Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/ [...truncated...]
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang [...truncated...]
Maintainer: Xiaolei Liu <xll198708@gmail.com>
Diff between rMVP versions 1.3.0 dated 2024-12-17 and 1.3.5 dated 2025-01-09
DESCRIPTION | 8 MD5 | 26 +- R/MVP.FarmCPU.r | 17 - R/MVP.GLM.r | 9 R/MVP.MLM.r | 9 R/MVP.r | 7 R/RcppExports.R | 20 - man/MVP.GLM.Rd | 3 man/MVP.MLM.Rd | 3 src/RcppExports.cpp | 59 +---- src/assoc.cpp | 61 ++--- src/impute.cpp | 32 +- src/kinship.cpp | 558 +++++++++++++++++++++++++--------------------------- src/rMVP.h | 1 14 files changed, 396 insertions(+), 417 deletions(-)
Title: Pattern Causality Algorithm
Description: A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.
Author: Stavros Stavroglou [aut] ,
Athanasios Pantelous [aut] ,
Hui Wang [aut, cre]
Maintainer: Hui Wang <huiw1128@gmail.com>
Diff between patterncausality versions 0.1.3 dated 2024-09-24 and 0.2.0 dated 2025-01-09
patterncausality-0.1.3/patterncausality/R/convertSignatureToValueOutOfSample.R |only patterncausality-0.1.3/patterncausality/R/pastNNsInfo_Lite.R |only patterncausality-0.1.3/patterncausality/R/plotEffect.R |only patterncausality-0.1.3/patterncausality/R/plotMatrix.R |only patterncausality-0.1.3/patterncausality/R/plotState.R |only patterncausality-0.1.3/patterncausality/man/convertSignatureToValue.Rd |only patterncausality-0.1.3/patterncausality/man/convertSignatureToValueOutOfSample.Rd |only patterncausality-0.1.3/patterncausality/man/dataBank.Rd |only patterncausality-0.1.3/patterncausality/man/distanceMatrix.Rd |only patterncausality-0.1.3/patterncausality/man/distanceVector.Rd |only patterncausality-0.1.3/patterncausality/man/fillPCMatrix.Rd |only patterncausality-0.1.3/patterncausality/man/firstCausalityPoint.Rd |only patterncausality-0.1.3/patterncausality/man/firstCausalityPointCHECK.Rd |only patterncausality-0.1.3/patterncausality/man/metricDistance.Rd |only patterncausality-0.1.3/patterncausality/man/natureOfCausality.Rd |only patterncausality-0.1.3/patterncausality/man/pastNNsInfo.Rd |only patterncausality-0.1.3/patterncausality/man/pastNNsInfo_Lite.Rd |only patterncausality-0.1.3/patterncausality/man/patternHashing.Rd |only patterncausality-0.1.3/patterncausality/man/patternSpace.Rd |only patterncausality-0.1.3/patterncausality/man/plotCV.Rd |only patterncausality-0.1.3/patterncausality/man/plotEffect.Rd |only patterncausality-0.1.3/patterncausality/man/plotMatrix.Rd |only patterncausality-0.1.3/patterncausality/man/plotState.Rd |only patterncausality-0.1.3/patterncausality/man/predictionY.Rd |only patterncausality-0.1.3/patterncausality/man/projectedNNsInfo.Rd |only patterncausality-0.1.3/patterncausality/man/projectedNNsInfo_Lite.Rd |only patterncausality-0.1.3/patterncausality/man/signatureSpace.Rd |only patterncausality-0.1.3/patterncausality/vignettes/djsmatrix.rds |only patterncausality-0.2.0/patterncausality/DESCRIPTION | 16 patterncausality-0.2.0/patterncausality/LICENSE | 19 patterncausality-0.2.0/patterncausality/MD5 | 201 ++-- patterncausality-0.2.0/patterncausality/NAMESPACE | 79 + patterncausality-0.2.0/patterncausality/NEWS.md |only patterncausality-0.2.0/patterncausality/R/PC.Mk.II.Full.Details.R | 274 +++--- patterncausality-0.2.0/patterncausality/R/PC.Mk.II.Lightweight.R | 190 ++-- patterncausality-0.2.0/patterncausality/R/classes.R |only patterncausality-0.2.0/patterncausality/R/convertSignatureToValue.R | 66 - patterncausality-0.2.0/patterncausality/R/data.R | 48 - patterncausality-0.2.0/patterncausality/R/dataBank.R | 124 +- patterncausality-0.2.0/patterncausality/R/distanceMatrix.R | 116 +- patterncausality-0.2.0/patterncausality/R/fillPCMatrix.R | 136 +- patterncausality-0.2.0/patterncausality/R/firstCausalityPoint.R | 110 +- patterncausality-0.2.0/patterncausality/R/firstCausalityPointCHECK.R | 95 +- patterncausality-0.2.0/patterncausality/R/geom-rtile.R |only patterncausality-0.2.0/patterncausality/R/interfaces.R |only patterncausality-0.2.0/patterncausality/R/natureOfCausality.R | 255 ++--- patterncausality-0.2.0/patterncausality/R/optimalParametersSearch.R | 215 +++- patterncausality-0.2.0/patterncausality/R/pastNNsInfo.R | 119 +- patterncausality-0.2.0/patterncausality/R/patternHashing.R | 87 + patterncausality-0.2.0/patterncausality/R/patternSpace.R | 83 + patterncausality-0.2.0/patterncausality/R/pattern_utils.R |only patterncausality-0.2.0/patterncausality/R/pcAccuracy.R | 146 ++- patterncausality-0.2.0/patterncausality/R/pcCV.R | 336 +++++-- patterncausality-0.2.0/patterncausality/R/pcCrossMatrix.R |only patterncausality-0.2.0/patterncausality/R/pcEffect.R | 142 ++- patterncausality-0.2.0/patterncausality/R/pcMatrix.R | 199 +++- patterncausality-0.2.0/patterncausality/R/pc_accuracy_methods.R |only patterncausality-0.2.0/patterncausality/R/pc_check.R |only patterncausality-0.2.0/patterncausality/R/pc_full_details_utils.R |only patterncausality-0.2.0/patterncausality/R/pc_lightweight_utils.R |only patterncausality-0.2.0/patterncausality/R/pc_nature.R |only patterncausality-0.2.0/patterncausality/R/pc_neighbors.R |only patterncausality-0.2.0/patterncausality/R/pc_params.R |only patterncausality-0.2.0/patterncausality/R/pc_point.R |only patterncausality-0.2.0/patterncausality/R/pc_strength.R |only patterncausality-0.2.0/patterncausality/R/predictionY.R | 128 +- patterncausality-0.2.0/patterncausality/R/projectedNNsInfo.R | 151 +-- patterncausality-0.2.0/patterncausality/R/signatureSpace.R | 79 + patterncausality-0.2.0/patterncausality/R/stateSpace.R | 89 + patterncausality-0.2.0/patterncausality/README.md | 120 +- patterncausality-0.2.0/patterncausality/build/partial.rdb |only patterncausality-0.2.0/patterncausality/build/vignette.rds |binary patterncausality-0.2.0/patterncausality/inst/CITATION |only patterncausality-0.2.0/patterncausality/inst/CONTRIBUTING.md |only patterncausality-0.2.0/patterncausality/inst/doc/advanced.R |only patterncausality-0.2.0/patterncausality/inst/doc/advanced.Rmd |only patterncausality-0.2.0/patterncausality/inst/doc/advanced.html |only patterncausality-0.2.0/patterncausality/inst/doc/dynamic.R |only patterncausality-0.2.0/patterncausality/inst/doc/dynamic.Rmd |only patterncausality-0.2.0/patterncausality/inst/doc/dynamic.html |only patterncausality-0.2.0/patterncausality/inst/doc/matrix.R | 72 + patterncausality-0.2.0/patterncausality/inst/doc/matrix.Rmd | 145 ++- patterncausality-0.2.0/patterncausality/inst/doc/matrix.html | 456 ++++++---- patterncausality-0.2.0/patterncausality/inst/doc/parallel.R |only patterncausality-0.2.0/patterncausality/inst/doc/parallel.Rmd |only patterncausality-0.2.0/patterncausality/inst/doc/parallel.html |only patterncausality-0.2.0/patterncausality/inst/doc/patterncausality.R | 41 patterncausality-0.2.0/patterncausality/inst/doc/patterncausality.Rmd | 82 + patterncausality-0.2.0/patterncausality/inst/doc/patterncausality.html | 138 +-- patterncausality-0.2.0/patterncausality/inst/doc/series.R | 59 + patterncausality-0.2.0/patterncausality/inst/doc/series.Rmd | 112 ++ patterncausality-0.2.0/patterncausality/inst/doc/series.html | 340 ++++++- patterncausality-0.2.0/patterncausality/inst/examples |only patterncausality-0.2.0/patterncausality/man/AUCO.Rd | 16 patterncausality-0.2.0/patterncausality/man/DJS.Rd | 16 patterncausality-0.2.0/patterncausality/man/climate_indices.Rd | 23 patterncausality-0.2.0/patterncausality/man/distanceMetric.Rd |only patterncausality-0.2.0/patterncausality/man/optimalParametersSearch.Rd | 66 + patterncausality-0.2.0/patterncausality/man/pcAccuracy.Rd | 58 + patterncausality-0.2.0/patterncausality/man/pcCrossMatrix.Rd |only patterncausality-0.2.0/patterncausality/man/pcCrossValidation.Rd | 121 ++ patterncausality-0.2.0/patterncausality/man/pcEffect.Rd | 53 + patterncausality-0.2.0/patterncausality/man/pcFullDetails.Rd | 72 + patterncausality-0.2.0/patterncausality/man/pcLightweight.Rd | 72 + patterncausality-0.2.0/patterncausality/man/pcMatrix.Rd | 62 + patterncausality-0.2.0/patterncausality/man/pc_cv.Rd |only patterncausality-0.2.0/patterncausality/man/pc_effect.Rd |only patterncausality-0.2.0/patterncausality/man/pc_matrix.Rd |only patterncausality-0.2.0/patterncausality/man/pc_params.Rd |only patterncausality-0.2.0/patterncausality/man/plot.pc_cv.Rd |only patterncausality-0.2.0/patterncausality/man/plot.pc_effect.Rd |only patterncausality-0.2.0/patterncausality/man/plot.pc_fit.Rd |only patterncausality-0.2.0/patterncausality/man/plot.pc_matrix.Rd |only patterncausality-0.2.0/patterncausality/man/plot.pc_state.Rd |only patterncausality-0.2.0/patterncausality/man/plot_causality.Rd |only patterncausality-0.2.0/patterncausality/man/plot_causality.pc_full_details.Rd |only patterncausality-0.2.0/patterncausality/man/plot_components.Rd |only patterncausality-0.2.0/patterncausality/man/plot_components.pc_fit.Rd |only patterncausality-0.2.0/patterncausality/man/plot_total.Rd |only patterncausality-0.2.0/patterncausality/man/plot_total.pc_fit.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_accuracy.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_cv.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_effect.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_fit.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_matrix.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_params.Rd |only patterncausality-0.2.0/patterncausality/man/print.pc_state.Rd |only patterncausality-0.2.0/patterncausality/man/print.summary.pc_accuracy.Rd |only patterncausality-0.2.0/patterncausality/man/stateSpace.Rd | 50 - patterncausality-0.2.0/patterncausality/man/stateSpaceMethod.Rd |only patterncausality-0.2.0/patterncausality/man/summary.pc_accuracy.Rd |only 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patterncausality-0.2.0/patterncausality/vignettes/patterncausality.Rmd | 82 + patterncausality-0.2.0/patterncausality/vignettes/series.Rmd | 112 ++ 147 files changed, 4097 insertions(+), 1919 deletions(-)
