Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] ,
Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalSL versions 0.94 dated 2024-03-19 and 0.96 dated 2024-08-26
DESCRIPTION | 9 + MD5 | 16 ++- NAMESPACE | 24 +---- R/LIB_PLANN.R |only R/predict.libsl.R | 35 +++++++ R/survivalSL.R | 247 +++++++++++++++++++++++++++++++++++++++++++++--------- R/tunePLANN.R |only R/tuneSNN.R | 4 man/LIB_PLANN.Rd |only man/survivalSL.Rd | 9 + man/tunePLANN.Rd |only 11 files changed, 272 insertions(+), 72 deletions(-)
Title: Simplified Fetching and Processing of Microarray and RNA-Seq
Data
Description: Wrapper around various existing tools and command-line interfaces,
providing a standard interface, simple parallelization, and detailed logging.
For microarray data, maps probe sets to standard gene IDs, building on
'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>,
'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>,
Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>,
and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>.
For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology
Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and
quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>,
performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>,
quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197& [...truncated...]
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between seeker versions 1.1.5 dated 2024-01-22 and 1.1.6 dated 2024-08-26
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/fetch.R | 7 ++++++- R/install_sys_deps.R | 7 ++++++- build/vignette.rds |binary inst/doc/introduction.html | 6 +++--- inst/doc/reproducibility.html | 14 +++++++------- tests/testthat/data/GPL6887.qs |binary tests/testthat/data/GPL7202.qs |binary tests/testthat/data/map_pkg_ver.qs |binary tests/testthat/data/multiqc_output.qs |binary tests/testthat/data/seeker_output_full.qs |binary tests/testthat/test-fetch.R | 2 ++ 13 files changed, 40 insertions(+), 28 deletions(-)
Title: Copula Based Cox Proportional Hazards Models for Dependent
Censoring
Description: Copula based Cox proportional hazards models for survival data subject to dependent
censoring. This approach does not assume that the parameter defining the copula is known. The
dependency parameter is estimated with other finite model parameters by maximizing a Pseudo
likelihood function. The cumulative hazard function is estimated via estimating equations
derived based on martingale ideas. Available copula functions include Frank, Gumbel and Normal
copulas. Only Weibull and lognormal models are allowed for the censoring model, even though any
parametric model that satisfies certain identifiability conditions could be used. Implemented
methods are described in the article "Copula based Cox proportional hazards models for dependent
censoring" by Deresa and Van Keilegom (2024) <doi:10.1080/01621459.2022.2161387>.
Author: Negera Wakgari Deresa [aut, cre]
,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between SemiPar.depCens versions 0.1.2 dated 2024-03-29 and 0.1.3 dated 2024-08-26
DESCRIPTION | 10 ++++---- MD5 | 20 ++++++++-------- NEWS.md | 3 ++ R/bootstrapFunctions.R | 11 ++++---- R/depCensoringFit-Results.R | 4 --- R/fitIndependentCensoringModels.R | 20 ++++++++-------- R/fitdependentCensorigModels.R | 47 ++++++++++++++++++-------------------- man/boot.fun.Rd | 3 ++ man/boot.funI.Rd | 3 ++ man/fitDepCens.Rd | 19 ++++++++------- man/fitIndepCens.Rd | 15 +++++++----- 11 files changed, 85 insertions(+), 70 deletions(-)
More information about SemiPar.depCens at CRAN
Permanent link
Title: The Free Algebra
Description: The free algebra in R with non-commuting indeterminates.
Uses 'disordR' discipline
(Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the
package in publications please use Hankin (2022)
<doi:10.48550/ARXIV.2211.04002>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between freealg versions 1.1-1 dated 2023-03-20 and 1.1-8 dated 2024-08-26
freealg-1.1-1/freealg/build/freealg.pdf |only freealg-1.1-1/freealg/vignettes/free.bib |only freealg-1.1-8/freealg/DESCRIPTION | 15 freealg-1.1-8/freealg/MD5 | 83 ++- freealg-1.1-8/freealg/NAMESPACE | 5 freealg-1.1-8/freealg/NEWS.md | 57 ++ freealg-1.1-8/freealg/R/free.R | 51 ++ freealg-1.1-8/freealg/R/freeops.R | 11 freealg-1.1-8/freealg/README.md | 20 freealg-1.1-8/freealg/build/partial.rdb |binary freealg-1.1-8/freealg/build/vignette.rds |binary freealg-1.1-8/freealg/data/dot.rda |binary freealg-1.1-8/freealg/inst/doc/adjoint.Rnw | 4 freealg-1.1-8/freealg/inst/doc/adjoint.pdf |binary freealg-1.1-8/freealg/inst/doc/freealg.R | 11 freealg-1.1-8/freealg/inst/doc/freealg.Rmd | 37 + freealg-1.1-8/freealg/inst/doc/freealg.html | 499 +++++++++++++++++------- freealg-1.1-8/freealg/inst/lettersymbols.rda |only freealg-1.1-8/freealg/inst/symb.Rmd |only freealg-1.1-8/freealg/man/Ops.freealg.Rd | 17 freealg-1.1-8/freealg/man/abelianize.Rd | 7 freealg-1.1-8/freealg/man/accessor.Rd | 27 - freealg-1.1-8/freealg/man/adjoint.Rd | 8 freealg-1.1-8/freealg/man/constant.Rd | 9 freealg-1.1-8/freealg/man/deriv.Rd | 8 freealg-1.1-8/freealg/man/dot.Rd | 15 freealg-1.1-8/freealg/man/drop.Rd | 6 freealg-1.1-8/freealg/man/freealg-class.Rd |only freealg-1.1-8/freealg/man/freealg.Rd | 17 freealg-1.1-8/freealg/man/grade.Rd | 40 + freealg-1.1-8/freealg/man/horner.Rd | 13 freealg-1.1-8/freealg/man/inverse.Rd |only freealg-1.1-8/freealg/man/letters.Rd |only freealg-1.1-8/freealg/man/linear.Rd | 18 freealg-1.1-8/freealg/man/nterms.Rd | 2 freealg-1.1-8/freealg/man/pepper.Rd | 13 freealg-1.1-8/freealg/man/print.Rd | 60 ++ freealg-1.1-8/freealg/man/rfalg.Rd | 8 freealg-1.1-8/freealg/src/free.cpp | 33 - freealg-1.1-8/freealg/tests/testthat/test_aaa.R | 11 freealg-1.1-8/freealg/tests/testthat/test_aad.R | 38 + freealg-1.1-8/freealg/tests/testthat/test_aag.R | 5 freealg-1.1-8/freealg/tests/testthat/test_aah.R |only freealg-1.1-8/freealg/tests/testthat/test_zzz.R | 37 + freealg-1.1-8/freealg/vignettes/adjoint.Rnw | 4 freealg-1.1-8/freealg/vignettes/freealg.Rmd | 37 + freealg-1.1-8/freealg/vignettes/freealg.bib |only 47 files changed, 878 insertions(+), 348 deletions(-)
Title: Using the Theory of Belief Functions
Description: Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Peiyuan Zhu [aut, cre],
Claude Boivin [aut]
Maintainer: Peiyuan Zhu <garyzhubc@gmail.com>
Diff between dst versions 1.7.0 dated 2024-06-06 and 1.7.1 dated 2024-08-26
DESCRIPTION | 21 +- MD5 | 54 ++--- NAMESPACE | 1 NEWS.md | 6 R/bcaPrintLarge.R | 6 R/belplauEval.R | 57 +++--- R/belplauPlot.R | 20 +- inst/doc/Bayes_Rule.R | 8 inst/doc/Bayes_Rule.Rmd | 11 - inst/doc/Bayes_Rule.html | 150 +++++++-------- inst/doc/Captain_Example.R | 12 - inst/doc/Captain_Example.Rmd | 12 - inst/doc/Captain_Example.html | 236 +++++++++++++++---------- inst/doc/Crime_Scene_Commonality.Rmd | 4 inst/doc/Crime_Scene_Commonality.html | 6 inst/doc/Introduction_to_Belief_Functions.html | 8 inst/doc/The_Monty_Hall_Game.html | 6 inst/doc/The_PJM_example.html | 2 inst/doc/Zadeh_Example.html | 2 inst/dst.pdf |binary man/bcaPrintLarge.Rd | 4 man/belplauEval.Rd | 25 +- man/belplauPlot.Rd | 20 +- tests/testthat/test_bcaPrintLarge.R | 1 tests/testthat/test_belplauEval.R | 2 vignettes/Bayes_Rule.Rmd | 11 - vignettes/Captain_Example.Rmd | 12 - vignettes/Crime_Scene_Commonality.Rmd | 4 28 files changed, 404 insertions(+), 297 deletions(-)
Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers both
distribution-free modeling using Taylor polynomials and parametric modeling
using the beta-binomial distribution. Originally developed for achievement
tests, it is applicable to a wide range of mental, physical, or other test
scores dependent on continuous or discrete explanatory variables. The package
provides several advantages: It minimizes deviations from representativeness
in subsamples, interpolates between discrete levels of explanatory variables,
and significantly reduces the required sample size compared to conventional
norming per age group. cNORM enables graphical and analytical evaluation of
model fit, accommodates a wide range of scales including those with negative
and descending values, and even supports conventional norming. It generates
norm tables including confidence intervals. It also includes methods for
addressing represent [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.2.0 dated 2024-08-17 and 3.3.0 dated 2024-08-26
DESCRIPTION | 12 MD5 | 76 ++-- NAMESPACE | 6 NEWS.md | 25 + R/betaBinomial.R | 18 - R/cNORM.R | 105 +++++- R/data.R | 2 R/modelling.R | 637 +++++++++++++++++++++++++-------------- R/plot.R | 128 +++++-- R/predict.R | 2 R/utilities.R | 31 - README.md | 9 inst/doc/BetaBinomial.html | 6 inst/doc/WeightedRegression.Rmd | 6 inst/doc/WeightedRegression.html | 37 +- inst/doc/cNORM-Demo.R | 2 inst/doc/cNORM-Demo.Rmd | 26 - inst/doc/cNORM-Demo.html | 165 +++++----- man/bestModel.Rd | 28 + man/buildCnormObject.Rd | 2 man/cNORM.Rd | 12 man/checkConsistency.Rd | 27 - man/check_monotonicity.Rd |only man/cnorm.betabinomial1.Rd | 6 man/cnorm.cv.Rd | 3 man/log_likelihood.Rd | 4 man/plotCnorm.Rd | 4 man/plotDerivative.Rd | 4 man/plotNorm.Rd | 3 man/plotPercentiles.Rd | 3 man/plotSubset.Rd | 3 man/ppvt.Rd | 2 man/predictCoefficients.Rd | 8 man/predictNorm.Rd | 2 man/taylorSwift.Rd |only man/weighted.quantile.Rd | 2 tests/testthat/test.modelling.R | 136 +++++++- vignettes/WeightedRegression.Rmd | 6 vignettes/beta.png |binary vignettes/cNORM-Demo.Rmd | 26 - 40 files changed, 1018 insertions(+), 556 deletions(-)
Title: Import XY-Data into R
Description: Provides access to the 'xylib' C library for to import xy
data from powder diffraction, spectroscopy and other experimental methods.
Author: Sebastian Kreutzer [aut, trl, cre]
,
Johannes Friedrich [aut] ,
RLum Team [ctb],
Marcin Wojdyr [cph] ,
Peng Zhang [cph]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between rxylib versions 0.2.12 dated 2023-11-03 and 0.2.13 dated 2024-08-26
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 7 ++----- R/rxylib-package.R | 3 +-- README.md | 2 ++ man/convert_xy2TKA.Rd | 2 +- man/read_xyData.Rd | 2 +- man/rxylib-package.Rd | 8 ++++++++ 8 files changed, 28 insertions(+), 22 deletions(-)
Title: Complementary Package to 'nicheROVER' and 'SIBER'
Description: Provides functions complementary to packages 'nicheROVER' and 'SIBER'
allowing the user to extract Bayesian estimates from data objects created
by the packages 'nicheROVER' and 'SIBER'. Please see the following
publications for detailed methods on 'nicheROVER' and 'SIBER'
Hansen et al. (2015) <doi:10.1890/14-0235.1>,
Jackson et al. (2011) <doi:10.1111/j.1365-2656.2011.01806.x>, and
Layman et al. (2007) <doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2>,
respectfully.
