Title: Test for Multivariate Normal Distribution Based on a
Characterization
Description: Provides a test of multivariate normality of an unknown sample
that does not require estimation of the nuisance parameters, the mean and covariance
matrix. Rather, a sequence of transformations removes these nuisance parameters and
results in a set of sample matrices that are positive definite. These matrices are
uniformly distributed on the space of positive definite matrices in the unit
hyper-rectangle if and only if the original data is multivariate normal (Fairweather,
1973, Doctoral dissertation, University of Washington). The package performs a
goodness of fit test of this hypothesis. In addition to the test, functions in the
package give visualizations of the support region of positive definite matrices for
bivariate samples.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between MVNtestchar versions 1.1.0 dated 2020-07-03 and 1.1.2 dated 2020-07-18
DESCRIPTION | 15 +++++++++------ MD5 | 11 ++++++++--- NEWS.md | 2 +- build/partial.rdb |binary build/vignette.rds |only inst |only vignettes |only 7 files changed, 18 insertions(+), 10 deletions(-)
Title: Candidate Prescriptions Discovery Based on Pathway Fingerprint
Description: The pathway fingerprint is a method to indicate the profile of significant pathways being influenced by drugs, which may hint drug functions. Through the similarity of pathway fingerprints, the potential relationship between disease and prescription can be found. Ye (2012) <doi: 10.1007/s13238-012-2011-z>.
Author: Yuanlong Hu [aut, cre]
Maintainer: Yuanlong Hu <huyuanlong1996@163.com>
Diff between immcp versions 0.8.3 dated 2020-06-09 and 0.9.1 dated 2020-07-18
immcp-0.8.3/immcp/R/00-AllClasses.R |only immcp-0.8.3/immcp/man/to_df.Rd |only immcp-0.8.3/immcp/man/to_list.Rd |only immcp-0.9.1/immcp/DESCRIPTION | 9 +- immcp-0.9.1/immcp/MD5 | 50 ++++++++------ immcp-0.9.1/immcp/NAMESPACE | 17 ++++ immcp-0.9.1/immcp/NEWS.md |only immcp-0.9.1/immcp/R/AllClasses.R |only immcp-0.9.1/immcp/R/AllGenerics.R |only immcp-0.9.1/immcp/R/do_geneset.R | 2 immcp-0.9.1/immcp/R/extrFP.R | 100 ++++++++++++++++++++++++++++- immcp-0.9.1/immcp/R/plot_network.R |only immcp-0.9.1/immcp/R/res_rank.R |only immcp-0.9.1/immcp/R/score_fp.R | 9 +- immcp-0.9.1/immcp/R/score_network.R | 20 +++-- immcp-0.9.1/immcp/R/sysdata.rda |binary immcp-0.9.1/immcp/README.md | 29 ++------ immcp-0.9.1/immcp/data/drugResult.rda |binary immcp-0.9.1/immcp/inst/doc/immcp.R | 2 immcp-0.9.1/immcp/inst/doc/immcp.Rmd | 4 - immcp-0.9.1/immcp/inst/doc/immcp.html | 15 ++-- immcp-0.9.1/immcp/man/ScoreFP-class.Rd | 4 - immcp-0.9.1/immcp/man/ScoreResult-class.Rd | 2 immcp-0.9.1/immcp/man/as.data.frame.Rd |only immcp-0.9.1/immcp/man/extrFP.Rd | 9 -- immcp-0.9.1/immcp/man/head.Rd |only immcp-0.9.1/immcp/man/overlap_pathway.Rd |only immcp-0.9.1/immcp/man/plot_network.Rd |only immcp-0.9.1/immcp/man/res_rank.Rd |only immcp-0.9.1/immcp/man/score_fp.Rd | 9 +- immcp-0.9.1/immcp/man/score_network.Rd | 2 immcp-0.9.1/immcp/man/tail.Rd |only immcp-0.9.1/immcp/vignettes/immcp.Rmd | 4 - 33 files changed, 200 insertions(+), 87 deletions(-)
Title: Deep Time Redox Analysis of the Geobiology Ontology Network
Description: Create, visualize, manipulate, and analyze bipartite mineral-chemistry
networks for set of focal element(s) across deep-time on Earth. The method is
described in Spielman and Moore (2020) <doi:10.31223/osf.io/z7k9q>.
Author: Stephanie J. Spielman [aut, cre]
(<https://orcid.org/0000-0002-9090-4788>)
Maintainer: Stephanie J. Spielman <spielman@rowan.edu>
Diff between dragon versions 1.0.0 dated 2020-07-16 and 1.0.1 dated 2020-07-18
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- README.md | 2 +- inst/doc/dragon.html | 4 ++-- inst/dragon |only tests/testthat/test_prepare-med-data.R | 8 +++----- 6 files changed, 14 insertions(+), 15 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Namita Gupta [aut],
Susanna Marquez [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Jason Vander Heiden [cre, aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between alakazam versions 1.0.1 dated 2020-05-11 and 1.0.2 dated 2020-07-18
DESCRIPTION | 8 - MD5 | 28 +++--- NAMESPACE | 3 NEWS.md | 16 +++ R/Alakazam.R | 2 R/Diversity.R | 29 ++++-- R/Gene.R | 168 +++++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary inst/doc/Lineage-Vignette.pdf |binary inst/doc/Topology-Vignette.pdf |binary man/alphaDiversity.Rd | 26 +++--- man/groupGenes.Rd | 126 ++++++++++++++++------------- 15 files changed, 236 insertions(+), 170 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment
trial data using parametric and non-parametric methods. Parametric
methods includes Additive Main Effects and Multiplicative Interaction
(AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>,
Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang
(2003) <doi:10.1201/9781420040371>, joint Regression Analysis by
Eberhart & Russel (1966)
(<doi:10.2135/cropsci1966.0011183X000600010011x>), ecovalence by
Wricke (1965), genotypic confidence index by Annicchiarico (1992),
Murakami & Cruz's (2004) method <doi:10.12702/1984-7033.v04n01a02>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted average of absolute scores by Olivoto et al. (2019a)
<doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by
Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>.
