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: Claude Boivin <webapp.cb@gmail.com> Peiyuan Zhu <garyzhubc@gmail.com>
Maintainer: Claude Boivin <webapp.cb@gmail.com>
Diff between dst versions 1.5.2 dated 2023-11-16 and 1.6.0 dated 2024-04-17
DESCRIPTION | 18 MD5 | 169 ++++- NAMESPACE | 37 + NEWS.md | 129 ++++ R/DoSSnames.R |only R/addTobca.R | 66 +- R/bca.R | 92 +-- R/bcaNorm.R |only R/bcaPrintLarge.R |only R/bcaRel.R | 4 R/bcaTrunc.R | 209 ++++++- R/belplau.R | 101 ++- R/belplauEval.R |only R/belplauH.R |only R/belplauHLogsumexp.R |only R/belplauLogsumexp.R |only R/belplauPlot.R |only R/data.R | 9 R/dotprod.R | 7 R/dsrwon.R | 434 ++++++++++----- R/dsrwonLogsumexp.R |only R/extFrame.R |only R/extmin.R | 30 - R/inters.R | 57 + R/intersBySSName.R |only R/logsum.R |only R/mFromMarginal.R |only R/nameRows.R | 5 R/nzdsr.R | 58 +- R/nzdsrLogsumexp.R |only R/plautrans.R | 8 R/tabresul.R | 2 R/ttmatrix.R |only R/ttmatrixFromMarginal.R |only R/ttmatrixPartition.R |only build/vignette.rds |binary data/captain_result.rda |only inst/doc/Bayes_Rule.R |only inst/doc/Bayes_Rule.Rmd |only inst/doc/Bayes_Rule.html |only inst/doc/Captain_Example.R | 352 ------------ inst/doc/Captain_Example.Rmd | 373 ------------ inst/doc/Captain_Example.html | 722 ++++++++----------------- inst/doc/Crime_Scene.R |only inst/doc/Crime_Scene.Rmd |only inst/doc/Crime_Scene.html |only inst/doc/Introduction_to_Belief_Functions.R | 14 inst/doc/Introduction_to_Belief_Functions.Rmd | 16 inst/doc/Introduction_to_Belief_Functions.html | 218 +++---- inst/doc/The_Monty_Hall_Game.R | 16 inst/doc/The_Monty_Hall_Game.Rmd | 16 inst/doc/The_Monty_Hall_Game.html | 108 +-- inst/doc/The_PJM_example.R |only inst/doc/The_PJM_example.Rmd |only inst/doc/The_PJM_example.html |only inst/doc/Zadeh_Example.R | 2 inst/doc/Zadeh_Example.Rmd | 2 inst/doc/Zadeh_Example.html | 28 inst/dst.pdf |binary man/DoSSnames.Rd |only man/addTobca.Rd | 3 man/bca.Rd | 25 man/bcaNorm.Rd |only man/bcaPrintLarge.Rd |only man/bcaRel.Rd | 2 man/bcaTrunc.Rd | 4 man/belplau.Rd | 16 man/belplauEval.Rd |only man/belplauH.Rd |only man/belplauHLogsumexp.Rd |only man/belplauLogsumexp.Rd |only man/belplauPlot.Rd |only man/captain_result.Rd |only man/dsrwon.Rd | 35 - man/dsrwonLogsumpexp.Rd |only man/extFrame.Rd |only man/inters.Rd | 18 man/intersBySSName.Rd |only man/logsum.Rd |only man/mFromMarginal.Rd |only man/nzdsr.Rd | 22 man/nzdsrLogsumexp.Rd |only man/plautrans.Rd | 2 man/ttmatrix.Rd |only man/ttmatrixFromMarginal.Rd |only man/ttmatrixPartition.Rd |only tests/testthat/test_DoSSnames.R |only tests/testthat/test_bca.R | 27 tests/testthat/test_bcaNorm.R |only tests/testthat/test_bcaPrintLarge.R |only tests/testthat/test_bcaTrunc.R | 17 tests/testthat/test_belplau.R | 8 tests/testthat/test_belplauEval.R |only tests/testthat/test_belplauH.R |only tests/testthat/test_belplauHLogsumexp.R |only tests/testthat/test_belplauLogsumexp.R |only tests/testthat/test_belplauPlot.R |only tests/testthat/test_dsrwon.R | 33 - tests/testthat/test_dsrwonLogsumexp.R |only tests/testthat/test_extFrame.R |only tests/testthat/test_extmin.R | 4 tests/testthat/test_inters.R | 7 tests/testthat/test_intersBySSName.R |only tests/testthat/test_logsum.R |only tests/testthat/test_mFromMarginal.R |only tests/testthat/test_nameRows.R | 2 tests/testthat/test_nzdsr.R | 12 tests/testthat/test_nzdsrLogsumexp.R |only tests/testthat/test_ttmatrix.R |only tests/testthat/test_ttmatrixPartition.R |only tests/testthat/ttmatrixFromMarginal.R |only vignettes/Bayes_Rule.Rmd |only vignettes/Captain_Example.Rmd | 373 ------------ vignettes/Crime_Scene.Rmd |only vignettes/Introduction_to_Belief_Functions.Rmd | 16 vignettes/The_Monty_Hall_Game.Rmd | 16 vignettes/The_PJM_example.Rmd |only vignettes/Zadeh_Example.Rmd | 2 118 files changed, 1769 insertions(+), 2177 deletions(-)
Title: Phylogeny-Guided OTU-Specific Association Test for Microbiome
Data
Description: Implements the Phylogeny-Guided Microbiome OTU-Specific Association
Test method, which boosts the testing power by adaptively borrowing
information from phylogenetically close OTUs (operational taxonomic units)
of the target OTU. This method
is built on a kernel machine regression framework and allows for flexible
modeling of complex microbiome effects, adjustments for covariates, and
can accommodate both continuous and binary outcomes.
Author: Caizhi Huang [aut],
Jung-Ying Tzeng [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between POSTm versions 1.3 dated 2023-12-13 and 1.4 dated 2024-04-17
DESCRIPTION | 10 MD5 | 21 - NEWS | 4 R/glmFit.R | 85 ++--- R/lmFit.R | 46 +- R/post.R | 726 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/POSTm_vignette.Rmd | 658 +++++++++++++++++++------------------- inst/doc/POSTm_vignette.pdf |binary tests |only vignettes/POSTm_vignette.Rmd | 658 +++++++++++++++++++------------------- 11 files changed, 1115 insertions(+), 1093 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre],
Sebastian Krantz [ctb],
Grant McDermott [ctb] ,
Russell Lenth [ctb]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between fixest versions 0.11.2 dated 2023-11-24 and 0.12.0 dated 2024-04-17
fixest-0.11.2/fixest/R/Deprecated_funs.R |only fixest-0.11.2/fixest/R/ESTIMATION_FUNS.R |only fixest-0.11.2/fixest/R/Lagging.R |only fixest-0.11.2/fixest/R/Methods.R |only fixest-0.11.2/fixest/R/MiscFuns.R |only fixest-0.11.2/fixest/R/VCOV_aliases.R |only fixest-0.11.2/fixest/R/etable_aliases.R |only fixest-0.11.2/fixest/R/xaxis.R |only fixest-0.12.0/fixest/DESCRIPTION | 21 fixest-0.12.0/fixest/MD5 | 289 fixest-0.12.0/fixest/NAMESPACE | 25 fixest-0.12.0/fixest/NEWS.md | 85 fixest-0.12.0/fixest/R/ML_Families.R | 32 fixest-0.12.0/fixest/R/RcppExports.R | 100 fixest-0.12.0/fixest/R/VCOV.R | 3359 ++--- fixest-0.12.0/fixest/R/alias_VCOV.R |only fixest-0.12.0/fixest/R/alias_etable.R |only fixest-0.12.0/fixest/R/alias_generator.R | 22 fixest-0.12.0/fixest/R/coefplot.R | 3442 ++--- fixest-0.12.0/fixest/R/ctb_emmeans.R |only fixest-0.12.0/fixest/R/data_tools.R | 1778 +- fixest-0.12.0/fixest/R/deprecated.R |only fixest-0.12.0/fixest/R/did.R | 769 - fixest-0.12.0/fixest/R/estimation.R |only 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912 - fixest-0.12.0/fixest/src/quf.cpp | 1836 +- fixest-0.12.0/fixest/src/vcov_related.cpp | 1007 - fixest-0.12.0/fixest/tests/fixest_tests.R | 1073 + fixest-0.12.0/fixest/vignettes/fixest_walkthrough.Rmd | 2 157 files changed, 28890 insertions(+), 24094 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2024) <doi:10.1093/jrsssc/qlad102>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 2.1-6 dated 2024-01-09 and 2.1-7 dated 2024-04-17
DESCRIPTION | 14 ++--- MD5 | 40 +++++++------- NEWS.md | 5 + R/BayesSUR.R | 6 +- R/RcppExports.R | 4 - README.md | 13 +++- build/vignette.rds |binary data/exampleGDSC.rda |binary inst/CITATION | 124 +++++++++++++++++++++++++++------------------- inst/doc/BayesSUR-RE.html | 2 man/BayesSUR.Rd | 4 + src/BayesSUR.cpp | 4 - src/ESS_Sampler.h | 9 ++- src/HRR_Chain.cpp | 55 +++++++++++++------- src/HRR_Chain.h | 5 + src/RcppExports.cpp | 9 +-- src/SUR_Chain.cpp | 30 +++++++---- src/SUR_Chain.h | 5 + src/drive.cpp | 25 +++++---- src/drive.h | 2 src/utils.h | 1 21 files changed, 217 insertions(+), 140 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph] ,
David Barnett [ctb],
Michael Brusco [ctb, cph],
