Title: Backfill Bayesian Optimal Interval Design Using Efficacy and
Toxicity
Description: The backfill Bayesian optimal interval design using efficacy and toxicity outcomes for
dose optimization (BF-BOIN-ET) design is a novel clinical trial design to allow patients to be
backfilled at lower doses during a dose-finding trial while prioritizing the dose-escalation
cohort to explore a higher dose. The advantages compared to the other designs in terms of the
percentage of correct optimal dose (OD) selection, reducing the sample size, and shortening the
duration of the trial, in various realistic setting.
Author: Jing Zhu [cre, aut],
Kentaro Takeda [aut]
Maintainer: Jing Zhu <zhujing716@gmail.com>
Diff between bfboinet versions 0.1.0 dated 2024-11-18 and 0.2.0 dated 2025-02-09
bfboinet |only 1 file changed
Title: Robust Bayesian Variable Selection for Gene-Environment
Interactions
Description: Gene-environment (G×E) interactions have important implications to elucidate the
etiology of complex diseases beyond the main genetic and environmental effects.
Outliers and data contamination in disease phenotypes of G×E studies have been commonly
encountered, leading to the development of a broad spectrum of robust penalization methods.
Nevertheless, within the Bayesian framework, the issue has not been taken care of in existing
studies. We develop a robust Bayesian variable selection method for G×E interaction
studies. The proposed Bayesian method can effectively accommodate heavy-tailed errors and
outliers in the response variable while conducting variable selection by accounting for
structural sparsity. In particular, the spike-and-slab priors have been imposed on both
individual and group levels to identify important main and interaction effects. An efficient
Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo
algorithms of the proposed a [...truncated...]
Author: Jie Ren [aut, cre],
Fei Zhou [aut],
Xiaoxi Li [aut],
Cen Wu [aut]
Maintainer: Jie Ren <renjie0910@gmail.com>
Diff between roben versions 0.1.1 dated 2024-03-12 and 0.1.2 dated 2025-02-09
DESCRIPTION | 28 ++++++++++++++++++++++------ MD5 | 9 +++++---- NEWS.md |only README.md | 12 ++++++------ build/partial.rdb |binary man/roben-package.Rd | 11 +++++++++++ 6 files changed, 44 insertions(+), 16 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of default Bayes factors
for testing statistical hypotheses under various statistical models. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
correlation analysis, generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., group means, regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. polychoric/polyserial/biserial/tetrachoric/product
moments correlations), among others.
The statistical underpinnings are
described in
O'Hagan (1995) <DOI:10.1111/j.2517-6161.1995.tb02017.x>,
De Santis and Spezzaferri (2001) <DOI:10.1016/S0378-3758(00)00240-8>,
Mulder and Xin (2022) <DOI:10.1080/00273171.2021.1904809& [...truncated...]
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Donald R. Williams [aut, ctb],
Xin Gu [aut, ctb],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Robbie van Aert [ctb],
Barry [...truncated...]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 1.4.0 dated 2024-12-03 and 1.4.2 dated 2025-02-09
DESCRIPTION | 13 +++++--- MD5 | 16 +++++----- NEWS.md | 12 +++++++ R/BF.cortest.R | 52 ++++++++++++++++++-------------- inst/doc/vignette_BFpack.html | 4 +- man/cor_test.Rd | 19 +++++++---- src/BFpack_init.c | 6 +-- src/bct_mixedordinal.f90 | 64 ++++++++++++++++++++++++++-------------- tests/testthat/test_BFcortest.R | 42 ++++++++++++++++---------- 9 files changed, 143 insertions(+), 85 deletions(-)
Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv.
Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci.
The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included.
Three standard color difference metrics are included, plus the forward direction of the 'CIECAM02' color appearance model.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesXYZ versions 1.4-0 dated 2025-01-17 and 1.5-1 dated 2025-02-09
DESCRIPTION | 10 MD5 | 31 - NAMESPACE | 7 NEWS.md | 4 R/CCT.R | 903 ++++++++++++++++++++++++++++------------------- R/CIECAM02.R |only R/basic.R | 184 +++++---- R/hooks.R | 22 - R/utils.R | 38 + inst/doc/adaptation.html | 8 inst/doc/isotherms.R | 18 inst/doc/isotherms.pdf |binary inst/doc/isotherms.rnw | 24 - man/CCT.Rd | 45 +- man/CIECAM02fromXYZ.Rd |only man/DeltaE_CAM02.Rd |only tests/test-CCT.R | 137 +++---- vignettes/isotherms.rnw | 24 - 18 files changed, 865 insertions(+), 590 deletions(-)
Title: Network-Based Regularization for Generalized Linear Models
Description: Network-based regularization has achieved success in variable selection for
high-dimensional biological data due to its ability to incorporate correlations among
genomic features. This package provides procedures of network-based variable selection
for generalized linear models (Ren et al. (2017) <doi:10.1186/s12863-017-0495-5> and
Ren et al.(2019) <doi:10.1002/gepi.22194>). Continuous, binary, and survival response
are supported. Robust network-based methods are available for continuous and survival
responses.
