Title: Using Cytogenetics Data in R
Description: Defines classes and methods to process text-based
cytogenetics using the CytoGPS web site, then import the results
into R for further analysis and graphing.
Author: Kevin R. Coombes, Dwayne Tally
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RCytoGPS versions 1.0.1 dated 2020-11-19 and 1.1.1 dated 2021-02-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++++++----- NAMESPACE | 2 +- NEWS | 10 +++++++++- R/102-preclean.R |only inst/PreClean |only inst/doc/Gallery.html | 6 +++--- inst/doc/IntroRCytoGPS.html | 8 ++++---- man/07-preclean.Rd |only tests/test101-preclean.R |only tests/test101-preclean.Rout.save |only 11 files changed, 34 insertions(+), 18 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.3.2 dated 2020-06-15 and 2.3.4 dated 2021-02-10
DESCRIPTION | 10 MD5 | 18 R/gjamHfunctions.R | 467 ++++++++----- R/gjamPriorTemplate.R | 7 build/vignette.rds |binary inst/doc/gjamVignette.R | 40 - inst/doc/gjamVignette.Rmd | 142 ++-- inst/doc/gjamVignette.html | 1503 +++++++++++++++++++++++++-------------------- man/gjam-package.Rd | 4 vignettes/gjamVignette.Rmd | 142 ++-- 10 files changed, 1372 insertions(+), 961 deletions(-)
Title: Politely Web Scrape Data from SquashInfo
Description: Scrape SquashInfo <http://www.squashinfo.com/> for data on the Professional Squash Association World Tour and other squash events. 'squashinformr' functions scrape, parse, and clean data associated with players, tournaments, and rankings.
Author: Hayden MacDonald [aut, cre]
Maintainer: Hayden MacDonald <hayden.macdonald.8778@gmail.com>
Diff between squashinformr versions 0.2.0 dated 2021-01-24 and 0.2.1 dated 2021-02-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/get_historical_rankings.R | 2 +- R/get_tournament_.R | 2 +- README.md | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: 'WebSocket' Client Library
Description: Provides a 'WebSocket' client interface for R.
'WebSocket' is a protocol for low-overhead real-time communication:
<https://en.wikipedia.org/wiki/WebSocket>.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
Alan Dipert [aut],
Barbara Borges [aut],
RStudio [cph],
Peter Thorson [ctb, cph] (WebSocket++ library),
René Nyffenegger [ctb, cph] (Base 64 library),
Micael Hildenborg [ctb, cph] (SHA1 library),
Aladdin Enterprises [cph] (MD5 library),
Bjoern Hoehrmann [ctb, cph] (UTF8 Validation library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between websocket versions 1.3.1 dated 2020-07-13 and 1.3.2 dated 2021-02-10
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 9 README.md | 230 ++++++++++++++++++++++-- build/vignette.rds |binary configure | 22 -- inst/doc/overview.html | 410 +++++++++++++++++-------------------------- src/wrapped_print.h | 2 tests/testthat/test-client.R | 12 - 9 files changed, 420 insertions(+), 287 deletions(-)
Title: ILO Open Data via Ilostat Bulk Download Facility or SDMX Web
Service
Description: Tools to download data from the ilostat database
<https://ilostat.ilo.org> together with search and
manipulation utilities.
Author: ILO Department of Statistics [cph, fnd],
David Bescond [aut, cre] (<https://orcid.org/0000-0002-1642-0304>),
Mabelin Villarreal-Fuentes [ctb]
(<https://orcid.org/0000-0001-5644-5760>)
Maintainer: David Bescond <bescond@ilo.org>
Diff between Rilostat versions 1.1 dated 2020-05-27 and 1.1.5 dated 2021-02-10
Rilostat-1.1.5/Rilostat/DESCRIPTION | 24 ++++++++++-------- Rilostat-1.1.5/Rilostat/MD5 | 32 ++++++++----------------- Rilostat-1.1.5/Rilostat/NEWS.md | 4 +++ Rilostat-1.1.5/Rilostat/R/Rilostat.R | 5 ++- Rilostat-1.1.5/Rilostat/R/get_ilostat_dic.R | 2 - Rilostat-1.1.5/Rilostat/R/get_ilostat_toc.R | 2 - Rilostat-1.1.5/Rilostat/R/runExplorer.R | 18 ++++---------- Rilostat-1.1.5/Rilostat/README.md | 2 - Rilostat-1.1.5/Rilostat/man/Rilostat.Rd | 4 +-- Rilostat-1.1.5/Rilostat/man/get_ilostat_dic.Rd | 2 - Rilostat-1.1.5/Rilostat/man/get_ilostat_toc.Rd | 3 -- Rilostat-1.1.5/Rilostat/man/runExplorer.Rd | 2 - Rilostat-1.1/Rilostat/build |only Rilostat-1.1/Rilostat/inst |only Rilostat-1.1/Rilostat/vignettes |only 15 files changed, 43 insertions(+), 57 deletions(-)
Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.20 dated 2021-01-06 and 0.21 dated 2021-02-10
DESCRIPTION | 6 ++-- MD5 | 30 ++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 16 +++++++++++ R/command.R | 39 ++++++++++++++++------------ R/io.R | 14 +++++++++- R/packages.R | 27 ++++++++++++++++++- R/revcheck.R | 5 ++- R/utils.R | 60 ++++++++++++++++++++++++++++++++++++++++++++ README.md | 11 ++++++++ inst/doc/xfun.html | 17 ++++++++---- man/Rscript_call.Rd | 7 +++++ man/bg_process.Rd | 16 +++++++---- man/exit_call.Rd |only man/pkg_attach.Rd | 16 +++++++++++ man/read_bin.Rd |only man/set_envvar.Rd |only tests/testit/test-command.R |only 18 files changed, 220 insertions(+), 48 deletions(-)
Title: Symbolic Representation of Matrix Determinant
Description: Creates a numeric guide for writing the formula for the determinant of a square matrix (a detguide) as a function of the elements of the matrix and writes out that formula, the symbolic representation.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between SymbolicDeterminants versions 1.3.0 dated 2021-01-05 and 2.0.0 dated 2021-02-10
DESCRIPTION | 11 +++--- MD5 | 38 +++++++++++++--------- NAMESPACE | 5 ++ NEWS.md | 11 ++++++ R/anewdetguide.R | 8 +--- R/anewminidet.r |only R/confirm.minidet.R |only R/detindex.R | 54 ++++++++++++++++++++++++------- R/parsedetguide.R | 39 ++++++++++++++++++---- R/parsemini.r |only R/retrieve.R | 80 +++++++++++++++++++++++++++++++---------------- R/retrieve.mini.R |only README.md | 53 ++++++++++++++++++++++++++++--- inst/doc/Background.Rmd | 26 +++++++++------ inst/doc/Background.html | 19 +++++++---- man/anewminidet.Rd |only man/confirm.det.Rd | 4 +- man/confirm.minidet.Rd |only man/detindex.Rd | 22 ++++++++---- man/parsedetguide.Rd | 13 ++++--- man/parsemini.Rd |only man/retrieve.Rd | 14 ++++---- man/retrieve.mini.Rd |only vignettes/Background.Rmd | 26 +++++++++------ 24 files changed, 302 insertions(+), 121 deletions(-)
More information about SymbolicDeterminants at CRAN
Permanent link
Title: C-Statistics for Risk Prediction Models with Censored Survival
Data
Description: Performs inference for C of risk prediction models with censored survival data, using the method proposed by Uno et al. (2011) <doi:10.1002/sim.4154>. Inference for the difference in C between two competing prediction models is also implemented.
Author: Hajime Uno
Maintainer: Hajime Uno <huno@jimmy.harvard.edu>
Diff between survC1 versions 1.0-2 dated 2013-02-14 and 1.0-3 dated 2021-02-10
DESCRIPTION | 18 ++++++++---------- MD5 | 29 ++++++++++++++++------------- NAMESPACE | 9 ++++++--- NEWS.md |only README.md |only man/Est.Cval.Rd | 17 ----------------- man/Est.PH.Rd | 18 ------------------ man/Inf.Cval.Delta.Rd | 18 ------------------ man/Inf.Cval.Rd | 18 ------------------ man/VEC2MAT.Rd | 27 --------------------------- man/conc.Rd | 34 +--------------------------------- man/cvC.Rd | 18 ------------------ man/kmcens.Rd | 34 +--------------------------------- man/survC1-package.Rd | 8 ++++---- man/unoCW.Rd | 33 +-------------------------------- man/unoU2P.Rd | 33 +-------------------------------- src/survC1_init.c |only 17 files changed, 38 insertions(+), 276 deletions(-)
Title: Using GPUs in Statistical Genomics
Description: Can be used to carry out
permutation resampling inference in the context of RNA
microarray studies.
Author: Ivo D. Shterev [aut, cre],
Kouros Owzar [aut],
Sin-Ho Jung [aut],
Stephen L. George [aut],
Brian J. Smith [ctb, cph] (wrote original version of configure.ac file),
Kenneth Wilder [ctb, cph] (wrote ranker.h),
Romain Francois [ctb, cph] (wrote original version of cleanup file),
Dirk Eddelbuettel [ctb, cph] (wrote original version of cleanup file)
Maintainer: Ivo D. Shterev <i.shterev@gmail.com>
Diff between permGPU versions 0.14.9 dated 2016-02-23 and 0.15 dated 2021-02-10
permGPU-0.14.9/permGPU/cleanup |only permGPU-0.15/permGPU/DESCRIPTION | 11 ++++----- permGPU-0.15/permGPU/MD5 | 17 ++++++-------- permGPU-0.15/permGPU/man/makeExprSet.Rd | 10 ++------ permGPU-0.15/permGPU/man/permGPU-package.Rd | 34 +++++++++++----------------- permGPU-0.15/permGPU/man/permgpu.Rd | 27 ++-------------------- permGPU-0.15/permGPU/man/scoregpu.Rd | 23 +----------------- permGPU-0.15/permGPU/man/test.permgpu.Rd | 8 +----- permGPU-0.15/permGPU/man/test.scoregpu.Rd | 7 +---- permGPU-0.15/permGPU/src/permGPU.cu | 15 ++++++++---- 10 files changed, 49 insertions(+), 103 deletions(-)
More information about behaviorchange at CRAN
Permanent link
Title: Moving Sum Based Procedures for Changes in the Mean
Description: Implementations of MOSUM-based statistical procedures and algorithms for detecting multiple changes in the mean. This comprises the MOSUM procedure for estimating multiple mean changes from Eichinger and Kirch (2018) <doi:10.3150/16-BEJ887> and the multiscale algorithmic extensions from Cho and Kirch (2019) <arXiv:1910.12486>.
Author: Alexander Meier [aut],
Haeran Cho [aut, cre],
Claudia Kirch [aut]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>
Diff between mosum versions 1.2.3 dated 2019-11-04 and 1.2.4 dated 2021-02-10
DESCRIPTION | 10 - MD5 | 109 ++++++++-------- NAMESPACE | 72 +++++------ R/RcppExports.R | 268 ++++++++++++++++++++--------------------- R/bandwidth.R | 4 R/bootstrap.R | 251 +++++++++++++++++++------------------- R/local_prune.R | 59 ++++++--- man/bandwidths.default.Rd | 77 +++++------ man/bootstrapped_timeSeries.Rd | 24 +-- man/comb_contains_cpt.Rd | 24 +-- man/confint.mosum.cpts.Rd | 91 ++++++------- man/confint.multiscale.cpts.Rd | 91 ++++++------- man/cpts_bootstrap.Rd | 24 +-- man/cpts_bootstrap_help.Rd | 24 +-- man/detect.interval.Rd |only man/dup.merge.Rd | 32 ++-- man/eta_criterion_help.Rd | 24 +-- man/exhaust_sc.Rd | 58 ++++---- man/extract_sub.Rd | 40 +++--- man/get_comb_ind.Rd | 32 ++-- man/get_k_star.Rd | 24 +-- man/get_local_costs.Rd | 28 ++-- man/is_child.Rd | 32 ++-- man/local.env.Rd | 24 +-- man/local.prune.Rd | 24 +-- man/mean_help.Rd | 24 +-- man/modelSignal.blocks.Rd | 56 ++++---- man/modelSignal.fms.Rd | 56 ++++---- man/modelSignal.mix.Rd | 56 ++++---- man/modelSignal.stairs10.Rd | 56 ++++---- man/modelSignal.teeth10.Rd | 56 ++++---- man/mosum.Rd | 215 +++++++++++++++++--------------- man/mosum.asymptoticA.Rd | 24 +-- man/mosum.asymptoticB.Rd | 24 +-- man/mosum.criticalValue.Rd | 62 ++++----- man/mosum.pValue.Rd | 44 +++--- man/mosum.stat.Rd | 110 ++++++++-------- man/multiscale.bottomUp.Rd | 180 ++++++++++++++------------- man/multiscale.grid.Rd | 68 +++++----- man/multiscale.localPrune.Rd | 208 ++++++++++++++++--------------- man/next_bit_permutation.Rd | 36 ++--- man/numberOfSetBits.Rd | 28 ++-- man/persp3D.multiscaleMosum.Rd | 156 ++++++++++++----------- man/plot.mosum.cpts.Rd | 94 +++++++------- man/plot.mosum.stat.Rd | 51 +++---- man/plot.multiscale.cpts.Rd | 121 +++++++++--------- man/print.mosum.cpts.Rd | 42 +++--- man/print.multiscale.cpts.Rd | 42 +++--- man/rolling_sum.Rd | 28 ++-- man/setBitNumber.Rd | 28 ++-- man/start_bit_permutations.Rd | 32 ++-- man/summary.mosum.cpts.Rd | 54 ++++---- man/summary.multiscale.cpts.Rd | 54 ++++---- man/testData.Rd | 142 +++++++++++---------- man/testSignal.Rd | 84 ++++++------ src/bootstrap.cpp | 20 +-- 56 files changed, 1898 insertions(+), 1799 deletions(-)
Title: Solar Radiation
Description: Functions to compute insolation on complex terrain.
