package.Rd |    4 
 man/g.analyse.Rd    |   15 
 12 files changed, 1372 insertions(+), 1328 deletions(-)

More information about GGIR at CRAN
Permanent link

Package GetTDData updated to version 1.2.3 with previous version 1.2.2 dated 2016-05-22

Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetTDData versions 1.2.2 dated 2016-05-22 and 1.2.3 dated 2016-05-24

 DESCRIPTION                 |    8 ++--
 MD5                         |   12 +++---
 NEWS.md                     |    3 +
 R/gtdd_download_TD_data.R   |   43 +++++++++++++++++++---
 inst/doc/gtdd-vignette.html |   10 +++--
 man/download.TD.data.Rd     |   86 ++++++++++++++++++++++----------------------
 man/read.TD.files.Rd        |   86 ++++++++++++++++++++++----------------------
 7 files changed, 144 insertions(+), 104 deletions(-)

More information about GetTDData at CRAN
Permanent link

Package rstanarm updated to version 2.9.0-4 with previous version 2.9.0-3 dated 2016-02-13

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates pre-compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Trustees of Columbia University [cph], R Core Deveopment Team [cph] (R/pp_data.R, R/stan_aov.R), Douglas Bates [cph] (R/pp_data.R), Martin Maechler [cph] (R/pp_data.R), Ben Bolker [cph] (R/pp_data.R), Steve Walker [cph] (R/pp_data.R), Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R), William Venables [cph] (R/stan_polr.R), Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

Diff between rstanarm versions 2.9.0-3 dated 2016-02-13 and 2.9.0-4 dated 2016-05-24

 rstanarm-2.9.0-3/rstanarm/data/example_model.rda                  |only
 rstanarm-2.9.0-3/rstanarm/man/plots.Rd                            |only
 rstanarm-2.9.0-4/rstanarm/DESCRIPTION                             |   12 
 rstanarm-2.9.0-4/rstanarm/MD5                                     |  196 -
 rstanarm-2.9.0-4/rstanarm/NAMESPACE                               |    7 
 rstanarm-2.9.0-4/rstanarm/R/adapt_delta.R                         |   31 
 rstanarm-2.9.0-4/rstanarm/R/as.matrix.stanreg.R                   |    4 
 rstanarm-2.9.0-4/rstanarm/R/example_model.R                       |    4 
 rstanarm-2.9.0-4/rstanarm/R/loo.R                                 |   70 
 rstanarm-2.9.0-4/rstanarm/R/misc.R                                |   80 
 rstanarm-2.9.0-4/rstanarm/R/plots.R                               |   39 
 rstanarm-2.9.0-4/rstanarm/R/posterior_interval.R                  |    5 
 rstanarm-2.9.0-4/rstanarm/R/posterior_predict.R                   |   66 
 rstanarm-2.9.0-4/rstanarm/R/posterior_vs_prior.R                  |only
 rstanarm-2.9.0-4/rstanarm/R/pp_check.R                            |   86 
 rstanarm-2.9.0-4/rstanarm/R/pp_data.R                             |   12 
 rstanarm-2.9.0-4/rstanarm/R/pp_validate.R                         |only
 rstanarm-2.9.0-4/rstanarm/R/print-and-summary.R                   |   19 
 rstanarm-2.9.0-4/rstanarm/R/priors.R                              |   50 
 rstanarm-2.9.0-4/rstanarm/R/rstanarm-package.R                    |    2 
 rstanarm-2.9.0-4/rstanarm/R/shinystan.R                           |   72 
 rstanarm-2.9.0-4/rstanarm/R/stan_gamm4.R                          |   11 
 rstanarm-2.9.0-4/rstanarm/R/stan_glm.R                            |    3 
 rstanarm-2.9.0-4/rstanarm/R/stan_glm.fit.R                        |   41 
 rstanarm-2.9.0-4/rstanarm/R/stan_glmer.R                          |   29 
 rstanarm-2.9.0-4/rstanarm/R/stan_lm.R                             |    8 
 rstanarm-2.9.0-4/rstanarm/R/stan_lm.fit.R                         |    4 
 rstanarm-2.9.0-4/rstanarm/R/stan_polr.R                           |  128 
 rstanarm-2.9.0-4/rstanarm/R/stan_polr.fit.R                       |    2 
 rstanarm-2.9.0-4/rstanarm/R/stanmodels.R                          |    4 
 rstanarm-2.9.0-4/rstanarm/R/stanreg-methods.R                     |   29 
 rstanarm-2.9.0-4/rstanarm/R/stanreg.R                             |   20 
 rstanarm-2.9.0-4/rstanarm/R/zzz.R                                 |    4 
 rstanarm-2.9.0-4/rstanarm/cleanup                                 |    1 
 rstanarm-2.9.0-4/rstanarm/cleanup.win                             |    1 
 rstanarm-2.9.0-4/rstanarm/exec/lm.stan                            |   10 
 rstanarm-2.9.0-4/rstanarm/inst/NEWS                               |   17 
 rstanarm-2.9.0-4/rstanarm/inst/chunks/priors_glm.stan             |   10 
 rstanarm-2.9.0-4/rstanarm/inst/chunks/tdata_glm.stan              |   15 
 rstanarm-2.9.0-4/rstanarm/inst/chunks/tparameters_glm.stan        |   23 
 rstanarm-2.9.0-4/rstanarm/inst/doc/aov.Rmd                        |   12 
 rstanarm-2.9.0-4/rstanarm/inst/doc/aov.html                       |   46 
 rstanarm-2.9.0-4/rstanarm/inst/doc/binomial.Rmd                   |   14 
 rstanarm-2.9.0-4/rstanarm/inst/doc/binomial.html                  |   42 
 rstanarm-2.9.0-4/rstanarm/inst/doc/continuous.Rmd                 |    8 
 rstanarm-2.9.0-4/rstanarm/inst/doc/continuous.html                |   82 
 rstanarm-2.9.0-4/rstanarm/inst/doc/count.Rmd                      |    8 
 rstanarm-2.9.0-4/rstanarm/inst/doc/count.html                     |   32 
 rstanarm-2.9.0-4/rstanarm/inst/doc/glmer.Rmd                      |    6 
 rstanarm-2.9.0-4/rstanarm/inst/doc/glmer.html                     |   18 
 rstanarm-2.9.0-4/rstanarm/inst/doc/lm.Rmd                         |   17 
 rstanarm-2.9.0-4/rstanarm/inst/doc/lm.html                        |   47 
 rstanarm-2.9.0-4/rstanarm/inst/doc/polr.Rmd                       |   17 
 rstanarm-2.9.0-4/rstanarm/inst/doc/polr.html                      |   32 
 rstanarm-2.9.0-4/rstanarm/inst/doc/pooling.Rmd                    |    2 
 rstanarm-2.9.0-4/rstanarm/inst/doc/pooling.html                   |  116 
 rstanarm-2.9.0-4/rstanarm/inst/doc/rstanarm.Rmd                   |    5 
 rstanarm-2.9.0-4/rstanarm/inst/doc/rstanarm.html                  |   32 
 rstanarm-2.9.0-4/rstanarm/man/adapt_delta.Rd                      |   31 
 rstanarm-2.9.0-4/rstanarm/man/as.matrix.stanreg.Rd                |    3 
 rstanarm-2.9.0-4/rstanarm/man/example_model.Rd                    |    4 
 rstanarm-2.9.0-4/rstanarm/man/loo.stanreg.Rd                      |   12 
 rstanarm-2.9.0-4/rstanarm/man/pairs.stanreg.Rd                    |    1 
 rstanarm-2.9.0-4/rstanarm/man/plot.stanreg.Rd                     |   19 
 rstanarm-2.9.0-4/rstanarm/man/posterior_interval.Rd               |    1 
 rstanarm-2.9.0-4/rstanarm/man/posterior_predict.Rd                |    3 
 rstanarm-2.9.0-4/rstanarm/man/posterior_vs_prior.Rd               |only
 rstanarm-2.9.0-4/rstanarm/man/pp_check.Rd                         |    5 
 rstanarm-2.9.0-4/rstanarm/man/pp_validate.Rd                      |only
 rstanarm-2.9.0-4/rstanarm/man/priors.Rd                           |   48 
 rstanarm-2.9.0-4/rstanarm/man/rstanarm-package.Rd                 |    2 
 rstanarm-2.9.0-4/rstanarm/man/rstanarm-plots.Rd                   |only
 rstanarm-2.9.0-4/rstanarm/man/shinystan.Rd                        |   69 
 rstanarm-2.9.0-4/rstanarm/man/stan_gamm4.Rd                       |   28 
 rstanarm-2.9.0-4/rstanarm/man/stan_glm.Rd                         |   28 
 rstanarm-2.9.0-4/rstanarm/man/stan_glmer.Rd                       |   29 
 rstanarm-2.9.0-4/rstanarm/man/stan_lm.Rd                          |    5 
 rstanarm-2.9.0-4/rstanarm/man/stanreg-methods.Rd                  |    5 
 rstanarm-2.9.0-4/rstanarm/man/summary.stanreg.Rd                  |    9 
 rstanarm-2.9.0-4/rstanarm/src/include/models.hpp                  | 1622 ++--------
 rstanarm-2.9.0-4/rstanarm/tests/testthat.R                        |    1 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_loo.R               |   74 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_methods.R           |   43 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_misc.R              |   31 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_plots.R             |   44 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_posterior_predict.R |  113 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_pp_check.R          |    2 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_pp_validate.R       |only
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_predict.R           |    2 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_functions.R    |   10 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_glm.R          |    6 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_glmer.R        |    9 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_lm.R           |   16 
 rstanarm-2.9.0-4/rstanarm/tests/testthat/test_stan_polr.R         |   21 
 rstanarm-2.9.0-4/rstanarm/vignettes/aov.Rmd                       |   12 
 rstanarm-2.9.0-4/rstanarm/vignettes/binomial.Rmd                  |   14 
 rstanarm-2.9.0-4/rstanarm/vignettes/continuous.Rmd                |    8 
 rstanarm-2.9.0-4/rstanarm/vignettes/count.Rmd                     |    8 
 rstanarm-2.9.0-4/rstanarm/vignettes/glmer.Rmd                     |    6 
 rstanarm-2.9.0-4/rstanarm/vignettes/lm.Rmd                        |   17 
 rstanarm-2.9.0-4/rstanarm/vignettes/polr.Rmd                      |   17 
 rstanarm-2.9.0-4/rstanarm/vignettes/pooling.Rmd                   |    2 
 rstanarm-2.9.0-4/rstanarm/vignettes/rstanarm.Rmd                  |    5 
 103 files changed, 1919 insertions(+), 2117 deletions(-)

More information about rstanarm at CRAN
Permanent link

Package rioja updated to version 0.9-7 with previous version 0.9-6 dated 2016-04-04

Title: Analysis of Quaternary Science Data
Description: Functions for the analysis of Quaternary science data, including constrained clustering, WA, WAPLS, IKFA, MLRC and MAT transfer functions, and stratigraphic diagrams.
Author: Steve Juggins
Maintainer: Steve Juggins <Stephen.Juggins@ncl.ac.uk>

Diff between rioja versions 0.9-6 dated 2016-04-04 and 0.9-7 dated 2016-05-24

 DESCRIPTION          |    8 +--
 MD5                  |   32 ++++++------
 R/MAT.r              |  100 ++++++++++++++++++++++++++++++++-------
 R/PTF.r              |    7 +-
 R/WAPLS.r            |   11 ++--
 R/inkspot.r          |   11 +++-
 R/strat.plot.r       |  129 +++++++++++++++++++++++++++++++++++----------------
 inst/ChangeLog       |    8 +++
 man/IKFA.Rd          |    2 
 man/MAT.Rd           |    2 
 man/MLRC.Rd          |    2 
 man/MR.Rd            |    2 
 man/WA.Rd            |    2 
 man/WAPLS.Rd         |    2 
 man/inkspot.Rd       |    3 +
 man/rioja.package.Rd |    6 +-
 man/strat.plot.Rd    |    8 +--
 17 files changed, 237 insertions(+), 98 deletions(-)

More information about rioja at CRAN
Permanent link

Package FreeSortR updated to version 1.2 with previous version 1.1 dated 2014-08-29

Title: Free Sorting Data Analysis
Description: Provides tools for describing and analysing free sorting data. Main methods are computation of consensus partition and factorial analysis of the dissimilarity matrix between stimuli (using multidimensional scaling approach).
Author: Philippe Courcoux
Maintainer: Philippe Courcoux <philippe.courcoux@oniris-nantes.fr>

Diff between FreeSortR versions 1.1 dated 2014-08-29 and 1.2 dated 2016-05-24

 DESCRIPTION |   12 ++++++------
 MD5         |    8 ++++----
 NAMESPACE   |    3 +++
 R/MdsDiss.R |    4 ++--
 R/MdsSort.R |    2 +-
 5 files changed, 16 insertions(+), 13 deletions(-)

More information about FreeSortR at CRAN
Permanent link

Package EpiModel updated to version 1.2.6 with previous version 1.2.5 dated 2016-03-09

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic agent-based, and stochastic network models. Network models use robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an easy API for extending these templates to address novel scientific research aims.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Emily Beylerian [ctb], Li Wang [ctb], Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>

Diff between EpiModel versions 1.2.5 dated 2016-03-09 and 1.2.6 dated 2016-05-24

 DESCRIPTION                          |   33 ++++++-------
 MD5                                  |   20 ++++----
 NEWS                                 |   17 ++++++
 R/EpiModel-package.r                 |    6 +-
 R/dcm.mods.R                         |   11 +---
 R/dendo.R                            |   86 ++++++++++++++++++++++-------------
 build/vignette.rds                   |binary
 inst/doc/Intro.html                  |   13 ++---
 man/EpiModel-package.Rd              |    6 +-
 man/as.phylo.transmat.Rd             |    4 +
 tests/testthat/test-transmat-dendo.R |   24 +++++++++
 11 files changed, 139 insertions(+), 81 deletions(-)

More information about EpiModel at CRAN
Permanent link

Package ragt2ridges updated to version 0.2.0 with previous version 0.1.9 dated 2016-05-10

Title: Ridge Estimation of the Vector Auto-Regressive (VAR) Processes
Description: Ridge maximum likelihood estimation of vector auto-regressive processes and supporting functions for their exploitation.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>

Diff between ragt2ridges versions 0.1.9 dated 2016-05-10 and 0.2.0 dated 2016-05-24

 DESCRIPTION                |    8 ++++----
 MD5                        |    7 ++++---
 inst/NEWS.Rd               |only
 man/evaluateVAR1fit.Rd     |    2 +-
 man/ragt2ridges-package.Rd |    2 +-
 5 files changed, 10 insertions(+), 9 deletions(-)

More information about ragt2ridges at CRAN
Permanent link

New package QCEWAS with initial version 1.0-6
Package: QCEWAS
Type: Package
Title: Fast & Easy Quality Control of EWAS Results Files
Version: 1.0-6
Date: 2016-05-24
Author: Peter J. van der Most, Leanne K. Kupers, Ilja M. Nolte
Maintainer: Peter J. van der Most <p.j.van.der.most@umcg.nl>
Depends: R (>= 3.0.0)
Description: Tools for (automated and manual) quality control of the results of Epigenome-Wide Association Studies.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2016-05-24 12:50:15 UTC; mostPJ
Repository: CRAN
Date/Publication: 2016-05-24 16:32:45

More information about QCEWAS at CRAN
Permanent link

Package goft updated to version 1.3.1 with previous version 1.2 dated 2015-09-22

Title: Tests of Fit for some Probability Distributions
Description: Goodness-of-fit tests for gamma, inverse Gaussian, lognormal, Weibull, Frechet, Gumbel, univariate normal, multivariate normal, Cauchy, Laplace or double exponential, exponential and generalized Pareto distributions. Parameter estimators for gamma, inverse Gaussian and generalized Pareto distributions.
Author: Elizabeth Gonzalez-Estrada, Jose A. Villasenor-Alva
Maintainer: Elizabeth Gonzalez-Estrada <egonzalez@colpos.mx>

