Thu, 18 May 2017

Package SSRMST updated to version 0.1.1 with previous version 0.1.0 dated 2015-08-24

Title: Sample Size Calculation using Restricted Mean Survival Time
Description: Calculates the power and sample size based on the difference in Restricted Mean Survival Time.
Author: Miki Horiguchi, Hajime Uno
Maintainer: Miki Horiguchi <horiguchimiki@gmail.com>

Diff between SSRMST versions 0.1.0 dated 2015-08-24 and 0.1.1 dated 2017-05-18

 DESCRIPTION                   |   16 +
 MD5                           |   23 +-
 NAMESPACE                     |    3 
 NEWS.md                       |only
 R/ssrmst.R                    |  338 +++++++++++++++++++++++++++++-------------
 build/vignette.rds            |binary
 inst/doc/vignette-ssrmst.R    |    8 
 inst/doc/vignette-ssrmst.Rmd  |   54 +++---
 inst/doc/vignette-ssrmst.html |  132 +++++++++-------
 man/SSRMST-package.Rd         |   54 +++---
 man/print.ssrmst.Rd           |    3 
 man/ssrmst.Rd                 |   47 +++--
 vignettes/vignette-ssrmst.Rmd |   54 +++---
 13 files changed, 447 insertions(+), 285 deletions(-)

More information about SSRMST at CRAN
Permanent link

Package REDCapR updated to version 0.9.8 with previous version 0.9.7 dated 2016-09-09

Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.
Author: Will Beasley [aut, cre], David Bard [ctb], Thomas Wilson [ctb], John J Aponte [ctb], Rollie Parrish [ctb], Benjamin Nutter [ctb], Andrew Peters [ctb], Hao Zhu [ctb]
Maintainer: Will Beasley <wibeasley@hotmail.com>

Diff between REDCapR versions 0.9.7 dated 2016-09-09 and 0.9.8 dated 2017-05-18

 REDCapR-0.9.7/REDCapR/R/validate-for-write.R                                               |only
 REDCapR-0.9.7/REDCapR/man/validate_for_write.Rd                                            |only
 REDCapR-0.9.7/REDCapR/tests/testthat/test-validate-for-write.R                             |only
 REDCapR-0.9.8/REDCapR/DESCRIPTION                                                          |   17 
 REDCapR-0.9.8/REDCapR/MD5                                                                  |  187 -
 REDCapR-0.9.8/REDCapR/NAMESPACE                                                            |   47 
 REDCapR-0.9.8/REDCapR/NEWS                                                                 |  237 -
 REDCapR-0.9.8/REDCapR/R/REDCapR-package.R                                                  |   88 
 REDCapR-0.9.8/REDCapR/R/create-batch-glossary.R                                            |  129 
 REDCapR-0.9.8/REDCapR/R/metadata-utilities.R                                               |  191 -
 REDCapR-0.9.8/REDCapR/R/project-simple.R                                                   |  208 -
 REDCapR-0.9.8/REDCapR/R/redcap-column-sanitize.R                                           |  100 
 REDCapR-0.9.8/REDCapR/R/redcap-download-file-oneshot.R                                     |  322 -
 REDCapR-0.9.8/REDCapR/R/redcap-metadata-read.R                                             |  287 -
 REDCapR-0.9.8/REDCapR/R/redcap-project.R                                                   |  222 -
 REDCapR-0.9.8/REDCapR/R/redcap-read-oneshot-eav.R                                          |only
 REDCapR-0.9.8/REDCapR/R/redcap-read-oneshot.R                                              |  455 +-
 REDCapR-0.9.8/REDCapR/R/redcap-read.R                                                      |  445 +-
 REDCapR-0.9.8/REDCapR/R/redcap-upload-file-oneshot.R                                       |  271 -
 REDCapR-0.9.8/REDCapR/R/redcap-variables.R                                                 |only
 REDCapR-0.9.8/REDCapR/R/redcap-version.R                                                   |only
 REDCapR-0.9.8/REDCapR/R/redcap-write-oneshot.R                                             |  348 -
 REDCapR-0.9.8/REDCapR/R/redcap-write.R                                                     |  297 -
 REDCapR-0.9.8/REDCapR/R/retrieve-credential.R                                              |  410 +-
 REDCapR-0.9.8/REDCapR/R/retrieve-token.R                                                   |  242 -
 REDCapR-0.9.8/REDCapR/R/sanitize-token.R                                                   |only
 REDCapR-0.9.8/REDCapR/R/utilities.R                                                        |   90 
 REDCapR-0.9.8/REDCapR/R/validate.R                                                         |only
 REDCapR-0.9.8/REDCapR/README.md                                                            |  220 -
 REDCapR-0.9.8/REDCapR/build/vignette.rds                                                   |binary
 REDCapR-0.9.8/REDCapR/inst/doc/BasicREDCapROperations.R                                    |  242 -
 REDCapR-0.9.8/REDCapR/inst/doc/BasicREDCapROperations.Rmd                                  |  356 +-
 REDCapR-0.9.8/REDCapR/inst/doc/BasicREDCapROperations.html                                 | 1770 +++++++---
 REDCapR-0.9.8/REDCapR/inst/doc/SecurityDatabase.Rmd                                        |  658 +--
 REDCapR-0.9.8/REDCapR/inst/doc/SecurityDatabase.html                                       |  770 ++--
 REDCapR-0.9.8/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd                                 |  788 ++--
 REDCapR-0.9.8/REDCapR/inst/doc/TroubleshootingApiCalls.html                                |  766 ++--
 REDCapR-0.9.8/REDCapR/inst/doc/advanced-redcapr-operations.R                               |only
 REDCapR-0.9.8/REDCapR/inst/doc/advanced-redcapr-operations.Rmd                             |only
 REDCapR-0.9.8/REDCapR/inst/doc/advanced-redcapr-operations.html                            |only
 REDCapR-0.9.8/REDCapR/inst/misc/bad.credentials                                            |   16 
 REDCapR-0.9.8/REDCapR/inst/misc/conflicting-rows.credentials                               |   16 
 REDCapR-0.9.8/REDCapR/inst/misc/example.credentials                                        |   20 
 REDCapR-0.9.8/REDCapR/inst/misc/out-of-order.credentials                                   |   16 
 REDCapR-0.9.8/REDCapR/inst/misc/vignette.css                                               |   72 
 REDCapR-0.9.8/REDCapR/inst/misc/zero-rows.credentials                                      |   12 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-color-boxes/Readme.md                         |  106 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-color-boxes/color-boxes-data-dictionary.csv   |    6 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-color-boxes/color-boxes-data.csv              |    8 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-longitudinal/longitudinal-data-dictionary.csv |  192 -
 REDCapR-0.9.8/REDCapR/inst/test-data/project-longitudinal/longitudinal-data.csv            |   38 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-russian/russian-data.csv                      |    8 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-simple/simple-data-dictionary.csv             |   34 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-simple/simple-data.csv                        |   32 
 REDCapR-0.9.8/REDCapR/inst/test-data/project-simple/simple-metadata.csv                    |   34 
 REDCapR-0.9.8/REDCapR/man/REDCapR-package.Rd                                               |   89 
 REDCapR-0.9.8/REDCapR/man/create_batch_glossary.Rd                                         |  105 
 REDCapR-0.9.8/REDCapR/man/metadata_utilities.Rd                                            |  148 
 REDCapR-0.9.8/REDCapR/man/redcap_column_sanitize.Rd                                        |   93 
 REDCapR-0.9.8/REDCapR/man/redcap_download_file_oneshot.Rd                                  |  194 -
 REDCapR-0.9.8/REDCapR/man/redcap_metadata_read.Rd                                          |  137 
 REDCapR-0.9.8/REDCapR/man/redcap_project.Rd                                                |  115 
 REDCapR-0.9.8/REDCapR/man/redcap_read.Rd                                                   |  207 -
 REDCapR-0.9.8/REDCapR/man/redcap_read_oneshot.Rd                                           |  222 -
 REDCapR-0.9.8/REDCapR/man/redcap_read_oneshot_eav.Rd                                       |only
 REDCapR-0.9.8/REDCapR/man/redcap_upload_file_oneshot.Rd                                    |  181 -
 REDCapR-0.9.8/REDCapR/man/redcap_variables.Rd                                              |only
 REDCapR-0.9.8/REDCapR/man/redcap_version.Rd                                                |only
 REDCapR-0.9.8/REDCapR/man/redcap_write.Rd                                                  |  199 -
 REDCapR-0.9.8/REDCapR/man/redcap_write_oneshot.Rd                                          |  169 
 REDCapR-0.9.8/REDCapR/man/replace_nas_with_explicit.Rd                                     |   73 
 REDCapR-0.9.8/REDCapR/man/retrieve_credential.Rd                                           |  133 
 REDCapR-0.9.8/REDCapR/man/retrieve_token.Rd                                                |  137 
 REDCapR-0.9.8/REDCapR/man/sanitize_token.Rd                                                |only
 REDCapR-0.9.8/REDCapR/man/validate.Rd                                                      |only
 REDCapR-0.9.8/REDCapR/tests/manual/README.md                                               |    8 
 REDCapR-0.9.8/REDCapR/tests/manual/test-could-not-connect-rate.R                           |  104 
 REDCapR-0.9.8/REDCapR/tests/manual/test-stress-test-serial.R                               |  224 -
 REDCapR-0.9.8/REDCapR/tests/test-all.R                                                     |   10 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-column-sanitize.R                                |   73 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-create-batch-glossary.R                          |  156 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-file-oneshot.R                                   |  426 +-
 REDCapR-0.9.8/REDCapR/tests/testthat/test-metadata-read.R                                  |  546 +--
 REDCapR-0.9.8/REDCapR/tests/testthat/test-metadata-utilities.R                             |   60 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-project.R                                        |  142 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-batch-longitudinal.R                        |  332 -
 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-batch-simple.R                              |  914 ++---
 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-errors.R                                    |  174 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-oneshot-eav.R                               |only
 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-oneshot.R                                   |  668 +--
 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-russian.R                                   |   92 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-credential-local.R                      |  304 -
 REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-credential-mssql.R                      |  312 -
 REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-token.R                                 |  230 -
 REDCapR-0.9.8/REDCapR/tests/testthat/test-sanitize.R                                       |only
 REDCapR-0.9.8/REDCapR/tests/testthat/test-utilities.R                                      |  140 
 REDCapR-0.9.8/REDCapR/tests/testthat/test-validate.R                                       |only
 REDCapR-0.9.8/REDCapR/tests/testthat/test-variables.R                                      |only
 REDCapR-0.9.8/REDCapR/tests/testthat/test-version.R                                        |only
 REDCapR-0.9.8/REDCapR/tests/testthat/test-write-batch.R                                    |  360 +-
 REDCapR-0.9.8/REDCapR/tests/testthat/test-write-oneshot.R                                  |  360 +-
 REDCapR-0.9.8/REDCapR/vignettes/BasicREDCapROperations.Rmd                                 |  356 +-
 REDCapR-0.9.8/REDCapR/vignettes/SecurityDatabase.Rmd                                       |  658 +--
 REDCapR-0.9.8/REDCapR/vignettes/TroubleshootingApiCalls.Rmd                                |  788 ++--
 REDCapR-0.9.8/REDCapR/vignettes/advanced-redcapr-operations.Rmd                            |only
 REDCapR-0.9.8/REDCapR/vignettes/styles.css                                                 |only
 106 files changed, 10751 insertions(+), 9661 deletions(-)

More information about REDCapR at CRAN
Permanent link

Package Opportunistic updated to version 1.1 with previous version 1.0 dated 2017-05-09

Title: Broadcasts, Transmissions and Receptions in an Opportunistic Network
Description: Computes the expectation of the number of broadcasts, transmissions and receptions considering an Opportunistic transport model. It provides theoretical results and also estimated values based on Monte Carlo simulations.
Author: Christian E. Galarza, Jonathan M. Olate
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>

Diff between Opportunistic versions 1.0 dated 2017-05-09 and 1.1 dated 2017-05-18

 DESCRIPTION    |   11 ++++++-----
 MD5            |    6 +++---
 R/Expected.R   |    3 ---
 R/MonteCarlo.R |    4 +---
 4 files changed, 10 insertions(+), 14 deletions(-)

More information about Opportunistic at CRAN
Permanent link

Package nleqslv updated to version 3.3 with previous version 3.2 dated 2017-03-04

Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>

Diff between nleqslv versions 3.2 dated 2017-03-04 and 3.3 dated 2017-05-18

 DESCRIPTION        |    8 ++++----
 MD5                |   10 +++++-----
 NEWS               |    7 +++++++
 man/searchzeros.Rd |    8 ++++----
 src/nleqslv.c      |   11 +++++++----
 src/nwclsh.f       |    5 +++--
 6 files changed, 30 insertions(+), 19 deletions(-)

More information about nleqslv at CRAN
Permanent link

Package GESE updated to version 2.0.1 with previous version 2.0.0 dated 2016-11-16

Title: Gene-Based Segregation Test
Description: Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hersh, C.P., et al. (2017). <DOI:10.1002/gepi.22037>. Gene-based segregation method for identifying rare variants for family-based sequencing studies. Genet Epidemiol 41(4):309-319. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.
Author: Dandi Qiao, Michael H. Cho
Maintainer: Dandi Qiao <redaq@channing.harvard.edu>