Michael Friendly [ctb],
Hans-Friedrich Koehn [ctb, cph],
Fionn Murtagh [ctb, cph],
Stephanie Stahl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.5.4 dated 2023-12-12 and 1.5.5 dated 2024-04-17
DESCRIPTION | 10 +- MD5 | 120 +++++++++++++++++----------------- NEWS.md | 4 + R/AAA_color_palette.R | 4 - R/AAA_registry_criterion.R | 24 ++++-- R/AAA_registry_seriate.R | 2 R/AAA_seriation-package.R | 25 ++++--- R/Chameleon.R | 1 R/Irish.R | 9 +- R/Munsingen.R | 11 +-- R/Psych24.R | 6 - R/SupremeCourt.R | 5 - R/Townships.R | 1 R/Wood.R | 7 - R/Zoo.R | 3 R/criterion.R | 47 ++++++------- R/criterion.dist.R | 61 ++++++++++++----- R/criterion.matrix.R | 11 +-- R/lines_and_ordered_data.R | 27 +++---- R/register_DendSer.R | 7 + R/register_GA.R | 14 +-- R/register_optics.R | 10 +- R/register_smacof.R | 22 +++++- R/register_tsne.R | 7 + R/robinson.R | 10 +- R/ser_dist.R | 12 +-- R/seriate.R | 88 ++++++++++++------------ R/seriate_best.R | 11 +-- R/uniscale.R | 29 +++++--- README.md | 10 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/seriation.pdf |binary man/Chameleon.Rd | 12 +++ man/Irish.Rd | 20 ++++- man/Munsingen.Rd | 20 ++++- man/Psych24.Rd | 6 - man/SupremeCourt.Rd | 16 +++- man/Townships.Rd | 12 +++ man/Wood.Rd | 18 +++-- man/Zoo.Rd | 14 +++ man/create_lines_data.Rd | 36 ++++++---- man/criterion.Rd | 29 +++----- man/get_order.Rd | 4 - man/is.robinson.Rd | 16 +++- man/palette.Rd | 4 - man/permutation_vector2matrix.Rd | 4 - man/permute.Rd | 4 - man/register_DendSer.Rd | 10 +- man/register_GA.Rd | 8 +- man/register_optics.Rd | 12 +-- man/register_smacof.Rd | 10 +- man/register_tsne.Rd | 11 +-- man/register_umap.Rd | 4 - man/registry_for_criterion_methods.Rd | 7 + man/registry_for_seriaiton_methods.Rd | 6 - man/ser_dist.Rd | 16 ++-- man/seriate.Rd | 52 +++++++------- man/seriate_best.Rd | 11 +-- man/seriation-package.Rd | 49 +++++++++++++ man/uniscale.Rd | 15 ++-- 61 files changed, 626 insertions(+), 398 deletions(-)
Title: Statistical Tolerance Intervals and Regions
Description: Statistical tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence. This package provides functions for estimating tolerance limits (intervals) for various univariate distributions (binomial, Cauchy, discrete Pareto, exponential, two-parameter exponential, extreme value, hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), Bayesian normal tolerance limits, multivariate normal tolerance regions, nonparametric tolerance intervals, tolerance bands for regression settings (linear regression, nonlinear regression, nonparametric regression, and multivariate regression), and analysis of variance tolerance intervals. Visualizations are also available for most of these settings.
Author: Derek S. Young [aut, cre] ,
Kedai Cheng [aut]
Maintainer: Derek S. Young <derek.young@uky.edu>
Diff between tolerance versions 2.0.0 dated 2020-02-05 and 3.0.0 dated 2024-04-17
tolerance-2.0.0/tolerance/R/regtolint.R |only tolerance-3.0.0/tolerance/DESCRIPTION | 18 tolerance-3.0.0/tolerance/MD5 | 88 +- tolerance-3.0.0/tolerance/NAMESPACE | 14 tolerance-3.0.0/tolerance/NEWS | 409 +++++++----- tolerance-3.0.0/tolerance/R/Kfactor.R | 7 tolerance-3.0.0/tolerance/R/accsamp.R | 68 +- tolerance-3.0.0/tolerance/R/bonftolint.R | 50 - tolerance-3.0.0/tolerance/R/diffprop.R | 130 ++- tolerance-3.0.0/tolerance/R/dparetoll.R | 2 tolerance-3.0.0/tolerance/R/gammatolint.R | 2 tolerance-3.0.0/tolerance/R/logistolint.R | 2 tolerance-3.0.0/tolerance/R/negbintolint.R | 12 tolerance-3.0.0/tolerance/R/nonlinregtolint.R | 195 +++-- tolerance-3.0.0/tolerance/R/nonparregtolint.R | 98 +- tolerance-3.0.0/tolerance/R/normss.R | 10 tolerance-3.0.0/tolerance/R/npbetolint.R | 32 tolerance-3.0.0/tolerance/R/nporder.R | 48 - tolerance-3.0.0/tolerance/R/plotly_anovatol.R |only tolerance-3.0.0/tolerance/R/plotly_controltol.R |only tolerance-3.0.0/tolerance/R/plotly_histtol.R |only tolerance-3.0.0/tolerance/R/plotly_multitol.R |only tolerance-3.0.0/tolerance/R/plotly_normOC.R |only tolerance-3.0.0/tolerance/R/plotly_npmvtol.R |only tolerance-3.0.0/tolerance/R/plotly_regtol.R |only tolerance-3.0.0/tolerance/R/plottol.R | 710 +++++++++++---------- tolerance-3.0.0/tolerance/R/poislindll.R | 6 tolerance-3.0.0/tolerance/R/poislindtolint.R | 2 tolerance-3.0.0/tolerance/R/regtol.int.R |only tolerance-3.0.0/tolerance/R/semiconttolint.R |only tolerance-3.0.0/tolerance/R/simnormtolint.R | 2 tolerance-3.0.0/tolerance/R/zipftolint.R | 178 ++--- tolerance-3.0.0/tolerance/R/zmll.R | 62 - tolerance-3.0.0/tolerance/R/zzz.R |only tolerance-3.0.0/tolerance/README.md |only tolerance-3.0.0/tolerance/inst/CITATION | 38 - tolerance-3.0.0/tolerance/man/Kfactor.Rd | 144 ++-- tolerance-3.0.0/tolerance/man/Kfactorsim.Rd | 2 tolerance-3.0.0/tolerance/man/bayesnormtolint.Rd | 4 tolerance-3.0.0/tolerance/man/gammatolint.Rd | 11 tolerance-3.0.0/tolerance/man/nonlinregtolint.Rd | 153 ++-- tolerance-3.0.0/tolerance/man/nonparregtolint.Rd | 146 ++-- tolerance-3.0.0/tolerance/man/nonpartolint.Rd | 4 tolerance-3.0.0/tolerance/man/npbetolint.Rd | 2 tolerance-3.0.0/tolerance/man/npmvtolregion.Rd | 10 tolerance-3.0.0/tolerance/man/plotly_anovatol.Rd |only tolerance-3.0.0/tolerance/man/plotly_controltol.Rd |only tolerance-3.0.0/tolerance/man/plotly_histtol.Rd |only tolerance-3.0.0/tolerance/man/plotly_multitol.Rd |only tolerance-3.0.0/tolerance/man/plotly_normOC.Rd |only tolerance-3.0.0/tolerance/man/plotly_npmvtol.Rd |only tolerance-3.0.0/tolerance/man/plotly_regtol.Rd |only tolerance-3.0.0/tolerance/man/regtolint.Rd | 3 tolerance-3.0.0/tolerance/man/semiconttolint.Rd |only tolerance-3.0.0/tolerance/man/simnormtolint.Rd | 8 55 files changed, 1494 insertions(+), 1176 deletions(-)
Title: Tau-Leaping Stochastic Simulation
Description: Implements adaptive tau leaping to approximate the
trajectory of a continuous-time stochastic process as
described by Cao et al. (2007) The Journal of Chemical Physics
<doi:10.1063/1.2745299> (aka. the Gillespie stochastic
simulation algorithm). This package is based upon work
supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip
Johnson and NIH R01-AI049334 to Rustom Antia.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between adaptivetau versions 2.3 dated 2023-11-28 and 2.3-1 dated 2024-04-17
DESCRIPTION | 10 +- MD5 | 12 +- NEWS | 10 ++ build/vignette.rds |binary inst/doc/adaptivetau.pdf |binary man/ssa.adaptivetau.Rd | 18 ++-- src/adaptivetau.cpp | 205 +++++++++++++++++++++++------------------------ 7 files changed, 134 insertions(+), 121 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via by ModSEM it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8 [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 0.1.1 dated 2024-04-15 and 0.1.2 dated 2024-04-17
DESCRIPTION | 6 +- MD5 | 22 ++++----- R/emLms.R | 31 ++++--------- R/equationsLms.R | 35 ++++++++------- R/equationsQml.R | 23 --------- R/modelLmsQml.R | 78 +++++++++------------------------ R/modsem.R | 25 ++++++++++ R/utilsLms.R | 70 +++++------------------------- R/utilsQml.R | 20 ++++---- man/modsem.Rd | 25 ++++++++++ tests/testthat/mplusResults.out | 8 +-- tests/testthat/testingLMS.R | 93 ++++++++++++++++++++-------------------- 12 files changed, 192 insertions(+), 244 deletions(-)
Title: Targets for JAGS Pipelines
Description: Bayesian data analysis usually incurs long runtimes
and cumbersome custom code.