Non-parametric methods includes superiority index by Lin & Binns
(1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic
stability by Huehn (1990)
<https://link.springer.com/article/10.1007/BF00024241>, TOP third
statistic by Fox et al. (1990) <doi:10.1007/BF00040364>, geometric
adaptability index described by Shahbazi (2019)
<doi:10.1016/j.scienta.2019.04.047>. Functions for computing
biometrical analysis such as path analysis, canonical correlation,
partial correlation, clustering analysis, and tools for inspecting,
manipulating, summarizing and plotting typical multi-environment
trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.6.1 dated 2020-06-07 and 1.7.0 dated 2020-07-18
DESCRIPTION | 12 MD5 | 189 NAMESPACE | 13 NEWS.md | 8 R/AMMI_indexes.R | 2 R/Annicchiarico.R | 2 R/Fox.R | 2 R/Huehn.R | 3 R/Schmildt.R | 2 R/Shukla.R | 2 R/Smith_Hazel.R | 9 R/Thennarasu.R | 2 R/anova_ind.R | 5 R/anova_joint.R | 5 R/barplots.R | 22 R/can_cor.R | 2 R/coincidence_index.R | 18 R/colindiag.R | 2 R/corr_ci.R | 17 R/corr_ss.R | 2 R/covcor_design.R | 3 R/cv_ammi.R | 3 R/cv_ammif.R | 3 R/cv_blup.R | 3 R/desc_stat.R | 73 R/ecovalence.R | 2 R/env_dissimilarity.R | 2 R/fai_blup.R | 13 R/find_outliers.R | 2 R/gafem.R | 5 R/gai.R | 2 R/gamem.R | 11 R/gamem_met.R | 17 R/ge_details.R | 2 R/ge_effects.R | 2 R/ge_factanal.R | 2 R/ge_means.R | 2 R/ge_reg.R | 4 R/ge_stats.R | 4 R/ge_winners.R | 2 R/get_model_data.R | 41 R/gge.R | 2 R/imput_miss_val.R | 8 R/mahala_design.R | 6 R/make_mat.R | 3 R/mgidi.R | 51 R/path_coeff.R | 2 R/performs_ammi.R | 5 R/plot_ci.R | 17 R/resca.R | 10 R/resp_surf.R | 4 R/superiority.R | 2 R/to_factor.R | 2 R/utilities.R | 163 R/utils-tidy-eval.R | 10 R/utils_na.R | 8 R/waas.R | 10 R/waas_means.R | 2 R/waasb.R | 23 R/wsmp.R | 3 R/zzz.R | 10 build/metan.pdf |27931 +++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/metan_start.html | 72 man/AMMI_indexes.Rd | 2 man/anova_ind.Rd | 1 man/anova_joint.Rd | 1 man/barplots.Rd | 13 man/can_corr.Rd | 2 man/coincidence_index.Rd | 4 man/colindiag.Rd | 2 man/corr_ci.Rd | 3 man/corr_ss.Rd | 2 man/cv_ammi.Rd | 1 man/cv_ammif.Rd | 1 man/cv_blup.Rd | 1 man/desc_stat.Rd | 1 man/figures/README-AMMI-1.png |binary man/figures/README-GGE-1.png |binary man/gafem.Rd | 1 man/gamem_met.Rd | 3 man/ge_reg.Rd | 2 man/ge_stats.Rd | 2 man/get_model_data.Rd | 7 man/impute_missing_val.Rd | 8 man/mgidi.Rd | 23 man/path_coeff.Rd | 2 man/performs_ammi.Rd | 1 man/reexports.Rd | 4 man/resca.Rd | 3 man/tidyeval.Rd | 10 man/utils_data.Rd |only man/utils_stats.Rd | 6 man/waas.Rd | 6 man/waasb.Rd | 9 vignettes/metanref.bib | 1 96 files changed, 14594 insertions(+), 14389 deletions(-)
Title: Calculation and Visualization of the Impact Effect Size Measure
Description: A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Author: Jorn Lotsch[aut,cre], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.loetsch@em.uni-frankfurt.de>
Diff between ImpactEffectsize versions 0.5.0 dated 2020-06-26 and 0.6.0 dated 2020-07-18
DESCRIPTION | 13 - MD5 | 19 +- NAMESPACE | 5 R/ClassGMD.R | 38 +++- R/Impact.R | 95 ++++++---- R/ParetoDensityEstimationIE.R | 368 +++++++++++++++++------------------------- R/RcppExports.R |only R/plot2Densities.R | 80 +++++---- man/Impact.Rd | 3 src |only 10 files changed, 317 insertions(+), 304 deletions(-)
More information about ImpactEffectsize at CRAN
Permanent link
Title: Dimension Reduction of Non-Normally Distributed Data
Description: Implements a generalized version of principal components analysis
(GLM-PCA) for dimension reduction of non-normally distributed data such as
counts or binary matrices.
Townes FW, Hicks SC, Aryee MJ, Irizarry RA (2019) <doi:10.1186/s13059-019-1861-6>.
Townes FW (2019) <arXiv:1907.02647>.
Author: F. William Townes [aut, cre, cph],
Kelly Street [aut],
Jake Yeung [ctb]
Maintainer: F. William Townes <will.townes@gmail.com>
Diff between glmpca versions 0.1.0 dated 2019-09-27 and 0.2.0 dated 2020-07-18
DESCRIPTION | 20 - LICENSE |only MD5 | 31 + NAMESPACE | 16 NEWS.md | 33 +- R/families.R |only R/glmpca.R | 692 ++++++++++++++++++++----------------------- R/initialization.R |only R/optimizers.R |only R/postprocess.R |only R/utils.R |only README.md | 19 - build/vignette.rds |binary inst/doc/glmpca.R | 38 +- inst/doc/glmpca.Rmd | 57 ++- inst/doc/glmpca.html | 152 +++------ man/glmpca.Rd | 206 +++++++++--- man/predict.glmpca.Rd |only tests/testthat/test_glmpca.R | 29 + vignettes/glmpca.Rmd | 57 ++- 20 files changed, 752 insertions(+), 598 deletions(-)
Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and robustness analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.21.0 dated 2020-06-02 and 1.22.0 dated 2020-07-18
DESCRIPTION | 6 MD5 | 52 +- NAMESPACE | 22 - NEWS | 14 R/PLIquantile.r | 730 +++++++++++++++++------------------ R/PLIsuperquantile.r | 62 +- R/base.R | 7 R/sensiHSIC.R | 872 +++++++++++++++++++++++++++++++++--------- R/shapleyBlockEstimation.R |only R/sobol.R | 384 +++++++++--------- R/sobol2002.R | 274 +++++++------ R/sobol2007.R | 276 +++++++------ R/sobolMultOut.R | 83 ++- R/soboljansen.R | 20 R/sobolmara.R | 230 ++++++----- man/PLIquantile.Rd | 29 + man/PLIsuperquantile.Rd | 27 - man/sensiHSIC.Rd | 396 ++++++++++--------- man/sensitivity-package.Rd | 5 man/shapleyBlockEstimation.Rd |only man/shapleyLinearGaussian.Rd | 2 man/sobol.Rd | 2 man/sobol2002.Rd | 2 man/sobol2007.Rd | 2 man/sobolMultOut.Rd | 123 +++-- man/soboljansen.Rd | 2 man/sobolmara.Rd | 2 man/sobolshap_knn.Rd | 2 28 files changed, 2193 insertions(+), 1433 deletions(-)
Title: Grammatical Evolution for R
Description: A native R implementation of grammatical evolution (GE).
GE facilitates the discovery of programs that can achieve a desired goal.
This is done by performing an evolutionary optimisation over a population
of R expressions generated via a user-defined context-free grammar (CFG)
and cost function.