Author: Javier G. Corripio
Maintainer: Javier G. Corripio <jgc@meteoexploration.com>
Diff between insol versions 1.2.1 dated 2019-12-17 and 1.2.2 dated 2021-02-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/insolation.R | 8 ++++---- man/aspect.Rd | 3 +-- man/cgrad.Rd | 3 +-- man/doshade.Rd | 2 +- man/insolation.Rd | 25 ++++++++++++++++++------- 7 files changed, 35 insertions(+), 26 deletions(-)
Title: Fuzzy Inference System Design and Optimization
Description: Fuzzy inference systems are based on fuzzy rules, which have a good capability for managing progressive phenomenons.
This package is a basic implementation of the main functions to use a Fuzzy Inference System (FIS) provided by the open source software 'FisPro' <https://www.fispro.org>.
'FisPro' allows to create fuzzy inference systems and to use them for reasoning purposes, especially for simulating a physical or biological system.
Author: Serge Guillaume [aut],
Brigitte Charnomordic [aut],
Jean-Luc Lablée [aut, cre],
Hazaël Jones [ctb],
Lydie Desperben [ctb],
INRAE [cph] (National Research Institute for Agriculture, Food and
Environment, France)
Maintainer: Jean-Luc Lablée <jean-luc.lablee@inrae.fr>
Diff between FisPro versions 1.0 dated 2019-06-14 and 1.1 dated 2021-02-10
FisPro-1.0/FisPro/R/RcppExports.R |only FisPro-1.0/FisPro/man/FisPro-package.Rd |only FisPro-1.0/FisPro/man/fis.Rd |only FisPro-1.0/FisPro/man/mf.Rd |only FisPro-1.0/FisPro/man/mf_trapezoidal.Rd |only FisPro-1.0/FisPro/man/mf_trapezoidal_inf.Rd |only FisPro-1.0/FisPro/man/mf_trapezoidal_sup.Rd |only FisPro-1.0/FisPro/man/mf_triangular.Rd |only FisPro-1.0/FisPro/src/Makevars.win |only FisPro-1.0/FisPro/src/aggreg.cpp |only FisPro-1.0/FisPro/src/common.cpp |only FisPro-1.0/FisPro/src/common.h |only FisPro-1.0/FisPro/src/defuz.cpp |only FisPro-1.0/FisPro/src/defuz.h |only FisPro-1.0/FisPro/src/fis.cpp |only FisPro-1.0/FisPro/src/fis.h |only FisPro-1.0/FisPro/src/fispro_module.cpp |only FisPro-1.0/FisPro/src/in.cpp |only FisPro-1.0/FisPro/src/mf.cpp |only FisPro-1.0/FisPro/src/mf.h |only FisPro-1.0/FisPro/src/mfdposs.cpp |only FisPro-1.0/FisPro/src/out.cpp |only FisPro-1.0/FisPro/src/pt.cpp |only FisPro-1.0/FisPro/src/pt.h |only FisPro-1.0/FisPro/src/rule.cpp |only FisPro-1.0/FisPro/src/rule.h |only FisPro-1.1/FisPro/DESCRIPTION | 29 - FisPro-1.1/FisPro/MD5 | 151 ++++- FisPro-1.1/FisPro/NAMESPACE | 34 + FisPro-1.1/FisPro/NEWS.md |only FisPro-1.1/FisPro/R/deprecated.r |only FisPro-1.1/FisPro/R/fis.R |only FisPro-1.1/FisPro/R/fisin.R |only FisPro-1.1/FisPro/R/fisout.R |only FisPro-1.1/FisPro/R/mf.R |only FisPro-1.1/FisPro/R/module.R | 48 + FisPro-1.1/FisPro/R/package.R | 61 +- FisPro-1.1/FisPro/R/rule.R |only FisPro-1.1/FisPro/build/partial.rdb |binary FisPro-1.1/FisPro/build/vignette.rds |only FisPro-1.1/FisPro/cleanup |only FisPro-1.1/FisPro/cleanup.win |only FisPro-1.1/FisPro/inst/doc |only FisPro-1.1/FisPro/inst/extdata/test.fis | 14 FisPro-1.1/FisPro/inst/extdata/test_data.csv |only FisPro-1.1/FisPro/inst/include |only FisPro-1.1/FisPro/man/Fis.Rd |only FisPro-1.1/FisPro/man/FisIn.Rd |only FisPro-1.1/FisPro/man/FisOut.Rd |only FisPro-1.1/FisPro/man/FisOutCrisp.Rd |only FisPro-1.1/FisPro/man/FisOutFuzzy.Rd |only FisPro-1.1/FisPro/man/FisPro-deprecated.Rd |only FisPro-1.1/FisPro/man/FisPro.Rd |only FisPro-1.1/FisPro/man/Mf.Rd |only FisPro-1.1/FisPro/man/MfTrapezoidal.Rd |only FisPro-1.1/FisPro/man/MfTrapezoidalInf.Rd |only FisPro-1.1/FisPro/man/MfTrapezoidalSup.Rd |only FisPro-1.1/FisPro/man/MfTriangular.Rd |only FisPro-1.1/FisPro/man/NewFis.Rd |only FisPro-1.1/FisPro/man/NewFisIn.Rd |only FisPro-1.1/FisPro/man/NewFisOutCrisp.Rd |only FisPro-1.1/FisPro/man/NewFisOutFuzzy.Rd |only FisPro-1.1/FisPro/man/NewMfTrapezoidal.Rd |only FisPro-1.1/FisPro/man/NewMfTrapezoidalInf.Rd |only FisPro-1.1/FisPro/man/NewMfTrapezoidalSup.Rd |only FisPro-1.1/FisPro/man/NewMfTriangular.Rd |only FisPro-1.1/FisPro/man/NewRule.Rd |only FisPro-1.1/FisPro/man/Rule.Rd |only FisPro-1.1/FisPro/man/fis-deprecated.Rd |only FisPro-1.1/FisPro/man/mf-deprecated.Rd |only FisPro-1.1/FisPro/man/mf_trapezoidal-deprecated.Rd |only FisPro-1.1/FisPro/man/mf_trapezoidal_inf-deprecated.Rd |only FisPro-1.1/FisPro/man/mf_trapezoidal_sup-deprecated.Rd |only FisPro-1.1/FisPro/man/mf_triangular-deprecated.Rd |only FisPro-1.1/FisPro/src/Makevars | 29 + FisPro-1.1/FisPro/src/RcppExports.cpp | 14 FisPro-1.1/FisPro/src/base |only FisPro-1.1/FisPro/src/deprecated_module.cpp |only FisPro-1.1/FisPro/src/fis_module.cpp |only FisPro-1.1/FisPro/src/fis_wrapper.cpp |only FisPro-1.1/FisPro/src/fisin_module.cpp |only FisPro-1.1/FisPro/src/fisin_wrapper.cpp |only FisPro-1.1/FisPro/src/fisout_module.cpp |only FisPro-1.1/FisPro/src/fisout_wrapper.cpp |only FisPro-1.1/FisPro/src/fuzzy_range.cpp |only FisPro-1.1/FisPro/src/fuzzy_range.h |only FisPro-1.1/FisPro/src/fuzzy_wrapper.cpp |only FisPro-1.1/FisPro/src/mf_module.cpp |only FisPro-1.1/FisPro/src/mf_wrapper.cpp |only FisPro-1.1/FisPro/src/rule_module.cpp |only FisPro-1.1/FisPro/src/rule_wrapper.cpp |only FisPro-1.1/FisPro/src/util |only FisPro-1.1/FisPro/tests/testthat/helper.R |only FisPro-1.1/FisPro/tests/testthat/helper_fis.R |only FisPro-1.1/FisPro/tests/testthat/test_1_output.fis |only FisPro-1.1/FisPro/tests/testthat/test_2_outputs.fis |only FisPro-1.1/FisPro/tests/testthat/test_data.csv |only FisPro-1.1/FisPro/tests/testthat/test_deprecated_fis.R |only FisPro-1.1/FisPro/tests/testthat/test_deprecated_mf_trapezoidal.R |only FisPro-1.1/FisPro/tests/testthat/test_deprecated_mf_trapezoidal_inf.R |only FisPro-1.1/FisPro/tests/testthat/test_deprecated_mf_trapezoidal_sup.R |only FisPro-1.1/FisPro/tests/testthat/test_deprecated_mf_triangular.R |only FisPro-1.1/FisPro/tests/testthat/test_fis.R | 271 +++++++++- FisPro-1.1/FisPro/tests/testthat/test_fisin.R |only FisPro-1.1/FisPro/tests/testthat/test_fisout.R |only FisPro-1.1/FisPro/tests/testthat/test_fisout_crisp.R |only FisPro-1.1/FisPro/tests/testthat/test_fisout_fuzzy.R |only FisPro-1.1/FisPro/tests/testthat/test_fuzzy.R |only FisPro-1.1/FisPro/tests/testthat/test_mf.R |only FisPro-1.1/FisPro/tests/testthat/test_mf_trapezoidal.R | 28 - FisPro-1.1/FisPro/tests/testthat/test_mf_trapezoidal_inf.R | 25 FisPro-1.1/FisPro/tests/testthat/test_mf_trapezoidal_sup.R | 25 FisPro-1.1/FisPro/tests/testthat/test_mf_triangular.R | 28 - FisPro-1.1/FisPro/tests/testthat/test_rule.R |only FisPro-1.1/FisPro/vignettes |only 115 files changed, 663 insertions(+), 94 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.2.1 dated 2020-11-13 and 0.3.0 dated 2021-02-10
DESCRIPTION | 10 - MD5 | 47 +++-- NEWS.md | 7 R/aaa.R |only R/cpp11.R | 6 R/shape_text.R | 3 README.md | 6 build/vignette.rds |binary inst/doc/c_interface.Rmd | 15 + inst/doc/c_interface.html | 7 inst/include/textshaping.h | 9 - man/figures |only man/shape_text.Rd | 2 src/Makevars.win | 2 src/cpp11.cpp | 1 src/face_feature.cpp | 23 +- src/string_metrics.cpp | 15 + src/string_metrics.h | 3 src/string_shape.cpp | 389 ++++++++++++++++++++++++++++++++++++++++----- src/string_shape.h | 28 +++ src/utils.h | 4 vignettes/c_interface.Rmd | 15 + 22 files changed, 490 insertions(+), 102 deletions(-)
Title: Innovative and/or Additive Outlier Robust Kalman Filtering
Description: Implements a series of robust Kalman filtering approaches. It implements the additive outlier robust filters of Ruckdeschel et al. (2014) <arXiv:1204.3358> and Agamennoni et al. (2018) <doi:10.1109/ICRA.2011.5979605>, the innovative outlier robust filter of Ruckdeschel et al. (2014) <arXiv:1204.3358>, as well as the innovative and additive outlier robust filter of Fisch et al. (2020) <arXiv:2007.03238>.