Author: Benjamin L. Hlina [aut, cre]
Maintainer: Benjamin L. Hlina <benjamin.hlina@gmail.com>
Diff between nichetools versions 0.2.0 dated 2024-06-07 and 0.3.0 dated 2024-08-26
nichetools-0.2.0/nichetools/R/summ-niche_ellipse.R |only nichetools-0.2.0/nichetools/R/util-extract_mu.R |only nichetools-0.2.0/nichetools/R/util-extract_niche_size.R |only nichetools-0.2.0/nichetools/R/util-extract_overlap.R |only nichetools-0.2.0/nichetools/R/util-extract_sigma.R |only nichetools-0.3.0/nichetools/DESCRIPTION | 28 +- nichetools-0.3.0/nichetools/MD5 | 60 +++-- nichetools-0.3.0/nichetools/NAMESPACE | 5 nichetools-0.3.0/nichetools/NEWS.md | 19 + nichetools-0.3.0/nichetools/R/create_comparison.R |only nichetools-0.3.0/nichetools/R/extract_group_metrics.R |only nichetools-0.3.0/nichetools/R/extract_layman.R |only nichetools-0.3.0/nichetools/R/extract_mu.R |only nichetools-0.3.0/nichetools/R/extract_niche_size.R |only nichetools-0.3.0/nichetools/R/extract_overlap.R |only nichetools-0.3.0/nichetools/R/extract_sigma.R |only nichetools-0.3.0/nichetools/R/extract_similarities.R |only nichetools-0.3.0/nichetools/R/niche_ellipse.R |only nichetools-0.3.0/nichetools/R/zzz.R | 10 nichetools-0.3.0/nichetools/README.md | 60 +++-- nichetools-0.3.0/nichetools/build/vignette.rds |binary nichetools-0.3.0/nichetools/inst/CITATION | 26 +- nichetools-0.3.0/nichetools/inst/doc/using-nichetools-with-the-package-SIBER.R |only nichetools-0.3.0/nichetools/inst/doc/using-nichetools-with-the-package-SIBER.Rmd |only nichetools-0.3.0/nichetools/inst/doc/using-nichetools-with-the-package-SIBER.html |only nichetools-0.3.0/nichetools/inst/doc/using-nichetools-with-the-package-nicheROVER.Rmd | 4 nichetools-0.3.0/nichetools/inst/doc/using-nichetools-with-the-package-nicheROVER.html | 17 - nichetools-0.3.0/nichetools/man/create_comparisons.Rd |only nichetools-0.3.0/nichetools/man/extract_group_metrics.Rd |only nichetools-0.3.0/nichetools/man/extract_layman.Rd |only nichetools-0.3.0/nichetools/man/extract_mu.Rd | 2 nichetools-0.3.0/nichetools/man/extract_niche_size.Rd | 53 +++- nichetools-0.3.0/nichetools/man/extract_overlap.Rd | 2 nichetools-0.3.0/nichetools/man/extract_sigma.Rd | 2 nichetools-0.3.0/nichetools/man/extract_similarities.Rd |only nichetools-0.3.0/nichetools/man/niche_ellipse.Rd | 2 nichetools-0.3.0/nichetools/man/nichetools-package.Rd | 4 nichetools-0.3.0/nichetools/tests/testthat/test-create_comparison.R |only nichetools-0.3.0/nichetools/tests/testthat/test-extract_group_metrics.R |only nichetools-0.3.0/nichetools/tests/testthat/test-extract_laymans.R |only nichetools-0.3.0/nichetools/tests/testthat/test-extract_niche_size.R | 113 ++++++++++ nichetools-0.3.0/nichetools/tests/testthat/test-extract_similarities.R |only nichetools-0.3.0/nichetools/vignettes/using-nichetools-with-the-package-SIBER.Rmd |only nichetools-0.3.0/nichetools/vignettes/using-nichetools-with-the-package-nicheROVER.Rmd | 4 44 files changed, 314 insertions(+), 97 deletions(-)
Title: Viral Quasispecies Comparison from Long-Read Sequencing Data
Description: Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
Author: Nakarin Pamornchainavakul [aut, cre]
Maintainer: Nakarin Pamornchainavakul <pamornakarin@gmail.com>
Diff between longreadvqs versions 0.1.2 dated 2024-04-14 and 0.1.3 dated 2024-08-26
DESCRIPTION | 15 MD5 | 65 +-- NAMESPACE | 8 NEWS.md | 12 R/AAcompare.R |only R/filtfast.R | 1 R/gapremove.R | 1 R/longreadvqs-package.R |only R/otucompare.R | 7 R/pctopt.R | 10 R/snvcompare.R | 2 R/vqsassess.R | 10 R/vqscompare.R | 341 ++++++++++++++- R/vqscustompct.R | 10 R/vqsout.R | 43 + R/vqsresub.R | 10 R/vqssub.R | 20 README.md | 284 +++++++++++++ build/partial.rdb |only inst/doc/longreadvqs-vignette.R | 8 inst/doc/longreadvqs-vignette.Rmd | 34 - inst/doc/longreadvqs-vignette.html | 798 +++++++++++++++++++------------------ man/AAcompare.Rd |only man/figures/fig0-1.png |only man/figures/fig1-1.png |only man/figures/fig2-1.png |only man/figures/fig3-1.png |only man/figures/fig4-1.png |only man/figures/fig5-1.png |only man/longreadvqs-package.Rd |only man/otucompare.Rd | 6 man/pctopt.Rd | 10 man/snvcompare.Rd | 2 man/vqsassess.Rd | 10 man/vqscompare.Rd | 10 man/vqscustompct.Rd | 10 man/vqsresub.Rd | 10 man/vqssub.Rd | 20 vignettes/longreadvqs-vignette.Rmd | 34 - 39 files changed, 1241 insertions(+), 550 deletions(-)
Title: Linear Mixed Model Solver
Description: An efficient and flexible system to solve sparse mixed model
equations. Important applications are the use of splines to model spatial or temporal
trends as described in Boer (2023). (<doi:10.1177/1471082X231178591>).
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.7 dated 2024-04-16 and 1.0.8 dated 2024-08-26
DESCRIPTION | 10 MD5 | 86 +- NAMESPACE | 1 NEWS.md | 12 R/DifferentiationCholesky.R | 10 R/LMMsolve-class.R | 148 ++++ R/LMMsolve.R | 30 - R/RcppExports.R | 8 R/data.R | 18 R/predictFunctions.R | 4 R/sparseMixedModels.R | 8 R/splinesFunctions.R | 7 R/utils.R | 46 + README.md | 116 +-- build/partial.rdb |binary build/vignette.rds |binary data/SeaSurfaceTemp.rda |only inst/doc/Solving_Linear_Mixed_Models.R | 396 +++++++++---- inst/doc/Solving_Linear_Mixed_Models.Rmd | 574 ++++++++++++++----- inst/doc/Solving_Linear_Mixed_Models.html | 900 +++++++++++++++++++----------- inst/tinytest/GLMMFull |binary inst/tinytest/LMMsolve0 |binary inst/tinytest/LMMsolve1 |binary inst/tinytest/LMMsolve2 |binary inst/tinytest/LMMsolve3 |binary inst/tinytest/LMMsolve4 |binary inst/tinytest/LMMsolve5 |binary inst/tinytest/cfFull |binary inst/tinytest/gam1DFull |binary inst/tinytest/spl1DFull |binary inst/tinytest/spl2DFull |binary inst/tinytest/spl3DFull |binary inst/tinytest/test_LMMsolve-class.R | 5 inst/tinytest/test_gam.R | 4 inst/tinytest/test_spl1D.R | 4 man/LMMsolve.Rd | 3 man/LMMsolveObject.Rd | 1 man/SeaSurfaceTemp.Rd |only man/deviance.LMMsolve.Rd | 10 man/figures/logo.png |only man/predict.LMMsolve.Rd |only src/ADcholesky.cpp | 28 src/RcppExports.cpp | 28 src/SparseMatrix.cpp | 138 ++++ vignettes/Solving_Linear_Mixed_Models.Rmd | 574 ++++++++++++++----- vignettes/bibliography.bib | 15 46 files changed, 2285 insertions(+), 899 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Estimation-bias corrections are available.
Author: Eric Marcon [aut, cre] ,
Bruno Herault [aut]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between entropart versions 1.6-13 dated 2023-09-26 and 1.6-15 dated 2024-08-26
DESCRIPTION | 11 ++++---- MD5 | 58 ++++++++++++++++++++++----------------------- NEWS.md | 2 - R/SpeciesDistribution.R | 4 +-- README.md | 6 ++-- build/vignette.rds |binary inst/doc/entropart.html | 8 +++--- man/AllenH.Rd | 2 - man/AlphaDiversity.Rd | 2 - man/AlphaEntropy.Rd | 2 - man/BetaDiversity.Rd | 2 - man/BetaEntropy.Rd | 2 - man/ChaoPD.Rd | 2 - man/DivEst.Rd | 4 +-- man/DivPart.Rd | 2 - man/DivProfile.Rd | 4 +-- man/GammaDiversity.Rd | 2 - man/GammaEntropy.Rd | 2 - man/GenSimpson.Rd | 2 - man/PDFD.Rd | 2 - man/PPtree.Rd | 4 +-- man/Paracou618.Taxonomy.Rd | 2 - man/PhyloApply.Rd | 2 - man/PhyloBetaEntropy.Rd | 2 - man/PhyloDiversity.Rd | 2 - man/PhyloEntropy.Rd | 2 - man/Preprocess.Tree.Rd | 4 +-- man/RAC.Rd | 2 - man/Rao.Rd | 2 - man/SpeciesDistribution.Rd | 2 - 30 files changed, 72 insertions(+), 71 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.1.1 dated 2024-07-16 and 1.5.1.2 dated 2024-08-26
DESCRIPTION | 8 - MD5 | 20 +-- configure.ac | 2 src/gpboost_R.cpp | 1 src/gpboost_R.h | 1 src/include/GPBoost/re_model_template.h | 7 + src/include/LightGBM/utils/log.h | 1 tests/testthat/test_GPModel_grouped_random_effects.R | 11 +- tests/testthat/test_GPModel_non_Gaussian_data.R | 45 ++++++-- tests/testthat/test_z_GPBoost_algorithm.R | 37 +++--- tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 65 +++++++----- 11 files changed, 127 insertions(+), 71 deletions(-)
Title: Fitting Hidden Markov Models to Financial Data
Description: Fitting (hierarchical) hidden Markov models to financial data
via maximum likelihood estimation. See Oelschläger, L. and Adam, T.
"Detecting Bearish and Bullish Markets in Financial Time Series Using
Hierarchical Hidden Markov Models" (2021, Statistical Modelling)
<doi:10.1177/1471082X211034048> for a reference on the method. A user guide
is provided by the accompanying software paper "fHMM: Hidden Markov Models
for Financial Time Series in R", Oelschläger, L., Adam, T., and Michels, R.
(2024, Journal of Statistical Software) <doi:10.18637/jss.v109.i09>.
Author: Lennart Oelschlaeger [aut, cre]
,
Timo Adam [aut] ,
Rouven Michels [aut]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between fHMM versions 1.3.1 dated 2024-05-31 and 1.4.0 dated 2024-08-26
DESCRIPTION | 6 MD5 | 277 NAMESPACE | 226 NEWS.md | 252 R/RcppExports.R | 22 R/compare_models.R | 152 R/compute_T_star.R | 174 R/compute_ci.R | 122 R/compute_residuals.R | 238 R/data_and_models.R | 632 R/decode_states.R | 350 R/download_data.R | 244 R/fHMM-package.R | 172 R/fHMM_colors.R | 152 R/fHMM_controls.R | 1848 +- R/fHMM_data.R | 432 R/fHMM_events.R | 116 R/fHMM_likelihood.R | 478 R/fHMM_model.R | 898 - R/fHMM_parameters.R | 2192 +- R/fHMM_sdds.R | 320 R/fit_model.R | 500 R/get_initial_values.R | 652 R/helpers.R |only R/parameter_labels.R | 132 R/plot.R | 1536 +- R/read_data.R | 453 R/reorder_states.R | 264 R/simulate_hmm.R | 416 README.md | 626 build/partial.rdb |binary build/vignette.rds |binary data/dax_model_2n.rda |binary data/dax_model_3t.rda |binary data/dax_vw_model.rda |binary data/sim_model_2gamma.rda |binary data/unemp_spx_model_3_2.rda |binary inst/doc/fHMM.R | 14 inst/doc/fHMM.Rmd | 108 inst/doc/fHMM.html | 934 - inst/doc/v01_model_definition.R | 14 inst/doc/v01_model_definition.Rmd | 104 inst/doc/v01_model_definition.html | 866 - inst/doc/v02_controls.R | 86 inst/doc/v02_controls.Rmd | 176 inst/doc/v02_controls.html | 1002 - inst/doc/v03_data_management.R | 88 inst/doc/v03_data_management.Rmd | 184 inst/doc/v03_data_management.html | 922 - inst/doc/v04_model_estimation.R | 82 inst/doc/v04_model_estimation.Rmd | 252 inst/doc/v04_model_estimation.html | 1136 - inst/doc/v05_state_decoding_and_prediction.R | 52 inst/doc/v05_state_decoding_and_prediction.Rmd | 148 inst/doc/v05_state_decoding_and_prediction.html | 948 - inst/doc/v06_model_checking.R | 46 inst/doc/v06_model_checking.Rmd | 132 inst/doc/v06_model_checking.html | 920 - inst/doc/v07_model_selection.R | 32 inst/doc/v07_model_selection.Rmd | 108 inst/doc/v07_model_selection.html | 914 - inst/extdata/dax.csv |18024 ++++++++++++------------ man/check_date.Rd |only man/compare_models.Rd | 60 man/compute_T_star.Rd | 58 man/compute_ci.Rd | 54 man/compute_residuals.Rd | 48 man/dax.Rd | 74 man/dax_model_2n.Rd | 82 man/dax_model_3t.Rd | 92 man/dax_vw_model.Rd | 94 man/decode_states.Rd | 138 man/download_data.Rd | 134 man/fHMM-package.Rd | 62 man/fHMM_colors.Rd | 80 man/fHMM_data.Rd | 140 man/fHMM_events.Rd | 82 man/fHMM_model.Rd | 178 man/fHMM_parameters.Rd | 324 man/fHMM_sdds.Rd | 126 man/figures/README-plot_model_fit-1.png |binary man/figures/README-plot_model_fit-2.png |binary man/figures/README-plot_model_residuals-1.png |binary man/figures/README-simulate-hmm-data-1.png |binary man/find_closest_year.Rd |only man/fit_model.Rd | 338 man/get_initial_values.Rd | 98 man/ll_hmm.Rd | 256 man/nLL_hhmm.Rd | 44 man/nLL_hmm.Rd | 44 man/parameter_labels.Rd | 40 man/parameter_transformations.Rd | 458 man/plot.fHMM_data.Rd | 70 man/plot.fHMM_model.Rd | 118 man/plot_ll.Rd | 46 man/plot_pr.Rd | 40 man/plot_sdds.Rd | 52 man/plot_ts.Rd | 86 man/prepare_data.Rd | 60 man/read_data.Rd | 58 man/reorder_states.Rd | 96 man/set_controls.Rd | 652 man/sim_model_2gamma.Rd | 78 man/simulate_hmm.Rd | 270 man/simulate_observations.Rd | 82 man/spx.Rd | 72 man/unemp.Rd | 54 man/unemp_spx_model_3_2.Rd | 93 man/vw.Rd | 70 tests/testthat.R | 8 tests/testthat/test-compare_models.R | 40 tests/testthat/test-compute_T_star.R | 84 tests/testthat/test-compute_ci.R | 26 tests/testthat/test-compute_residuals.R | 46 tests/testthat/test-data_and_models.R |only tests/testthat/test-decode_states.R | 60 tests/testthat/test-download_data.R | 122 tests/testthat/test-fHMM_colors.R | 70 tests/testthat/test-fHMM_controls.R | 1250 - tests/testthat/test-fHMM_data.R | 120 tests/testthat/test-fHMM_events.R | 56 tests/testthat/test-fHMM_likelihood.R | 66 tests/testthat/test-fHMM_model.R | 96 tests/testthat/test-fHMM_parameters.R | 426 tests/testthat/test-fHMM_sdds.R | 214 tests/testthat/test-fit_model.R | 178 tests/testthat/test-get_initial_values.R | 118 tests/testthat/test-helpers.R |only tests/testthat/test-parameter_labels.R | 68 tests/testthat/test-plot.R | 232 tests/testthat/test-read_data.R | 42 tests/testthat/test-reorder_states.R | 12 tests/testthat/test-simulate_hmm.R | 100 vignettes/fHMM.Rmd | 108 vignettes/ref.bib | 662 vignettes/v01_model_definition.Rmd | 104 vignettes/v02_controls.Rmd | 176 vignettes/v03_data_management.Rmd | 184 vignettes/v04_model_estimation.Rmd | 252 vignettes/v05_state_decoding_and_prediction.Rmd | 148 vignettes/v06_model_checking.Rmd | 132 vignettes/v07_model_selection.Rmd | 108 142 files changed, 25790 insertions(+), 25793 deletions(-)
Title: Basic Calculations for PK/PD Modeling
Description: Essentials for PK/PD (pharmacokinetics/pharmacodynamics) such as area under the curve, (geometric) coefficient of variation, and other calculations that are not part of base R. This is not a noncompartmental analysis (NCA) package.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMcalc versions 0.0.3 dated 2024-01-08 and 0.0.4 dated 2024-08-26
DESCRIPTION | 10 ++++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 1 + NEWS.md | 11 ++++++++++- R/CVlnorm.R | 9 +++++++++ R/logit.R | 2 ++ R/quantbin.R | 20 +++++++++++++++++--- man/CVlnorm.Rd |only man/invlogit.Rd | 3 +++ man/logit.Rd | 3 +++ man/quantbin.Rd | 6 +++++- tests/testthat.R |only 12 files changed, 67 insertions(+), 18 deletions(-)
Title: Incomplete Block Designs using Hadamard Matrix (HadIBDs)
Description: Hadamard matrix based statistical designs are of immense importance as the resultant designs carry various desirable characterizing properties. Constructing Partially Balanced Incomplete Block Designs (PBIBds) using Kronecker product of incidence matrices of Balanced Incomplete Block (BIB) and Partially Balanced Incomplete Block (PBIB) designs is much evident from literature. Here, we have constructed Incomplete Block Designs (IBDs) based on Hadamard matrices and Kronecker product of Hadamard matrices.