Diff between goft versions 1.2 dated 2015-09-22 and 1.3.1 dated 2016-05-24

 goft-1.2/goft/R/gpd.fit.R             |only
 goft-1.2/goft/R/gpd.test-internal.R   |only
 goft-1.2/goft/R/gpd.test.R            |only
 goft-1.2/goft/R/ig.test-internal.R    |only
 goft-1.2/goft/man/gpd.fit.Rd          |only
 goft-1.2/goft/man/gpd.test.Rd         |only
 goft-1.3.1/goft/DESCRIPTION           |   13 ++---
 goft-1.3.1/goft/MD5                   |   60 +++++++++++++++---------
 goft-1.3.1/goft/NAMESPACE             |   11 ++--
 goft-1.3.1/goft/R/cauchy.test.R       |only
 goft-1.3.1/goft/R/de.test.R           |only
 goft-1.3.1/goft/R/ev.test.R           |only
 goft-1.3.1/goft/R/exp.test.R          |only
 goft-1.3.1/goft/R/gamma.fit.R         |   26 ++++++----
 goft-1.3.1/goft/R/gamma.test.R        |   33 +++++++------
 goft-1.3.1/goft/R/gp.fit.R            |only
 goft-1.3.1/goft/R/gp.test.R           |only
 goft-1.3.1/goft/R/ig.fit.R            |   17 +++----
 goft-1.3.1/goft/R/ig.test.R           |   82 +++++++++++++++++++++++++++-------
 goft-1.3.1/goft/R/lnorm.test.R        |only
 goft-1.3.1/goft/R/mvShapiro.Test.R    |   43 +++++++++--------
 goft-1.3.1/goft/R/normal.R            |   43 ++++++++---------
 goft-1.3.1/goft/R/weibull.test.R      |only
 goft-1.3.1/goft/data/o3.RData         |only
 goft-1.3.1/goft/data/o3max.RData      |only
 goft-1.3.1/goft/data/strength.RData   |only
 goft-1.3.1/goft/inst/history.txt      |   25 +++++++---
 goft-1.3.1/goft/man/cauchy.test.Rd    |only
 goft-1.3.1/goft/man/de.test.Rd        |only
 goft-1.3.1/goft/man/ev.test.Rd        |only
 goft-1.3.1/goft/man/exp.test.Rd       |only
 goft-1.3.1/goft/man/gamma.fit.Rd      |   19 ++++---
 goft-1.3.1/goft/man/gamma.test.Rd     |   24 ++++++---
 goft-1.3.1/goft/man/goats.Rd          |    6 +-
 goft-1.3.1/goft/man/gp.fit.Rd         |only
 goft-1.3.1/goft/man/gp.test.Rd        |only
 goft-1.3.1/goft/man/ig.fit.Rd         |   10 ++--
 goft-1.3.1/goft/man/ig.test.Rd        |   42 ++++++++++++-----
 goft-1.3.1/goft/man/lnorm.test.Rd     |only
 goft-1.3.1/goft/man/mvShapiro.Test.Rd |   23 ++++-----
 goft-1.3.1/goft/man/normal.Rd         |   17 +++----
 goft-1.3.1/goft/man/o3max.Rd          |only
 goft-1.3.1/goft/man/ozone.Rd          |only
 goft-1.3.1/goft/man/strength.Rd       |only
 goft-1.3.1/goft/man/weibull.test.Rd   |only
 45 files changed, 306 insertions(+), 188 deletions(-)

More information about goft at CRAN
Permanent link

New package bayesbio with initial version 1.0.0
Package: bayesbio
Title: Miscellaneous Functions for Bioinformatics and Bayesian Statistics
Version: 1.0.0
Authors@R: person("Andrew", "McKenzie", email = "amckenz@gmail.com", role = c("aut", "cre"))
Description: A hodgepodge of hopefully helpful functions. Two of these perform shrinkage estimation: one using a simple weighted method where the user can specify the degree of shrinkage required, and one using James-Stein shrinkage estimation for the case of unequal variances.
Depends: R (>= 3.2.0)
Suggests: ggplot2, RISmed, testthat
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-24 13:50:20 UTC; amckenz
Author: Andrew McKenzie [aut, cre]
Maintainer: Andrew McKenzie <amckenz@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-24 16:32:42

More information about bayesbio at CRAN
Permanent link

New package DBItest with initial version 1.2
Package: DBItest
Title: Testing 'DBI' Back Ends
Version: 1.2
Date: 2016-05-21
Authors@R: c( person(given = "Kirill", family = "Müller", role = c("aut", "cre"), email = "krlmlr+r@mailbox.org"), person("RStudio", role = "cph") )
Description: A helper that tests 'DBI' back ends for conformity to the interface, currently work in progress.
Depends: R (>= 3.0.0)
Imports: methods, testthat (>= 1.0.2), withr, DBI (>= 0.4-1)
Suggests: devtools, lintr, knitr, rmarkdown
License: LGPL (>= 2)
LazyData: true
Encoding: UTF-8
BugReports: https://github.com/rstats-db/DBItest/issues
Collate: 'DBItest.R' 'context.R' 'expectations.R' 'import-dbi.R' 'import-testthat.R' 'run.R' 'test_all.R' 'test_getting_started.R' 'test_driver.R' 'test_connection.R' 'test_result.R' 'test_sql.R' 'test_meta.R' 'test_compliance.R' 'tweaks.R' 'utf8.R' 'utils.R'
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-24 12:15:07 UTC; muelleki
Author: Kirill Müller [aut, cre], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Repository: CRAN
Date/Publication: 2016-05-24 14:49:34

More information about DBItest at CRAN
Permanent link

Package biogas updated to version 1.4.0 with previous version 1.3.0 dated 2016-04-15

Title: Process Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>

Diff between biogas versions 1.3.0 dated 2016-04-15 and 1.4.0 dated 2016-05-24

 biogas-1.3.0/biogas/R/densBg.R                               |only
 biogas-1.4.0/biogas/ChangeLog                                |   91 +++
 biogas-1.4.0/biogas/DESCRIPTION                              |   10 
 biogas-1.4.0/biogas/MD5                                      |   57 +-
 biogas-1.4.0/biogas/NEWS                                     |   21 
 biogas-1.4.0/biogas/R/checkArgClassValue.R                   |    6 
 biogas-1.4.0/biogas/R/cumBg.R                                |  268 ++++++++---
 biogas-1.4.0/biogas/R/interp.R                               |    4 
 biogas-1.4.0/biogas/R/stdVol.R                               |   11 
 biogas-1.4.0/biogas/R/summBg.R                               |    8 
 biogas-1.4.0/biogas/build/vignette.rds                       |binary
 biogas-1.4.0/biogas/data/comp.rda                            |binary
 biogas-1.4.0/biogas/data/comp2.rda                           |binary
 biogas-1.4.0/biogas/data/mass.rda                            |binary
 biogas-1.4.0/biogas/data/massw.rda                           |binary
 biogas-1.4.0/biogas/data/setup.rda                           |binary
 biogas-1.4.0/biogas/data/setup2.rda                          |binary
 biogas-1.4.0/biogas/data/strawComp.rda                       |only
 biogas-1.4.0/biogas/data/strawMass.rda                       |only
 biogas-1.4.0/biogas/data/strawPressure.rda                   |only
 biogas-1.4.0/biogas/data/strawSetup.rda                      |only
 biogas-1.4.0/biogas/data/vol.rda                             |binary
 biogas-1.4.0/biogas/data/vol2.rda                            |binary
 biogas-1.4.0/biogas/inst/doc/biogas_quick_start.Rnw          |    2 
 biogas-1.4.0/biogas/inst/doc/biogas_quick_start.pdf          |binary
 biogas-1.4.0/biogas/inst/doc/predBg_function.pdf             |binary
 biogas-1.4.0/biogas/man/cumBg.Rd                             |  179 +++++--
 biogas-1.4.0/biogas/man/stdVol.Rd                            |    9 
 biogas-1.4.0/biogas/man/strawComp.Rd                         |only
 biogas-1.4.0/biogas/man/strawMass.Rd                         |only
 biogas-1.4.0/biogas/man/strawPressure.Rd                     |only
 biogas-1.4.0/biogas/man/strawSetup.Rd                        |only
 biogas-1.4.0/biogas/tests/testthat/test_HighLevelFunctions.R |   20 
 biogas-1.4.0/biogas/vignettes/biogas_quick_start.Rnw         |    2 
 34 files changed, 524 insertions(+), 164 deletions(-)

More information about biogas at CRAN
Permanent link

Package BAMMtools updated to version 2.1.3 with previous version 2.1.1 dated 2016-03-03

Title: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>

Diff between BAMMtools versions 2.1.1 dated 2016-03-03 and 2.1.3 dated 2016-05-24

 BAMMtools-2.1.1/BAMMtools/R/BAMMlikelihood.R                 |only
 BAMMtools-2.1.1/BAMMtools/R/print.credibleshiftset.R         |only
 BAMMtools-2.1.1/BAMMtools/R/richColors.R                     |only
 BAMMtools-2.1.1/BAMMtools/man/BAMMtools-internal.Rd          |only
 BAMMtools-2.1.1/BAMMtools/man/BAMMtools-package.Rd           |only
 BAMMtools-2.1.3/BAMMtools/DESCRIPTION                        |   24 
 BAMMtools-2.1.3/BAMMtools/MD5                                |  198 ++--
 BAMMtools-2.1.3/BAMMtools/NAMESPACE                          |  128 +-
 BAMMtools-2.1.3/BAMMtools/R/BAMMtools-data.R                 |only
 BAMMtools-2.1.3/BAMMtools/R/BAMMtools-package.R              |only
 BAMMtools-2.1.3/BAMMtools/R/addBAMMlegend.R                  |   76 +
 BAMMtools-2.1.3/BAMMtools/R/addBAMMshifts.R                  |   66 +
 BAMMtools-2.1.3/BAMMtools/R/as.bammdata.R                    |    5 
 BAMMtools-2.1.3/BAMMtools/R/as.phylo.bammdata.R              |    1 
 BAMMtools-2.1.3/BAMMtools/R/assignColorBreaks.R              |   59 +
 BAMMtools-2.1.3/BAMMtools/R/bammLikelihood.R                 |only
 BAMMtools-2.1.3/BAMMtools/R/bammcolors.R                     |   20 
 BAMMtools-2.1.3/BAMMtools/R/barLegend.R                      |   38 
 BAMMtools-2.1.3/BAMMtools/R/cohorts.R                        |   59 +
 BAMMtools-2.1.3/BAMMtools/R/colorMap.R                       |   10 
 BAMMtools-2.1.3/BAMMtools/R/computeBayesFactors.R            |   54 +
 BAMMtools-2.1.3/BAMMtools/R/credibleShiftSet.R               |  224 ++++-
 BAMMtools-2.1.3/BAMMtools/R/cumulativeShiftProbsTree.R       |    2 
 BAMMtools-2.1.3/BAMMtools/R/distinctShiftConfigurations.R    |   75 +
 BAMMtools-2.1.3/BAMMtools/R/dtRates.R                        |   57 +
 BAMMtools-2.1.3/BAMMtools/R/generateControlFile.R            |   44 -
 BAMMtools-2.1.3/BAMMtools/R/getBestShiftConfiguration.R      |   75 +
 BAMMtools-2.1.3/BAMMtools/R/getBranchShiftPriors.R           |   49 +
 BAMMtools-2.1.3/BAMMtools/R/getCladeRates.R                  |   74 +
 BAMMtools-2.1.3/BAMMtools/R/getCohortMatrix.R                |   52 +
 BAMMtools-2.1.3/BAMMtools/R/getEventData.R                   |  157 +++
 BAMMtools-2.1.3/BAMMtools/R/getJenksBreaks.R                 |   53 +
 BAMMtools-2.1.3/BAMMtools/R/getMarginalBranchRateMatrix.R    |   39 
 BAMMtools-2.1.3/BAMMtools/R/getMeanBranchLengthTree.R        |   39 
 BAMMtools-2.1.3/BAMMtools/R/getRateThroughTimeMatrix.R       |  111 ++
 BAMMtools-2.1.3/BAMMtools/R/getShiftNodesFromIndex.R         |   37 
 BAMMtools-2.1.3/BAMMtools/R/getTipRates.R                    |   76 +
 BAMMtools-2.1.3/BAMMtools/R/getmrca.R                        |   26 
 BAMMtools-2.1.3/BAMMtools/R/marginalOddsRatioBranches.R      |   46 +
 BAMMtools-2.1.3/BAMMtools/R/marginalShiftProbsTree.R         |   68 +
 BAMMtools-2.1.3/BAMMtools/R/maximumShiftCredibility.R        |   64 +
 BAMMtools-2.1.3/BAMMtools/R/plot.bammdata.R                  |  245 +++++
 BAMMtools-2.1.3/BAMMtools/R/plot.bammshifts.R                |   78 +
 BAMMtools-2.1.3/BAMMtools/R/plot.credibleshiftset.R          |   63 +
 BAMMtools-2.1.3/BAMMtools/R/plotPrior.R                      |   24 
 BAMMtools-2.1.3/BAMMtools/R/plotRateThroughTime.R            |  132 +++
 BAMMtools-2.1.3/BAMMtools/R/print.bammdata.R                 |    1 
 BAMMtools-2.1.3/BAMMtools/R/rateLegend.R                     |    4 
 BAMMtools-2.1.3/BAMMtools/R/ratesHistogram.R                 |   44 +
 BAMMtools-2.1.3/BAMMtools/R/samplingProbs.R                  |   68 +
 BAMMtools-2.1.3/BAMMtools/R/setBAMMpriors.R                  |   73 +
 BAMMtools-2.1.3/BAMMtools/R/speciesByRatesMatrix.R           |   52 +
 BAMMtools-2.1.3/BAMMtools/R/subsetEventData.R                |   29 
 BAMMtools-2.1.3/BAMMtools/R/subtreeBAMM.R                    |   38 
 BAMMtools-2.1.3/BAMMtools/R/summary.bammdata.R               |   30 
 BAMMtools-2.1.3/BAMMtools/R/summary.credibleshiftset.R       |   50 +
 BAMMtools-2.1.3/BAMMtools/R/testTimeVariableBranches.R       |  114 ++
 BAMMtools-2.1.3/BAMMtools/R/traitDependentBAMM.R             |  130 ++
 BAMMtools-2.1.3/BAMMtools/R/transparentColor.R               |   20 
 BAMMtools-2.1.3/BAMMtools/R/writeEventData.R                 |   20 
 BAMMtools-2.1.3/BAMMtools/man/BAMMlikelihood.Rd              |  128 +-
 BAMMtools-2.1.3/BAMMtools/man/BAMMtools-data.Rd              |  151 ++-
 BAMMtools-2.1.3/BAMMtools/man/BAMMtools.Rd                   |only
 BAMMtools-2.1.3/BAMMtools/man/ShiftProbsTree.Rd              |   93 +-
 BAMMtools-2.1.3/BAMMtools/man/addBAMMlegend.Rd               |  151 +--
 BAMMtools-2.1.3/BAMMtools/man/addBAMMshifts.Rd               |  118 +-
 BAMMtools-2.1.3/BAMMtools/man/assignColorBreaks.Rd           |  126 +-
 BAMMtools-2.1.3/BAMMtools/man/cohorts.Rd                     |  124 +-
 BAMMtools-2.1.3/BAMMtools/man/computeBayesFactors.Rd         |   73 -
 BAMMtools-2.1.3/BAMMtools/man/credibleShiftSet.Rd            |  345 ++++---
 BAMMtools-2.1.3/BAMMtools/man/distinctShiftConfigurations.Rd |  123 +-
 BAMMtools-2.1.3/BAMMtools/man/dtRates.Rd                     |   98 +-
 BAMMtools-2.1.3/BAMMtools/man/generateControlFile.Rd         |   73 -
 BAMMtools-2.1.3/BAMMtools/man/getBestShiftConfiguration.Rd   |   95 +-
 BAMMtools-2.1.3/BAMMtools/man/getBranchShiftPriors.Rd        |   77 -
 BAMMtools-2.1.3/BAMMtools/man/getCladeRates.Rd               |  100 +-
 BAMMtools-2.1.3/BAMMtools/man/getCohortMatrix.Rd             |   71 -
 BAMMtools-2.1.3/BAMMtools/man/getEventData.Rd                |  276 +++---
 BAMMtools-2.1.3/BAMMtools/man/getJenksBreaks.Rd              |   88 --
 BAMMtools-2.1.3/BAMMtools/man/getMarginalBranchRateMatrix.Rd |   63 -
 BAMMtools-2.1.3/BAMMtools/man/getMeanBranchLengthTree.Rd     |   65 -
 BAMMtools-2.1.3/BAMMtools/man/getRateThroughTimeMatrix.Rd    |  187 ++--
 BAMMtools-2.1.3/BAMMtools/man/getShiftNodesFromIndex.Rd      |   55 -
 BAMMtools-2.1.3/BAMMtools/man/getTipRates.Rd                 |  132 +--
 BAMMtools-2.1.3/BAMMtools/man/getmrca.Rd                     |   48 -
 BAMMtools-2.1.3/BAMMtools/man/marginalOddsRatioBranches.Rd   |   78 -
 BAMMtools-2.1.3/BAMMtools/man/maximumShiftCredibility.Rd     |   98 +-
 BAMMtools-2.1.3/BAMMtools/man/plot.bammdata.Rd               |  483 +++++------
 BAMMtools-2.1.3/BAMMtools/man/plot.bammshifts.Rd             |  159 +--
 BAMMtools-2.1.3/BAMMtools/man/plot.credibleshiftset.Rd       |  151 +--
 BAMMtools-2.1.3/BAMMtools/man/plotPrior.Rd                   |   63 -
 BAMMtools-2.1.3/BAMMtools/man/plotRateThroughTime.Rd         |  339 +++----
 BAMMtools-2.1.3/BAMMtools/man/ratesHistogram.Rd              |  106 +-
 BAMMtools-2.1.3/BAMMtools/man/richColors.Rd                  |only
 BAMMtools-2.1.3/BAMMtools/man/samplingProbs.Rd               |  110 +-
 BAMMtools-2.1.3/BAMMtools/man/setBAMMpriors.Rd               |  134 +--
 BAMMtools-2.1.3/BAMMtools/man/speciesByRatesMatrix.Rd        |   87 +
 BAMMtools-2.1.3/BAMMtools/man/subsetEventData.Rd             |   52 -
 BAMMtools-2.1.3/BAMMtools/man/subtreeBAMM.Rd                 |   62 -
 BAMMtools-2.1.3/BAMMtools/man/summary.bammdata.Rd            |   65 -
 BAMMtools-2.1.3/BAMMtools/man/summary.credibleshiftset.Rd    |   86 -
 BAMMtools-2.1.3/BAMMtools/man/testTimeVariableBranches.Rd    |  125 +-
 BAMMtools-2.1.3/BAMMtools/man/traitDependentBAMM.Rd          |  222 +++--
 BAMMtools-2.1.3/BAMMtools/man/transparentColor.Rd            |   35 
 BAMMtools-2.1.3/BAMMtools/man/writeEventData.Rd              |   38 
 105 files changed, 5911 insertions(+), 2763 deletions(-)