Diff between GESE versions 2.0.0 dated 2016-11-16 and 2.0.1 dated 2017-05-18

 DESCRIPTION               |   10 +++++-----
 MD5                       |   28 ++++++++++++++--------------
 R/GESE.R                  |   11 ++++++++---
 build/partial.rdb         |binary
 data/database.rda         |binary
 inst/doc/my-vignette.Rmd  |    2 +-
 inst/doc/my-vignette.pdf  |binary
 man/GESE-internal.Rd      |    2 +-
 man/GESE-package.Rd       |    3 ++-
 man/GESE.Rd               |    4 ++--
 man/condSegProbF.Rd       |    3 ++-
 man/getSegInfo.Rd         |    3 ++-
 man/trim_oneLineage.Rd    |    3 +--
 man/trim_unrelated.Rd     |    2 +-
 vignettes/my-vignette.Rmd |    2 +-
 15 files changed, 40 insertions(+), 33 deletions(-)

More information about GESE at CRAN
Permanent link

Package dplR updated to version 1.6.6 with previous version 1.6.5 dated 2017-02-03

Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology building, and cross dating. Read and write standard file formats used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>

Diff between dplR versions 1.6.5 dated 2017-02-03 and 1.6.6 dated 2017-05-18

 ChangeLog                    |   79 +++++++++++++++++++++++++++++++++++++++++++
 DESCRIPTION                  |   23 +++++-------
 MD5                          |   60 +++++++++++++++++---------------
 NAMESPACE                    |   13 ++-----
 R/exactmean.R                |    2 -
 R/helpers.R                  |   16 ++++++++
 R/latexify.R                 |    8 ++--
 R/rasterPlot.R               |    7 ++-
 R/rcs.R                      |   68 ++++++++++++++++++++-----------------
 R/read.tucson.R              |    3 +
 R/redfit.R                   |   36 ++++++++++---------
 build/vignette.rds           |binary
 inst/doc/chron-dplR.pdf      |binary
 inst/doc/intro-dplR.pdf      |binary
 inst/doc/timeseries-dplR.pdf |binary
 inst/doc/xdate-dplR.pdf      |binary
 man/detrend.series.Rd        |    4 +-
 man/rcs.Rd                   |    9 +++-
 man/redfit.Rd                |   11 +++--
 src/Makevars                 |only
 src/dplR-win.def             |only
 src/exactmean.c              |    1 
 src/gini.c                   |    1 
 src/init.c                   |only
 src/rcompact.c               |    1 
 src/readloop.c               |    1 
 src/redfit.c                 |   16 +++-----
 src/registered.h             |only
 src/sens.c                   |    1 
 src/tbrm.c                   |    1 
 tests/testthat.R             |    5 +-
 tests/testthat/test-chron.R  |    4 +-
 tests/testthat/test-dplR.R   |    4 +-
 33 files changed, 245 insertions(+), 129 deletions(-)

More information about dplR at CRAN
Permanent link

Package powerplus updated to version 3.1 with previous version 3.0 dated 2016-08-18

Title: Exponentiation Operations
Description: Computation of matrix and scalar exponentiation.
Author: Albert Dorador
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>

Diff between powerplus versions 3.0 dated 2016-08-18 and 3.1 dated 2017-05-18

 powerplus-3.0/powerplus/R/MatpowV3.R  |only
 powerplus-3.0/powerplus/R/explusV2.R  |only
 powerplus-3.1/powerplus/DESCRIPTION   |   14 +++++++-------
 powerplus-3.1/powerplus/MD5           |   10 +++++-----
 powerplus-3.1/powerplus/R/MatpowV4.R  |only
 powerplus-3.1/powerplus/R/explusV3.R  |only
 powerplus-3.1/powerplus/man/Matpow.Rd |   18 ++++++++----------
 powerplus-3.1/powerplus/man/explus.Rd |   19 ++++++++++++-------
 8 files changed, 32 insertions(+), 29 deletions(-)

More information about powerplus at CRAN
Permanent link

New package LZeroSpikeInference with initial version 1.0.1
Package: LZeroSpikeInference
Type: Package
Title: Exact Spike Train Inference via L0 Optimization
Version: 1.0.1
Authors@R: person("Sean", "Jewell", email = "swjewell@uw.edu", role = c("aut", "cre"))
Description: An implementation of algorithms described in Jewell and Witten (2017) <arXiv:1703.08644>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat
Imports: graphics, stats
NeedsCompilation: no
Packaged: 2017-05-18 16:07:32 UTC; jewellsean
Author: Sean Jewell [aut, cre]
Maintainer: Sean Jewell <swjewell@uw.edu>
Repository: CRAN
Date/Publication: 2017-05-18 16:16:25 UTC

More information about LZeroSpikeInference at CRAN
Permanent link

Package tensorBSS updated to version 0.3 with previous version 0.2 dated 2016-08-25

Title: Blind Source Separation Methods for Tensor-Valued Observations
Description: Contains several utility functions for manipulating tensor-valued data (centering, multiplication from a single mode etc.) and the implementations of the following blind source separation methods for tensor-valued data: 'tPCA', 'tFOBI', 'tJADE', 'tgFOBI', 'tgJADE', 'tSOBI', 'tNSS.SD', 'tNSS.JD' and 'tNSS.TD.JD'.
Author: Joni Virta, Bing Li, Klaus Nordhausen, Hannu Oja
Maintainer: Joni Virta <jomivi@utu.fi>

Diff between tensorBSS versions 0.2 dated 2016-08-25 and 0.3 dated 2017-05-18

 tensorBSS-0.2/tensorBSS/R/eigenVectors.R     |only
 tensorBSS-0.2/tensorBSS/R/mAutoCovMatrix.R   |only
 tensorBSS-0.2/tensorBSS/R/mFOBIMatrix.R      |only
 tensorBSS-0.2/tensorBSS/R/mJADEMatrix.R      |only
 tensorBSS-0.2/tensorBSS/R/mTGFOBIMatrix.R    |only
 tensorBSS-0.2/tensorBSS/R/mTGJADEMatrix.R    |only
 tensorBSS-0.2/tensorBSS/R/matrixCovariance.R |only
 tensorBSS-0.2/tensorBSS/R/symmetricPower.R   |only
 tensorBSS-0.2/tensorBSS/src/tBSS.cpp         |only
 tensorBSS-0.2/tensorBSS/src/tBSS.h           |only
 tensorBSS-0.3/tensorBSS/DESCRIPTION          |   10 +++----
 tensorBSS-0.3/tensorBSS/MD5                  |   34 ++++++++++++++-------------
 tensorBSS-0.3/tensorBSS/NAMESPACE            |    4 +--
 tensorBSS-0.3/tensorBSS/R/RcppExports.R      |only
 tensorBSS-0.3/tensorBSS/R/arraySelectLast.R  |only
 tensorBSS-0.3/tensorBSS/R/tJADE.R            |    2 -
 tensorBSS-0.3/tensorBSS/R/tJADERotate.R      |   15 +++++++++--
 tensorBSS-0.3/tensorBSS/R/tNSS.JD.R          |only
 tensorBSS-0.3/tensorBSS/R/tNSS.SD.R          |only
 tensorBSS-0.3/tensorBSS/R/tNSS.TD.JD.R       |only
 tensorBSS-0.3/tensorBSS/inst/ChangeLog       |    9 ++++++-
 tensorBSS-0.3/tensorBSS/man/tFOBI.Rd         |    2 -
 tensorBSS-0.3/tensorBSS/man/tNSS.JD.Rd       |only
 tensorBSS-0.3/tensorBSS/man/tNSS.SD.Rd       |only
 tensorBSS-0.3/tensorBSS/man/tNSS.TD.JD.Rd    |only
 tensorBSS-0.3/tensorBSS/src/RcppExports.cpp  |only
 tensorBSS-0.3/tensorBSS/src/tensorBSS.cpp    |only
 tensorBSS-0.3/tensorBSS/src/tensorBSS.h      |only
 tensorBSS-0.3/tensorBSS/src/tensorBSS_init.c |only
 29 files changed, 47 insertions(+), 29 deletions(-)

More information about tensorBSS at CRAN
Permanent link

Package provenance updated to version 1.7 with previous version 1.6 dated 2017-05-03

Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov- Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances. Also included are tools to plot compositional data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between provenance versions 1.6 dated 2017-05-03 and 1.7 dated 2017-05-18

 DESCRIPTION                        |   13 
 MD5                                |   96 +--
 NAMESPACE                          |    1 
 R/gui.R                            |   30 -
 R/provenance.R                     |  980 -------------------------------------
 R/toolbox.R                        |only
 man/CLR.Rd                         |    3 
 man/GPA.Rd                         |    3 
 man/KDE.Rd                         |    1 
 man/KDEs.Rd                        |    1 
 man/KS.diss.Rd                     |    3 
 man/Kuiper.diss.Rd                 |only
 man/MDS.Rd                         |   23 
 man/Namib.Rd                       |    7 
 man/PCA.Rd                         |    3 
 man/SH.diss.Rd                     |    7 
 man/amalgamate.Rd                  |    7 
 man/as.acomp.Rd                    |    3 
 man/as.compositional.Rd            |    3 
 man/as.data.frame.compositional.Rd |    3 
 man/botev.Rd                       |    7 
 man/bray.diss.Rd                   |    3 
 man/combine.Rd                     |    3 
 man/densities.Rd                   |    7 
 man/diss.Rd                        |   11 
 man/endmembers.Rd                  |    7 
 man/get.f.Rd                       |    3 
 man/get.n.Rd                       |    3 
 man/get.p.Rd                       |    3 
 man/indscal.Rd                     |    7 
 man/minsorting.Rd                  |    7 
 man/plot.GPA.Rd                    |    1 
 man/plot.INDSCAL.Rd                |    1 
 man/plot.KDE.Rd                    |    1 
 man/plot.MDS.Rd                    |    1 
 man/plot.PCA.Rd                    |    1 
 man/plot.compositional.Rd          |    1 
 man/plot.distributional.Rd         |    1 
 man/plot.minsorting.Rd             |    1 
 man/plot.ternary.Rd                |    1 
 man/procrustes.Rd                  |    9 
 man/provenance.Rd                  |   35 +
 man/read.compositional.Rd          |    3 
 man/read.densities.Rd              |    3 
 man/read.distributional.Rd         |    6 
 man/restore.Rd                     |    7 
 man/subset.compositional.Rd        |    3 
 man/subset.distributional.Rd       |    3 
 man/summaryplot.Rd                 |    1 
 man/ternary.Rd                     |    3 
 50 files changed, 189 insertions(+), 1141 deletions(-)

More information about provenance at CRAN
Permanent link

New package osmdata with initial version 0.0.0
Package: osmdata
Version: 0.0.0
Authors@R: c( person("Mark", "Padgham", email="mark.padgham@email.com", role=c("aut", "cre")), person("Bob", "Rudis", role="aut"), person("Robin", "Lovelace", role="aut"), person("Maëlle", "Salmon", role="aut"), person("Andrew", "Smith", role="ctb"), person("Marcin", "Kalicinski", role=c("ctb", "cph"), comment="Author of included RapidXML code"), person("Finkelstein", "Noam", role=c("ctb","cph"), comment="Author of included stub.R code"), person ("Bartnik", "Lukasz", role=c("ctb","cph"), comment="Author of included stub.R code"))
Maintainer: Mark Padgham <mark.padgham@email.com>
Title: Import OpenStreetMap Data as Simple Features or Spatial Objects
Description: Download and import of "OpenStreetMap" ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server and processed with very fast 'C++' routines for return to 'R'.
Depends: R (>= 3.2.4)
License: GPL-3
SystemRequirements: C++11
NeedsCompilation: yes
LazyData: true
Imports: curl, httr, lubridate, methods, Rcpp (>= 0.12.4), rvest, jsonlite, sp, utils, xml2
Suggests: devtools, knitr, microbenchmark, rmarkdown, roxygen2, sf, testthat
LinkingTo: Rcpp
URL: https://github.com/osmdatar/osmdata
BugReports: https://github.com/osmdatar/osmdata/issues
Encoding: UTF-8
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Packaged: 2017-05-18 15:20:27 UTC; markus
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maëlle Salmon [aut], Andrew Smith [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Repository: CRAN
Date/Publication: 2017-05-18 15:38:24 UTC

More information about osmdata at CRAN
Permanent link

Package condformat updated to version 0.6.0 with previous version 0.5.0 dated 2017-01-23

Title: Conditional Formatting in Data Frames
Description: Apply and visualize conditional formatting to data frames in R. It renders a data frame with cells formatted according to criteria defined by rules, using a syntax similar to 'ggplot2'. The table is printed either opening a web browser or within the 'RStudio' viewer if available. The conditional formatting rules allow to highlight cells matching a condition or add a gradient background to a given column. This package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and exporting to an 'xlsx' file.
Author: Sergio Oller Moreno [aut, cph, cre]
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>

Diff between condformat versions 0.5.0 dated 2017-01-23 and 0.6.0 dated 2017-05-18