Author: Alexander Fisch [aut],
Daniel Grose [aut, cre],
Idris Eckley [ths],
Paul Fearnhead [ths],
Bardwell Lawrence [ctb]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between RobKF versions 1.0.0 dated 2020-09-01 and 1.0.1 dated 2021-02-10
DESCRIPTION | 8 +-- MD5 | 27 +++++------ build/partial.rdb |binary src/Get_Particle_Additive_Descendents.cpp | 6 +- src/Get_Particle_Descendents.cpp | 6 +- src/Get_Particle_Descendents_V.cpp | 4 - src/Get_Particle_Descendents_W.cpp | 4 - src/Get_Particle_Descendents_typical.cpp | 4 - src/Get_Particle_Innovative_Descendents.cpp | 6 +- src/Particle.cpp |only src/Particle.h | 67 ++++++++++++++-------------- src/Subsample_Particles.cpp | 2 src/initiate_Particle.cpp | 4 - src/prepare_Particles.cpp | 4 - src/update_Particle.cpp | 2 15 files changed, 73 insertions(+), 71 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 3.1.5 dated 2021-01-18 and 3.1.6 dated 2021-02-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ inst/WORDLIST | 1 + tests/testthat/helper_rfishbase.R | 9 +++------ tests/testthat/test-db_create.R | 1 + 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Rcpp Bindings for Sequential Monte Carlo
Description: R access to the Sequential Monte Carlo Template Classes
by Johansen <doi:10.18637/jss.v030.i06> is provided. At present, four
additional examples have been added, and the first example from the JSS
paper has been extended. Further integration and extensions are planned.
Author: Dirk Eddelbuettel, Adam M. Johansen and Leah F. South
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSMC versions 0.2.2 dated 2020-08-30 and 0.2.3 dated 2021-02-10
ChangeLog | 36 +++++++ DESCRIPTION | 8 - MD5 | 46 ++++----- R/RcppExports.R | 62 ++++++------- README.md | 3 inst/NEWS.Rd | 8 + inst/include/LinReg.h | 20 +++- inst/include/LinReg_LA.h | 21 +++- inst/include/LinReg_LA_adapt.h | 27 ++++- inst/include/blockpfgaussianopt.h | 16 ++- inst/include/moveset.h | 178 +++++++++++--------------------------- inst/include/nonLinPMMH.h | 16 ++- inst/include/pflineart.h | 18 +++ inst/include/pfnonlinbs.h | 21 +++- inst/include/sampler.h | 77 ++++++++++++++-- inst/include/smctc.h | 24 ++--- src/LinReg.cpp | 47 +++++----- src/LinReg_LA.cpp | 13 +- src/LinReg_LA_adapt.cpp | 12 +- src/RcppExports.cpp | 24 ++--- src/blockpfgaussianopt.cpp | 11 +- src/nonLinPMMH.cpp | 11 +- src/pflineart.cpp | 12 +- src/pfnonlinbs.cpp | 11 +- 24 files changed, 420 insertions(+), 302 deletions(-)
Title: A Platform for the Study of Macro-Ecology of Life History Traits
Description: Tools for generation of (life-history) traits and diversity maps on hexagonal or square grids. Valcu et al.(2012) <doi:10.1111/j.1466-8238.2011.00739.x>.
Author: Mihai Valcu [aut, cre] (<https://orcid.org/0000-0002-6907-7802>),
James Dale [aut] (<https://orcid.org/0000-0001-5950-5829>),
Joan Maspons [ctb]
Maintainer: Mihai Valcu <valcu@orn.mpg.de>
Diff between rangeMapper versions 2.0.0 dated 2021-02-05 and 2.0.1 dated 2021-02-10
DESCRIPTION | 10 MD5 | 52 ++-- NAMESPACE | 1 R/2_prepare.R | 301 +++++++++++++++++----------- R/3_subset.R | 5 R/4_maps.R | 2 R/5_get.R | 2 R/utils.R | 4 R/zzz.R | 26 ++ README.md |only inst/doc/Case_studies_Valcu_et_al_2012.R | 16 + inst/doc/Case_studies_Valcu_et_al_2012.Rmd | 16 + inst/doc/Case_studies_Valcu_et_al_2012.html | 53 ++-- inst/doc/rangeMapper.R | 2 inst/doc/rangeMapper.Rmd | 2 inst/doc/rangeMapper.html | 2 man/rangeMapper.Rd |only man/rmap_prepare.Rd | 29 +- man/rmap_save_map.Rd | 2 man/rmap_save_subset.Rd | 4 man/rmap_to_sf.Rd | 2 tests/testthat/test-1_utilities.R | 4 tests/testthat/test-2_prepare.R | 60 +++++ tests/testthat/test-3_subsets.R | 2 tests/testthat/test-4_maps.R | 2 tests/testthat/test-5_get.R | 2 vignettes/Case_studies_Valcu_et_al_2012.Rmd | 16 + vignettes/rangeMapper.Rmd | 2 28 files changed, 404 insertions(+), 215 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout variable importance. Visualize trees on your Safari or Google Chrome browser.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.10.0 dated 2021-01-31 and 2.10.1 dated 2021-02-10
DESCRIPTION | 10 +++---- MD5 | 33 +++++++++++------------ R/anonymous.utilities.R |only R/generic.predict.rfsrc.R | 18 +++++++++++- R/get.tree.rfsrc.R | 3 -- R/partial.rfsrc.R | 10 +++++-- R/rfsrc.R | 4 +- R/utilities.R | 2 - configure | 18 ++++++------ configure.ac | 2 - inst/NEWS | 4 +- man/holdout.vimp.rfsrc.Rd | 5 +++ man/max.subtree.rfsrc.Rd | 2 - man/rfsrc.Rd | 61 +++++++++++++++++++++++++++---------------- man/vimp.rfsrc.Rd | 5 ++- src/R_init_randomForestSRC.c | 4 +- src/randomForestSRC.c | 2 - src/randomForestSRC.h | 4 +- 18 files changed, 116 insertions(+), 71 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Build MultiClass Pair-Based Classifiers using TSPs or RF
Description: A toolbox to train a single sample classifier that uses in-sample feature relationships. The relationships are represented as feature1 < feature2 (e.g. gene1 < gene2). We provide two options to go with. First is based on 'switchBox' package which uses Top-score pairs algorithm. Second is a novel implementation based on random forest algorithm. For simple problems we recommend to use one-vs-rest using TSP option due to its simplicity and for being easy to interpret. For complex problems RF performs better. Both lines filter the features first then combine the filtered features to make the list of all the possible rules (i.e. rule1: feature1 < feature2, rule2: feature1 < feature3, etc...). Then the list of rules will be filtered and the most important and informative rules will be kept. The informative rules will be assembled in an one-vs-rest model or in an RF model. We provide a detailed description with each function in this package to explain the filtration and training methodology in each line. Reference: Marzouka & Eriksson (2021) <doi:10.1093/bioinformatics/btab088>.
Author: Nour-al-dain Marzouka
Maintainer: Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>
Diff between multiclassPairs versions 0.4.1 dated 2021-01-26 and 0.4.2 dated 2021-02-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/doc/Tutorial.html | 30 +++++++++++++++--------------- 3 files changed, 21 insertions(+), 21 deletions(-)
More information about multiclassPairs at CRAN
Permanent link
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using automatically generated C functions. Please
note that no warranty is implied for correctness of results or fitness for a
particular purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb] (contributed to mkinresplot()),
René Lehmann [ctb] (ilr() and invilr()),
Eurofins Regulatory AG [cph] (copyright for some of the contributions
of JR 2012-2014)
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 1.0.0 dated 2021-02-03 and 1.0.1 dated 2021-02-10
mkin-1.0.0/mkin/man/print.mmkin.Rd |only mkin-1.0.1/mkin/DESCRIPTION | 8 mkin-1.0.1/mkin/MD5 | 51 ++--- mkin-1.0.1/mkin/NEWS.md | 12 + mkin-1.0.1/mkin/R/confint.mkinfit.R | 8 mkin-1.0.1/mkin/R/logLik.mkinfit.R | 6 mkin-1.0.1/mkin/R/mkinfit.R | 2 mkin-1.0.1/mkin/R/mkinresplot.R | 2 mkin-1.0.1/mkin/R/mmkin.R | 1 mkin-1.0.1/mkin/R/nlme.mmkin.R | 36 ++-- mkin-1.0.1/mkin/R/transform_odeparms.R | 18 +- mkin-1.0.1/mkin/README.md | 2 mkin-1.0.1/mkin/build/partial.rdb |binary mkin-1.0.1/mkin/inst/doc/FOCUS_D.html | 35 ++-- mkin-1.0.1/mkin/inst/doc/FOCUS_L.html | 155 +++++++++--------- mkin-1.0.1/mkin/inst/doc/mkin.html | 35 ++-- mkin-1.0.1/mkin/inst/doc/twa.html | 37 +++- mkin-1.0.1/mkin/man/confint.mkinfit.Rd | 8 mkin-1.0.1/mkin/man/logLik.mkinfit.Rd | 6 mkin-1.0.1/mkin/man/mkinresplot.Rd | 2 mkin-1.0.1/mkin/man/mmkin.Rd | 7 mkin-1.0.1/mkin/man/nlme.mmkin.Rd | 37 ++-- mkin-1.0.1/mkin/man/transform_odeparms.Rd | 18 +- mkin-1.0.1/mkin/tests/testthat/print_mmkin_parent.txt | 12 - mkin-1.0.1/mkin/tests/testthat/test_confidence.R | 9 - mkin-1.0.1/mkin/tests/testthat/test_error_models.R | 8 mkin-1.0.1/mkin/tests/testthat/test_mixed.R | 2 27 files changed, 302 insertions(+), 215 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories
(also known as a Sankey diagram), flow charts by extending the grid package,
a method for variable selection based on the SVD, Bézier lines with arrows
complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.11.0 dated 2020-07-03 and 2.0.1 dated 2021-02-10
DESCRIPTION | 10 +- MD5 | 48 ++++++------ NEWS | 4 + R/docx_document.R | 4 - R/fastDoCall.R | 2 R/mergeLists.R | 49 +++++++++++-- build/vignette.rds |binary inst/doc/Descriptives.Rmd | 2 inst/doc/Descriptives.html | 97 ++++++++++++-------------- inst/doc/Grid-based_flowcharts.html | 39 ++++------ inst/doc/Transition-class.R | 3 inst/doc/Transition-class.Rmd | 3 inst/doc/Transition-class.html | 43 +++++------ inst/doc/transitionPlot.R | 3 inst/doc/transitionPlot.Rmd | 3 inst/doc/transitionPlot.html | 40 +++++----- man/docx_document.Rd | 2 man/fastDoCall.Rd | 2 man/mergeLists.Rd | 9 ++ tests/testthat/Rplots.pdf |binary tests/testthat/test-mergeLists.R | 49 ++++++++----- tests/visual_tests/FTP_test/Setup_and_munge.R | 9 +- vignettes/Descriptives.Rmd | 2 vignettes/Transition-class.Rmd | 3 vignettes/transitionPlot.Rmd | 3 25 files changed, 238 insertions(+), 191 deletions(-)
Title: Create Constraints for Small Test Assembly Problems
Description: Provides simple functions to create constraints for small test assembly problems
(e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently,
'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from
any mainstream repository; see <https://www.gurobi.com/downloads/>.
