Fri, 11 Oct 2019

Package stringdist updated to version 0.9.5.3 with previous version 0.9.5.2 dated 2019-06-06

Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native 'match' function. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences. This package is built for speed and runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
Author: Mark van der Loo [aut, cre], Jan van der Laan [ctb], R Core Team [ctb], Nick Logan [ctb], Chris Muir [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

Diff between stringdist versions 0.9.5.2 dated 2019-06-06 and 0.9.5.3 dated 2019-10-11

 DESCRIPTION                          |    6 +++---
 MD5                                  |   26 +++++++++++++-------------
 NEWS                                 |    3 +++
 R/amatch.R                           |    2 ++
 R/phonetic.R                         |    2 +-
 R/qgrams.R                           |    4 ++--
 R/stringdist.R                       |    4 +++-
 R/stringsim.R                        |    2 +-
 R/utils.R                            |    2 +-
 build/vignette.rds                   |binary
 inst/doc/RJournal_6_111-122-2014.pdf |binary
 inst/doc/stringdist_C-Cpp_api.pdf    |binary
 inst/tinytest/test_gh_issue_59.R     |    2 +-
 inst/tinytest/test_stringsim.R       |    5 +++++
 14 files changed, 35 insertions(+), 23 deletions(-)

More information about stringdist at CRAN
Permanent link

Package ckanr updated to version 0.4.0 with previous version 0.3.0 dated 2019-07-23

Title: Client for the Comprehensive Knowledge Archive Network ('CKAN') API
Description: Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Imanuel Costigan [aut], Wush Wu [aut] (<https://orcid.org/0000-0001-5180-0567>), Florian Mayer [aut] (<https://orcid.org/0000-0003-4269-4242>), Sharla Gelfand [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between ckanr versions 0.3.0 dated 2019-07-23 and 0.4.0 dated 2019-10-11

 ckanr-0.3.0/ckanr/inst/vign                       |only
 ckanr-0.4.0/ckanr/DESCRIPTION                     |   11 
 ckanr-0.4.0/ckanr/MD5                             |   32 
 ckanr-0.4.0/ckanr/NEWS.md                         |   20 
 ckanr-0.4.0/ckanr/R/ckan_fetch.R                  |   63 +
 ckanr-0.4.0/ckanr/R/ckan_info.R                   |   19 
 ckanr-0.4.0/ckanr/R/package_search.R              |   22 
 ckanr-0.4.0/ckanr/R/zzz.R                         |   37 -
 ckanr-0.4.0/ckanr/README.md                       |   15 
 ckanr-0.4.0/ckanr/build/vignette.rds              |binary
 ckanr-0.4.0/ckanr/inst/doc/ckanr.R                |only
 ckanr-0.4.0/ckanr/inst/doc/ckanr.Rmd              |  304 +-------
 ckanr-0.4.0/ckanr/inst/doc/ckanr.html             |  779 +++++++++-------------
 ckanr-0.4.0/ckanr/man/ckan_fetch.Rd               |   28 
 ckanr-0.4.0/ckanr/man/ckan_info.Rd                |    2 
 ckanr-0.4.0/ckanr/man/package_search.Rd           |    9 
 ckanr-0.4.0/ckanr/tests/testthat/test-ckan_info.R |only
 ckanr-0.4.0/ckanr/vignettes/ckanr.Rmd             |  304 +-------
 18 files changed, 660 insertions(+), 985 deletions(-)

More information about ckanr at CRAN
Permanent link

Package optmatch updated to version 0.9-12 with previous version 0.9-11 dated 2019-07-12

Title: Functions for Optimal Matching
Description: Distance based bipartite matching using the RELAX-IV minimum cost flow solver, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson <mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson, Adam Rauh and Peter Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas <dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>

Diff between optmatch versions 0.9-11 dated 2019-07-12 and 0.9-12 dated 2019-10-11

 DESCRIPTION                                 |    6 +++---
 MD5                                         |   18 +++++++++---------
 NEWS                                        |   10 ++++++++++
 R/match_on.R                                |   10 +++++-----
 R/summary.optmatch.R                        |    5 +++--
 inst/doc/fullmatch-vignette.pdf             |binary
 inst/doc/matching-from-foreign-software.pdf |binary
 inst/doc/matching-within-subgroups.pdf      |binary
 tests/testthat/test.InfinitySparseMatrix.R  |   12 +++++++++---
 tests/testthat/test.summary.optmatch.R      |   17 +++++++++++++++++
 10 files changed, 56 insertions(+), 22 deletions(-)

More information about optmatch at CRAN
Permanent link

Package lpirfs updated to version 0.1.6 with previous version 0.1.5 dated 2019-04-11

Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and plot linear as well as nonlinear impulse responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
Author: Philipp Adämmer [aut, cre] (<https://orcid.org/0000-0003-3770-0097>), James P. LeSage [ctb], Mehmet Balcilar [ctb], Jon Danielsson [ctb]
Maintainer: Philipp Adämmer <adaemmer@hsu-hh.de>