Author: Mohd Harun [aut, ctb],
Cini Varghese [aut, ctb],
Ashutosh Dalal [aut, cre]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between HadIBDs versions 1.0.0 dated 2023-11-29 and 1.0.1 dated 2024-08-26
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/HadIBDs.R | 25 ++++++++++++++++++++++++- 3 files changed, 32 insertions(+), 9 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.2 dated 2024-07-15 and 0.1.3 dated 2024-08-26
NMsim-0.1.2/NMsim/inst/examples/R |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr021.dir1 |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr021.msf |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr021.xml |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr021_ETAS.msf |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr021_RMAT.msf |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr021_SMAT.msf |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr032.dir1 |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr032.msf |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr032.xml |only NMsim-0.1.2/NMsim/inst/examples/nonmem/xgxr032_ETAS.msf |only NMsim-0.1.3/NMsim/DESCRIPTION | 16 NMsim-0.1.3/NMsim/MD5 | 173 +---- NMsim-0.1.3/NMsim/NAMESPACE | 3 NMsim-0.1.3/NMsim/NEWS.md | 71 ++ NMsim-0.1.3/NMsim/R/NMcreateMatLines.R | 16 NMsim-0.1.3/NMsim/R/NMexec.R | 140 ++-- NMsim-0.1.3/NMsim/R/NMexecDirectory.R | 32 NMsim-0.1.3/NMsim/R/NMreadSim.R | 2 NMsim-0.1.3/NMsim/R/NMreadSimModTab.R | 40 - NMsim-0.1.3/NMsim/R/NMrunWin.R | 72 +- NMsim-0.1.3/NMsim/R/NMsim.R | 186 ++--- NMsim-0.1.3/NMsim/R/NMsimTestConf.R |only NMsim-0.1.3/NMsim/R/NMsim_EBE.R | 9 NMsim-0.1.3/NMsim/R/NMsim_NWPRI.R |only NMsim-0.1.3/NMsim/R/NMsim_VarCov.R | 27 NMsim-0.1.3/NMsim/R/NMsim_helpers.R | 15 NMsim-0.1.3/NMsim/R/addEVID2.R | 2 NMsim-0.1.3/NMsim/R/addParType.R |only NMsim-0.1.3/NMsim/R/getSystemType.R | 8 NMsim-0.1.3/NMsim/R/modifyHelpers.R | 7 NMsim-0.1.3/NMsim/R/prettyMatLines.R |only NMsim-0.1.3/NMsim/R/readParsWide.R | 1 NMsim-0.1.3/NMsim/R/searchExecutable.R |only NMsim-0.1.3/NMsim/R/typicalize.R | 24 NMsim-0.1.3/NMsim/README.md | 2 NMsim-0.1.3/NMsim/inst/examples/derived/dat_sim1.csv | 344 +++++----- NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.coi |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.cor |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.cov |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.ext |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.lst |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.mod |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.phi |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033.shk |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033_etas.txt |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033_input.rds |only NMsim-0.1.3/NMsim/inst/examples/nonmem/xgxr033_res.txt |only NMsim-0.1.3/NMsim/man/NMcreateMatLines.Rd | 4 NMsim-0.1.3/NMsim/man/NMexec.Rd | 18 NMsim-0.1.3/NMsim/man/NMexecDirectory.Rd | 11 NMsim-0.1.3/NMsim/man/NMsim.Rd | 15 NMsim-0.1.3/NMsim/man/NMsimTestConf.Rd |only NMsim-0.1.3/NMsim/man/NMsim_EBE.Rd | 4 NMsim-0.1.3/NMsim/man/NMsim_NWPRI.Rd |only NMsim-0.1.3/NMsim/man/NMsim_VarCov.Rd | 25 NMsim-0.1.3/NMsim/man/cleanStrings.Rd | 6 NMsim-0.1.3/NMsim/man/prettyMatLines.Rd |only NMsim-0.1.3/NMsim/tests/testthat/simulate-results |only NMsim-0.1.3/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.1.3/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail_input.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/NMreadSim_03.rds |only NMsim-0.1.3/NMsim/tests/testthat/testReference/NMsim_02.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/NMsim_EBE_03.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/NMsim_NWPRI_01.rds |only NMsim-0.1.3/NMsim/tests/testthat/testReference/addEVID2_01.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/addEVID2_02.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/addEVID2_03.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/addEVID2_04.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/addEVID2_05.rds |binary NMsim-0.1.3/NMsim/tests/testthat/testReference/addEVID2_06.rds |binary NMsim-0.1.3/NMsim/tests/testthat/test_NMreadSim.R | 120 ++- NMsim-0.1.3/NMsim/tests/testthat/test_NMsim.R | 55 + NMsim-0.1.3/NMsim/tests/testthat/test_NMsim_NWPRI.R |only NMsim-0.1.3/NMsim/tests/testthat/test_addEVID2.R | 38 - 76 files changed, 884 insertions(+), 604 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: Color schemes ready for each type of data (qualitative,
diverging or sequential), with colors that are distinct for all
people, including color-blind readers. This package provides an
implementation of Paul Tol (2018) and Fabio Crameri (2018)
<doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics'
or 'ggplot2'. It provides tools to simulate color-blindness and to
test how well the colors of any palette are identifiable. Several
scientific thematic schemes (geologic timescale, land cover, FAO
soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Vincent Arel-Bundock [ctb] ,
Ulrik Stervbo [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.13.0 dated 2024-07-01 and 1.14.0 dated 2024-08-26
DESCRIPTION | 8 +-- MD5 | 96 ++++++++++++++++++++-------------------- NEWS.md | 6 ++ R/info.R | 4 - R/khroma-package.R | 2 R/palettes.R | 17 +++++-- README.md | 6 +- inst/doc/crameri.html | 62 ++++++++++++------------- inst/doc/tol.html | 48 ++++++++++---------- inst/tinytest/test_palettes.R | 10 +++- man/crameri.Rd | 4 - man/khroma-package.Rd | 2 man/palette_color_continuous.Rd | 7 ++ man/palette_color_discrete.Rd | 5 +- man/scale_crameri_acton.Rd | 2 man/scale_crameri_bam.Rd | 2 man/scale_crameri_bamO.Rd | 2 man/scale_crameri_bamako.Rd | 2 man/scale_crameri_batlow.Rd | 2 man/scale_crameri_batlowK.Rd | 2 man/scale_crameri_batlowW.Rd | 2 man/scale_crameri_berlin.Rd | 2 man/scale_crameri_bilbao.Rd | 2 man/scale_crameri_broc.Rd | 2 man/scale_crameri_brocO.Rd | 2 man/scale_crameri_buda.Rd | 2 man/scale_crameri_bukavu.Rd | 2 man/scale_crameri_cork.Rd | 2 man/scale_crameri_corkO.Rd | 2 man/scale_crameri_davos.Rd | 2 man/scale_crameri_devon.Rd | 2 man/scale_crameri_fes.Rd | 2 man/scale_crameri_grayC.Rd | 2 man/scale_crameri_hawaii.Rd | 2 man/scale_crameri_imola.Rd | 2 man/scale_crameri_lajolla.Rd | 2 man/scale_crameri_lapaz.Rd | 2 man/scale_crameri_lisbon.Rd | 2 man/scale_crameri_nuuk.Rd | 2 man/scale_crameri_oleron.Rd | 2 man/scale_crameri_oslo.Rd | 2 man/scale_crameri_roma.Rd | 2 man/scale_crameri_romaO.Rd | 2 man/scale_crameri_tofino.Rd | 2 man/scale_crameri_tokyo.Rd | 2 man/scale_crameri_turku.Rd | 2 man/scale_crameri_vanimo.Rd | 2 man/scale_crameri_vik.Rd | 2 man/scale_crameri_vikO.Rd | 2 49 files changed, 186 insertions(+), 161 deletions(-)
More information about htrSPRanalysis at CRAN
Permanent link
Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE')
on 'tibble' format. 'Banco de España' is the national central bank
and, within the framework of the Single Supervisory Mechanism ('SSM'),
the supervisor of the Spanish banking system along with the European
Central Bank. This package is in no way sponsored endorsed or
administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.3.6 dated 2024-04-22 and 0.3.7 dated 2024-08-26
DESCRIPTION | 12 - MD5 | 30 +-- NEWS.md | 8 R/catalogs.R | 21 -- R/indicators.R | 29 +-- R/scales.R | 19 -- R/series.R | 239 +++++++++++++---------------- R/utils.R | 37 ++-- README.md | 25 --- build/vignette.rds |binary inst/CITATION | 11 - inst/doc/tidyBdE.Rmd | 12 - inst/schemaorg.json | 6 tests/testthat/_snaps/bde_tidy_palettes.md | 30 +-- tests/testthat/_snaps/superseded.md | 36 ++-- vignettes/tidyBdE.Rmd | 12 - 16 files changed, 238 insertions(+), 289 deletions(-)
Title: Linked Micromap Plots
Description: This group of functions simplifies the creation of linked micromap plots. Please
see <https://www.jstatsoft.org/v63/i02/> for additional details.
Author: Quinn Payton [aut],
Tony Olsen [aut],
Marc Weber [ctb],
Michael McManus [ctb],
Tom Kincaid [ctb],
Marcus W. Beck [cre, ctb]
Maintainer: Marcus W. Beck <mbeck@tbep.org>
Diff between micromap versions 1.9.8 dated 2024-02-06 and 1.9.9 dated 2024-08-26
DESCRIPTION | 8 MD5 | 58 +-- NAMESPACE | 106 ++--- R/AttDefaults.r | 2 R/PanelBuilding.r | 12 R/mmPlot.r | 2 inst/NEWS.Rd | 16 inst/doc/Introduction_Guide.Rnw | 13 inst/doc/Introduction_Guide.pdf |binary man/OrEcoLevel3.Rd | 46 +- man/USstates.Rd | 48 +- man/WSA3.Rd | 46 +- man/alterForMedian.Rd | 54 +- man/assimilatePlot.Rd | 68 +-- man/create_map_table.Rd | 74 +-- man/edPov.Rd | 50 +- man/internal.Rd | 54 +- man/labels_att.Rd | 58 +-- man/labels_build.Rd | 68 +-- man/lungMort.Rd | 70 +-- man/mmplot.Rd | 748 +++++++++++++++++++-------------------- man/print.mm.Rd | 56 +- man/printLMPlot.Rd | 52 +- man/right.Rd | 44 +- man/sample_att.Rd | 106 ++--- man/statesFlatfile.Rd | 50 +- man/vegCov.Rd | 70 +-- vignettes/Introduction_Guide.Rnw | 13 vignettes/Introduction_Guide.pdf |binary vignettes/Introduction_Guide.tex | 13 30 files changed, 1006 insertions(+), 999 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre]
,
Pino Nicolas [ctb] ,
Riquelme Joaquin [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.0.3 dated 2023-06-20 and 1.0.4 dated 2024-08-26
datana-1.0.3/datana/R/deleteRight.R |only datana-1.0.3/datana/R/extractRight.R |only datana-1.0.3/datana/R/findcolumn.byname.R |only datana-1.0.3/datana/R/valesta.R |only datana-1.0.3/datana/data/airquality.rda |only datana-1.0.3/datana/data/airquality2.rda |only datana-1.0.3/datana/data/anscombe.rda |only datana-1.0.3/datana/data/anscombe2.rda |only datana-1.0.3/datana/data/boreal.rda |only datana-1.0.3/datana/data/boreal2.rda |only datana-1.0.3/datana/data/carbohydrates.rda |only datana-1.0.3/datana/data/carbohydrates2.rda |only datana-1.0.3/datana/data/chickgr.rda |only datana-1.0.3/datana/data/chickgr2.rda |only datana-1.0.3/datana/data/crownradii.rda |only datana-1.0.3/datana/data/crownradii2.rda |only datana-1.0.3/datana/data/demograph2.rda |only datana-1.0.3/datana/data/dgorange.rda |only datana-1.0.3/datana/data/dgorange2.rda |only datana-1.0.3/datana/data/diamgr.rda |only datana-1.0.3/datana/data/diamgr2.rda |only datana-1.0.3/datana/data/eucaplotsampleh.rda |only datana-1.0.3/datana/data/eucaplotsampleh2.rda |only datana-1.0.3/datana/data/grGrandfir.rda |only datana-1.0.3/datana/data/grGrandfir2.rda |only datana-1.0.3/datana/data/hdptorico.rda |only datana-1.0.3/datana/data/hdptorico2.rda |only datana-1.0.3/datana/data/hgrowthlenga.rda |only datana-1.0.3/datana/data/hgrowthlenga2.rda |only datana-1.0.3/datana/data/populavolplots.rda |only datana-1.0.3/datana/data/populavolplots2.rda |only datana-1.0.3/datana/data/psptime.rda |only datana-1.0.3/datana/data/psptime2.rda |only datana-1.0.3/datana/data/ptaeda2.rda |only datana-1.0.3/datana/data/redoakvol.rda |only datana-1.0.3/datana/data/redoakvol2.rda |only datana-1.0.3/datana/man/airquality.Rd |only datana-1.0.3/datana/man/airquality2.Rd |only datana-1.0.3/datana/man/anscombe.Rd |only datana-1.0.3/datana/man/anscombe2.Rd |only datana-1.0.3/datana/man/boreal.Rd |only datana-1.0.3/datana/man/boreal2.Rd |only datana-1.0.3/datana/man/carbohydrates.Rd |only datana-1.0.3/datana/man/carbohydrates2.Rd |only datana-1.0.3/datana/man/chickgr.Rd |only datana-1.0.3/datana/man/chickgr2.Rd |only datana-1.0.3/datana/man/crownradii.Rd |only datana-1.0.3/datana/man/crownradii2.Rd |only datana-1.0.3/datana/man/deleteRight.Rd |only datana-1.0.3/datana/man/demograph2.Rd |only datana-1.0.3/datana/man/dgorange.Rd |only datana-1.0.3/datana/man/dgorange2.Rd |only datana-1.0.3/datana/man/diamgr.Rd |only datana-1.0.3/datana/man/diamgr2.Rd |only datana-1.0.3/datana/man/eucaplotsampleh.Rd |only datana-1.0.3/datana/man/eucaplotsampleh2.Rd |only datana-1.0.3/datana/man/extractRight.Rd |only datana-1.0.3/datana/man/findColumn.byname.Rd |only datana-1.0.3/datana/man/grGrandfir.Rd |only datana-1.0.3/datana/man/grGrandfir2.Rd |only datana-1.0.3/datana/man/hdptorico.Rd |only datana-1.0.3/datana/man/hdptorico2.Rd |only datana-1.0.3/datana/man/hgrowthlenga.Rd |only datana-1.0.3/datana/man/hgrowthlenga2.Rd |only datana-1.0.3/datana/man/populavolplots.Rd |only datana-1.0.3/datana/man/populavolplots2.Rd |only datana-1.0.3/datana/man/psptime.Rd |only datana-1.0.3/datana/man/psptime2.Rd |only datana-1.0.3/datana/man/ptaeda2.Rd |only datana-1.0.3/datana/man/redoakvol.Rd |only datana-1.0.3/datana/man/redoakvol2.Rd |only datana-1.0.3/datana/man/valesta.Rd |only datana-1.0.4/datana/DESCRIPTION | 35 datana-1.0.4/datana/MD5 | 476 +--- datana-1.0.4/datana/NAMESPACE | 4 datana-1.0.4/datana/R/describe_datas.R | 2270 +++++++-------------- datana-1.0.4/datana/R/descstat.R | 9 datana-1.0.4/datana/R/xyBoxplot.R | 32 datana-1.0.4/datana/R/xyHist.R | 12 datana-1.0.4/datana/build/partial.rdb |binary datana-1.0.4/datana/data/aboutrsq.rda |only datana-1.0.4/datana/data/aboutrsq2.rda |only datana-1.0.4/datana/data/airnyc.rda |only datana-1.0.4/datana/data/airnyc2.rda |only datana-1.0.4/datana/data/annualppCities.rda |binary datana-1.0.4/datana/data/annualppCities2.rda |binary datana-1.0.4/datana/data/araucaria.rda |binary datana-1.0.4/datana/data/araucaria2.rda |binary datana-1.0.4/datana/data/baiTreelines.rda |binary datana-1.0.4/datana/data/baiTreelines2.rda |binary datana-1.0.4/datana/data/bears.rda |binary datana-1.0.4/datana/data/bears2.rda |binary datana-1.0.4/datana/data/bearsDepu.rda |binary datana-1.0.4/datana/data/bearsDepu2.rda |binary datana-1.0.4/datana/data/beetles.rda |binary datana-1.0.4/datana/data/beetles2.rda |binary datana-1.0.4/datana/data/biomass.rda |binary datana-1.0.4/datana/data/biomass2.rda |binary datana-1.0.4/datana/data/carbohydrateTreelines.rda |only datana-1.0.4/datana/data/chicksw.rda |only datana-1.0.4/datana/data/corkoak.rda |binary datana-1.0.4/datana/data/corkoak2.rda |binary datana-1.0.4/datana/data/crown.rda |only datana-1.0.4/datana/data/crown2.rda |only datana-1.0.4/datana/data/deadForestCA.rda |binary datana-1.0.4/datana/data/deadForestCA2.rda |binary datana-1.0.4/datana/data/deadLianas.rda |binary datana-1.0.4/datana/data/deadLianas2.rda |binary datana-1.0.4/datana/data/demograph.rda |binary datana-1.0.4/datana/data/election.rda |binary datana-1.0.4/datana/data/election2.rda |binary datana-1.0.4/datana/data/eucaleaf.rda |binary datana-1.0.4/datana/data/eucaleaf2.rda |binary datana-1.0.4/datana/data/eucaleafAll.rda |only datana-1.0.4/datana/data/eucaleafAll2.rda |only datana-1.0.4/datana/data/eucaplot.rda |binary datana-1.0.4/datana/data/eucaplot2.rda |binary datana-1.0.4/datana/data/fertilizaexpe.rda |binary datana-1.0.4/datana/data/fertilizaexpe2.rda |binary datana-1.0.4/datana/data/fishgrowth.rda |binary datana-1.0.4/datana/data/fishgrowth2.rda |binary datana-1.0.4/datana/data/floraChile.rda |binary datana-1.0.4/datana/data/floraChile2.rda |binary datana-1.0.4/datana/data/football.rda |binary datana-1.0.4/datana/data/football2.rda |binary datana-1.0.4/datana/data/forestFire.rda |binary datana-1.0.4/datana/data/forestFire2.rda |binary datana-1.0.4/datana/data/forestHawaii.rda |binary datana-1.0.4/datana/data/hawaii.rda |binary datana-1.0.4/datana/data/hawaii2.rda |binary datana-1.0.4/datana/data/hgrowthDfir.rda |binary datana-1.0.4/datana/data/hgrowthDfir2.rda |binary datana-1.0.4/datana/data/idahohd.rda |binary datana-1.0.4/datana/data/idahohd2.rda |binary datana-1.0.4/datana/data/invasivesRCI.rda |binary datana-1.0.4/datana/data/landCoverSantiago.rda |binary datana-1.0.4/datana/data/landCoverSantiago2.rda |binary datana-1.0.4/datana/data/lleuque.rda |binary datana-1.0.4/datana/data/orange.rda |only datana-1.0.4/datana/data/orange2.rda |only datana-1.0.4/datana/data/pinaster.rda |binary datana-1.0.4/datana/data/pinaster2.rda |binary datana-1.0.4/datana/data/pinusContorta.rda |binary datana-1.0.4/datana/data/pinusContorta2.rda |binary datana-1.0.4/datana/data/pinusSpp.rda |binary datana-1.0.4/datana/data/pinusSpp2.rda |binary datana-1.0.4/datana/data/plantsHawaii.rda |binary datana-1.0.4/datana/data/presenceIce.rda |binary datana-1.0.4/datana/data/presidentChile.rda |binary datana-1.0.4/datana/data/presidentChile2.rda |binary datana-1.0.4/datana/data/primary.rda |only datana-1.0.4/datana/data/primary2.rda |only datana-1.0.4/datana/data/pspLlancahue.rda |binary datana-1.0.4/datana/data/pspLlancahue2.rda |binary datana-1.0.4/datana/data/pspRuca.rda |binary datana-1.0.4/datana/data/pspRuca2.rda |binary datana-1.0.4/datana/data/ptaeda.rda |binary datana-1.0.4/datana/data/radiatapl.rda |binary datana-1.0.4/datana/data/raulihg.rda |binary datana-1.0.4/datana/data/raulihg2.rda |binary datana-1.0.4/datana/data/regNothofagus.rda |binary datana-1.0.4/datana/data/simula.rda |binary datana-1.0.4/datana/data/slashpine.rda |binary datana-1.0.4/datana/data/slashpine2.rda |binary datana-1.0.4/datana/data/sludge.rda |binary datana-1.0.4/datana/data/snaspeChile.rda |binary datana-1.0.4/datana/data/snaspeChile2.rda |binary datana-1.0.4/datana/data/soiltreat.rda |binary datana-1.0.4/datana/data/soiltreat2.rda |binary datana-1.0.4/datana/data/spatAustria.rda |binary datana-1.0.4/datana/data/speciesList.rda |binary datana-1.0.4/datana/data/sppAbundance.rda |binary datana-1.0.4/datana/data/sppTraits.rda |binary datana-1.0.4/datana/data/standLleuque.rda |binary datana-1.0.4/datana/data/standLleuque2.rda |binary datana-1.0.4/datana/data/trailCameraTrap.rda |binary datana-1.0.4/datana/data/traits.rda |binary datana-1.0.4/datana/data/traits2.rda |binary datana-1.0.4/datana/data/treegrowth.rda |binary datana-1.0.4/datana/data/treegrowth2.rda |binary datana-1.0.4/datana/data/treelistinve.rda |binary datana-1.0.4/datana/data/treelistinve2.rda |binary datana-1.0.4/datana/data/treevol.rda |binary datana-1.0.4/datana/data/treevol2.rda |binary datana-1.0.4/datana/data/treevolroble.rda |binary datana-1.0.4/datana/data/treevolroble2.rda |binary datana-1.0.4/datana/data/treevolruca.rda |binary datana-1.0.4/datana/data/treevolruca2.rda |binary datana-1.0.4/datana/inst/CITATION | 19 datana-1.0.4/datana/man/aboutrsq.Rd |only datana-1.0.4/datana/man/aboutrsq2.Rd |only datana-1.0.4/datana/man/airnyc.Rd |only datana-1.0.4/datana/man/airnyc2.Rd |only datana-1.0.4/datana/man/annualppCities.Rd | 14 datana-1.0.4/datana/man/annualppCities2.Rd | 16 datana-1.0.4/datana/man/araucaria.Rd | 41 datana-1.0.4/datana/man/araucaria2.Rd | 43 datana-1.0.4/datana/man/baiTreelines.Rd | 9 datana-1.0.4/datana/man/baiTreelines2.Rd | 27 datana-1.0.4/datana/man/bears2.Rd | 10 datana-1.0.4/datana/man/bearsDepu.Rd | 2 datana-1.0.4/datana/man/bearsDepu2.Rd | 4 datana-1.0.4/datana/man/beetles.Rd | 50 datana-1.0.4/datana/man/beetles2.Rd | 51 datana-1.0.4/datana/man/biomass.Rd | 22 datana-1.0.4/datana/man/biomass2.Rd | 30 datana-1.0.4/datana/man/carbohydrateTreelines.Rd |only datana-1.0.4/datana/man/chicksw.Rd |only datana-1.0.4/datana/man/corkoak.Rd | 12 datana-1.0.4/datana/man/crown.Rd |only datana-1.0.4/datana/man/crown2.Rd |only datana-1.0.4/datana/man/datana-package.Rd | 20 datana-1.0.4/datana/man/deadForestCA.Rd | 15 datana-1.0.4/datana/man/deadForestCA2.Rd | 49 datana-1.0.4/datana/man/deadLianas.Rd | 6 datana-1.0.4/datana/man/deadLianas2.Rd | 34 datana-1.0.4/datana/man/demograph.Rd | 38 datana-1.0.4/datana/man/descstat.Rd | 11 datana-1.0.4/datana/man/election.Rd | 6 datana-1.0.4/datana/man/election2.Rd | 10 datana-1.0.4/datana/man/eucaleaf.Rd | 2 datana-1.0.4/datana/man/eucaleaf2.Rd | 8 datana-1.0.4/datana/man/eucaleafAll.Rd |only datana-1.0.4/datana/man/eucaleafAll2.Rd |only datana-1.0.4/datana/man/eucaplot.Rd | 6 datana-1.0.4/datana/man/eucaplot2.Rd | 8 datana-1.0.4/datana/man/fertilizaexpe.Rd | 2 datana-1.0.4/datana/man/fishgrowth2.Rd | 2 datana-1.0.4/datana/man/floraChile.Rd | 2 datana-1.0.4/datana/man/floraChile2.Rd | 4 datana-1.0.4/datana/man/football.Rd | 26 datana-1.0.4/datana/man/football2.Rd | 26 datana-1.0.4/datana/man/forestFire.Rd | 14 datana-1.0.4/datana/man/forestFire2.Rd | 29 datana-1.0.4/datana/man/forestHawaii.Rd | 8 datana-1.0.4/datana/man/hawaii.Rd | 4 datana-1.0.4/datana/man/hawaii2.Rd | 12 datana-1.0.4/datana/man/hgrowthDfir2.Rd | 8 datana-1.0.4/datana/man/idahohd2.Rd | 10 datana-1.0.4/datana/man/landCoverSantiago.Rd | 2 datana-1.0.4/datana/man/landCoverSantiago2.Rd | 18 datana-1.0.4/datana/man/orange.Rd |only datana-1.0.4/datana/man/orange2.Rd |only datana-1.0.4/datana/man/pinaster.Rd | 13 datana-1.0.4/datana/man/pinaster2.Rd | 18 datana-1.0.4/datana/man/pinusContorta.Rd | 8 datana-1.0.4/datana/man/pinusContorta2.Rd | 14 datana-1.0.4/datana/man/pinusSpp.Rd | 7 datana-1.0.4/datana/man/pinusSpp2.Rd | 23 datana-1.0.4/datana/man/plantsHawaii.Rd | 2 datana-1.0.4/datana/man/presenceIce.Rd | 2 datana-1.0.4/datana/man/presidentChile.Rd | 26 datana-1.0.4/datana/man/presidentChile2.Rd | 45 datana-1.0.4/datana/man/primary.Rd |only datana-1.0.4/datana/man/primary2.Rd |only datana-1.0.4/datana/man/pspLlancahue.Rd | 13 datana-1.0.4/datana/man/pspLlancahue2.Rd | 23 datana-1.0.4/datana/man/pspRuca.Rd | 12 datana-1.0.4/datana/man/pspRuca2.Rd | 26 datana-1.0.4/datana/man/ptaeda.Rd | 10 datana-1.0.4/datana/man/raulihg.Rd | 18 datana-1.0.4/datana/man/raulihg2.Rd | 14 datana-1.0.4/datana/man/regNothofagus.Rd | 4 datana-1.0.4/datana/man/simula.Rd | 8 datana-1.0.4/datana/man/slashpine.Rd | 2 datana-1.0.4/datana/man/slashpine2.Rd | 12 datana-1.0.4/datana/man/snaspeChile.Rd | 2 datana-1.0.4/datana/man/snaspeChile2.Rd | 6 datana-1.0.4/datana/man/soiltreat.Rd | 29 datana-1.0.4/datana/man/soiltreat2.Rd | 33 datana-1.0.4/datana/man/spatAustria.Rd | 4 datana-1.0.4/datana/man/speciesList.Rd | 4 datana-1.0.4/datana/man/sppAbundance.Rd | 10 datana-1.0.4/datana/man/sppTraits.Rd | 6 datana-1.0.4/datana/man/standLleuque2.Rd | 9 datana-1.0.4/datana/man/trailCameraTrap.Rd | 4 datana-1.0.4/datana/man/traits.Rd | 2 datana-1.0.4/datana/man/traits2.Rd | 2 datana-1.0.4/datana/man/treegrowth.Rd | 4 datana-1.0.4/datana/man/treegrowth2.Rd | 14 datana-1.0.4/datana/man/treelistinve.Rd | 13 datana-1.0.4/datana/man/treelistinve2.Rd | 34 datana-1.0.4/datana/man/treevol.Rd | 19 datana-1.0.4/datana/man/treevol2.Rd | 10 datana-1.0.4/datana/man/treevolroble.Rd | 14 datana-1.0.4/datana/man/treevolroble2.Rd | 17 datana-1.0.4/datana/man/treevolruca.Rd | 6 datana-1.0.4/datana/man/treevolruca2.Rd | 12 datana-1.0.4/datana/man/xyBoxplot.Rd | 6 289 files changed, 1763 insertions(+), 2365 deletions(-)
Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>)
by geography, state, measure, and release year. This package also contains a
function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>
Diff between CDCPLACES versions 1.1.6 dated 2024-07-28 and 1.1.7 dated 2024-08-26
DESCRIPTION | 9 MD5 | 12 - NAMESPACE | 15 - NEWS.md | 5 R/get_dictionary.R | 14 - R/get_places.R | 587 ++++++++++++++++++++------------------------------ man/get_dictionary.Rd | 1 7 files changed, 268 insertions(+), 375 deletions(-)
Title: Retrieving and Analyzing Air Quality and Weather Data from ARPA
Lombardia
Description: Contains functions for retrieving, managing and analysing air quality and weather data from Regione Lombardia open database (<https://www.dati.lombardia.it/>).