A pipeline toolkit tailored to Bayesian statisticians,
the 'jagstargets' R package is leverages
'targets' and 'R2jags' to ease this burden.
'jagstargets' makes it super easy to set up scalable
JAGS pipelines that automatically parallelize the computation
and skip expensive steps when the results are already up to date.
Minimal custom code is required, and there is no need to manually
configure branching, so usage is much easier than 'targets' alone.
For the underlying methodology, please refer
to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS'
(Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.
Author: William Michael Landau [aut, cre]
,
David Lawrence Miller [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between jagstargets versions 1.1.0 dated 2023-01-06 and 1.2.0 dated 2024-04-17
DESCRIPTION | 22 MD5 | 48 - NAMESPACE | 5 NEWS.md | 11 R/tar_jags.R | 27 - R/tar_jags_package.R | 6 R/tar_jags_rep.R | 26 - R/tar_jags_rep_dic.R | 6 R/tar_jags_rep_draws.R | 6 R/tar_jags_rep_summary.R | 6 R/utils_data.R | 2 build/vignette.rds |binary inst/CITATION | 20 inst/doc/introduction.R | 22 inst/doc/introduction.html | 600 ++++++++++++----------- inst/doc/simulation.R | 18 inst/doc/simulation.html | 735 +++++++++++++++-------------- man/jagstargets-package.Rd | 1 man/tar_jags.Rd | 29 - man/tar_jags_rep.Rd | 29 - man/tar_jags_rep_dic.Rd | 29 - man/tar_jags_rep_draws.Rd | 29 - man/tar_jags_rep_summary.Rd | 29 - tests/testthat/test-tar_jags.R | 2 tests/testthat/test-tar_jags_rep_summary.R | 2 25 files changed, 956 insertions(+), 754 deletions(-)
Title: Interpolation and Extrapolation with Beta Diversity for Three
Dimensions of Biodiversity
Description: As a sequel to 'iNEXT', the 'iNEXT.beta3D' package provides functions to compute
standardized taxonomic, phylogenetic, and functional diversity (3D) estimates
with a common sample size (for alpha and gamma diversity) or sample coverage
(for alpha, beta, gamma diversity as well as dissimilarity or turnover indices).
Hill numbers and their generalizations are used to quantify 3D and to make
multiplicative decomposition (gamma = alpha x beta). The package also features
size- and coverage-based rarefaction and extrapolation sampling curves to
facilitate rigorous comparison of beta diversity across datasets.
See Chao et al. (2023) <doi:10.1002/ecm.1588> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.beta3D versions 1.0.1 dated 2024-03-25 and 1.0.2 dated 2024-04-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 6 ++++-- R/MainFun.r | 16 ++++++++-------- inst/doc/Introduction.pdf |binary 5 files changed, 19 insertions(+), 17 deletions(-)
Title: Analysis of Ecological Dynamic Regimes
Description: A toolbox for implementing the Ecological Dynamic Regime framework
(Sánchez-Pinillos et al., 2023 <doi:10.1002/ecm.1589>) to characterize and
compare groups of ecological trajectories in multidimensional spaces defined
by state variables. The package includes the RETRA-EDR algorithm to identify
representative trajectories, functions to generate, summarize, and visualize
representative trajectories, and several metrics to quantify the distribution
and heterogeneity of trajectories in an ecological dynamic regime and quantify
the dissimilarity between two or more ecological dynamic regimes. The package
also includes a set of functions to assess ecological resilience based on
ecological dynamic regimes (Sánchez-Pinillos et al., 2024 <doi:10.1016/j.biocon.2023.110409>).
Author: Martina Sanchez-Pinillos [aut, cre, cph]
Maintainer: Martina Sanchez-Pinillos <martina.sanchez.pinillos@gmail.com>
Diff between ecoregime versions 0.1.3 dated 2023-09-10 and 0.2.0 dated 2024-04-17
DESCRIPTION | 33 ++-- MD5 | 58 ++++--- NAMESPACE | 5 NEWS.md | 24 +++ R/EDR_data.R | 29 ++- R/EDR_metrics.R | 2 R/define_retra.R | 5 R/deviation_metrics.R |only R/dist_edr.R | 10 - R/retra_edr.R | 3 R/state_to_trajectory.R |only README.md | 101 +++++++++++-- build/partial.rdb |binary build/vignette.rds |binary data/EDR_data.rda |binary inst/CITATION | 18 ++ inst/doc/EDR_framework.R | 8 - inst/doc/EDR_framework.Rmd | 6 inst/doc/EDR_framework.html | 223 ++++++++++++++---------------- inst/doc/Resilience.R |only inst/doc/Resilience.Rmd |only inst/doc/Resilience.html |only man/EDR_data.Rd | 29 ++- man/deviation_metrics.Rd |only man/dist_edr.Rd | 10 - man/ecoregime-package.Rd | 2 man/figures/README-plotEDR-1.png |binary man/state_to_trajectory.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-EDR_metrics.R | 27 +++ tests/testthat/test-deviation_metrics.R |only tests/testthat/test-plot.R | 15 ++ tests/testthat/test-state_to_trajectory.R |only vignettes/EDR_framework.Rmd | 6 vignettes/Resilience.Rmd |only 35 files changed, 396 insertions(+), 218 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.10.0 dated 2024-02-22 and 0.11.0.1 dated 2024-04-17
adbcsqlite-0.10.0/adbcsqlite/NEWS.md |only adbcsqlite-0.10.0/adbcsqlite/src/init.c |only adbcsqlite-0.10.0/adbcsqlite/src/nanoarrow |only adbcsqlite-0.10.0/adbcsqlite/src/sqlite.c |only adbcsqlite-0.10.0/adbcsqlite/src/statement_reader.c |only adbcsqlite-0.10.0/adbcsqlite/src/statement_reader.h |only adbcsqlite-0.10.0/adbcsqlite/src/types.h |only adbcsqlite-0.11.0.1/adbcsqlite/DESCRIPTION | 6 +- adbcsqlite-0.11.0.1/adbcsqlite/MD5 | 53 +++++++++++++++----- adbcsqlite-0.11.0.1/adbcsqlite/cleanup | 3 - adbcsqlite-0.11.0.1/adbcsqlite/src/Makevars.in | 15 +++-- adbcsqlite-0.11.0.1/adbcsqlite/src/c |only adbcsqlite-0.11.0.1/adbcsqlite/src/init.cc |only 13 files changed, 57 insertions(+), 20 deletions(-)
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are
described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>,
Fritz et al. (2012) <doi:10.18637/jss.v047.i12>,
Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Valentin Todorov [aut, cre] ,
Luis Angel Garcia Escudero [aut],
Agustin Mayo Iscar [aut],
Javier Crespo Guerrero [aut],
Heinrich Fritz [aut]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between tclust versions 1.5-6 dated 2024-02-09 and 2.0-3 dated 2024-04-17
tclust-1.5-6/tclust/R/ScaleAdv.R |only tclust-1.5-6/tclust/R/plot.DiscrFact.R |only tclust-1.5-6/tclust/R/plot_DiscrFact_p2.R |only tclust-1.5-6/tclust/R/plot_DiscrFact_p3.R |only tclust-1.5-6/tclust/R/print.DiscrFact.R |only tclust-1.5-6/tclust/R/summary.DiscrFact.R |only tclust-1.5-6/tclust/R/tclust.opt.restr.R |only tclust-1.5-6/tclust/R/tkmeans.C.R |only tclust-1.5-6/tclust/inst/work/clust.cpp |only tclust-1.5-6/tclust/inst/work/clust.h |only tclust-1.5-6/tclust/inst/work/tclust-notes.txt |only tclust-1.5-6/tclust/man/discr_coords.Rd |only tclust-1.5-6/tclust/src/ML_meal.cpp |only tclust-1.5-6/tclust/src/ML_meal.h |only tclust-1.5-6/tclust/src/ML_package.cpp |only tclust-1.5-6/tclust/src/ML_package.h |only tclust-1.5-6/tclust/src/ML_passrng.cpp |only tclust-1.5-6/tclust/src/ML_passrng.h |only tclust-1.5-6/tclust/src/R.Inc.h |only tclust-1.5-6/tclust/src/R_meal.cpp |only tclust-1.5-6/tclust/src/R_meal.h |only tclust-1.5-6/tclust/src/R_meal_BLAS.cpp |only tclust-1.5-6/tclust/src/R_package.cpp |only tclust-1.5-6/tclust/src/R_package.h |only tclust-1.5-6/tclust/src/clust.cpp |only tclust-1.5-6/tclust/src/clust.h |only tclust-1.5-6/tclust/src/perftimer.h |only tclust-1.5-6/tclust/src/restr.cpp |only tclust-1.5-6/tclust/src/restr_eigen.cpp |only tclust-1.5-6/tclust/src/smat.base.h |only tclust-1.5-6/tclust/src/smat.cpp |only tclust-1.5-6/tclust/src/smat.def.h |only tclust-1.5-6/tclust/src/smat.elop.h |only tclust-1.5-6/tclust/src/smat.h |only tclust-1.5-6/tclust/src/smat.math.h |only tclust-1.5-6/tclust/src/smat.matop.h |only tclust-1.5-6/tclust/src/smat.meal.h |only tclust-1.5-6/tclust/src/smat.mem.h |only tclust-1.5-6/tclust/src/smat.misc.h |only tclust-1.5-6/tclust/src/smat.random.h |only tclust-1.5-6/tclust/src/smat.sort.h |only tclust-1.5-6/tclust/src/smat.stat.h |only tclust-1.5-6/tclust/src/smat_meal_passrng.h |only tclust-1.5-6/tclust/src/smat_meal_passrng_hpp.h |only tclust-1.5-6/tclust/src/tclust.h |only tclust-1.5-6/tclust/src/tclust_init.c |only tclust-1.5-6/tclust/src/tkmeans.h |only tclust-2.0-3/tclust/ChangeLog | 9 tclust-2.0-3/tclust/DESCRIPTION | 35 tclust-2.0-3/tclust/MD5 | 139 - tclust-2.0-3/tclust/NAMESPACE | 57 tclust-2.0-3/tclust/R/DiscrFact.R | 347 ++++ tclust-2.0-3/tclust/R/R_restr.eigen.R | 187 +- tclust-2.0-3/tclust/R/R_tclust.R | 18 tclust-2.0-3/tclust/R/RcppExports.R |only tclust-2.0-3/tclust/R/ctlcurves.R | 358 ++-- tclust-2.0-3/tclust/R/data.R |only tclust-2.0-3/tclust/R/discr_coords.R | 91 - tclust-2.0-3/tclust/R/myscale.r |only tclust-2.0-3/tclust/R/plot.rlg.R |only tclust-2.0-3/tclust/R/plot.tclust.R | 88 + tclust-2.0-3/tclust/R/print.tclust.R | 18 tclust-2.0-3/tclust/R/rlg.R |only tclust-2.0-3/tclust/R/simul_rlg.R |only tclust-2.0-3/tclust/R/simul_tclust.R |only tclust-2.0-3/tclust/R/tclust-internal.R | 89 - tclust-2.0-3/tclust/R/tclust.R | 876 ++++++----- tclust-2.0-3/tclust/R/tkmeans.R | 324 ++++ tclust-2.0-3/tclust/R/zzz.R |only tclust-2.0-3/tclust/README.md | 8 tclust-2.0-3/tclust/data/LG5data.RData |only tclust-2.0-3/tclust/data/M5data.RData |only tclust-2.0-3/tclust/data/pine.rda |only tclust-2.0-3/tclust/data/wholesale.rda |only tclust-2.0-3/tclust/inst/doc/tclust.R | 279 +-- tclust-2.0-3/tclust/inst/doc/tclust.pdf |binary tclust-2.0-3/tclust/inst/doc/tclust.rnw | 348 ++-- tclust-2.0-3/tclust/inst/work/dmnorm-old.R |only tclust-2.0-3/tclust/man/DiscrFact.Rd | 109 - tclust-2.0-3/tclust/man/LG5data.Rd |only tclust-2.0-3/tclust/man/M5data.Rd | 47 tclust-2.0-3/tclust/man/ctlcurves.Rd | 207 +- tclust-2.0-3/tclust/man/geyser2.Rd | 68 tclust-2.0-3/tclust/man/pine.Rd |only tclust-2.0-3/tclust/man/plot.DiscrFact.Rd | 147 - tclust-2.0-3/tclust/man/plot.ctlcurves.Rd | 172 +- tclust-2.0-3/tclust/man/plot.rlg.Rd |only tclust-2.0-3/tclust/man/plot.tclust.Rd | 209 +- tclust-2.0-3/tclust/man/rlg.Rd |only tclust-2.0-3/tclust/man/simula.rlg.Rd |only tclust-2.0-3/tclust/man/simula.tclust.Rd |only tclust-2.0-3/tclust/man/summary.DiscrFact.Rd | 97 - tclust-2.0-3/tclust/man/swissbank.Rd | 53 tclust-2.0-3/tclust/man/tclust.Rd | 647 ++++---- tclust-2.0-3/tclust/man/tkmeans.Rd | 313 +--- tclust-2.0-3/tclust/man/wholesale.Rd |only tclust-2.0-3/tclust/src/Makevars | 16 tclust-2.0-3/tclust/src/Makevars.win |only tclust-2.0-3/tclust/src/RcppExports.cpp |only tclust-2.0-3/tclust/src/rlg.cpp |only tclust-2.0-3/tclust/src/tclust.cpp | 1787 ++++++++++-------------- tclust-2.0-3/tclust/src/tclust_types.h |only tclust-2.0-3/tclust/src/tkmeans.cpp | 346 +++- tclust-2.0-3/tclust/tests/ttclust.R | 78 - tclust-2.0-3/tclust/tests/ttclust.Rout.save | 589 ++++--- tclust-2.0-3/tclust/vignettes/tclust.rnw | 348 ++-- 106 files changed, 4563 insertions(+), 3941 deletions(-)
Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed
Models
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
Author: Maude Wagner [aut, cre] ,
Emmanuelle Comets [ctb],
Ana W. Capuano [aut]
Maintainer: Maude Wagner <maude_wagner@rush.edu>
Diff between nlive versions 0.2.0 dated 2023-10-30 and 0.3.0 dated 2024-04-17
DESCRIPTION | 22 ++-- MD5 | 26 ++--- NAMESPACE | 1 R/globals.R | 4 R/nlive.R | 150 ++++++++++++++++++++++++++++--- R/nlive.inspect.R | 1 R/nlive.pmma.R | 241 ++++++++++++++++++++++++++++++++------------------- R/nlive.pmms.R | 144 ++++++++++++++++++++++-------- R/nlive.smm.R | 142 +++++++++++++++++++++--------- man/nlive.Rd | 9 + man/nlive.inspect.Rd | 1 man/nlive.pmma.Rd | 5 - man/nlive.pmms.Rd | 5 - man/nlive.smm.Rd | 5 - 14 files changed, 545 insertions(+), 211 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.6.0 dated 2024-03-13 and 1.7.0 dated 2024-04-17
targets-1.6.0/targets/R/utils_digest.R |only targets-1.6.0/targets/tests/testthat/test-utils_digest.R |only targets-1.7.0/targets/DESCRIPTION | 15 - targets-1.7.0/targets/MD5 | 130 +++++----- targets-1.7.0/targets/NAMESPACE | 17 - targets-1.7.0/targets/NEWS.md | 14 + targets-1.7.0/targets/R/class_aws.R | 2 targets-1.7.0/targets/R/class_builder.R | 11 targets-1.7.0/targets/R/class_clustermq.R | 1 targets-1.7.0/targets/R/class_command.R | 2 targets-1.7.0/targets/R/class_crew.R | 5 targets-1.7.0/targets/R/class_database.R | 74 +++++ targets-1.7.0/targets/R/class_database_aws.R | 6 targets-1.7.0/targets/R/class_database_gcp.R | 6 targets-1.7.0/targets/R/class_database_local.R | 6 targets-1.7.0/targets/R/class_file.R | 8 targets-1.7.0/targets/R/class_future.R | 1 targets-1.7.0/targets/R/class_gcp.R | 2 targets-1.7.0/targets/R/class_inventory_aws.R | 2 targets-1.7.0/targets/R/class_inventory_gcp.R | 2 targets-1.7.0/targets/R/class_mermaid.R | 2 targets-1.7.0/targets/R/class_meta.R | 4 targets-1.7.0/targets/R/class_pattern.R | 16 + targets-1.7.0/targets/R/class_pipeline.R | 3 targets-1.7.0/targets/R/class_progress.R | 1 targets-1.7.0/targets/R/class_resources_custom_format.R |only targets-1.7.0/targets/R/class_store_custom.R | 15 + targets-1.7.0/targets/R/class_target.R | 10 targets-1.7.0/targets/R/class_value.R | 2 targets-1.7.0/targets/R/tar_cue.R | 2 targets-1.7.0/targets/R/tar_package.R | 7 targets-1.7.0/targets/R/tar_resources.R | 7 targets-1.7.0/targets/R/tar_resources_custom_format.R |only targets-1.7.0/targets/R/utils_assert.R | 42 +++ targets-1.7.0/targets/R/utils_callr.R | 14 + targets-1.7.0/targets/R/utils_hash.R |only targets-1.7.0/targets/R/utils_imports.R | 18 - targets-1.7.0/targets/R/utils_time.R | 2 targets-1.7.0/targets/R/utils_url.R | 2 targets-1.7.0/targets/man/tar_cue.Rd | 2 targets-1.7.0/targets/man/tar_resources.Rd | 9 targets-1.7.0/targets/man/tar_resources_aws.Rd | 1 targets-1.7.0/targets/man/tar_resources_clustermq.Rd | 1 targets-1.7.0/targets/man/tar_resources_crew.Rd | 1 targets-1.7.0/targets/man/tar_resources_custom_format.Rd |only targets-1.7.0/targets/man/tar_resources_feather.Rd | 1 targets-1.7.0/targets/man/tar_resources_fst.Rd | 1 targets-1.7.0/targets/man/tar_resources_future.Rd | 1 targets-1.7.0/targets/man/tar_resources_gcp.Rd | 1 targets-1.7.0/targets/man/tar_resources_network.Rd | 1 targets-1.7.0/targets/man/tar_resources_parquet.Rd | 1 targets-1.7.0/targets/man/tar_resources_qs.Rd | 1 targets-1.7.0/targets/man/tar_resources_url.Rd | 1 targets-1.7.0/targets/tests/aws/test-class_inventory_aws.R | 2 targets-1.7.0/targets/tests/gcp/test-class_inventory_gcp.R | 2 targets-1.7.0/targets/tests/hpc/sge_batchtools.tmpl | 2 targets-1.7.0/targets/tests/hpc/sge_clustermq.tmpl | 2 targets-1.7.0/targets/tests/interactive/test-tar_assert_store_noninvalidating.R |only targets-1.7.0/targets/tests/testthat/helper-aws.R | 2 targets-1.7.0/targets/tests/testthat/test-class_database.R | 80 +++--- targets-1.7.0/targets/tests/testthat/test-class_group.R | 4 targets-1.7.0/targets/tests/testthat/test-class_imports.R | 10 targets-1.7.0/targets/tests/testthat/test-class_list.R | 6 targets-1.7.0/targets/tests/testthat/test-class_meta.R | 2 targets-1.7.0/targets/tests/testthat/test-class_resources_custom_format.R |only targets-1.7.0/targets/tests/testthat/test-class_vector.R | 4 targets-1.7.0/targets/tests/testthat/test-tar_format.R | 57 ++++ targets-1.7.0/targets/tests/testthat/test-tar_resources_custom_format.R |only targets-1.7.0/targets/tests/testthat/test-utils_hash.R |only targets-1.7.0/targets/tests/testthat/test-utils_packages.R | 2 targets-1.7.0/targets/tests/testthat/test-utils_time.R | 1 71 files changed, 478 insertions(+), 171 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible pipelines concisely and compactly.