Diff between lpirfs versions 0.1.5 dated 2019-04-11 and 0.1.6 dated 2019-10-11

 lpirfs-0.1.5/lpirfs/R/se_hc_panel_cluster.R             |only
 lpirfs-0.1.5/lpirfs/man/se_hc_panel_cluster.Rd          |only
 lpirfs-0.1.6/lpirfs/DESCRIPTION                         |   20 -
 lpirfs-0.1.6/lpirfs/MD5                                 |   95 ++++--
 lpirfs-0.1.6/lpirfs/NAMESPACE                           |   24 +
 lpirfs-0.1.6/lpirfs/NEWS.md                             |   14 
 lpirfs-0.1.6/lpirfs/R/RcppExports.R                     |   91 +++++-
 lpirfs-0.1.6/lpirfs/R/get_robust_cov_panel.R            |only
 lpirfs-0.1.6/lpirfs/R/get_robust_vcxt_panel.R           |only
 lpirfs-0.1.6/lpirfs/R/get_std_err.R                     |only
 lpirfs-0.1.6/lpirfs/R/get_std_err_tsls.R                |only
 lpirfs-0.1.6/lpirfs/R/lp_lin.R                          |  195 ++++++++++---
 lpirfs-0.1.6/lpirfs/R/lp_lin_iv.R                       |  234 ++++++++++-----
 lpirfs-0.1.6/lpirfs/R/lp_lin_panel.R                    |   68 ++--
 lpirfs-0.1.6/lpirfs/R/lp_nl.R                           |  185 ++++++++++--
 lpirfs-0.1.6/lpirfs/R/lp_nl_iv.R                        |  238 ++++++++++------
 lpirfs-0.1.6/lpirfs/R/lp_nl_panel.R                     |   64 ++--
 lpirfs-0.1.6/lpirfs/R/lpirfs_obj-methods-base.R         |only
 lpirfs-0.1.6/lpirfs/R/zzz.R                             |    3 
 lpirfs-0.1.6/lpirfs/README.md                           |    4 
 lpirfs-0.1.6/lpirfs/build                               |only
 lpirfs-0.1.6/lpirfs/inst/doc                            |only
 lpirfs-0.1.6/lpirfs/man/get_robust_cov_panel.Rd         |only
 lpirfs-0.1.6/lpirfs/man/get_robust_vcxt_panel.Rd        |only
 lpirfs-0.1.6/lpirfs/man/get_std_err.Rd                  |only
 lpirfs-0.1.6/lpirfs/man/get_std_err_tsls.Rd             |only
 lpirfs-0.1.6/lpirfs/man/lp_lin.Rd                       |   45 +--
 lpirfs-0.1.6/lpirfs/man/lp_lin_iv.Rd                    |   42 +-
 lpirfs-0.1.6/lpirfs/man/lp_lin_panel.Rd                 |   35 +-
 lpirfs-0.1.6/lpirfs/man/lp_nl.Rd                        |   46 +--
 lpirfs-0.1.6/lpirfs/man/lp_nl_iv.Rd                     |   36 +-
 lpirfs-0.1.6/lpirfs/man/lp_nl_panel.Rd                  |   37 +-
 lpirfs-0.1.6/lpirfs/man/lpirfs_obj-methods-base.Rd      |only
 lpirfs-0.1.6/lpirfs/man/newey_west.Rd                   |    5 
 lpirfs-0.1.6/lpirfs/man/newey_west_pw.Rd                |only
 lpirfs-0.1.6/lpirfs/man/newey_west_tsls.Rd              |    4 
 lpirfs-0.1.6/lpirfs/man/ols_diagnost.Rd                 |only
 lpirfs-0.1.6/lpirfs/man/plot.lpirfs_lin_iv_obj.Rd       |only
 lpirfs-0.1.6/lpirfs/man/plot.lpirfs_lin_obj.Rd          |only
 lpirfs-0.1.6/lpirfs/man/plot.lpirfs_lin_panel_obj.Rd    |only
 lpirfs-0.1.6/lpirfs/man/plot.lpirfs_nl_iv_obj.Rd        |only
 lpirfs-0.1.6/lpirfs/man/plot.lpirfs_nl_obj.Rd           |only
 lpirfs-0.1.6/lpirfs/man/plot.lpirfs_nl_panel_obj.Rd     |only
 lpirfs-0.1.6/lpirfs/man/summary.lpirfs_lin_iv_obj.Rd    |only
 lpirfs-0.1.6/lpirfs/man/summary.lpirfs_lin_obj.Rd       |only
 lpirfs-0.1.6/lpirfs/man/summary.lpirfs_lin_panel_obj.Rd |only
 lpirfs-0.1.6/lpirfs/man/summary.lpirfs_nl_iv_obj.Rd     |only
 lpirfs-0.1.6/lpirfs/man/summary.lpirfs_nl_obj.Rd        |only
 lpirfs-0.1.6/lpirfs/man/summary.lpirfs_nl_panel_obj.Rd  |only
 lpirfs-0.1.6/lpirfs/man/var_one.Rd                      |only
 lpirfs-0.1.6/lpirfs/src/RcppExports.cpp                 |   40 ++
 lpirfs-0.1.6/lpirfs/src/get_vals_lagcrit.cpp            |    6 
 lpirfs-0.1.6/lpirfs/src/newey_west.cpp                  |   27 +
 lpirfs-0.1.6/lpirfs/src/newey_west_pw.cpp               |only
 lpirfs-0.1.6/lpirfs/src/newey_west_tsls.cpp             |   29 +
 lpirfs-0.1.6/lpirfs/src/ols_diagnost.cpp                |only
 lpirfs-0.1.6/lpirfs/src/var_one.cpp                     |only
 lpirfs-0.1.6/lpirfs/tests/testthat/test-diagnost_ols.R  |only
 lpirfs-0.1.6/lpirfs/tests/testthat/test-lp_lin.R        |  114 +++++++
 lpirfs-0.1.6/lpirfs/tests/testthat/test-lp_lin_iv.R     |  163 ++++++++++
 lpirfs-0.1.6/lpirfs/tests/testthat/test-lp_lin_panel.R  |  106 ++++++-
 lpirfs-0.1.6/lpirfs/tests/testthat/test-lp_nl.R         |   87 +++++
 lpirfs-0.1.6/lpirfs/tests/testthat/test-lp_nl_panel.R   |   50 +--
 lpirfs-0.1.6/lpirfs/tests/testthat/test-newey_west.R    |only
 lpirfs-0.1.6/lpirfs/vignettes                           |only
 65 files changed, 1614 insertions(+), 493 deletions(-)

More information about lpirfs at CRAN
Permanent link

Package pcFactorStan updated to version 1.2.0 with previous version 1.1.0 dated 2019-09-22

Title: Stan Models for the Paired Comparison Factor Model
Description: Provides convenience functions and pre-programmed Stan models related to the paired comparison factor model. Its purpose is to make fitting paired comparison data using Stan easy.
Author: Joshua N. Pritikin [aut, cre] (<https://orcid.org/0000-0002-9862-5484>), Daniel C. Furr [ctb], Trustees of Columbia University [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between pcFactorStan versions 1.1.0 dated 2019-09-22 and 1.2.0 dated 2019-10-11

 DESCRIPTION                       |    6 
 MD5                               |   38 +++---
 NEWS                              |    4 
 R/fit.R                           |   41 ++++++
 inst/doc/manual.R                 |   24 ++-
 inst/doc/manual.Rmd               |   90 ++++++++------
 inst/doc/manual.html              |  237 ++++++++++++++++++--------------------
 man/findModel.Rd                  |    3 
 man/prepFactorModel.Rd            |   17 ++
 src/stan_files/factor.stan        |   20 ++-
 src/stan_files/factor1.stan       |only
 src/stan_files/factor1_ll.stan    |only
 src/stan_files/factor_ll.stan     |   20 ++-
 tests/testthat/test-3data.R       |   10 +
 tests/testthat/test-4likelihood.R |    4 
 tests/testthat/test-5loo.R        |   19 ---
 tests/testthat/test-6explorer.R   |    2 
 tests/testthat/test-7report.R     |    2 
 tools/build                       |    2 
 tools/genStan                     |   64 +++++++---
 vignettes/manual.Rmd              |   90 ++++++++------
 21 files changed, 402 insertions(+), 291 deletions(-)

More information about pcFactorStan at CRAN
Permanent link

Package AlphaSimR updated to version 0.11.0 with previous version 0.10.0 dated 2019-03-15

Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>), Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>), David Wilson [ctb], Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>), John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>)
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>

Diff between AlphaSimR versions 0.10.0 dated 2019-03-15 and 0.11.0 dated 2019-10-11