Author: Jie Ren [aut, cre],
Luann C. Jung [aut],
Yinhao Du [aut],
Cen Wu [aut],
Yu Jiang [aut],
Junhao Liu [aut]
Maintainer: Jie Ren <renjie0910@gmail.com>
Diff between regnet versions 1.0.1 dated 2024-02-21 and 1.0.2 dated 2025-02-09
DESCRIPTION | 25 +++-- MD5 | 36 +++---- NAMESPACE | 18 +-- NEWS.md | 6 + R/plot.regnet.R | 6 - R/print.regnet.R | 2 README.md | 7 + build/partial.rdb |binary man/cv.regnet.Rd | 242 ++++++++++++++++++++++++------------------------- man/plot.regnet.Rd | 10 +- man/print.cv.regnet.Rd | 42 ++++---- man/print.regnet.Rd | 2 man/regnet-package.Rd | 161 +++++++++++++++++--------------- man/regnet.Rd | 216 +++++++++++++++++++++---------------------- man/rgn.Rd | 62 ++++++------ src/QR.cpp | 26 ++++- src/QR.h | 4 src/RunCont.cpp | 4 src/RunSurv.cpp | 4 19 files changed, 466 insertions(+), 407 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>.
'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Author: Eric Marcon [aut, cre]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between divent versions 0.4-4 dated 2024-11-06 and 0.5-2 dated 2025-02-09
DESCRIPTION | 23 MD5 | 208 ++--- NAMESPACE | 37 NEWS.md | 20 R/RcppExports.R |only R/abd_freq_count.R | 100 +- R/abd_species.R | 29 R/accum_div_phylo.R | 251 +++--- R/accum_hill.R | 218 ++--- R/accum_sp.R |only R/accum_sp_hill.R |only R/alpha_hull.R |only R/autoplot.accumulation.R | 58 - R/autoplot.profile.R | 36 R/coverage.R | 234 +++-- R/div_gen_simpson.R |only R/div_hill.R | 283 ++++--- R/div_hurlbert.R | 111 +- R/div_part.R | 73 - R/div_pd.R |only R/div_phylo.R | 120 +- R/div_richness.R | 242 +++--- R/div_similarity.R | 101 +- R/e_n_q.R | 34 R/ent_allen.R |only R/ent_gen_simpson.R |only R/ent_hurlbert.R | 97 +- R/ent_phylo.R | 255 ++++-- R/ent_rao.R | 146 ++- R/ent_shannon.R | 281 +++--- R/ent_similarity.R | 269 ++++-- R/ent_simpson.R | 158 ++- R/ent_sp_simpson.R |only R/ent_tsallis.R | 367 ++++----- R/exp_q.R | 41 - R/fit_rac.R | 73 - R/fun_ordinariness.R | 24 R/fun_similarity.R | 32 R/ln_q.R | 28 R/metacommunity.R | 64 - R/package.R | 1250 ++++++++++++++++++++----------- R/phylo_divent.R | 42 - R/plot.phylo_divent.R | 9 R/plot.species_distribution.R | 147 +-- R/probabilities.R | 345 ++++---- R/profile_hill.R | 161 ++- R/profile_phylo.R | 196 ++-- R/profile_similarity.R | 154 ++- R/rcommunity.R | 387 ++++++--- R/rlseries.R | 43 - R/species_distribution.R | 463 ++++++++--- README.md | 187 ++++ build/partial.rdb |binary build/vignette.rds |binary data/non_species_columns.rda |only inst/REFERENCES.bib | 124 +++ inst/doc/divent.R | 2 inst/doc/divent.Rmd | 6 inst/doc/divent.html | 166 ++-- man/abd_freq_count.Rd | 25 man/abd_species.Rd | 9 man/accum_div_phylo.Rd | 32 man/accum_hill.Rd | 26 man/accum_sp.Rd |only man/accum_sp_hill.Rd |only man/alphahull.Rd |only man/autoplot.accumulation.Rd | 4 man/autoplot.profile.Rd | 4 man/autoplot.wmppp.Rd |only man/check_divent_args.Rd | 149 +++ man/coverage.Rd | 4 man/div_gen_simpson.Rd |only man/div_hill.Rd | 44 - man/div_hurlbert.Rd | 12 man/div_part.Rd | 30 man/div_pd.Rd |only man/div_phylo.Rd | 34 man/div_richness.Rd | 15 man/div_similarity.Rd | 26 man/ent_allen.Rd |only man/ent_gen_simpson.Rd |only man/ent_hurlbert.Rd | 132 +-- man/ent_phylo.Rd | 34 man/ent_rao.Rd | 18 man/ent_shannon.Rd | 23 man/ent_similarity.Rd | 26 man/ent_simpson.Rd | 23 man/ent_sp_simpson.Rd |only man/ent_tsallis.Rd | 27 man/exp_q.Rd | 7 man/figures/README-MetaCommunitydf-1.png |only man/figures/README-div_profile-1.png |only man/figures/README-rcommunity-1.png |only man/figures/README-unnamed-chunk-2-1.png |only man/fit_rac.Rd | 2 man/fun_ordinariness.Rd | 8 man/fun_similarity.Rd | 6 man/ln_q.Rd | 6 man/metacommunity.Rd | 8 man/non_species_columns.Rd |only man/paracou_6.Rd | 5 man/paracou_6_fundist.Rd | 3 man/phylo_divent.Rd | 2 man/plot.species_distribution.Rd | 4 man/probabilities.Rd | 14 man/profile_hill.Rd | 37 man/profile_phylo.Rd | 32 man/profile_similarity.Rd | 28 man/rcommunity.Rd | 131 ++- man/reexports.Rd | 5 man/rlseries.Rd | 96 +- man/species_distribution.Rd | 49 + src |only tests/testthat/test_coverage.R | 17 tests/testthat/test_div_richness.R | 11 tests/testthat/test_rcommunity.R | 2 vignettes/divent.Rmd | 6 117 files changed, 5458 insertions(+), 3413 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. This packaged is described by