More information about patterncausality at CRAN
Permanent link
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple
rectangular data. The 'rtables' package provides a framework for
declaring complex multi-level tabulations and then applying them to
data. This framework models both tabulation and the resulting tables
as hierarchical, tree-like objects which support sibling sub-tables,
arbitrary splitting or grouping of data in row and column dimensions,
cells containing multiple values, and the concept of contextual
summary computations. A convenient pipe-able interface is provided for
declaring table layouts and the corresponding computations, and then
applying them to data.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [ctb],
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables versions 0.6.10 dated 2024-09-20 and 0.6.11 dated 2025-01-09
rtables-0.6.10/rtables/R/tt_as_flextable.R |only rtables-0.6.10/rtables/man/export_as_docx.Rd |only rtables-0.6.10/rtables/man/figures/logo.png |only rtables-0.6.10/rtables/man/tt_to_flextable.Rd |only rtables-0.6.10/rtables/tests/testthat/test-tt_as_flextable.R |only rtables-0.6.11/rtables/DESCRIPTION | 43 rtables-0.6.11/rtables/MD5 | 111 +- rtables-0.6.11/rtables/NAMESPACE | 13 rtables-0.6.11/rtables/NEWS.md | 20 rtables-0.6.11/rtables/R/00tabletrees.R | 3 rtables-0.6.11/rtables/R/colby_constructors.R | 13 rtables-0.6.11/rtables/R/tree_accessors.R | 28 rtables-0.6.11/rtables/R/tt_afun_utils.R | 36 rtables-0.6.11/rtables/R/tt_as_df.R | 516 ++++++---- rtables-0.6.11/rtables/R/tt_export.R | 183 --- rtables-0.6.11/rtables/R/utils.R | 6 rtables-0.6.11/rtables/README.md | 2 rtables-0.6.11/rtables/build/vignette.rds |binary rtables-0.6.11/rtables/inst/WORDLIST | 4 rtables-0.6.11/rtables/inst/doc/advanced_usage.html | 22 rtables-0.6.11/rtables/inst/doc/ard_how_to.R |only rtables-0.6.11/rtables/inst/doc/ard_how_to.Rmd |only rtables-0.6.11/rtables/inst/doc/ard_how_to.html |only rtables-0.6.11/rtables/inst/doc/baseline.html | 13 rtables-0.6.11/rtables/inst/doc/clinical_trials.html | 59 - rtables-0.6.11/rtables/inst/doc/col_counts.R | 28 rtables-0.6.11/rtables/inst/doc/col_counts.html | 25 rtables-0.6.11/rtables/inst/doc/custom_appearance.html | 34 rtables-0.6.11/rtables/inst/doc/example_analysis_coxreg.html | 18 rtables-0.6.11/rtables/inst/doc/exploratory_analysis.R | 8 rtables-0.6.11/rtables/inst/doc/exploratory_analysis.Rmd | 2 rtables-0.6.11/rtables/inst/doc/exploratory_analysis.html | 32 rtables-0.6.11/rtables/inst/doc/format_precedence.html | 23 rtables-0.6.11/rtables/inst/doc/introspecting_tables.html | 25 rtables-0.6.11/rtables/inst/doc/manual_table_construction.html | 13 rtables-0.6.11/rtables/inst/doc/rtables.html | 26 rtables-0.6.11/rtables/inst/doc/sorting_pruning.html | 38 rtables-0.6.11/rtables/inst/doc/split_functions.html | 19 rtables-0.6.11/rtables/inst/doc/subsetting_tables.html | 28 rtables-0.6.11/rtables/inst/doc/tabulation_concepts.html | 28 rtables-0.6.11/rtables/inst/doc/tabulation_dplyr.Rmd | 6 rtables-0.6.11/rtables/inst/doc/tabulation_dplyr.html | 28 rtables-0.6.11/rtables/inst/doc/title_footer.html | 18 rtables-0.6.11/rtables/man/CellValue.Rd | 6 rtables-0.6.11/rtables/man/data.frame_export.Rd | 71 - rtables-0.6.11/rtables/man/figures/logo.svg |only rtables-0.6.11/rtables/man/in_rows.Rd | 13 rtables-0.6.11/rtables/man/int_methods.Rd | 15 rtables-0.6.11/rtables/man/rcell.Rd | 12 rtables-0.6.11/rtables/man/rtables-package.Rd | 8 rtables-0.6.11/rtables/tests/testthat.R | 7 rtables-0.6.11/rtables/tests/testthat/test-binding.R | 5 rtables-0.6.11/rtables/tests/testthat/test-colby_constructors.R |only rtables-0.6.11/rtables/tests/testthat/test-default_split_funs.R | 3 rtables-0.6.11/rtables/tests/testthat/test-exporters.R | 42 rtables-0.6.11/rtables/tests/testthat/test-lyt-tabulation.R | 3 rtables-0.6.11/rtables/tests/testthat/test-printing.R | 21 rtables-0.6.11/rtables/tests/testthat/test-result_data_frame.R | 304 +++++ rtables-0.6.11/rtables/tests/testthat/test-subset-access.R | 3 rtables-0.6.11/rtables/vignettes/ard_how_to.Rmd |only rtables-0.6.11/rtables/vignettes/exploratory_analysis.Rmd | 2 rtables-0.6.11/rtables/vignettes/tabulation_dplyr.Rmd | 6 62 files changed, 987 insertions(+), 1005 deletions(-)
Title: Miscellaneous Descriptive Functions
Description: Helper functions for descriptive tasks such as making print-friendly bivariate
tables, sample size flow counts, and visualizing sample distributions. Also
contains 'R' approximations of some common 'SAS' and 'Stata' functions such
as 'PROC MEANS' from 'SAS' and 'ladder', 'gladder', and 'pwcorr' from 'Stata'.
Author: Craig McGowan [aut, cre]
Maintainer: Craig McGowan <mcgowan.cj@gmail.com>
Diff between describedata versions 0.1.0 dated 2019-08-02 and 0.1.1 dated 2025-01-09
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 5 ++++- README.md | 25 +++++++++++++++++++------ tests/testthat/test-bivariate_compare.R | 10 +++++----- 5 files changed, 37 insertions(+), 20 deletions(-)
Title: 'C++' Standard Template Library Containers
Description: Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps,
unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.
Author: Christian Dueben [aut, cre]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>
Diff between cppcontainers versions 1.0.1 dated 2024-11-14 and 1.0.3 dated 2025-01-09
DESCRIPTION | 6 +-- MD5 | 13 ++++---- NEWS.md |only README.md | 72 +++++++++++++++++++++++++-------------------- inst/doc/introduction.Rmd | 13 ++++---- inst/doc/introduction.html | 21 ++++++------- src/to_r.cpp | 4 +- vignettes/introduction.Rmd | 13 ++++---- 8 files changed, 78 insertions(+), 64 deletions(-)
Title: Bootstrap for Regression Effect Sizes
Description: Generates nonparametric bootstrap confidence intervals
(Efron and Tibshirani, 1993: <doi:10.1201/9780429246593>)
for standardized regression coefficients (beta) and other effect sizes,
including multiple correlation, semipartial correlations,
improvement in R-squared, squared partial correlations,
and differences in standardized regression coefficients,
for models fitted by lm().