Data are collected by ARPA Lombardia (Lombardia Environmental Protection Agency), Italy, through its ground monitoring network (<https://www.dati.lombardia.it/stories/s/auv9-c2sj>).
See the webpage <https://www.arpalombardia.it/> for further information on ARPA Lombardia's activities and history.
Data quality (e.g. missing values, exported values, graphical mapping) has been checked involving members of the ARPA Lombardia's office for air quality control.
The package makes available observations since 1989 (for weather) and 1968 (for air quality) and are updated with daily frequency by the regional agency.
Full description of the package can be retrieved in the companion paper Maranzano \& Algieri (2024), "ARPALData: an R package for retrieving and analyzing air quality
and weather data from ARPA Lombardia [...truncated...]
Author: Paolo Maranzano [aut, cre, cph]
,
Andrea Algieri [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
Diff between ARPALData versions 1.5.2 dated 2024-03-16 and 1.6.0 dated 2024-08-26
ARPALData-1.5.2/ARPALData/R/url_dataset_year.R |only ARPALData-1.6.0/ARPALData/DESCRIPTION | 8 ARPALData-1.6.0/ARPALData/MD5 | 23 ARPALData-1.6.0/ARPALData/NAMESPACE | 2 ARPALData-1.6.0/ARPALData/R/W_download_current.R |only ARPALData-1.6.0/ARPALData/R/W_download_past.R |only ARPALData-1.6.0/ARPALData/R/W_metadata_reshape.R | 8 ARPALData-1.6.0/ARPALData/R/get_ARPA_Lombardia_AQ_data.R | 6 ARPALData-1.6.0/ARPALData/R/get_ARPA_Lombardia_AQ_municipal_data.R | 16 ARPALData-1.6.0/ARPALData/R/get_ARPA_Lombardia_W_data.R | 372 +--------- ARPALData-1.6.0/ARPALData/R/url_AQ_year_dataset.R |only ARPALData-1.6.0/ARPALData/R/url_W_year_par.R |only ARPALData-1.6.0/ARPALData/man/get_ARPA_Lombardia_AQ_data.Rd | 4 ARPALData-1.6.0/ARPALData/man/get_ARPA_Lombardia_AQ_municipal_data.Rd | 12 ARPALData-1.6.0/ARPALData/man/get_ARPA_Lombardia_W_data.Rd | 4 15 files changed, 115 insertions(+), 340 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre],
Eric Anderson [ctb],
Matthew Fidler [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.1.6 dated 2024-04-23 and 0.1.7 dated 2024-08-26
NMdata-0.1.6/NMdata/inst/examples/nonmem/xgxr002.lst |only NMdata-0.1.6/NMdata/inst/examples/nonmem/xgxr002.mod |only NMdata-0.1.6/NMdata/inst/examples/nonmem/xgxr002.phi |only NMdata-0.1.6/NMdata/inst/examples/nonmem/xgxr002_res.txt |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/NMexec.pnm |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr001.dir1 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr001dir/input.ext |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr001dir/input.phi |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr014.dir1 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr014.dir2 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr023.dir1 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr023.dir2 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr023.dir3 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr023.dir4 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr028.dir1 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr028.dir2 |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.coi |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.cor |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.cov |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.lst |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.msf |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.phi |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031.shk |only NMdata-0.1.6/NMdata/tests/testthat/testData/nonmem/xgxr031_res.txt |only NMdata-0.1.6/NMdata/tests/testthat/testReference/NMorderColumns_1.rds |only NMdata-0.1.7/NMdata/DESCRIPTION | 25 NMdata-0.1.7/NMdata/MD5 | 451 NMdata-0.1.7/NMdata/NAMESPACE | 2 NMdata-0.1.7/NMdata/NEWS.md | 129 NMdata-0.1.7/NMdata/R/NMapplyFilters.R | 2 NMdata-0.1.7/NMdata/R/NMcheckData.R | 48 NMdata-0.1.7/NMdata/R/NMcheckDataFile.R | 3 NMdata-0.1.7/NMdata/R/NMdataConf.R | 24 NMdata-0.1.7/NMdata/R/NMexpandDoses.R | 5 NMdata-0.1.7/NMdata/R/NMextractDataFile.R | 2 NMdata-0.1.7/NMdata/R/NMextractText.R | 43 NMdata-0.1.7/NMdata/R/NMgenText.R | 17 NMdata-0.1.7/NMdata/R/NMorderColumns.R | 18 NMdata-0.1.7/NMdata/R/NMreadCov.R | 17 NMdata-0.1.7/NMdata/R/NMreadCsv.R | 59 NMdata-0.1.7/NMdata/R/NMreadExt.R | 106 NMdata-0.1.7/NMdata/R/NMreadParsText.R | 376 NMdata-0.1.7/NMdata/R/NMreadPhi.R | 3 NMdata-0.1.7/NMdata/R/NMreadSection.R | 18 NMdata-0.1.7/NMdata/R/NMreadShk.R | 20 NMdata-0.1.7/NMdata/R/NMreadTab.R | 11 NMdata-0.1.7/NMdata/R/NMreadTabSlow.R | 1 NMdata-0.1.7/NMdata/R/NMrelate.R |only NMdata-0.1.7/NMdata/R/NMrelateOne.R |only NMdata-0.1.7/NMdata/R/NMreplaceDataFile.R | 4 NMdata-0.1.7/NMdata/R/NMscanData.R | 6 NMdata-0.1.7/NMdata/R/NMscanInput.R | 16 NMdata-0.1.7/NMdata/R/NMscanMultiple.R | 19 NMdata-0.1.7/NMdata/R/NMscanTables.R | 3 NMdata-0.1.7/NMdata/R/NMtransInp.R | 13 NMdata-0.1.7/NMdata/R/NMwriteData.R | 25 NMdata-0.1.7/NMdata/R/NMwriteSectionOne.R | 13 NMdata-0.1.7/NMdata/R/addOmegaCorr.R | 14 NMdata-0.1.7/NMdata/R/addParType.R |only NMdata-0.1.7/NMdata/R/addTAPD.R | 8 NMdata-0.1.7/NMdata/R/addTableStep.R | 4 NMdata-0.1.7/NMdata/R/cleanSpaces.R |only NMdata-0.1.7/NMdata/R/compareCols.R | 2 NMdata-0.1.7/NMdata/R/deprecatedArg.R | 4 NMdata-0.1.7/NMdata/R/dims.R | 4 NMdata-0.1.7/NMdata/R/dt2mat.R | 23 NMdata-0.1.7/NMdata/R/findCovs.R | 3 NMdata-0.1.7/NMdata/R/findVars.R | 3 NMdata-0.1.7/NMdata/R/flagsAssign.R | 4 NMdata-0.1.7/NMdata/R/getArgs.R | 34 NMdata-0.1.7/NMdata/R/getFilePaths.R | 12 NMdata-0.1.7/NMdata/R/getLines.R |only NMdata-0.1.7/NMdata/R/mat2dt.R | 4 NMdata-0.1.7/NMdata/R/mergeCheck.R | 75 NMdata-0.1.7/NMdata/R/tmpcol.R | 6 NMdata-0.1.7/NMdata/README.md | 22 NMdata-0.1.7/NMdata/inst/examples/data/xgxr2covs.csv |only NMdata-0.1.7/NMdata/inst/examples/data/xgxr2covs.rds |only NMdata-0.1.7/NMdata/inst/examples/data/xgxr2covs_meta.txt |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr018.lst | 6246 +++++++++- NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr018_res.txt | 1810 +- NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr018_res_fo.txt | 300 NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr018_res_vols.txt | 1810 +- NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.coi |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.cor |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.cov |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.ext |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.lst |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.mod |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.msf |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.phi |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.shk |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132.xml |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132_ETAS.msf |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132_etas.txt |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr132_res.txt |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr133.cov |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr133.ext |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr133.lst |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr133.mod |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr133.shk |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.coi |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.cor |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.cov |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.ext |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.lst |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.mod |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.msf |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.phi |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.shk |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.xml |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134_ETAS.msf |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134_etas.txt |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134_res.txt |only NMdata-0.1.7/NMdata/inst/examples/scripts |only NMdata-0.1.7/NMdata/man/NMextractDataFile.Rd | 2 NMdata-0.1.7/NMdata/man/NMextractText.Rd | 5 NMdata-0.1.7/NMdata/man/NMgenText.Rd | 2 NMdata-0.1.7/NMdata/man/NMorderColumns.Rd | 6 NMdata-0.1.7/NMdata/man/NMreadCov.Rd | 7 NMdata-0.1.7/NMdata/man/NMreadCsv.Rd | 8 NMdata-0.1.7/NMdata/man/NMreadExt.Rd | 6 NMdata-0.1.7/NMdata/man/NMreadParsText.Rd | 99 NMdata-0.1.7/NMdata/man/NMreadSection.Rd | 3 NMdata-0.1.7/NMdata/man/NMreadShk.Rd | 7 NMdata-0.1.7/NMdata/man/NMreadTab.Rd | 2 NMdata-0.1.7/NMdata/man/NMrelate.Rd |only NMdata-0.1.7/NMdata/man/NMtransInp.Rd | 4 NMdata-0.1.7/NMdata/man/addOmegaCorr.Rd | 6 NMdata-0.1.7/NMdata/man/cleanSpaces.Rd |only NMdata-0.1.7/NMdata/man/dt2mat.Rd | 6 NMdata-0.1.7/NMdata/man/figures/README-NMscanData-example1-plot-1.png |binary NMdata-0.1.7/NMdata/man/figures/README-unnamed-chunk-2-1.png |binary NMdata-0.1.7/NMdata/man/getArgs.Rd | 15 NMdata-0.1.7/NMdata/man/getFilePaths.Rd | 10 NMdata-0.1.7/NMdata/man/mergeCheck.Rd | 27 NMdata-0.1.7/NMdata/man/splitFields.Rd |only NMdata-0.1.7/NMdata/man/tmpcol.Rd | 12 NMdata-0.1.7/NMdata/tests/testthat/testData/nonmem/xgxr018.ext | 16 NMdata-0.1.7/NMdata/tests/testthat/testData/nonmem/xgxr018.lst | 6246 +++++++++- NMdata-0.1.7/NMdata/tests/testthat/testData/nonmem/xgxr018.phi | 262 NMdata-0.1.7/NMdata/tests/testthat/testData/nonmem/xgxr018_res.txt | 1810 +- NMdata-0.1.7/NMdata/tests/testthat/testData/nonmem/xgxr018_res_fo.txt | 300 NMdata-0.1.7/NMdata/tests/testthat/testData/nonmem/xgxr018_res_vols.txt | 1810 +- NMdata-0.1.7/NMdata/tests/testthat/testData/simulations/xgxr014_subprobs/NMsim_xgxr014_subprobs.ext |only NMdata-0.1.7/NMdata/tests/testthat/testData/simulations/xgxr014_subprobs/NMsim_xgxr014_subprobs.lst |only NMdata-0.1.7/NMdata/tests/testthat/testData/simulations/xgxr014_subprobs/NMsim_xgxr014_subprobs.mod |only NMdata-0.1.7/NMdata/tests/testthat/testOutput/NMwriteData_13.csv |only NMdata-0.1.7/NMdata/tests/testthat/testOutput/NMwriteData_13.fst |only NMdata-0.1.7/NMdata/tests/testthat/testOutput/NMwriteData_13_meta.txt |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMdataConf_01.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMdataConf_02.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMorderColumns_01.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMorderColumns_02.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadExt_01.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadExt_02.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadExt_03.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadExt_04.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadExt_05.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadExt_06.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadParText_02.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadParText_03.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadParText_04.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadParText_05.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadParText_06.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadParText_07.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMreadShk_01.rds |binary NMdata-0.1.7/NMdata/tests/testthat/testReference/NMrelateOne_01.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMrelate_01.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMrelate_02.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMrelate_03.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMwriteData_13.rds |only NMdata-0.1.7/NMdata/tests/testthat/testReference/splitFields_01.rds |only NMdata-0.1.7/NMdata/tests/testthat/test_NMdataConf.R | 76 NMdata-0.1.7/NMdata/tests/testthat/test_NMdata_utils.R | 11 NMdata-0.1.7/NMdata/tests/testthat/test_NMorderColumns.R | 30 NMdata-0.1.7/NMdata/tests/testthat/test_NMreadExt.R | 53 NMdata-0.1.7/NMdata/tests/testthat/test_NMreadParText.R | 179 NMdata-0.1.7/NMdata/tests/testthat/test_NMreadShk.R | 3 NMdata-0.1.7/NMdata/tests/testthat/test_NMrelate.R |only NMdata-0.1.7/NMdata/tests/testthat/test_NMscanData.R | 21 NMdata-0.1.7/NMdata/tests/testthat/test_NMscanInput.R | 8 NMdata-0.1.7/NMdata/tests/testthat/test_NMscanTables.R | 5 NMdata-0.1.7/NMdata/tests/testthat/test_NMwriteData.R | 45 NMdata-0.1.7/NMdata/tests/testthat/test_deprecatedArg.R | 3 NMdata-0.1.7/NMdata/tests/testthat/test_getArgs.R | 3 186 files changed, 18081 insertions(+), 4894 deletions(-)