 DESCRIPTION                        |   14 +++---
 MD5                                |   64 ++++++++++++++--------------
 NAMESPACE                          |    1 
 NEWS                               |   10 ++++
 R/condformat.R                     |    2 
 R/condformat_render.R              |   82 ++++++++++++++++++++-----------------
 R/shiny.R                          |   35 +++++----------
 build/vignette.rds                 |binary
 inst/doc/introduction.html         |    8 +--
 inst/shinyexample/server.R         |   30 ++++++++++++-
 inst/shinyexample/ui.R             |   28 ++++++++++--
 man/condformat-shiny.Rd            |    7 +--
 man/condformat.Rd                  |    1 
 man/condformat2excel.Rd            |    1 
 man/condformat2html.Rd             |    1 
 man/condformat2latex.Rd            |    1 
 man/condformat2widget.Rd           |    5 +-
 man/get_css_field.Rd               |    1 
 man/knit_print.condformat_tbl.Rd   |    1 
 man/lock_cells.Rd                  |    1 
 man/plus-.condformat_tbl.Rd        |    1 
 man/print.condformat_tbl.Rd        |    5 +-
 man/reexports.Rd                   |    2 
 man/render_rules_condformat_tbl.Rd |    1 
 man/rule_fill_discrete.Rd          |    1 
 man/rule_fill_discrete_.Rd         |    1 
 man/rule_fill_gradient.Rd          |    1 
 man/rule_fill_gradient2.Rd         |    1 
 man/rule_fill_gradient2_.Rd        |    1 
 man/rule_fill_gradient_.Rd         |    1 
 man/show_columns.Rd                |    1 
 man/show_rows.Rd                   |    2 
 man/theme_htmlTable.Rd             |    1 
 33 files changed, 175 insertions(+), 137 deletions(-)

More information about condformat at CRAN
Permanent link

New package afc with initial version 1.4.0
Package: afc
Version: 1.4.0
Date: 2017-05-18
Title: Generalized Discrimination Score
Authors@R: c(person("Andreas", "Weigel", email="", role = "aut"), person("MeteoSwiss", "", role=c('cph')), person("Jonas", "Bhend", email="jonas.bhend@meteoswiss.ch", role = c('cre', 'ctb')))
Description: This is an implementation of the Generalized Discrimination Score (also known as Two Alternatives Forced Choice Score, 2AFC) for various representations of forecasts and verifying observations. The Generalized Discrimination Score is a generic forecast verification framework which can be applied to any of the following verification contexts: dichotomous, polychotomous (ordinal and nominal), continuous, probabilistic, and ensemble. A comprehensive description of the Generalized Discrimination Score, including all equations used in this package, is provided by Mason and Weigel (2009) <doi:10.1175/MWR-D-10-05069.1>.
License: GPL-3
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-18 15:05:00 UTC; bhj
Author: Andreas Weigel [aut], MeteoSwiss [cph], Jonas Bhend [cre, ctb]
Maintainer: Jonas Bhend <jonas.bhend@meteoswiss.ch>
Repository: CRAN
Date/Publication: 2017-05-18 15:23:57 UTC

More information about afc at CRAN
Permanent link

New package GUIgems with initial version 0.1
Type: Package
Package: GUIgems
Title: Graphical User Interface for Generalized Multistate Simulation Model
Version: 0.1
Date: 2017-04-30
Author: Zofia Baranczuk, Janne Estill, Nello Blaser, Luisa Salazar Vizcaya, Olivia Keiser
Description: A graphical user interface for the R package Gems. Apart from the functionality of Gems package in the Graphical User interface, GUIgems allows adding states to a defined model, merging states for the analysis and plotting progression paths between states based on the simulated cohort. There is also a module in the GUIgems which allows to compare costs and QALYs between different cohorts.
Maintainer: Zofia Baranczuk <zofia.baranczuk@math.uzh.ch>
Imports: rpanel, igraph, ggplot2, plyr, tools, msm, MASS, stringr, methods, utils, graphics, stats
License: GPL-3
RoxygenNote: 6.0.1.9000
NeedsCompilation: no
Packaged: 2017-05-18 13:47:23 UTC; Zofia
Repository: CRAN
Date/Publication: 2017-05-18 14:14:46 UTC

More information about GUIgems at CRAN
Permanent link

Package grpreg updated to version 3.1-0 with previous version 3.0-2 dated 2016-07-11

Title: Regularization Paths for Regression Models with Grouped Covariates
Description: Efficient algorithms for fitting the regularization path of linear or logistic regression models with grouped penalties. This includes group selection methods such as group lasso, group MCP, and group SCAD as well as bi-level selection methods such as the group exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny [aut, cre], Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

Diff between grpreg versions 3.0-2 dated 2016-07-11 and 3.1-0 dated 2017-05-18

 grpreg-3.0-2/grpreg/src/grpreg.c                                   |only
 grpreg-3.0-2/grpreg/tests                                          |only
 grpreg-3.1-0/grpreg/DESCRIPTION                                    |   12 
 grpreg-3.1-0/grpreg/MD5                                            |   89 +-
 grpreg-3.1-0/grpreg/NEWS                                           |  293 +++----
 grpreg-3.1-0/grpreg/R/cv.grpreg.R                                  |   44 -
 grpreg-3.1-0/grpreg/R/cv.grpsurv.R                                 |    6 
 grpreg-3.1-0/grpreg/R/gBridge.R                                    |  143 +--
 grpreg-3.1-0/grpreg/R/grpreg.R                                     |  157 +--
 grpreg-3.1-0/grpreg/R/grpsurv.R                                    |  113 +-
 grpreg-3.1-0/grpreg/R/multi.R                                      |    3 
 grpreg-3.1-0/grpreg/R/newS.R                                       |only
 grpreg-3.1-0/grpreg/R/newXG.R                                      |only
 grpreg-3.1-0/grpreg/R/newY.R                                       |only
 grpreg-3.1-0/grpreg/R/reorderGroups.R                              |    4 
 grpreg-3.1-0/grpreg/R/setupLambda.R                                |   30 
 grpreg-3.1-0/grpreg/build/vignette.rds                             |binary
 grpreg-3.1-0/grpreg/inst/doc/penalties.Rnw                         |   10 
 grpreg-3.1-0/grpreg/inst/doc/penalties.pdf                         |binary
 grpreg-3.1-0/grpreg/inst/doc/quick-start.Rnw                       |    2 
 grpreg-3.1-0/grpreg/inst/doc/quick-start.pdf                       |binary
 grpreg-3.1-0/grpreg/inst/tests/agreement.R                         |only
 grpreg-3.1-0/grpreg/inst/tests/basic-functionality.R               |  120 +-
 grpreg-3.1-0/grpreg/inst/tests/coerce.R                            |   16 
 grpreg-3.1-0/grpreg/inst/tests/cv.R                                |only
 grpreg-3.1-0/grpreg/inst/tests/extra-features.R                    |   43 -
 grpreg-3.1-0/grpreg/inst/tests/grpsurv.R                           |    2 
 grpreg-3.1-0/grpreg/inst/tests/multitask.R                         |    3 
 grpreg-3.1-0/grpreg/inst/tests/standardization-orthogonalization.R |    1 
 grpreg-3.1-0/grpreg/man/Lung.Rd                                    |    2 
 grpreg-3.1-0/grpreg/man/gBridge.Rd                                 |    4 
 grpreg-3.1-0/grpreg/man/grpreg-internal.Rd                         |    2 
 grpreg-3.1-0/grpreg/man/grpreg.Rd                                  |   50 -
 grpreg-3.1-0/grpreg/man/grpsurv.Rd                                 |   14 
 grpreg-3.1-0/grpreg/src/gdfit_binomial.c                           |   49 -
 grpreg-3.1-0/grpreg/src/gdfit_cox.c                                |   57 -
 grpreg-3.1-0/grpreg/src/gdfit_gaussian.c                           |  417 ++++++++--
 grpreg-3.1-0/grpreg/src/gdfit_poisson.c                            |   52 -
 grpreg-3.1-0/grpreg/src/grpreg_init.c                              |only
 grpreg-3.1-0/grpreg/src/lcdfit_binomial.c                          |   56 -
 grpreg-3.1-0/grpreg/src/lcdfit_cox.c                               |   60 -
 grpreg-3.1-0/grpreg/src/lcdfit_gaussian.c                          |   60 -
 grpreg-3.1-0/grpreg/src/lcdfit_poisson.c                           |   54 -
 grpreg-3.1-0/grpreg/src/maxprod.c                                  |    8 
 grpreg-3.1-0/grpreg/src/standardize.c                              |    4 
 grpreg-3.1-0/grpreg/vignettes/penalties.Rnw                        |   10 
 grpreg-3.1-0/grpreg/vignettes/quick-start.Rnw                      |    2 
 47 files changed, 1130 insertions(+), 862 deletions(-)

More information about grpreg at CRAN
Permanent link

Package easyVerification updated to version 0.4.2 with previous version 0.4.1 dated 2017-03-13

Title: Ensemble Forecast Verification for Large Data Sets
Description: Set of tools to simplify application of atomic forecast verification metrics for (comparative) verification of ensemble forecasts to large data sets. The forecast metrics are imported from the 'SpecsVerification' package, and additional forecast metrics are provided with this package. Alternatively, new user-defined forecast scores can be implemented using the example scores provided and applied using the functionality of this package.
Author: MeteoSwiss [aut, cph], Jonas Bhend [cre], Jacopo Ripoldi [ctb], Claudia Mignani [ctb], Irina Mahlstein [ctb], Rebecca Hiller [ctb], Christoph Spirig [ctb], Mark Liniger [ctb], Andreas Weigel [ctb], Joaqu'in Bedia Jimenez [ctb], Matteo De Felice [ctb], Stefan Siegert [ctb]
Maintainer: Jonas Bhend <jonas.bhend@meteoswiss.ch>

Diff between easyVerification versions 0.4.1 dated 2017-03-13 and 0.4.2 dated 2017-05-18

 DESCRIPTION                     |   12 ++++-----
 MD5                             |   52 ++++++++++++++++++++--------------------
 NEWS                            |    5 +++
 R/convert2prob.R                |   20 ++++++++++-----
 R/veriApply.R                   |    2 +
 R/veriUnwrap.R                  |    2 +
 build/vignette.rds              |binary
 man/Ens2AFC.Rd                  |    1 
 man/EnsCorr.Rd                  |    1 
 man/EnsError.Rd                 |    3 --
 man/EnsErrorss.Rd               |    1 
 man/EnsIgn.Rd                   |    2 -
 man/EnsRoca.Rd                  |    5 ++-
 man/EnsSprErr.Rd                |    1 
 man/FairSprErr.Rd               |    1 
 man/changearg.Rd                |    1 
 man/climFairRpss.Rd             |    1 
 man/convert2prob.Rd             |    4 +--
 man/count2prob.Rd               |    2 -
 man/easyVerification.Rd         |    1 
 man/generateRef.Rd              |    3 +-
 man/size.Rd                     |    1 
 man/toymodel.Rd                 |    4 +--
 man/veriApply.Rd                |    2 -
 man/veriUnwrap.Rd               |    1 
 man/weisheimer.Rd               |    1 
 tests/testthat/test_veriApply.R |    7 ++++-
 27 files changed, 73 insertions(+), 63 deletions(-)

More information about easyVerification at CRAN
Permanent link

New package uncmbb with initial version 0.1.0
Package: uncmbb
Type: Package
Title: UNC Men's Basketball Match Results Since 1949-1950 Season
Version: 0.1.0
Authors@R: c(person("Jay", "Lee", email = "joongsup@gmail.com", role = c("aut", "cre")))
Description: Dataset contains select attributes for each match result since 1949-1950 season for UNC men's basketball team.
Depends: R (>= 3.3.2)
License: CC0
Encoding: UTF-8
LazyData: true
URL: http://github.com/joongsup/uncmbb
BugReports: https://github.com/joongsup/uncmbb/issues
RoxygenNote: 5.0.1
Suggests: dplyr
NeedsCompilation: no
Packaged: 2017-05-18 12:47:38 UTC; jl939a
Author: Jay Lee [aut, cre]
Maintainer: Jay Lee <joongsup@gmail.com>
Repository: CRAN
Date/Publication: 2017-05-18 13:47:23 UTC

More information about uncmbb at CRAN
Permanent link

Package sdcTable updated to version 0.22.6 with previous version 0.22.4 dated 2017-04-07

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>

Diff between sdcTable versions 0.22.4 dated 2017-04-07 and 0.22.6 dated 2017-05-18

 DESCRIPTION              |    8 -
 MD5                      |   18 ++--
 R/classes_tauBatch.r     |    4 
 R/createArgusInput.R     |only
 R/export_functions.r     |  193 -----------------------------------------------
 R/runArgusBatchFile.R    |only
 R/tauBatch_helpers.R     |  141 ++++++++++++++++++++--------------
 build/vignette.rds       |binary
 inst/doc/sdcTable.pdf    |binary
 man/createArgusInput.Rd  |    4 
 man/runArgusBatchFile.Rd |   13 +--
 11 files changed, 109 insertions(+), 272 deletions(-)

More information about sdcTable at CRAN
Permanent link

Package clickstream updated to version 1.2.1 with previous version 1.2.0 dated 2017-04-10

Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e., clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>

Diff between clickstream versions 1.2.0 dated 2017-04-10 and 1.2.1 dated 2017-05-18

 DESCRIPTION                |   10 +++++-----
 MD5                        |   17 +++++++++--------
 NAMESPACE                  |    2 ++
 NEWS                       |    6 ++++++
 R/Clickstream.r            |   30 ++++++++++++++++++++++++++++++
 R/MarkovChain.r            |   13 +++++++++++--
 R/clickstream-package.R    |    4 ++--
 man/as.ClickClust.Rd       |only
 man/clickstream-package.Rd |    2 +-
 man/hmPlot-methods.Rd      |    4 +++-
 10 files changed, 69 insertions(+), 19 deletions(-)