The methods in this package were influenced by the 'drake' R package
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between tarchetypes versions 0.8.0 dated 2024-03-18 and 0.9.0 dated 2024-04-17
tarchetypes-0.8.0/tarchetypes/R/utils_data.R |only tarchetypes-0.9.0/tarchetypes/DESCRIPTION | 10 +-- tarchetypes-0.9.0/tarchetypes/MD5 | 20 +++--- tarchetypes-0.9.0/tarchetypes/NAMESPACE | 2 tarchetypes-0.9.0/tarchetypes/NEWS.md | 6 ++ tarchetypes-0.9.0/tarchetypes/R/tar_map.R | 8 -- tarchetypes-0.9.0/tarchetypes/R/tar_package.R | 2 tarchetypes-0.9.0/tarchetypes/R/tar_render_rep_raw.R | 4 - tarchetypes-0.9.0/tarchetypes/R/utils_hash.R |only tarchetypes-0.9.0/tarchetypes/tests/testthat/test-tar_map_rep.R | 12 ++-- tarchetypes-0.9.0/tarchetypes/tests/testthat/test-tar_rep.R | 30 +++++++--- tarchetypes-0.9.0/tarchetypes/tests/testthat/test-tar_rep2.R | 24 ++++---- 12 files changed, 64 insertions(+), 54 deletions(-)
Title: Read and Write QOI Images
Description: The new QOI file format offers a very simple but efficient image compression algorithm. This package provides an easy and simple way to read, write and display bitmap images stored in the QOI (Quite Ok Image) format. It can read and write both files and in-memory raw vectors.
Author: Johannes Friedrich [aut, trl, cre],
Dominic Szablewski [cph]
Maintainer: Johannes Friedrich <Johannes.Friedrich@posteo.de>
Diff between qoi versions 0.0.4 dated 2023-02-07 and 0.1.0 dated 2024-04-17
DESCRIPTION | 14 ++++++++------ LICENSE |only MD5 | 10 +++++++--- src/qoi.h | 31 ++++++++----------------------- src/write.c | 8 ++++---- tests |only 6 files changed, 27 insertions(+), 36 deletions(-)
Title: Functions for Estimating Centrographic Statistics
Description: A collection of functions for computing centrographic
statistics (e.g., standard distance, standard deviation
ellipse, standard deviation box) for observations taken at
point locations. Separate plotting functions have been
developed for each measure. Users interested in writing results
to ESRI shapefiles can do so by using results from 'aspace'
functions as inputs to the convert.to.shapefile() and
write.shapefile() functions in the 'shapefiles' library. We intend to
provide 'terra' integration for geographic data in a future release.
The 'aspace' package was originally conceived to aid in the analysis of
spatial patterns of travel behaviour (see Buliung and Remmel 2008
<doi:10.1007/s10109-008-0063-7>).
Author: Tarmo K. Remmel [aut, cre] ,
Randy Bui [aut],
Ron N. Buliung [aut]
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Diff between aspace versions 4.1.0 dated 2023-09-05 and 4.1.1 dated 2024-04-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/plot_centres.R | 4 ++-- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Relative Quantification of Gene Expression using Delta Ct
Methods
Description: The commonly used methods for relative quantification of gene expression levels obtained in real-time PCR (Polymerase Chain Reaction) experiments are the delta Ct methods, encompassing 2^-dCt and 2^-ddCt methods, originally proposed by Kenneth J. Livak and Thomas D. Schmittgen (2001) <doi:10.1006/meth.2001.1262>. The main idea is to normalise gene expression values using endogenous control gene, present gene expression levels in linear form by using the 2^-(value)^ transformation, and calculate differences in gene expression levels between groups of samples (or technical replicates of a single sample). The 'RQdeltaCT' package offers functions that cover both methods for comparison of either independent groups of samples or groups with paired samples, together with importing expression datasets, performing multi-step quality control of data, enabling numerous data visualisations, enrichment of the standard workflow with additional useful analyses (correlation analysis, Receiver Op [...truncated...]