 AlphaSimR-0.10.0/AlphaSimR/man/GCAsol-class.Rd          |only
 AlphaSimR-0.10.0/AlphaSimR/man/RRDsol-class.Rd          |only
 AlphaSimR-0.10.0/AlphaSimR/man/SCAsol-class.Rd          |only
 AlphaSimR-0.10.0/AlphaSimR/man/SimParam_setRecRatio.Rd  |only
 AlphaSimR-0.10.0/AlphaSimR/src/GEBV.cpp                 |only
 AlphaSimR-0.10.0/AlphaSimR/vignettes/bibliography.bib   |only
 AlphaSimR-0.11.0/AlphaSimR/DESCRIPTION                  |   12 
 AlphaSimR-0.11.0/AlphaSimR/MD5                          |  134 +-
 AlphaSimR-0.11.0/AlphaSimR/NAMESPACE                    |    9 
 AlphaSimR-0.11.0/AlphaSimR/NEWS                         |   21 
 AlphaSimR-0.11.0/AlphaSimR/R/AlphaSimR.R                |    3 
 AlphaSimR-0.11.0/AlphaSimR/R/Class-LociMap.R            |  228 ---
 AlphaSimR-0.11.0/AlphaSimR/R/Class-Pop.R                |   45 
 AlphaSimR-0.11.0/AlphaSimR/R/Class-RRsol.R              |only
 AlphaSimR-0.11.0/AlphaSimR/R/Class-SimParam.R           |  127 +-
 AlphaSimR-0.11.0/AlphaSimR/R/GS.R                       |  701 +++++++++---
 AlphaSimR-0.11.0/AlphaSimR/R/RcppExports.R              |  116 --
 AlphaSimR-0.11.0/AlphaSimR/R/crossing.R                 |  146 ++
 AlphaSimR-0.11.0/AlphaSimR/R/founderPop.R               |   58 -
 AlphaSimR-0.11.0/AlphaSimR/R/mergePops.R                |    3 
 AlphaSimR-0.11.0/AlphaSimR/R/misc.R                     |  150 ++
 AlphaSimR-0.11.0/AlphaSimR/R/phenotypes.R               |    4 
 AlphaSimR-0.11.0/AlphaSimR/R/popSummary.R               |    4 
 AlphaSimR-0.11.0/AlphaSimR/R/pullGeno.R                 |   45 
 AlphaSimR-0.11.0/AlphaSimR/R/selection.R                |    8 
 AlphaSimR-0.11.0/AlphaSimR/build/vignette.rds           |binary
 AlphaSimR-0.11.0/AlphaSimR/inst/doc/intro.R             |    7 
 AlphaSimR-0.11.0/AlphaSimR/inst/doc/intro.Rmd           |   23 
 AlphaSimR-0.11.0/AlphaSimR/inst/doc/intro.html          |  193 ++-
 AlphaSimR-0.11.0/AlphaSimR/inst/doc/traits.Rmd          |only
 AlphaSimR-0.11.0/AlphaSimR/inst/doc/traits.pdf          |only
 AlphaSimR-0.11.0/AlphaSimR/man/MapPop-class.Rd          |    2 
 AlphaSimR-0.11.0/AlphaSimR/man/Pop-class.Rd             |    9 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP.Rd                |    5 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP2.Rd               |    5 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUPMemUse.Rd          |    2 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP_D.Rd              |    6 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP_D2.Rd             |    5 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP_GCA.Rd            |    6 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP_GCA2.Rd           |    6 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP_SCA.Rd            |    6 
 AlphaSimR-0.11.0/AlphaSimR/man/RRBLUP_SCA2.Rd           |only
 AlphaSimR-0.11.0/AlphaSimR/man/RRsol-class.Rd           |   18 
 AlphaSimR-0.11.0/AlphaSimR/man/RawPop-class.Rd          |    9 
 AlphaSimR-0.11.0/AlphaSimR/man/SimParam.Rd              |    2 
 AlphaSimR-0.11.0/AlphaSimR/man/SimParam_addTraitADE.Rd  |    4 
 AlphaSimR-0.11.0/AlphaSimR/man/SimParam_addTraitADEG.Rd |    4 
 AlphaSimR-0.11.0/AlphaSimR/man/SimParam_addTraitAE.Rd   |    4 
 AlphaSimR-0.11.0/AlphaSimR/man/SimParam_addTraitAEG.Rd  |    4 
 AlphaSimR-0.11.0/AlphaSimR/man/SimParam_setMeiosis.Rd   |only
 AlphaSimR-0.11.0/AlphaSimR/man/TraitA-class.Rd          |    2 
 AlphaSimR-0.11.0/AlphaSimR/man/TraitA2-class.Rd         |only
 AlphaSimR-0.11.0/AlphaSimR/man/TraitA2D-class.Rd        |only
 AlphaSimR-0.11.0/AlphaSimR/man/genParam.Rd              |    4 
 AlphaSimR-0.11.0/AlphaSimR/man/makeDH.Rd                |    6 
 AlphaSimR-0.11.0/AlphaSimR/man/mutate.Rd                |only
 AlphaSimR-0.11.0/AlphaSimR/man/pedigreeCross.Rd         |   22 
 AlphaSimR-0.11.0/AlphaSimR/man/self.Rd                  |    6 
 AlphaSimR-0.11.0/AlphaSimR/man/setEBV.Rd                |   32 
 AlphaSimR-0.11.0/AlphaSimR/src/MME.cpp                  |  774 +++++++++++--
 AlphaSimR-0.11.0/AlphaSimR/src/RcppExports.cpp          |  330 ++---
 AlphaSimR-0.11.0/AlphaSimR/src/alphasimr.h              |    1 
 AlphaSimR-0.11.0/AlphaSimR/src/calcGenParam.cpp         |  185 +--
 AlphaSimR-0.11.0/AlphaSimR/src/getGeno.cpp              |  299 +++--
 AlphaSimR-0.11.0/AlphaSimR/src/getGeno.h                |   27 
 AlphaSimR-0.11.0/AlphaSimR/src/getGv.cpp                |  134 +-
 AlphaSimR-0.11.0/AlphaSimR/src/getHybridGv.cpp          |  177 ++-
 AlphaSimR-0.11.0/AlphaSimR/src/init.c                   |   94 -
 AlphaSimR-0.11.0/AlphaSimR/src/meiosis.cpp              |  916 ++++++++++------
 AlphaSimR-0.11.0/AlphaSimR/src/misc.cpp                 |  127 +-
 AlphaSimR-0.11.0/AlphaSimR/src/misc.h                   |    2 
 AlphaSimR-0.11.0/AlphaSimR/src/packHaplo.cpp            |   57 
 AlphaSimR-0.11.0/AlphaSimR/src/simulator.cpp            |  129 +-
 AlphaSimR-0.11.0/AlphaSimR/vignettes/AlphaSimR.bib      |only
 AlphaSimR-0.11.0/AlphaSimR/vignettes/intro.Rmd          |   23 
 AlphaSimR-0.11.0/AlphaSimR/vignettes/traits.Rmd         |only
 76 files changed, 3726 insertions(+), 1755 deletions(-)

More information about AlphaSimR at CRAN
Permanent link

Package tidyquant updated to version 0.5.8 with previous version 0.5.7 dated 2019-09-20

Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

Diff between tidyquant versions 0.5.7 dated 2019-09-20 and 0.5.8 dated 2019-10-11

 DESCRIPTION                                            |    8 +-
 MD5                                                    |   18 ++---
 NEWS.md                                                |    4 +
 R/tq_stock_list.R                                      |    7 +-
 inst/doc/TQ00-introduction-to-tidyquant.html           |    4 -
 inst/doc/TQ01-core-functions-in-tidyquant.html         |   56 ++++++++---------
 inst/doc/TQ02-quant-integrations-in-tidyquant.html     |   24 +++----
 inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html |   30 ++++-----
 inst/doc/TQ04-charting-with-tidyquant.html             |    4 -
 inst/doc/TQ05-performance-analysis-with-tidyquant.html |   12 +--
 10 files changed, 87 insertions(+), 80 deletions(-)