More information about PoSIAdjRSquared at CRAN
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Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph] [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.7.2 dated 2024-03-17 and 0.8.0 dated 2024-08-26
pak-0.7.2/pak/src/library/callr/R/errors.R |only pak-0.8.0/pak/DESCRIPTION | 17 pak-0.8.0/pak/MD5 | 135 +- pak-0.8.0/pak/NEWS.md | 30 pak-0.8.0/pak/R/embed.R | 4 pak-0.8.0/pak/R/package.R | 4 pak-0.8.0/pak/R/push-packages.R | 12 pak-0.8.0/pak/R/repo.R | 2 pak-0.8.0/pak/R/subprocess.R | 6 pak-0.8.0/pak/R/sysreqs.R | 19 pak-0.8.0/pak/R/system-requirements.R | 4 pak-0.8.0/pak/README.md |only pak-0.8.0/pak/inst/header.md | 2 pak-0.8.0/pak/man/chunks/FAQ.Rmd | 5 pak-0.8.0/pak/man/chunks/features.Rmd | 9 pak-0.8.0/pak/man/chunks/sysreqs.Rmd | 10 pak-0.8.0/pak/man/chunks/sysreqs.md | 540 ++++----- pak-0.8.0/pak/man/faq.Rd | 5 pak-0.8.0/pak/man/features.Rd | 9 pak-0.8.0/pak/man/pkg_sysreqs.Rd | 15 pak-0.8.0/pak/man/repo_add.Rd | 2 pak-0.8.0/pak/man/sysreqs.Rd | 541 ++++------ pak-0.8.0/pak/src/install-embedded.R | 4 pak-0.8.0/pak/src/library/callr/DESCRIPTION | 12 pak-0.8.0/pak/src/library/callr/NEWS.md | 7 pak-0.8.0/pak/src/library/callr/R/load-client.R | 2 pak-0.8.0/pak/src/library/callr/R/standalone-errors.R |only pak-0.8.0/pak/src/library/callr/R/test-helpers.R |only pak-0.8.0/pak/src/library/callr/R/x-client.R | 2 pak-0.8.0/pak/src/library/callr/inst/WORDLIST | 4 pak-0.8.0/pak/src/library/pkgcache/DESCRIPTION | 9 pak-0.8.0/pak/src/library/pkgcache/NEWS.md | 20 pak-0.8.0/pak/src/library/pkgcache/R/aaa-async.R | 264 ++++ pak-0.8.0/pak/src/library/pkgcache/R/archive.R | 2 pak-0.8.0/pak/src/library/pkgcache/R/installed.R | 2 pak-0.8.0/pak/src/library/pkgcache/R/metadata-cache.R | 3 pak-0.8.0/pak/src/library/pkgcache/R/onload.R | 438 -------- pak-0.8.0/pak/src/library/pkgcache/R/packages-gz.R | 15 pak-0.8.0/pak/src/library/pkgcache/R/platform.R | 12 pak-0.8.0/pak/src/library/pkgcache/R/ppm.R | 39 pak-0.8.0/pak/src/library/pkgcache/R/repo-set.R | 16 pak-0.8.0/pak/src/library/pkgcache/src/lib.c | 4 pak-0.8.0/pak/src/library/pkgdepends/DESCRIPTION | 16 pak-0.8.0/pak/src/library/pkgdepends/NAMESPACE | 4 pak-0.8.0/pak/src/library/pkgdepends/R/builder.R |only pak-0.8.0/pak/src/library/pkgdepends/R/gh-mirror.R |only pak-0.8.0/pak/src/library/pkgdepends/R/gh-releases.R |only pak-0.8.0/pak/src/library/pkgdepends/R/gh-repo.R |only pak-0.8.0/pak/src/library/pkgdepends/R/ghcr.R |only pak-0.8.0/pak/src/library/pkgdepends/R/git-app.R | 7 pak-0.8.0/pak/src/library/pkgdepends/R/git-auth.R | 21 pak-0.8.0/pak/src/library/pkgdepends/R/git-protocol.R | 79 + pak-0.8.0/pak/src/library/pkgdepends/R/git-submodules.R |only pak-0.8.0/pak/src/library/pkgdepends/R/install-plan.R | 58 - pak-0.8.0/pak/src/library/pkgdepends/R/iso-date.R |only pak-0.8.0/pak/src/library/pkgdepends/R/parse-remotes.R | 13 pak-0.8.0/pak/src/library/pkgdepends/R/repo.R |only pak-0.8.0/pak/src/library/pkgdepends/R/resolution-df.R | 6 pak-0.8.0/pak/src/library/pkgdepends/R/resolution.R | 2 pak-0.8.0/pak/src/library/pkgdepends/R/solve.R | 34 pak-0.8.0/pak/src/library/pkgdepends/R/time.R | 2 pak-0.8.0/pak/src/library/pkgdepends/R/type-git.R | 43 pak-0.8.0/pak/src/library/pkgdepends/R/type-gitlab.R | 34 pak-0.8.0/pak/src/library/pkgdepends/R/utils.R | 14 pak-0.8.0/pak/src/library/pkgdepends/R/zzz-pkgdepends-config.R | 12 pak-0.8.0/pak/src/library/pkgdepends/inst/WORDLIST | 3 pak-0.8.0/pak/src/library/pkgdepends/inst/docs/download-result.rds |binary pak-0.8.0/pak/src/library/pkgdepends/inst/docs/pak-config-docs.rds |binary pak-0.8.0/pak/src/library/pkgdepends/inst/docs/pkg-refs.rds |binary pak-0.8.0/pak/src/library/pkgdepends/inst/docs/resolution-result.rds |binary pak-0.8.0/pak/src/library/zip/src/init.c | 1 pak-0.8.0/pak/tests/testthat/fixtures |only pak-0.8.0/pak/tests/testthat/test-failure-output.R |only pak-0.8.0/pak/tools/docs |only 74 files changed, 1296 insertions(+), 1279 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels
(Autonomous Communities, Provinces, Municipalities) based on the
'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco>
and 'CartoBase SIANE' from 'Instituto Geografico Nacional'
<https://www.ign.es/>. It also provides a 'leaflet' plugin and the
ability of downloading and processing static tiles.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.9.1 dated 2024-06-10 and 0.9.2 dated 2024-08-26
DESCRIPTION | 8 MD5 | 44 +- NEWS.md | 5 R/esp_dict.R | 28 + R/esp_get_ccaa.R | 2 R/esp_get_hypsobath.R | 1 R/sysdata.rda |binary R/utils_siane.R | 13 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary data/esp_codelist.rda |binary data/esp_munic.sf.rda |binary data/esp_nuts.sf.rda |binary data/esp_tiles_providers.rda |binary data/leaflet.providersESP.df.rda |binary data/pobmun19.rda |binary inst/schemaorg.json | 4 tests/testthat/test-esp_dict.R | 19 + tests/testthat/test-esp_getTiles.R | 611 +++++++++++++++++----------------- tests/testthat/test-esp_get_capimun.R | 64 +-- tests/testthat/test-esp_get_comarca.R | 54 +-- tests/testthat/test-esp_get_munic.R | 3 23 files changed, 463 insertions(+), 397 deletions(-)
Title: Generalized Hyperbolic Distribution and Its Special Cases
Description: Detailed functionality for working
with the univariate and multivariate Generalized Hyperbolic
distribution and its special cases (Hyperbolic (hyp), Normal
Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t
and Gaussian distribution). Especially, it contains fitting
procedures, an AIC-based model selection routine, and functions
for the computation of density, quantile, probability, random
variates, expected shortfall and some portfolio optimization
and plotting routines as well as the likelihood ratio test. In
addition, it contains the Generalized Inverse Gaussian
distribution. See Chapter 3 of A. J. McNeil, R. Frey, and P. Embrechts.
Quantitative risk management: Concepts, techniques and tools.
Princeton University Press, Princeton (2005).
Author: Marc Weibel [aut, cre],
David Luethi [aut],
Henriette-Elise Breymann [aut]
Maintainer: Marc Weibel <marc.weibel@quantsulting.ch>
Diff between ghyp versions 1.6.4 dated 2023-08-21 and 1.6.5 dated 2024-08-26
ghyp-1.6.4/ghyp/inst/Fixme |only ghyp-1.6.5/ghyp/DESCRIPTION | 22 ghyp-1.6.5/ghyp/MD5 | 13 ghyp-1.6.5/ghyp/build/vignette.rds |binary ghyp-1.6.5/ghyp/inst/doc/Generalized_Hyperbolic_Distribution.Rnw | 2766 +++++----- ghyp-1.6.5/ghyp/inst/doc/Generalized_Hyperbolic_Distribution.pdf |binary ghyp-1.6.5/ghyp/src/rgig.c | 21 ghyp-1.6.5/ghyp/vignettes/Generalized_Hyperbolic_Distribution.Rnw | 2766 +++++----- 8 files changed, 2793 insertions(+), 2795 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.8.1 dated 2024-07-30 and 0.9.0 dated 2024-08-26
dimensio-0.8.1/dimensio/R/predicates.R |only dimensio-0.8.1/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_group.svg |only dimensio-0.8.1/dimensio/man/get_distances.Rd |only dimensio-0.8.1/dimensio/man/prepare.Rd |only dimensio-0.9.0/dimensio/DESCRIPTION | 8 dimensio-0.9.0/dimensio/MD5 | 178 ++-- dimensio-0.9.0/dimensio/NAMESPACE | 8 dimensio-0.9.0/dimensio/NEWS.md | 10 dimensio-0.9.0/dimensio/R/AllClasses.R | 31 dimensio-0.9.0/dimensio/R/AllGenerics.R | 103 +- dimensio-0.9.0/dimensio/R/augment.R | 11 dimensio-0.9.0/dimensio/R/biplot.R | 36 - dimensio-0.9.0/dimensio/R/dimensio-internal.R | 198 ----- dimensio-0.9.0/dimensio/R/dimensio-package.R | 5 dimensio-0.9.0/dimensio/R/get_coordinates.R | 11 dimensio-0.9.0/dimensio/R/get_distances.R | 2 dimensio-0.9.0/dimensio/R/get_eigenvalues.R | 17 dimensio-0.9.0/dimensio/R/mutators.R | 44 + dimensio-0.9.0/dimensio/R/pca.R | 5 dimensio-0.9.0/dimensio/R/pcoa.R |only dimensio-0.9.0/dimensio/R/plot.R |only dimensio-0.9.0/dimensio/R/reexport.R | 4 dimensio-0.9.0/dimensio/R/screeplot.R | 51 + dimensio-0.9.0/dimensio/R/viz_coordinates.R | 338 +++++++-- dimensio-0.9.0/dimensio/README.md | 81 ++ dimensio-0.9.0/dimensio/inst/doc/pca.R | 32 dimensio-0.9.0/dimensio/inst/doc/pca.Rmd | 33 dimensio-0.9.0/dimensio/inst/doc/pca.html | 50 - dimensio-0.9.0/dimensio/inst/examples/ex-ca.R | 16 dimensio-0.9.0/dimensio/inst/examples/ex-envelopes.R | 8 dimensio-0.9.0/dimensio/inst/examples/ex-pca.R | 18 dimensio-0.9.0/dimensio/inst/examples/ex-pcoa.R |only dimensio-0.9.0/dimensio/inst/examples/ex-plot.R | 12 dimensio-0.9.0/dimensio/inst/tinytest/_snaps/pcoa_points.rds |only dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_col_0-0.svg | 2 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_col_0-1.svg | 5 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_col_1-0.svg | 7 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_col_1-1.svg | 2 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_row_0-0.svg | 10 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_row_0-1.svg | 5 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_row_1-0.svg | 15 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/CA_row_1-1.svg | 10 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_0-0.svg | 20 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_0-1.svg | 5 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_1-0.svg | 25 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_1-1.svg | 20 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_highlight_quali.svg | 357 +++++----- dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_ind_highlight_quali_quanti.svg |only dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_var_0-1.svg | 5 dimensio-0.9.0/dimensio/inst/tinytest/_tinysnapshot/PCA_var_1-0.svg | 5 dimensio-0.9.0/dimensio/inst/tinytest/test_bootstrap_ca.R | 3 dimensio-0.9.0/dimensio/inst/tinytest/test_bootstrap_pca.R | 3 dimensio-0.9.0/dimensio/inst/tinytest/test_ca.R | 3 dimensio-0.9.0/dimensio/inst/tinytest/test_pcoa.R |only dimensio-0.9.0/dimensio/inst/tinytest/test_plot_ca.R | 4 dimensio-0.9.0/dimensio/inst/tinytest/test_plot_pca.R | 25 dimensio-0.9.0/dimensio/man/BootstrapCA-class.Rd | 3 dimensio-0.9.0/dimensio/man/BootstrapPCA-class.Rd | 3 dimensio-0.9.0/dimensio/man/CA-class.Rd | 19 dimensio-0.9.0/dimensio/man/MCA-class.Rd | 3 dimensio-0.9.0/dimensio/man/MultivariateAnalysis.Rd | 3 dimensio-0.9.0/dimensio/man/MultivariateBootstrap.Rd | 3 dimensio-0.9.0/dimensio/man/MultivariateResults.Rd | 3 dimensio-0.9.0/dimensio/man/MultivariateSummary.Rd | 3 dimensio-0.9.0/dimensio/man/PCA-class.Rd | 21 dimensio-0.9.0/dimensio/man/PCOA-class.Rd |only dimensio-0.9.0/dimensio/man/biplot.Rd | 1 dimensio-0.9.0/dimensio/man/ca.Rd | 17 dimensio-0.9.0/dimensio/man/dimensio-package.Rd | 2 dimensio-0.9.0/dimensio/man/dimnames.Rd | 5 dimensio-0.9.0/dimensio/man/figures/README-biplot-1.png |binary dimensio-0.9.0/dimensio/man/figures/README-plot-var-1.png |binary dimensio-0.9.0/dimensio/man/get_contributions.Rd | 12 dimensio-0.9.0/dimensio/man/get_coordinates.Rd | 13 dimensio-0.9.0/dimensio/man/get_data.Rd | 10 dimensio-0.9.0/dimensio/man/get_eigenvalues.Rd | 39 - dimensio-0.9.0/dimensio/man/loadings.Rd | 5 dimensio-0.9.0/dimensio/man/mca.Rd | 1 dimensio-0.9.0/dimensio/man/pca.Rd | 19 dimensio-0.9.0/dimensio/man/pcoa.Rd |only dimensio-0.9.0/dimensio/man/plot.Rd |only dimensio-0.9.0/dimensio/man/predict.Rd | 3 dimensio-0.9.0/dimensio/man/prepare_legend.Rd | 6 dimensio-0.9.0/dimensio/man/prepare_plot.Rd |only dimensio-0.9.0/dimensio/man/reexports.Rd | 3 dimensio-0.9.0/dimensio/man/screeplot.Rd | 11 dimensio-0.9.0/dimensio/man/subset.Rd | 5 dimensio-0.9.0/dimensio/man/viz_biplot.Rd | 4 dimensio-0.9.0/dimensio/man/viz_contributions.Rd | 1 dimensio-0.9.0/dimensio/man/viz_individuals.Rd | 62 + dimensio-0.9.0/dimensio/man/viz_labels.Rd | 10 dimensio-0.9.0/dimensio/man/viz_points.Rd | 38 - dimensio-0.9.0/dimensio/man/viz_variables.Rd | 83 +- dimensio-0.9.0/dimensio/man/viz_wrap.Rd | 12 dimensio-0.9.0/dimensio/man/wrap.Rd | 4 dimensio-0.9.0/dimensio/vignettes/bibliography.bib | 105 +- dimensio-0.9.0/dimensio/vignettes/pca.Rmd | 33 97 files changed, 1441 insertions(+), 965 deletions(-)
Title: Client for World Banks's 'Indicators' and 'Poverty and
Inequality Platform (PIP)' APIs
Description: Download and search data from the 'World Bank Indicators
API', which provides access to nearly 16,000 time series indicators.