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian <farzad.noorian@gmail.com>
Diff between gramEvol versions 2.1-3 dated 2016-07-04 and 2.1-4 dated 2020-07-18
DESCRIPTION | 18 MD5 | 119 +- NAMESPACE | 121 +- NEWS.md | 133 +- R/CreateGrammar.R | 106 +- R/EvalExpressions.R | 110 +- R/EvolutionStrategy.int.R | 371 +++---- R/GEPhenotype.R | 54 - R/GERule.R | 84 - R/GERule_Concat.R | 48 R/GeneticAlg.int.R | 496 +++++---- R/GeneticAlg_helpers.R | 128 +- R/GrammarGetDepth.R | 54 - R/GrammarGetFirstSequence.R | 206 ++-- R/GrammarGetNextSequence.R | 184 +-- R/GrammarIsRecursive.R | 92 - R/GrammarIsTerminal.R | 16 R/GrammarMap.R | 82 - R/GrammarMaxRuleSize.R | 12 R/GrammarMaxSequenceLen.R | 72 - R/GrammarMaxSequenceRange.R | 201 ++- R/GrammarNumOfExpressions.R | 60 - R/GrammarOverflow.R | 26 R/GrammarRandomExpression.R | 74 - R/GrammarStartSymbol.R | 6 R/GrammarVerboseMap.R | 164 +-- R/Grammar_escape.R | 28 R/Grammar_helpers.R | 224 ++-- R/GrammaticalEvolution.R | 337 +++--- R/GrammaticalExhaustiveSearch.R | 120 +- R/GrammaticalRandomSearch.R | 142 +- R/ReadBNFFile.R | 62 - R/ReplaceInExpression.R |only R/SymbolicRuleToListRule.R | 164 +-- R/print.GESearch.R | 108 +- R/print.grammar.R | 72 - R/summary.grammar.R | 50 README.md | 123 +- build/vignette.rds |binary inst/CITATION | 48 inst/doc/ge-intro.R | 541 ++++------ inst/doc/ge-intro.Rnw | 2015 ++++++++++++++++++++-------------------- inst/doc/ge-intro.pdf |binary man/GeneticAlg.int.Rd | 3 man/GrammarRandomExpression.Rd | 179 +-- man/GrammaticalEvolution.Rd | 3 man/ReplaceInExpression.Rd |only man/c.GERule.Rd | 74 - man/summary.grammar.Rd | 5 tests/bnf.R | 36 tests/es.R | 62 - tests/exhaustive.R | 60 - tests/ga.R | 62 - tests/ge.R | 78 - tests/grammar_newstyle.R | 228 ++-- tests/grammar_oldstyle.R | 162 +-- tests/grammar_sequence.R | 76 - tests/randomsearch.R | 62 - tests/replace_exp.R |only tests/test.bnf | 10 vignettes/ge-intro.Rnw | 2015 ++++++++++++++++++++-------------------- vignettes/vig_refs.bib | 813 ++++++++-------- 62 files changed, 5567 insertions(+), 5432 deletions(-)
Title: Testing for Change in C-Statistic
Description: Calculate the confidence interval and p value for change in C-statistic. The adjusted C-statistic is calculated by using formula as "Somers' Dxy rank correlation"/2+0.5. The confidence interval was calculated by using the bootstrap method. The p value was calculated by using the Z testing method. Please refer to the article of Peter Ganz et al. (2016) <doi:10.1001/jama.2016.5951>.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between CsChange versions 0.1.5 dated 2018-12-11 and 0.1.6 dated 2020-07-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/CsChange.R | 35 +++++++++++++++++++++-------------- 3 files changed, 26 insertions(+), 19 deletions(-)
Title: Modeling Spatially Varying Coefficients
Description: Implements a maximum likelihood estimation (MLE)
method for estimation and prediction in spatially varying coefficient
(SVC) models (Dambon et al. (2020) <arXiv:2001.08089>). Covariance
tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can be
applied such that the method scales to large data.
Author: Jakob A. Dambon [aut, cre] (<https://orcid.org/0000-0001-5855-2017>),
Fabio Sigrist [ctb] (<https://orcid.org/0000-0002-3994-2244>),
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>)
Maintainer: Jakob A. Dambon <jakob.dambon@math.uzh.ch>
Diff between varycoef versions 0.2.11 dated 2020-04-14 and 0.2.12 dated 2020-07-18
varycoef-0.2.11/varycoef/R/eff_dof.R |only varycoef-0.2.12/varycoef/DESCRIPTION | 10 varycoef-0.2.12/varycoef/MD5 | 42 +- varycoef-0.2.12/varycoef/NAMESPACE | 1 varycoef-0.2.12/varycoef/R/SVC_mle.R | 232 +++++++++-- varycoef-0.2.12/varycoef/R/data.R |only varycoef-0.2.12/varycoef/R/example.R | 60 ++- varycoef-0.2.12/varycoef/R/fitted-SVC_mle.R | 2 varycoef-0.2.12/varycoef/R/print-SVC_mle.R | 3 varycoef-0.2.12/varycoef/R/residuals-SVC_mle.R | 6 varycoef-0.2.12/varycoef/build/partial.rdb |binary varycoef-0.2.12/varycoef/build/vignette.rds |binary varycoef-0.2.12/varycoef/data |only varycoef-0.2.12/varycoef/inst/doc/example.html.asis | 2 varycoef-0.2.12/varycoef/inst/doc/manual.html | 370 +++++++++---------- varycoef-0.2.12/varycoef/man/SVC_mle.Rd | 58 ++ varycoef-0.2.12/varycoef/man/SVC_mle_control.Rd | 109 ++++- varycoef-0.2.12/varycoef/man/fitted.SVC_mle.Rd | 2 varycoef-0.2.12/varycoef/man/fullSVC_reggrid.Rd | 47 +- varycoef-0.2.12/varycoef/man/house.Rd |only varycoef-0.2.12/varycoef/man/predict.SVC_mle.Rd | 43 +- varycoef-0.2.12/varycoef/man/print.SVC_mle.Rd | 3 varycoef-0.2.12/varycoef/man/residuals.SVC_mle.Rd | 6 varycoef-0.2.12/varycoef/vignettes/example.html.asis | 2 24 files changed, 634 insertions(+), 364 deletions(-)
Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
A modern take on the 'Tufte' design for pdf and html vignettes,
building on the 'tufte' package with additional contributions
from the 'knitr' and 'ggtufte' package, and also acknowledging
the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel and Jonathan Gilligan
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.1.2 dated 2019-04-19 and 0.1.3 dated 2020-07-18
ChangeLog | 40 +++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 30 ++++++++++++++------------ R/html.R | 26 ++++++++++++++-------- R/utils.R | 1 README.md | 20 ++++++++++++++--- build/vignette.rds |binary cleanup | 8 ++++--- inst/NEWS.Rd | 16 ++++++++++++-- inst/doc/tintHtmlIntro.R | 6 ++--- inst/doc/tintHtmlIntro.Rmd | 13 ++++++----- inst/doc/tintHtmlIntro.html | 48 ++++++++++++++++++++++++++++-------------- inst/doc/tintPdfIntro.R | 6 ++--- inst/doc/tintPdfIntro.pdf |binary inst/examples/tintBibDemo.Rmd |only inst/examples/tintBibDemo.bib |only vignettes/tintHtmlIntro.Rmd | 13 ++++++----- 17 files changed, 166 insertions(+), 69 deletions(-)
Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Neal Fultz,
Sebastian Gibb, Colin Gillespie, Jan Górecki, Matt Jones, Thomas Leeper,
Steven Pav, Jan Schulz, Christoph Stepper, Felix G.M. Ernst and Patrick
Schratz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.1.7 dated 2020-07-10 and 0.1.8 dated 2020-07-18
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README.md | 40 ++++++++++++++++++++-------------------- inst/NEWS.Rd | 7 +++++++ tests/skeleton_git2r.R | 13 ++++++++++--- 6 files changed, 54 insertions(+), 32 deletions(-)
Title: Statistical Methods for Interval-Censored Data
Description: Functions that provide statistical methods for interval-censored (grouped) data. The package supports the estimation of linear and linear mixed regression models with interval-censored dependent variables. Parameter estimates are obtained by a stochastic expectation maximization algorithm. Furthermore, the package enables the direct (without covariates) estimation of statistical indicators from interval-censored data via an iterative kernel density algorithm. Survey and Organisation for Economic Co-operation and Development (OECD) weights can be included into the direct estimation (see, Walter, P. (2019) <doi:10.17169/refubium-1621>).