Author: Daniel Zalewski [aut, cre]
Maintainer: Daniel Zalewski <daniel.piotr.zalewski@gmail.com>
Diff between RQdeltaCT versions 1.2.1 dated 2024-04-02 and 1.3.0 dated 2024-04-17
RQdeltaCT-1.2.1/RQdeltaCT/man/RQ_exp_Ct_dCt.Rd |only RQdeltaCT-1.2.1/RQdeltaCT/man/RQ_plot.Rd |only RQdeltaCT-1.2.1/RQdeltaCT/man/RQ_volcano.Rd |only RQdeltaCT-1.2.1/RQdeltaCT/man/exp_Ct_dCt.Rd |only RQdeltaCT-1.3.0/RQdeltaCT/DESCRIPTION | 8 RQdeltaCT-1.3.0/RQdeltaCT/MD5 | 65 RQdeltaCT-1.3.0/RQdeltaCT/NAMESPACE | 7 RQdeltaCT-1.3.0/RQdeltaCT/R/RQdeltaCT.R | 664 +-- RQdeltaCT-1.3.0/RQdeltaCT/build/vignette.rds |binary RQdeltaCT-1.3.0/RQdeltaCT/inst/doc/my-vignette.R | 151 RQdeltaCT-1.3.0/RQdeltaCT/inst/doc/my-vignette.Rmd | 402 -- RQdeltaCT-1.3.0/RQdeltaCT/inst/doc/my-vignette.html | 2825 +++++++-------- RQdeltaCT-1.3.0/RQdeltaCT/man/FCh_plot.Rd |only RQdeltaCT-1.3.0/RQdeltaCT/man/ROCh.Rd | 7 RQdeltaCT-1.3.0/RQdeltaCT/man/RQ_dCt.Rd |only RQdeltaCT-1.3.0/RQdeltaCT/man/RQ_ddCt.Rd | 11 RQdeltaCT-1.3.0/RQdeltaCT/man/control_boxplot_gene.Rd | 5 RQdeltaCT-1.3.0/RQdeltaCT/man/control_boxplot_sample.Rd | 5 RQdeltaCT-1.3.0/RQdeltaCT/man/control_cluster_gene.Rd | 5 RQdeltaCT-1.3.0/RQdeltaCT/man/control_cluster_sample.Rd | 6 RQdeltaCT-1.3.0/RQdeltaCT/man/control_pca_gene.Rd | 6 RQdeltaCT-1.3.0/RQdeltaCT/man/control_pca_sample.Rd | 6 RQdeltaCT-1.3.0/RQdeltaCT/man/corr_gene.Rd | 5 RQdeltaCT-1.3.0/RQdeltaCT/man/corr_sample.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/man/delta_Ct.Rd | 22 RQdeltaCT-1.3.0/RQdeltaCT/man/filter_transformed_data.Rd | 12 RQdeltaCT-1.3.0/RQdeltaCT/man/log_reg.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/man/parallel_plot.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/man/pca_kmeans.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/man/results_barplot.Rd | 9 RQdeltaCT-1.3.0/RQdeltaCT/man/results_boxplot.Rd | 15 RQdeltaCT-1.3.0/RQdeltaCT/man/results_heatmap.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/man/results_volcano.Rd |only RQdeltaCT-1.3.0/RQdeltaCT/man/single_pair_gene.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/man/single_pair_sample.Rd | 2 RQdeltaCT-1.3.0/RQdeltaCT/vignettes/figure1ok.png |binary RQdeltaCT-1.3.0/RQdeltaCT/vignettes/my-vignette.Rmd | 402 -- 37 files changed, 2200 insertions(+), 2452 deletions(-)
Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] ,
Graph Builder [ctb, cph] ,
Brett Woolridge [ctb, cph]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnect versions 1.0.8 dated 2024-01-30 and 1.0.9 dated 2024-04-17
XLConnect-1.0.8/XLConnect/inst/java/XLConnect-2.0.0-SNAPSHOT.jar |only XLConnect-1.0.9/XLConnect/DESCRIPTION | 6 +-- XLConnect-1.0.9/XLConnect/MD5 | 16 +++++----- XLConnect-1.0.9/XLConnect/NEWS | 4 ++ XLConnect-1.0.9/XLConnect/build/vignette.rds |binary XLConnect-1.0.9/XLConnect/inst/doc/XLConnect.pdf |binary XLConnect-1.0.9/XLConnect/inst/doc/XLConnectImpatient.pdf |binary XLConnect-1.0.9/XLConnect/inst/java/XLConnect-2.0.1.jar |only XLConnect-1.0.9/XLConnect/inst/unitTests/runit.loadWorkbook.R | 5 +++ XLConnect-1.0.9/XLConnect/tests/run_tests.R | 16 +++++++--- 10 files changed, 32 insertions(+), 15 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in \doi{10.1007/s11222-019-09870-4}.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-5 dated 2022-01-14 and 0.3-6 dated 2024-04-17
tbm-0.3-5/tbm/tests/Rplots.pdf |only tbm-0.3-6/tbm/DESCRIPTION | 8 ++++---- tbm-0.3-6/tbm/MD5 | 15 +++++++-------- tbm-0.3-6/tbm/build/vignette.rds |binary tbm-0.3-6/tbm/inst/CITATION | 13 +++---------- tbm-0.3-6/tbm/inst/NEWS.Rd | 6 ++++++ tbm-0.3-6/tbm/inst/doc/tbm_supplement.pdf |binary tbm-0.3-6/tbm/man/ctmboost.Rd | 2 +- tbm-0.3-6/tbm/man/stmboost.Rd | 2 +- 9 files changed, 22 insertions(+), 24 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 ML framework with spatio-temporal resampling
methods to account for the presence of spatiotemporal autocorrelation
(STAC) in predictor variables. STAC may cause highly biased
performance estimates in cross-validation if ignored.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.3.0 dated 2024-01-22 and 2.3.1 dated 2024-04-17
DESCRIPTION | 8 MD5 | 196 +++++----- NEWS.md | 7 R/ResamplingRepeatedSpCVBlock.R | 28 - R/ResamplingRepeatedSpCVCoords.R | 8 R/ResamplingRepeatedSpCVDisc.R | 16 R/ResamplingRepeatedSpCVEnv.R | 10 R/ResamplingRepeatedSpCVTiles.R | 26 - R/ResamplingRepeatedSpCVknndm.R | 44 +- R/ResamplingRepeatedSptCVCstf.R | 10 R/ResamplingSpCVBlock.R | 24 - R/ResamplingSpCVBuffer.R | 10 R/ResamplingSpCVCoords.R | 6 R/ResamplingSpCVDisc.R | 14 R/ResamplingSpCVEnv.R | 8 R/ResamplingSpCVKnndm.R | 38 - R/ResamplingSpCVTiles.R | 24 - R/ResamplingSptCVCstf.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mlr3spatiotempcv.html | 55 +- inst/doc/spatiotemp-viz.html | 2 man/mlr_resamplings_repeated_spcv_knndm.Rd | 26 - man/mlr_resamplings_spcv_knndm.Rd | 24 - tests/testthat/_snaps/1-autoplot/autoplot-show-blocks-true-show-labels-true.svg | 4 tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2-sample-fold-n.svg | 8 tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2.svg | 8 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More information about mlr3spatiotempcv at CRAN
Permanent link
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] ,
Wil Davis [ctb] ,
Spencer Matthews [ctb] ,
JavaScript and CSS libraries authors [ctb, cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.8.4 dated 2024-04-04 and 0.8.5 dated 2024-04-17
DESCRIPTION | 6 +-- MD5 | 19 +++++----- NAMESPACE | 1 NEWS.md | 7 +++ R/WinBox.R | 20 +++++++++-- R/input-noUiSlider.R | 2 - inst/examples/WinBox/apply-method.R |only inst/packer/WinBox.js | 2 - man/WinBox.Rd | 65 ++++++++++++++++++++++++++++++++++++ man/noUiSliderInput.Rd | 2 - man/wbOptions.Rd | 2 - 11 files changed, 108 insertions(+), 18 deletions(-)
Title: Thurstonian IRT Models
Description: Fit Thurstonian Item Response Theory (IRT) models in R. This
package supports fitting Thurstonian IRT models and its extensions using
'Stan', 'lavaan', or 'Mplus' for the model estimation. Functionality for
extracting results, making predictions, and simulating data is provided as
well. References:
Brown & Maydeu-Olivares (2011) <doi:10.1177/0013164410375112>;
Bürkner et al. (2019) <doi:10.1177/0013164419832063>.
Author: Paul-Christian Buerkner [aut, cre],
Angus Hughes [ctb],
Trustees of Columbia University [cph]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between thurstonianIRT versions 0.12.4 dated 2023-12-19 and 0.12.5 dated 2024-04-17
DESCRIPTION | 10 MD5 | 24 NEWS.md | 7 R/data-helpers.R | 12 R/datasets.R | 14 inst/doc/TIRT_sim_tests.Rmd | 399 +-- inst/doc/TIRT_sim_tests.html | 14 man/set_block.Rd | 12 man/thurstonianIRT-package.Rd | 18 man/triplets.Rd | 14 src/stanExports_thurstonian_irt_model.h | 2743 +++++++++++------------- src/stanExports_thurstonian_irt_model_newdata.h | 1810 +++++++-------- vignettes/TIRT_sim_tests.Rmd | 399 +-- 13 files changed, 2673 insertions(+), 2803 deletions(-)
More information about thurstonianIRT at CRAN
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Title: Chacko Test for Order-Restriction with Permutation
Description: Implements an extension of the Chacko chi-square test for
ordered vectors (Chacko, 1966, <https://www.jstor.org/stable/25051572>).
Our extension brings the Chacko test to the computer age by implementing
a permutation test to offer a numeric estimate of the p-value, which is
particularly useful when the analytic solution is not available.