More information about tidyquant at CRAN
Permanent link

Package mlxR updated to version 4.1.0 with previous version 4.0.6 dated 2019-06-28

Title: Simulation of Longitudinal Data
Description: Simulation and visualization of complex models for longitudinal data. The models are encoded using the model coding language 'Mlxtran' and automatically converted into C++ codes. That allows one to implement very easily complex ODE-based models and complex statistical models, including mixed effects models, for continuous, count, categorical, and time-to-event data.
Author: Marc Lavielle [aut, cre], Esther Ilinca [ctb], Raphael Kuate [ctb]
Maintainer: Marc Lavielle <Marc.Lavielle@inria.fr>

Diff between mlxR versions 4.0.6 dated 2019-06-28 and 4.1.0 dated 2019-10-11

 DESCRIPTION            |    6 
 MD5                    |   22 -
 R/convertmlx.R         |  584 ++++++++++++++++++++++++-------------------------
 R/exposure.R           |  261 ++++++++++++---------
 R/monolix2simulx.R     |    2 
 R/processing_monolix.R |  115 +++++++--
 R/readdatamlx.R        |  135 +++++++----
 R/simpopmlx.R          |    6 
 R/simulx.R             |   12 -
 R/toolsmlx.R           |   69 ++---
 R/translateIOV.R       |    1 
 R/writeDatamlx.R       |   30 +-
 12 files changed, 691 insertions(+), 552 deletions(-)

More information about mlxR at CRAN
Permanent link

New package discrim with initial version 0.0.1
Package: discrim
Title: Model Wrappers for Discriminant Analysis
Version: 0.0.1
Authors@R: c( person(given = "Max", family = "Kuhn", email = "max@rstudio.com", role = c("aut", "cre")), person("RStudio", role = "cph") )
Description: Bindings for additional classification models for use with the 'parsnip' package. Models include flavors of discriminant analysis, such as linear (Fisher (1936) <doi:10.1111/j.1469-1809.1936.tb02137.x>), regularized (Friedman (1989) <doi:10.1080/01621459.1989.10478752>), and flexible (Hastie, Tibshirani, and Buja (1994) <doi:10.1080/01621459.1994.10476866>), as well as naive Bayes classifiers (Hand and Yu (2007) <doi:10.1111/j.1751-5823.2001.tb00465.x>).
License: GPL-2
Depends: parsnip, R (>= 2.10)
Imports: purrr, rlang, tibble, withr, dials
Suggests: testthat, MASS, mda, klaR, earth, mlbench, covr, ggplot2, xml2, spelling
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2019-10-10 16:56:57 UTC; max
Author: Max Kuhn [aut, cre], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Repository: CRAN
Date/Publication: 2019-10-11 12:10:02 UTC

More information about discrim at CRAN
Permanent link

New package BayesBEKK with initial version 0.1.0
Package: BayesBEKK
Type: Package
Title: Bayesian Estimation of Bivariate Volatility Model
Version: 0.1.0
Author: Achal Lama, Girish K Jha, K N Singh and Bishal Gurung
Maintainer: Achal Lama <achal.lama@icar.gov.in>
Depends: R (>= 3.3.0),MTS,coda,mvtnorm
Description: The Multivariate Generalized Autoregressive Conditional Heteroskedasticity (MGARCH) models are used for modelling the volatile multivariate data sets. In this package a variant of MGARCH called BEKK (Baba, Engle, Kraft, Kroner) proposed by Engle and Kroner (1995) <http://www.jstor.org/stable/3532933> has been used to estimate the bivariate time series data using Bayesian technique.
Encoding: UTF-8
LazyData: true
License: GPL-3
NeedsCompilation: no
Packaged: 2019-10-11 11:28:22 UTC; USER
Repository: CRAN
Date/Publication: 2019-10-11 12:10:05 UTC

More information about BayesBEKK at CRAN
Permanent link

New package usefun with initial version 0.4.1
Package: usefun
Type: Package
Title: A Collection of Useful Functions by John
Version: 0.4.1
Authors@R: person("John", "Zobolas", role = c("aut", "cph", "cre"), email = "bblodfon@gmail.com", comment = c(ORCID = "0000-0002-3609-8674"))
Description: A set of general functions that I have used in various projects and in other R packages. They support some miscellaneous operations on data frames, matrices and vectors: adding a row on a ternary (3-value) data.frame based on positive and negative vector-indicators, rearranging a list of data.frames by rownames, pruning rows or columns of a data.frame that contain only one specific value given by the user, checking for matrix equality, pruning and reordering a vector according to the common elements between its names and elements of another given vector, finding the non-common elements between two vectors (outer-section), normalization of a vector, matrix or data.frame's numeric values in a specified range, pretty printing of vector names and values in an R notebook (common names and values between two vectors also supported), retrieving the parent directory of any string path, checking whether a numeric value is inside a given interval, trim the decimal points of a given numeric value, quick saving of data to a file, making a multiple densities plot and a color bar plot and executing a plot string expression while generating the result to the specified file format.
License: MIT + file LICENSE
URL: https://github.com/bblodfon/usefun
BugReports: https://github.com/bblodfon/usefun/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: grDevices, graphics, stats, utils
Suggests: testthat, covr
NeedsCompilation: no
Packaged: 2019-10-10 13:07:02 UTC; john
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-11 11:40:02 UTC

More information about usefun at CRAN
Permanent link

New package tangles with initial version 0.8.1
Package: tangles
Type: Package
Title: Anonymization of Spatial Point Patterns and Raster Objects
Version: 0.8.1
Date: 2019-10-10
Authors@R: c(person("Brendan", "Malone", email = "brendan.malone@csiro.au", role = c("cre", "aut")))
Description: Spatial data anonymization preserves confidentiality. Using methods described in Zandbergen (2014) <doi:10.1155/2014/567049>, spatial data anonymization is achieved by dithering original spatial coordinates with combinations of randomized vertical, horizontal and rotational shifts. This can apply to non-grid spatial point patterns and raster objects, and the methods preserve the same spatial characteristics and relationships of the original data. Unique hash keying enables data subjected to anonymization sequences to be re-identified where required.
Depends: R (>= 3.0.1)
Imports: raster, digest, sp
Suggests: rasterVis, rgdal, knitr, rmarkdown
VignetteBuilder: knitr
License: GPL-2
LazyData: no
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-10-10 09:18:20 UTC; mal181
Author: Brendan Malone [cre, aut]
Maintainer: Brendan Malone <brendan.malone@csiro.au>
Repository: CRAN
Date/Publication: 2019-10-11 11:30:02 UTC