See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>
for further details about the API.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between worldbank versions 0.2.0 dated 2024-07-31 and 0.3.0 dated 2024-08-26
worldbank-0.2.0/worldbank/R/api.R |only worldbank-0.2.0/worldbank/tests/testthat/test-api.R |only worldbank-0.3.0/worldbank/DESCRIPTION | 9 +- worldbank-0.3.0/worldbank/MD5 | 48 +++++++------ worldbank-0.3.0/worldbank/NAMESPACE | 11 ++ worldbank-0.3.0/worldbank/NEWS.md | 5 + worldbank-0.3.0/worldbank/R/assertions.R | 16 +++- worldbank-0.3.0/worldbank/R/indicators.R |only worldbank-0.3.0/worldbank/R/pip.R |only worldbank-0.3.0/worldbank/R/utils.R | 7 - worldbank-0.3.0/worldbank/R/worldbank-package.R | 3 worldbank-0.3.0/worldbank/README.md | 14 ++- worldbank-0.3.0/worldbank/man/pip_aux.Rd |only worldbank-0.3.0/worldbank/man/pip_citation.Rd |only worldbank-0.3.0/worldbank/man/pip_data.Rd |only worldbank-0.3.0/worldbank/man/pip_group.Rd |only worldbank-0.3.0/worldbank/man/pip_health_check.Rd |only worldbank-0.3.0/worldbank/man/pip_info.Rd |only worldbank-0.3.0/worldbank/man/pip_valid_params.Rd |only worldbank-0.3.0/worldbank/man/pip_versions.Rd |only worldbank-0.3.0/worldbank/man/wb_country.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_country_indicator.Rd | 4 - worldbank-0.3.0/worldbank/man/wb_income_level.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_indicator.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_language.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_lending_type.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_region.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_source.Rd | 15 +++- worldbank-0.3.0/worldbank/man/wb_topic.Rd | 15 +++- worldbank-0.3.0/worldbank/man/worldbank-package.Rd | 2 worldbank-0.3.0/worldbank/tests/testthat/test-indicators.R |only worldbank-0.3.0/worldbank/tests/testthat/test-pip.R |only 32 files changed, 181 insertions(+), 58 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut] ,
Eduard Szoecs [aut],
Zachary Foster [aut, cre],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzo [...truncated...]
Maintainer: ORPHANED
Diff between taxize versions 0.9.100 dated 2022-04-22 and 0.9.100.1 dated 2024-08-26
DESCRIPTION | 21 +++++++++++++-------- MD5 | 8 ++++---- NAMESPACE | 4 ++-- R/bold_search.R | 9 ++++++--- R/get_boldid.R | 18 +++++++++++------- 5 files changed, 36 insertions(+), 24 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between curl versions 5.2.1 dated 2024-03-01 and 5.2.2 dated 2024-08-26
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS | 4 + build/vignette.rds |binary configure | 15 ++---- inst/doc/intro.html | 88 ++++++++++++++++++------------------- src/handle.c | 7 ++ tests/testthat/test-certificates.R | 10 ++-- tests/testthat/test-connection.R | 2 9 files changed, 78 insertions(+), 70 deletions(-)
Title: Generalized Reporter Score-Based Enrichment Analysis for Omics
Data
Description: Inspired by the classic 'RSA', we developed the improved 'Generalized Reporter
Score-based Analysis (GRSA)' method, implemented in the R package 'ReporterScore', along
with comprehensive visualization methods and pathway databases. 'GRSA' is a threshold-free
method that works well with all types of biomedical features, such as genes, chemical compounds,
and microbial species. Importantly, the 'GRSA' supports multi-group and longitudinal experimental
designs, because of the included multi-group-compatible statistical methods.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between ReporterScore versions 0.1.7 dated 2024-08-21 and 0.1.8 dated 2024-08-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/enrichment.R | 7 ------- inst/doc/ReporterScore.html | 2 +- man/KO_enrich.Rd | 8 -------- 5 files changed, 8 insertions(+), 23 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-02 1.3.0
2021-05-11 1.2.0
2020-06-17 1.1.0
2020-05-01 1.0.0
2019-06-27 0.9.0
2018-12-14 0.8.6
2018-10-26 0.8.0
2017-07-21 0.5.0
2017-01-06 0.4.0
2016-03-29 0.3.5
2016-03-23 0.3.4
2015-09-16 0.3.0
2015-04-18 0.2.6
2014-08-20 0.2.0
2014-07-24 0.1.2
2014-05-28 0.1.0
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.1.6 dated 2024-08-17 and 0.1.7 dated 2024-08-26
yulab.utils-0.1.6/yulab.utils/R/exec.R |only yulab.utils-0.1.7/yulab.utils/DESCRIPTION | 13 +-- yulab.utils-0.1.7/yulab.utils/MD5 | 27 +++--- yulab.utils-0.1.7/yulab.utils/NAMESPACE | 6 - yulab.utils-0.1.7/yulab.utils/NEWS.md | 11 ++ yulab.utils-0.1.7/yulab.utils/R/download.R | 20 ++--- yulab.utils-0.1.7/yulab.utils/R/file.R | 8 +- yulab.utils-0.1.7/yulab.utils/R/os.R |only yulab.utils-0.1.7/yulab.utils/R/regexpr.R | 3 yulab.utils-0.1.7/yulab.utils/R/str-utils.R | 59 ++++++--------- yulab.utils-0.1.7/yulab.utils/R/yulab-msg.R | 17 ++++ yulab.utils-0.1.7/yulab.utils/inst |only yulab.utils-0.1.7/yulab.utils/man/exec.Rd | 2 yulab.utils-0.1.7/yulab.utils/man/has_internet.Rd |only yulab.utils-0.1.7/yulab.utils/man/str-detect.Rd |only yulab.utils-0.1.7/yulab.utils/man/str_wrap.Rd | 2 yulab.utils-0.1.7/yulab.utils/man/yulab.utils-package.Rd | 1 17 files changed, 93 insertions(+), 76 deletions(-)
Title: 'AlphaSimR' Extension for Simulating Honeybee Populations and
Breeding Programmes
Description: An extension of the 'AlphaSimR' package
(<https://cran.r-project.org/package=AlphaSimR>) for stochastic simulations of
honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of
individual bees that form a colony, which includes a queen, fathers (drones
the queen mated with), virgin queens, workers, and drones. Multiple colony can
be merged into a population of colonies, such as an apiary or a whole country
of colonies. Functions enable operations on castes, colony, or colonies, to
ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with
respect to genomes and genetic and phenotype values is available and further
extended for honeybees, including haplo-diploidy, complementary sex determiner
locus, colony events (swarming, supersedure, etc.), and colony phenotype values.
Author: Jana Obsteter [aut, cre] ,
Laura Strachan [aut] ,
Jernej Bubnic [aut] ,
Gregor Gorjanc [aut]
Maintainer: Jana Obsteter <obsteter.jana@gmail.com>
Diff between SIMplyBee versions 0.3.0 dated 2022-12-15 and 0.4.0 dated 2024-08-26
SIMplyBee-0.3.0/SIMplyBee/man/createRandomCrossPlan.Rd |only SIMplyBee-0.3.0/SIMplyBee/man/figures/Hex_sticker_SIMplyBee.R |only SIMplyBee-0.3.0/SIMplyBee/man/figures/SIMplyBee_logo_hex.png |only SIMplyBee-0.3.0/SIMplyBee/man/figures/SIMplyBeelogo_small.png |only SIMplyBee-0.3.0/SIMplyBee/man/figures/collapse.pdf |only SIMplyBee-0.3.0/SIMplyBee/man/figures/collapse.png |only SIMplyBee-0.3.0/SIMplyBee/man/figures/founderpop.pdf |only SIMplyBee-0.3.0/SIMplyBee/man/figures/founderpop.png |only SIMplyBee-0.3.0/SIMplyBee/man/figures/split.pdf |only SIMplyBee-0.3.0/SIMplyBee/man/figures/split.png |only SIMplyBee-0.3.0/SIMplyBee/man/figures/supersede.pdf |only SIMplyBee-0.3.0/SIMplyBee/man/figures/supersede.png |only SIMplyBee-0.3.0/SIMplyBee/man/figures/swarm.pdf |only SIMplyBee-0.3.0/SIMplyBee/man/figures/swarm.png |only SIMplyBee-0.4.0/SIMplyBee/DESCRIPTION | 17 SIMplyBee-0.4.0/SIMplyBee/LICENSE | 2 SIMplyBee-0.4.0/SIMplyBee/MD5 | 326 +- SIMplyBee-0.4.0/SIMplyBee/NAMESPACE | 12 SIMplyBee-0.4.0/SIMplyBee/NEWS.md | 66 SIMplyBee-0.4.0/SIMplyBee/R/Class-Colony.R | 31 SIMplyBee-0.4.0/SIMplyBee/R/Class-MultiColony.R | 25 SIMplyBee-0.4.0/SIMplyBee/R/Class-SimParamBee.R | 273 + SIMplyBee-0.4.0/SIMplyBee/R/Functions_L0_auxilary.R | 1522 ++++++---- SIMplyBee-0.4.0/SIMplyBee/R/Functions_L1_Pop.R | 728 ++-- SIMplyBee-0.4.0/SIMplyBee/R/Functions_L2_Colony.R | 447 +- SIMplyBee-0.4.0/SIMplyBee/R/Functions_L3_Colonies.R | 86 SIMplyBee-0.4.0/SIMplyBee/R/RcppExports.R |only SIMplyBee-0.4.0/SIMplyBee/R/SIMplyBee.R | 27 SIMplyBee-0.4.0/SIMplyBee/README.md | 24 SIMplyBee-0.4.0/SIMplyBee/build/partial.rdb |binary SIMplyBee-0.4.0/SIMplyBee/build/vignette.rds |binary SIMplyBee-0.4.0/SIMplyBee/inst/CITATION |only SIMplyBee-0.4.0/SIMplyBee/inst/doc/A_Honeybee_biology.R | 28 SIMplyBee-0.4.0/SIMplyBee/inst/doc/A_Honeybee_biology.Rmd | 84 SIMplyBee-0.4.0/SIMplyBee/inst/doc/A_Honeybee_biology.html | 668 ++-- SIMplyBee-0.4.0/SIMplyBee/inst/doc/B_Multiple_colonies.R | 24 SIMplyBee-0.4.0/SIMplyBee/inst/doc/B_Multiple_colonies.Rmd | 34 SIMplyBee-0.4.0/SIMplyBee/inst/doc/B_Multiple_colonies.html | 312 +- SIMplyBee-0.4.0/SIMplyBee/inst/doc/C_Colony_events.R | 18 SIMplyBee-0.4.0/SIMplyBee/inst/doc/C_Colony_events.Rmd | 20 SIMplyBee-0.4.0/SIMplyBee/inst/doc/C_Colony_events.html | 618 ++-- SIMplyBee-0.4.0/SIMplyBee/inst/doc/D_Crossing.R | 190 - SIMplyBee-0.4.0/SIMplyBee/inst/doc/D_Crossing.Rmd | 488 ++- SIMplyBee-0.4.0/SIMplyBee/inst/doc/D_Crossing.html | 472 +-- SIMplyBee-0.4.0/SIMplyBee/inst/doc/E_Genomics.R | 5 SIMplyBee-0.4.0/SIMplyBee/inst/doc/E_Genomics.Rmd | 8 SIMplyBee-0.4.0/SIMplyBee/inst/doc/E_Genomics.html | 470 +-- SIMplyBee-0.4.0/SIMplyBee/inst/doc/F_Quantitative_Genetics.R |only SIMplyBee-0.4.0/SIMplyBee/inst/doc/F_Quantitative_Genetics.Rmd |only SIMplyBee-0.4.0/SIMplyBee/inst/doc/F_Quantitative_Genetics.html |only SIMplyBee-0.4.0/SIMplyBee/inst/doc/G_Sampling_functions.R | 6 SIMplyBee-0.4.0/SIMplyBee/inst/doc/G_Sampling_functions.Rmd | 2 SIMplyBee-0.4.0/SIMplyBee/inst/doc/G_Sampling_functions.html | 68 SIMplyBee-0.4.0/SIMplyBee/inst/doc/Z_FAQ.R | 4 SIMplyBee-0.4.0/SIMplyBee/inst/doc/Z_FAQ.Rmd | 6 SIMplyBee-0.4.0/SIMplyBee/inst/doc/Z_FAQ.html | 174 - SIMplyBee-0.4.0/SIMplyBee/man/Colony-class.Rd | 23 SIMplyBee-0.4.0/SIMplyBee/man/MultiColony-class.Rd | 25 SIMplyBee-0.4.0/SIMplyBee/man/SIMplyBee-package.Rd | 12 SIMplyBee-0.4.0/SIMplyBee/man/SimParamBee.Rd | 113 SIMplyBee-0.4.0/SIMplyBee/man/addCastePop.Rd | 11 SIMplyBee-0.4.0/SIMplyBee/man/buildUp.Rd | 19 SIMplyBee-0.4.0/SIMplyBee/man/calcBeeGRMIbd.Rd | 11 SIMplyBee-0.4.0/SIMplyBee/man/calcBeeGRMIbs.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/calcColonyValue.Rd | 13 SIMplyBee-0.4.0/SIMplyBee/man/calcInheritanceCriterion.Rd | 25 SIMplyBee-0.4.0/SIMplyBee/man/calcPerformanceCriterion.Rd | 18 SIMplyBee-0.4.0/SIMplyBee/man/calcQueensPHomBrood.Rd | 15 SIMplyBee-0.4.0/SIMplyBee/man/calcSelectionCriterion.Rd | 18 SIMplyBee-0.4.0/SIMplyBee/man/collapse.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/combine.Rd | 7 SIMplyBee-0.4.0/SIMplyBee/man/combineBeeGametes.Rd | 10 SIMplyBee-0.4.0/SIMplyBee/man/combineBeeGametesHaploDiploid.Rd | 10 SIMplyBee-0.4.0/SIMplyBee/man/combineNULLAndPop.Rd | 4 SIMplyBee-0.4.0/SIMplyBee/man/createCastePop.Rd | 36 SIMplyBee-0.4.0/SIMplyBee/man/createColony.Rd | 13 SIMplyBee-0.4.0/SIMplyBee/man/createCrossPlan.Rd |only SIMplyBee-0.4.0/SIMplyBee/man/createDCA.Rd | 11 SIMplyBee-0.4.0/SIMplyBee/man/createMatingStationDCA.Rd | 7 SIMplyBee-0.4.0/SIMplyBee/man/createMultiColony.Rd | 20 SIMplyBee-0.4.0/SIMplyBee/man/cross.Rd | 184 - SIMplyBee-0.4.0/SIMplyBee/man/downsize.Rd | 13 SIMplyBee-0.4.0/SIMplyBee/man/downsizePFun.Rd | 6 SIMplyBee-0.4.0/SIMplyBee/man/editCsdLocus.Rd | 6 SIMplyBee-0.4.0/SIMplyBee/man/figures/founderpop-1.png |only SIMplyBee-0.4.0/SIMplyBee/man/getAa.Rd | 20 SIMplyBee-0.4.0/SIMplyBee/man/getBv.Rd | 20 SIMplyBee-0.4.0/SIMplyBee/man/getCaste.Rd | 15 SIMplyBee-0.4.0/SIMplyBee/man/getCasteId.Rd | 27 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SIMplyBee-0.4.0/SIMplyBee/man/getSnpHaplo.Rd | 21 SIMplyBee-0.4.0/SIMplyBee/man/hasCollapsed.