Collyer & Adams (2018). Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] ,
Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 2.1.0 dated 2025-01-31 and 2.1.1 dated 2025-02-09
DESCRIPTION | 6 ++-- MD5 | 21 ++++++++------- NAMESPACE | 1 NEWS.md | 8 ++++++ R/RRPP.support.code.r | 2 + R/RRPP.utils.r | 56 +++++++++++++++++++++++++++++++++--------- R/base_lm.rrpp.r | 9 ++++++ inst/doc/ANOVA.vs.MANOVA.html | 4 +-- inst/doc/Using.RRPP.html | 4 +-- man/print.betaTest.Rd | 6 ---- man/print.summary.betaTest.Rd |only man/summary.betaTest.Rd | 6 +++- 12 files changed, 88 insertions(+), 35 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme-value and other copula families, as well as their rotations,
mixtures and asymmetrizations. Nested Archimedean copulas, related
tools and special functions. Methods for density, distribution, random
number generation, bivariate dependence measures, Rosenblatt transform,
Kendall distribution function, perspective and contour plots. Fitting of
copula models with potentially partly fixed parameters, including
standard errors. Serial independence tests, copula specification tests
(independence, exchangeability, radial symmetry, extreme-value
dependence, goodness-of-fit) and model selection based on
cross-validation. Empirical copula, smoothed versions, and
non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] ,
Ivan Kojadinovic [aut] ,
Martin Maechler [aut, cre] ,
Jun Yan [aut] ,
Johanna G. Neslehova [ctb] ,
<https://orcid.org/0000-0001-9634-4796>),
Rebecca Morger [ctb] : code for free mixCopula weight
parameters)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 1.1-4 dated 2024-08-17 and 1.1-5 dated 2025-02-09
DESCRIPTION | 20 ++++++------ MD5 | 60 ++++++++++++++++++------------------- R/Auxiliaries.R | 2 - R/cop_objects.R | 30 +++++++++++++++--- R/fitCopula.R | 14 ++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 29 +++++++++++++++++- inst/doc/AC_Liouville.html | 4 +- inst/doc/AR_Clayton.html | 8 ++--- inst/doc/Frank-Rmpfr.pdf |binary inst/doc/GIG.html | 14 ++++---- inst/doc/HAXC.html | 4 +- inst/doc/NALC.html | 8 ++--- inst/doc/copula_GARCH.html | 4 +- inst/doc/dNAC.html | 4 +- inst/doc/empiricial_copulas.html | 4 +- inst/doc/logL_visualization.html | 62 +++++++++++++++++++-------------------- inst/doc/nacopula-pkg.pdf |binary inst/doc/qrng.html | 4 +- inst/doc/rhoAMH-dilog.Rnw | 6 +-- inst/doc/rhoAMH-dilog.pdf |binary inst/doc/wild_animals.html | 62 +++++++++++++++++++-------------------- man/cCopula.Rd | 8 +++-- man/copula-package.Rd | 4 +- man/fitCopula.Rd | 25 ++++++++------- man/indepTest.Rd | 2 - man/multIndepTest.Rd | 7 ++-- tests/Stirling-etc.R | 12 +++++-- tests/ggraph-tst.R | 4 ++ vignettes/rhoAMH-dilog.Rnw | 6 +-- 31 files changed, 238 insertions(+), 169 deletions(-)
Title: Analyze Nominal Response Data with the Multinomial-Poisson Trick
Description: Dichotomous responses having two categories can be analyzed
with stats::glm() or lme4::glmer() using the family=binomial option.
Unfortunately, polytomous responses with three or more unordered
categories cannot be analyzed similarly because there is no analogous
family=multinomial option. For between-subjects data,
nnet::multinom() can address this need, but it cannot handle random
factors and therefore cannot handle repeated measures. To address this
gap, we transform nominal response data into counts for each categorical
alternative. These counts are then analyzed using (mixed) Poisson regression
as per Baker (1994) <doi:10.2307/2348134>. Omnibus analyses of variance can be
run along with post hoc pairwise comparisons. For users wishing to analyze nominal
responses from surveys or experiments, the functions in this package essentially
act as though stats::glm() or lme4::glmer() provide a family=multinomial option.