More information about tangles at CRAN
Permanent link

New package SailoR with initial version 1.0
Package: SailoR
Type: Package
Title: An Extension of the Taylor Diagram to Two-Dimensional Vector Data
Version: 1.0
Date: 2019-10-09
Authors@R: c(person(given = "Jon", family = "Sáenz", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-5920-7570")), person(given = "Sheila", family = "Carreno-Madinabeitia", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-4625-6178")), person(given = "Santos J.", family = "González-Rojí", role = c("aut", "cre", "cph"), email = "santosjose.gonzalez@ehu.eus", comment = c(ORCID = "0000-0003-4737-0984")), person(given = "Ganix", family = "Esnaola", role = c("ctb","cph"), comment = c(ORCID = "0000-0001-9058-043X")), person(given = "Gabriel", family = "Ibarra-Berastegi", role = c("ctb","cph"), comment = c(ORCID = "0000-0001-8681-3755")), person(given = "Alain", family = "Ulazia", role = c("ctb","cph"), comment = c(ORCID = "0000-0002-4124-2853")))
Author: Jon Sáenz [aut, cph] (<https://orcid.org/0000-0002-5920-7570>), Sheila Carreno-Madinabeitia [aut, cph] (<https://orcid.org/0000-0003-4625-6178>), Santos J. González-Rojí [aut, cre, cph] (<https://orcid.org/0000-0003-4737-0984>), Ganix Esnaola [ctb, cph] (<https://orcid.org/0000-0001-9058-043X>), Gabriel Ibarra-Berastegi [ctb, cph] (<https://orcid.org/0000-0001-8681-3755>), Alain Ulazia [ctb, cph] (<https://orcid.org/0000-0002-4124-2853>)
Maintainer: Santos J. González-Rojí <santosjose.gonzalez@ehu.eus>
Description: A new diagram for the verification of vector variables (wind, current, etc) generated by multiple models against a set of observations is presented in this package. It has been designed as a generalization of the Taylor diagram to two dimensional quantities. It is based on the analysis of the two-dimensional structure of the mean squared error matrix between model and observations. The matrix is divided into the part corresponding to the relative rotation and the bias of the empirical orthogonal functions of the data. The full set of diagnostics produced by the analysis of the errors between model and observational vector datasets comprises the errors in the means, the analysis of the total variance of both datasets, the rotation matrix corresponding to the principal components in observation and model, the angle of rotation of model-derived empirical orthogonal functions respect to the ones from observations, the standard deviation of model and observations, the root mean squared error between both datasets and the squared two-dimensional correlation coefficient. See the output of function UVError() in this package.
Depends: R (>= 3.5.0)
License: GPL-3
Repository: CRAN
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-10-10 12:05:37 UTC; Santitxu
Date/Publication: 2019-10-11 11:40:05 UTC

More information about SailoR at CRAN
Permanent link

New package GRPtests with initial version 0.1.0
Package: GRPtests
Type: Package
Title: Goodness-of-Fit Tests in High-Dimensional GLMs
Version: 0.1.0
Date: 2019-09-14
Author: Jana Jankova [aut, cre], Rajen Shah [aut], Peter Buehlmann [aut], Richard Samworth [aut]
Maintainer: Jana Jankova <jana.jankova@gmail.com>
Description: Methodology for testing nonlinearity in the conditional mean function in low- or high-dimensional generalized linear models, and the significance of (potentially large) groups of predictors. Details on the algorithms can be found in the paper by Jankova, Shah, Buehlmann and Samworth (2019) <arXiv:1908.03606>.
License: GPL
Imports: glmnet, randomForest, MASS, stats, RPtests
Suggests: xyz
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-10 14:50:53 UTC; janajankova
Repository: CRAN
Date/Publication: 2019-10-11 12:00:04 UTC

More information about GRPtests at CRAN
Permanent link

New package chlorpromazineR with initial version 0.1.2
Package: chlorpromazineR
Title: Convert Antipsychotic Doses to Chlorpromazine Equivalents
Version: 0.1.2
Authors@R: c(person("Eric", "Brown", role = c("aut", "cre"), email = "eb@ericebrown.com", comment = c(ORCID = "0000-0002-1575-2606")), person("Parita", "Shah", role = "aut", comment = c(ORCID = "0000-0002-7302-0411")), person("Julia", "Kim", role = "aut", comment = c(ORCID = "0000-0002-0379-1333")), person("Frederick", "Boehm", role = "rev", comment = c(ORCID = "0000-0002-1644-5931")))
Description: As different antipsychotic medications have different potencies, the doses of different medications cannot be directly compared. Various strategies are used to convert doses into a common reference so that comparison is meaningful. Chlorpromazine (CPZ) has historically been used as a reference medication into which other antipsychotic doses can be converted, as "chlorpromazine-equivalent doses". Using conversion keys generated from widely-cited scientific papers (Gardner et. al 2010 <doi:10.1176/appi.ajp.2009.09060802>, Leucht et al. 2016 <doi:10.1093/schbul/sbv167>), antipsychotic doses are converted to CPZ (or any specified antipsychotic) equivalents. The use of the package is described in the included vignette. Not for clinical use.
URL: https://github.com/ropensci/chlorpromazineR
BugReports: https://github.com/ropensci/chlorpromazineR/issues
Depends: R (>= 3.5)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-10 15:55:55 UTC; ericbrown
Author: Eric Brown [aut, cre] (<https://orcid.org/0000-0002-1575-2606>), Parita Shah [aut] (<https://orcid.org/0000-0002-7302-0411>), Julia Kim [aut] (<https://orcid.org/0000-0002-0379-1333>), Frederick Boehm [rev] (<https://orcid.org/0000-0002-1644-5931>)
Maintainer: Eric Brown <eb@ericebrown.com>
Repository: CRAN
Date/Publication: 2019-10-11 12:00:02 UTC

More information about chlorpromazineR at CRAN
Permanent link

New package pedtools with initial version 0.9.0
Package: pedtools
Type: Package
Title: Creating and Working with Pedigrees and Marker Data
Version: 0.9.0
Authors@R: person("Magnus Dehli", "Vigeland", email = "m.d.vigeland@medisin.uio.no", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9134-4962"))
Description: A lightweight, but comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. Pedigree plots are produced by wrapping the plotting functionality of the 'kinship2' package.
License: GPL-3
URL: https://github.com/magnusdv/pedtools
Encoding: UTF-8
Language: en-GB
LazyData: true
Imports: kinship2
Suggests: testthat, igraph, knitr, rmarkdown, pedmut, kableExtra
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-09 21:16:29 UTC; magnusdv
Author: Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Repository: CRAN
Date/Publication: 2019-10-11 11:00:02 UTC

More information about pedtools at CRAN
Permanent link

New package fgdr with initial version 1.0.0
Package: fgdr
Title: Utilities for Fundamental Geo-Spatial Data
Version: 1.0.0
Authors@R: c( person(given = "Shinya", family = "Uryu", email = "suika1127@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0493-6186")) )
Description: Read and Parse for Fundamental Geo-Spatial Data (FGD) which downloads XML file from providing site (<https://fgd.gsi.go.jp/download/menu.php>). The JPGIS format file provided by FGD so that it can be handled as an R spatial object such as 'sf' and 'raster' or 'stars'. Supports the FGD version 4.1, and accepts fundamental items and digital elevation models.
License: MIT + file LICENSE
Imports: jpmesh (>= 1.1.1), magrittr (>= 1.5), purrr (>= 0.2.5), raster (>= 2.6.7), readr (>= 1.3.1), rlang (>= 0.2.2), sf (>= 0.6.3), sp (>= 1.3.1), stars (>= 0.3-1), stringr (>= 1.3.1), tibble (>= 1.4.2), xml2 (>= 1.2.0)
Encoding: UTF-8
LazyData: true
URL: https://github.com/uribo/fgdr
BugReports: https://github.com/uribo/fgdr/issues
RoxygenNote: 6.1.1
Suggests: covr, roxygen2 (>= 6.1.1), testthat
Depends: R (>= 3.1)
NeedsCompilation: no
Packaged: 2019-10-09 22:51:41 UTC; suryu
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-11 10:30:03 UTC