Author: Waldir Leoncio [aut, cre] ,
Graeme Ruxton [aut],
Morten Wang Fagerland [aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between permChacko versions 0.2.0 dated 2023-11-07 and 1.0.0 dated 2024-04-17
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/permChacko.R | 7 ++++++- R/print.R | 25 +++++++++++++++++++++---- inst/doc/improving_chacko.html | 10 ++++++---- man/permChacko-package.Rd | 1 - tests/testthat/test-print-and-summary.R | 6 +++++- 8 files changed, 55 insertions(+), 23 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function knn() from package 'nabor' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Dominic Russel [ctb],
Luigi Ranghetti [ctb],
Attilio Benini [ctb],
Arnaud Tarroux [ctb],
Felipe Matas [ctb],
Charles F.F Karney [ctb, cph]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.4.7 dated 2023-04-24 and 0.4.8 dated 2024-04-17
DESCRIPTION | 8 +++++--- MD5 | 16 ++++++++-------- NEWS.md | 19 +++---------------- R/st_nn.R | 2 +- R/st_nn_pnt_proj.R | 30 ++---------------------------- build/vignette.rds |binary inst/doc/intro.pdf |binary man/nngeo-package.Rd | 1 + man/st_nn.Rd | 2 +- 9 files changed, 21 insertions(+), 57 deletions(-)
Title: Inferring Cell-Specific Gene Regulatory Network
Description: A method for inferring cell-specific gene regulatory network from single-cell sequencing data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.0.1 dated 2024-03-15 and 1.0.3 dated 2024-04-17
inferCSN-1.0.1/inferCSN/man/filter.sort.matrix.Rd |only inferCSN-1.0.3/inferCSN/DESCRIPTION | 8 inferCSN-1.0.3/inferCSN/MD5 | 43 ++-- inferCSN-1.0.3/inferCSN/NAMESPACE | 6 inferCSN-1.0.3/inferCSN/R/calculate.gene.rank.R | 36 ++-- inferCSN-1.0.3/inferCSN/R/crossweight.R |only inferCSN-1.0.3/inferCSN/R/data.R | 8 inferCSN-1.0.3/inferCSN/R/import.R |only inferCSN-1.0.3/inferCSN/R/inferCSN.R | 2 inferCSN-1.0.3/inferCSN/R/network.visualization.R | 157 ++++++++++++++++-- inferCSN-1.0.3/inferCSN/R/performance.calculate.R | 20 +- inferCSN-1.0.3/inferCSN/R/sparse.regression.R | 7 inferCSN-1.0.3/inferCSN/R/utils.R | 50 +++-- inferCSN-1.0.3/inferCSN/R/weight_filter.R |only inferCSN-1.0.3/inferCSN/README.md | 7 inferCSN-1.0.3/inferCSN/data/example_ground_truth.rda |binary inferCSN-1.0.3/inferCSN/data/example_matrix.rda |binary inferCSN-1.0.3/inferCSN/data/example_meta_data.rda |only inferCSN-1.0.3/inferCSN/man/acc.calculate.Rd | 3 inferCSN-1.0.3/inferCSN/man/auc.calculate.Rd | 3 inferCSN-1.0.3/inferCSN/man/calculate.gene.rank.Rd | 19 +- inferCSN-1.0.3/inferCSN/man/crossweight.Rd |only inferCSN-1.0.3/inferCSN/man/crossweight_params.Rd |only inferCSN-1.0.3/inferCSN/man/example_meta_data.Rd |only inferCSN-1.0.3/inferCSN/man/filter_sort_matrix.Rd |only inferCSN-1.0.3/inferCSN/man/network.heatmap.Rd | 37 +++- inferCSN-1.0.3/inferCSN/man/normalization.Rd |only inferCSN-1.0.3/inferCSN/man/weight_filter.Rd |only 28 files changed, 302 insertions(+), 104 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-10 1.2.2
2023-08-24 1.2.1
2022-11-30 1.1.21
2022-11-16 1.1.20
2022-03-16 1.1.18
2022-01-07 1.1.17
2021-12-21 1.1.16
Title: Create Common TLGs Used in Clinical Trials
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
Author: Joe Zhu [aut, cre],
Daniel Sabanes Bove [aut],
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Heng Wang [aut],
Francois Collin [aut],
Adrian Waddell [aut],
Pawel Rucki [aut],
Chendi Liao [aut],
Jennifer [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern versions 0.9.3 dated 2023-12-08 and 0.9.4 dated 2024-04-17
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tern-0.9.4/tern/man/estimate_coef.Rd | 18 tern-0.9.4/tern/man/estimate_multinomial_rsp.Rd | 14 tern-0.9.4/tern/man/estimate_proportions.Rd | 14 tern-0.9.4/tern/man/ex_data.Rd | 18 tern-0.9.4/tern/man/explicit_na.Rd | 6 tern-0.9.4/tern/man/extract_by_name.Rd | 2 tern-0.9.4/tern/man/extract_rsp_biomarkers.Rd | 10 tern-0.9.4/tern/man/extract_rsp_subgroups.Rd | 6 tern-0.9.4/tern/man/extract_survival_biomarkers.Rd | 4 tern-0.9.4/tern/man/extract_survival_subgroups.Rd | 4 tern-0.9.4/tern/man/extreme_format.Rd | 12 tern-0.9.4/tern/man/f_pval.Rd | 2 tern-0.9.4/tern/man/fct_collapse_only.Rd | 4 tern-0.9.4/tern/man/fct_discard.Rd | 4 tern-0.9.4/tern/man/fct_explicit_na_if.Rd | 8 tern-0.9.4/tern/man/fit_coxreg.Rd | 6 tern-0.9.4/tern/man/fit_logistic.Rd | 2 tern-0.9.4/tern/man/fit_rsp_step.Rd | 8 tern-0.9.4/tern/man/fit_survival_step.Rd | 4 tern-0.9.4/tern/man/forest_viewport.Rd | 18 tern-0.9.4/tern/man/format_auto.Rd | 14 tern-0.9.4/tern/man/format_count_fraction.Rd | 10 tern-0.9.4/tern/man/format_count_fraction_fixed_dp.Rd | 12 tern-0.9.4/tern/man/format_count_fraction_lt10.Rd | 12 tern-0.9.4/tern/man/format_extreme_values.Rd | 10 tern-0.9.4/tern/man/format_extreme_values_ci.Rd | 8 tern-0.9.4/tern/man/format_fraction.Rd | 10 tern-0.9.4/tern/man/format_fraction_fixed_dp.Rd | 12 tern-0.9.4/tern/man/format_fraction_threshold.Rd | 8 tern-0.9.4/tern/man/format_sigfig.Rd | 14 tern-0.9.4/tern/man/format_xx.Rd | 8 tern-0.9.4/tern/man/formatting_functions.Rd | 8 tern-0.9.4/tern/man/g_forest.Rd | 103 - tern-0.9.4/tern/man/g_ipp.Rd |only tern-0.9.4/tern/man/g_km.Rd | 239 +- tern-0.9.4/tern/man/g_lineplot.Rd | 74 tern-0.9.4/tern/man/g_step.Rd | 4 tern-0.9.4/tern/man/g_waterfall.Rd | 21 tern-0.9.4/tern/man/get_covariates.Rd | 4 tern-0.9.4/tern/man/get_smooths.Rd | 10 tern-0.9.4/tern/man/groups_list_to_df.Rd | 4 tern-0.9.4/tern/man/h_adlb_abnormal_by_worst_grade.Rd | 14 tern-0.9.4/tern/man/h_adlb_worsen.Rd | 16 tern-0.9.4/tern/man/h_adsl_adlb_merge_using_worst_flag.Rd | 15 tern-0.9.4/tern/man/h_ancova.Rd | 6 tern-0.9.4/tern/man/h_append_grade_groups.Rd | 22 tern-0.9.4/tern/man/h_col_indices.Rd | 4 tern-0.9.4/tern/man/h_count_cumulative.Rd | 10 tern-0.9.4/tern/man/h_cox_regression.Rd | 2 tern-0.9.4/tern/man/h_data_plot.Rd | 12 tern-0.9.4/tern/man/h_decompose_gg.Rd | 8 tern-0.9.4/tern/man/h_format_row.Rd | 2 tern-0.9.4/tern/man/h_g_ipp.Rd | 12 tern-0.9.4/tern/man/h_ggkm.Rd | 47 tern-0.9.4/tern/man/h_glm_count.Rd | 25 tern-0.9.4/tern/man/h_grob_coxph.Rd | 14 tern-0.9.4/tern/man/h_grob_median_surv.Rd | 14 tern-0.9.4/tern/man/h_grob_tbl_at_risk.Rd | 16 tern-0.9.4/tern/man/h_grob_y_annot.Rd | 10 tern-0.9.4/tern/man/h_incidence_rate.Rd | 12 tern-0.9.4/tern/man/h_km_layout.Rd | 12 tern-0.9.4/tern/man/h_logistic_regression.Rd | 15 tern-0.9.4/tern/man/h_map_for_count_abnormal.Rd | 7 tern-0.9.4/tern/man/h_odds_ratio.Rd | 4 tern-0.9.4/tern/man/h_pkparam_sort.Rd | 8 tern-0.9.4/tern/man/h_prop_diff.Rd | 18 tern-0.9.4/tern/man/h_prop_diff_test.Rd | 10 tern-0.9.4/tern/man/h_proportions.Rd | 10 tern-0.9.4/tern/man/h_response_biomarkers_subgroups.Rd | 10 tern-0.9.4/tern/man/h_response_subgroups.Rd | 20 tern-0.9.4/tern/man/h_split_by_subgroups.Rd | 4 tern-0.9.4/tern/man/h_split_param.Rd | 2 tern-0.9.4/tern/man/h_stack_by_baskets.Rd | 15 tern-0.9.4/tern/man/h_step.Rd | 16 tern-0.9.4/tern/man/h_survival_biomarkers_subgroups.Rd | 10 tern-0.9.4/tern/man/h_survival_duration_subgroups.Rd | 20 tern-0.9.4/tern/man/h_tab_one_biomarker.Rd | 4 tern-0.9.4/tern/man/h_tbl_coxph_pairwise.Rd | 16 tern-0.9.4/tern/man/h_tbl_median_surv.Rd | 8 tern-0.9.4/tern/man/h_worsen_counter.Rd | 10 tern-0.9.4/tern/man/h_xticks.Rd | 16 tern-0.9.4/tern/man/imputation_rule.Rd | 10 tern-0.9.4/tern/man/incidence_rate.Rd | 16 tern-0.9.4/tern/man/labels_or_names.Rd | 4 tern-0.9.4/tern/man/labels_use_control.Rd | 6 tern-0.9.4/tern/man/logistic_regression_cols.Rd | 4 tern-0.9.4/tern/man/logistic_summary_by_flag.Rd | 2 tern-0.9.4/tern/man/make_names.Rd | 4 tern-0.9.4/tern/man/month2day.Rd | 6 tern-0.9.4/tern/man/muffled_car_anova.Rd | 2 tern-0.9.4/tern/man/n_available.Rd | 4 tern-0.9.4/tern/man/odds_ratio.Rd | 14 tern-0.9.4/tern/man/prop_diff.Rd | 16 tern-0.9.4/tern/man/prop_diff_test.Rd | 20 tern-0.9.4/tern/man/prune_occurrences.Rd | 4 tern-0.9.4/tern/man/range_noinf.Rd | 6 tern-0.9.4/tern/man/reapply_varlabels.Rd | 2 tern-0.9.4/tern/man/response_biomarkers_subgroups.Rd | 2 tern-0.9.4/tern/man/response_subgroups.Rd | 6 tern-0.9.4/tern/man/rtable2gg.Rd | 14 tern-0.9.4/tern/man/rtables_access.Rd | 4 tern-0.9.4/tern/man/s_cox_multivariate.Rd | 12 tern-0.9.4/tern/man/sas_na.Rd | 8 tern-0.9.4/tern/man/score_occurrences.Rd | 4 tern-0.9.4/tern/man/split_cols_by_groups.Rd | 4 tern-0.9.4/tern/man/split_text_grob.Rd | 8 tern-0.9.4/tern/man/stack_grobs.Rd | 14 tern-0.9.4/tern/man/stat_mean_ci.Rd | 8 tern-0.9.4/tern/man/stat_mean_pval.Rd | 6 tern-0.9.4/tern/man/stat_median_ci.Rd | 6 tern-0.9.4/tern/man/stat_propdiff_ci.Rd | 6 tern-0.9.4/tern/man/strata_normal_quantile.Rd | 2 tern-0.9.4/tern/man/study_arm.Rd | 2 tern-0.9.4/tern/man/summarize_ancova.Rd | 26 tern-0.9.4/tern/man/summarize_change.Rd | 12 tern-0.9.4/tern/man/summarize_colvars.Rd | 7 tern-0.9.4/tern/man/summarize_functions.Rd | 4 tern-0.9.4/tern/man/summarize_glm_count.Rd | 28 tern-0.9.4/tern/man/summarize_logistic.Rd | 6 tern-0.9.4/tern/man/summarize_num_patients.Rd | 20 tern-0.9.4/tern/man/summarize_patients_exposure_in_cols.Rd | 12 tern-0.9.4/tern/man/survival_biomarkers_subgroups.Rd | 2 tern-0.9.4/tern/man/survival_coxph_pairwise.Rd | 32 tern-0.9.4/tern/man/survival_duration_subgroups.Rd | 8 tern-0.9.4/tern/man/survival_time.Rd | 20 tern-0.9.4/tern/man/survival_timepoint.Rd | 24 tern-0.9.4/tern/man/tern-package.Rd | 6 tern-0.9.4/tern/man/tidy.glm.Rd | 6 tern-0.9.4/tern/man/tidy.step.Rd | 6 tern-0.9.4/tern/man/tidy_coxreg.Rd | 4 tern-0.9.4/tern/man/to_n.Rd | 4 tern-0.9.4/tern/man/to_string_matrix.Rd | 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tern-0.9.4/tern/tests/testthat/test-decorate_grob.R | 132 - tern-0.9.4/tern/tests/testthat/test-fit_rsp_step.R | 14 tern-0.9.4/tern/tests/testthat/test-formatting_functions.R |only tern-0.9.4/tern/tests/testthat/test-g_forest.R | 154 + tern-0.9.4/tern/tests/testthat/test-g_km.R | 253 ++- tern-0.9.4/tern/tests/testthat/test-g_lineplot.R | 72 tern-0.9.4/tern/tests/testthat/test-g_step.R | 10 tern-0.9.4/tern/tests/testthat/test-g_waterfall.R | 13 tern-0.9.4/tern/tests/testthat/test-h_km.R |only tern-0.9.4/tern/tests/testthat/test-h_logistic_regression.R | 36 tern-0.9.4/tern/tests/testthat/test-h_response_biomarkers_subgroups.R | 101 - tern-0.9.4/tern/tests/testthat/test-h_response_subgroups.R | 38 tern-0.9.4/tern/tests/testthat/test-h_step.R | 30 tern-0.9.4/tern/tests/testthat/test-h_survival_duration_subgroups.R | 2 tern-0.9.4/tern/tests/testthat/test-logistic_regression.R | 44 tern-0.9.4/tern/tests/testthat/test-odds_ratio.R | 65 tern-0.9.4/tern/tests/testthat/test-response_biomarkers_subgroups.R | 42 tern-0.9.4/tern/tests/testthat/test-response_subgroups.R | 16 tern-0.9.4/tern/tests/testthat/test-score_occurrences.R | 2 tern-0.9.4/tern/tests/testthat/test-summarize_ancova.R | 54 tern-0.9.4/tern/tests/testthat/test-summarize_coxreg.R | 17 tern-0.9.4/tern/tests/testthat/test-summarize_glm_count.R | 215 ++ tern-0.9.4/tern/tests/testthat/test-survival_coxph_pairwise.R | 18 tern-0.9.4/tern/tests/testthat/test-test_proportion_diff.R | 14 tern-0.9.4/tern/tests/testthat/test-utils.R | 7 tern-0.9.4/tern/tests/testthat/test-utils_checkmate.R | 12 tern-0.9.4/tern/tests/testthat/test-utils_default_stats_formats_labels.R | 14 tern-0.9.4/tern/tests/testthat/test-utils_ggplot.R | 64 tern-0.9.4/tern/tests/testthat/test-utils_grid.R | 20 tern-0.9.4/tern/tests/testthat/test-utils_rtables.R | 4 tern-0.9.4/tern/vignettes/tables.Rmd | 50 tern-0.9.4/tern/vignettes/tern.Rmd | 30 447 files changed, 4865 insertions(+), 4150 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.8 dated 2024-03-18 and 0.1.9 dated 2024-04-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- data/UserGS.rda |binary data/UserGST.rda |binary inst/doc/vignette.html | 44 ++++++++++++++++++-------------------------- 5 files changed, 26 insertions(+), 34 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.3.0 dated 2024-01-21 and 0.4.0 dated 2024-04-17
DESCRIPTION | 10 MD5 | 42 NAMESPACE | 4 R/const_dmd.R | 572 +-- R/data.R | 59 R/drp.R | 2006 ++++++------- R/light_proj_inv.R | 948 +++--- R/month_to_week.R | 7 R/proj_git.R |only R/proj_inv.R | 1405 ++++----- R/ssl.R |only README.md | 252 + build/vignette.rds |binary data/demo_in_transit.rda |only data/slob.rda |only inst/doc/get_started.R | 2 inst/doc/get_started.html | 1787 ++++++------ inst/doc/user_cases.R | 2 inst/doc/user_cases.html | 6063 ++++++++++++++++++++--------------------- man/blueprint.Rd | 3 man/demo_in_transit.Rd |only man/month_to_week.Rd | 4 man/proj_git.Rd |only man/slob.Rd |only man/ssl.Rd |only tests/testthat/test-proj_git.R |only tests/testthat/test-ssl.R |only 27 files changed, 6627 insertions(+), 6539 deletions(-)
Title: Neutrosophic Distributions
Description: Computes the pdf, cdf, quantile function and generating random numbers for neutrosophic distributions. This family have been developed by different authors in the recent years. See Patro and Smarandache (2016) <doi:10.5281/zenodo.571153> and Rao et al (2023) <doi:10.5281/zenodo.7832786>.
Author: Danial Mazarei [aut, cre] ,
Mina Norouzirad [aut] ,
Amin Roshani [aut] ,
Gadde Srinivasa Rao [ctb] ,
Foad Esmaeili [ctb] ,
FCT, I.P. [fnd] )
Maintainer: Danial Mazarei <danial.mazarei@gmail.com>
Diff between ntsDists versions 2.1.0 dated 2024-04-14 and 2.1.1 dated 2024-04-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 12 +++++++----- README.md | 12 ++++-------- 4 files changed, 17 insertions(+), 19 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] ,
Austin Dickey [ctb],
Matthias Grenie [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb],
Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.16 dated 2023-03-19 and 0.4.17 dated 2024-04-17
DESCRIPTION | 10 - MD5 | 46 ++--- NEWS.md | 4 R/fortify_surv.R | 6 R/ggfortify.R | 3 R/plotlib.R | 5 build/vignette.rds |binary inst/doc/basics.R | 36 ++-- inst/doc/basics.html | 329 +++++++++++++++++------------------------- inst/doc/plot_dist.R | 8 - inst/doc/plot_dist.html | 311 ++++++++++++++++----------------------- inst/doc/plot_lm.R | 14 - inst/doc/plot_lm.html | 315 ++++++++++++++++------------------------ inst/doc/plot_map.R | 14 - inst/doc/plot_map.html | 321 +++++++++++++++++------------------------ inst/doc/plot_pca.R | 40 ++--- inst/doc/plot_pca.html | 351 ++++++++++++++++++--------------------------- inst/doc/plot_surv.R | 6 inst/doc/plot_surv.html | 315 ++++++++++++++++------------------------ inst/doc/plot_ts.R | 54 +++--- inst/doc/plot_ts.html | 341 ++++++++++++++++++------------------------- man/ggbiplot.Rd | 3 man/ggfortify.Rd | 29 +++ tests/testthat/test-surv.R | 2 24 files changed, 1110 insertions(+), 1453 deletions(-)