Author: Paul Walter
Maintainer: Paul Walter <paul.walter@fu-berlin.de>
Diff between smicd versions 1.1.0 dated 2020-04-30 and 1.1.1 dated 2020-07-18
DESCRIPTION | 18 +-- MD5 | 82 +++++++-------- NAMESPACE | 2 NEWS.md | 6 + R/Exam.R | 2 R/ICD.R | 19 +-- R/boxcox.lm.est.R | 35 +++--- R/boxcox.lme.est.R | 142 +++++++++++--------------- R/dclassICD.R | 240 ++++++++++++++++++++++++--------------------- R/icc.est.R | 3 R/indicators.est.R | 98 +++++++++--------- R/kde.algo.R | 129 +++++++++++++----------- R/kdeAlgoObject.R | 7 - R/lambda.lm.est.R | 55 +++++----- R/lambda.lme.est.R | 48 ++++----- R/log.est.R | 3 R/midpoints.est.R | 19 ++- R/parameters.est.R | 6 - R/parameters.est.ma.R | 13 +- R/plot.kdeAlgo.R | 155 ++++++++++++++++------------- R/plot.sem.R | 218 ++++++++++++++++++++++++---------------- R/print.kdeAlgo.R | 2 R/print.sem.R | 38 ++++--- R/sem.lm.R | 157 ++++++++++++++++------------- R/sem.lme.R | 225 ++++++++++++++++++++++-------------------- R/semObject.R | 12 +- R/standardError.est.R | 41 ++++--- R/standardErrorLM.est.R | 39 ++++--- R/standardErrorLME.est.R | 149 +++++++++++++++------------ R/summary.sem.R | 101 +++++++++++------- build/vignette.rds |binary inst/doc/vignetteSmicd.pdf |binary man/Exam.Rd | 2 man/kdeAlgo.Rd | 52 +++++---- man/kdeAlgoObject.Rd | 7 - man/plot.kdeAlgo.Rd | 8 - man/plot.sem.Rd | 24 ++-- man/semLm.Rd | 42 ++++--- man/semLme.Rd | 56 +++++----- man/semObject.Rd | 12 +- man/smicd.Rd | 19 +-- man/summary.sem.Rd | 2 42 files changed, 1236 insertions(+), 1052 deletions(-)
Title: Filter Based Feature Selection for 'mlr3'
Description: Extends 'mlr3' with filter methods for feature
selection. Besides standalone filter methods built-in methods of any
machine-learning algorithm are supported. Partial scoring of
multivariate filter methods is supported.
Author: Patrick Schratz [aut, cre] (<https://orcid.org/0000-0003-0748-6624>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Martin Binder [aut]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3filters versions 0.2.0 dated 2020-03-12 and 0.3.0 dated 2020-07-18
mlr3filters-0.2.0/mlr3filters/man/mlr_filters_variable_importance.Rd |only mlr3filters-0.3.0/mlr3filters/DESCRIPTION | 14 mlr3filters-0.3.0/mlr3filters/MD5 | 120 +-- mlr3filters-0.3.0/mlr3filters/NAMESPACE | 2 mlr3filters-0.3.0/mlr3filters/NEWS.md | 21 mlr3filters-0.3.0/mlr3filters/R/Filter.R | 310 +++++----- mlr3filters-0.3.0/mlr3filters/R/FilterAUC.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterAnova.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterCMIM.R | 6 mlr3filters-0.3.0/mlr3filters/R/FilterCarScore.R | 11 mlr3filters-0.3.0/mlr3filters/R/FilterCorrelation.R | 16 mlr3filters-0.3.0/mlr3filters/R/FilterDISR.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterFindCorrelation.R | 16 mlr3filters-0.3.0/mlr3filters/R/FilterImportance.R | 9 mlr3filters-0.3.0/mlr3filters/R/FilterInformationGain.R | 10 mlr3filters-0.3.0/mlr3filters/R/FilterJMI.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterJMIM.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterKruskalTest.R | 14 mlr3filters-0.3.0/mlr3filters/R/FilterMIM.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterMRMR.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterNJMIM.R | 7 mlr3filters-0.3.0/mlr3filters/R/FilterPerformance.R | 16 mlr3filters-0.3.0/mlr3filters/R/FilterPermutation.R |only mlr3filters-0.3.0/mlr3filters/R/FilterVariance.R | 13 mlr3filters-0.3.0/mlr3filters/R/flt.R | 9 mlr3filters-0.3.0/mlr3filters/R/mlr_filters.R | 84 +- mlr3filters-0.3.0/mlr3filters/R/reexports.R | 18 mlr3filters-0.3.0/mlr3filters/R/zzz.R | 27 mlr3filters-0.3.0/mlr3filters/README.md | 42 - mlr3filters-0.3.0/mlr3filters/man/Filter.Rd | 31 - mlr3filters-0.3.0/mlr3filters/man/as.data.table.Rd | 26 mlr3filters-0.3.0/mlr3filters/man/flt.Rd | 9 mlr3filters-0.3.0/mlr3filters/man/mlr3filters-package.Rd | 66 +- mlr3filters-0.3.0/mlr3filters/man/mlr_filters.Rd | 7 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_anova.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_auc.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_carscore.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_cmim.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_correlation.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_disr.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_find_correlation.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_importance.Rd |only mlr3filters-0.3.0/mlr3filters/man/mlr_filters_information_gain.Rd | 14 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_jmi.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_jmim.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_kruskal_test.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_mim.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_mrmr.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_njmim.Rd | 6 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_performance.Rd | 14 mlr3filters-0.3.0/mlr3filters/man/mlr_filters_permutation.Rd |only mlr3filters-0.3.0/mlr3filters/man/mlr_filters_variance.Rd | 8 mlr3filters-0.3.0/mlr3filters/tests/testthat.R | 8 mlr3filters-0.3.0/mlr3filters/tests/testthat/helper.R | 6 mlr3filters-0.3.0/mlr3filters/tests/testthat/setup.R | 24 mlr3filters-0.3.0/mlr3filters/tests/testthat/teardown.R | 4 mlr3filters-0.3.0/mlr3filters/tests/testthat/test_FilterFindCorrelation.R | 10 mlr3filters-0.3.0/mlr3filters/tests/testthat/test_FilterImportance.R | 18 mlr3filters-0.3.0/mlr3filters/tests/testthat/test_filter.R | 64 +- mlr3filters-0.3.0/mlr3filters/tests/testthat/test_filter_classif.R | 5 mlr3filters-0.3.0/mlr3filters/tests/testthat/test_filter_regr.R | 4 mlr3filters-0.3.0/mlr3filters/tests/testthat/test_mlr_filters.R | 10 mlr3filters-0.3.0/mlr3filters/tests/testthat/test_partial_scoring.R | 4 63 files changed, 694 insertions(+), 530 deletions(-)
Title: A Tool Kit for Working with Time Series in R
Description: Easy visualization, wrangling, and feature engineering of time series data for
forecasting and machine learning prediction.