More information about clickstream at CRAN
Permanent link

New package ccRemover with initial version 1.0.1
Package: ccRemover
Type: Package
Title: Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data
Version: 1.0.1
Authors@R: c( person("Jun", "Li", email = "jun.li@nd.edu",role = c("aut","cre")), person("Martin", "Barron", email = "mbarron2@nd.edu",role = c("aut")))
Description: Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.
Depends: R (>= 2.10.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: stats, utils
NeedsCompilation: no
Packaged: 2017-05-18 05:11:03 UTC; Administrator
Author: Jun Li [aut, cre], Martin Barron [aut]
Maintainer: Jun Li <jun.li@nd.edu>
Repository: CRAN
Date/Publication: 2017-05-18 13:48:53 UTC

More information about ccRemover at CRAN
Permanent link

Package atlantistools updated to version 0.4.2 with previous version 0.4.1 dated 2017-05-09

Title: Process and Visualise Output from Atlantis Models
Description: Atlantis is an end-to-end marine ecosystem modelling framework. It was originally developed in Australia by E.A. Fulton, A.D.M. Smith and D.C. Smith (2007) and has since been adopted in many marine ecosystems around the world (<http://atlantis.cmar.csiro.au/www/en/atlantis.html>). The output of an Atlantis simulation is stored in various file formats like .netcdf and .txt and different output structures are used for the output variables like e.g. productivity or biomass. This package is used to convert the different output types to a unified format according to the "tidy-data" approach by H. Wickham (2014) <DOI:10.18637/jss.v059.i10>. Additionally, ecological metrics like for example spatial overlap of predator and prey or consumption can be calculated and visualised with this package. Due to the unified data structure it is very easy to share model output with each other and perform model comparisons.
Author: Alexander Keth [aut, cre]
Maintainer: Alexander Keth <alexander.keth@uni-hamburg.de>

Diff between atlantistools versions 0.4.1 dated 2017-05-09 and 0.4.2 dated 2017-05-18

 atlantistools-0.4.1/atlantistools/tests/figs/plot-species/line-plot.svg                    |only
 atlantistools-0.4.2/atlantistools/DESCRIPTION                                              |   14 
 atlantistools-0.4.2/atlantistools/MD5                                                      |  187 +++++-----
 atlantistools-0.4.2/atlantistools/R/agg-data.R                                             |    2 
 atlantistools-0.4.2/atlantistools/R/calculate-biomass-spatial.R                            |    6 
 atlantistools-0.4.2/atlantistools/R/calculate-consumed-biomass.R                           |    2 
 atlantistools-0.4.2/atlantistools/R/change-avail.R                                         |    2 
 atlantistools-0.4.2/atlantistools/R/change-prm-cohort.R                                    |    2 
 atlantistools-0.4.2/atlantistools/R/change-prm.R                                           |    5 
 atlantistools-0.4.2/atlantistools/R/combine-groups.R                                       |    4 
 atlantistools-0.4.2/atlantistools/R/data.R                                                 |   32 -
 atlantistools-0.4.2/atlantistools/R/flip-layers.R                                          |   10 
 atlantistools-0.4.2/atlantistools/R/get-boundary.R                                         |    3 
 atlantistools-0.4.2/atlantistools/R/get-colpal.R                                           |    2 
 atlantistools-0.4.2/atlantistools/R/get-groups.R                                           |   12 
 atlantistools-0.4.2/atlantistools/R/get-growth-fishbase.R                                  |    4 
 atlantistools-0.4.2/atlantistools/R/get-ids-fishbase.R                                     |    2 
 atlantistools-0.4.2/atlantistools/R/load-dietcheck.R                                       |    4 
 atlantistools-0.4.2/atlantistools/R/load-init-age.R                                        |    4 
 atlantistools-0.4.2/atlantistools/R/load-nc-physics.R                                      |    4 
 atlantistools-0.4.2/atlantistools/R/pipe.R                                                 |    2 
 atlantistools-0.4.2/atlantistools/R/plot-bar.R                                             |    2 
 atlantistools-0.4.2/atlantistools/R/plot-consumed-biomass.R                                |    4 
 atlantistools-0.4.2/atlantistools/R/plot-diet-bec-dev.R                                    |    4 
 atlantistools-0.4.2/atlantistools/R/plot-diet.R                                            |    2 
 atlantistools-0.4.2/atlantistools/R/plot-spatial-box.R                                     |    6 
 atlantistools-0.4.2/atlantistools/R/plot-spatial-ts.R                                      |    4 
 atlantistools-0.4.2/atlantistools/R/plot-species.R                                         |    4 
 atlantistools-0.4.2/atlantistools/R/preprocess-txt.R                                       |    4 
 atlantistools-0.4.2/atlantistools/R/sc-init.R                                              |    6 
 atlantistools-0.4.2/atlantistools/R/str-split-twice.R                                      |    2 
 atlantistools-0.4.2/atlantistools/R/theme-atlantis.R                                       |    4 
 atlantistools-0.4.2/atlantistools/R/utils.R                                                |   13 
 atlantistools-0.4.2/atlantistools/README.md                                                |   10 
 atlantistools-0.4.2/atlantistools/build/vignette.rds                                       |binary
 atlantistools-0.4.2/atlantistools/inst/doc/model-calibration-species.Rmd                   |    2 
 atlantistools-0.4.2/atlantistools/inst/doc/model-calibration-species.pdf                   |binary
 atlantistools-0.4.2/atlantistools/inst/doc/model-calibration.Rmd                           |    2 
 atlantistools-0.4.2/atlantistools/inst/doc/model-calibration.pdf                           |binary
 atlantistools-0.4.2/atlantistools/inst/doc/model-comparison.Rmd                            |    2 
 atlantistools-0.4.2/atlantistools/inst/doc/model-comparison.pdf                            |binary
 atlantistools-0.4.2/atlantistools/inst/doc/model-preprocess.Rmd                            |    2 
 atlantistools-0.4.2/atlantistools/inst/doc/model-preprocess.html                           |    6 
 atlantistools-0.4.2/atlantistools/inst/doc/package-demo.Rmd                                |    2 
 atlantistools-0.4.2/atlantistools/inst/doc/package-demo.html                               |    6 
 atlantistools-0.4.2/atlantistools/man/agg_data.Rd                                          |    2 
 atlantistools-0.4.2/atlantistools/man/calculate_biomass_spatial.Rd                         |    6 
 atlantistools-0.4.2/atlantistools/man/calculate_consumed_biomass.Rd                        |    2 
 atlantistools-0.4.2/atlantistools/man/change_avail.Rd                                      |    2 
 atlantistools-0.4.2/atlantistools/man/change_prm.Rd                                        |    4 
 atlantistools-0.4.2/atlantistools/man/change_prm_cohort.Rd                                 |    2 
 atlantistools-0.4.2/atlantistools/man/combine_groups.Rd                                    |    2 
 atlantistools-0.4.2/atlantistools/man/fishbase_data.Rd                                     |    2 
 atlantistools-0.4.2/atlantistools/man/flip_layers.Rd                                       |   10 
 atlantistools-0.4.2/atlantistools/man/get_colpal.Rd                                        |    2 
 atlantistools-0.4.2/atlantistools/man/get_groups.Rd                                        |   12 
 atlantistools-0.4.2/atlantistools/man/get_growth_fishbase.Rd                               |    4 
 atlantistools-0.4.2/atlantistools/man/get_ids_fishbase.Rd                                  |    2 
 atlantistools-0.4.2/atlantistools/man/load_dietcheck.Rd                                    |    2 
 atlantistools-0.4.2/atlantistools/man/load_init_age.Rd                                     |    4 
 atlantistools-0.4.2/atlantistools/man/load_nc_physics.Rd                                   |    2 
 atlantistools-0.4.2/atlantistools/man/plot_bar.Rd                                          |    2 
 atlantistools-0.4.2/atlantistools/man/plot_consumed_biomass.Rd                             |    6 
 atlantistools-0.4.2/atlantistools/man/plot_diet.Rd                                         |    2 
 atlantistools-0.4.2/atlantistools/man/plot_diet_bec_dev.Rd                                 |    4 
 atlantistools-0.4.2/atlantistools/man/plot_spatial_box.Rd                                  |    8 
 atlantistools-0.4.2/atlantistools/man/plot_spatial_ts.Rd                                   |    6 
 atlantistools-0.4.2/atlantistools/man/plot_species.Rd                                      |    4 
 atlantistools-0.4.2/atlantistools/man/preprocess_txt.Rd                                    |    4 
 atlantistools-0.4.2/atlantistools/man/ref_bio_cons.Rd                                      |    2 
 atlantistools-0.4.2/atlantistools/man/ref_bio_sp.Rd                                        |    6 
 atlantistools-0.4.2/atlantistools/man/ref_dietmatrix.Rd                                    |    2 
 atlantistools-0.4.2/atlantistools/man/ref_dm.Rd                                            |    2 
 atlantistools-0.4.2/atlantistools/man/ref_eat.Rd                                           |    2 
 atlantistools-0.4.2/atlantistools/man/ref_grazing.Rd                                       |    2 
 atlantistools-0.4.2/atlantistools/man/ref_growth.Rd                                        |    2 
 atlantistools-0.4.2/atlantistools/man/ref_n.Rd                                             |    2 
 atlantistools-0.4.2/atlantistools/man/ref_nums.Rd                                          |    2 
 atlantistools-0.4.2/atlantistools/man/ref_physics.Rd                                       |    2 
 atlantistools-0.4.2/atlantistools/man/ref_resn.Rd                                          |    2 
 atlantistools-0.4.2/atlantistools/man/ref_structn.Rd                                       |    2 
 atlantistools-0.4.2/atlantistools/man/ref_vol.Rd                                           |    2 
 atlantistools-0.4.2/atlantistools/man/ref_vol_dz.Rd                                        |    2 
 atlantistools-0.4.2/atlantistools/man/sc_init.Rd                                           |    2 
 atlantistools-0.4.2/atlantistools/man/str_split_twice.Rd                                   |    2 
 atlantistools-0.4.2/atlantistools/man/theme_atlantis.Rd                                    |    4 
 atlantistools-0.4.2/atlantistools/tests/figs/plot-species/line-plot-preprocess-biomass.svg |only
 atlantistools-0.4.2/atlantistools/tests/testthat/helper-fontconfig.R                       |only
 atlantistools-0.4.2/atlantistools/tests/testthat/test-conv-mg-n-bio-t.R                    |    8 
 atlantistools-0.4.2/atlantistools/tests/testthat/test-load-dietmatrix.R                    |    2 
 atlantistools-0.4.2/atlantistools/tests/testthat/test-plot-species.R                       |    6 
 atlantistools-0.4.2/atlantistools/vignettes/model-calibration-species.Rmd                  |    2 
 atlantistools-0.4.2/atlantistools/vignettes/model-calibration.Rmd                          |    2 
 atlantistools-0.4.2/atlantistools/vignettes/model-comparison.Rmd                           |    2 
 atlantistools-0.4.2/atlantistools/vignettes/model-preprocess.Rmd                           |    2 
 atlantistools-0.4.2/atlantistools/vignettes/package-demo.Rmd                               |    2 
 96 files changed, 290 insertions(+), 262 deletions(-)

More information about atlantistools at CRAN
Permanent link

New package moveVis with initial version 0.9
Package: moveVis
Type: Package
Title: Movement Data Visualization
Version: 0.9
Depends: R (>= 2.10)
Date: 2017-04-28
Authors@R: person("Jakob", "Schwalb-Willmann", email = "movevis@schwalb-willmann.de", role = c("aut", "cre"))
Description: Tools to visualize movement data of any kind, e. g by creating path animations from GPS point data.
License: GPL-3
RoxygenNote: 6.0.1
Imports: animation, xts, maptools, ggplot2, grid, rasterVis, raster, sp, geosphere, dismo, utils, grDevices, methods, stats, move, RCurl
NeedsCompilation: no
Packaged: 2017-05-18 10:46:15 UTC; jakob
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>
Repository: CRAN
Date/Publication: 2017-05-18 11:33:45 UTC

More information about moveVis at CRAN
Permanent link

New package meltt with initial version 0.3.0
Package: meltt
Type: Package
Title: Matching Event Data by Location, Time and Type
Version: 0.3.0
Date: 2017-05-18
Author: Karsten Donnay and Eric Dunford
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Description: Framework for merging and disambiguating event data based on spatiotemporal co-occurrence and secondary event characteristics. It can account for intrinsic "fuzziness" in the coding of events, varying event taxonomies and different geo-precision codes.
License: LGPL-3
Depends: R (>= 2.6)
Imports: sp, reticulate, graphics, scales, ggmap, ggplot2, plotGoogleMaps, plyr
SystemRequirements: Python (>= 2.7)
NeedsCompilation: no
Packaged: 2017-05-18 09:50:44 UTC; kdonnay
Repository: CRAN
Date/Publication: 2017-05-18 11:34:56 UTC

More information about meltt at CRAN
Permanent link

Package numOSL updated to version 2.3 with previous version 2.2 dated 2017-04-04

Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation, dose rate determination, growth curve fitting, decay curve decomposition, statistical age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre], Bo Li [aut], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Paul Gilbert [ctb], Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>