More information about BAMMtools at CRAN
Permanent link

Package AlignStat updated to version 1.2.1 with previous version 1.1.3 dated 2016-03-18

Title: Comparison of Alternative Multiple Sequence Alignments
Description: Methods for comparing two alternative multiple sequence alignments (MSAs) to determine whether they align homologous residues in the same columns as one another. It then classifies similarities and differences into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative to the other. Summarising these categories for each MSA column yields information on which sequence regions are agreed upon my both MSAs, and which differ. Several plotting functions enable easily visualisation of the comparison data for analysis.
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee@gmail.com>

Diff between AlignStat versions 1.1.3 dated 2016-03-18 and 1.2.1 dated 2016-05-24

 DESCRIPTION                              |   12 +-
 MD5                                      |   38 +++---
 NAMESPACE                                |    1 
 R/AlignStat.R                            |    1 
 R/Plots.R                                |   51 ++++++++
 R/compare_alignments.R                   |  181 ++++++++++++++++++++++++++-----
 README.md                                |   46 ++++++-
 data/comparison_alignment.rda            |binary
 data/reference_alignment.rda             |binary
 man/AlignStat.Rd                         |    1 
 man/compare_alignments.Rd                |   13 +-
 man/plot_SP_summary.Rd                   |only
 tests/testthat/AlignmentA.fasta          |only
 tests/testthat/AlignmentB.clustal        |only
 tests/testthat/AlignmentB.fasta          |only
 tests/testthat/GrammicidinsClustal.fasta |only
 tests/testthat/GrammicidinsMuscle.fasta  |only
 tests/testthat/categories.rda            |binary
 tests/testthat/means.rda                 |binary
 tests/testthat/prepared_com.rda          |binary
 tests/testthat/prepared_ref.rda          |binary
 tests/testthat/results.rda               |binary
 tests/testthat/test-align.R              |   47 ++++++--
 23 files changed, 324 insertions(+), 67 deletions(-)

More information about AlignStat at CRAN
Permanent link

New package adespatial with initial version 0.0-2
Package: adespatial
Title: Multivariate Multiscale Spatial Analysis
Version: 0.0-2
Date: 2016-05-24
Author: Stéphane Dray, Guillaume Blanchet, Guillaume Guenard, Thibaut Jombart, Pierre Legendre, Helene H Wagner
Description: Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Imports: ade4 (>= 1.7-1), adegraphics, sp, spdep, lattice, methods, grDevices, graphics, stats, utils, vegan
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2016-05-24 11:55:17 UTC; stephane
Repository: CRAN
Date/Publication: 2016-05-24 14:49:37

More information about adespatial at CRAN
Permanent link

Package surveyplanning updated to version 1.6 with previous version 1.4 dated 2016-04-14

Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>

Diff between surveyplanning versions 1.4 dated 2016-04-14 and 1.6 dated 2016-05-24

 DESCRIPTION                   |    8 ++++----
 MD5                           |    6 +++---
 R/expsize.R                   |    3 ++-
 man/surveyplanning-package.Rd |    4 ++--
 4 files changed, 11 insertions(+), 10 deletions(-)

More information about surveyplanning at CRAN
Permanent link

Package scatterplot3d updated to version 0.3-37 with previous version 0.3-36 dated 2015-07-29

Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>

Diff between scatterplot3d versions 0.3-36 dated 2015-07-29 and 0.3-37 dated 2016-05-24

 CHANGES              |    1 +
 DESCRIPTION          |    8 ++++----
 MD5                  |   14 +++++++-------
 NAMESPACE            |    2 +-
 R/scatterplot3d.R    |   22 +++++++++++++++++-----
 build/vignette.rds   |binary
 inst/doc/s3d.pdf     |binary
 man/scatterplot3d.Rd |    8 ++++++--
 8 files changed, 36 insertions(+), 19 deletions(-)

More information about scatterplot3d at CRAN
Permanent link

Package RJSDMX updated to version 1.6-2 with previous version 1.6-1 dated 2016-04-07

Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers that disseminate data by means of SDMX web services. SDMX (Statistical Data and Metadata eXchange) is a standard that has been developed with the aim of simplifying the exchange of statistical information. More about the SDMX standard and the SDMX Web Services can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>

Diff between RJSDMX versions 1.6-1 dated 2016-04-07 and 1.6-2 dated 2016-05-24

 DESCRIPTION        |    6 +++---
 MD5                |    4 ++--
 inst/java/SDMX.jar |binary
 3 files changed, 5 insertions(+), 5 deletions(-)

More information about RJSDMX at CRAN
Permanent link

Package eVenn updated to version 2.3.2 with previous version 2.3.1 dated 2016-04-26

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 2.3.1 dated 2016-04-26 and 2.3.2 dated 2016-05-24

 DESCRIPTION          |    8 
 MD5                  |   12 -
 R/autoevenn.R        |    4 
 R/evenn.R            |  478 ++++++++++++++++++++++++++++++---------------------
 man/autoevenn.Rd     |    5 
 man/eVenn-package.Rd |    4 
 man/evenn.Rd         |    5 
 7 files changed, 305 insertions(+), 211 deletions(-)

More information about eVenn at CRAN
Permanent link

Package spaMM updated to version 1.9.0 with previous version 1.8.0 dated 2016-04-08

Title: Mixed Models, Particularly Spatial GLMMs
Description: Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [ctb], Dirk Eddelbuettel [ctb] (ziggurat rnorm sources), GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between spaMM versions 1.8.0 dated 2016-04-08 and 1.9.0 dated 2016-05-24

 spaMM-1.8.0/spaMM/src/Makevars                      |only
 spaMM-1.9.0/spaMM/DESCRIPTION                       |   14 
 spaMM-1.9.0/spaMM/MD5                               |  143 ++---
 spaMM-1.9.0/spaMM/NAMESPACE                         |   12 
 spaMM-1.9.0/spaMM/R/COMPoisson.R                    |    5 
 spaMM-1.9.0/spaMM/R/CanonizeRanPars.R               |only
 spaMM-1.9.0/spaMM/R/GLM.fit.R                       |   27 
 spaMM-1.9.0/spaMM/R/HLCor.R                         |  141 +----
 spaMM-1.9.0/spaMM/R/HLFactorList.R                  |   58 +-
 spaMM-1.9.0/spaMM/R/HLfit.R                         |  559 +++++++-------------
 spaMM-1.9.0/spaMM/R/HLfit_Internals.R               |  476 ++++++++++++-----
 spaMM-1.9.0/spaMM/R/LR.R                            |   11 
 spaMM-1.9.0/spaMM/R/LevenbergMstep.R                |    4 
 spaMM-1.9.0/spaMM/R/MakeCovEst.R                    |   12 
 spaMM-1.9.0/spaMM/R/RcppExports.R                   |   32 -
 spaMM-1.9.0/spaMM/R/SEMbetalambda.R                 |  290 ++++------
 spaMM-1.9.0/spaMM/R/auglinmodfit.R                  |   75 +-
 spaMM-1.9.0/spaMM/R/bloc_lambda.R                   |only
 spaMM-1.9.0/spaMM/R/confint.R                       |   33 -
 spaMM-1.9.0/spaMM/R/corrHLfit-internals.R           |  124 ++--
 spaMM-1.9.0/spaMM/R/corrHLfit.R                     |  122 +---
 spaMM-1.9.0/spaMM/R/corrMM.LRT.R                    |  114 ++--
 spaMM-1.9.0/spaMM/R/correlationFns.R                |   26 
 spaMM-1.9.0/spaMM/R/dispGammaGLM.R                  |    2 
 spaMM-1.9.0/spaMM/R/extractors.R                    |   68 ++
 spaMM-1.9.0/spaMM/R/fitme.R                         |  301 ++++++----
 spaMM-1.9.0/spaMM/R/iterateSmooth.R                 |   19 
 spaMM-1.9.0/spaMM/R/locoptimthroughsmooth.R         |   23 
 spaMM-1.9.0/spaMM/R/logL_from_SEMsample.R           |only
 spaMM-1.9.0/spaMM/R/mapMM.R                         |   11 
 spaMM-1.9.0/spaMM/R/migraineLike.R                  |    3 
 spaMM-1.9.0/spaMM/R/negbin.R                        |   59 +-
 spaMM-1.9.0/spaMM/R/plot.HLfit.R                    |    2 
 spaMM-1.9.0/spaMM/R/predict.R                       |   32 -
 spaMM-1.9.0/spaMM/R/preprocess.R                    |   64 +-
 spaMM-1.9.0/spaMM/R/simulate.HL.R                   |    6 
 spaMM-1.9.0/spaMM/R/summary.HL.R                    |  182 +++---
 spaMM-1.9.0/spaMM/R/update.HL.R                     |   17 
 spaMM-1.9.0/spaMM/data/Loaloa.RData                 |binary
 spaMM-1.9.0/spaMM/data/arabidopsis.RData            |binary
 spaMM-1.9.0/spaMM/data/blackcap.RData               |binary
 spaMM-1.9.0/spaMM/data/freight.RData                |binary
 spaMM-1.9.0/spaMM/data/landMask.RData               |binary
 spaMM-1.9.0/spaMM/data/oceanmask.RData              |binary
 spaMM-1.9.0/spaMM/data/salamander.RData             |binary
 spaMM-1.9.0/spaMM/data/scotlip.RData                |binary
 spaMM-1.9.0/spaMM/data/seaMask.RData                |binary
 spaMM-1.9.0/spaMM/data/seeds.RData                  |binary
 spaMM-1.9.0/spaMM/data/wafers.RData                 |binary
 spaMM-1.9.0/spaMM/data/welding.RData                |binary
 spaMM-1.9.0/spaMM/data/worldcountries.RData         |binary
 spaMM-1.9.0/spaMM/inst/NEWS.Rd                      |   27 
 spaMM-1.9.0/spaMM/man/COMPoisson.Rd                 |   22 
 spaMM-1.9.0/spaMM/man/GLM.fit.Rd                    |   12 
 spaMM-1.9.0/spaMM/man/HLCor.Rd                      |   20 
 spaMM-1.9.0/spaMM/man/HLfit.Rd                      |   33 -
 spaMM-1.9.0/spaMM/man/corrHLfit.Rd                  |    4 
 spaMM-1.9.0/spaMM/man/corrMatrix.Rd                 |only
 spaMM-1.9.0/spaMM/man/designL.from.Corr.Rd          |    5 
 spaMM-1.9.0/spaMM/man/extractors.Rd                 |   18 
 spaMM-1.9.0/spaMM/man/fitme.Rd                      |only
 spaMM-1.9.0/spaMM/man/fixed.LRT.Rd                  |   16 
 spaMM-1.9.0/spaMM/man/mapMM.Rd                      |   46 -
 spaMM-1.9.0/spaMM/man/negbin.Rd                     |only
 spaMM-1.9.0/spaMM/man/options.Rd                    |    2 
 spaMM-1.9.0/spaMM/man/predict.Rd                    |    2 
 spaMM-1.9.0/spaMM/man/spaMM-internal-Rcpp.Rd        |    8 
 spaMM-1.9.0/spaMM/man/spaMM-internal.Rd             |   17 
 spaMM-1.9.0/spaMM/man/spaMM.Rd                      |    2 
 spaMM-1.9.0/spaMM/src/Makevars.win                  |    8 
 spaMM-1.9.0/spaMM/src/RcppExports.cpp               |  133 +++-
 spaMM-1.9.0/spaMM/src/Rcpp_gibbs.cpp                |only
 spaMM-1.9.0/spaMM/src/Zigg.h                        |only
 spaMM-1.9.0/spaMM/src/Ziggurat.h                    |only
 spaMM-1.9.0/spaMM/src/pMVN.cpp                      |    1 
 spaMM-1.9.0/spaMM/src/spaMM_linear.cpp              |  242 ++++----
 spaMM-1.9.0/spaMM/src/zrnorm.cpp                    |only
 spaMM-1.9.0/spaMM/tests/testthat/test-multinomial.R |    2 
 78 files changed, 2061 insertions(+), 1626 deletions(-)

More information about spaMM at CRAN
Permanent link

Package pubprint updated to version 0.2.1 with previous version 0.2 dated 2016-05-12

Title: Printing Results of Statistical Computing in a Publishable Way
Description: Takes the output of statistical tests and transforms it in a publish-friendly pattern. Currently only APA (American Psychological Association) style is supported with output to HTML, LaTeX, Markdown and plain text. It is easily customizable, extendable and can be used well with 'knitr'. Additionally 'pubprint' offers a memory system that allows to save and retrieve results of computations.
Author: Rudolf Siegel [aut, cre]
Maintainer: Rudolf Siegel <rs.os@t-online.de>

Diff between pubprint versions 0.2 dated 2016-05-12 and 0.2.1 dated 2016-05-24

 DESCRIPTION            |    8 +++---
 MD5                    |   14 +++++-----
 NEWS.md                |    6 ++++
 R/out_html.R           |   64 ++++++++++++++++++++++++++-----------------------
 README.md              |    4 +--
 inst/doc/pubprint.Rnw  |    2 -
 inst/doc/pubprint.pdf  |binary
 vignettes/pubprint.Rnw |    2 -
 8 files changed, 56 insertions(+), 44 deletions(-)