Author: Benjamin Becker [aut, cre],
Dries Debeer [aut]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatATA versions 0.9.1 dated 2020-12-07 and 0.10.0 dated 2021-02-10
eatATA-0.10.0/eatATA/DESCRIPTION | 12 eatATA-0.10.0/eatATA/MD5 | 162 +++--- eatATA-0.10.0/eatATA/NAMESPACE | 68 +- eatATA-0.10.0/eatATA/NEWS.md | 20 eatATA-0.10.0/eatATA/R/analyzeBlockExclusion.R | 39 - eatATA-0.10.0/eatATA/R/analyzeComplexBlockExclusion.R |only eatATA-0.10.0/eatATA/R/appendSolution.R | 22 eatATA-0.10.0/eatATA/R/autoItemValuesMinMax.R | 31 - eatATA-0.10.0/eatATA/R/calculateIIF.R | 33 - eatATA-0.10.0/eatATA/R/check_solverOut.R | 5 eatATA-0.10.0/eatATA/R/computeTargetValues.R | 4 eatATA-0.10.0/eatATA/R/constraint-methods.R |only eatATA-0.10.0/eatATA/R/depletePoolConstraint.R | 10 eatATA-0.10.0/eatATA/R/input_checks.R | 19 eatATA-0.10.0/eatATA/R/inspectSolution.R | 37 - eatATA-0.10.0/eatATA/R/itemCategoryConstraint.R | 40 - eatATA-0.10.0/eatATA/R/itemCategoryMinMax.R | 64 ++ eatATA-0.10.0/eatATA/R/itemExclusionConstraint.R | 106 +++- eatATA-0.10.0/eatATA/R/itemUsageConstraint.R | 59 +- eatATA-0.10.0/eatATA/R/itemValuesConstraint.R | 60 +- eatATA-0.10.0/eatATA/R/itemValuesMinMax.R | 69 ++ eatATA-0.10.0/eatATA/R/itemsPerFormConstraint.R | 23 eatATA-0.10.0/eatATA/R/items_sim.R |only eatATA-0.10.0/eatATA/R/matrixExlusionTuples.R | 94 +-- eatATA-0.10.0/eatATA/R/objectiveConstraint.R |only eatATA-0.10.0/eatATA/R/useSolver.R | 175 ++++-- eatATA-0.10.0/eatATA/R/utils.R |only eatATA-0.10.0/eatATA/README.md | 4 eatATA-0.10.0/eatATA/build/vignette.rds |binary eatATA-0.10.0/eatATA/data/items_sim.rda |only eatATA-0.10.0/eatATA/inst/doc/minimal_example.R |only eatATA-0.10.0/eatATA/inst/doc/minimal_example.Rmd |only eatATA-0.10.0/eatATA/inst/doc/minimal_example.html |only eatATA-0.10.0/eatATA/inst/doc/overview.R |only eatATA-0.10.0/eatATA/inst/doc/overview.Rmd |only eatATA-0.10.0/eatATA/inst/doc/overview.html |only eatATA-0.10.0/eatATA/inst/doc/use_case_pilot_study.R |only eatATA-0.10.0/eatATA/inst/doc/use_case_pilot_study.Rmd |only eatATA-0.10.0/eatATA/inst/doc/use_case_pilot_study.html |only eatATA-0.10.0/eatATA/man/analyzeBlockExclusion.Rd | 127 ++--- eatATA-0.10.0/eatATA/man/analyzeComplexBlockExclusion.Rd | 4 eatATA-0.10.0/eatATA/man/appendSolution.Rd | 86 +-- eatATA-0.10.0/eatATA/man/autoItemValuesMinMax.Rd | 94 ++- eatATA-0.10.0/eatATA/man/calculateExpectedRT.Rd | 120 ++-- eatATA-0.10.0/eatATA/man/calculateIIF.Rd | 81 +-- eatATA-0.10.0/eatATA/man/cappedMaximinConstraint.Rd |only eatATA-0.10.0/eatATA/man/combineConstraints.Rd |only eatATA-0.10.0/eatATA/man/computeTargetValues.Rd | 252 +++++----- eatATA-0.10.0/eatATA/man/depletePoolConstraint.Rd | 50 + eatATA-0.10.0/eatATA/man/dummiesToFactor.Rd | 68 +- eatATA-0.10.0/eatATA/man/inspectSolution.Rd | 106 ++-- eatATA-0.10.0/eatATA/man/itemCategoryConstraint.Rd | 102 ++-- eatATA-0.10.0/eatATA/man/itemCategoryRange.Rd | 195 ++++--- eatATA-0.10.0/eatATA/man/itemExclusionConstraint.Rd | 110 ++-- eatATA-0.10.0/eatATA/man/itemExclusionTuples.Rd | 76 +-- eatATA-0.10.0/eatATA/man/itemUsageConstraint.Rd | 105 ++-- eatATA-0.10.0/eatATA/man/itemValuesConstraint.Rd | 97 ++- eatATA-0.10.0/eatATA/man/itemValuesRange.Rd | 181 ++++--- eatATA-0.10.0/eatATA/man/items.Rd | 48 - eatATA-0.10.0/eatATA/man/itemsPerFormConstraint.Rd | 91 +-- eatATA-0.10.0/eatATA/man/items_sim.Rd |only eatATA-0.10.0/eatATA/man/matrixExclusionTuples.Rd | 68 +- eatATA-0.10.0/eatATA/man/maxConstraint.Rd |only eatATA-0.10.0/eatATA/man/maximinConstraint.Rd |only eatATA-0.10.0/eatATA/man/minConstraint.Rd |only eatATA-0.10.0/eatATA/man/minimaxConstraint.Rd |only eatATA-0.10.0/eatATA/man/useSolver.Rd | 137 ++--- eatATA-0.10.0/eatATA/tests/testthat/helper_complexBlockExclusions.RData |binary eatATA-0.10.0/eatATA/tests/testthat/test_analyzeBlockExclusion.R | 17 eatATA-0.10.0/eatATA/tests/testthat/test_analyzeComplexBlockExclusion.R |only eatATA-0.10.0/eatATA/tests/testthat/test_appendSolution.R | 24 eatATA-0.10.0/eatATA/tests/testthat/test_autoItemValuesMinMax.R | 54 +- eatATA-0.10.0/eatATA/tests/testthat/test_check_solverOut.R | 26 - eatATA-0.10.0/eatATA/tests/testthat/test_depletePoolConstraint.R | 8 eatATA-0.10.0/eatATA/tests/testthat/test_input_checks.R | 23 eatATA-0.10.0/eatATA/tests/testthat/test_inspectSolution.R | 28 - eatATA-0.10.0/eatATA/tests/testthat/test_itemCategoryConstraint.R | 83 +-- eatATA-0.10.0/eatATA/tests/testthat/test_itemExclusionConstraint.R | 82 ++- eatATA-0.10.0/eatATA/tests/testthat/test_itemUsageConstraint.R | 51 +- eatATA-0.10.0/eatATA/tests/testthat/test_itemValuesConstraint.R | 75 +- eatATA-0.10.0/eatATA/tests/testthat/test_itemsPerFormConstraint.R | 25 eatATA-0.10.0/eatATA/tests/testthat/test_matrixExclusionTuples.R | 64 +- eatATA-0.10.0/eatATA/tests/testthat/test_objectiveConstraint.R |only eatATA-0.10.0/eatATA/tests/testthat/test_useSolver.R | 102 +++- eatATA-0.10.0/eatATA/tests/testthat/test_utils.R |only eatATA-0.10.0/eatATA/vignettes/minimal_example.Rmd |only eatATA-0.10.0/eatATA/vignettes/overview.Rmd |only eatATA-0.10.0/eatATA/vignettes/use_case_output.RDS |only eatATA-0.10.0/eatATA/vignettes/use_case_pilot_study.Rmd |only eatATA-0.10.0/eatATA/vignettes/use_case_solver_out.RDS |only eatATA-0.9.1/eatATA/R/analyzeComplexeBlockExclusion.R |only eatATA-0.9.1/eatATA/R/gurobiExample.R |only eatATA-0.9.1/eatATA/R/itemExclusionTuples.R |only eatATA-0.9.1/eatATA/R/itemTargetConstraint.R |only eatATA-0.9.1/eatATA/data/gurobiExample.rda |only eatATA-0.9.1/eatATA/inst/doc/eatATA.R |only eatATA-0.9.1/eatATA/inst/doc/eatATA.Rmd |only eatATA-0.9.1/eatATA/inst/doc/eatATA.html |only eatATA-0.9.1/eatATA/man/gurobiExample.Rd |only eatATA-0.9.1/eatATA/man/itemTargetConstraint.Rd |only eatATA-0.9.1/eatATA/tests/testthat/test_analyzeComplexeBlockExclusion.R |only eatATA-0.9.1/eatATA/tests/testthat/test_itemExclusionTuples.R |only eatATA-0.9.1/eatATA/tests/testthat/test_itemTargetConstraint.R |only eatATA-0.9.1/eatATA/vignettes/eatATA.Rmd |only 104 files changed, 2344 insertions(+), 1672 deletions(-)
Title: Interactive and Reproducible Data Cleaning
Description: Flexible and efficient cleaning of data with interactivity.
'datacleanr' facilitates best practices in data analyses and reproducibility with built-in features and by translating interactive/manual operations to code.
The package is designed for interoperability, and so seamlessly fits into reproducible analyses pipelines in 'R'.
Author: Alexander Hurley [cre, aut, cph]
(<https://orcid.org/0000-0002-9641-2805>),
Richard Peters [ctb] (<https://orcid.org/0000-0002-7441-1297>),
Christoforos Pappas [ctb] (<https://orcid.org/0000-0001-5721-557X>)
Maintainer: Alexander Hurley <agl.hurley@gmail.com>
Diff between datacleanr versions 1.0.0 dated 2020-11-02 and 1.0.1 dated 2021-02-10
DESCRIPTION | 20 MD5 | 76 NEWS.md | 13 R/datacleaner_ui.R | 689 ++--- R/datacleanr_app.R | 83 R/datacleanr_server.R | 2880 ++++++++++++----------- R/module_annotation_button.R | 71 R/module_annotation_table.R | 134 - R/module_apply_reset.R | 53 R/module_data_summary.R | 89 R/module_dynamic_histograms.R | 228 - R/module_extract_code_box.R | 603 ++-- R/module_extract_code_fileconfig.R | 373 +- R/module_filter_df.R | 118 R/module_filter_str_select_box.R | 122 R/module_group_selector_table.R | 48 R/module_grouptable_relayout.R | 101 R/module_plot_lowercontrol_buttons.R | 198 - R/module_plot_selectable.R | 254 +- R/module_plot_selectorcontrols.R | 144 - R/module_render_group_summary_checkbox.R | 59 R/module_set_grouping_selection.R | 60 R/utils.R | 1234 ++++----- README.md | 15 man/dcr_app.Rd | 14 man/filter_scoped_df.Rd | 17 man/module_server_summary.Rd | 16 man/navbarPageWithInputs.Rd | 3 tests/testthat/test-check_individual_statement.R | 40 tests/testthat/test-dcr_checks.R | 130 - tests/testthat/test-filter_scoped.R | 207 - tests/testthat/test-make_group_table.R | 6 tests/testthat/test.get_factor_cols_idx.R | 13 tests/testthat/test_apply_df_setup.R | 21 tests/testthat/test_calc_limits_per_groups.R | 230 - tests/testthat/test_extend_palette.R | 20 tests/testthat/test_hide_trace_idx.R | 46 tests/testthat/test_make_save_filepath.R | 17 tests/testthat/test_sel_outliers.R | 85 39 files changed, 4393 insertions(+), 4137 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the project to download a template to create a structure of directories and scripts.
Author: Sergio Ibarra-Espinosa [aut, cre, wdc]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between vein versions 0.9.0.1 dated 2020-10-13 and 0.9.1 dated 2021-02-10
vein-0.9.0.1/vein/tests |only vein-0.9.1/vein/DESCRIPTION | 10 vein-0.9.1/vein/MD5 | 146 +------ vein-0.9.1/vein/NAMESPACE | 10 vein-0.9.1/vein/NEWS.md | 33 + vein-0.9.1/vein/R/GriddedEmissionsArray.R | 167 +++++--- vein-0.9.1/vein/R/colplot.R | 398 +++++-------------- vein-0.9.1/vein/R/ef_cetesb.R | 462 ++++++++++++++++++---- vein-0.9.1/vein/R/ef_emfac.R |only vein-0.9.1/vein/R/ef_hdv_speed.R | 23 - vein-0.9.1/vein/R/emis.R | 165 ++++++- vein-0.9.1/vein/R/emis_chem2.R |only vein-0.9.1/vein/R/emis_cold_td.R | 319 ++++++++++++--- vein-0.9.1/vein/R/emis_hot_td.R | 392 +++++++++++++++--- vein-0.9.1/vein/R/emis_order.R | 2 vein-0.9.1/vein/R/get_project.R | 98 ++++ vein-0.9.1/vein/R/speciate.R | 563 +++++++++++++-------------- vein-0.9.1/vein/R/sysdata.rda |binary vein-0.9.1/vein/R/threads.R |only vein-0.9.1/vein/build/vignette.rds |binary vein-0.9.1/vein/data/pollutants.rda |binary vein-0.9.1/vein/inst/README.Rmd | 137 +----- vein-0.9.1/vein/inst/doc/basics.Rmd | 8 vein-0.9.1/vein/inst/doc/basics.html | 297 -------------- vein-0.9.1/vein/man/GriddedEmissionsArray.Rd | 32 + vein-0.9.1/vein/man/check_nt.Rd |only vein-0.9.1/vein/man/colplot.Rd | 3 vein-0.9.1/vein/man/ef_cetesb.Rd | 50 +- vein-0.9.1/vein/man/ef_emfac.Rd |only vein-0.9.1/vein/man/ef_hdv_speed.Rd | 23 - vein-0.9.1/vein/man/emis.Rd | 6 vein-0.9.1/vein/man/emis_chem2.Rd |only vein-0.9.1/vein/man/emis_cold_td.Rd | 6 vein-0.9.1/vein/man/emis_hot_td.Rd | 14 vein-0.9.1/vein/man/get_project.Rd | 18 vein-0.9.1/vein/man/speciate.Rd | 137 ++++-- vein-0.9.1/vein/src/Makevars | 3 vein-0.9.1/vein/src/e_bottomup.f95 | 101 ++++ vein-0.9.1/vein/src/e_topdown.f95 | 469 +++++++++++++++++++++- vein-0.9.1/vein/src/init.c | 56 ++ vein-0.9.1/vein/src/threads.f95 |only vein-0.9.1/vein/vignettes/basics.Rmd | 8 42 files changed, 2601 insertions(+), 1555 deletions(-)
Title: Residential Energy Consumption Data
Description: Datasets with energy consumption data of different data measurement frequencies.