Diff between numOSL versions 2.2 dated 2017-04-04 and 2.3 dated 2017-05-18

 DESCRIPTION           |    8 
 MD5                   |   48 +--
 R/analyseBINdata.R    |   55 +++
 R/as_analyseBIN.R     |   43 +-
 R/calED.R             |  310 +++++++++++--------
 R/calSARED.R          |  418 +++++++++++++++-----------
 R/calSGCED.R          |  782 ++++++++++++++++++++++++++++++++++++++------------
 R/fastED.R            |   18 -
 R/fitGrowth.R         |  151 ++++++++-
 R/lsNORM.R            |  218 +++++++++----
 R/pickSARdata.R       |  382 +++++++++++++++---------
 R/scaleSGCN.R         |  393 +++++++++++++++++++++----
 man/analyseBINdata.Rd |   23 +
 man/as_analyseBIN.Rd  |   13 
 man/calED.Rd          |   35 +-
 man/calSARED.Rd       |   21 -
 man/calSGCED.Rd       |   79 +++--
 man/decomp.Rd         |    4 
 man/fitGrowth.Rd      |   50 ++-
 man/loadBINdata.Rd    |    2 
 man/lsNORM.Rd         |    3 
 man/numOSL-package.Rd |    4 
 man/pickBINdata.Rd    |    4 
 man/pickSARdata.Rd    |    4 
 man/scaleSGCN.Rd      |   45 ++
 25 files changed, 2184 insertions(+), 929 deletions(-)

More information about numOSL at CRAN
Permanent link

Package rmdformats updated to version 0.3.3 with previous version 0.3.2 dated 2017-03-21

Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra features such as automatic table of contents, lightboxed figures, dynamic crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>

Diff between rmdformats versions 0.3.2 dated 2017-03-21 and 0.3.3 dated 2017-05-18

 DESCRIPTION                                |   10 ++++----
 MD5                                        |   36 ++++++++++++++---------------
 NEWS                                       |    9 +++++++
 R/html_dependencies.R                      |    2 -
 build/vignette.rds                         |binary
 inst/doc/introduction.html                 |    6 ++--
 inst/templates/html_clean/clean.css        |   15 ++++++++++++
 inst/templates/html_docco/docco.css        |   13 ++++++++++
 inst/templates/material/material.css       |   33 ++++++++++++++++++++++++++
 inst/templates/material/material.js        |    9 +++++--
 inst/templates/readthedown/readthedown.css |   13 ++++++++++
 man/create.doc.Rd                          |    1 
 man/html_clean.Rd                          |    1 
 man/html_docco.Rd                          |    1 
 man/knit_print.pilltabs.Rd                 |    1 
 man/material.Rd                            |    1 
 man/pilltabs.Rd                            |    1 
 man/print.pilltabs.Rd                      |    1 
 man/readthedown.Rd                         |    1 
 19 files changed, 117 insertions(+), 37 deletions(-)

More information about rmdformats at CRAN
Permanent link

Package knitr updated to version 1.16 with previous version 1.15.1 dated 2016-11-22

Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Author: Yihui Xie [aut, cre], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Ben Baumer [ctb], Brian Diggs [ctb], Cassio Pereira [ctb], David Robinson [ctb], Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty), Doug Hemken [ctb], Duncan Murdoch [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Gregoire Detrez [ctb], Hadley Wickham [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Noam Ross [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Romain Francois [ctb], Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between knitr versions 1.15.1 dated 2016-11-22 and 1.16 dated 2017-05-18

 DESCRIPTION                   |   28 +++--
 MD5                           |  213 +++++++++++++++++++++---------------------
 NAMESPACE                     |    3 
 R/block.R                     |   29 ++++-
 R/cache.R                     |    6 -
 R/citation.R                  |    2 
 R/defaults.R                  |    8 -
 R/engine.R                    |   65 +++++++++++-
 R/hooks-extra.R               |    4 
 R/hooks-html.R                |   19 ++-
 R/hooks-latex.R               |    6 -
 R/hooks-md.R                  |   27 ++++-
 R/hooks.R                     |    6 -
 R/output.R                    |   15 +-
 R/package.R                   |    4 
 R/pandoc.R                    |    2 
 R/parser.R                    |   10 +
 R/pattern.R                   |    8 -
 R/plot.R                      |   11 +-
 R/spin.R                      |    2 
 R/table.R                     |   31 ++++--
 R/utils-conversion.R          |   28 +++++
 R/utils-rd2html.R             |    2 
 R/utils-sweave.R              |    2 
 R/utils-upload.R              |    2 
 R/utils-vignettes.R           |    4 
 R/utils.R                     |   50 +++++++++
 build/knitr.pdf               |binary
 build/vignette.rds            |binary
 inst/doc/docco-classic.html   |    6 -
 inst/doc/docco-linear.html    |    5 
 inst/doc/knit_expand.html     |    4 
 inst/doc/knit_print.html      |    8 -
 inst/doc/knitr-intro.html     |   14 +-
 inst/doc/knitr-markdown.html  |    4 
 inst/doc/knitr-refcard.pdf    |binary
 inst/misc/docco-classic.html  |    4 
 inst/misc/docco-template.html |    3 
 man/Sweave2knitr.Rd           |    3 
 man/all_labels.Rd             |    1 
 man/all_patterns.Rd           |    3 
 man/asis_output.Rd            |    1 
 man/chunk_hook.Rd             |    9 -
 man/clean_cache.Rd            |    1 
 man/combine_words.Rd          |    1 
 man/current_input.Rd          |    1 
 man/dep_auto.Rd               |    3 
 man/dep_prev.Rd               |    3 
 man/engine_output.Rd          |    1 
 man/fig_chunk.Rd              |    1 
 man/fig_path.Rd               |    1 
 man/hook_animation.Rd         |    3 
 man/hook_document.Rd          |    3 
 man/hook_plot.Rd              |   10 +
 man/image_uri.Rd              |    7 -
 man/imgur_upload.Rd           |    9 -
 man/include_graphics.Rd       |    1 
 man/include_url.Rd            |    3 
 man/inline_expr.Rd            |    1 
 man/kable.Rd                  |    8 -
 man/knit.Rd                   |   11 +-
 man/knit2html.Rd              |    1 
 man/knit2pandoc.Rd            |only
 man/knit2pdf.Rd               |    7 -
 man/knit2wp.Rd                |    7 -
 man/knit_child.Rd             |    3 
 man/knit_engines.Rd           |    5 
 man/knit_exit.Rd              |    1 
 man/knit_expand.Rd            |    1 
 man/knit_filter.Rd            |    1 
 man/knit_global.Rd            |    1 
 man/knit_hooks.Rd             |    5 
 man/knit_meta.Rd              |    1 
 man/knit_params.Rd            |    1 
 man/knit_params_yaml.Rd       |    1 
 man/knit_patterns.Rd          |    5 
 man/knit_print.Rd             |    1 
 man/knit_rd.Rd                |    1 
 man/knit_theme.Rd             |    7 -
 man/knit_watch.Rd             |    1 
 man/knitr-package.Rd          |   11 +-
 man/load_cache.Rd             |    1 
 man/opts_chunk.Rd             |    5 
 man/opts_hooks.Rd             |    3 
 man/opts_knit.Rd              |    5 
 man/opts_template.Rd          |    1 
 man/output_hooks.Rd           |   12 +-
 man/pandoc.Rd                 |    3 
 man/pat_fun.Rd                |    7 -
 man/plot_crop.Rd              |    1 
 man/rand_seed.Rd              |    3 
 man/raw_output.Rd             |    3 
 man/read_chunk.Rd             |    7 -
 man/read_rforge.Rd            |    1 
 man/rocco.Rd                  |    7 -
 man/rst2pdf.Rd                |    7 -
 man/set_alias.Rd              |    1 
 man/set_header.Rd             |    1 
 man/set_parent.Rd             |    3 
 man/spin.Rd                   |   11 +-
 man/spin_child.Rd             |    1 
 man/stitch.Rd                 |    1 
 man/vignette_engines.Rd       |    3 
 man/wrap_rmd.Rd               |    1 
 man/write_bib.Rd              |    1 
 tests/testit/test-hooks.R     |    3 
 tests/testit/test-plot.R      |    3 
 tests/testit/test-utils.R     |    7 +
 108 files changed, 582 insertions(+), 301 deletions(-)

More information about knitr at CRAN
Permanent link

Package huxtable updated to version 0.3.0 with previous version 0.2.2 dated 2017-04-27

Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar functionality to 'xtable', but does more, with a simpler interface.
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

Diff between huxtable versions 0.2.2 dated 2017-04-27 and 0.3.0 dated 2017-05-18

 DESCRIPTION                      |    9 -
 MD5                              |   56 +++----
 NAMESPACE                        |    2 
 NEWS.md                          |    9 +
 R/HTML.R                         |    5 
 R/LaTeX.R                        |    6 
 R/attributes.R                   |   69 ++++++++
 R/dplyr.R                        |    2 
 R/huxreg.R                       |    4 
 R/huxtable.R                     |    4 
 R/screen.R                       |    2 
 README.md                        |    6 
 inst/doc/design-principles.R     |    2 
 inst/doc/design-principles.Rmd   |    2 
 inst/doc/design-principles.html  |   11 -
 inst/doc/huxreg.html             |  304 +++++++++++++++++++--------------------
 inst/doc/huxtable.R              |   11 +
 inst/doc/huxtable.Rmd            |   14 +
 inst/doc/huxtable.html           |  245 ++++++++++++++++---------------
 man/caption_pos.Rd               |    8 -
 man/dplyr-verbs.Rd               |    2 
 man/get_default_properties.Rd    |only
 man/huxreg.Rd                    |    8 -
 man/left_border.Rd               |    4 
 man/position.Rd                  |    4 
 man/set_default_properties.Rd    |only
 tests/testthat/test-attributes.R |   11 +
 tests/testthat/test-huxreg.R     |   14 +
 vignettes/design-principles.Rmd  |    2 
 vignettes/huxtable.Rmd           |   14 +
 30 files changed, 489 insertions(+), 341 deletions(-)

More information about huxtable at CRAN
Permanent link

Package GSED updated to version 1.5 with previous version 1.4 dated 2017-05-04

Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between GSED versions 1.4 dated 2017-05-04 and 1.5 dated 2017-05-18

 DESCRIPTION         |    8 ++++----
 MD5                 |    6 +++---
 R/GSED.R            |    8 +++++---
 man/GSED-package.Rd |    4 ++--
 4 files changed, 14 insertions(+), 12 deletions(-)

More information about GSED at CRAN
Permanent link

New package GeneralizedUmatrix with initial version 0.9.4
Package: GeneralizedUmatrix
Type: Package
Title: Credible Visualization for Two-Dimensional Projections of Data
Version: 0.9.4
Date: 2017-05-17
Author: Michael Thrun, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Description: Projections from a high-dimensional data space onto a two-dimensional plane are used to detect structures, such as clusters, in multivariate data. The generalized Umatrix is able to visualize errors of these two-dimensional scatter plots by using a 3D topographic map.
License: GPL-3
Imports: Rcpp
Suggests: matrixStats, rgl, ggplot2, grid, mgcv
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.0)
NeedsCompilation: yes
LazyLoad: yes
LazyData: TRUE
URL: https://www.uni-marburg.de/fb12/datenbionik/software-en
Encoding: UTF-8
Packaged: 2017-05-18 09:09:12 UTC; MCT
Repository: CRAN
Date/Publication: 2017-05-18 09:23:46 UTC

More information about GeneralizedUmatrix at CRAN
Permanent link

New package FHDI with initial version 1.0
Package: FHDI
Version: 1.0
Date: 2017-05-13
Title: Fractional Hot Deck and Fully Efficient Fractional Imputation
Authors@R: c(person("Jongho","Im", role="aut",email="jonghoim@iastate.edu"), person("Inho","Cho", role=c("aut","cre"), email="icho@iastate.edu"), person("Jaekwang","Kim", role="aut", email="jkim@iastate.edu"))
Author: Jongho Im [aut], Inho Cho [aut, cre], Jaekwang Kim [aut]
Maintainer: Inho Cho <icho@iastate.edu>
Description: Impute general multivariate missing data with the fractional hot deck imputation.
License: GPL (>= 2)
URL: https://www.r-project.org, https://sites.google.com/view/jaekwangkim/software
BugReports: <mailto:icho@iastate.edu>
NeedsCompilation: yes
Packaged: 2017-05-17 21:20:10 UTC; ihcho_000
Repository: CRAN
Date/Publication: 2017-05-18 09:50:00 UTC

More information about FHDI at CRAN
Permanent link

New package dwapi with initial version 0.1.0
Package: dwapi
Title: A Client for Data.world's REST API
Version: 0.1.0
Authors@R: c( person("Rafael", "Pereira", email = "rafael.pereira@data.world", role = c("aut", "cre")), person("Triet", "Le", email = "triet.le@data.world", role = c("aut")), person("Bryon", "Jacob", email = "bryon.jacob@data.world", role = c("aut")))
Description: A set of wrapper functions for data.world's REST API endpoints.
Depends: R (>= 3.3.0)
Imports: httr, readr, rjson, xml2
Suggests: knitr, rmarkdown, testthat
License: Apache License 2.0
Encoding: UTF-8
LazyData: true
URL: https://github.com/datadotworld/dwapi-r
BugReports: https://github.com/datadotworld/dwapi-r/issues
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-05-12 14:26:23 UTC; rafael
Author: Rafael Pereira [aut, cre], Triet Le [aut], Bryon Jacob [aut]
Maintainer: Rafael Pereira <rafael.pereira@data.world>
Repository: CRAN
Date/Publication: 2017-05-18 09:30:21 UTC

More information about dwapi at CRAN
Permanent link

Package ROI.plugin.glpk updated to version 0.2-5 with previous version 0.2-1 dated 2016-06-19