More information about fgdr at CRAN
Permanent link

New package dynwrap with initial version 1.1.4
Package: dynwrap
Type: Package
Title: Representing and Inferring Single-Cell Trajectories
Description: Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Version: 1.1.4
Authors@R: c( person( "Robrecht", "Cannoodt", email = "rcannood@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood") ), person( "Wouter", "Saelens", email = "wouter.saelens@ugent.be", role = c("aut"), comment = c(ORCID = "0000-0002-7114-6248", github = "zouter") ) )
URL: https://github.com/dynverse/dynwrap
BugReports: https://github.com/dynverse/dynwrap/issues
License: GPL-3
LazyData: TRUE
RoxygenNote: 6.1.1
Encoding: UTF-8
Depends: R (>= 3.0.0)
Imports: assertthat, babelwhale, dplyr, dynutils (>= 1.0.3), dynparam, FNN, hdf5r, igraph, glue, jsonlite, magrittr, Matrix, methods, purrr, processx, readr, stringr, reshape2, testthat, tibble, tidyr, yaml, crayon
Suggests: curl, devtools, dyndimred, ggplot2, knitr, lhs, pkgload, ranger, rmarkdown, viridis
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-10 15:34:51 UTC; rcannood
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-11 10:40:02 UTC

More information about dynwrap at CRAN
Permanent link

Package cairoDevice updated to version 2.28 with previous version 2.27 dated 2019-08-02

Title: Embeddable Cairo Graphics Device Driver
Description: This device uses Cairo and GTK to draw to the screen, file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or Cairo context). The screen device may be embedded into RGtk2 interfaces and supports all interactive features of other graphics devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>

Diff between cairoDevice versions 2.27 dated 2019-08-02 and 2.28 dated 2019-10-11

 DESCRIPTION |    6 +++---
 MD5         |    4 ++--
 src/gtk.c   |   16 ++++++++++------
 3 files changed, 15 insertions(+), 11 deletions(-)

More information about cairoDevice at CRAN
Permanent link

New package BlythStillCasellaCI with initial version 1.0.0
Package: BlythStillCasellaCI
Title: Blyth-Still-Casella Exact Binomial Confidence Intervals
Version: 1.0.0
Authors@R: c( person("Ron", "Yu", email = "ronyu5135@gmail.com", role = c("aut", "cre")), person("Peiwen", "Wu", email = "pwu.stat@gmail.com", role = "aut"))
Description: Computes Blyth-Still-Casella exact binomial confidence intervals based on a refining procedure proposed by George Casella (1986) <doi:10.2307/3314658>.
Depends: R (>= 3.2.0)
License: GPL-3
RoxygenNote: 6.1.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2019-10-09 16:21:10 UTC; pwu01
Author: Ron Yu [aut, cre], Peiwen Wu [aut]
Maintainer: Ron Yu <ronyu5135@gmail.com>
Repository: CRAN
Date/Publication: 2019-10-11 10:30:06 UTC

More information about BlythStillCasellaCI at CRAN
Permanent link

New package xlsx2dfs with initial version 0.1.0
Package: xlsx2dfs
Type: Package
Title: Read and Write 'Excel' Sheets into and from List of Data Frames
Version: 0.1.0
Authors@R: person("Gwang-Jin", "Kim", email = "gwang.jin.kim.phd@gmail.com", role = c("aut", "cre"))
Maintainer: Gwang-Jin Kim <gwang.jin.kim.phd@gmail.com>
Description: Reading and writing sheets of a single 'Excel' file into and from a list of data frames. Eases I/O of tabular data in bioinformatics while keeping them in a human readable format.
Depends: openxlsx
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-10 08:40:32 UTC; josephus
Author: Gwang-Jin Kim [aut, cre]
Repository: CRAN
Date/Publication: 2019-10-11 09:10:02 UTC

More information about xlsx2dfs at CRAN
Permanent link

New package varycoef with initial version 0.2.9
Package: varycoef
Type: Package
Title: Varying Coefficients
Version: 0.2.9
Authors@R: c(person("Jakob", "Dambon", role = c("aut", "cre"), email = "jakob.dambon@math.uzh.ch"), person("Fabio", "Sigrist", role = c("ctb")), person("Reinhard", "Furrer", role = c("ctb")))
Depends: spam
Imports: fields, methods, sp, RandomFields
Suggests: tmap, knitr, rmarkdown, microbenchmark
Description: Gives maximum likelihood estimation (MLE) method to estimate and predict spatially varying coefficient (SVC) Models. It supports covariance tapering by Furrer et al. (2006) <doi:10.1198/106186006X132178> to allow MLE on large data.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-10-10 12:50:06 UTC; jdambo
Author: Jakob Dambon [aut, cre], Fabio Sigrist [ctb], Reinhard Furrer [ctb]
Maintainer: Jakob Dambon <jakob.dambon@math.uzh.ch>
Repository: CRAN
Date/Publication: 2019-10-11 09:20:02 UTC

More information about varycoef at CRAN
Permanent link

New package nhm with initial version 0.1.0
Package: nhm
Type: Package
Title: Non-Homogeneous Markov and Hidden Markov Multistate Models
Version: 0.1.0
Authors@R: person("Andrew", "Titman", role=c("aut", "cre"), email = "a.titman@lancaster.ac.uk")
Maintainer: Andrew Titman <a.titman@lancaster.ac.uk>
Description: Fits non-homogeneous Markov multistate models and misclassification-type hidden Markov models in continuous time to intermittently observed data. Implements the methods in Titman (2011) <doi:10.1111/j.1541-0420.2010.01550.x>. Uses direct numerical solution of the Kolmogorov forward equations to calculate the transition probabilities.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: stats, deSolve, maxLik, mvtnorm
Suggests: msm, parallel, splines
NeedsCompilation: yes
Packaged: 2019-10-10 11:14:34 UTC; andre
Author: Andrew Titman [aut, cre]
Repository: CRAN
Date/Publication: 2019-10-11 09:10:05 UTC

More information about nhm at CRAN
Permanent link

New package mnj with initial version 1.0
Package: mnj
Title: Machine Learning and Judgement
Version: 1.0
Authors@R: person(given = "Yong-Seok", family = "Jeon", role = c("aut","cre"), email = "flywade@skku.edu")
Description: Perform FlexBoost in R. FlexBoost is a newly suggested algorithm based on AdaBoost by adjusting adaptive loss functions. Not only FlexBoost but also other machine learning algorithms (e.g. Support Vector Machines) will be added. For more details on FlexBoost see Jeon, Y. S., Yang, D. H., & Lim, D. J. (2019) <doi:10.1109/access.2019.2938356>.
Imports: rpart(>= 4.1-15)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-10 10:01:30 UTC; jeon
Author: Yong-Seok Jeon [aut, cre]
Maintainer: Yong-Seok Jeon <flywade@skku.edu>
Repository: CRAN
Date/Publication: 2019-10-11 09:10:08 UTC