The data stems from several publicly funded research projects of the Chair of Information
Systems and Energy Efficient Systems at the University of Bamberg.
Author: Konstantin Hopf [aut, cre] (<https://orcid.org/0000-0002-5452-0672>),
Andreas Weigert [aut] (<https://orcid.org/0000-0002-8093-3710>),
Nicolai Weinig [ctb],
Thorsten Staake [aut] (<https://orcid.org/0000-0003-1399-4676>)
Maintainer: Konstantin Hopf <konstantin.hopf@uni-bamberg.de>
Diff between ResidentialEnergyConsumption versions 1.0.1 dated 2020-08-17 and 1.1.0 dated 2021-02-10
DESCRIPTION | 19 ++++++++++--------- MD5 | 18 +++++++++--------- R/data.R | 39 +++++++++++++++++++++++++++------------ data/elcons_15min.rda |binary data/heatinginfo_15min.rda |binary data/solarcadaster_features.rda |binary data/weather_data.rda |binary man/heatinginfo_15min.Rd | 6 +++++- man/solarcadaster_features.Rd | 10 +++++----- man/weather_data.Rd | 23 ++++++++++++++++++----- 10 files changed, 74 insertions(+), 41 deletions(-)
More information about ResidentialEnergyConsumption at CRAN
Permanent link
Title: Pretty Base Graphics
Description: Drop-in replacements for standard base graphics
functions. The replacements are prettier versions of the originals.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between prettyB versions 0.2.1 dated 2019-05-17 and 0.2.2 dated 2021-02-10
prettyB-0.2.1/prettyB/R/qqnorm.R |only prettyB-0.2.1/prettyB/tests/testthat/test_lint.R |only prettyB-0.2.2/prettyB/DESCRIPTION | 31 - prettyB-0.2.2/prettyB/MD5 | 68 +- prettyB-0.2.2/prettyB/NAMESPACE | 2 prettyB-0.2.2/prettyB/NEWS.md | 9 prettyB-0.2.2/prettyB/R/barplot.R | 29 - prettyB-0.2.2/prettyB/R/par.R | 22 prettyB-0.2.2/prettyB/R/plot.R | 78 ++ prettyB-0.2.2/prettyB/R/prettyB-package.R | 3 prettyB-0.2.2/prettyB/R/qqnorm_minimal.R | 4 prettyB-0.2.2/prettyB/R/ticks_title.R | 12 prettyB-0.2.2/prettyB/R/zzz.R | 2 prettyB-0.2.2/prettyB/README.md | 42 - prettyB-0.2.2/prettyB/build/vignette.rds |binary prettyB-0.2.2/prettyB/inst/doc/introduction.R | 18 prettyB-0.2.2/prettyB/inst/doc/introduction.html | 272 +--------- prettyB-0.2.2/prettyB/man/add_y_axis.Rd |only prettyB-0.2.2/prettyB/man/barplot.prettyB.Rd | 80 ++ prettyB-0.2.2/prettyB/man/boxplot.prettyB.Rd | 44 + prettyB-0.2.2/prettyB/man/figures/README-plot-minimal-1.png |binary prettyB-0.2.2/prettyB/man/figures/README-plot-minimal-full-1.png |binary prettyB-0.2.2/prettyB/man/figures/README-unnamed-chunk-6-1.png |binary prettyB-0.2.2/prettyB/man/figures/README-unnamed-chunk-7-1.png |binary prettyB-0.2.2/prettyB/man/hist.prettyB.Rd | 58 +- prettyB-0.2.2/prettyB/man/plot.prettyB.Rd | 51 + prettyB-0.2.2/prettyB/man/prettyB-package.Rd | 3 prettyB-0.2.2/prettyB/tests/figs/barplot/barplot-basic-no-axisnames.svg |only prettyB-0.2.2/prettyB/tests/figs/deps.txt | 4 prettyB-0.2.2/prettyB/tests/figs/plotting/plot-x-y-mat-single-vector.svg |only prettyB-0.2.2/prettyB/tests/figs/plotting/plot-x-y-mat-single.svg |only prettyB-0.2.2/prettyB/tests/figs/plotting/plot-x-y-mat.svg |only prettyB-0.2.2/prettyB/tests/testthat.R | 4 prettyB-0.2.2/prettyB/tests/testthat/helper-utils.R |only prettyB-0.2.2/prettyB/tests/testthat/test_barplot.R | 10 prettyB-0.2.2/prettyB/tests/testthat/test_boxplot.R | 9 prettyB-0.2.2/prettyB/tests/testthat/test_hist.R | 9 prettyB-0.2.2/prettyB/tests/testthat/test_plot.R | 31 - prettyB-0.2.2/prettyB/tests/testthat/test_s3_plot.R | 2 39 files changed, 465 insertions(+), 432 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut],
Yan-Han Chen [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-29 dated 2020-05-11 and 0.1-30 dated 2021-02-10
ChangeLog | 3 +++ DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- inst/doc/index_doc.html | 16 ++++++++-------- inst/doc/phyclust-guide.Rnw | 6 +----- inst/doc/phyclust-guide.pdf |binary vignettes/index_doc.html | 16 ++++++++-------- vignettes/phyclust-guide.Rnw | 6 +----- vignettes/phyclust-include/01-introduction.tex | 6 +++--- vignettes/phyclust-include/03-msseqgen.tex | 2 +- vignettes/phyclust-include/04-phyclust.tex | 2 +- vignettes/phyclust-include/05-paml_baseml.tex | 2 +- 12 files changed, 43 insertions(+), 48 deletions(-)
Title: Calculating Ontological Similarities
Description: Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologySimilarity versions 2.4 dated 2021-02-10 and 2.5 dated 2021-02-10
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- inst/doc/ontologySimilarity-GO-example.R | 1 - inst/doc/ontologySimilarity-GO-example.Rmd | 1 - inst/doc/ontologySimilarity-GO-example.html | 6 +++--- inst/doc/ontologySimilarity-examples.R | 3 --- inst/doc/ontologySimilarity-examples.Rmd | 4 ---- inst/doc/ontologySimilarity-examples.html | 8 ++++---- inst/doc/ontologySimilarity-introduction.html | 4 ++-- vignettes/ontologySimilarity-GO-example.Rmd | 1 - vignettes/ontologySimilarity-examples.Rmd | 4 ---- 11 files changed, 24 insertions(+), 38 deletions(-)
More information about ontologySimilarity at CRAN
Permanent link
Title: Scaling with Ranked Subsampling
Description: Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is a popular method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. An alternative to rarefying is scaling with ranked subsampling (SRS). SRS consists of two steps. In the first step, the total counts for all OTUs (operational taxonomic units) or species in each sample are divided by a scaling factor chosen in such a way that the sum of the scaled counts Cscaled equals Cmin. In the second step, the non-integer Cscaled values are converted into integers by an algorithm that we dub ranked subsampling. The Cscaled value for each OTU or species is split into the integer part Cint (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cints). Since the sum of Cint is smaller or equal to Cmin, additional delta C = Cmin - the sum of Cint counts have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values. Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches delta C and the sum of all counts in the normalized library equals Cmin. When the lowest Cfrag involved in picking delta C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. OTUs with identical Cfrag as well as Cint are sampled randomly without replacement. See Beule & Karlovsky (2020) <doi:10.7717/peerj.9593> for details.
Author: Lukas Beule [aut, cre],
Vitor Heidrich [aut],
Devon O'rourke [aut],
Petr Karlovsky [aut]
Maintainer: Lukas Beule <lukas.beule@agr.uni-goettingen.de>
Diff between SRS versions 0.2.1 dated 2020-11-17 and 0.2.2 dated 2021-02-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/SRScurve.R | 10 ++++++---- 3 files changed, 11 insertions(+), 9 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
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.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 0.9.6 dated 2020-11-14 and 0.9.7 dated 2021-02-10
pedtools-0.9.6/pedtools/R/deprecated.R |only pedtools-0.9.7/pedtools/DESCRIPTION | 6 pedtools-0.9.7/pedtools/MD5 | 54 ++--- pedtools-0.9.7/pedtools/NAMESPACE | 5 pedtools-0.9.7/pedtools/NEWS.md | 28 ++ pedtools-0.9.7/pedtools/R/marker_accessors.R | 8 pedtools-0.9.7/pedtools/R/marker_transfer.R | 24 +- pedtools-0.9.7/pedtools/R/ped.R | 128 +++++++----- pedtools-0.9.7/pedtools/R/ped_accessors.R | 45 ++-- pedtools-0.9.7/pedtools/R/ped_connected.R | 25 +- pedtools-0.9.7/pedtools/R/ped_internal.R | 78 +++++-- pedtools-0.9.7/pedtools/R/ped_modify.R | 31 ++ pedtools-0.9.7/pedtools/R/ped_plot.R | 4 pedtools-0.9.7/pedtools/R/ped_subgroups.R | 39 ++- pedtools-0.9.7/pedtools/R/ped_utils.R | 15 + pedtools-0.9.7/pedtools/inst/doc/pedtools.html | 44 ---- pedtools-0.9.7/pedtools/man/connectedComponents.Rd | 15 - pedtools-0.9.7/pedtools/man/getComponent.Rd | 13 - pedtools-0.9.7/pedtools/man/getSex.Rd | 7 pedtools-0.9.7/pedtools/man/marker_getset.Rd | 3 pedtools-0.9.7/pedtools/man/newPed.Rd |only pedtools-0.9.7/pedtools/man/ped.Rd | 13 - pedtools-0.9.7/pedtools/man/ped_internal.Rd | 22 +- pedtools-0.9.7/pedtools/man/ped_modify.Rd | 2 pedtools-0.9.7/pedtools/man/ped_subgroups.Rd | 21 + pedtools-0.9.7/pedtools/man/transferMarkers.Rd | 12 - pedtools-0.9.7/pedtools/tests/testthat/test-ped-relatives.R | 16 + pedtools-0.9.7/pedtools/tests/testthat/test-ped-utils.R | 22 ++ pedtools-0.9.7/pedtools/tests/testthat/test-singleton.R | 7 29 files changed, 458 insertions(+), 229 deletions(-)
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Description: Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written to standard file formats.
Author: Lucas A. Nell [cph, aut, cre] (<https://orcid.org/0000-0003-3209-0517>)
Maintainer: Lucas A. Nell <lucas@lucasnell.com>
Diff between jackalope versions 1.1.1 dated 2020-06-15 and 1.1.2 dated 2021-02-10
DESCRIPTION | 10 MD5 | 31 +-- R/data.R | 2 README.md | 22 +- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/doc/jackalope-intro.Rmd | 2 inst/doc/jackalope-intro.html | 434 ++++++++++++------------------------------ inst/doc/sub-models.html | 193 +----------------- man/evo_rates.Rd | 8 man/haplotypes.Rd | 18 + man/ref_genome.Rd | 16 + src/hap_classes.h | 2 src/hts.h | 2 src/ref_hap_access.cpp | 2 vignettes/jackalope-intro.Rmd | 2 17 files changed, 225 insertions(+), 527 deletions(-)
Title: Systematic Screening of Study Data for Subgroup Effects
Description: Identifying outcome relevant subgroups has now become as simple as possible! The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation.
The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup.
The diagram may show thousands of them. The position of the dot in the diagram is determined by the
sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The
sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore,
the diagram shows the line of no effect and the overall study results. For small subgroups, which
are found on the left side of the plot, larger random deviations from the mean study effect are expected,
while for larger subgroups only small deviations from the study mean can be expected to be chance findings.