Methods discussed herein are commonplace in machine learning, and have been cited
in various literature. Refer to "Calendar Effects" in papers such as
Taieb, Souhaib Ben. "Machine learning strategies for multi-step-ahead time series
forecasting." Universit Libre de Bruxelles, Belgium (2014): 75-86.
<http://souhaib-bentaieb.com/pdf/2014_phd.pdf>.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between timetk versions 2.1.0 dated 2020-07-03 and 2.2.0 dated 2020-07-18
timetk-2.1.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.R |only timetk-2.1.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.Rmd |only timetk-2.1.0/timetk/inst/doc/TK03_Forecasting_Using_Time_Series_Signature.html |only timetk-2.1.0/timetk/vignettes/TK03_Forecasting_Using_Time_Series_Signature.Rmd |only timetk-2.1.0/timetk/vignettes/timetk_version_2.jpg |only timetk-2.2.0/timetk/DESCRIPTION | 20 +- timetk-2.2.0/timetk/MD5 | 68 +++++----- timetk-2.2.0/timetk/NAMESPACE | 5 timetk-2.2.0/timetk/NEWS.md | 12 + timetk-2.2.0/timetk/R/00_global_vars.R | 3 timetk-2.2.0/timetk/R/diagnostics-tk_acf_diagnostics.R | 7 + timetk-2.2.0/timetk/R/dplyr-mutate_by_time.R |only timetk-2.2.0/timetk/R/dplyr-pad_by_time.R | 55 ++++++-- timetk-2.2.0/timetk/R/dplyr-slidify.R | 27 --- timetk-2.2.0/timetk/R/dplyr-summarise_by_time.R | 2 timetk-2.2.0/timetk/R/plot-acf_diagnostics.R | 50 ++++++- timetk-2.2.0/timetk/R/plot-time_series.R | 18 -- timetk-2.2.0/timetk/R/vec-box_cox.R | 2 timetk-2.2.0/timetk/R/vec-log_interval.R |only timetk-2.2.0/timetk/README.md | 65 +-------- timetk-2.2.0/timetk/build/vignette.rds |binary timetk-2.2.0/timetk/inst/doc/TK04_Plotting_Time_Series.R | 5 timetk-2.2.0/timetk/inst/doc/TK04_Plotting_Time_Series.Rmd | 7 - timetk-2.2.0/timetk/inst/doc/TK04_Plotting_Time_Series.html | 9 - timetk-2.2.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.R | 2 timetk-2.2.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.Rmd | 2 timetk-2.2.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.html | 10 - timetk-2.2.0/timetk/man/figures/README-unnamed-chunk-4-1.png |binary timetk-2.2.0/timetk/man/figures/README-unnamed-chunk-5-1.png |binary timetk-2.2.0/timetk/man/figures/README-unnamed-chunk-6-1.png |binary timetk-2.2.0/timetk/man/log_interval_vec.Rd |only timetk-2.2.0/timetk/man/mutate_by_time.Rd |only timetk-2.2.0/timetk/man/pad_by_time.Rd | 19 ++ timetk-2.2.0/timetk/man/plot_acf_diagnostics.Rd | 16 ++ timetk-2.2.0/timetk/man/plot_time_series.Rd | 18 -- timetk-2.2.0/timetk/man/slidify.Rd | 27 --- timetk-2.2.0/timetk/vignettes/TK04_Plotting_Time_Series.Rmd | 7 - timetk-2.2.0/timetk/vignettes/TK05_Plotting_Seasonality_and_Correlation.Rmd | 2 timetk-2.2.0/timetk/vignettes/temp_archive/TK03_Forecasting_Using_Time_Series_Signature.Rmd |only timetk-2.2.0/timetk/vignettes/temp_archive/TK07_Time_Series_Data_Wrangling.Rmd | 2 40 files changed, 223 insertions(+), 237 deletions(-)
Title: Persistent Large Data Array with Lazy-Loading on Demand
Description: Multi-threaded serialization of compressed array that
fully utilizes modern solid state drives. It allows
to store and load extremely large data on demand within seconds
without occupying too much memories. With data stored on hard drive,
a lazy-array data can be loaded, shared across multiple R sessions.
For arrays with partition mode on, multiple R sessions can write to
a same array simultaneously along the last dimension (partition).
The internal storage format is provided by 'fstcore' package geared by
'LZ4' and 'ZSTD' compressors.