Title: ROI Plug-in GLPK
Description: Enhances the R Optimization Infrastructure ('ROI') package by registering the free 'GLPK' solver. It allows for solving mixed integer linear programming (MILP) problems as well as all variants/combinations of LP, IP.
Author: Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>

Diff between ROI.plugin.glpk versions 0.2-1 dated 2016-06-19 and 0.2-5 dated 2017-05-18

 DESCRIPTION       |   14 +++----
 MD5               |   11 +++---
 NAMESPACE         |    4 +-
 R/plugin.R        |   95 ++++++++++++++++++++++++++++++++++++++++++++----------
 R/zzz.R           |   19 +++++++---
 man               |only
 tests/test_glpk.R |    2 +
 7 files changed, 109 insertions(+), 36 deletions(-)

More information about ROI.plugin.glpk at CRAN
Permanent link

Package Rglpk updated to version 0.6-3 with previous version 0.6-2 dated 2016-06-14

Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programming Kit. 'GLPK' is open source software for solving large-scale linear programming (LP), mixed integer linear programming ('MILP') and other related problems.
Author: Stefan Theussl [aut, cre], Kurt Hornik [aut], Christian Buchta [ctb], Florian Schwendinger [ctb], Heinrich Schuchardt [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>

Diff between Rglpk versions 0.6-2 dated 2016-06-14 and 0.6-3 dated 2017-05-18

 DESCRIPTION           |   13 ++++++-----
 MD5                   |   22 ++++++++++--------
 NAMESPACE             |    2 -
 R/Rglpk_solve.R       |   58 ++++++++++++++++++++++++++++++++++++--------------
 R/Rglpk_write_file.R  |only
 R/bounds.R            |    2 -
 R/filereader.R        |    6 ++---
 R/zzz.R               |    4 +--
 inst/CHANGELOG        |    6 +++++
 man/Rglpk_solve.Rd    |   11 ++++++---
 src/Rglpk_read_file.c |   26 +++++++++++++++++++---
 src/Rglpk_solve.c     |   20 ++++++++++++++++-
 src/init.c            |only
 13 files changed, 123 insertions(+), 47 deletions(-)

More information about Rglpk at CRAN
Permanent link

Package flexrsurv updated to version 1.4.1 with previous version 1.3.3 dated 2016-04-26

Title: Flexible Relative Survival Analysis
Description: Package for parametric relative survival analyses. It allows to model non-linear and non-proportional effects using splines (B-spline and truncated power basis). It also includes both non proportional and non linear effects of Remontet, L. et al. (2007) <DOI:10.1002/sim.2656> and Mahboubi, A. et al. (2011) <DOI:10.1002/sim.4208>.
Author: Isabelle Clerc-Urms [aut], Michel Grzebyk [aut, cre], Guy Hdelin [ctb], CENSUR working survival group [ctb]
Maintainer: Michel Grzebyk <michel.grzebyk@inrs.fr>

Diff between flexrsurv versions 1.3.3 dated 2016-04-26 and 1.4.1 dated 2017-05-18

 DESCRIPTION                               |   25 -
 MD5                                       |  153 ++++++----
 NAMESPACE                                 |    6 
 NEWS                                      |only
 R/AllClass.R                              |   20 +
 R/NLL.NPH.func.R                          |    6 
 R/ReadDesignFlexrsurv.R                   |    4 
 R/SplineParam.R                           |  433 +++++++++++++++++++++++++++---
 R/computeCumulativeHazard.R               |  410 +++++++++++++++++++++++++++-
 R/computeLinearPredictor.R                |   50 ++-
 R/computeStdErrorCumulativeHazard.R       |only
 R/computeStdErrorLinearPredictor.R        |  139 +++------
 R/converged.R                             |    2 
 R/cutT.R                                  |    4 
 R/default_bands.R                         |    3 
 R/flexrsurv.glm.fit.R                     |    2 
 R/flexrsurv.glmiterative.fit.R            |    8 
 R/flexrsurv.ll.R                          |    1 
 R/flexrsurv.ll.fit.R                      |   57 ++-
 R/flexrsurv.ll.fromto.fit.R               |   94 +++---
 R/get_list_var.R                          |    6 
 R/gr_cumhaz_flexrsurv_GA0B0AB.R           |only
 R/gr_cumhaz_flexrsurv_GA0B0AB_bh.R        |only
 R/gr_cumhaz_flexrsurv_fromto_GA0B0AB.R    |only
 R/gr_cumhaz_flexrsurv_fromto_GA0B0AB_bh.R |only
 R/gr_linkrate_flexrsurv_GA0B0AB.R         |only
 R/gr_linkrate_flexrsurv_fromto_GA0B0AB.R  |only
 R/gr_ll_flexrsurv_GA0B0AB.R               |   50 +--
 R/gr_ll_flexrsurv_GA0B0AB_bh.R            |   91 +++---
 R/gr_ll_flexrsurv_fromto_GA0B0AB.R        |   50 ++-
 R/gr_ll_flexrsurv_fromto_GA0B0AB_bh.R     |   57 ++-
 R/intTDfromto_base.R                      |   19 -
 R/ll_flexrsurv_GA0B0AB.R                  |   41 +-
 R/ll_flexrsurv_GA0B0AB_bh.R               |   40 +-
 R/ll_flexrsurv_alpha0alpha.R              |   32 +-
 R/ll_flexrsurv_alpha0alpha_bh.R           |   38 +-
 R/ll_flexrsurv_beta0beta.R                |   35 +-
 R/ll_flexrsurv_beta0beta_bh.R             |   41 +-
 R/ll_flexrsurv_fromto_GA0B0AB.R           |   24 +
 R/ll_flexrsurv_fromto_GA0B0AB_bh.R        |   33 +-
 R/ll_flexrsurv_fromto_alpha0alpha.R       |   32 +-
 R/ll_flexrsurv_fromto_alpha0alpha_bh.R    |   32 +-
 R/ll_flexrsurv_fromto_beta0beta.R         |   36 +-
 R/ll_flexrsurv_fromto_beta0beta_bh.R      |   36 +-
 R/ll_flexrsurv_fromto_gamma0.R            |   36 +-
 R/ll_flexrsurv_fromto_gamma0_bh.R         |   40 +-
 R/ll_flexrsurv_gamma0.R                   |   28 +
 R/ll_flexrsurv_gamma0_bh.R                |   41 +-
 R/make.formulastep.formula.R              |    8 
 R/make.formulastep.terms.R                |   10 
 R/make.glm.formula.R                      |    4 
 R/nl.td.func.R                            |   20 -
 R/opg_flexrsurv_G0A0B0AB.R                |   51 ++-
 R/opg_flexrsurv_G0A0B0AB_bh.R             |   57 ++-
 R/opg_flexrsurv_fromto_G0A0B0AB.R         |   45 ++-
 R/opg_flexrsurv_fromto_G0A0B0AB_bh.R      |   62 ++--
 R/predict.flexrsurv.R                     |only
 R/predictCumulativeHazard.flexrsurv.R     |only
 R/predictHazard.flexrsurv.R               |only
 R/rateTD.R                                |   44 ++-
 R/rateTD_bh.R                             |   41 +-
 R/zzz.R                                   |    6 
 build/partial.rdb                         |binary
 inst                                      |only
 man/Flexrsurv.Rd                          |   43 ++
 man/Flexrsurvpackage.Rd                   |   21 -
 man/NLLbetaNPHalpha.Rd                    |    4 
 man/NPH.Rd                                |    4 
 man/NPHNLL.Rd                             |    4 
 man/flexrsurv-internal.Rd                 |   11 
 man/predict.flexrsurv.Rd                  |only
 man/summary.flexrsurv.Rd                  |    8 
 src/EvaluateCLLinExSplineBasis.c          |only
 src/EvaluateCLSplineBasis.c               |   77 ++++-
 src/EvaluateESplineBasis.c                |only
 src/EvaluateLinExSplineBasis.c            |only
 src/EvaluateSplineBasis.c                 |  146 ++++------
 src/EvaluateTPSplineBasis.c               |  106 -------
 src/GradientWeightedCumulativeExposure.c  |only
 src/PredictESplineBasis.c                 |only
 src/PredictLinExSplineBasis.c             |only
 src/PredictSplineBasis.c                  |  192 +++++++------
 src/PredictTPSplineBasis.c                |   41 --
 src/SplineParam.h                         |only
 src/WeightedCumulativeExposure.c          |  398 +++++++++++++++++----------
 src/flexrsurv.h                           |   47 ++-
 src/init.c                                |only
 src/slowPredictLinExSplineBasis.c         |only
 src/slowPredictSplineBasis.c              |only
 89 files changed, 2457 insertions(+), 1248 deletions(-)

More information about flexrsurv at CRAN
Permanent link

Package complexplus updated to version 2.1 with previous version 2.0 dated 2016-11-23

Title: Functions of Complex or Real Variable
Description: Extension of several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.
Author: Albert Dorador and Uffe Høgsbro Thygesen
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>

Diff between complexplus versions 2.0 dated 2016-11-23 and 2.1 dated 2017-05-18

 complexplus-2.0/complexplus/R/matlog.R      |only
 complexplus-2.1/complexplus/DESCRIPTION     |   12 ++++++------
 complexplus-2.1/complexplus/MD5             |   20 ++++++++++----------
 complexplus-2.1/complexplus/R/DetV2.R       |    2 +-
 complexplus-2.1/complexplus/R/Imzap.R       |    4 ++--
 complexplus-2.1/complexplus/R/matexp.R      |    2 +-
 complexplus-2.1/complexplus/R/matlogV2.R    |only
 complexplus-2.1/complexplus/man/Det.Rd      |    1 -
 complexplus-2.1/complexplus/man/Imzap.Rd    |    3 +--
 complexplus-2.1/complexplus/man/matclass.Rd |    1 -
 complexplus-2.1/complexplus/man/matexp.Rd   |    7 +++----
 complexplus-2.1/complexplus/man/matlog.Rd   |    9 ++++-----
 12 files changed, 28 insertions(+), 33 deletions(-)

More information about complexplus at CRAN
Permanent link

New package AR with initial version 1.0
Package: AR
Type: Package
Title: Another Look at the Acceptance-Rejection Method
Version: 1.0
Date: 2017-05-16
Author: Abbas Parchami (Department of Statistics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Kerman, Iran)
Maintainer: Abbas Parchami <parchami@uk.ac.ir>
Description: In mathematics, 'rejection sampling' is a basic technique used to generate observations from a distribution. It is also commonly called 'the Acceptance-Rejection method' or 'Accept-Reject algorithm' and is a type of Monte Carlo method. 'Acceptance-Rejection method' is based on the observation that to sample a random variable one can perform a uniformly random sampling of the 2D cartesian graph, and keep the samples in the region under the graph of its density function. Package 'AR' is able to generate/simulate random data from a probability density function by Acceptance-Rejection method. Moreover, this package is a useful teaching resource for graphical presentation of Acceptance-Rejection method. From the practical point of view, the user needs to calculate a constant in Acceptance-Rejection method, which package 'AR' is able to compute this constant by optimization tools. Several numerical examples are provided to illustrate the graphical presentation for the Acceptance-Rejection Method.
License: LGPL (>= 3)
Imports: DISTRIB
NeedsCompilation: no
Packaged: 2017-05-18 08:08:43 UTC; parchami
Repository: CRAN
Date/Publication: 2017-05-18 08:28:44 UTC

More information about AR at CRAN
Permanent link

Package metaSEM updated to version 0.9.14 with previous version 0.9.12 dated 2017-01-23

Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a structural equation modeling (SEM) approach via the 'OpenMx' package. It also implements the two-stage SEM approach to conduct meta-analytic structural equation modeling on correlation and covariance matrices.
Author: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Maintainer: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>

Diff between metaSEM versions 0.9.12 dated 2017-01-23 and 0.9.14 dated 2017-05-18

 DESCRIPTION            |   12 -
 MD5                    |   95 ++++-----
 NAMESPACE              |    6 
 NEWS                   |    9 
 R/genCor.R             |only
 R/impliedR.R           |   80 +++++++
 R/meta.R               |    3 
 R/smd.R                |only
 R/summary.R            |    3 
 R/tssem.R              |    6 
 R/uniR.R               |    8 
 build/vignette.rds     |binary
 data/Aloe14.rda        |binary
 data/BCG.rda           |binary
 data/Becker09.rda      |binary
 data/Becker83.rda      |binary
 data/Becker92.rda      |binary
 data/Becker94.rda      |binary
 data/Berkey98.rda      |binary
 data/Boer16.rda        |binary
 data/Bornmann07.rda    |binary
 data/Cheung00.rda      |binary
 data/Cheung09.rda      |binary
 data/Cooke16.rda       |binary
 data/Cooper03.rda      |binary
 data/Digman97.rda      |binary
 data/HedgesOlkin85.rda |binary
 data/Hox02.rda         |binary
 data/Hunter83.rda      |binary
 data/Jaramillo05.rda   |binary
 data/Mak09.rda         |binary
 data/Nohe15A1.rda      |binary
 data/Nohe15A2.rda      |binary
 data/Norton13.rda      |binary
 data/Roorda11.rda      |binary
 data/issp05.rda        |binary
 data/issp89.rda        |binary
 data/wvs94a.rda        |binary
 data/wvs94b.rda        |binary
 inst/CITATION          |    4 
 inst/doc/Examples.html |  491 +++++++++++++++++++++++++------------------------
 inst/doc/metaSEM.pdf   |binary
 man/Becker09.Rd        |    4 
 man/impliedR.Rd        |   17 +
 man/metaSEM-package.Rd |    4 
 man/rCorSam.Rd         |only
 man/smdMES.Rd          |only
 man/smdMTS.Rd          |only
 man/summary.Rd         |   14 -
 man/uniR1.Rd           |    4 
 man/uniR2.Rd           |    2 
 51 files changed, 456 insertions(+), 306 deletions(-)