So for a study with no conspicuous subgroup effects, the dots in the figure are expected to form a
kind of funnel. Any deviations from this funnel shape hint to conspicuous subgroups.
This approach was presented in Muysers (2020) <doi:10.1007/s43441-019-00082-6> and referenced in Ballarini (2020) <doi:10.1002/pst.2012>.
New to version 3 is the Automatic Screening of one- or MUlti-factorial Subgroups (ASMUS) for documentation of the structured review of subgroup findings.
Author: Bodo Kirsch, Steffen Jeske, Susanne Lippert, Thomas Schmelter, Christoph Muysers, Hermann Kulmann
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Diff between subscreen versions 3.0.4 dated 2021-02-04 and 3.0.5 dated 2021-02-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/subscreencalc.R | 2 +- inst/doc/subscreen.html | 4 ++-- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Mass Spectrometry Tools
Description: Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element
isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks,
examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI)
ion sources.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between MSbox versions 1.2.2 dated 2020-08-10 and 1.3.8 dated 2021-02-10
MSbox-1.2.2/MSbox/R/Adduct.R |only MSbox-1.3.8/MSbox/DESCRIPTION | 9 +++-- MSbox-1.3.8/MSbox/MD5 | 50 ++++++++++++++++++++++--------- MSbox-1.3.8/MSbox/NAMESPACE | 38 +++++++++++++++++++++++ MSbox-1.3.8/MSbox/R/adduct.R |only MSbox-1.3.8/MSbox/R/contaminant.R | 2 - MSbox-1.3.8/MSbox/R/describe.R |only MSbox-1.3.8/MSbox/R/doNormalization.R |only MSbox-1.3.8/MSbox/R/doStat.R |only MSbox-1.3.8/MSbox/R/getCV.R |only MSbox-1.3.8/MSbox/R/getFC.R |only MSbox-1.3.8/MSbox/R/getMax.R |only MSbox-1.3.8/MSbox/R/getOPLSDA.R |only MSbox-1.3.8/MSbox/R/getP.R |only MSbox-1.3.8/MSbox/R/mass.R | 20 +++++++++--- MSbox-1.3.8/MSbox/R/mz.R | 33 +++++++++++++++----- MSbox-1.3.8/MSbox/R/sysdata.rda |binary MSbox-1.3.8/MSbox/R/viewPCA.R |only MSbox-1.3.8/MSbox/R/viewTIC.R |only MSbox-1.3.8/MSbox/R/viewVolcano.R |only MSbox-1.3.8/MSbox/R/what.R | 33 +++++++------------- MSbox-1.3.8/MSbox/README.md | 27 +++++----------- MSbox-1.3.8/MSbox/man/adduct.Rd | 2 - MSbox-1.3.8/MSbox/man/contam.Rd | 6 +-- MSbox-1.3.8/MSbox/man/describe.Rd |only MSbox-1.3.8/MSbox/man/doNormalization.Rd |only MSbox-1.3.8/MSbox/man/doStat.Rd |only MSbox-1.3.8/MSbox/man/getCV.Rd |only MSbox-1.3.8/MSbox/man/getFC.Rd |only MSbox-1.3.8/MSbox/man/getMax.Rd |only MSbox-1.3.8/MSbox/man/getOPLSDA.Rd |only MSbox-1.3.8/MSbox/man/getP.Rd |only MSbox-1.3.8/MSbox/man/mass.Rd | 15 ++++++--- MSbox-1.3.8/MSbox/man/mz.Rd | 20 ++++++++---- MSbox-1.3.8/MSbox/man/viewPCA.Rd |only MSbox-1.3.8/MSbox/man/viewTIC.Rd |only MSbox-1.3.8/MSbox/man/viewVolcano.Rd |only MSbox-1.3.8/MSbox/man/what.Rd | 1 38 files changed, 170 insertions(+), 86 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are
otherwise performed manually. This includes setting up unit testing,
test coverage, continuous integration, Git, 'GitHub', licenses,
'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between usethis versions 2.0.0 dated 2020-12-10 and 2.0.1 dated 2021-02-10
usethis-2.0.0/usethis/build |only usethis-2.0.1/usethis/DESCRIPTION | 9 - usethis-2.0.1/usethis/MD5 | 129 ++++++++-------- usethis-2.0.1/usethis/NAMESPACE | 3 usethis-2.0.1/usethis/NEWS.md | 26 ++- usethis-2.0.1/usethis/R/badge.R | 25 --- usethis-2.0.1/usethis/R/browse.R | 12 - usethis-2.0.1/usethis/R/ci.R | 2 usethis-2.0.1/usethis/R/create.R | 31 +++ usethis-2.0.1/usethis/R/data-table.R | 2 usethis-2.0.1/usethis/R/edit.R | 39 ++++ usethis-2.0.1/usethis/R/git.R | 2 usethis-2.0.1/usethis/R/github-actions.R | 11 - usethis-2.0.1/usethis/R/github-labels.R | 8 usethis-2.0.1/usethis/R/github-pages.R | 2 usethis-2.0.1/usethis/R/github.R | 18 +- usethis-2.0.1/usethis/R/helpers.R | 7 usethis-2.0.1/usethis/R/lifecycle.R | 30 +-- usethis-2.0.1/usethis/R/line-ending.R | 2 usethis-2.0.1/usethis/R/pkgdown.R | 52 ++---- usethis-2.0.1/usethis/R/pr.R | 14 - usethis-2.0.1/usethis/R/proj.R | 33 +--- usethis-2.0.1/usethis/R/readme.R | 30 ++- usethis-2.0.1/usethis/R/release.R | 52 ++++-- usethis-2.0.1/usethis/R/revdep.R | 5 usethis-2.0.1/usethis/R/roxygen.R | 4 usethis-2.0.1/usethis/R/rstudio.R | 2 usethis-2.0.1/usethis/R/tidyverse.R | 12 + usethis-2.0.1/usethis/R/tutorial.R | 6 usethis-2.0.1/usethis/R/usethis-defunct.R | 2 usethis-2.0.1/usethis/R/utils-github.R | 7 usethis-2.0.1/usethis/R/utils.R | 16 + usethis-2.0.1/usethis/R/version.R | 7 usethis-2.0.1/usethis/R/vignette.R | 22 +- usethis-2.0.1/usethis/README.md | 10 - usethis-2.0.1/usethis/inst/templates/pipe.R | 3 usethis-2.0.1/usethis/man/badges.Rd | 16 - usethis-2.0.1/usethis/man/ci.Rd | 2 usethis-2.0.1/usethis/man/create_from_github.Rd | 20 +- usethis-2.0.1/usethis/man/edit_file.Rd | 8 usethis-2.0.1/usethis/man/git_credentials.Rd | 2 usethis-2.0.1/usethis/man/tidyverse.Rd | 20 -- usethis-2.0.1/usethis/man/use_data_table.Rd | 2 usethis-2.0.1/usethis/man/use_github.Rd | 10 - usethis-2.0.1/usethis/man/use_github_labels.Rd | 8 usethis-2.0.1/usethis/man/use_github_links.Rd | 6 usethis-2.0.1/usethis/man/use_github_pages.Rd | 2 usethis-2.0.1/usethis/man/use_github_release.Rd | 6 usethis-2.0.1/usethis/man/use_lifecycle.Rd | 11 - usethis-2.0.1/usethis/man/use_pkgdown.Rd | 31 ++- usethis-2.0.1/usethis/tests/testthat/_snaps/badge.md |only usethis-2.0.1/usethis/tests/testthat/_snaps/release.md | 29 ++- usethis-2.0.1/usethis/tests/testthat/_snaps/vignette.md |only usethis-2.0.1/usethis/tests/testthat/test-badge.R | 8 usethis-2.0.1/usethis/tests/testthat/test-course.R | 7 usethis-2.0.1/usethis/tests/testthat/test-cpp11.R | 2 usethis-2.0.1/usethis/tests/testthat/test-create.R | 11 + usethis-2.0.1/usethis/tests/testthat/test-data-table.R | 2 usethis-2.0.1/usethis/tests/testthat/test-edit.R | 7 usethis-2.0.1/usethis/tests/testthat/test-lifecycle.R | 2 usethis-2.0.1/usethis/tests/testthat/test-pkgdown.R | 6 usethis-2.0.1/usethis/tests/testthat/test-rcpp.R | 4 usethis-2.0.1/usethis/tests/testthat/test-rstudio.R | 7 usethis-2.0.1/usethis/tests/testthat/test-tidyverse.R | 19 +- usethis-2.0.1/usethis/tests/testthat/test-tutorial.R | 2 usethis-2.0.1/usethis/tests/testthat/test-utils-git.R | 6 usethis-2.0.1/usethis/tests/testthat/test-vignette.R | 40 +++- 67 files changed, 529 insertions(+), 402 deletions(-)
Title: Sub-National Geospatial Data Archive: Geoprocessing Toolkit
Description: Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System (<https://www.nsf.gov/awardsearch/showAward?AWD_ID=1925693&HistoricalAwards=false>).
Author: Jason Byers, Marty Davidson, Yuri M. Zhukov
Maintainer: Yuri M. Zhukov <zhukov@umich.edu>
Diff between SUNGEO versions 0.2.0 dated 2020-12-14 and 0.2.1 dated 2021-02-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/point2poly_simp.R | 11 +++++++---- README.md | 2 +- man/point2poly_simp.Rd | 5 ++++- 5 files changed, 20 insertions(+), 14 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>),
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
Ray Cartwright [ctb],
Richard Condit [ctb],
Francis Crick [ctb],
Marcelino de la Cruz Rot [ctb],
Jack Cuzick [ctb],
Peter Diggle [ctb],
Michael Drinkwater [ctb],
Stephen Eglen [ctb],
Robert Edwards [ctb],
AE Esler [ctb],
Gregory Evans [ctb],
Bernard Fingleton [ctb],
Olivier Flores [ctb],
David Ford [ctb],
Robin Foster [ctb],
Janet Franklin [ctb],
Neba Funwi-Gabga [ctb],
DJ Gerrard [ctb],
Andy Green [ctb],
Tim Griffin [ctb],
Ute Hahn [ctb],
RD Harkness [ctb],
Arthur Hickman [ctb],
Stephen Hubbell [ctb],
Austin Hughes [ctb],
Jonathan Huntington [ctb],
MJ Hutchings [ctb],
Valerie Isham [ctb],
Aruna Jammalamadaka [ctb],
Carl Knox-Robinson [ctb],
Mahdieh Khanmohammadi [ctb],
Tero Kokkila [ctb],
Bas Kooijman [ctb],
Kenneth Kosik [ctb],
Peter Kovesi [ctb],
Lily Kozmian-Ledward [ctb],
Robert Lamb [ctb],
NA Laskurain [ctb],
George Leser [ctb],
Marie-Colette van Lieshout [ctb],
AF Mark [ctb],
Jorge Mateu [ctb],
Annikki Makela [ctb],
Enrique Miranda [ctb],
Nicoletta Nava [ctb],
M Numata [ctb],
Matti Nummelin [ctb],
Jens Randel Nyengaard [ctb],
Yosihiko Ogata [ctb],
Antti Penttinen [ctb],
Sandra Pereira [ctb],
Nicolas Picard [ctb],
William Platt [ctb],
Stephen Rathbun [ctb],
Brian Ripley [ctb],
Dietrich Stoyan [ctb],
David Strauss [ctb],
L Strand [ctb],
Masaharu Tanemura [ctb],
Graham Upton [ctb],
Bill Venables [ctb],
Sasha Voss [ctb],
Rasmus Waagepetersen [ctb],
Keith Watkins [ctb],
H Wendrock [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 1.7-0 dated 2020-12-16 and 2.0-0 dated 2021-02-10
DESCRIPTION | 169 ++++++++++++++++++++++++++++++++++++++++--- MD5 | 112 ++++++++++++++-------------- inst/doc/packagesizes.txt | 1 man/Kovesi.Rd | 4 - man/amacrine.Rd | 2 man/anemones.Rd | 4 - man/ants.Rd | 4 - man/austates.Rd | 2 man/bdspots.Rd | 2 man/bei.Rd | 4 - man/betacells.Rd | 4 - man/bramblecanes.Rd | 2 man/bronzefilter.Rd | 4 - man/cells.Rd | 2 man/cetaceans.Rd | 8 +- man/chicago.Rd | 6 - man/chorley.Rd | 8 +- man/clmfires.Rd | 6 - man/concrete.Rd | 6 - man/copper.Rd | 8 +- man/demohyper.Rd | 4 - man/demopat.Rd | 2 man/dendrite.Rd | 4 - man/finpines.Rd | 4 - man/flu.Rd | 6 - man/ganglia.Rd | 2 man/gordon.Rd | 2 man/gorillas.Rd | 10 +- man/hamster.Rd | 2 man/humberside.Rd | 8 +- man/hyytiala.Rd | 2 man/japanesepines.Rd | 2 man/lansing.Rd | 8 +- man/letterR.Rd | 2 man/longleaf.Rd | 4 - man/mucosa.Rd | 4 - man/murchison.Rd | 6 - man/nbfires.Rd | 10 +- man/nztrees.Rd | 2 man/osteo.Rd | 4 - man/paracou.Rd | 6 - man/ponderosa.Rd | 4 - man/pyramidal.Rd | 2 man/redwood.Rd | 6 - man/redwoodfull.Rd | 4 - man/residualspaper.Rd | 6 - man/shapley.Rd | 8 +- man/simdat.Rd | 2 man/spatstat.data-package.Rd | 2 man/spiders.Rd | 2 man/sporophores.Rd | 2 man/spruces.Rd | 6 - man/swedishpines.Rd | 4 - man/urkiola.Rd | 2 man/vesicles.Rd | 6 - man/waka.Rd | 2 man/waterstriders.Rd | 2 57 files changed, 331 insertions(+), 181 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 2.4-2 dated 2021-01-31 and 2.4-3 dated 2021-02-10
robustlmm-2.4-2/robustlmm/vignettes/jss.dtx |only robustlmm-2.4-3/robustlmm/DESCRIPTION | 8 - robustlmm-2.4-3/robustlmm/MD5 | 15 +-- robustlmm-2.4-3/robustlmm/build/vignette.rds |binary robustlmm-2.4-3/robustlmm/inst/doc/rlmer.R | 10 +- robustlmm-2.4-3/robustlmm/inst/doc/rlmer.Rnw | 122 +++++++++++++------------- robustlmm-2.4-3/robustlmm/inst/doc/rlmer.pdf |binary robustlmm-2.4-3/robustlmm/vignettes/rlmer.Rnw | 122 +++++++++++++------------- robustlmm-2.4-3/robustlmm/vignettes/rlmer.sty | 42 ++++---- 9 files changed, 159 insertions(+), 160 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 2.4.1 dated 2020-10-14 and 2.4.2 dated 2021-02-10
REndo-2.4.1/REndo/R/f_copulacorrection_LL.R |only REndo-2.4.2/REndo/DESCRIPTION | 8 ++++---- REndo-2.4.2/REndo/MD5 | 13 ++++++------- REndo-2.4.2/REndo/NAMESPACE | 1 - REndo-2.4.2/REndo/NEWS.md | 7 +++++++ REndo-2.4.2/REndo/R/f_copulacorrection_optimizeLL.R | 4 ++-- REndo-2.4.2/REndo/src/RcppExports.cpp | 8 ++++---- REndo-2.4.2/REndo/src/f_copulacorrection_LL_rcpp.cpp | 18 ++++++++---------- 8 files changed, 31 insertions(+), 28 deletions(-)
Title: Permutation Based Gene Expression Pathway Analysis
Description: Can be used to carry out permutation based gene expression pathway analysis. This work was supported by a National Institute of Allergy and Infectious Disease/National Institutes of Health contract (No. HHSN272200900059C).