More information about pubprint at CRAN
Permanent link

New package photobiologyInOut with initial version 0.4.4
Package: photobiologyInOut
Type: Package
Title: Read Spectral Data from Foreign Files
Version: 0.4.4
Date: 2016-05-22
Author: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Description: Functions for reading and writing foreign files containing spectral data from spectrometers and their associated software, and output from simulation models in common use.
License: GPL (>= 3)
VignetteBuilder: knitr
Depends: R (>= 3.2.0)
Imports: lubridate (>= 1.5.6), tibble (>= 1.0), dplyr (>= 0.4.3), readr (>= 0.2.2), photobiology (>= 0.9.8), reshape2 (>= 1.4.1), hyperSpec (>= 0.98), pavo (>= 0.5-5), lazyeval (>= 0.1.10), methods
Suggests: knitr (>= 1.13), ggspectra (>= 0.1.7), photobiologyWavebands (>= 0.4.0), ggplot2 (>= 2.1.0), ggmap (>= 2.6.1), testthat (>= 1.0.2)
LazyLoad: yes
LazyData: yes
ByteCompile: true
Encoding: UTF-8
URL: http://www.r4photobiology.info
BugReports: https://bitbucket.org/aphalo/photobiologyinout/
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 11:39:18 UTC; aphalo
Repository: CRAN
Date/Publication: 2016-05-24 11:02:23

More information about photobiologyInOut at CRAN
Permanent link

Package MAPA updated to version 1.9.1 with previous version 1.9 dated 2014-11-21

Title: Multiple Aggregation Prediction Algorithm
Description: Functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts time series at multiple temporal aggregation levels, thus strengthening and attenuating the various time series components for better holistic estimation of its structure.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>

Diff between MAPA versions 1.9 dated 2014-11-21 and 1.9.1 dated 2016-05-24

 ChangeLog   |    4 ++++
 DESCRIPTION |   10 +++++-----
 MD5         |    8 ++++----
 NAMESPACE   |    3 +++
 R/MAPA.R    |    2 ++
 5 files changed, 18 insertions(+), 9 deletions(-)

More information about MAPA at CRAN
Permanent link

Package stpm updated to version 1.3.1 with previous version 1.2.1 dated 2016-04-12

Title: Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided. For more information, see: (i) "Life tables with covariates: Dynamic model for nonlinear analysis of longitudinal data" by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80), <DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al. (2007), Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>; (iii) "Health decline, aging and mortality: how are they related?" by Yashin A. et al. (2007), Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>

Diff between stpm versions 1.2.1 dated 2016-04-12 and 1.3.1 dated 2016-05-24

 stpm-1.2.1/stpm/R/simdata_gen.R              |only
 stpm-1.2.1/stpm/man/fill_last.Rd             |only
 stpm-1.2.1/stpm/man/optimize.Rd              |only
 stpm-1.2.1/stpm/man/setlb.Rd                 |only
 stpm-1.2.1/stpm/man/setub.Rd                 |only
 stpm-1.2.1/stpm/man/simdata_cont2.Rd         |only
 stpm-1.3.1/stpm/DESCRIPTION                  |    8 
 stpm-1.3.1/stpm/MD5                          |   65 -
 stpm-1.3.1/stpm/NAMESPACE                    |    3 
 stpm-1.3.1/stpm/R/prepare_data.R             |  131 ++-
 stpm-1.3.1/stpm/R/simdata_cont.R             |  228 -----
 stpm-1.3.1/stpm/R/simdata_discr.R            |   28 
 stpm-1.3.1/stpm/R/simdata_gen_cont.R         |only
 stpm-1.3.1/stpm/R/simdata_time-dep.R         |   51 -
 stpm-1.3.1/stpm/R/spm.R                      |   28 
 stpm-1.3.1/stpm/R/spm_continuous.R           |  166 ++--
 stpm-1.3.1/stpm/R/spm_discrete.R             |    9 
 stpm-1.3.1/stpm/R/spm_gen.R                  |  433 +++++++---
 stpm-1.3.1/stpm/R/spm_projection.R           |   40 -
 stpm-1.3.1/stpm/R/spm_time-dependent.R       |  735 +++++++++---------
 stpm-1.3.1/stpm/R/stpm-package.R             |    4 
 stpm-1.3.1/stpm/man/prepare_data.Rd          |   29 
 stpm-1.3.1/stpm/man/prepare_data_discr.Rd    |    3 
 stpm-1.3.1/stpm/man/simdata_cont.Rd          |   38 
 stpm-1.3.1/stpm/man/simdata_discr.Rd         |   13 
 stpm-1.3.1/stpm/man/simdata_gen.Rd           |   69 +
 stpm-1.3.1/stpm/man/simdata_time_dep.Rd      |   14 
 stpm-1.3.1/stpm/man/spm.Rd                   |   23 
 stpm-1.3.1/stpm/man/spm_continuous.Rd        |    9 
 stpm-1.3.1/stpm/man/spm_discrete.Rd          |    4 
 stpm-1.3.1/stpm/man/spm_gen.Rd               |   73 +
 stpm-1.3.1/stpm/man/spm_projection.Rd        |   24 
 stpm-1.3.1/stpm/man/spm_time_dep.Rd          |   10 
 stpm-1.3.1/stpm/src/simdataND.cpp            |  141 ---
 stpm-1.3.1/stpm/src/spm_integral_MD.cpp      | 1064 +++++++++++++++++++++------
 stpm-1.3.1/stpm/vignettes/stpm-vignette.Rmd  |  216 +++--
 stpm-1.3.1/stpm/vignettes/stpm-vignette.html |  513 ++++++++-----
 37 files changed, 2559 insertions(+), 1613 deletions(-)

More information about stpm at CRAN
Permanent link

Package dlsem updated to version 1.0.1 with previous version 1.0 dated 2016-05-19

Title: Distributed-Lag Structural Equation Modelling
Description: Fit distributed-lag structural equation models and perform path analysis at different time lags.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>

Diff between dlsem versions 1.0 dated 2016-05-19 and 1.0.1 dated 2016-05-24

 DESCRIPTION          |    8 ++++----
 MD5                  |   22 +++++++++++-----------
 R/dlsem.r            |   13 +++++++++----
 data/agres.rda       |binary
 man/agres.Rd         |    2 +-
 man/dlaglm.Rd        |    8 ++++----
 man/dlsem-package.Rd |   12 ++++++------
 man/dlsem.Rd         |   46 +++++++++++++++++++++++++++-------------------
 man/isIndep.Rd       |   10 +++++-----
 man/lagPlot.Rd       |   14 +++++++-------
 man/pathAnal.Rd      |   10 +++++-----
 man/pathCoeff.Rd     |   10 +++++-----
 12 files changed, 84 insertions(+), 71 deletions(-)

More information about dlsem at CRAN
Permanent link

New package ChangepointTesting with initial version 1.0
Package: ChangepointTesting
Type: Package
Title: Change Point Estimation for Clustered Signals
Version: 1.0
Date: 2016-02-01
Author: Hongyuan Cao, Wei Biao Wu, and Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Description: A multiple testing procedure for clustered alternative hypotheses. It is assumed that the p-values under the null hypotheses follow U(0,1) and that the distributions of p-values from the alternative hypotheses are stochastically smaller than U(0,1). By aggregating information, this method is more sensitive to detecting signals of low magnitude than standard methods. Additionally, sporadic small p-values appearing within a null hypotheses sequence are avoided by averaging on the neighboring p-values.
License: GPL-2
Depends: graphics, methods, stats
NeedsCompilation: no
Packaged: 2016-05-23 22:36:17 UTC; sthollow
Repository: CRAN
Date/Publication: 2016-05-24 05:38:52

More information about ChangepointTesting at CRAN
Permanent link

Package ape updated to version 3.5 with previous version 3.4 dated 2015-11-29

Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph], Simon Blomberg [aut, cph], Ben Bolker [aut, cph], Julien Claude [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph], Benoit Durand [aut, cph], Julien Dutheil [aut, cph], Olivier Gascuel [aut, cph], Christoph Heibl [aut, cph], Anthony Ives [aut, cph], Daniel Lawson [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre [aut, cph], Jim Lemon [aut, cph], Rosemary McCloskey [aut, cph], Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph], Korbinian Strimmer [aut, cph], Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>

Diff between ape versions 3.4 dated 2015-11-29 and 3.5 dated 2016-05-24

 DESCRIPTION                    |    8 
 MD5                            |   77 ++++-----
 NAMESPACE                      |    8 
 R/DNA.R                        |  346 +++++++++++++++++++++++++++++++++++++++--
 R/clustal.R                    |   27 ++-
 R/dist.topo.R                  |   91 ++++------
 R/plot.phylo.R                 |   20 +-
 R/plot.phyloExtra.R            |only
 R/read.nexus.R                 |    2 
 R/root.R                       |   29 +--
 build/vignette.rds             |binary
 data/hivtree.newick.rda        |binary
 data/landplants.newick.rda     |binary
 data/opsin.newick.rda          |binary
 inst/doc/MoranI.Rnw            |    2 
 inst/doc/MoranI.pdf            |binary
 man/AAbin.Rd                   |only
 man/DNAbin.Rd                  |    2 
 man/DNAbin2indel.Rd            |    3 
 man/LTT.Rd                     |    3 
 man/additive.Rd                |    1 
 man/all.equal.phylo.Rd         |    2 
 man/alview.Rd                  |   12 -
 man/ape-internal.Rd            |    1 
 man/boot.phylo.Rd              |   48 ++++-
 man/checkAlignment.Rd          |only
 man/clustal.Rd                 |    2 
 man/def.Rd                     |    2 
 man/del.gaps.Rd                |   29 ++-
 man/dist.dna.Rd                |    6 
 man/diversity.contrast.test.Rd |    2 
 man/image.DNAbin.Rd            |    3 
 man/makeNodeLabel.Rd           |    2 
 man/mcmc.popsize.Rd            |    8 
 man/plot.phyloExtra.Rd         |only
 man/read.GenBank.Rd            |    2 
 man/root.Rd                    |    2 
 man/trans.Rd                   |only
 man/write.nexus.data.Rd        |    4 
 src/ape.c                      |    6 
 src/dist_dna.c                 |  218 +++++++++++++++++++++++++
 vignettes/MoranI.Rnw           |    2 
 42 files changed, 794 insertions(+), 176 deletions(-)

More information about ape at CRAN
Permanent link

Mon, 23 May 2016

Package uskewFactors updated to version 2.0 with previous version 1.0 dated 2014-09-18

Title: Model-Based Clustering via Mixtures of Unrestricted Skew-t Sactor Analyzer Models
Description: Implements mixtures of unrestricted skew-t factor analyzer models via the EM algorithm.
Author: Paula M. Murray, Ryan P. Browne, and Paul D. McNicholas
Maintainer: Paula M. Murray <paula.murray@math.mcmaster.ca>

Diff between uskewFactors versions 1.0 dated 2014-09-18 and 2.0 dated 2016-05-23

 DESCRIPTION                 |   18 ++++++-------
 MD5                         |   10 +++----
 NAMESPACE                   |    1 
 R/uSkewFactors.R            |   57 ++++++++++++++++++++++----------------------
 man/uskewFA.Rd              |   19 ++++++--------
 man/uskewFactors-package.Rd |    6 ++--
 6 files changed, 56 insertions(+), 55 deletions(-)

More information about uskewFactors at CRAN
Permanent link

Package sommer updated to version 1.7 with previous version 1.6 dated 2016-05-19

Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures of random effects. ML/REML estimates are obtained using the Average Information, Expectation-Maximization, Newton-Raphson, or Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>

Diff between sommer versions 1.6 dated 2016-05-19 and 1.7 dated 2016-05-23

 CHANGELOG             |   16 
 DESCRIPTION           |   10 
 MD5                   |   52 -
 NAMESPACE             |    8 
 R/AI.R                |  960 ++++++++++++++++--------------
 R/AI2.R               |  452 +++++++-------
 R/AI3.R               |  456 +++++++-------
 R/EM.R                |  633 +++++++++-----------
 R/EM2.R               |  366 +++++------
 R/NR.R                | 1573 +++++++++++++++++++++++++++-----------------------
 R/NR22.R              |only
 R/R.mat.R             |only
 R/fdr.R               |   32 -
 R/mmer.R              |  235 +++++--
 R/mmer2.R             |    4 
 R/score.calc.R        |   14 
 data/PolyData.RData   |binary
 inst/doc/sommer.R     |    2 
 inst/doc/sommer.Rmd   |    2 
 inst/doc/sommer.pdf   |binary
 man/NR.Rd             |   36 +
 man/NR22.Rd           |only
 man/PolyData.Rd       |   13 
 man/R.mat.Rd          |only
 man/fdr.Rd            |    2 
 man/mmer.Rd           |    4 
 man/mmer2.Rd          |    5 
 vignettes/sommer.Rmd  |    2 
 vignettes/sommer.html |   49 -
 29 files changed, 2655 insertions(+), 2271 deletions(-)

More information about sommer at CRAN
Permanent link

New package sjstats with initial version 0.1.0
Package: sjstats
Type: Package
Encoding: UTF-8
Title: Collection of Convenient Functions for Common Statistical Computations
Version: 0.1.0
Date: 2016-05-23
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Description: Collection of convenient functions for common statistical computations, which are not directly provided by R's base or stats packages. This package aims at providing, first, shortcuts for statistical measures, which otherwise could only be calculated with additional effort (like standard errors or root mean squared errors). Second, these shortcut functions are generic (if appropriate), and can be applied not only to vectors, but also to other objects as well (e.g., the Coefficient of Variation can be computed for vectors, linear models, or linear mixed models; the r2()-function returns the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects). The focus of most functions lies on summary statistics or fit measures for regression models, including generalized linear models and mixed effects models. However, some of the functions also deal with other statistical measures, like Cronbach's Alpha, Cramer's V, Phi etc.
License: GPL-3
Depends: R (>= 3.2), stats, utils
Imports: coin, lme4, MASS, Matrix, nlme, sjmisc
Suggests: AER, arm, pwr
URL: https://github.com/sjPlot/sjstats
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 16:52:26 UTC; Standardbenutzer
Repository: CRAN
Date/Publication: 2016-05-23 23:37:22

More information about sjstats at CRAN
Permanent link

New package SafeBayes with initial version 1.0
Package: SafeBayes
Type: Package
Title: Generalized and Safe-Bayesian Ridge and Lasso Regression
Version: 1.0
Date: 2016-05-21
Authors@R: c(person("Rianne", "de Heide", role = c("aut", "cre"), email = "r.de.heide@cwi.nl"), person("Gustavo", "de los Campos", role = "ctb"), person("Paulino", "Perez Rodriguez", role = "ctb"), person("Bob", "Wheeler", role = "ctb"))
Depends: R (>= 3.1.2), stats
Description: Functions for Generalized and Safe-Bayesian Ridge and Lasso Regression models with both fixed and varying variance.
License: GPL-2
NeedsCompilation: yes
LazyLoad: true
Packaged: 2016-05-23 14:48:19 UTC; Rianne
Author: Rianne de Heide [aut, cre], Gustavo de los Campos [ctb], Paulino Perez Rodriguez [ctb], Bob Wheeler [ctb]
Maintainer: Rianne de Heide <r.de.heide@cwi.nl>
Repository: CRAN
Date/Publication: 2016-05-23 17:05:40

More information about SafeBayes at CRAN
Permanent link

Package MFAg updated to version 1.4 with previous version 1.3 dated 2015-10-06

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 1.3 dated 2015-10-06 and 1.4 dated 2016-05-23

 DESCRIPTION         |    8 ++++----
 MD5                 |    6 +++---
 R/Plot.MFA.R        |    2 +-
 man/MFAg-package.Rd |    4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