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaNB versions 1.0.4 dated 2024-04-14 and 1.0.5 dated 2025-01-09
DESCRIPTION | 10 ++--- LICENSE | 2 - MD5 | 48 ++++++++++++------------- NEWS.md | 6 +++ R/betaNB-beta-nb.R | 6 ++- R/betaNB-ci.R | 6 --- R/betaNB-delta-r-sq-nb.R | 4 +- R/betaNB-diff-beta-nb.R | 4 +- R/betaNB-nb.R | 6 +++ R/betaNB-p-cor-nb.R | 4 +- R/betaNB-r-sq-nb.R | 4 +- R/betaNB-s-cor-nb.R | 4 +- R/processLM-process-lm-dot.R | 6 --- build/partial.rdb |binary data/nas1982.rda |binary inst/CITATION | 3 - man/BetaNB.Rd | 2 + man/betaNB-package.Rd | 2 - tests/testthat/test-betaNB-beta-nb-est.R | 1 tests/testthat/test-betaNB-delta-r-sq-nb-est.R | 2 + tests/testthat/test-betaNB-diff-beta-nb-est.R | 2 + tests/testthat/test-betaNB-nb.R | 1 tests/testthat/test-betaNB-p-cor-nb-est.R | 2 + tests/testthat/test-betaNB-r-sq-nb-est.R | 2 + tests/testthat/test-betaNB-s-cor-nb-est.R | 2 + 25 files changed, 72 insertions(+), 57 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 1.0.0 dated 2024-11-26 and 1.0.1 dated 2025-01-09
DESCRIPTION | 27 MD5 | 182 +- NAMESPACE | 10 NEWS.md | 30 R/check_if_installed.R | 2 R/clean_names.R | 4 R/clean_parameters.R | 13 R/compute_variances.R | 34 R/display.R | 3 R/ellipsis_info.R | 2 R/export_table.R | 17 R/find_formula.R | 39 R/find_parameters.R | 8 R/find_parameters_bayesian.R | 1 R/find_parameters_other.R | 12 R/find_predictors.R | 6 R/find_response.R | 2 R/find_statistic.R | 5 R/find_terms.R | 15 R/find_variables.R | 2 R/format_ci.R | 2 R/format_message.R | 2 R/format_number.R | 5 R/format_table.R | 26 R/format_value.R | 4 R/get_auxiliary.R | 2 R/get_data.R | 14 R/get_datagrid.R | 93 + R/get_deviance.R | 2 R/get_df.R | 1 R/get_modelmatrix.R | 1 R/get_parameters.R | 30 R/get_parameters_bayesian.R | 3 R/get_parameters_emmeans.R | 2 R/get_parameters_gam.R | 2 R/get_parameters_htest.R | 5 R/get_parameters_mfx.R | 2 R/get_parameters_mixed.R | 2 R/get_parameters_others.R | 14 R/get_parameters_zi.R | 3 R/get_predicted.R | 45 R/get_predicted_args.R | 12 R/get_predicted_bayesian.R | 8 R/get_predicted_ci.R | 15 R/get_predicted_ci_zeroinflated.R | 10 R/get_predicted_gam.R | 2 R/get_predicted_methods.R | 4 R/get_predicted_mixed.R | 5 R/get_predicted_ordinal.R | 4 R/get_predicted_other.R | 1 R/get_predicted_se.R | 3 R/get_priors.R | 7 R/get_residuals.R | 7 R/get_sigma.R | 19 R/get_statistic.R | 46 R/get_varcov.R | 15 R/get_weights.R | 1 R/has_intercept.R | 10 R/helper_functions.R | 12 R/is_model.R | 5 R/is_model_supported.R | 4 R/link_function.R | 32 R/link_inverse.R | 23 R/model_info.R | 45 R/n_obs.R | 6 R/n_parameters.R | 5 R/standardize_names.R | 8 R/utilities.R | 3 R/utils_get_data.R | 24 README.md | 69 - inst/WORDLIST | 1 inst/doc/display.html | 220 +-- man/find_formula.Rd | 2 man/format_table.Rd | 3 man/get_datagrid.Rd | 15 man/get_datagrid.emmGrid.Rd |only man/get_predicted.Rd | 4 tests/testthat/_snaps/export_table.md | 1690 +++++++++++++------------- tests/testthat/_snaps/format_table.md | 32 tests/testthat/_snaps/windows/format_table.md | 56 