Author: Ivo D. Shterev [aut, cre],
Kouros Owzar [aut],
Gregory D. Sempowski [aut],
Kenneth Wilder [ctb, cph] (wrote original version of ranker.h)
Maintainer: Ivo D. Shterev <i.shterev@gmail.com>
Diff between permPATH versions 1.1 dated 2017-06-09 and 1.2 dated 2021-02-10
permPATH-1.1/permPATH/R/permPath-internal.R |only permPATH-1.2/permPATH/DESCRIPTION | 11 +++++------ permPATH-1.2/permPATH/MD5 | 11 +++++------ permPATH-1.2/permPATH/build/vignette.rds |binary permPATH-1.2/permPATH/inst/doc/permPATHmanual.R | 6 +++--- permPATH-1.2/permPATH/inst/doc/permPATHmanual.pdf |binary permPATH-1.2/permPATH/man/permPATH2HTML.Rd | 4 ---- 7 files changed, 13 insertions(+), 19 deletions(-)
More information about PolyHaplotyper at CRAN
Permanent link
More information about ontologySimilarity at CRAN
Permanent link
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables, and functions to work with
hierarchical/multilevel batches of parameters
(Fernández-i-Marín, 2016 <doi:10.18637/jss.v070.i09>).
Author: Xavier Fernández i Marín [aut, cre]
(<https://orcid.org/0000-0002-9522-8870>)
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>
Diff between ggmcmc versions 1.5.0 dated 2020-08-29 and 1.5.1.1 dated 2021-02-10
DESCRIPTION | 9 MD5 | 20 - NAMESPACE | 2 R/ggs_pcp.R | 2 R/ggs_separation.R | 2 R/help.R | 2 inst/doc/using_ggmcmc.html | 529 ++++++++++++++++++++++++++++++++------------- inst/doc/v70i09.R | 2 inst/doc/v70i09.Rnw | 2 inst/doc/v70i09.pdf |binary vignettes/v70i09.Rnw | 2 11 files changed, 406 insertions(+), 166 deletions(-)
Title: Chaotic Time Series Analysis
Description: Chaos theory has been hailed as a revolution of thoughts and attracting ever increasing
attention of many scientists from diverse disciplines. Chaotic systems are nonlinear deterministic
dynamic systems which can behave like an erratic and apparently random motion. A relevant field
inside chaos theory and nonlinear time series analysis is the detection of a chaotic behaviour
from empirical time series data. One of the main features of chaos is the well known initial value
sensitivity property. Methods and techniques related to test the hypothesis of chaos try to quantify
the initial value sensitive property estimating the Lyapunov exponents. The DChaos package
provides different useful tools and efficient algorithms which test robustly the hypothesis of chaos
based on the Lyapunov exponent in order to know if the data generating process behind time series
behave chaotically or not.
Author: Julio E. Sandubete [aut, cre],
Lorenzo Escot [aut]
Maintainer: Julio E. Sandubete <jsandube@ucm.es>
Diff between DChaos versions 0.1-5 dated 2020-05-10 and 0.1-6 dated 2021-02-10
DESCRIPTION | 8 MD5 | 38 +-- R/embedding.R | 160 +++++++------ R/gauss.sim.R | 29 +- R/henon.sim.R | 46 +-- R/jacobian.net.R | 55 ++-- R/logistic.sim.R | 31 +- R/lyapunov.R | 197 +++++++++-------- R/lyapunov.max.R | 364 ++++++++++++++++--------------- R/lyapunov.spec.R | 590 +++++++++++++++++++++++++-------------------------- R/netfit.R | 73 +++--- R/rossler.sim.R | 94 ++++---- R/summary.lyapunov.R | 36 +-- R/w0.net.R | 39 ++- man/henon.sim.Rd | 4 man/jacobian.net.Rd | 5 man/lyapunov.Rd | 7 man/netfit.Rd | 5 man/rossler.sim.Rd | 4 man/w0.net.Rd | 5 20 files changed, 941 insertions(+), 849 deletions(-)
Title: Interface to the 'ASSP' Library
Description: A wrapper around Michel Scheffers's 'libassp' (<http://libassp.sourceforge.net/>).
The 'libassp' (Advanced Speech Signal Processor) library aims at providing
functionality for handling speech signal files in most common audio formats
and for performing analyses common in phonetic science/speech science. This
includes the calculation of formants, fundamental frequency, root mean
square, auto correlation, a variety of spectral analyses, zero crossing
rate, filtering etc. This wrapper provides R with a large subset of
'libassp's signal processing functions and provides them to the user in a
(hopefully) user-friendly manner.
Author: Raphael Winkelmann [aut, cre],
Lasse Bombien [aut],
Michel Scheffers [aut]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between wrassp versions 0.1.9 dated 2020-02-15 and 1.0.0 dated 2021-02-10
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 10 - README.md | 14 - build/vignette.rds |binary inst/doc/wrassp_intro.html | 410 ++++++++++++------------------------------- src/assp/asspfio.c | 177 +++++++++++------- src/dataobj.c | 4 tests/testthat/test_fileIO.R | 23 ++ 9 files changed, 284 insertions(+), 376 deletions(-)
Title: Multilingual Stopword Lists
Description: Provides multiple sources of stopwords, for use in text analysis and natural language processing.
Author: Kenneth Benoit [aut, cre],
David Muhr [aut],
Kohei Watanabe [aut]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between stopwords versions 2.1 dated 2020-12-08 and 2.2 dated 2021-02-10
stopwords-2.1/stopwords/R/use_stopwords.R |only stopwords-2.1/stopwords/inst/templates |only stopwords-2.1/stopwords/man/use_stopwords.Rd |only stopwords-2.2/stopwords/DESCRIPTION | 8 ++-- stopwords-2.2/stopwords/MD5 | 15 +++----- stopwords-2.2/stopwords/NAMESPACE | 4 -- stopwords-2.2/stopwords/NEWS.md | 4 ++ stopwords-2.2/stopwords/README.md | 50 ++++++++++++++------------- stopwords-2.2/stopwords/build/partial.rdb |binary stopwords-2.2/stopwords/inst/WORDLIST | 6 ++- 10 files changed, 45 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-05 0.4.1
2021-01-27 0.4.0
2020-11-17 0.3.14
2020-01-09 0.3.13
2019-10-21 0.3.12
2019-08-19 0.3.11
2019-03-16 0.3.9
2019-02-10 0.3.8
2018-07-21 0.3.2
2018-04-27 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-05 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-07 0.3.2
2020-03-20 0.3.0
Title: Perform the Joint Graphical Lasso and Selects Tuning Parameters
Description: Can be used to simultaneously estimate networks (Gaussian Graphical Models) in data from different groups or classes via Joint Graphical Lasso. Tuning parameters are selected via information criteria (AIC / BIC / extended BIC) or cross validation.
Author: Giulio Costantini, Nils Kappelmann, Sacha Epskamp
Maintainer: Giulio Costantini <giulio.costantini@unimib.it>
Diff between EstimateGroupNetwork versions 0.2.2 dated 2020-01-08 and 0.3.1 dated 2021-02-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/BootTable.R | 2 ++ R/GroupBootPlot.R | 5 +++-- R/GroupNetworkBoot.R | 9 ++++++++- man/BootTable.Rd | 2 ++ man/GroupBootPlot.Rd | 5 ++++- 8 files changed, 35 insertions(+), 14 deletions(-)
More information about EstimateGroupNetwork at CRAN
Permanent link
Title: Programming with Big Data -- Interface to 'ZeroMQ'
Description: 'ZeroMQ' is a well-known library for high-performance
asynchronous messaging in scalable, distributed applications. This
package provides high level R wrapper functions to easily utilize
'ZeroMQ'. We mainly focus on interactive client/server programming
frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2)
is shipped with 'pbdZMQ', which can be used if no system installation
of 'ZeroMQ' is available. A few wrapper functions compatible with
'rzmq' are also provided.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Christian Heckendorf [aut] (file transfer),
George Ostrouchov [aut] (Mac OSX),
Whit Armstrong [ctb] (some functions are modified from the rzmq package
for backwards compatibility),
Brian Ripley [ctb] (C code of shellexec, and Solaris),
R Core team [ctb] (some functions are modified from the R source code),
Philipp A. [ctb] (Fedora),
Elliott Sales de Andrade [ctb] (sprintf),
Spencer Aiello [ctb] (windows conf),
Paul Andrey [ctb] (Mac OSX conf),
Panagiotis Cheilaris [ctb] (add serialize version)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdZMQ versions 0.3-4 dated 2020-12-13 and 0.3-5 dated 2021-02-10
ChangeLog | 3 DESCRIPTION | 8 MD5 | 8 src/zmqsrc/config/config.guess | 1106 +++++++++-------- src/zmqsrc/config/config.sub | 2625 +++++++++++++++++++++-------------------- 5 files changed, 1982 insertions(+), 1768 deletions(-)
Title: Measurement of Biodiversity
Description: Functions for calculating metrics for the measurement biodiversity
and its changes across scales, treatments, and gradients. The methods
implemented in this package are described in:
Chase, J.M., et al. (2018) <doi:10.1111/ele.13151>,
McGlinn, D.J., et al. (2019) <doi:10.1111/2041-210X.13102>, and
McGlinn, D.J., et al. (2021) <doi:10.1002/ecy.3233>.