More information about MFAg at CRAN
Permanent link

New package extremefit with initial version 0.1
Package: extremefit
Type: Package
Title: Estimation of Extreme Conditional Quantiles and Probabilities
Version: 0.1
Date: 2016-05-23
Author: Gilles Durrieu, Ion Grama, Kevin Jaunatre, Quang-Khoai Pham, Jean-Marie Tricot
Depends: R (>= 2.10)
Maintainer: Kevin Jaunatre <kevin.jaunatre@univ-ubs.fr>
Description: Extreme value theory, nonparametric kernel estimation, tail conditional probabilities, extreme conditional quantile, adaptive estimation, quantile regression, survival probabilities.
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 13:56:08 UTC; kevin
Repository: CRAN
Date/Publication: 2016-05-23 16:28:14

More information about extremefit at CRAN
Permanent link

Package tgcd updated to version 1.9 with previous version 1.8 dated 2016-01-19

Title: Thermoluminescence Glow Curve Deconvolution
Description: Deconvolving thermoluminescence glow curves according to the general-order empirical expression or the semi-analytical expression derived from the one trap- one recombination (OTOR) model based on the Lambert's W function using a modified Levenberg-Marquardt algorithm. It provides the possibility of setting constraints or fixing any of parameters. It offers an interactive way to initialize parameters by clicking with a mouse on a plot at positions where peak maxima should be located. The optimal estimate is obtained by "trial-and-error". It also provides routines for simulating first-order, second-order, and general-order glow peaks (curves).
Author: Jun Peng [aut, cre], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Linda R. Petzold [ctb], Alan C. Hindmarsh [ctb], R. Woodrow Setzer [ctb], Andrew Horchler [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>

Diff between tgcd versions 1.8 dated 2016-01-19 and 1.9 dated 2016-05-23

 DESCRIPTION         |   52 +++++---
 MD5                 |   17 +-
 R/simPeak.R         |   44 ++++---
 R/simqOTOR.R        |   50 ++++----
 R/tgcd.R            |  297 +++++++++++++++++++++++++++++++-----------------
 man/tgcd.Rd         |  124 ++++++++++++--------
 src/calcD.f90       |only
 src/calcei.f90      |only
 src/tgcd.f90        |  318 ++++++++++++++++++++++++++++++++++++----------------
 src/tgcd1.f90       |  223 ++++++++++++++++++++++++------------
 src/wrightOmega.f90 |only
 11 files changed, 739 insertions(+), 386 deletions(-)

More information about tgcd at CRAN
Permanent link

Package OptimaRegion updated to version 0.2 with previous version 0.1.0 dated 2016-03-11

Title: Confidence Regions for Optima
Description: Computes confidence regions on the location of response surface optima.
Author: Enrique del Castillo, John Hunt, and James Rapkin
Maintainer: Enrique del Castillo <exd13@psu.edu>

Diff between OptimaRegion versions 0.1.0 dated 2016-03-11 and 0.2 dated 2016-05-23

 OptimaRegion-0.1.0/OptimaRegion/data/Drug.txt                   |only
 OptimaRegion-0.2/OptimaRegion/DESCRIPTION                       |   10 ++--
 OptimaRegion-0.2/OptimaRegion/MD5                               |   18 ++++---
 OptimaRegion-0.2/OptimaRegion/NAMESPACE                         |    2 
 OptimaRegion-0.2/OptimaRegion/R/CRcompare.R                     |only
 OptimaRegion-0.2/OptimaRegion/R/OptRegionQuad.R                 |    3 -
 OptimaRegion-0.2/OptimaRegion/data/Drug.txt.gz                  |only
 OptimaRegion-0.2/OptimaRegion/inst/doc/OptimaRegion-manual.pdf  |binary
 OptimaRegion-0.2/OptimaRegion/inst/doc/OptimaRegionVignette.pdf |only
 OptimaRegion-0.2/OptimaRegion/man/CRcompare.Rd                  |only
 OptimaRegion-0.2/OptimaRegion/man/OptRegionQuad.Rd              |   24 +++++-----
 OptimaRegion-0.2/OptimaRegion/man/OptRegionTps.Rd               |   19 +++----
 OptimaRegion-0.2/OptimaRegion/man/OptimaRegion-package.Rd       |only
 13 files changed, 42 insertions(+), 34 deletions(-)

More information about OptimaRegion at CRAN
Permanent link

Package OneArmPhaseTwoStudy updated to version 0.1.6 with previous version 0.1.4 dated 2015-11-26

Title: Planing, Monitoring and Evaluating Oncological Phase 2 Studies
Description: Purpose of this package is it to plan, monitor and evaluate oncological phase II studies. In general this kind of studies are single-arm trials with planned interim analysis and binary endpoint. To meet the resulting requirements, the package provides functions to calculate and evaluate 'Simon's two-stage designs' and 'so-called' 'subset designs'. If you are unfamiliar with this package a good starting point is to take a closer look at the functions getSolutions() and getSolutionsSub1().The web-based tool (https://imbi.shinyapps.io/phaseII-app/) extends the functionality of our R package by means of a proper dealing with over- and underrunning. The R function binom.test of the 'stats' R package and the package 'binom' might be helpful to assess the performance of the corresponding one-stage design as a reference.
Author: Marius Wirths
Maintainer: Marius Wirths <wirths@imbi.uni-heidelberg.de>

Diff between OneArmPhaseTwoStudy versions 0.1.4 dated 2015-11-26 and 0.1.6 dated 2016-05-23

 DESCRIPTION                              |   22 ++++++---
 MD5                                      |   74 +++++++++++++++----------------
 R/zzz.R                                  |   40 +++++++++++++++-
 man/getCE.Rd                             |    3 -
 man/getCP.Rd                             |    9 ++-
 man/getCP_simon.Rd                       |    3 -
 man/getD_distributeToOne.Rd              |    5 +-
 man/getD_equally.Rd                      |    7 +-
 man/getD_none.Rd                         |    5 +-
 man/getD_proportionally.Rd               |    9 ++-
 man/getN2.Rd                             |    3 -
 man/getP.Rd                              |    3 -
 man/getSolutions.Rd                      |   11 ++--
 man/getSolutionsSub1.Rd                  |    7 +-
 man/get_CI.Rd                            |    3 -
 man/get_UMVUE_GMS.Rd                     |    3 -
 man/get_UMVUE_GMS_subset_second_only.Rd  |    5 +-
 man/get_UMVUE_GMS_subset_second_total.Rd |    3 -
 man/get_conditionalPower.Rd              |    5 +-
 man/get_confidence_set.Rd                |    5 +-
 man/get_p_KC.Rd                          |    3 -
 man/get_p_exact_subset.Rd                |    3 -
 man/get_r2_flex.Rd                       |    5 +-
 man/plot_confidence_set.Rd               |    3 -
 man/plot_simon_study_state.Rd            |    5 +-
 man/plot_sub1_study_state.Rd             |    5 +-
 man/setSimonParams.Rd                    |    3 -
 man/setSub1Params.Rd                     |    3 -
 man/setupSimon.Rd                        |    3 -
 man/setupSub1Design.Rd                   |    3 -
 man/toDataframe.Rd                       |    5 +-
 src/Makevars.win                         |    4 -
 src/design.cpp                           |    2 
 src/design.h                             |    2 
 src/simonModule.h                        |    1 
 src/sub1.cpp                             |    2 
 src/sub1.h                               |    2 
 src/sub1Module.h                         |    3 -
 38 files changed, 181 insertions(+), 101 deletions(-)

More information about OneArmPhaseTwoStudy at CRAN
Permanent link

Package filematrix updated to version 1.1.0 with previous version 1.0 dated 2015-06-12

Title: File-Backed Matrix Class with Convenient Read and Write Access
Description: Interface for working with large matrices stored in files, not in computer memory. Supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. Supports very large matrices. Tested on multi-terabyte matrices. Allows for more than 2^32 rows or columns. Allows for quick addition of extra columns to a filematrix. Cross-platform as the package has R code only.
Author: Andrey A Shabalin
Maintainer: Andrey A Shabalin <ashabalin@vcu.edu>

Diff between filematrix versions 1.0 dated 2015-06-12 and 1.1.0 dated 2016-05-23

 filematrix-1.0/filematrix/R/filematrix.r              |only
 filematrix-1.1.0/filematrix/DESCRIPTION               |   34 ++++--
 filematrix-1.1.0/filematrix/MD5                       |   27 ++++-
 filematrix-1.1.0/filematrix/NAMESPACE                 |    9 -
 filematrix-1.1.0/filematrix/R/filematrix.R            |only
 filematrix-1.1.0/filematrix/build                     |only
 filematrix-1.1.0/filematrix/inst                      |only
 filematrix-1.1.0/filematrix/man/filematrix-class.Rd   |   91 ++++++++----------
 filematrix-1.1.0/filematrix/man/filematrix-package.Rd |   31 +++---
 filematrix-1.1.0/filematrix/man/fm.create.Rd          |   82 +++++++---------
 filematrix-1.1.0/filematrix/tests                     |only
 filematrix-1.1.0/filematrix/vignettes                 |only
 12 files changed, 149 insertions(+), 125 deletions(-)

More information about filematrix at CRAN
Permanent link

New package ILS with initial version 0.1.0
Package: ILS
Type: Package
Title: Interlaboratory Study
Version: 0.1.0
Date: 2016-05-22
Authors@R: c( person("Miguel","Flores",role=c("aut","cre"), email="ma.flores@outlook.com"), person("Salvador","Naya",role="ctb"), person("Javier","Tarrio-Saavedra",role="ctb"), person("Ruben","Fernandez",role="ctb"), person("Rubi","Arias",role="ctb") )
Depends: R (>= 3.1.0), multcomp, depthTools, fda.usc, MASS
Description: It performs interlaboratory studies (ILS) to detect those laboratories that provide non-consistent results when comparing to others. It permits to work simultaneously with various testing materials, from standard univariate, and functional data analysis (FDA) perspectives. The univariate approach based on ASTM E691-08 consist of estimating the Mandel's h and k statistics to identify those laboratories that provide more significant different results, testing also the presence of outliers by Cochran and Grubbs tests, Analysis of variance (ANOVA) techniques are provided (F and Tuckey tests) to test differences in means corresponding to different laboratories per each material. Taking into account the functional nature of data retrieved in analytical chemistry, applied physics and engineering (spectra, thermograms, etc.). ILS package provides a FDA approach for finding the Mandel's k and h statistics distribution by smoothing bootstrap resampling.
License: GPL (>= 2)
LazyData: yes
Author: Miguel Flores [aut, cre], Salvador Naya [ctb], Javier Tarrio-Saavedra [ctb], Ruben Fernandez [ctb], Rubi Arias [ctb]
Maintainer: Miguel Flores <ma.flores@outlook.com>
Repository: CRAN
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-23 10:48:30 UTC; MiguelA
Date/Publication: 2016-05-23 13:04:51

More information about ILS at CRAN
Permanent link

Package asd updated to version 2.2 with previous version 2.0 dated 2013-11-26

Title: Simulations for Adaptive Seamless Designs
Description: Package runs simulations for adaptive seamless designs with and without early outcomes for treatment selection and subpopulation type designs.
Author: Nick Parsons
Maintainer: Nick Parsons <nick.parsons@warwick.ac.uk>

Diff between asd versions 2.0 dated 2013-11-26 and 2.2 dated 2016-05-23

 DESCRIPTION          |   10 +++++-----
 MD5                  |   10 +++++-----
 NAMESPACE            |   21 ++++++++++++++-------
 man/asd-package.Rd   |    4 ++--
 man/gsubpop.sim.Rd   |    2 +-
 man/gtreatsel.sim.Rd |    2 +-
 6 files changed, 28 insertions(+), 21 deletions(-)

More information about asd at CRAN
Permanent link

Package topicmodels updated to version 0.2-4 with previous version 0.2-3 dated 2016-02-17

Title: Topic Models
Description: Provides an interface to the C code for Latent Dirichlet Allocation (LDA) models and Correlated Topics Models (CTM) by David M. Blei and co-authors and the C++ code for fitting LDA models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
Author: Bettina Grün [aut, cre], Kurt Hornik [aut]
Maintainer: Bettina Grün <Bettina.Gruen@jku.at>

Diff between topicmodels versions 0.2-3 dated 2016-02-17 and 0.2-4 dated 2016-05-23

 DESCRIPTION              |    6 +++---
 MD5                      |   12 ++++++------
 build/vignette.rds       |binary
 data/AssociatedPress.rda |binary
 inst/NEWS.Rd             |    7 +++++++
 inst/doc/topicmodels.pdf |binary
 src/rGibbslda.cpp        |   37 +++++++++++++++++++------------------
 7 files changed, 35 insertions(+), 27 deletions(-)

More information about topicmodels at CRAN
Permanent link

Package YplantQMC updated to version 0.6-6 with previous version 0.6-4 dated 2014-12-03

Title: Plant Architectural Analysis with Yplant and QuasiMC
Description: An R implementation of Yplant, combined with the QuasiMC raytracer. Calculate radiation absorption, transmission and scattering, photosynthesis and transpiration of virtual 3D plants.
Author: Remko Duursma. QuasiMC by Mik Cieslak. Uses code by Robert Pearcy (Yplant) and Belinda Medlyn (MAESTRA)
Maintainer: Remko Duursma <remkoduursma@gmail.com>

Diff between YplantQMC versions 0.6-4 dated 2014-12-03 and 0.6-6 dated 2016-05-23