Author: Jacob O. Wobbrock [aut, cre, cph]
Maintainer: Jacob O. Wobbrock <wobbrock@uw.edu>
Diff between multpois versions 0.3.2 dated 2025-01-29 and 0.3.3 dated 2025-02-09
DESCRIPTION | 8 ++-- MD5 | 40 +++++++++++------------ NEWS.md | 11 ++++++ R/Anova.mp.R | 26 ++++++++------- R/Data.R | 83 +++++++++++++++++++++++++------------------------ R/glm.mp.R | 13 ++++--- R/glm.mp.con.R | 26 ++++++++------- R/glmer.mp.R | 43 ++++++++++++++----------- R/glmer.mp.con.R | 49 +++++++++++++++------------- inst/WORDLIST | 67 +++++++++++++++++++-------------------- inst/doc/multpois.html | 4 +- man/Anova.mp.Rd | 26 ++++++++------- man/bs2.Rd | 15 ++++---- man/bs3.Rd | 17 +++++----- man/glm.mp.Rd | 13 ++++--- man/glm.mp.con.Rd | 26 ++++++++------- man/glmer.mp.Rd | 43 ++++++++++++++----------- man/glmer.mp.con.Rd | 49 +++++++++++++++------------- man/icecream.Rd | 23 +++++++------ man/ws2.Rd | 13 ++++--- man/ws3.Rd | 15 ++++---- 21 files changed, 330 insertions(+), 280 deletions(-)
Title: Generic PK/PD Simulation Platform CAMPSIS
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on R
packages 'rxode2' and 'mrgsolve'. CAMPSIS provides an abstraction
layer over the underlying processes of writing a PK/PD model,
assembling a custom dataset and running a simulation. CAMPSIS has a
strong dependency to the R package 'campsismod', which allows to
read/write a model from/to files and adapt it further on the fly in
the R environment. Package 'campsis' allows the user to assemble a
dataset in an intuitive manner. Once the user’s dataset is ready, the
package is in charge of preparing the simulation, calling 'rxode2' or
'mrgsolve' (at the user's choice) and returning the results, for the
given model, dataset and desired simulation settings.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsis versions 1.5.5 dated 2024-11-26 and 1.6.0 dated 2025-02-09
campsis-1.5.5/campsis/R/parameter_uncertainty.R |only campsis-1.5.5/campsis/tests/testthat/testParameterUncertainty.R |only campsis-1.6.0/campsis/DESCRIPTION | 24 +- campsis-1.6.0/campsis/MD5 | 48 ++--- campsis-1.6.0/campsis/NAMESPACE | 6 campsis-1.6.0/campsis/NEWS.md | 13 + campsis-1.6.0/campsis/R/simulate.R | 89 ++++++---- campsis-1.6.0/campsis/R/simulate_preprocess.R | 20 +- campsis-1.6.0/campsis/R/simulation_settings.R | 21 +- campsis-1.6.0/campsis/build/vignette.rds |binary campsis-1.6.0/campsis/inst/doc/campsis.html | 2 campsis-1.6.0/campsis/man/Outfun.Rd | 60 +++--- campsis-1.6.0/campsis/man/Settings.Rd | 2 campsis-1.6.0/campsis/man/onCI.Rd | 30 +-- campsis-1.6.0/campsis/man/onCran.Rd | 34 +-- campsis-1.6.0/campsis/man/output_function-class.Rd | 42 ++-- campsis-1.6.0/campsis/man/preprocessOutfun.Rd | 36 ++-- campsis-1.6.0/campsis/man/preprocessReplicates.Rd | 6 campsis-1.6.0/campsis/man/preprocessTablefun.Rd | 36 ++-- campsis-1.6.0/campsis/man/sample.Rd | 6 campsis-1.6.0/campsis/man/simulate.Rd | 16 + campsis-1.6.0/campsis/man/simulation_settings-class.Rd | 2 campsis-1.6.0/campsis/tests/testthat/testSettings.R | 9 + campsis-1.6.0/campsis/tests/testthat/testSimulateReplicates.R | 58 ++++++ campsis-1.6.0/campsis/tests/testthat/testSimulateWeirdCases.R | 39 ++++ campsis-1.6.0/campsis/tests/testthat/testUtils.R | 4 26 files changed, 394 insertions(+), 209 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.6.4 dated 2024-04-26 and 0.7.0 dated 2025-02-09
svrep-0.6.4/svrep/R/rescale_reps.R |only svrep-0.7.0/svrep/DESCRIPTION | 12 svrep-0.7.0/svrep/MD5 | 95 +- svrep-0.7.0/svrep/NAMESPACE | 10 svrep-0.7.0/svrep/NEWS.md | 335 +++++----- svrep-0.7.0/svrep/R/as_bootstrap_design.R | 2 svrep-0.7.0/svrep/R/as_jackknife_design.R | 25 svrep-0.7.0/svrep/R/fays_generalized_replication.R | 46 - svrep-0.7.0/svrep/R/generalized-replication-helpers.R |only svrep-0.7.0/svrep/R/generalized_bootstrap.R | 85 +- svrep-0.7.0/svrep/R/hadamard-matrix-helpers.R |only svrep-0.7.0/svrep/R/make_bootstrap_weights.R | 20 svrep-0.7.0/svrep/R/quadratic_forms.R | 302 ++++++++- svrep-0.7.0/svrep/R/quadratic_forms_of_survey_design_objects.R | 93 ++ svrep-0.7.0/svrep/R/rescale_replicates.R |only svrep-0.7.0/svrep/R/successive-difference-replication.R |only svrep-0.7.0/svrep/R/svrep-package-options.R |only svrep-0.7.0/svrep/R/svrep-package.R | 6 svrep-0.7.0/svrep/R/variance-estimators.R | 73 ++ svrep-0.7.0/svrep/README.md | 5 svrep-0.7.0/svrep/build/partial.rdb |binary svrep-0.7.0/svrep/build/vignette.rds |binary svrep-0.7.0/svrep/inst/CITATION | 6 svrep-0.7.0/svrep/inst/doc/bootstrap-replicates.Rmd | 4 svrep-0.7.0/svrep/inst/doc/bootstrap-replicates.html | 28 svrep-0.7.0/svrep/inst/doc/nonresponse-adjustments.html | 9 svrep-0.7.0/svrep/inst/doc/sample-based-calibration.html | 26 svrep-0.7.0/svrep/inst/doc/two-phase-sampling.Rmd | 2 svrep-0.7.0/svrep/inst/doc/two-phase-sampling.html | 18 svrep-0.7.0/svrep/man/as_bootstrap_design.Rd | 2 svrep-0.7.0/svrep/man/as_fays_gen_rep_design.Rd | 27 svrep-0.7.0/svrep/man/as_gen_boot_design.Rd | 31 svrep-0.7.0/svrep/man/as_random_group_jackknife_design.Rd | 8 svrep-0.7.0/svrep/man/as_sdr_design.Rd |only svrep-0.7.0/svrep/man/assign_hadamard_rows.Rd |only svrep-0.7.0/svrep/man/compute_eigen_decomposition.Rd |only svrep-0.7.0/svrep/man/find_minimum_hadamard_order.Rd |only svrep-0.7.0/svrep/man/get_design_quad_form.Rd | 36 - svrep-0.7.0/svrep/man/make_fays_gen_rep_factors.Rd | 6 svrep-0.7.0/svrep/man/make_gen_boot_factors.Rd | 9 svrep-0.7.0/svrep/man/make_kernel_var_matrix.Rd |only svrep-0.7.0/svrep/man/make_ppswor_approx_matrix.Rd | 22 svrep-0.7.0/svrep/man/make_quad_form_matrix.Rd | 11 svrep-0.7.0/svrep/man/make_rwyb_bootstrap_weights.Rd | 19 svrep-0.7.0/svrep/man/make_sdr_replicate_factors.Rd |only svrep-0.7.0/svrep/man/rescale_replicates.Rd |only svrep-0.7.0/svrep/man/rescale_reps.Rd | 7 svrep-0.7.0/svrep/man/svrep-package-options.Rd |only svrep-0.7.0/svrep/man/variance-estimators.Rd | 76 ++ svrep-0.7.0/svrep/tests/testthat/test-database-backed-designs.R | 33 svrep-0.7.0/svrep/tests/testthat/test-fays-generalized-replication.R | 40 + svrep-0.7.0/svrep/tests/testthat/test-generalized-bootstrap.R | 8 svrep-0.7.0/svrep/tests/testthat/test-quadratic-forms.R | 171 +++++ svrep-0.7.0/svrep/tests/testthat/test-successive-difference-replication.R |only svrep-0.7.0/svrep/vignettes/bootstrap-replicates.Rmd | 4 svrep-0.7.0/svrep/vignettes/two-phase-sampling.Rmd | 2 56 files changed, 1327 insertions(+), 387 deletions(-)
Title: Generate Dockerfiles for 'Shiny' Applications
Description: Automates the creation of Dockerfiles for deploying 'Shiny' applications.
By integrating with 'renv' for dependency management and leveraging Docker-based
solutions, it simplifies the process of containerizing 'Shiny' apps,
ensuring reproducibility and consistency across different environments.
Additionally, it facilitates the setup of CI/CD pipelines for building Docker images
on both GitLab and GitHub.
Author: Vincent Guyader [aut, cre]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between shiny2docker versions 0.0.1 dated 2025-02-04 and 0.0.2 dated 2025-02-09
DESCRIPTION | 10 MD5 | 27 - NAMESPACE | 20 NEWS.md | 7 R/set_github_action.R |only R/set_gitlab_ci.R | 54 +- README.md | 283 +++++++------ build/vignette.rds |binary inst/doc/introduction.R | 83 ++-- inst/doc/introduction.Rmd | 32 + inst/doc/introduction.html | 923 ++++++++++++++++++++++----------------------- inst/docker-build.yml |only inst/gitlab-ci.yml | 2 man/set_github_action.Rd |only man/set_gitlab_ci.Rd | 18 vignettes/introduction.Rmd | 32 + 16 files changed, 803 insertions(+), 688 deletions(-)
Title: KPI Widgets for Quarto Dashboards with Crosstalk
Description: Provides an easy way to create interactive KPI (key performance indicator) widgets for 'Quarto' dashboards using 'Crosstalk'. The package enables visualization of key metrics in a structured format, supporting interactive filtering and linking with other 'Crosstalk'-enabled components. Designed for use in 'Quarto' Dashboards.