More information about mnj at CRAN
Permanent link

New package LogrankPower with initial version 1.0.0
Package: LogrankPower
Type: Package
Title: Log-Rank Test Power Calculation
Version: 1.0.0
Date: 2019-10-10
Author: Rong Lu
Maintainer: Rong Lu <rong.lu@utsw.edu>
Depends: R (>= 2.15.0), survival, survminer
Description: Power of the log-rank test is estimated using simulation datasets, with user specified total sample size (in one simulation dataset), type I error, effect size, the total number of simulation datasets, sample size ratio between two comparison groups, the death rate in the reference group, and the distribution of follow-up time (simulated from a negative binomial distribution). Method reference: Hogg, R. V., McKean, J., and Craig, A. T. (2004, ISBN 10: 0130085073). <https://github.com/RongUTSW/Methods/blob/master/LRPowerSimulation.pdf>.
License: GPL-2
NeedsCompilation: no
Packaged: 2019-10-10 15:10:41 UTC; ronglu
Repository: CRAN
Date/Publication: 2019-10-11 09:20:08 UTC

More information about LogrankPower at CRAN
Permanent link

New package locStra with initial version 1.0
Package: locStra
Type: Package
Title: Fast Implementation of (Local) Population Stratification Methods
Version: 1.0
Date: 2019-10-07
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Description: Fast and fully sparse 'cpp' implementations to compute the genetic covariance matrix, the genomic relationship matrix, the Jaccard matrix, and the s-matrix of an input matrix. Full support for sparse matrices from the R-package 'Matrix'. Additionally, a 'cpp' implementation of the power method (von Mises iteration) algorithm to compute the largest eigenvector of a matrix is included, and a function to compute sliding windows.
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.13), Rdpack, Matrix
RdMacros: Rdpack
LinkingTo: Rcpp, RcppEigen
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-10-10 16:02:05 UTC; acer
Repository: CRAN
Date/Publication: 2019-10-11 09:20:05 UTC

More information about locStra at CRAN
Permanent link

New package linearOrdering with initial version 1.0.0
Package: linearOrdering
Type: Package
Title: Methods of Linear Ordering of Data
Version: 1.0.0
Authors@R: person("Antoni", "Baum", email = "antoni.baum@protonmail.com", role = c("aut", "cre"))
Description: Provides various methods of linear ordering of data. Supports weights and positive/negative impacts. Currently included methods: * Sum of ranks * Standardized sums * Hellwig's (Hellwig, 1968, <https://unesdoc.unesco.org/ark:/48223/pf0000158559.locale=en>) * TOPSIS (Yoon & Hwang, 1981, ISBN:978-3-642-48318-9).
URL: https://github.com/Yard1/linearOrdering
BugReports: https://github.com/Yard1/linearOrdering/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-10-10 00:08:53 UTC; baum
Author: Antoni Baum [aut, cre]
Maintainer: Antoni Baum <antoni.baum@protonmail.com>
Repository: CRAN
Date/Publication: 2019-10-11 09:30:02 UTC

More information about linearOrdering at CRAN
Permanent link

New package GWASbyCluster with initial version 0.1.7
Package: GWASbyCluster
Type: Package
Title: Identifying Significant SNPs in Genome Wide Association Studies (GWAS) via Clustering
Version: 0.1.7
Date: 2019-10-09
Author: Yan Xu, Li Xing, Jessica Su, Xuekui Zhang<UBC.X.Zhang@gmail.com>, Weiliang Qiu <Weiliang.Qiu@gmail.com>
Maintainer: Li Xing <sfulxing@gmail.com>
Depends: R (>= 3.5.0), Biobase
Imports: stats, snpStats, methods, rootSolve, limma
Description: Identifying disease-associated significant SNPs using clustering approach. This package is implementation of method proposed in Xu et al (2019) <DOI:10.1038/s41598-019-50229-6>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2019-10-10 01:10:31 UTC; weiliangqiu
Repository: CRAN
Date/Publication: 2019-10-11 09:30:06 UTC

More information about GWASbyCluster at CRAN
Permanent link

Package miscTools updated to version 0.6-24 with previous version 0.6-22 dated 2016-11-25

Title: Miscellaneous Tools and Utilities
Description: Miscellaneous small tools and utilities. Many of them facilitate the work with matrices, e.g. inserting rows or columns, creating symmetric matrices, or checking for semidefiniteness. Other tools facilitate the work with regression models, e.g. extracting the standard errors, obtaining the number of (estimated) parameters, or calculating R-squared values.
Author: Arne Henningsen, Ott Toomet
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between miscTools versions 0.6-22 dated 2016-11-25 and 0.6-24 dated 2019-10-11

 miscTools-0.6-22/miscTools/R/logDataSet.R                    |only
 miscTools-0.6-24/miscTools/DESCRIPTION                       |    9 +--
 miscTools-0.6-24/miscTools/MD5                               |   21 ++++---
 miscTools-0.6-24/miscTools/NAMESPACE                         |    4 +
 miscTools-0.6-24/miscTools/NEWS                              |   10 +++
 miscTools-0.6-24/miscTools/R/semidef.R                       |   30 ++++++----
 miscTools-0.6-24/miscTools/R/summarizeDF.R                   |only
 miscTools-0.6-24/miscTools/man/miscTools-internal.Rd         |    1 
 miscTools-0.6-24/miscTools/man/semidefiniteness.Rd           |   31 ++++++-----
 miscTools-0.6-24/miscTools/man/summarizeDF.Rd                |only
 miscTools-0.6-24/miscTools/tests/stdErTests.R                |   12 ++--
 miscTools-0.6-24/miscTools/tests/stdErTests.Rout.save        |   26 ++++-----
 miscTools-0.6-24/miscTools/tests/summarizeDF_tests.R         |only
 miscTools-0.6-24/miscTools/tests/summarizeDF_tests.Rout.save |only
 14 files changed, 87 insertions(+), 57 deletions(-)

More information about miscTools at CRAN
Permanent link

New package labelmachine with initial version 1.0.0
Package: labelmachine
Title: Make Labeling of R Data Sets Easy
Version: 1.0.0
Authors@R: person(given = "Adrian", family = "Maldet", role = c("aut", "cre"), email = "maldet@posteo.at")
Description: Assign meaningful labels to data frame columns. 'labelmachine' manages your label assignment rules in 'yaml' files and makes it easy to use the same labels in multiple projects.
Depends: R (>= 3.5.0)
Imports: yaml (>= 2.2.0)
Suggests: testthat (>= 2.1.0), roxygen2 (>= 6.1.1), magrittr (>= 1.5), rlang (>= 0.4.0), covr, knitr, rmarkdown
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 6.1.1
License: GPL-3
URL: https://a-maldet.github.io/labelmachine, https://github.com/a-maldet/labelmachine
BugReports: https://github.com/a-maldet/labelmachine/issues
Collate: 'composerr.R' 'imports.R' 'utilities.R' 'lama_dictionary.R' 'lama_merge.R' 'lama_mutate.R' 'lama_read.R' 'lama_select.R' 'lama_rename.R' 'lama_translate.R' 'lama_translate_all.R' 'lama_write.R' 'lappli.R'
NeedsCompilation: no
Packaged: 2019-10-08 08:58:31 UTC; maldet
Author: Adrian Maldet [aut, cre]
Maintainer: Adrian Maldet <maldet@posteo.at>
Repository: CRAN
Date/Publication: 2019-10-11 07:30:03 UTC