 YplantQMC-0.6-4/YplantQMC/README.md                     |only
 YplantQMC-0.6-6/YplantQMC/DESCRIPTION                   |   13 
 YplantQMC-0.6-6/YplantQMC/MD5                           |  273 ++--
 YplantQMC-0.6-6/YplantQMC/NAMESPACE                     |   38 
 YplantQMC-0.6-6/YplantQMC/R/DAPA.R                      |    6 
 YplantQMC-0.6-6/YplantQMC/R/DAPA.plant3d.R              |   90 -
 YplantQMC-0.6-6/YplantQMC/R/DAPAQMC.R                   |   50 
 YplantQMC-0.6-6/YplantQMC/R/Farquhar.R                  |  362 +++---
 YplantQMC-0.6-6/YplantQMC/R/GramSchmidt.R               |   60 -
 YplantQMC-0.6-6/YplantQMC/R/KE.R                        |   72 -
 YplantQMC-0.6-6/YplantQMC/R/Kn.R                        |   96 -
 YplantQMC-0.6-6/YplantQMC/R/STARbar.R                   |  665 +++++------
 YplantQMC-0.6-6/YplantQMC/R/Silhouette.R                |   86 -
 YplantQMC-0.6-6/YplantQMC/R/VPDTdiurnal.R               |   76 -
 YplantQMC-0.6-6/YplantQMC/R/VPDtoRH.R                   |   12 
 YplantQMC-0.6-6/YplantQMC/R/YplantDay.R                 |  597 ++++-----
 YplantQMC-0.6-6/YplantQMC/R/acosangle.R                 |   26 
 YplantQMC-0.6-6/YplantQMC/R/areapoly.R                  |    6 
 YplantQMC-0.6-6/YplantQMC/R/as.data.frame.STARbarlist.R |   20 
 YplantQMC-0.6-6/YplantQMC/R/calcparhrly.R               |  104 -
 YplantQMC-0.6-6/YplantQMC/R/checkHemi.R                 |   20 
 YplantQMC-0.6-6/YplantQMC/R/checkInstallation.R         |   28 
 YplantQMC-0.6-6/YplantQMC/R/constructplant.R            |  958 ++++++++--------
 YplantQMC-0.6-6/YplantQMC/R/crownhull.R                 |  150 +-
 YplantQMC-0.6-6/YplantQMC/R/esat.R                      |   20 
 YplantQMC-0.6-6/YplantQMC/R/evalHemi.R                  |   88 -
 YplantQMC-0.6-6/YplantQMC/R/getR.R                      |  150 +-
 YplantQMC-0.6-6/YplantQMC/R/getangles.R                 |  136 +-
 YplantQMC-0.6-6/YplantQMC/R/getleafnormal.R             |   18 
 YplantQMC-0.6-6/YplantQMC/R/getpsil.R                   |  440 +++----
 YplantQMC-0.6-6/YplantQMC/R/gridtrace.R                 |  284 ++--
 YplantQMC-0.6-6/YplantQMC/R/includePhy.R                |  116 -
 YplantQMC-0.6-6/YplantQMC/R/installQuasiMC.R            |   10 
 YplantQMC-0.6-6/YplantQMC/R/leafdata.R                  |   82 -
 YplantQMC-0.6-6/YplantQMC/R/leafdispersion.R            |  174 +-
 YplantQMC-0.6-6/YplantQMC/R/lightresponse.R             |   52 
 YplantQMC-0.6-6/YplantQMC/R/madeleafdirection.R         |   82 -
 YplantQMC-0.6-6/YplantQMC/R/makeQMCinput.R              |  100 -
 YplantQMC-0.6-6/YplantQMC/R/makeStand.R                 |  210 +--
 YplantQMC-0.6-6/YplantQMC/R/makesolarvec.R              |   20 
 YplantQMC-0.6-6/YplantQMC/R/makevector.R                |    2 
 YplantQMC-0.6-6/YplantQMC/R/makeviewplane.R             |   22 
 YplantQMC-0.6-6/YplantQMC/R/pathlen.R                   |  262 ++--
 YplantQMC-0.6-6/YplantQMC/R/photosyn.R                  |  276 ++--
 YplantQMC-0.6-6/YplantQMC/R/plot.leaffile.R             |  108 -
 YplantQMC-0.6-6/YplantQMC/R/plot.plant3d.R              |  578 ++++-----
 YplantQMC-0.6-6/YplantQMC/R/plot.projectedplant3d.R     |  112 -
 YplantQMC-0.6-6/YplantQMC/R/plot.tracedplant.R          |   58 
 YplantQMC-0.6-6/YplantQMC/R/plot.yphemi.R               |  196 +--
 YplantQMC-0.6-6/YplantQMC/R/plot.yplantsim.R            |  190 +--
 YplantQMC-0.6-6/YplantQMC/R/plot.yplocation.R           |   20 
 YplantQMC-0.6-6/YplantQMC/R/plot.ypmet.R                |   90 -
 YplantQMC-0.6-6/YplantQMC/R/plot3dcylinder.R            |   68 -
 YplantQMC-0.6-6/YplantQMC/R/plotstemsections.R          |   50 
 YplantQMC-0.6-6/YplantQMC/R/print.STAR.R                |   30 
 YplantQMC-0.6-6/YplantQMC/R/print.plant3d.R             |   38 
 YplantQMC-0.6-6/YplantQMC/R/print.plant3dlist.R         |   18 
 YplantQMC-0.6-6/YplantQMC/R/print.projectedplant3d.R    |   18 
 YplantQMC-0.6-6/YplantQMC/R/print.stand3d.R             |   20 
 YplantQMC-0.6-6/YplantQMC/R/print.summary.plant3d.R     |   70 -
 YplantQMC-0.6-6/YplantQMC/R/print.yplantsim.R           |   46 
 YplantQMC-0.6-6/YplantQMC/R/print.yplantsimlist.R       |   22 
 YplantQMC-0.6-6/YplantQMC/R/print.yplocation.R          |   28 
 YplantQMC-0.6-6/YplantQMC/R/print.ypmet.R               |   50 
 YplantQMC-0.6-6/YplantQMC/R/print.ypphy.R               |   24 
 YplantQMC-0.6-6/YplantQMC/R/projectplant.R              |  212 +--
 YplantQMC-0.6-6/YplantQMC/R/psrdata.R                   |   34 
 YplantQMC-0.6-6/YplantQMC/R/randomplant.R               |  318 ++---
 YplantQMC-0.6-6/YplantQMC/R/readCAN.R                   |   74 -
 YplantQMC-0.6-6/YplantQMC/R/readQMCout.R                |   54 
 YplantQMC-0.6-6/YplantQMC/R/readl.R                     |  224 +--
 YplantQMC-0.6-6/YplantQMC/R/readp.R                     |  134 +-
 YplantQMC-0.6-6/YplantQMC/R/replaceangles.R             |  438 +++----
 YplantQMC-0.6-6/YplantQMC/R/runQMCUOC.R                 |   82 -
 YplantQMC-0.6-6/YplantQMC/R/runYplant.R                 |  647 +++++-----
 YplantQMC-0.6-6/YplantQMC/R/runquasimc.R                |   64 -
 YplantQMC-0.6-6/YplantQMC/R/setHemi.R                   |  202 +--
 YplantQMC-0.6-6/YplantQMC/R/setLocation.R               |  148 +-
 YplantQMC-0.6-6/YplantQMC/R/setMet.R                    |  534 ++++----
 YplantQMC-0.6-6/YplantQMC/R/setPhy.R                    |  146 +-
 YplantQMC-0.6-6/YplantQMC/R/shiftplant.R                |  138 +-
 YplantQMC-0.6-6/YplantQMC/R/summary.plant3d.R           |  464 +++----
 YplantQMC-0.6-6/YplantQMC/R/summary.plant3dlist.R       |  158 +-
 YplantQMC-0.6-6/YplantQMC/R/summary.yplantsimlist.R     |  186 +--
 YplantQMC-0.6-6/YplantQMC/R/viewplot.R                  |  172 +-
 YplantQMC-0.6-6/YplantQMC/R/writeOUTfile.R              |   26 
 YplantQMC-0.6-6/YplantQMC/R/writePSRfile.R              |  120 +-
 YplantQMC-0.6-6/YplantQMC/R/writecfg.R                  |  172 +-
 YplantQMC-0.6-6/YplantQMC/R/writerandomdiffuse.R        |   24 
 YplantQMC-0.6-6/YplantQMC/R/writeturtlediffuse.R        |   46 
 YplantQMC-0.6-6/YplantQMC/R/xmastime.R                  |   80 -
 YplantQMC-0.6-6/YplantQMC/R/xprod.R                     |   12 
 YplantQMC-0.6-6/YplantQMC/R/yplantqmc-package.R         |  276 ++--
 YplantQMC-0.6-6/YplantQMC/R/ypreport.R                  |  354 ++---
 YplantQMC-0.6-6/YplantQMC/R/zenaz.R                     |  488 ++++----
 YplantQMC-0.6-6/YplantQMC/R/zzz.R                       |   66 -
 YplantQMC-0.6-6/YplantQMC/data/hemiphotos.RData         |binary
 YplantQMC-0.6-6/YplantQMC/data/plantexamples.RData      |binary
 YplantQMC-0.6-6/YplantQMC/data/turtle.RData             |binary
 YplantQMC-0.6-6/YplantQMC/data/turtle244.RData          |binary
 YplantQMC-0.6-6/YplantQMC/data/turtle482.RData          |binary
 YplantQMC-0.6-6/YplantQMC/data/yplantaltaz.RData        |binary
 YplantQMC-0.6-6/YplantQMC/man/Farquhar.Rd               |    7 
 YplantQMC-0.6-6/YplantQMC/man/ModifyPfiles.Rd           |   17 
 YplantQMC-0.6-6/YplantQMC/man/STARbar.Rd                |   26 
 YplantQMC-0.6-6/YplantQMC/man/Silhouette.Rd             |    8 
 YplantQMC-0.6-6/YplantQMC/man/YplantDay.Rd              |   50 
 YplantQMC-0.6-6/YplantQMC/man/constructplant.Rd         |   13 
 YplantQMC-0.6-6/YplantQMC/man/crownhull.Rd              |    6 
 YplantQMC-0.6-6/YplantQMC/man/examplehemi.Rd            |    6 
 YplantQMC-0.6-6/YplantQMC/man/getR.Rd                   |    3 
 YplantQMC-0.6-6/YplantQMC/man/getangles.Rd              |    9 
 YplantQMC-0.6-6/YplantQMC/man/installQuasiMC.Rd         |   11 
 YplantQMC-0.6-6/YplantQMC/man/leafdispersion.Rd         |    8 
 YplantQMC-0.6-6/YplantQMC/man/lightresponse.Rd          |    3 
 YplantQMC-0.6-6/YplantQMC/man/makeStand.Rd              |    6 
 YplantQMC-0.6-6/YplantQMC/man/plantexamples.Rd          |    7 
 YplantQMC-0.6-6/YplantQMC/man/plot.leaffile.Rd          |    6 
 YplantQMC-0.6-6/YplantQMC/man/plot.plant3d.Rd           |    9 
 YplantQMC-0.6-6/YplantQMC/man/projectplant.Rd           |   14 
 YplantQMC-0.6-6/YplantQMC/man/psrdata.Rd                |    3 
 YplantQMC-0.6-6/YplantQMC/man/randomplant.Rd            |   17 
 YplantQMC-0.6-6/YplantQMC/man/readl.Rd                  |    3 
 YplantQMC-0.6-6/YplantQMC/man/readp.Rd                  |    3 
 YplantQMC-0.6-6/YplantQMC/man/runYplant.Rd              |   13 
 YplantQMC-0.6-6/YplantQMC/man/setHemi.Rd                |    5 
 YplantQMC-0.6-6/YplantQMC/man/setLocation.Rd            |    8 
 YplantQMC-0.6-6/YplantQMC/man/setMet.Rd                 |   15 
 YplantQMC-0.6-6/YplantQMC/man/setPhy.Rd                 |   21 
 YplantQMC-0.6-6/YplantQMC/man/summary.plant3d.Rd        |   56 
 YplantQMC-0.6-6/YplantQMC/man/turtle.Rd                 |    5 
 YplantQMC-0.6-6/YplantQMC/man/turtle244.Rd              |    7 
 YplantQMC-0.6-6/YplantQMC/man/turtle482.Rd              |    7 
 YplantQMC-0.6-6/YplantQMC/man/viewplot.Rd               |    8 
 YplantQMC-0.6-6/YplantQMC/man/xmastime.Rd               |    3 
 YplantQMC-0.6-6/YplantQMC/man/yplantaltaz.Rd            |    5 
 YplantQMC-0.6-6/YplantQMC/man/ypreport.Rd               |    3 
 YplantQMC-0.6-6/YplantQMC/man/zenaz.Rd                  |    6 
 138 files changed, 7399 insertions(+), 7277 deletions(-)

More information about YplantQMC at CRAN
Permanent link

Package nhanesA updated to version 0.6.4 with previous version 0.6.3.1 dated 2016-03-28

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 0.6.3.1 dated 2016-03-28 and 0.6.4 dated 2016-05-23

 DESCRIPTION                       |    8 
 MD5                               |   30 +--
 NAMESPACE                         |    4 
 R/nhanes.R                        |  353 +++++++++++++++++++++++++++++---------
 build/vignette.rds                |binary
 inst/doc/Introducing_nhanesA.R    |   13 +
 inst/doc/Introducing_nhanesA.Rmd  |   24 ++
 inst/doc/Introducing_nhanesA.html |   64 +++++-
 man/browseNHANES.Rd               |    7 
 man/nhanesDXA.Rd                  |    2 
 man/nhanesSearch.Rd               |   15 -
 man/nhanesSearchTableNames.Rd     |only
 man/nhanesSearchVarName.Rd        |only
 man/nhanesTableVars.Rd            |    6 
 man/nhanesTables.Rd               |    6 
 man/nhanesTranslate.Rd            |   10 -
 vignettes/Introducing_nhanesA.Rmd |   24 ++
 17 files changed, 427 insertions(+), 139 deletions(-)

More information about nhanesA at CRAN
Permanent link

Package MXM updated to version 0.8.7 with previous version 0.8.5 dated 2016-04-26

Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis, Anna Roumpelaki
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>

Diff between MXM versions 0.8.5 dated 2016-04-26 and 0.8.7 dated 2016-05-23

 DESCRIPTION            |   11 +-
 MD5                    |   62 ++++++++--------
 NAMESPACE              |    9 +-
 R/SES.R                |    1 
 R/bic.fsreg.R          |    4 -
 R/bic.glm.fsreg.R      |  188 +++++++++++++++++++++++++------------------------
 R/dag2eg.R             |    8 +-
 R/fs.reg.R             |    5 -
 R/glm.bsreg.R          |only
 R/glm.fsreg.R          |  179 +++++++++++++++++++++++-----------------------
 R/lm.fsreg.R           |    2 
 R/model.R              |   50 ++++++-------
 R/pc.con.R             |    5 +
 R/pc.or.R              |   35 +++++----
 R/rdag.R               |    8 +-
 R/reg.fit.R            |   16 ++--
 R/ridge.plot.R         |    6 -
 R/ridgereg.cv.R        |    8 +-
 R/testIndLogistic.R    |   16 ++--
 R/testIndPois.R        |   16 ++--
 man/MXM-internal.Rd    |    4 -
 man/MXM-package.Rd     |    4 -
 man/bic.fsreg.Rd       |    9 +-
 man/bic.glm.fsreg.Rd   |   14 +--
 man/fs.reg.Rd          |   12 +--
 man/glm.bsreg.Rd       |only
 man/glm.fsreg.Rd       |   18 ++--
 man/lm.fsreg.Rd        |    4 -
 man/pc.or.Rd           |    7 +
 man/testIndFisher.Rd   |    2 
 man/testIndLogistic.Rd |    2 
 man/testIndPois.Rd     |    2 
 man/testIndReg.Rd      |    2 
 33 files changed, 366 insertions(+), 343 deletions(-)

More information about MXM at CRAN
Permanent link

Package hqreg updated to version 1.3 with previous version 1.2 dated 2016-02-16

Title: Regularization Paths for Lasso or Elastic-Net Penalized Huber Loss Regression and Quantile Regression
Description: Efficient algorithms for fitting regularization paths for lasso or elastic-net penalized regression models with Huber loss, quantile loss or squared loss.
Author: Congrui Yi
Maintainer: Congrui Yi <congrui-yi@uiowa.edu>

Diff between hqreg versions 1.2 dated 2016-02-16 and 1.3 dated 2016-05-23

 hqreg-1.2/hqreg/R/init.R             |only
 hqreg-1.2/hqreg/R/loss.hqreg.R       |only
 hqreg-1.3/hqreg/DESCRIPTION          |   18 
 hqreg-1.3/hqreg/MD5                  |   34 
 hqreg-1.3/hqreg/NAMESPACE            |    3 
 hqreg-1.3/hqreg/NEWS                 |    8 
 hqreg-1.3/hqreg/R/cv.hqreg.R         |   63 +
 hqreg-1.3/hqreg/R/hqreg.R            |   55 -
 hqreg-1.3/hqreg/R/measure.hqreg.R    |only
 hqreg-1.3/hqreg/R/plot.cv.hqreg.R    |    6 
 hqreg-1.3/hqreg/R/plot.hqreg.R       |    7 
 hqreg-1.3/hqreg/R/predict.cv.hqreg.R |    5 
 hqreg-1.3/hqreg/man/cv.hqreg.Rd      |   28 
 hqreg-1.3/hqreg/man/hqreg-package.Rd |   20 
 hqreg-1.3/hqreg/man/hqreg.Rd         |   14 
 hqreg-1.3/hqreg/man/plot.cv.hqreg.Rd |    6 
 hqreg-1.3/hqreg/man/plot.hqreg.Rd    |    9 
 hqreg-1.3/hqreg/src/data_process.c   |only
 hqreg-1.3/hqreg/src/hqreg.c          | 1487 +++++++++++++++--------------------
 hqreg-1.3/hqreg/src/init.c           |only
 hqreg-1.3/hqreg/src/util.c           |only
 21 files changed, 824 insertions(+), 939 deletions(-)