Author: Arnold Kakas [aut, cre, cph]
Maintainer: Arnold Kakas <kakasarnold@gmail.com>
Diff between kpiwidget versions 0.1.0 dated 2025-02-04 and 0.1.1 dated 2025-02-09
DESCRIPTION | 10 MD5 | 20 NEWS.md | 2 R/kpiwidget.R | 8 README.md | 135 +- inst/doc/getting_started.R | 18 inst/doc/getting_started.Rmd | 619 ++++++------ inst/doc/getting_started.html | 2022 +++++++++++++++++++++++++++++++++++++++++- inst/htmlwidgets/kpiwidget.js | 17 man/kpiwidget.Rd | 8 vignettes/getting_started.Rmd | 619 ++++++------ 11 files changed, 2739 insertions(+), 739 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-18 0.1.0
2019-08-19 0.0.11
2016-11-07 0.0.10
2016-10-19 0.0.9
2016-07-06 0.0.7
2016-06-13 0.0.5
2016-05-04 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-15 0.1.8
2024-06-04 0.1.7
2022-05-10 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-08 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-21 1.3.1
2018-10-03 1.3.0
2017-12-20 1.2.0
2017-07-20 1.0.1
2016-10-06 0.5.4
2015-12-18 0.5.0
2015-09-15 0.4.7
2014-10-18 0.3.0
2014-10-06 0.2.0
2014-08-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-09 0.1.0
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 13. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond [aut, cre]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.3.9 dated 2025-01-09 and 0.4.0 dated 2025-02-09
DESCRIPTION | 6 ++-- MD5 | 21 ++++++++++------- R/All.R | 63 +++++++++++++++++++++++++++++++++------------------ R/FlowAnalysis.R | 6 ++-- R/GetData.R | 9 ++++--- R/RainfallAnalysis.R | 5 ++-- data/AMSP.csv |only data/NRFAData.csv |only data/QMEDData.csv |only data/ThamesPQ.csv |only data/UKOutline.csv |only man/DDFExtract.Rd | 4 ++- man/FlowSplit.Rd | 4 +-- man/QMED.Rd | 2 - 14 files changed, 74 insertions(+), 46 deletions(-)
Title: Evaluating Bias and Precision in Method Comparison Studies
Description: Evaluate bias and precision in method comparison
studies. One provides measurements for each method and it takes care of
the estimates. Multiple plots to evaluate bias, precision and compare
methods.
Author: Thomas Blomet [aut, cre],
Mingkai Peng [aut],
Patrick Taffe [aut],
Tyler Williamson [aut]
Maintainer: Thomas Blomet <thomas.blomet@alumni.epfl.ch>
Diff between MethodCompare versions 1.0.0 dated 2024-07-30 and 1.1.0 dated 2025-02-09
DESCRIPTION | 6 - MD5 | 48 ++++++----- NAMESPACE | 2 R/aggregate_data.R |only R/agreement0.R | 58 +++++++++---- R/agreement1.R | 58 +++++++++---- R/bias_plot.R | 26 +++--- R/compare_plot.R | 10 +- R/complete_data.R |only R/measure_compare.R | 191 +++++++++++++++++++++------------------------- R/mse.R | 49 ++++++++--- R/pct_agreement0.R | 50 ++++++------ R/pct_agreement1.R | 39 ++++----- R/precision_plot.R | 93 +++++++++++++++------- R/precision_simulation.R | 74 ++++++++++++----- R/sqrt_mse.R | 49 ++++++++--- R/total_bias_plot.R | 34 ++++++-- R/total_bias_simulation.R | 8 - R/var_blup.R | 27 +----- man/agreement0.Rd | 5 - man/agreement1.Rd | 5 - man/measure_compare.Rd | 20 ++-- man/mse.Rd | 5 - man/precision_plot.Rd | 8 + man/sqrt_mse.Rd | 5 - man/total_bias_plot.Rd | 5 - 26 files changed, 533 insertions(+), 342 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert [aut, cre, cph]
,
ZeroMQ authors [aut, cph]
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.9.6 dated 2025-01-10 and 0.9.7 dated 2025-02-09
DESCRIPTION | 8 MD5 | 132 NEWS.md | 5 R/Q.r | 16 R/util.r | 2 README.md | 46 inst/doc/faq.html | 5 inst/doc/technicaldocs.html | 5 inst/doc/userguide.R | 9 inst/doc/userguide.Rmd | 15 inst/doc/userguide.html | 343 - man/Q.Rd | 3 src/libzmq/Makefile.in | 547 +- src/libzmq/aclocal.m4 | 466 -- src/libzmq/builds/Makefile.in | 19 src/libzmq/builds/deprecated-msvc/Makefile.in | 19 src/libzmq/config.log |only src/libzmq/config/compile | 11 src/libzmq/config/config.guess | 112 src/libzmq/config/config.sub | 251 - src/libzmq/config/depcomp | 15 src/libzmq/config/install-sh | 14 src/libzmq/config/ltmain.sh | 735 +-- src/libzmq/config/missing | 75 src/libzmq/config/test-driver | 15 src/libzmq/configure | 5811 +++++++++----------------- src/libzmq/doc/Makefile.in | 28 src/libzmq/doc/zmq.7 |only src/libzmq/doc/zmq_atomic_counter_dec.3 |only src/libzmq/doc/zmq_atomic_counter_destroy.3 |only src/libzmq/doc/zmq_atomic_counter_inc.3 |only src/libzmq/doc/zmq_atomic_counter_new.3 |only src/libzmq/doc/zmq_atomic_counter_set.3 |only src/libzmq/doc/zmq_atomic_counter_value.3 |only src/libzmq/doc/zmq_bind.3 |only src/libzmq/doc/zmq_close.3 |only src/libzmq/doc/zmq_connect.3 |only src/libzmq/doc/zmq_connect_peer.3 |only src/libzmq/doc/zmq_ctx_get.3 |only src/libzmq/doc/zmq_ctx_new.3 |only src/libzmq/doc/zmq_ctx_set.3 |only src/libzmq/doc/zmq_ctx_shutdown.3 |only src/libzmq/doc/zmq_ctx_term.3 |only src/libzmq/doc/zmq_curve.7 |only src/libzmq/doc/zmq_curve_keypair.3 |only src/libzmq/doc/zmq_curve_public.3 |only src/libzmq/doc/zmq_disconnect.3 |only src/libzmq/doc/zmq_errno.3 |only src/libzmq/doc/zmq_getsockopt.3 |only src/libzmq/doc/zmq_gssapi.7 |only src/libzmq/doc/zmq_has.3 |only src/libzmq/doc/zmq_inproc.7 |only src/libzmq/doc/zmq_ipc.7 |only src/libzmq/doc/zmq_msg_close.3 |only src/libzmq/doc/zmq_msg_copy.3 |only src/libzmq/doc/zmq_msg_data.3 |only src/libzmq/doc/zmq_msg_get.3 |only src/libzmq/doc/zmq_msg_gets.3 |only src/libzmq/doc/zmq_msg_init.3 |only src/libzmq/doc/zmq_msg_init_buffer.3 |only src/libzmq/doc/zmq_msg_init_data.3 |only src/libzmq/doc/zmq_msg_init_size.3 |only src/libzmq/doc/zmq_msg_more.3 |only src/libzmq/doc/zmq_msg_move.3 |only src/libzmq/doc/zmq_msg_recv.3 |only src/libzmq/doc/zmq_msg_routing_id.3 |only src/libzmq/doc/zmq_msg_send.3 |only src/libzmq/doc/zmq_msg_set.3 |only src/libzmq/doc/zmq_msg_set_routing_id.3 |only src/libzmq/doc/zmq_msg_size.3 |only src/libzmq/doc/zmq_null.7 |only src/libzmq/doc/zmq_pgm.7 |only src/libzmq/doc/zmq_plain.7 |only src/libzmq/doc/zmq_poll.3 |only src/libzmq/doc/zmq_poller.3 |only src/libzmq/doc/zmq_ppoll.3 |only src/libzmq/doc/zmq_proxy.3 |only src/libzmq/doc/zmq_proxy_steerable.3 |only src/libzmq/doc/zmq_recv.3 |only src/libzmq/doc/zmq_recvmsg.3 |only src/libzmq/doc/zmq_send.3 |only src/libzmq/doc/zmq_send_const.3 |only src/libzmq/doc/zmq_sendmsg.3 |only src/libzmq/doc/zmq_setsockopt.3 |only src/libzmq/doc/zmq_socket.3 |only src/libzmq/doc/zmq_socket_monitor.3 |only src/libzmq/doc/zmq_socket_monitor_versioned.3 |only src/libzmq/doc/zmq_strerror.3 |only src/libzmq/doc/zmq_tcp.7 |only src/libzmq/doc/zmq_timers.3 |only src/libzmq/doc/zmq_tipc.7 |only src/libzmq/doc/zmq_udp.7 |only src/libzmq/doc/zmq_unbind.3 |only src/libzmq/doc/zmq_version.3 |only src/libzmq/doc/zmq_vmci.7 |only src/libzmq/doc/zmq_z85_decode.3 |only src/libzmq/doc/zmq_z85_encode.3 |only src/libzmq/include/zmq_utils.h | 23 src/libzmq/include/zmq_utils.h.orig | 23 src/libzmq/src/platform.hpp.in | 61 src/libzmq/src/zmq_utils.h.orig |only tests/testthat/test-0-util.r | 10 vignettes/userguide.Rmd | 15 103 files changed, 3265 insertions(+), 5574 deletions(-)
Title: The First Software for Quantitative Trajectory Inference
Description: Perform two types of analysis: 1) checking the
goodness-of-fit of tree models to your single-cell gene expression
data; and 2) deciding which tree best fits your data.
Author: Momoko Hayamizu [aut] ,
Kouhei Sutou [aut, cre] ,
Ryohei Suzuki [aut] ,
Hiromi Ishii [aut]
Maintainer: Kouhei Sutou <kou@clear-code.com>
Diff between treefit versions 1.0.2 dated 2022-01-18 and 1.0.3 dated 2025-02-09
DESCRIPTION | 8 MD5 | 18 - NEWS.md | 7 README.md | 43 ++ build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/treefit.html | 555 +++++++++++++++++++++++--------------- inst/doc/working-with-seurat.R | 10 inst/doc/working-with-seurat.html | 394 +++++++++++++++----------- tests/testthat/test-treefit.R | 4 10 files changed, 642 insertions(+), 400 deletions(-)
Title: Produces an Odds Ratio Plot from a Logistic Regression Model
Description: Produces an Odds Ratio (OR) Plot to visualise the result of a
logistic regression analysis.
Provide it with a binomial regression model produced by 'glm()' and it will
convert the estimates to odds ratios with a 95% confidence interval and
plot the results using 'ggplot2'.