Author: Daniel McGlinn [aut, cre],
Xiao Xiao [aut],
Brian McGill [aut],
Felix May [aut],
Thore Engel [aut],
Caroline Oliver [aut],
Shane Blowes [aut],
Tiffany Knight [aut],
Oliver Purschke [aut],
Nicholas Gotelli [aut],
Jon Chase [aut]
Maintainer: Daniel McGlinn <danmcglinn@gmail.com>
Diff between mobr versions 2.0.0 dated 2020-09-21 and 2.0.2 dated 2021-02-10
DESCRIPTION | 10 ++-- MD5 | 36 ++++++++-------- NEWS.md | 20 +++++++++ R/mobr.R | 83 +++++++++++++++++++++++--------------- R/mobr_boxplots.R | 70 +++++++++++++++++++------------- README.md | 29 +++++++++---- inst/doc/mobr_intro.R | 30 ++++++------- inst/doc/mobr_intro.Rmd | 34 +++++++-------- inst/doc/mobr_intro.pdf |binary man/get_group_delta.Rd | 2 man/get_mob_stats.Rd | 12 ++++- man/plot_abu.Rd | 15 ++++-- man/plot_rarefaction.Rd | 21 +++++---- tests/testthat/test_rarefaction.R | 6 +- vignettes/fire_stats.Rdata |binary vignettes/inv_stats.Rdata |binary vignettes/mobr_intro.Rmd | 34 +++++++-------- vignettes/mobr_intro.html | 72 ++++++++++++++++---------------- vignettes/tank_stats.Rdata |binary 19 files changed, 281 insertions(+), 193 deletions(-)
Title: Explore the Innards of 'ggplot2' Objects
Description: Extensions to 'ggplot2' providing low-level debug tools: statistics
and geometries echoing their data argument. Layer manipulation: deletion,
insertion, extraction and reordering of layers. Deletion of unused variables
from the data object embedded in "ggplot" objects.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between gginnards versions 0.0.3 dated 2019-11-26 and 0.0.4 dated 2021-02-10
gginnards-0.0.3/gginnards/NEWS |only gginnards-0.0.4/gginnards/DESCRIPTION | 28 gginnards-0.0.4/gginnards/MD5 | 45 gginnards-0.0.4/gginnards/NAMESPACE | 2 gginnards-0.0.4/gginnards/NEWS.md |only gginnards-0.0.4/gginnards/R/data-manip.R | 13 gginnards-0.0.4/gginnards/R/geom-debug.R | 18 gginnards-0.0.4/gginnards/R/layer-manip.R | 47 gginnards-0.0.4/gginnards/README.md | 34 gginnards-0.0.4/gginnards/build/vignette.rds |binary gginnards-0.0.4/gginnards/inst/doc/user-guide-1.html | 585 +++------- gginnards-0.0.4/gginnards/inst/doc/user-guide-2.html | 445 ++----- gginnards-0.0.4/gginnards/man/delete_layers.Rd | 34 gginnards-0.0.4/gginnards/man/drop_vars.Rd | 9 gginnards-0.0.4/gginnards/man/figures/README-unnamed-chunk-2-1.png |binary gginnards-0.0.4/gginnards/man/figures/README-unnamed-chunk-3-1.png |binary gginnards-0.0.4/gginnards/man/figures/README-unnamed-chunk-4-1.png |binary gginnards-0.0.4/gginnards/man/figures/README-unnamed-chunk-5-1.png |binary gginnards-0.0.4/gginnards/man/figures/README-unnamed-chunk-6-1.png |binary gginnards-0.0.4/gginnards/man/figures/README-unnamed-chunk-6-2.png |binary gginnards-0.0.4/gginnards/man/figures/logo-gginnards.png |only gginnards-0.0.4/gginnards/man/geom_debug.Rd | 7 gginnards-0.0.4/gginnards/man/geom_null.Rd | 9 gginnards-0.0.4/gginnards/man/gginnards-ggproto.Rd | 30 gginnards-0.0.4/gginnards/man/gginnards-package.Rd | 12 25 files changed, 566 insertions(+), 752 deletions(-)
Title: Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Description: Local inferential feature significance for multivariate kernel density estimation.
Author: Tarn Duong [aut, cre],
Matt Wand [aut]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between feature versions 1.2.14 dated 2020-10-15 and 1.2.15 dated 2021-02-10
feature-1.2.14/feature/R/zzz.R |only feature-1.2.15/feature/DESCRIPTION | 15 +- feature-1.2.15/feature/MD5 | 35 ++-- feature-1.2.15/feature/R/SiZer.R | 5 feature-1.2.15/feature/R/addSignifFeatureData.R | 12 + feature-1.2.15/feature/R/addSignifFeatureRegion.R | 16 +- feature-1.2.15/feature/R/featureSignif.R | 1 feature-1.2.15/feature/R/featureSignifGUI.R | 18 -- feature-1.2.15/feature/R/plot.fs.R | 69 +++++---- feature-1.2.15/feature/build/vignette.rds |binary feature-1.2.15/feature/data/earthquake.RData |binary feature-1.2.15/feature/inst/doc/feature.R | 8 - feature-1.2.15/feature/inst/doc/feature.Rmd | 17 +- feature-1.2.15/feature/inst/doc/feature.html | 164 ++++++---------------- feature-1.2.15/feature/man/feature-package.Rd | 2 feature-1.2.15/feature/man/featureSignif.Rd | 29 +-- feature-1.2.15/feature/man/featureSignifGUI.Rd | 6 feature-1.2.15/feature/man/plot.fs.Rd | 14 + feature-1.2.15/feature/vignettes/feature.Rmd | 17 +- 19 files changed, 203 insertions(+), 225 deletions(-)
Title: Tsallis q-Exp Distribution
Description: Tsallis distribution also known as the q-exponential family distribution. Provide distribution d, p, q, r functions, fitting and testing functions. Project initiated by Paul Higbie and based on Cosma Shalizi's code.
Author: Cosma Shalizi [aut] (original R code), Christophe Dutang [cre] (R code packaging)
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between tsallisqexp versions 0.9-3 dated 2018-08-07 and 0.9-4 dated 2021-02-10
tsallisqexp-0.9-3/tsallisqexp/vignettes/qexpfamily-concordance.tex |only tsallisqexp-0.9-3/tsallisqexp/vignettes/qexpfamily.tex |only tsallisqexp-0.9-4/tsallisqexp/DESCRIPTION | 6 tsallisqexp-0.9-4/tsallisqexp/MD5 | 24 +-- tsallisqexp-0.9-4/tsallisqexp/build/vignette.rds |binary tsallisqexp-0.9-4/tsallisqexp/inst/NEWS | 6 tsallisqexp-0.9-4/tsallisqexp/inst/doc/qexpfamily.Rnw | 67 +--------- tsallisqexp-0.9-4/tsallisqexp/inst/doc/qexpfamily.pdf |binary tsallisqexp-0.9-4/tsallisqexp/man/tsal-boot.Rd | 2 tsallisqexp-0.9-4/tsallisqexp/man/tsal-cens.Rd | 2 tsallisqexp-0.9-4/tsallisqexp/man/tsal-distr.Rd | 2 tsallisqexp-0.9-4/tsallisqexp/man/tsal-fit.Rd | 2 tsallisqexp-0.9-4/tsallisqexp/man/tsal-test.Rd | 2 tsallisqexp-0.9-4/tsallisqexp/vignettes/qexpfamily.Rnw | 67 +--------- 14 files changed, 51 insertions(+), 129 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut, ctb, cph],
Marco A. Aquino Lopez [aut],
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.5.0 dated 2020-10-28 and 2.5.1 dated 2021-02-10
DESCRIPTION | 15 - MD5 | 87 +++--- NAMESPACE | 1 NEWS.md | 15 + R/Bacon.R | 67 ++--- R/MCMC.R | 18 - R/accrate.R | 209 ++++++---------- R/agedepth.R | 41 +-- R/calc.R | 51 +-- R/calibrate.R | 159 +++++------- R/internal_plots.R | 69 ++--- R/plots.R | 7 R/read_write.R | 19 - R/read_write_plum.R | 6 build |only man/AgesOfEvents.Rd | 4 man/Bacon.Age.d.Rd | 8 man/Bacon.Rd | 35 +- man/Bacon.cleanup.Rd | 3 man/Bacon.d.Age.Rd | 8 man/Bacon.hist.Rd | 8 man/Baconvergence.Rd | 6 man/accrate.age.Rd | 8 man/accrate.age.ghost.Rd | 38 -- man/accrate.depth.Rd | 8 man/accrate.depth.ghost.Rd | 8 man/add.dates.Rd | 50 ++- man/agedepth.Rd | 23 + man/agemodel.it.Rd | 8 man/bacon2clam.Rd | 3 man/calib.plot.Rd | 18 - man/calib.plumbacon.plot.Rd | 9 man/clam2bacon.Rd | 3 man/flux.age.ghost.Rd | 8 man/proxy.ghost.Rd | 8 man/scissors.Rd | 8 man/thinner.Rd | 8 src/bacon.cpp | 12 src/bacon.h | 573 ++++++++++++++++++++++++++++++-------------- src/cal.h | 158 ++++++++++-- src/input.cpp | 153 ++++++++++- src/input.h | 9 src/kernel.cpp | 4 src/twalk.h | 8 src/vector.cpp | 5 45 files changed, 1115 insertions(+), 851 deletions(-)
Title: Manipulate and Map Origin-Destination Data
Description: The aim of 'od' is to provide tools and example datasets for working with
origin-destination ('OD') datasets of the type used to describe aggregate
urban mobility patterns (Carey et al. 1981) <doi:10.1287/trsc.15.1.32>.
The package builds on functions for working with 'OD' data in the package 'stplanr',
(Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053> with a focus on computational
efficiency and support for the 'sf' class system (Pebesma 2018) <doi:10.32614/RJ-2018-009>.
With few dependencies and a simple class system based on data frames,
the package is intended to facilitate efficient analysis of 'OD' datasets
and to provide a place for developing new functions.
The package enables the creation and analysis of geographic entities
representing large scale mobility patterns,
from daily travel between zones in cities to migration between countries.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
David Cooley [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between od versions 0.0.1 dated 2020-09-09 and 0.1.0 dated 2021-02-10
od-0.0.1/od/man/od_to_sf_network.Rd |only od-0.1.0/od/DESCRIPTION | 6 od-0.1.0/od/MD5 | 46 +- od-0.1.0/od/NAMESPACE | 3 od-0.1.0/od/NEWS.md |only od-0.1.0/od/R/aggregate.R |only od-0.1.0/od/R/data.R | 99 +++++ od-0.1.0/od/R/network.R |only od-0.1.0/od/R/od-funs.R | 132 +++---- od-0.1.0/od/README.md | 49 +- od-0.1.0/od/build/vignette.rds |binary od-0.1.0/od/data/od_data_buildings.rda |only od-0.1.0/od/data/od_data_centroids2.rda |only od-0.1.0/od/data/od_data_destinations.rda |only od-0.1.0/od/data/od_data_df2.rda |only od-0.1.0/od/data/od_data_zones_small.rda |only od-0.1.0/od/inst/doc/od.Rmd | 4 od-0.1.0/od/inst/doc/od.html | 505 +++++++++--------------------- od-0.1.0/od/man/od_coordinates.Rd | 9 od-0.1.0/od/man/od_data_buildings.Rd |only od-0.1.0/od/man/od_data_centroids.Rd | 1 od-0.1.0/od/man/od_data_centroids2.Rd |only od-0.1.0/od/man/od_data_destinations.Rd |only od-0.1.0/od/man/od_data_df.Rd | 3 od-0.1.0/od/man/od_data_df2.Rd |only od-0.1.0/od/man/od_data_network.Rd | 1 od-0.1.0/od/man/od_data_zones_small.Rd |only od-0.1.0/od/man/od_disaggregate.Rd |only od-0.1.0/od/man/od_to_network.Rd |only od-0.1.0/od/man/od_to_odmatrix.Rd | 3 od-0.1.0/od/man/od_to_sf.Rd | 18 + od-0.1.0/od/vignettes/od.Rmd | 4 32 files changed, 405 insertions(+), 478 deletions(-)
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 5.0.0 dated 2020-08-27 and 5.1.0 dated 2021-02-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/ecm.R | 6 +++--- README.md | 2 +- man/ecm.Rd | 2 +- 5 files changed, 12 insertions(+), 12 deletions(-)