More information about hqreg at CRAN
Permanent link

New package eechidna with initial version 0.1
Package: eechidna
Version: 0.1
Title: Exploring Election and Census Highly Informative Data Nationally for Australia
Description: Data from the 2013 Australian Federal Election (House of Representatives) and the 2011 Australian Census. Includes tools for visualizing and analysing the data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission) 2016.
Depends: R (>= 3.2.3)
Imports: dplyr, ggplot2 (>= 2.0.0), tidyr, shiny, plotly (>= 3.5.2), ggthemes, shinyjs, methods
Suggests: testthat, knitr, rmarkdown, maptools, purrr, sp, GGally, corrplot, broom, plyr, scales, readr, gridExtra
Authors@R: c(person("Di", "Cook", role = c("aut")), person("Heike", "Hofmann", role = c("aut")), person("Rob", "Hyndman", role = c("aut")), person("Thomas", "Lumley", role = c("aut")), person("Ben", "Marwick", role = c("aut", "cre"), email = "benmarwick@gmail.com"), person("Carson", "Sievert", role = c("aut")), person("Nicholas", "Tierney", role = c("aut")), person("Nathaniel", "Tomasetti", role = c("aut")), person("Fang", "Zhou", role = c("aut")), person("Commonwealth of Australia", "AEC", role = c("cph")))
Maintainer: Ben Marwick <benmarwick@gmail.com>
LazyData: true
ByteCompile: TRUE
License: GPL (>= 2)
URL: https://github.com/ropenscilabs/eechidna
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-22 23:28:11 UTC; marwick
Author: Di Cook [aut], Heike Hofmann [aut], Rob Hyndman [aut], Thomas Lumley [aut], Ben Marwick [aut, cre], Carson Sievert [aut], Nicholas Tierney [aut], Nathaniel Tomasetti [aut], Fang Zhou [aut], Commonwealth of Australia AEC [cph]
Repository: CRAN
Date/Publication: 2016-05-23 06:01:37

More information about eechidna at CRAN
Permanent link

Sun, 22 May 2016

Package icenReg updated to version 1.3.5 with previous version 1.3.4 dated 2016-03-19

Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH, proportional odds, and accelerated failure time models. Allows for both semi and fully parametric models (parametric only for accelerated failure time models). Includes functions for easy visual diagnostics of model fits and imputation of censored data.
Author: Clifford Anderson-Bergman; uses Marloes Maathuis's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>

Diff between icenReg versions 1.3.4 dated 2016-03-19 and 1.3.5 dated 2016-05-22

 DESCRIPTION                             |   10 -
 MD5                                     |   36 ++++--
 NEWS                                    |    6 +
 R/Utilities.R                           |    8 +
 R/referenceClasses.R                    |    3 
 R/user_functions.R                      |   72 +++++++++----
 build                                   |only
 inst                                    |only
 man/diag_covar.Rd                       |    2 
 man/ic_par.Rd                           |    4 
 man/imputeCens.Rd                       |    2 
 src/icenReg.cpp                         |    3 
 src/icenReg_files/ic_par.cpp            |  120 ++++++++++------------
 src/icenReg_files/ic_par.h              |   20 ++-
 src/icenReg_files/ic_par_aft.cpp        |only
 src/icenReg_files/ic_par_aft.h          |only
 src/icenReg_files/ic_sp_ch.cpp          |   67 +++++++++++-
 src/icenReg_files/ic_sp_ch.h            |   14 +-
 src/icenReg_files/ic_sp_gradDescent.cpp |  171 ++++++++++++++++++++++++++++++--
 vignettes                               |only
 20 files changed, 395 insertions(+), 143 deletions(-)

More information about icenReg at CRAN
Permanent link

New package VDAP with initial version 2.0.0
Package: VDAP
Type: Package
Title: Peptide Array Analysis Tools
Version: 2.0.0
Date: 2016-04-26
Author: Cody Moore
Maintainer: Cody Moore <Jumper9400@gmail.com>
Description: Analyze Peptide Array Data and characterize peptide sequence space. Allows for high level visualization of global signal, Quality control based on replicate correlation and/or relative Kd, calculation of peptide Length/Charge/Kd parameters, Hits selection based on RFU Signal, and amino acid composition/basic motif recognition with RFU signal weighting. Basic signal trends can be used to generate peptides that follow the observed compositional trends.
License: GPL-2
Imports: stringr, drc, ggplot2, reshape2
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-05-22 19:13:48 UTC; Draguru
Repository: CRAN
Date/Publication: 2016-05-22 22:54:19

More information about VDAP at CRAN
Permanent link

Package tsDyn updated to version 0.9-44 with previous version 0.9-43 dated 2015-04-24

Title: Nonlinear Time Series Models with Regime Switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut], Jose Luis Aznarte [ctb], Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>

Diff between tsDyn versions 0.9-43 dated 2015-04-24 and 0.9-44 dated 2016-05-22

 DESCRIPTION                       |   10 
 MD5                               |   47 
 NAMESPACE                         |   19 
 R/TVAR_LRtest.R                   |   55 
 R/TVARestim.R                     |   16 
 R/VAR.sim.R                       |   15 
 R/coefECT.R                       |   20 
 R/lineVar.R                       |   66 
 R/misc.R                          |    4 
 R/nlVar-methods.R                 |    9 
 R/vcov.R                          |only
 R/vec2var.tsDyn.R                 |    1 
 build/vignette.rds                |binary
 data/barry.rda                    |binary
 data/zeroyld.rda                  |binary
 inst/CITATION                     |    4 
 inst/ChangeLog                    |   10 
 inst/doc/ThCointOverview.pdf      |binary
 inst/doc/tsDyn.pdf                |binary
 tests/00SetarAndFriends.R         |    3 
 tests/00SetarAndFriends.Rout.save |  191 +
 tests/TVECM.sim.Rout.save         |    4 
 tests/VAR.R                       |   13 
 tests/VAR.Rout.save               | 4585 ++++++++++++++++++++++++++++++++++++--
 tests/VECM.Rout.save              |    6 
 25 files changed, 4829 insertions(+), 249 deletions(-)

More information about tsDyn at CRAN
Permanent link

Package GetTDData updated to version 1.2.2 with previous version 1.2.1 dated 2016-05-04

Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetTDData versions 1.2.1 dated 2016-05-04 and 1.2.2 dated 2016-05-22

 DESCRIPTION                 |    6 -
 MD5                         |   24 ++---
 NEWS.md                     |    5 +
 R/gtdd_download_TD_data.R   |   91 +++++++++++++++-----
 R/gtdd_read_TD_files.R      |   69 +++++++++++++--
 build/vignette.rds          |binary
 inst/doc/gtdd-vignette.R    |   15 ++-
 inst/doc/gtdd-vignette.Rmd  |   19 ++--
 inst/doc/gtdd-vignette.html |  193 ++++++++++++++++++++++----------------------
 man/download.TD.data.Rd     |   83 +++++++++---------
 man/read.TD.files.Rd        |   82 +++++++++---------
 tests/testthat/test_gtdd.R  |    4 
 vignettes/gtdd-vignette.Rmd |   19 ++--
 13 files changed, 364 insertions(+), 246 deletions(-)

More information about GetTDData at CRAN
Permanent link

New package LindleyR with initial version 1.0.0
Package: LindleyR
Type: Package
Title: The Lindley Distribution and Its Modifications
Version: 1.0.0
License: GPL (>= 2)
Date: 2016-05-22
Author: Josmar Mazucheli and Larissa B. Fernandes
Maintainer: Josmar Mazucheli <jmazucheli@gmail.com>
Description: Implements the probability density function, quantile function, cumulative distribution function, random number generation and the hazard rate function for the continuous one-parameter Lindley distribution as well as for 15 of its modifications. Also is it possible to draw censored random samples, with a desired censoring rate, when the event times are any continuous lifetime distribution supported by R.
Depends: R (>= 3.0.2), actuar, LambertW, VGAM, zipfR
Imports: stats
Suggests: fitdistrplus
RoxygenNote: 5.0.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2016-05-22 18:30:17 UTC; josmar
Repository: CRAN
Date/Publication: 2016-05-22 22:54:21

More information about LindleyR at CRAN
Permanent link

Package switchr updated to version 0.10.14 with previous version 0.10.13 dated 2016-05-12

Title: Installing, Managing, and Switching Between Distinct Sets of Installed Packages
Description: Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a development/production release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>

Diff between switchr versions 0.10.13 dated 2016-05-12 and 0.10.14 dated 2016-05-22

 DESCRIPTION               |    6 ++---
 MD5                       |   12 +++++------
 build/vignette.rds        |binary
 inst/doc/switchrvign.R    |   49 ++++++++++++++++++++++++++++++----------------
 inst/doc/switchrvign.Rnw  |   30 ++++++++++++++++++++++++++++
 inst/doc/switchrvign.pdf  |binary
 vignettes/switchrvign.Rnw |   30 ++++++++++++++++++++++++++++
 7 files changed, 101 insertions(+), 26 deletions(-)

More information about switchr at CRAN
Permanent link

New package GRANBase with initial version 1.1.14
Package: GRANBase
Type: Package
Title: Creating Continuously Integrated Package Repositories from Manifests
Version: 1.1.14
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Copyright: Genentech Inc
Description: Repository based tools for department and analysis level reproducibility. 'GRANBase' allows creation of custom branched, continuous integration-ready R repositories, including incremental testing of only packages which have changed versions since the last repository build.
License: Artistic-2.0
Imports: tools, hwriter
Depends: switchr (>= 0.9.28), methods
Suggests: parallel, BiocStyle, RUnit
SystemRequirements: svn, git
URL: https://github.com/gmbecker/gRAN
BugReports: https://github.com/gmbecker/gRAN/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-22 17:15:05 UTC; beckerg4
Repository: CRAN
Date/Publication: 2016-05-22 20:34:42

More information about GRANBase at CRAN
Permanent link

Package rio updated to version 0.4.6 with previous version 0.4.5 dated 2016-05-20

Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that the user is probably willing to make: 'import()' and 'export()' determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate.
Author: Jason Becker [ctb], Chung-hong Chan [aut], Geoffrey CH Chan [ctb], Thomas J. Leeper [aut, cre], Christopher Gandrud [ctb], Andrew MacDonald [ctb], Ista Zahn [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between rio versions 0.4.5 dated 2016-05-20 and 0.4.6 dated 2016-05-22

 DESCRIPTION                    |    8 ++++----
 MD5                            |    6 +++---
 R/compression.R                |    3 ++-
 tests/testthat/test_compress.R |    6 +++---
 4 files changed, 12 insertions(+), 11 deletions(-)

More information about rio at CRAN
Permanent link

New package prof.tree with initial version 0.1.0
Package: prof.tree
Type: Package
Title: An Alternative Display Profiling Data as Tree Structure
Description: An alternative data structure for the profiling information generated by Rprof().
Version: 0.1.0
Author: Artem Kelvtsov [aut, cre]
Maintainer: Artem Kelvtsov <a.a.klevtsov@gmail.com>
URL: https://github.com/artemklevtsov/prof.tree
BugReports: https://github.com/artemklevtsov/prof.tree/issues
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Imports: data.tree
RoxygenNote: 5.0.1
Collate: 'env.R' 'parse.R' 'prof-tree.R'
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2016-05-22 14:56:53 UTC; xxx
Repository: CRAN
Date/Publication: 2016-05-22 17:23:47

More information about prof.tree at CRAN
Permanent link

New package kinn with initial version 0.1
Package: kinn
Type: Package
Title: An Implementation of 'kinn' Algorithm, a Graph Based Regression Model
Version: 0.1
Date: 2016-05-22
Author: Yossi Keshet
Maintainer: Yossi Keshet <jossiekat@icloud.com>
Description: A graph based regression model from flat unstructured dataset. Each line in the input data set is treated as a node from which an edge to another line (node) can be formed. In the training process, a model is created which contains sparse graph adjacency matrix. This model is then used for prediction by taking a predictor and the model as inputs and outputs a prediction which is an average of the most similar node and its neighbours in the model graph.
Depends: R (>= 3.2.4)
Imports: stringr,igraph,KRLS,caTools,mclust,caret,stats,graphics
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-22 15:32:02 UTC; josephkeshet
Repository: CRAN
Date/Publication: 2016-05-22 17:40:26

More information about kinn at CRAN
Permanent link

Package IMak updated to version 1.1.2 with previous version 1.1.1 dated 2016-03-21

Title: Item Maker
Description: This is an Automatic Item Generator for Psychological Testing. It is recommended for research purposes only.
Author: Diego Blum [aut, cre]
Maintainer: Diego Blum <blumworx@gmail.com>

Diff between IMak versions 1.1.1 dated 2016-03-21 and 1.1.2 dated 2016-05-22

 DESCRIPTION |    6 +++---
 MD5         |    6 +++---
 R/plotfa.R  |    2 +-
 man/IMak.Rd |    2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

More information about IMak at CRAN
Permanent link

Package aws.signature updated to version 0.2.2 with previous version 0.2.0 dated 2015-12-21

Title: Amazon Web Services Request Signatures
Description: Generates request signatures for Amazon Web Services (AWS) APIs.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between aws.signature versions 0.2.0 dated 2015-12-21 and 0.2.2 dated 2016-05-22

 DESCRIPTION                  |   10 +++++-----
 MD5                          |   20 +++++++++++---------
 NAMESPACE                    |    2 ++
 NEWS                         |    8 ++++++++
 R/v2.R                       |only
 R/v4.R                       |    6 ++++++
 README.md                    |   31 +++++++++++++++++++++++++------
 man/authorization.Rd         |    2 +-
 man/aws.signature-package.Rd |    2 +-
 man/v2.Rd                    |only
 man/v4.Rd                    |    2 +-
 tests/testthat/tests.R       |   43 +++++++++++++++++++++++++++++++++++++++++++
 12 files changed, 103 insertions(+), 23 deletions(-)

More information about aws.signature at CRAN
Permanent link

New package landscapeR with initial version 1.0.0
Package: landscapeR
Type: Package
Title: Categorical Landscape Simulation Facility
Version: 1.0.0
Date: 2016-05-22
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dmasan@ceh.ac.uk>
URL: https://github.com/dariomasante/landscapeR
Imports: raster, fastmatch
Description: This set of functions allows the simulation of categorical maps from scratch in a geographically referenced landscape or the manipulation of existing ones. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion), therefore expands more or less circularly picking cells at the edges randomly.
License: GPL (>= 3)
LazyLoad: yes
LazyData: TRUE
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-22 11:31:43 UTC; dmasan
Repository: CRAN
Date/Publication: 2016-05-22 16:02:06

More information about landscapeR at CRAN
Permanent link

Package ShrinkCovMat updated to version 1.1.2 with previous version 1.1.1 dated 2015-09-08

Title: Shrinkage Covariance Matrix Estimators
Description: Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>

Diff between ShrinkCovMat versions 1.1.1 dated 2015-09-08 and 1.1.2 dated 2016-05-22

 ShrinkCovMat-1.1.1/ShrinkCovMat/R/covmat.R                   |only
 ShrinkCovMat-1.1.1/ShrinkCovMat/R/covmat.default.R           |only
 ShrinkCovMat-1.1.1/ShrinkCovMat/R/print.covmat.R             |only
 ShrinkCovMat-1.1.2/ShrinkCovMat/DESCRIPTION                  |    8 
 ShrinkCovMat-1.1.2/ShrinkCovMat/MD5                          |   34 +-
 ShrinkCovMat-1.1.2/ShrinkCovMat/NAMESPACE                    |    2 
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/print.shrinkcovmathat.R    |only
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/shrinkcovmat.equal.R       |   91 +++---
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/shrinkcovmat.identity.R    |   88 +++---
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/shrinkcovmat.unequal.R     |  143 ++++++---
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/shrinkcovmathat.R          |only
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/shrinkcovmathat.default.R  |only
 ShrinkCovMat-1.1.2/ShrinkCovMat/R/targetselection.R          |  161 +++++++----
 ShrinkCovMat-1.1.2/ShrinkCovMat/inst/CITATION                |    6 
 ShrinkCovMat-1.1.2/ShrinkCovMat/inst/NEWS                    |    7 
 ShrinkCovMat-1.1.2/ShrinkCovMat/man/ShrinkCovMat-package.Rd  |   27 -
 ShrinkCovMat-1.1.2/ShrinkCovMat/man/colon.Rd                 |    7 
 ShrinkCovMat-1.1.2/ShrinkCovMat/man/shrinkcovmat.equal.Rd    |   21 -
 ShrinkCovMat-1.1.2/ShrinkCovMat/man/shrinkcovmat.identity.Rd |   20 -
 ShrinkCovMat-1.1.2/ShrinkCovMat/man/shrinkcovmat.unequal.Rd  |   20 -
 ShrinkCovMat-1.1.2/ShrinkCovMat/man/targetselection.Rd       |   13 
 21 files changed, 384 insertions(+), 264 deletions(-)