Author: Craig Parylo [aut, cre, cph]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between plotor versions 0.5.1 dated 2024-09-27 and 0.5.2 dated 2025-02-09
DESCRIPTION | 14 LICENSE | 4 MD5 | 32 NAMESPACE | 8 NEWS.md | 18 R/plot_or.R | 734 ++++++++------- R/plotor-package.R |only README.md | 251 ++--- build/vignette.rds |binary inst/doc/using_plotor.R | 292 +++--- inst/doc/using_plotor.Rmd | 580 ++++++------ inst/doc/using_plotor.html | 1432 +++++++++++++++---------------- man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-4-1.svg | 1234 +++++++++++++------------- man/plot_or.Rd | 104 +- man/plotor-package.Rd |only man/validate_glm_model.Rd |only tests |only vignettes/using_plotor.Rmd | 580 ++++++------ 19 files changed, 2701 insertions(+), 2582 deletions(-)
Title: Spread the Love for R Packages with Poetry
Description: Uses large language models to create poems about R packages.
Currently contains the roses() function to make "roses are red, ..." style
poems and the prompt() function to only assemble the prompt without submitting
it to the model.
Author: Romain Francois [aut, cre]
Maintainer: Romain Francois <romain@tada.science>
Diff between valentine versions 2024.2.14 dated 2024-02-13 and 2025.2.14 dated 2025-02-09
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NAMESPACE | 4 +++- NEWS.md | 6 +++++- R/roses.R | 53 ++++++++++++++++++++++++++++++----------------------- README.md | 48 +++++++++++++++++++++++++++++++++++------------- man/roses.Rd | 21 +++++++++++++++++---- 7 files changed, 103 insertions(+), 55 deletions(-)
Title: Create Details HTML Tag for Markdown and Package Documentation
Description: Create a details HTML tag around R objects to place
in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between details versions 0.3.0 dated 2022-03-27 and 0.4.0 dated 2025-02-09
details-0.3.0/details/inst/doc/tests_and_coverage.R |only details-0.3.0/details/inst/doc/tests_and_coverage.Rmd |only details-0.3.0/details/inst/doc/tests_and_coverage.html |only details-0.3.0/details/man/pipe.Rd |only details-0.3.0/details/vignettes/tests_and_coverage.Rmd |only details-0.4.0/details/DESCRIPTION | 14 details-0.4.0/details/LICENSE | 4 details-0.4.0/details/MD5 | 103 - details-0.4.0/details/NAMESPACE | 84 - details-0.4.0/details/NEWS.md | 60 details-0.4.0/details/R/build.R | 102 - details-0.4.0/details/R/details.R | 242 +-- details-0.4.0/details/R/device.R | 170 +- details-0.4.0/details/R/engine.R | 192 +- details-0.4.0/details/R/fold.R | 126 - details-0.4.0/details/R/parts.R | 54 details-0.4.0/details/R/print.R | 185 +- details-0.4.0/details/R/read.R | 81 - details-0.4.0/details/R/use.R | 192 +- details-0.4.0/details/R/utils.R | 14 details-0.4.0/details/README.md | 587 ++++---- details-0.4.0/details/build/vignette.rds |binary details-0.4.0/details/inst/doc/custom.R | 118 - details-0.4.0/details/inst/doc/custom.Rmd | 196 +- details-0.4.0/details/inst/doc/custom.html | 904 ++++++++----- details-0.4.0/details/inst/doc/documentation.R | 12 details-0.4.0/details/inst/doc/documentation.Rmd | 80 - details-0.4.0/details/inst/doc/documentation.html | 362 ++++- details-0.4.0/details/inst/doc/engine.R | 50 details-0.4.0/details/inst/doc/engine.Rmd | 344 ++--- details-0.4.0/details/inst/doc/engine.html | 976 ++++++++------ details-0.4.0/details/inst/doc/objects.R | 75 - details-0.4.0/details/inst/doc/objects.Rmd | 149 +- details-0.4.0/details/inst/doc/objects.html | 1139 +++++++++-------- details-0.4.0/details/inst/doc/sessioninfo.R | 36 details-0.4.0/details/inst/doc/sessioninfo.Rmd | 66 details-0.4.0/details/inst/doc/sessioninfo.html | 673 ++++++---- details-0.4.0/details/man/details.Rd | 216 +-- details-0.4.0/details/man/fold.Rd | 96 - details-0.4.0/details/man/macros/fold.Rd | 6 details-0.4.0/details/man/use_details.Rd | 62 details-0.4.0/details/tests/README.md | 202 +-- details-0.4.0/details/tests/testthat.R | 8 details-0.4.0/details/tests/testthat/helpers.R | 120 - details-0.4.0/details/tests/testthat/test-basic.R | 96 - details-0.4.0/details/tests/testthat/test-collapse.R | 52 details-0.4.0/details/tests/testthat/test-device.R | 96 - details-0.4.0/details/tests/testthat/test-print.R | 64 details-0.4.0/details/tests/testthat/test-use.R | 214 +-- details-0.4.0/details/tests/testthat/test-utils.R | 82 - details-0.4.0/details/vignettes/custom.Rmd | 196 +- details-0.4.0/details/vignettes/documentation.Rmd | 80 - details-0.4.0/details/vignettes/engine.Rmd | 344 ++--- details-0.4.0/details/vignettes/objects.Rmd | 149 +- details-0.4.0/details/vignettes/sessioninfo.Rmd | 66 55 files changed, 5276 insertions(+), 4263 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-16 2.0.0
2023-01-20 1.1.2
2023-01-18 1.1.1
2022-11-28 1.1.0
2022-11-17 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-17 0.15.3
2024-04-25 0.15.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-07 0.1.1
2023-03-08 0.1.0