Author: Zhengjia Wang [aut, cre, cph],
Mark Klik [ctb, cph] (Copyright holder of fstcore package)
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between lazyarray versions 1.0.0 dated 2020-06-24 and 1.1.0 dated 2020-07-18
lazyarray-1.0.0/lazyarray/man/LazyArray.Rd |only lazyarray-1.1.0/lazyarray/DESCRIPTION | 16 - lazyarray-1.1.0/lazyarray/MD5 | 43 ++-- lazyarray-1.1.0/lazyarray/NAMESPACE | 5 lazyarray-1.1.0/lazyarray/NEWS.md | 8 lazyarray-1.1.0/lazyarray/R/RcppExports.R | 4 lazyarray-1.1.0/lazyarray/R/aaa.R | 3 lazyarray-1.1.0/lazyarray/R/class-lazyarray.R | 73 ++++++ lazyarray-1.1.0/lazyarray/R/create_array.R | 58 ++++- lazyarray-1.1.0/lazyarray/R/lazyarray.R |only lazyarray-1.1.0/lazyarray/R/utils.R | 9 lazyarray-1.1.0/lazyarray/build/vignette.rds |binary lazyarray-1.1.0/lazyarray/inst/WORDLIST | 3 lazyarray-1.1.0/lazyarray/inst/doc/basic-usage-of-lazyarray.Rmd | 2 lazyarray-1.1.0/lazyarray/inst/doc/basic-usage-of-lazyarray.html | 106 +++++----- lazyarray-1.1.0/lazyarray/man/ClassLazyArray.Rd |only lazyarray-1.1.0/lazyarray/man/auto_clear_lazyarray.Rd |only lazyarray-1.1.0/lazyarray/man/create_lazyarray.Rd | 32 ++- lazyarray-1.1.0/lazyarray/man/lazyarray.Rd |only lazyarray-1.1.0/lazyarray/man/load_lazyarray.Rd | 2 lazyarray-1.1.0/lazyarray/src/RcppExports.cpp | 12 + lazyarray-1.1.0/lazyarray/src/lazyarray.cpp | 10 lazyarray-1.1.0/lazyarray/src/misc.cpp | 9 lazyarray-1.1.0/lazyarray/tests/testthat/test.setget.R | 4 lazyarray-1.1.0/lazyarray/vignettes/basic-usage-of-lazyarray.Rmd | 2 25 files changed, 293 insertions(+), 108 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Quantitative proteomics (Schubert et al 2017 <doi:10.1038/nprot.2017.040>) measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons.
The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values.
Dedicated filtering and statistical testing using the framework of package 'limma' <doi:10.18129/B9.bioc.limma> can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events.
Multi-species samples, as frequently used in benchmark-tests (eg Navarro et al 2016 <doi:10.1038/nbt.3685>, Ramus et al 2016 <doi:10.1016/j.jprot.2015.11.011>), can be run with special options separating the data into sub-groups during normalization and testing.
Subsequently, ROC curves (Hand and Till 2001 <doi:10.1023/A:1010920819831>) can be constructed to compare multiple analysis approaches.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrProteo versions 1.1.2 dated 2020-07-15 and 1.1.3 dated 2020-07-18
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- R/convAASeq2mass.R | 16 ++++++++-------- R/readUCSCtable.R | 31 ++++++++++++++++++------------- R/readUniProtExport.R | 26 ++++++++++++++++---------- inst/doc/wrProteoVignette1.R | 5 +++++ inst/doc/wrProteoVignette1.Rmd | 19 ++++++++++++++++--- inst/doc/wrProteoVignette1.html | 24 +++++++++++++++--------- man/convAASeq2mass.Rd | 8 ++++---- man/readUCSCtable.Rd | 12 ++++++++---- man/readUniProtExport.Rd | 20 ++++++++++++-------- vignettes/wrProteoVignette1.Rmd | 19 ++++++++++++++++--- 12 files changed, 135 insertions(+), 79 deletions(-)
Title: Collecting Social Media Data and Generating Networks for
Analysis
Description: A suite of tools for collecting and constructing networks from social media data.
Provides easy-to-use functions for collecting data across popular platforms (Twitter, YouTube
and Reddit) and generating different types of networks for analysis.
Author: Timothy Graham, Robert Ackland, Chung-hong Chan, Bryan Gertzel
Maintainer: Bryan Gertzel <bryan.gertzel@anu.edu.au>
Diff between vosonSML versions 0.29.10 dated 2020-04-25 and 0.29.13 dated 2020-07-18
DESCRIPTION | 11 - MD5 | 68 +++--- NEWS.md | 21 ++ R/AddText.R | 38 ++- R/AddUserData.R | 25 -- R/AddVideoData.R | 2 R/Authenticate.twitter.R | 33 ++- R/Collect.reddit.R | 33 +-- R/Collect.twitter.R | 6 R/Collect.youtube.R | 4 R/Create.R | 2 R/Create.activity.reddit.R | 15 - R/Create.activity.twitter.R | 19 - R/Create.activity.youtube.R | 11 - R/Create.actor.reddit.R | 12 - R/Create.actor.twitter.R | 9 R/Create.actor.youtube.R | 12 - R/Create.semantic.twitter.R | 17 + R/Create.twomode.twitter.R | 20 + R/Graph.R | 2 R/Utils.R | 4 README.md | 36 +-- build/vignette.rds |binary inst/doc/Intro-to-vosonSML.R | 6 inst/doc/Intro-to-vosonSML.Rmd | 16 + inst/doc/Intro-to-vosonSML.html | 48 +++- man/Authenticate.twitter.Rd | 129 ++++++------ man/Collect.youtube.Rd | 2 man/Create.semantic.twitter.Rd | 210 ++++++++++---------- man/Create.twomode.twitter.Rd | 111 +++++----- man/vosonSML-colon-colon-AddText.activity.reddit.Rd | 52 ++-- man/vosonSML-colon-colon-AddText.actor.reddit.Rd | 52 ++-- man/vosonSML-colon-colon-AddText.actor.youtube.Rd | 90 ++++---- man/vosonSML-colon-colon-AddUserData.Rd | 52 ++-- vignettes/Intro-to-vosonSML.Rmd | 16 + 35 files changed, 662 insertions(+), 522 deletions(-)
Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between set6 versions 0.1.6 dated 2020-07-17 and 0.1.7 dated 2020-07-18
DESCRIPTION | 6 +- MD5 | 66 ++++++++++++------------ NEWS.md | 6 ++ R/SetWrapper_ExponentSet.R | 73 +++++++++++++++++---------- R/Set_Interval.R | 4 + R/operation_cleaner.R | 5 + R/operation_setcomplement.R | 2 R/operation_setpower.R | 44 +++++++++++----- R/operation_setproduct.R | 6 ++ R/operation_setunion.R | 5 + inst/doc/set6.html | 18 ++---- man/ConditionalSet.Rd | 3 - man/ExponentSet.Rd | 13 ++-- man/FuzzySet.Rd | 3 - man/FuzzyTuple.Rd | 3 - man/Interval.Rd | 5 - man/LogicalSet.Rd | 3 - man/Set.Rd | 3 - man/Tuple.Rd | 3 - man/UniversalSet.Rd | 3 - man/as.FuzzySet.Rd | 14 ++--- man/as.Interval.Rd | 15 +++-- man/as.Set.Rd | 3 - man/listSpecialSets.Rd | 6 +- man/powerset.Rd | 8 +- man/setcomplement.Rd | 15 ++--- man/setintersect.Rd | 13 ++-- man/setpower.Rd | 26 ++++++--- man/setproduct.Rd | 19 +++---- man/setsymdiff.Rd | 5 - man/setunion.Rd | 13 ++-- man/useUnicode.Rd | 2 tests/testthat/test_operations_setpower.R | 21 ++++++- tests/testthat/test_setwrapper_exponentset.R | 2 34 files changed, 257 insertions(+), 179 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <fh@fharrell.com>
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.0-0 dated 2020-06-04 and 6.0-1 dated 2020-07-18
rms-6.0-0/rms/R/Glm.s |only rms-6.0-0/rms/R/blrm.r |only rms-6.0-0/rms/R/stanMisc.r |only rms-6.0-0/rms/inst/tests/blrm-contrast.r |only rms-6.0-0/rms/inst/tests/blrm-po.r |only rms-6.0-0/rms/inst/tests/blrm-ppo.r |only rms-6.0-0/rms/inst/tests/blrm-pred.r |only rms-6.0-0/rms/inst/tests/blrm.Rmd |only rms-6.0-0/rms/man/ExProb.blrm.Rd |only rms-6.0-0/rms/man/HPDint.Rd |only rms-6.0-0/rms/man/Mean.blrm.Rd |only rms-6.0-0/rms/man/PostF.Rd |only rms-6.0-0/rms/man/Quantile.blrm.Rd |only rms-6.0-0/rms/man/blrm.Rd |only rms-6.0-0/rms/man/blrmStats.Rd |only rms-6.0-0/rms/man/coef.rmsb.Rd |only rms-6.0-0/rms/man/compareBmods.Rd |only rms-6.0-0/rms/man/distSym.Rd |only rms-6.0-0/rms/man/pdensityContour.Rd |only rms-6.0-0/rms/man/plot.PostF.Rd |only rms-6.0-0/rms/man/plot.rmsb.Rd |only rms-6.0-0/rms/man/predict.blrm.Rd |only rms-6.0-0/rms/man/print.blrm.Rd |only rms-6.0-0/rms/man/print.blrmStats.Rd |only rms-6.0-0/rms/man/print.predict.blrm.Rd |only rms-6.0-0/rms/man/print.rmsb.Rd |only rms-6.0-0/rms/man/selectedQr.Rd |only rms-6.0-0/rms/man/stanCompile.Rd |only rms-6.0-0/rms/man/stanDx.Rd |only rms-6.0-0/rms/man/stanDxplot.Rd |only rms-6.0-0/rms/man/stanGet.Rd |only rms-6.0-0/rms/man/tauFetch.Rd |only rms-6.0-0/rms/man/vcov.rmsb.Rd |only rms-6.0-1/rms/DESCRIPTION | 21 ++-- rms-6.0-1/rms/MD5 | 134 ++++++++++---------------- rms-6.0-1/rms/NAMESPACE | 18 --- rms-6.0-1/rms/NEWS | 16 +++ rms-6.0-1/rms/R/Glm.r |only rms-6.0-1/rms/R/Predict.s | 114 +++++++++++++++++----- rms-6.0-1/rms/R/Rq.s | 28 +++-- rms-6.0-1/rms/R/anova.rms.s | 6 - rms-6.0-1/rms/R/bj.s | 28 ++--- rms-6.0-1/rms/R/calibrate.cph.s | 63 +++--------- rms-6.0-1/rms/R/contrast.s | 53 +++++++--- rms-6.0-1/rms/R/cph.s | 78 +++++---------- rms-6.0-1/rms/R/ggplot.Predict.s | 3 rms-6.0-1/rms/R/lrm.fit.s | 10 - rms-6.0-1/rms/R/lrm.s | 51 +++++---- rms-6.0-1/rms/R/ols.s | 35 ++---- rms-6.0-1/rms/R/orm.s | 38 +++---- rms-6.0-1/rms/R/plot.contrast.r | 21 ++-- rms-6.0-1/rms/R/predictrms.s | 54 ++++++---- rms-6.0-1/rms/R/psm.s | 47 +++------ rms-6.0-1/rms/R/rms.s | 159 ++++++++++++++++++++++++++++++- rms-6.0-1/rms/R/rmsMisc.s | 3 rms-6.0-1/rms/R/summary.rms.s | 4 rms-6.0-1/rms/R/survplotp.npsurv.s | 12 +- rms-6.0-1/rms/R/val.surv.s | 5 rms-6.0-1/rms/inst/tests/calibrate.cph.r | 4 rms-6.0-1/rms/inst/tests/modelData.r |only rms-6.0-1/rms/man/Glm.Rd | 81 ++++++++------- rms-6.0-1/rms/man/Predict.Rd | 16 ++- rms-6.0-1/rms/man/Rq.Rd | 3 rms-6.0-1/rms/man/bj.Rd | 7 - rms-6.0-1/rms/man/bplot.Rd | 4 rms-6.0-1/rms/man/contrast.Rd | 11 +- rms-6.0-1/rms/man/cph.Rd | 4 rms-6.0-1/rms/man/ggplot.Predict.Rd | 4 rms-6.0-1/rms/man/latex.cph.Rd | 2 rms-6.0-1/rms/man/lrm.Rd | 3 rms-6.0-1/rms/man/ols.Rd | 2 rms-6.0-1/rms/man/orm.Rd | 6 - rms-6.0-1/rms/man/orm.fit.Rd | 2 rms-6.0-1/rms/man/plot.contrast.rms.Rd | 6 - rms-6.0-1/rms/man/plotp.Predict.Rd | 2 rms-6.0-1/rms/man/predictrms.Rd | 20 ++- rms-6.0-1/rms/man/print.Glm.Rd |only rms-6.0-1/rms/man/psm.Rd | 4 rms-6.0-1/rms/man/residuals.lrm.Rd | 12 +- rms-6.0-1/rms/man/rms-internal.Rd | 1 rms-6.0-1/rms/man/rms.Rd | 39 +++++-- rms-6.0-1/rms/man/rmsMisc.Rd | 26 ++--- rms-6.0-1/rms/man/setPb.Rd | 2 rms-6.0-1/rms/man/survplot.Rd | 4 rms-6.0-1/rms/man/validate.Rd | 2 rms-6.0-1/rms/man/validate.cph.Rd | 2 86 files changed, 748 insertions(+), 522 deletions(-)
Title: Diversity Indices for Numerical Matrices
Description: Providing functions to calculate indices of diversity on numerical matrices based on information theory. The rationale behind the package is described in Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039>.