More information about metaSEM at CRAN
Permanent link

Package emdi updated to version 1.1.0 with previous version 1.0.0 dated 2016-11-08

Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation and the model-based approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel.
Author: Ann-Kristin Kreutzmann [aut], Soeren Pannier [aut, cre], Natalia Rojas-Perilla [aut], Timo Schmid [aut], Matthias Templ [aut], Nikos Tzavidis [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>

Diff between emdi versions 1.0.0 dated 2016-11-08 and 1.1.0 dated 2017-05-18

 emdi-1.0.0/emdi/R/framework.R                           |only
 emdi-1.0.0/emdi/R/indicator_functions.R                 |only
 emdi-1.0.0/emdi/tests/testthat/ebp_test.xlsx            |only
 emdi-1.0.0/emdi/tests/testthat/excel_output_all.xlsx    |only
 emdi-1.1.0/emdi/DESCRIPTION                             |   37 +
 emdi-1.1.0/emdi/MD5                                     |  119 +++--
 emdi-1.1.0/emdi/NAMESPACE                               |   13 
 emdi-1.1.0/emdi/NEWS.md                                 |only
 emdi-1.1.0/emdi/R/check_direct_arguments.R              |only
 emdi-1.1.0/emdi/R/check_ebp_arguments.R                 |   15 
 emdi-1.1.0/emdi/R/direct_estimation.R                   |only
 emdi-1.1.0/emdi/R/direct_variance.R                     |only
 emdi-1.1.0/emdi/R/ebp.R                                 |   99 ++--
 emdi-1.1.0/emdi/R/emdi.R                                |   17 
 emdi-1.1.0/emdi/R/emdiObject.R                          |   43 +
 emdi-1.1.0/emdi/R/estimators.emdi.R                     |  130 +++++
 emdi-1.1.0/emdi/R/eusilcA_pop.R                         |    8 
 emdi-1.1.0/emdi/R/eusilcA_smp.R                         |    9 
 emdi-1.1.0/emdi/R/framework_direct.R                    |only
 emdi-1.1.0/emdi/R/framework_ebp.R                       |only
 emdi-1.1.0/emdi/R/load_shape.R                          |only
 emdi-1.1.0/emdi/R/map_plot.R                            |  162 ++++---
 emdi-1.1.0/emdi/R/mse_emdi.R                            |   46 --
 emdi-1.1.0/emdi/R/mse_estimation.R                      |  245 +++++++---
 emdi-1.1.0/emdi/R/optimal_parameter.R                   |   68 ---
 emdi-1.1.0/emdi/R/plot.emdi.R                           |   47 +-
 emdi-1.1.0/emdi/R/point_estimation.R                    |   81 ---
 emdi-1.1.0/emdi/R/point_estimation_direct.R             |only
 emdi-1.1.0/emdi/R/print.emdi.R                          |  102 ++--
 emdi-1.1.0/emdi/R/summary.emdi.R                        |  358 ++++++++--------
 emdi-1.1.0/emdi/R/transformation_functions.R            |    2 
 emdi-1.1.0/emdi/R/write.excel.emdi.R                    |  130 +++++
 emdi-1.1.0/emdi/build                                   |only
 emdi-1.1.0/emdi/data/eusilcA_pop.RData                  |only
 emdi-1.1.0/emdi/data/eusilcA_pop.rda                    |binary
 emdi-1.1.0/emdi/data/eusilcA_smp.RData                  |only
 emdi-1.1.0/emdi/data/eusilcA_smp.rda                    |binary
 emdi-1.1.0/emdi/inst/doc                                |only
 emdi-1.1.0/emdi/man/as.data.frame.estimators.emdi.Rd    |only
 emdi-1.1.0/emdi/man/as.matrix.estimators.emdi.Rd        |only
 emdi-1.1.0/emdi/man/data_transformation.Rd              |    1 
 emdi-1.1.0/emdi/man/direct.Rd                           |only
 emdi-1.1.0/emdi/man/ebp.Rd                              |   73 +--
 emdi-1.1.0/emdi/man/emdi.Rd                             |   18 
 emdi-1.1.0/emdi/man/emdiObject.Rd                       |   44 +
 emdi-1.1.0/emdi/man/estimators.Rd                       |    1 
 emdi-1.1.0/emdi/man/estimators.emdi.Rd                  |   24 -
 emdi-1.1.0/emdi/man/eusilcA_pop.Rd                      |    9 
 emdi-1.1.0/emdi/man/eusilcA_smp.Rd                      |   10 
 emdi-1.1.0/emdi/man/head.estimators.emdi.Rd             |   28 +
 emdi-1.1.0/emdi/man/load_shapeaustria.Rd                |only
 emdi-1.1.0/emdi/man/map_plot.Rd                         |   55 +-
 emdi-1.1.0/emdi/man/plot.emdi.Rd                        |   42 -
 emdi-1.1.0/emdi/man/print.emdi.Rd                       |    5 
 emdi-1.1.0/emdi/man/print.estimators.emdi.Rd            |    1 
 emdi-1.1.0/emdi/man/print.summary.emdi.Rd               |    1 
 emdi-1.1.0/emdi/man/subset.estimators.emdi.Rd           |only
 emdi-1.1.0/emdi/man/summary.emdi.Rd                     |   73 +--
 emdi-1.1.0/emdi/man/tail.estimators.emdi.Rd             |   28 +
 emdi-1.1.0/emdi/man/write.excel.Rd                      |   50 +-
 emdi-1.1.0/emdi/tests/testthat/arpr_all.csv             |only
 emdi-1.1.0/emdi/tests/testthat/arpr_all_cali.csv        |only
 emdi-1.1.0/emdi/tests/testthat/arpr_all_naive.csv       |only
 emdi-1.1.0/emdi/tests/testthat/eusilc.RData             |only
 emdi-1.1.0/emdi/tests/testthat/eusilc.csv               |only
 emdi-1.1.0/emdi/tests/testthat/gini_all.csv             |only
 emdi-1.1.0/emdi/tests/testthat/gini_all_cali.csv        |only
 emdi-1.1.0/emdi/tests/testthat/gini_all_naive.csv       |only
 emdi-1.1.0/emdi/tests/testthat/qsr_all.csv              |only
 emdi-1.1.0/emdi/tests/testthat/qsr_all_cali.csv         |only
 emdi-1.1.0/emdi/tests/testthat/qsr_all_naive.csv        |only
 emdi-1.1.0/emdi/tests/testthat/test_direct_estimation.R |only
 emdi-1.1.0/emdi/tests/testthat/test_ebp.R               |    8 
 emdi-1.1.0/emdi/tests/testthat/test_mse_estimation.R    |    3 
 emdi-1.1.0/emdi/tests/testthat/test_optimal_par.R       |    2 
 emdi-1.1.0/emdi/tests/testthat/test_point_estimation.R  |    2 
 emdi-1.1.0/emdi/vignettes                               |only
 77 files changed, 1304 insertions(+), 905 deletions(-)

More information about emdi at CRAN
Permanent link

Package vcfR updated to version 1.5.0 with previous version 1.4.0 dated 2017-01-07

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

Diff between vcfR versions 1.4.0 dated 2017-01-07 and 1.5.0 dated 2017-05-18

 vcfR-1.4.0/vcfR/tests/testthat/test_windowing.R     |only
 vcfR-1.5.0/vcfR/DESCRIPTION                         |   44 ++---
 vcfR-1.5.0/vcfR/MD5                                 |  161 ++++++++++----------
 vcfR-1.5.0/vcfR/NAMESPACE                           |    4 
 vcfR-1.5.0/vcfR/R/RcppExports.R                     |    4 
 vcfR-1.5.0/vcfR/R/chromR-method.R                   |   22 ++
 vcfR-1.5.0/vcfR/R/chromR_functions.R                |   28 ++-
 vcfR-1.5.0/vcfR/R/chromo_plot.R                     |   22 ++
 vcfR-1.5.0/vcfR/R/create_chromR.R                   |   25 +++
 vcfR-1.5.0/vcfR/R/genetic_diff.R                    |only
 vcfR-1.5.0/vcfR/R/queryMETA.R                       |    5 
 vcfR-1.5.0/vcfR/R/vcfR-method.R                     |  137 ++++++++---------
 vcfR-1.5.0/vcfR/R/vcfR.R                            |    7 
 vcfR-1.5.0/vcfR/R/vcfR2DNAbin.R                     |    9 -
 vcfR-1.5.0/vcfR/R/vcfR_test.R                       |    2 
 vcfR-1.5.0/vcfR/README.md                           |   15 +
 vcfR-1.5.0/vcfR/build/vignette.rds                  |binary
 vcfR-1.5.0/vcfR/inst/CITATION                       |    7 
 vcfR-1.5.0/vcfR/inst/doc/converting_data.html       |   31 ++-
 vcfR-1.5.0/vcfR/inst/doc/filtering_data.html        |   20 +-
 vcfR-1.5.0/vcfR/inst/doc/intro_to_vcfR.html         |   20 +-
 vcfR-1.5.0/vcfR/inst/doc/ranking_data.html          |   18 +-
 vcfR-1.5.0/vcfR/inst/doc/sequence_coverage.html     |   11 -
 vcfR-1.5.0/vcfR/inst/doc/vcf_data.html              |   61 +++----
 vcfR-1.5.0/vcfR/inst/doc/visualization_1.html       |   20 +-
 vcfR-1.5.0/vcfR/inst/doc/visualization_2.html       |    8 
 vcfR-1.5.0/vcfR/inst/doc/workflow.html              |    8 
 vcfR-1.5.0/vcfR/man/AD_frequency.Rd                 |    1 
 vcfR-1.5.0/vcfR/man/INFO2df.Rd                      |    1 
 vcfR-1.5.0/vcfR/man/addID.Rd                        |    1 
 vcfR-1.5.0/vcfR/man/chromR-class.Rd                 |    1 
 vcfR-1.5.0/vcfR/man/chromR-method.Rd                |   13 -
 vcfR-1.5.0/vcfR/man/chromR_functions.Rd             |    6 
 vcfR-1.5.0/vcfR/man/chrom_to_vcfR.Rd                |    1 
 vcfR-1.5.0/vcfR/man/chromo_plot.Rd                  |    7 
 vcfR-1.5.0/vcfR/man/create_chromR.Rd                |    7 
 vcfR-1.5.0/vcfR/man/drplot.Rd                       |    3 
 vcfR-1.5.0/vcfR/man/extract_gt.Rd                   |    1 
 vcfR-1.5.0/vcfR/man/fasta_output.Rd                 |    1 
 vcfR-1.5.0/vcfR/man/freq_peak.Rd                    |    1 
 vcfR-1.5.0/vcfR/man/genetic_diff.Rd                 |only
 vcfR-1.5.0/vcfR/man/genotype_matrix.Rd              |    1 
 vcfR-1.5.0/vcfR/man/getFIX.Rd                       |   31 +--
 vcfR-1.5.0/vcfR/man/heatmap_bp.Rd                   |    1 
 vcfR-1.5.0/vcfR/man/io_vcfR.Rd                      |    1 
 vcfR-1.5.0/vcfR/man/is_het.Rd                       |    3 
 vcfR-1.5.0/vcfR/man/maf.Rd                          |    1 
 vcfR-1.5.0/vcfR/man/masplit.Rd                      |    1 
 vcfR-1.5.0/vcfR/man/ordisample.Rd                   |    1 
 vcfR-1.5.0/vcfR/man/pipe.Rd                         |    1 
 vcfR-1.5.0/vcfR/man/proc_chromR.Rd                  |    5 
 vcfR-1.5.0/vcfR/man/queryMETA.Rd                    |    1 
 vcfR-1.5.0/vcfR/man/query_gt.Rd                     |    5 
 vcfR-1.5.0/vcfR/man/ranking.Rd                      |    1 
 vcfR-1.5.0/vcfR/man/summary_tables.Rd               |    1 
 vcfR-1.5.0/vcfR/man/vcfR-method.Rd                  |   50 +++---
 vcfR-1.5.0/vcfR/man/vcfR.Rd                         |    5 
 vcfR-1.5.0/vcfR/man/vcfR2DNAbin.Rd                  |    3 
 vcfR-1.5.0/vcfR/man/vcfR_conversion.Rd              |    3 
 vcfR-1.5.0/vcfR/man/vcfR_example.Rd                 |    3 
 vcfR-1.5.0/vcfR/man/vcfR_test.Rd                    |    3 
 vcfR-1.5.0/vcfR/man/vcfR_to_tidy_conversion.Rd      |   11 -
 vcfR-1.5.0/vcfR/man/windowing.Rd                    |    5 
 vcfR-1.5.0/vcfR/src/Makevars                        |    8 
 vcfR-1.5.0/vcfR/src/RcppExports.cpp                 |    9 +
 vcfR-1.5.0/vcfR/src/extractGT2NM.cpp                |   25 ++-
 vcfR-1.5.0/vcfR/src/gt_to_popsum.cpp                |   25 ++-
 vcfR-1.5.0/vcfR/src/init.c                          |only
 vcfR-1.5.0/vcfR/src/is_het.cpp                      |    1 
 vcfR-1.5.0/vcfR/src/vcfRCommon.cpp                  |   10 +
 vcfR-1.5.0/vcfR/tests/testthat.R                    |   37 +++-
 vcfR-1.5.0/vcfR/tests/testthat/test_1_vcf.R         |    2 
 vcfR-1.5.0/vcfR/tests/testthat/test_2_chromR.R      |   22 ++
 vcfR-1.5.0/vcfR/tests/testthat/test_3_extract_gt.R  |   34 ++++
 vcfR-1.5.0/vcfR/tests/testthat/test_chromR_method.R |   14 +
 vcfR-1.5.0/vcfR/tests/testthat/test_chromo_plot.R   |   34 +++-
 vcfR-1.5.0/vcfR/tests/testthat/test_genetic_diff.R  |only
 vcfR-1.5.0/vcfR/tests/testthat/test_get.R           |    4 
 vcfR-1.5.0/vcfR/tests/testthat/test_io.R            |   17 --
 vcfR-1.5.0/vcfR/tests/testthat/test_is_het.R        |    3 
 vcfR-1.5.0/vcfR/tests/testthat/test_proc_chromR.R   |only
 vcfR-1.5.0/vcfR/tests/testthat/test_rank_variants.R |   25 +--
 vcfR-1.5.0/vcfR/tests/testthat/test_var_window.R    |   25 +--
 vcfR-1.5.0/vcfR/tests/testthat/test_vcfR_methods.R  |   31 +++
 vcfR-1.5.0/vcfR/tools                               |only
 85 files changed, 735 insertions(+), 461 deletions(-)