More information about ShrinkCovMat at CRAN
Permanent link

Package label.switching updated to version 1.6 with previous version 1.5 dated 2016-02-01

Title: Relabelling MCMC Outputs of Mixture Models
Description: The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>

Diff between label.switching versions 1.5 dated 2016-02-01 and 1.6 dated 2016-05-22

 DESCRIPTION                |    8 ++++----
 MD5                        |    4 ++--
 R/relabelling_algorithms.R |    2 ++
 3 files changed, 8 insertions(+), 6 deletions(-)

More information about label.switching at CRAN
Permanent link

Package asnipe updated to version 0.91 with previous version 0.90 dated 2016-04-08

Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>

Diff between asnipe versions 0.90 dated 2016-04-08 and 0.91 dated 2016-05-22

 DESCRIPTION             |    8 ++++----
 MD5                     |    8 ++++----
 R/network_permutation.R |    4 ++--
 R/network_swap.R        |    4 ++--
 man/asnipe-package.Rd   |    4 ++--
 5 files changed, 14 insertions(+), 14 deletions(-)

More information about asnipe at CRAN
Permanent link

Package spaero updated to version 0.1.1 with previous version 0.1.0 dated 2016-04-06

Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication of infectious diseases from surveillance time series. Also provides support for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>

Diff between spaero versions 0.1.0 dated 2016-04-06 and 0.1.1 dated 2016-05-22

 spaero-0.1.0/spaero/inst/doc/spaero-introduction.R    |only
 spaero-0.1.1/spaero/DESCRIPTION                       |   12 +-
 spaero-0.1.1/spaero/MD5                               |   24 ++--
 spaero-0.1.1/spaero/NEWS.md                           |only
 spaero-0.1.1/spaero/R/analysis.R                      |   58 ++++++----
 spaero-0.1.1/spaero/R/simulation.R                    |    2 
 spaero-0.1.1/spaero/build/vignette.rds                |binary
 spaero-0.1.1/spaero/inst/doc/spaero-introduction.Rmd  |   48 ++++----
 spaero-0.1.1/spaero/inst/doc/spaero-introduction.pdf  |binary
 spaero-0.1.1/spaero/man/create_simulator.Rd           |    2 
 spaero-0.1.1/spaero/man/get_stats.Rd                  |   36 +++---
 spaero-0.1.1/spaero/tests/testthat/test-simulator.R   |   22 +++
 spaero-0.1.1/spaero/tests/testthat/test-stats.R       |  100 +++++++++---------
 spaero-0.1.1/spaero/vignettes/spaero-introduction.Rmd |   48 ++++----
 14 files changed, 200 insertions(+), 152 deletions(-)

More information about spaero at CRAN
Permanent link

New package rosetteApi with initial version 1.0
Package: rosetteApi
Type: Package
Title: Rosette API
Version: 1.0
Date: 2016-04-26
Author: Sam Hausmann
Maintainer: Sam Hausmann <shausmann@basistech.com>
Description: Rosette is an API for multilingual text analysis and information extraction. More information can be found at https://developer.rosette.com.
License: Apache License
Depends: R (>= 3.1.0), httr, rjson
URL: https://developer.rosette.com
BugReports: https://developer.rosette.com/support-ticket
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 16:03:41 UTC; shausmann
Repository: CRAN
Date/Publication: 2016-05-22 09:21:04

More information about rosetteApi at CRAN
Permanent link

Package qtlbook updated to version 0.18-5 with previous version 0.18-3 dated 2015-09-20

Title: Datasets for the R/qtl Book
Description: Datasets for the book, A Guide to QTL Mapping with R/qtl.
Author: Karl W Broman <kbroman@biostat.wisc.edu>
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>

Diff between qtlbook versions 0.18-3 dated 2015-09-20 and 0.18-5 dated 2016-05-22

 DESCRIPTION          |    8 ++++----
 MD5                  |   24 ++++++++++++------------
 data/ch3a.RData      |binary
 data/ch3b.RData      |binary
 data/ch3c.RData      |binary
 data/gutlength.RData |binary
 data/iron.RData      |binary
 data/myocard.RData   |binary
 data/nf1.RData       |binary
 data/ovar.RData      |binary
 data/trout.RData     |binary
 inst/CITATION        |   11 +++++------
 inst/STATUS.txt      |    7 ++++++-
 13 files changed, 27 insertions(+), 23 deletions(-)

More information about qtlbook at CRAN
Permanent link

Package negenes updated to version 1.0-5 with previous version 1.0-3 dated 2015-09-11

Title: Estimating the Number of Essential Genes in a Genome
Description: Estimating the number of essential genes in a genome on the basis of data from a random transposon mutagenesis experiment, through the use of a Gibbs sampler.
Author: Karl W Broman <kbroman@biostat.wisc.edu>
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>

Diff between negenes versions 1.0-3 dated 2015-09-11 and 1.0-5 dated 2016-05-22

 DESCRIPTION         |    8 ++++----
 MD5                 |   20 ++++++++++----------
 R/negenes.R         |   18 ++++++++++--------
 README.md           |    1 +
 data/Mtb80.RData    |binary
 inst/CITATION       |   19 +++++++++----------
 inst/INSTALL_ME.txt |   12 ++++++------
 inst/README.md      |    1 +
 inst/STATUS.txt     |    7 ++++++-
 man/negenes.Rd      |   30 +++++++++++++++++-------------
 man/sim.mutants.Rd  |    8 ++++----
 11 files changed, 68 insertions(+), 56 deletions(-)

More information about negenes at CRAN
Permanent link

New package pETM with initial version 0.1.5
Package: pETM
Type: Package
Title: Penalized Exponential Tilt Model
Version: 0.1.5
Date: 2016-05-21
Author: Hokeun Sun
Depends: Matrix (>= 1.0-6), utils
Maintainer: Hokeun Sun <hsun@pusan.ac.kr>
Description: In analysis of high-dimensional DNA methylation data, a penalized exponential tilt model can identify differentially methylated loci between cases and controls, using network based regularization. It is able to detect any differences in means only, in variances only or in both means and variances.
License: GPL-2
Repository: CRAN
NeedsCompilation: yes
Packaged: 2016-05-21 12:40:08 UTC; root
Date/Publication: 2016-05-22 09:21:01

More information about pETM at CRAN
Permanent link

Package LatticeKrig updated to version 5.5 with previous version 5.4-1 dated 2015-11-05

Title: Multiresolution Kriging Based on Markov Random Fields
Description: Methods 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 and this package makes of the R spam package for this. An extension of this version over previous ones ( < 5.4 ) is the support for different geometries besides a rectangular domain. The Markov random field approach combined with a basis function representation makes the implementation of different geometries simple where only a few specific functions need to be added with most of the computation and evaluation done by generic routines that have been tuned to be efficient. 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 and also the case when the observations are a linear combination (e.g. an integral) of the spatial process. 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 5.4-1 dated 2015-11-05 and 5.5 dated 2016-05-22

 LatticeKrig-5.4-1/LatticeKrig/R/BACK                                      |only
 LatticeKrig-5.4-1/LatticeKrig/R/LKrigCovWieghtedObs.R                     |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKDistance.Rd                           |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKRing.Rd                               |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKgeometry.Rd                           |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKrig.fixed.Rd                          |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKrig.internal.Rd                       |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKrig.misc.Rd                           |only
 LatticeKrig-5.4-1/LatticeKrig/man/LKrigNormalizeBasisFast.Rd              |only
 LatticeKrig-5.5/LatticeKrig/DESCRIPTION                                   |   46 
 LatticeKrig-5.5/LatticeKrig/MD5                                           |  226 -
 LatticeKrig-5.5/LatticeKrig/NAMESPACE                                     |    4 
 LatticeKrig-5.5/LatticeKrig/R/GridList.R                                  |    4 
 LatticeKrig-5.5/LatticeKrig/R/LKDist.R                                    |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKDistComponents.R                          |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKDistGrid.R                                |    4 
 LatticeKrig-5.5/LatticeKrig/R/LKDistGridComponents.R                      |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKGridCheck.R                               |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKGridFindNmax.R                            |    3 
 LatticeKrig-5.5/LatticeKrig/R/LKRectangleFastNormalization.R              |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKinfoCheck.R                               |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKinfoUpdate.R                              |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.MLE.R                                 |   13 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.R                                     |   49 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.basis.R                               |   24 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.coef.R                                |   30 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.cov.R                                 |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.cov.plot.R                            |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.lnPlike.R                             |   95 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.make.par.grid.R                       |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.misc.R                                |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.precision.R                           |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.quadraticform.R                       |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.sim.R                                 |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.sim.conditional.R                     |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.spind2spam.R                          |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrig.traceA.R                              |    6 
 LatticeKrig-5.5/LatticeKrig/R/LKrigCovWeightedObs.R                       |only
 LatticeKrig-5.5/LatticeKrig/R/LKrigDefaultFixedFunction.R                 |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigDistance.R                             |    4 
 LatticeKrig-5.5/LatticeKrig/R/LKrigFindLambda.R                           |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigLatticeCenters.R                       |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigLatticeScales.R                        |only
 LatticeKrig-5.5/LatticeKrig/R/LKrigMakewU.R                               |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigMakewX.R                               |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigMarginalVariance.R                     |only
 LatticeKrig-5.5/LatticeKrig/R/LKrigNormalizeBasis.R                       |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigSAR.R                                  |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigSetup.R                                |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigSetupAlpha.R                           |   11 
 LatticeKrig-5.5/LatticeKrig/R/LKrigSetupAwght.R                           |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigSetupLattice.R                         |    2 
 LatticeKrig-5.5/LatticeKrig/R/LKrigUnrollGrid.R                           |    2 
 LatticeKrig-5.5/LatticeKrig/R/LatticeKrig.R                               |    2 
 LatticeKrig-5.5/LatticeKrig/R/LatticeKrigEasyDefaults.R                   |    2 
 LatticeKrig-5.5/LatticeKrig/R/ModelBox.R                                  |    6 
 LatticeKrig-5.5/LatticeKrig/R/ModelCylinder.R                             |    4 
 LatticeKrig-5.5/LatticeKrig/R/ModelInterval.R                             |   28 
 LatticeKrig-5.5/LatticeKrig/R/ModelRectangle.R                            |   56 
 LatticeKrig-5.5/LatticeKrig/R/ModelRing.R                                 |    4 
 LatticeKrig-5.5/LatticeKrig/R/Radial.basis.R                              |    2 
 LatticeKrig-5.5/LatticeKrig/R/Tensor.basis.R                              |    2 
 LatticeKrig-5.5/LatticeKrig/R/WendlandFunction.R                          |    5 
 LatticeKrig-5.5/LatticeKrig/R/convertIndexPeriodic.R                      |    2 
 LatticeKrig-5.5/LatticeKrig/R/createLKrigObject.R                         |    5 
 LatticeKrig-5.5/LatticeKrig/R/directionCosines.R                          |    4 
 LatticeKrig-5.5/LatticeKrig/R/predict.LKrig.R                             |    2 
 LatticeKrig-5.5/LatticeKrig/R/predictLKrigFixedFunction.R                 |    2 
 LatticeKrig-5.5/LatticeKrig/R/predictSE.LKrig.R                           |    6 
 LatticeKrig-5.5/LatticeKrig/R/predictSurface.LKrig.R                      |    2 
 LatticeKrig-5.5/LatticeKrig/R/print.LKinfo.R                              |    2 
 LatticeKrig-5.5/LatticeKrig/R/print.LKrig.R                               |    2 
 LatticeKrig-5.5/LatticeKrig/R/print.LatticeKrig.R                         |    2 
 LatticeKrig-5.5/LatticeKrig/R/setDefaultsLKinfo.R                         |    2 
 LatticeKrig-5.5/LatticeKrig/R/surface.LKrig.R                             |    2 
 LatticeKrig-5.5/LatticeKrig/R/triWeight.R                                 |    2 
 LatticeKrig-5.5/LatticeKrig/R/zzz.R                                       |    2 
 LatticeKrig-5.5/LatticeKrig/inst                                          |only
 LatticeKrig-5.5/LatticeKrig/man/LKDist.Rd                                 |only
 LatticeKrig-5.5/LatticeKrig/man/LKGeometry.Rd                             |only
 LatticeKrig-5.5/LatticeKrig/man/LKinfoCheck.Rd                            |   19 
 LatticeKrig-5.5/LatticeKrig/man/LKrig.MLE.Rd                              |   34 
 LatticeKrig-5.5/LatticeKrig/man/LKrig.Rd                                  |   77 
 LatticeKrig-5.5/LatticeKrig/man/LKrig.basis.Rd                            |   51 
 LatticeKrig-5.5/LatticeKrig/man/LKrig.sim.Rd                              |   23 
 LatticeKrig-5.5/LatticeKrig/man/LKrigDefaultFixedFunction.Rd              |only
 LatticeKrig-5.5/LatticeKrig/man/LKrigDistance-methods.Rd                  |   17 
 LatticeKrig-5.5/LatticeKrig/man/LKrigInternal.Rd                          |only
 LatticeKrig-5.5/LatticeKrig/man/LKrigLatticeCenters.Rd                    |   49 
 LatticeKrig-5.5/LatticeKrig/man/LKrigMiscellaneous.Rd                     |only
 LatticeKrig-5.5/LatticeKrig/man/LKrigNormalizeBasis.Rd                    |only
 LatticeKrig-5.5/LatticeKrig/man/LKrigSAR.Rd                               |   21 
 LatticeKrig-5.5/LatticeKrig/man/LKrigSetup.Rd                             |   46 
 LatticeKrig-5.5/LatticeKrig/man/LKrigSetupAlpha.Rd                        |   19 
 LatticeKrig-5.5/LatticeKrig/man/LKrigSetupAwght.Rd                        |   21 
 LatticeKrig-5.5/LatticeKrig/man/LKrigSetupLattice.Rd                      |   43 
 LatticeKrig-5.5/LatticeKrig/man/LatticeKrig.Rd                            |   65 
 LatticeKrig-5.5/LatticeKrig/man/PeriodicGeometry.Rd                       |only
 LatticeKrig-5.5/LatticeKrig/man/Radial.Basis.Rd                           |    5 
 LatticeKrig-5.5/LatticeKrig/man/gridList-class.Rd                         |  137 
 LatticeKrig-5.5/LatticeKrig/man/setDefaultsLKinfo.Rd                      |   29 
 LatticeKrig-5.5/LatticeKrig/src/LKdist.f                                  |   16 
 LatticeKrig-5.5/LatticeKrig/src/LKdistgrid.f                              |   16 
 LatticeKrig-5.5/LatticeKrig/src/dfind1d.f                                 |   16 
 LatticeKrig-5.5/LatticeKrig/src/dfind2d.f                                 |   17 
 LatticeKrig-5.5/LatticeKrig/src/findNorm.f                                |   19 
 LatticeKrig-5.5/LatticeKrig/src/multBasis.f                               |   19 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.FindNorm.test.Rout.save           |   43 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.LKCylinder.test.Rout.save         |only
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.LKCylinder.test.inverse.Rout.save |only
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.basis.test.R                      |   19 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.basis.test.Rout.save              |   63 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.lnPLike.test.R                    |   46 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.lnPlike.test.Rout.save            |   51 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.nullspace.test.Rout.save          |   19 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.precision.test.Rout.save          |   67 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.se.test.Rout.save                 |   43 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.test.3D.Rout.save                 | 1450 +++++++++-
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.test.R                            |   29 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.test.Rout.save                    |  135 
 LatticeKrig-5.5/LatticeKrig/tests/LKrig.test.inverse.Rout.save            |only
 LatticeKrig-5.5/LatticeKrig/tests/LKrigMarginalVariance.test.R            |only
 LatticeKrig-5.5/LatticeKrig/tests/LKrigMarginalVariance.test.Rout.save    |only
 123 files changed, 2700 insertions(+), 745 deletions(-)

More information about LatticeKrig at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.