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/hasSplit.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/hasSuperseded.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/hasSwarmed.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/isCaste.Rd | 17 SIMplyBee-0.4.0/SIMplyBee/man/isCsdActive.Rd | 6 SIMplyBee-0.4.0/SIMplyBee/man/isCsdHeterozygous.Rd | 9 SIMplyBee-0.4.0/SIMplyBee/man/isDronesPresent.Rd | 9 SIMplyBee-0.4.0/SIMplyBee/man/isEmpty.Rd | 11 SIMplyBee-0.4.0/SIMplyBee/man/isFathersPresent.Rd | 11 SIMplyBee-0.4.0/SIMplyBee/man/isGenoHeterozygous.Rd | 2 SIMplyBee-0.4.0/SIMplyBee/man/isNULLColonies.Rd | 3 SIMplyBee-0.4.0/SIMplyBee/man/isProductive.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/isQueenPresent.Rd | 9 SIMplyBee-0.4.0/SIMplyBee/man/isSimParamBee.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/isVirginQueensPresent.Rd | 28 SIMplyBee-0.4.0/SIMplyBee/man/isWorkersPresent.Rd | 13 SIMplyBee-0.4.0/SIMplyBee/man/mapCasteToColonyValue.Rd | 29 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SIMplyBee-0.4.0/SIMplyBee/man/resetEvents.Rd | 5 SIMplyBee-0.4.0/SIMplyBee/man/selectColonies.Rd | 12 SIMplyBee-0.4.0/SIMplyBee/man/setLocation.Rd | 40 SIMplyBee-0.4.0/SIMplyBee/man/setMisc.Rd |only SIMplyBee-0.4.0/SIMplyBee/man/setQueensYearOfBirth.Rd | 15 SIMplyBee-0.4.0/SIMplyBee/man/simulateHoneyBeeGenomes.Rd | 10 SIMplyBee-0.4.0/SIMplyBee/man/split.Rd | 11 SIMplyBee-0.4.0/SIMplyBee/man/splitPFun.Rd | 7 SIMplyBee-0.4.0/SIMplyBee/man/supersede.Rd | 15 SIMplyBee-0.4.0/SIMplyBee/man/swarm.Rd | 37 SIMplyBee-0.4.0/SIMplyBee/man/swarmPFun.Rd | 6 SIMplyBee-0.4.0/SIMplyBee/src |only SIMplyBee-0.4.0/SIMplyBee/tests |only SIMplyBee-0.4.0/SIMplyBee/vignettes/A_Honeybee_biology.Rmd | 84 SIMplyBee-0.4.0/SIMplyBee/vignettes/B_Multiple_colonies.Rmd | 34 SIMplyBee-0.4.0/SIMplyBee/vignettes/C_Colony_events.Rmd | 20 SIMplyBee-0.4.0/SIMplyBee/vignettes/D_Crossing.Rmd | 488 ++- SIMplyBee-0.4.0/SIMplyBee/vignettes/E_Genomics.Rmd | 8 SIMplyBee-0.4.0/SIMplyBee/vignettes/F_Quantitative_Genetics.Rmd |only SIMplyBee-0.4.0/SIMplyBee/vignettes/G_Sampling_functions.Rmd | 2 SIMplyBee-0.4.0/SIMplyBee/vignettes/Z_FAQ.Rmd | 6 SIMplyBee-0.4.0/SIMplyBee/vignettes/collapse.pdf |only SIMplyBee-0.4.0/SIMplyBee/vignettes/collapse.png |only SIMplyBee-0.4.0/SIMplyBee/vignettes/decisionTreeCrossing.png |only SIMplyBee-0.4.0/SIMplyBee/vignettes/founderpop.pdf |only SIMplyBee-0.4.0/SIMplyBee/vignettes/founderpop.png |only SIMplyBee-0.4.0/SIMplyBee/vignettes/split.pdf |only SIMplyBee-0.4.0/SIMplyBee/vignettes/split.png |only SIMplyBee-0.4.0/SIMplyBee/vignettes/supersede.pdf |only SIMplyBee-0.4.0/SIMplyBee/vignettes/supersede.png |only SIMplyBee-0.4.0/SIMplyBee/vignettes/swarm.pdf |only SIMplyBee-0.4.0/SIMplyBee/vignettes/swarm.png |only 179 files changed, 5683 insertions(+), 3971 deletions(-)
Title: Phylogenetic Tree Statistics
Description: Collection of phylogenetic tree statistics,
collected throughout the literature. All functions have been
written to maximize computation speed. The package includes
umbrella functions to calculate all statistics, all balance
associated statistics, or all branching time related statistics.
Furthermore, the 'treestats' package supports summary statistic
calculations on Ltables, provides speed-improved coding of
branching times, Ltable conversion and includes algorithms to
create intermediately balanced trees. Full description can be
found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.
Author: Thijs Janzen [cre, aut]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between treestats versions 1.70.4 dated 2024-07-17 and 1.70.5 dated 2024-08-26
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- R/calc_all_stats.R | 8 ++++++-- inst/CITATION | 10 ++++++---- inst/doc/Example_abc.html | 36 ++++++++++++++++++------------------ inst/doc/Example_data.html | 4 ++-- inst/doc/Getting_started.html | 28 ++++++++++++++-------------- inst/doc/Speed_improvement.html | 4 ++-- 9 files changed, 66 insertions(+), 55 deletions(-)
Title: Lightweight Extension of the Base R Graphics System
Description: Lightweight extension of the base R graphics system, with support
for automatic legends, facets, and various other enhancements.
Author: Grant McDermott [aut, cre] ,
Vincent Arel-Bundock [aut] ,
Achim Zeileis [aut] ,
Etienne Bacher [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Diff between tinyplot versions 0.2.0 dated 2024-07-31 and 0.2.1 dated 2024-08-26
tinyplot-0.2.0/tinyplot/R/density.R |only tinyplot-0.2.0/tinyplot/R/histogram.R |only tinyplot-0.2.1/tinyplot/DESCRIPTION | 10 tinyplot-0.2.1/tinyplot/MD5 | 39 tinyplot-0.2.1/tinyplot/NAMESPACE | 1 tinyplot-0.2.1/tinyplot/NEWS.md | 50 tinyplot-0.2.1/tinyplot/R/aesthetics.R |only tinyplot-0.2.1/tinyplot/R/draw_elements.R | 306 ++-- tinyplot-0.2.1/tinyplot/R/facet.R | 366 +++++ tinyplot-0.2.1/tinyplot/R/get_saved_par.R | 4 tinyplot-0.2.1/tinyplot/R/lim.R |only tinyplot-0.2.1/tinyplot/R/tinyAxis.R |only tinyplot-0.2.1/tinyplot/R/tinyformula.R |only tinyplot-0.2.1/tinyplot/R/tinyplot.R | 761 ++--------- tinyplot-0.2.1/tinyplot/R/type_area.R |only tinyplot-0.2.1/tinyplot/R/type_boxplot.R |only tinyplot-0.2.1/tinyplot/R/type_density.R |only tinyplot-0.2.1/tinyplot/R/type_histogram.R |only tinyplot-0.2.1/tinyplot/R/type_jitter.R |only tinyplot-0.2.1/tinyplot/R/type_pointrange.R |only tinyplot-0.2.1/tinyplot/R/type_ribbon.R |only tinyplot-0.2.1/tinyplot/R/zzz.R | 52 tinyplot-0.2.1/tinyplot/man/figures/README-quickstart2-1.png |binary tinyplot-0.2.1/tinyplot/man/figures/README-quickstart3-1.png |binary tinyplot-0.2.1/tinyplot/man/figures/README-quickstart4-1.png |binary tinyplot-0.2.1/tinyplot/man/figures/README-quickstart5-1.png |binary tinyplot-0.2.1/tinyplot/man/tinyplot.Rd | 233 +-- 27 files changed, 956 insertions(+), 866 deletions(-)
Title: Utilities to Weave Hydrologic Fabrics
Description: A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>), Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
Author: David Blodgett [aut, cre]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydroloom versions 1.0.2 dated 2024-01-15 and 1.1.0 dated 2024-08-26
DESCRIPTION | 13 +- MD5 | 105 +++++++++++---------- NAMESPACE | 1 NEWS.md | 11 ++ R/00_hydroloom.R | 12 ++ R/add_divergence.R | 4 R/add_levelpaths.R | 58 +++++++++-- R/add_pathlength.R | 17 ++- R/add_streamorder-level.R | 2 R/add_toids.R | 9 + R/index_points_to_lines.R | 22 +++- R/make_attribute_topology.R | 2 R/make_fromids.R | 32 +++++- R/make_index_ids.R | 34 +++++- R/make_node_topology.R | 27 +++++ R/navigate_connected_paths.R | 3 R/navigate_network_dfs.R | 128 +++++++++++++++++++++----- R/navigation_network.R | 32 +++++- R/sort_network.R | 10 +- R/to_flownetwork.R |only R/utils.R | 5 + build/vignette.rds |binary inst/doc/advanced_network.R | 3 inst/doc/advanced_network.Rmd | 3 inst/doc/advanced_network.html | 70 ++++++-------- inst/doc/flow-table.R | 5 - inst/doc/flow-table.Rmd | 5 - inst/doc/flow-table.html | 53 +++++++--- inst/doc/hydroloom.Rmd | 2 inst/doc/hydroloom.html | 32 +++--- inst/doc/network_navigation.R |only inst/doc/network_navigation.Rmd |only inst/doc/network_navigation.html |only inst/doc/non-dendritic.html | 12 +- man/add_levelpaths.Rd | 10 ++ man/add_pathlength.Rd | 2 man/index_points_to_waterbodies.Rd | 4 man/make_fromids.Rd | 6 + man/navigate_hydro_network.Rd | 6 + man/navigate_network_dfs.Rd | 28 +++++ man/to_flownetwork.Rd |only tests/testthat/test_add_levelpaths.R | 26 +++++ tests/testthat/test_add_pfafstetter.R | 2 tests/testthat/test_add_toids.R | 8 + tests/testthat/test_get_hydro_location.R | 2 tests/testthat/test_hydroloom.R | 8 + tests/testthat/test_index.R | 19 ++- tests/testthat/test_make_attribute_topology.R | 6 - tests/testthat/test_make_index_ids.R | 19 +++ tests/testthat/test_navigate_network_dfs.R | 35 +++++++ tests/testthat/test_sort_network.R | 49 +++++++++ tests/testthat/test_streamorder-level.R | 12 ++ tests/testthat/test_to_flownetwork.R |only vignettes/advanced_network.Rmd | 3 vignettes/flow-table.Rmd | 5 - vignettes/hydroloom.Rmd | 2 vignettes/network_navigation.Rmd |only 57 files changed, 743 insertions(+), 221 deletions(-)
Title: Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Description: Implements various procedures for finding
multiple change-points from Matteson D. et al (2013)
<doi:10.1080/01621459.2013.849605>, Zhang W. et al (2017)
<doi:10.1109/ICDMW.2017.44>, Arlot S. et al (2019).
Two methods make use of dynamic
programming and pruning, with no distributional
assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods
are included. All methods return the set of estimated change-
points as well as other summary information.
Author: Nicholas A. James [aut],
Wenyu Zhang [aut, cre],
David S. Matteson [aut]
Maintainer: Wenyu Zhang <wz258@cornell.edu>
Diff between ecp versions 3.1.5 dated 2023-07-01 and 3.1.6 dated 2024-08-26
DESCRIPTION | 22 +++++++++++++++++----- MD5 | 6 +++--- NEWS | 6 ++++++ man/e.divisive.Rd | 2 ++ 4 files changed, 28 insertions(+), 8 deletions(-)
Title: Cluster Adjusted t Statistic Applications
Description: Simulation results detailed in Esarey and Menger (2019) <doi:10.1017/psrm.2017.42>
demonstrate that cluster adjusted t statistics (CATs) are an effective method
for correcting standard errors in scenarios with a small number of clusters.
The 'mmiCATs' package offers a suite of tools for working with CATs. The
mmiCATs() function initiates a 'shiny' web application, facilitating
the analysis of data utilizing CATs, as implemented in the cluster.im.glm()
function from the 'clusterSEs' package. Additionally, the pwr_func_lmer()
function is designed to simplify the process of conducting simulations to
compare mixed effects models with CATs models. For educational purposes, the
CloseCATs() function launches a 'shiny' application card game, aimed at enhancing
users' understanding of the conditions under which CATs should be preferred
over random intercept models.
Author: Mackson Ncube [aut, cre],
mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Diff between mmiCATs versions 0.1.1 dated 2024-02-21 and 0.2.0 dated 2024-08-26
DESCRIPTION | 10 MD5 | 35 + NAMESPACE | 3 R/CloseCATs.R | 598 +++++++++++++++--------------- R/KenRCATs.R |only R/KenRCATs_helpers.R |only R/cc_game_mgmt.R | 458 +++++++++++------------ R/helpers.R | 69 ++- R/kenward_roger.R |only R/mmiCATs.R | 641 ++++++++++++++++++--------------- R/pwr_func_lmer.R | 588 +++++++++++++++++------------- man/KenRCATs.Rd |only man/append_KenRCATs.Rd |only man/format_citation.Rd |only man/getUIParams.Rd |only man/kenward_roger.Rd |only man/list_null.Rd |only man/parse_list_input.Rd |only man/pwr_func_lmer.Rd | 41 +- man/sig_null.Rd |only man/text_to_vector.Rd |only man/vec_null.Rd |only tests/testthat/test-cc_game_mgmt.R | 2 tests/testthat/test-cluster_im_lmRob.R | 282 +++++++------- tests/testthat/test-pwr_func_lmer.R | 306 +++++++++------ 25 files changed, 1676 insertions(+), 1357 deletions(-)