More information about vcfR at CRAN
Permanent link

Package shinydashboard updated to version 0.6.0 with previous version 0.5.3 dated 2016-09-20

Title: Create Dashboards with 'Shiny'
Description: Create dashboards with 'Shiny'. This package provides a theme on top of 'Shiny', making it easy to create attractive dashboards.
Author: Winston Chang [aut, cre], Barbara Borges Ribeiro [aut], RStudio [cph], Almasaeed Studio [ctb, cph] (AdminLTE theme for Bootstrap), Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang <winston@rstudio.com>

Diff between shinydashboard versions 0.5.3 dated 2016-09-20 and 0.6.0 dated 2017-05-18

 shinydashboard-0.5.3/shinydashboard/inst/AdminLTE/README-shiny-mods.md |only
 shinydashboard-0.6.0/shinydashboard/DESCRIPTION                        |   10 
 shinydashboard-0.6.0/shinydashboard/LICENSE                            |    8 
 shinydashboard-0.6.0/shinydashboard/MD5                                |   99 +-
 shinydashboard-0.6.0/shinydashboard/NEWS.md                            |   51 +
 shinydashboard-0.6.0/shinydashboard/R/dashboardHeader.R                |   15 
 shinydashboard-0.6.0/shinydashboard/R/dashboardPage.R                  |   12 
 shinydashboard-0.6.0/shinydashboard/R/dashboardSidebar.R               |   65 +
 shinydashboard-0.6.0/shinydashboard/R/deps.R                           |    4 
 shinydashboard-0.6.0/shinydashboard/R/utils.R                          |   21 
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/AdminLTE.css         |   73 +
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/AdminLTE.min.css     |    4 
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/_all-skins.css       |  103 --
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/_all-skins.min.css   |    2 
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.js               |  165 ++--
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.js.map           |only
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.min.js           |    2 
 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.min.js.map       |    2 
 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.css            |   28 
 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.js             |  400 ++++++----
 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.js.map         |only
 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.min.js         |only
 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.min.js.map     |only
 shinydashboard-0.6.0/shinydashboard/man/box.Rd                         |    1 
 shinydashboard-0.6.0/shinydashboard/man/dashboardBody.Rd               |    1 
 shinydashboard-0.6.0/shinydashboard/man/dashboardHeader.Rd             |    1 
 shinydashboard-0.6.0/shinydashboard/man/dashboardPage.Rd               |    1 
 shinydashboard-0.6.0/shinydashboard/man/dashboardSidebar.Rd            |    5 
 shinydashboard-0.6.0/shinydashboard/man/dropdownMenu.Rd                |   10 
 shinydashboard-0.6.0/shinydashboard/man/dropdownMenuOutput.Rd          |    1 
 shinydashboard-0.6.0/shinydashboard/man/infoBox.Rd                     |    1 
 shinydashboard-0.6.0/shinydashboard/man/menuItemOutput.Rd              |    1 
 shinydashboard-0.6.0/shinydashboard/man/menuOutput.Rd                  |    1 
 shinydashboard-0.6.0/shinydashboard/man/messageItem.Rd                 |    1 
 shinydashboard-0.6.0/shinydashboard/man/notificationItem.Rd            |    1 
 shinydashboard-0.6.0/shinydashboard/man/renderDropdownMenu.Rd          |    1 
 shinydashboard-0.6.0/shinydashboard/man/renderMenu.Rd                  |    1 
 shinydashboard-0.6.0/shinydashboard/man/renderValueBox.Rd              |    3 
 shinydashboard-0.6.0/shinydashboard/man/shinydashboard.Rd              |    1 
 shinydashboard-0.6.0/shinydashboard/man/sidebarMenu.Rd                 |   16 
 shinydashboard-0.6.0/shinydashboard/man/sidebarMenuOutput.Rd           |    1 
 shinydashboard-0.6.0/shinydashboard/man/sidebarSearchForm.Rd           |    1 
 shinydashboard-0.6.0/shinydashboard/man/sidebarUserPanel.Rd            |    1 
 shinydashboard-0.6.0/shinydashboard/man/tabBox.Rd                      |    1 
 shinydashboard-0.6.0/shinydashboard/man/tabItem.Rd                     |    1 
 shinydashboard-0.6.0/shinydashboard/man/tabItems.Rd                    |    1 
 shinydashboard-0.6.0/shinydashboard/man/tagAssert.Rd                   |    1 
 shinydashboard-0.6.0/shinydashboard/man/taskItem.Rd                    |    1 
 shinydashboard-0.6.0/shinydashboard/man/updateTabItems.Rd              |    1 
 shinydashboard-0.6.0/shinydashboard/man/validColors.Rd                 |    1 
 shinydashboard-0.6.0/shinydashboard/man/validStatuses.Rd               |    1 
 shinydashboard-0.6.0/shinydashboard/man/valueBox.Rd                    |    1 
 shinydashboard-0.6.0/shinydashboard/man/valueBoxOutput.Rd              |    3 
 53 files changed, 712 insertions(+), 414 deletions(-)

More information about shinydashboard at CRAN
Permanent link

Package rlang updated to version 0.1.1 with previous version 0.1 dated 2017-05-06

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between rlang versions 0.1 dated 2017-05-06 and 0.1.1 dated 2017-05-18

 rlang-0.1.1/rlang/DESCRIPTION                          |    8 
 rlang-0.1.1/rlang/MD5                                  |   86 ++--
 rlang-0.1.1/rlang/NAMESPACE                            |    3 
 rlang-0.1.1/rlang/NEWS.md                              |   54 +++
 rlang-0.1.1/rlang/R/attr.R                             |    5 
 rlang-0.1.1/rlang/R/cnd.R                              |    4 
 rlang-0.1.1/rlang/R/compat-lazyeval.R                  |    2 
 rlang-0.1.1/rlang/R/compat-oldrel.R                    |    2 
 rlang-0.1.1/rlang/R/compat-purrr.R                     |    2 
 rlang-0.1.1/rlang/R/dots.R                             |   16 
 rlang-0.1.1/rlang/R/env.R                              |   63 ++-
 rlang-0.1.1/rlang/R/eval-tidy.R                        |   19 -
 rlang-0.1.1/rlang/R/expr-lang.R                        |   29 +
 rlang-0.1.1/rlang/R/expr-node.R                        |   34 +
 rlang-0.1.1/rlang/R/operators.R                        |    2 
 rlang-0.1.1/rlang/R/stack.R                            |    3 
 rlang-0.1.1/rlang/R/vector-coercion.R                  |   12 
 rlang-0.1.1/rlang/README.md                            |   32 +
 rlang-0.1.1/rlang/build/vignette.rds                   |binary
 rlang-0.1.1/rlang/inst/doc/tidy-evaluation.R           |    2 
 rlang-0.1.1/rlang/inst/doc/tidy-evaluation.Rmd         |   70 +---
 rlang-0.1.1/rlang/inst/doc/tidy-evaluation.html        |   32 -
 rlang-0.1.1/rlang/man/dots_list.Rd                     |   16 
 rlang-0.1.1/rlang/man/env.Rd                           |   30 +
 rlang-0.1.1/rlang/man/env_unbind.Rd                    |    4 
 rlang-0.1.1/rlang/man/is_pairlist.Rd                   |   17 
 rlang-0.1.1/rlang/man/lang.Rd                          |   17 
 rlang-0.1.1/rlang/man/new_cnd.Rd                       |    4 
 rlang-0.1.1/rlang/man/pairlist.Rd                      |    4 
 rlang-0.1.1/rlang/man/set_attrs.Rd                     |    5 
 rlang-0.1.1/rlang/man/stack.Rd                         |    3 
 rlang-0.1.1/rlang/src/capture.c                        |    4 
 rlang-0.1.1/rlang/src/formula.c                        |    6 
 rlang-0.1.1/rlang/src/init.c                           |   86 ++--
 rlang-0.1.1/rlang/src/lang.c                           |only
 rlang-0.1.1/rlang/src/replace-na.c                     |    2 
 rlang-0.1.1/rlang/src/unquote.c                        |    2 
 rlang-0.1.1/rlang/src/utils.h                          |    1 
 rlang-0.1.1/rlang/tests/testthat/test-env.R            |   15 
 rlang-0.1.1/rlang/tests/testthat/test-quo-enquo.R      |   18 +
 rlang-0.1.1/rlang/tests/testthat/test-tidy-eval.R      |    9 
 rlang-0.1.1/rlang/tests/testthat/test-types-coercion.R |    5 
 rlang-0.1.1/rlang/vignettes/releases/rlang-0.1.Rmd     |  293 +++++++----------
 rlang-0.1.1/rlang/vignettes/tidy-evaluation.Rmd        |   70 +---
 rlang-0.1/rlang/src/symbol.h                           |only
 45 files changed, 656 insertions(+), 435 deletions(-)

More information about rlang at CRAN
Permanent link

Package SKAT updated to version 1.3.0 with previous version 1.2.1 dated 2016-06-28

Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>

Diff between SKAT versions 1.2.1 dated 2016-06-28 and 1.3.0 dated 2017-05-18

 SKAT-1.2.1/SKAT/src/Binary_resampling.c     |only
 SKAT-1.2.1/SKAT/src/interface.cpp           |only
 SKAT-1.2.1/SKAT/src/kernel_func.c           |only
 SKAT-1.3.0/SKAT/DESCRIPTION                 |    8 -
 SKAT-1.3.0/SKAT/MD5                         |   57 +++----
 SKAT-1.3.0/SKAT/NAMESPACE                   |    2 
 SKAT-1.3.0/SKAT/R/Binary_MAIN.R             |   10 -
 SKAT-1.3.0/SKAT/R/Joint_CommonRare.R        |   12 -
 SKAT-1.3.0/SKAT/R/MAIN.R                    |   43 ++++-
 SKAT-1.3.0/SKAT/R/Main_SSD.R                |   10 -
 SKAT-1.3.0/SKAT/R/SKAT_EMMAX.R              |   66 +++++++-
 SKAT-1.3.0/SKAT/R/SKAT_Linear.R             |   11 +
 SKAT-1.3.0/SKAT/R/SKAT_Logistic.R           |    9 -
 SKAT-1.3.0/SKAT/R/SKAT_Meta_Optimal.R       |only
 SKAT-1.3.0/SKAT/build/vignette.rds          |binary
 SKAT-1.3.0/SKAT/data/SKAT.example.ChrX.rda  |binary
 SKAT-1.3.0/SKAT/data/SKAT.example.rda       |binary
 SKAT-1.3.0/SKAT/data/SKAT.fam.example.rda   |binary
 SKAT-1.3.0/SKAT/data/SKAT.haplotypes.rda    |binary
 SKAT-1.3.0/SKAT/data/SKATBinary.example.rda |binary
 SKAT-1.3.0/SKAT/inst/doc/SKAT.R             |  116 +++++++++++++--
 SKAT-1.3.0/SKAT/inst/doc/SKAT.Rnw           |  208 +++++++++++++++++++---------
 SKAT-1.3.0/SKAT/inst/doc/SKAT.pdf           |binary
 SKAT-1.3.0/SKAT/man/SKAT.rd                 |    7 
 SKAT-1.3.0/SKAT/man/SKAT_ChrX.rd            |    6 
 SKAT-1.3.0/SKAT/man/SKAT_NULL_emmaX.rd      |    4 
 SKAT-1.3.0/SKAT/src/Binary_global.cpp       |    8 -
 SKAT-1.3.0/SKAT/src/Binary_global.h         |   18 +-
 SKAT-1.3.0/SKAT/src/Binary_resampling.cpp   |only
 SKAT-1.3.0/SKAT/src/interface_new.cpp       |only
 SKAT-1.3.0/SKAT/src/kernel_func.cpp         |only
 SKAT-1.3.0/SKAT/src/qfc.cpp                 |    6 
 SKAT-1.3.0/SKAT/vignettes/SKAT.Rnw          |  208 +++++++++++++++++++---------
 33 files changed, 564 insertions(+), 245 deletions(-)

More information about SKAT at CRAN
Permanent link


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