Author: Matteo Marcantonio [aut, cre],
Martina Iannacito [aut, ctb],
Elisa Thouverai [aut, ctb],
Daniele Da Re [aut],
Clara Tattoni [aut],
Giovanni Bacaro [aut],
Saverio Vicario [aut, ctb],
Carlo Ricotta [aut],
Duccio Rocchini [aut, ctb]
Maintainer: Matteo Marcantonio <marcantoniomatteo@gmail.com>
Diff between rasterdiv versions 0.2-0 dated 2020-06-11 and 0.2-1 dated 2020-07-18
rasterdiv-0.2-0/rasterdiv/inst/doc/vignettes_rasterdiv.R |only rasterdiv-0.2-0/rasterdiv/inst/doc/vignettes_rasterdiv.Rmd |only rasterdiv-0.2-0/rasterdiv/inst/doc/vignettes_rasterdiv.html |only rasterdiv-0.2-0/rasterdiv/vignettes/vignettes_rasterdiv.Rmd |only rasterdiv-0.2-1/rasterdiv/DESCRIPTION | 10 ++-- rasterdiv-0.2-1/rasterdiv/MD5 | 24 ++++++---- rasterdiv-0.2-1/rasterdiv/NAMESPACE | 10 +--- rasterdiv-0.2-1/rasterdiv/NEWS.md | 10 ++-- rasterdiv-0.2-1/rasterdiv/R/accRao.R |only rasterdiv-0.2-1/rasterdiv/build/vignette.rds |binary rasterdiv-0.2-1/rasterdiv/data/copNDVI.rda |binary rasterdiv-0.2-1/rasterdiv/inst/doc/rasterdiv_advanced_accRao.R |only rasterdiv-0.2-1/rasterdiv/inst/doc/rasterdiv_advanced_accRao.Rmd |only rasterdiv-0.2-1/rasterdiv/inst/doc/rasterdiv_advanced_accRao.html |only rasterdiv-0.2-1/rasterdiv/inst/doc/rasterdiv_basics.R |only rasterdiv-0.2-1/rasterdiv/inst/doc/rasterdiv_basics.Rmd |only rasterdiv-0.2-1/rasterdiv/inst/doc/rasterdiv_basics.html |only rasterdiv-0.2-1/rasterdiv/man/accRao.Rd |only rasterdiv-0.2-1/rasterdiv/vignettes/rasterdiv_advanced_accRao.Rmd |only rasterdiv-0.2-1/rasterdiv/vignettes/rasterdiv_basics.Rmd |only 20 files changed, 31 insertions(+), 23 deletions(-)
Title: Number Names
Description: Converts numeric vectors to character vectors of
English number names. Provides conversion to cardinals, ordinals,
numerators, and denominators. Supports negative and non-integer
numbers.
Author: Alexander Rossell Hayes [aut, cre]
(<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between nombre versions 0.1.0 dated 2020-05-25 and 0.2.0 dated 2020-07-18
DESCRIPTION | 11 +- MD5 | 38 ++++++--- NAMESPACE | 5 + NEWS.md | 37 +++++++++ R/adverbial.R |only R/cardinal.R | 148 +++++++++++++++++--------------------- R/collective.R |only R/convert_fraction.R | 32 +++++++- R/denominator.R | 34 +++----- R/nombre-package.R |only R/ordinal.R | 18 +--- README.md | 44 ++++++----- inst |only man/adverbial.Rd |only man/cardinal.Rd | 51 ++++++++++--- man/collective.Rd |only man/denominator.Rd | 38 ++++----- man/nombre-package.Rd |only man/ordinal.Rd | 27 +++--- tests/testthat/test-adverbial.R |only tests/testthat/test-cardinal.R | 27 +++--- tests/testthat/test-collective.R |only tests/testthat/test-denominator.R | 20 +++++ tests/testthat/test-ordinal.R | 8 ++ 24 files changed, 334 insertions(+), 204 deletions(-)
Title: Creates and Manages Folder Functions for Portable Large-Scale R
Analysis
Description: If you find yourself working on multiple different projects in R, you'll want a
series of folders pointing to raw data, processed data, plot results, intermediate table
outputs, etc. This package makes it easier to do that by providing a quick and easy way
to create and use functions for project-level directories.
Author: Nathan C. Sheffield [aut, cre],
Michal Stolarczyk [ctb],
Vince Reuter [ctb]
Maintainer: Nathan C. Sheffield <nathan@code.databio.org>
Diff between folderfun versions 0.1.3 dated 2020-07-14 and 0.1.4 dated 2020-07-18
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md | 5 +++++ README.md | 2 +- inst/doc/intro.html | 4 ++-- tests/check_CRAN.sh |only tests/testthat/helper-all.R | 11 +++++++---- tests/testthat/test_setff.R | 14 +++++--------- 8 files changed, 31 insertions(+), 26 deletions(-)
Title: Diet Estimated Trophic Levels
Description: Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Froese & Pauly (2000, ISBN: 9718709991).
Author: Samuel R. Borstein <sam@borstein.com>
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between dietr versions 1.0 dated 2019-11-13 and 1.1.0 dated 2020-07-18
DESCRIPTION | 10 - MD5 | 78 ++++++++++----- NAMESPACE | 4 NEWS.md |only R/CompositeIndices.R |only R/DataDoc.R | 39 +++++++ R/DietTroph.R | 50 +++++++++ R/Electivity.R | 13 +- R/FoodTroph.R | 2 R/FullnessIndex.R |only R/PlotElectivity.R |only R/VacuityIndex.R |only R/pkgname.R | 8 - build/vignette.rds |binary data/Casaux1998.RData |only data/Horn1982.RData |binary data/SebastesStomachs.RData |only inst/doc/dietr-vignette.R |only inst/doc/dietr-vignette.Rmd | 153 ++++++++++++++++++++++-------- inst/doc/dietr-vignette.pdf |binary man/Casaux1998.Rd |only man/CompositeIndices.Rd |only man/CortesPreyVals.Rd | 6 - man/DietTroph.Rd | 57 ++++++++++- man/Electivity.Rd | 23 +++- man/FishBasePreyVals.Rd | 6 - man/FoodTroph.Rd | 10 + man/GastrosomaticIndex.Rd |only man/Herichthys.Rd | 4 man/Horn1982.Rd | 6 - man/PlotElectivity.Rd |only man/SebastesStomachs.Rd |only man/VacuityIndex.Rd |only man/dietr.Rd | 9 - tests/testthat/test_ConvertFishbaseDiet.R | 14 +- tests/testthat/test_ConvertFishbaseFood.R | 14 +- tests/testthat/test_FoodTroph.R | 6 - vignettes/dietr-vignette.Rmd | 153 ++++++++++++++++++++++-------- vignettes/dietr-vignette_files |only 39 files changed, 515 insertions(+), 150 deletions(-)
Title: Decomposition of Bulk Expression with Single-Cell Sequencing
Description: Provides tools to accurately estimate cell type abundances
from heterogeneous bulk expression. A reference-based method utilizes
single-cell information to generate a signature matrix and transformation
of bulk expression for accurate regression based estimates. A marker-based
method utilizes known cell-specific marker genes to measure relative
abundances across samples.
For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.
Author: Brandon Jew [aut, cre],
Marcus Alvarez [aut]
Maintainer: Brandon Jew <brandon.jew@ucla.edu>
Diff between BisqueRNA versions 1.0.3 dated 2020-05-04 and 1.0.4 dated 2020-07-18
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NAMESPACE | 2 + R/reference_based.R | 53 +++++++++++++++++++++++++++++-------- man/GetCTP.Rd | 14 ++++++++- man/MarkerBasedDecomposition.Rd | 16 ++++++++--- man/ReferenceBasedDecomposition.Rd | 28 ++++++++++++++++--- man/SeuratToExpressionSet.Rd | 8 ++++- 8 files changed, 109 insertions(+), 34 deletions(-)