More information about labelmachine at CRAN
Permanent link

Package emld updated to version 0.3.0 with previous version 0.2.0 dated 2019-03-06

Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between emld versions 0.2.0 dated 2019-03-06 and 0.3.0 dated 2019-10-11

 emld-0.2.0/emld/inst/tests/eml-2.2.0/moduleEML                                   |only
 emld-0.2.0/emld/tests/testthat/test-rdf-roundtrip.R                              |only
 emld-0.3.0/emld/DESCRIPTION                                                      |    6 
 emld-0.3.0/emld/MD5                                                              |  234 -
 emld-0.3.0/emld/NEWS.md                                                          |    5 
 emld-0.3.0/emld/R/as_emld.R                                                      |    4 
 emld-0.3.0/emld/R/as_jsonlist.R                                                  |    2 
 emld-0.3.0/emld/R/as_xml.R                                                       |   15 
 emld-0.3.0/emld/R/eml_version.R                                                  |   37 
 emld-0.3.0/emld/R/validate_units.R                                               |   16 
 emld-0.3.0/emld/README.md                                                        |    4 
 emld-0.3.0/emld/build/vignette.rds                                               |binary
 emld-0.3.0/emld/inst/context/eml-2.2.0/eml-context.json                          |    6 
 emld-0.3.0/emld/inst/doc/tutorial.html                                           |   22 
 emld-0.3.0/emld/inst/examples/eml-data-paper.xml                                 |    8 
 emld-0.3.0/emld/inst/extdata/example.xml                                         |    6 
 emld-0.3.0/emld/inst/extdata/semantic-eml.xml                                    |   10 
 emld-0.3.0/emld/inst/frame/eml-2.2.0/eml-frame.json                              |    6 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.201.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.202.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.203.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.211.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.231.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.232.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.233.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.279.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.280.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.284.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.285.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.289.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.296.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.297.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.50.xml        |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/citation-sbclter-bibliography.51.xml        |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-2.1.1-all-units.xml                     |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-access.xml                              |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-attribute.xml                           |    6 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-citationWithContact.xml                 |    2 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-citationWithContactReference.xml        |    2 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-data-paper.xml                          |    8 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-dataTable.xml                           |    6 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-dataset.xml                             |   14 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetGRing.xml                        |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetGringpoint.xml                   |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetMultipleDistribution.xml         |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWhitespacePatterns.xml           |    5 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithAccess.xml                   |   16 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithAccessOverride.xml           |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithAccessUnitsLiteralLayout.xml |   96 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithAttributelevelMethods.xml    |    2 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithCitation.xml                 |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithNonwordCharacters.xml        |    2 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-datasetWithUnits.xml                    |    6 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-entity.xml                              |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-i18n.xml                                |   26 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-inline.xml                              |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-literature.xml                          |    6 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-literatureInPress.xml                   |    6 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-method.xml                              |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-offline.xml                             |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-party.xml                               |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-physical-inline-cdatasection.xml        |    8 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-physical-inline.xml                     |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-physical.xml                            |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-project.xml                             |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-protocol.xml                            |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-sample.xml                              |   10 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-semantics.xml                           |   12 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-software-dependency.xml                 |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-software.xml                            |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-softwareWithAcessDistribution.xml       |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-spatialVector.xml                       |    8 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-storedProcedure.xml                     |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-text.xml                                |   10 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-unitDictionary.xml                      |   14 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml-view.xml                                |    4 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/eml.xml                                     |    5 
 emld-0.3.0/emld/inst/tests/eml-2.2.0/stmml_dictionaryWithDefintion.xml           |   10 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-access.xsd                                |  203 -
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-attribute.xsd                             |  161 -
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-constraint.xsd                            |   69 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-coverage.xsd                              | 1214 ++++------
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-dataTable.xsd                             |   56 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-dataset.xsd                               |   53 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-documentation.xsd                         |    8 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-entity.xsd                                |   41 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-literature.xsd                            |   35 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-methods.xsd                               |   79 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-party.xsd                                 |   93 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-physical.xsd                              |   84 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-project.xsd                               |   41 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-protocol.xsd                              |   24 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-resource.xsd                              |   54 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-semantics.xsd                             |   29 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-software.xsd                              |   28 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-spatialRaster.xsd                         |   85 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-spatialReference.xsd                      |   24 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-spatialVector.xsd                         |   48 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-storedProcedure.xsd                       |   66 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-text.xsd                                  |   19 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-unitTypeDefinitions.xsd                   | 1007 +++-----
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml-view.xsd                                  |   51 
 emld-0.3.0/emld/inst/xsd/eml-2.2.0/eml.xsd                                       |   56 
 emld-0.3.0/emld/man/as_xml.Rd                                                    |    3 
 emld-0.3.0/emld/man/eml_ns.Rd                                                    |only
 emld-0.3.0/emld/man/eml_version.Rd                                               |    6 
 emld-0.3.0/emld/tests/testthat.R                                                 |    2 
 emld-0.3.0/emld/tests/testthat/test-validate.R                                   |    4 
 emld-0.3.0/emld/tests/testthat/test-version.R                                    |only
 109 files changed, 1865 insertions(+), 2587 deletions(-)

More information about emld at CRAN
Permanent link

Package spc updated to version 0.6.2 with previous version 0.6.1 dated 2019-06-19

Title: Statistical Process Control -- Calculation of ARL and Other Control Chart Performance Measures
Description: Evaluation of control charts by means of the zero-state, steady-state ARL (Average Run Length) and RL quantiles. Setting up control charts for given in-control ARL. The control charts under consideration are one- and two-sided EWMA, CUSUM, and Shiryaev-Roberts schemes for monitoring the mean or variance of normally distributed independent data. ARL calculation of the same set of schemes under drift (in the mean) are added. Eventually, all ARL measures for the multivariate EWMA (MEWMA) are provided.
Author: Sven Knoth
Maintainer: Sven Knoth <Sven.Knoth@gmx.de>

Diff between spc versions 0.6.1 dated 2019-06-19 and 0.6.2 dated 2019-10-11

 DESCRIPTION                     |    8 
 MD5                             |   18 
 NAMESPACE                       |    1 
 R/pois.cusum.arl.R              |only
 R/pois.cusum.crit.L0L1.R        |only
 R/pois.cusum.crit.R             |only
 man/pois.crit.L0L1.Rd           |only
 man/pois.cusum.arl.Rd           |only
 man/pois.cusum.crit.Rd          |only
 man/quadrature.nodes.weights.Rd |    2 
 src/allspc.c                    |  799 ++++++++++++++++++++++++++++++++++++++++
 src/ccusum_arl_be.c             |only
 src/ccusum_crit_be.c            |only
 src/spc_init.c                  |    4 
 14 files changed, 822 insertions(+), 10 deletions(-)

More information about spc at CRAN
Permanent link


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