tests/testthat/test-BayesFactorBF.R | 3 tests/testthat/test-afex_aov.R | 2 tests/testthat/test-brms_von_mises.R |only tests/testthat/test-fixest.R | 11 tests/testthat/test-format_table.R | 9 tests/testthat/test-geeglm.R | 6 tests/testthat/test-get_datagrid.R | 22 tests/testthat/test-get_modelmatrix.R | 4 tests/testthat/test-get_predicted-iv.R | 1 tests/testthat/test-get_predicted.R | 42 tests/testthat/test-marginaleffects.R | 6 tests/testthat/test-mipo.R | 3 tests/testthat/test-r2_nakagawa_negbin.R | 1 93 files changed, 1599 insertions(+), 1613 deletions(-)
Title: Regional Spatial Modeling with Continuous Borders
Description: Automatically creates separate regression models for different spatial
regions. The prediction surface is smoothed using a regional border smoothing
method. If regional models are continuous, the resulting prediction surface is
continuous across the spatial dimensions, even at region borders. Methodology
is described in Wagstaff and Bean (2023) <doi:10.32614/RJ-2023-004>.
Author: Jadon Wagstaff [aut, cre],
Brennan Bean [aut]
Maintainer: Jadon Wagstaff <jadonw@gmail.com>
Diff between remap versions 0.3.1 dated 2023-06-14 and 0.3.2 dated 2025-01-09
remap-0.3.1/remap/data/utsnow.rda |only remap-0.3.1/remap/data/utws.rda |only remap-0.3.2/remap/DESCRIPTION | 8 remap-0.3.2/remap/MD5 | 44 ++-- remap-0.3.2/remap/NEWS.md | 14 + remap-0.3.2/remap/R/data.R | 24 ++ remap-0.3.2/remap/R/redist.R | 97 +++++++--- remap-0.3.2/remap/R/remap.R | 163 +++++++++++------- remap-0.3.2/remap/R/utils.R | 6 remap-0.3.2/remap/build/vignette.rds |binary remap-0.3.2/remap/data/utsnow.R |only remap-0.3.2/remap/data/utws.R |only remap-0.3.2/remap/inst/doc/Introduction_to_remap.R | 9 remap-0.3.2/remap/inst/doc/Introduction_to_remap.Rmd | 9 remap-0.3.2/remap/inst/doc/Introduction_to_remap.html | 78 ++++---- remap-0.3.2/remap/inst/extdata |only remap-0.3.2/remap/man/predict.remap.Rd | 12 - remap-0.3.2/remap/man/redist.Rd | 8 remap-0.3.2/remap/man/remap.Rd | 18 + remap-0.3.2/remap/man/utsnow.Rd | 12 + remap-0.3.2/remap/man/utws.Rd | 8 remap-0.3.2/remap/vignettes/Introduction_to_remap.Rmd | 9 22 files changed, 332 insertions(+), 187 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning
Description: Functions for parameter descriptions and operations in
black-box optimization, tuning and machine learning. Parameters can be
described (type, constraints, defaults, etc.), combined to parameter
sets and can in general be programmed on. A useful OptPath object
(archive) to log function evaluations is also provided.
Author: Bernd Bischl [aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Jakob Bossek [aut],
Daniel Horn [aut],
Karin Schork [ctb],
Pascal Kerschke [aut],
Martin Binder [ctb, cre]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between ParamHelpers versions 1.14.1 dated 2022-07-04 and 1.14.2 dated 2025-01-09
DESCRIPTION | 37 +++--- MD5 | 154 ++++++++++++------------- NAMESPACE | 5 NEWS.md | 6 R/OptPath_plotYTraces.R | 6 R/ParamSet.R | 3 R/convertParamSetToIrace.R | 7 - R/evaluateParamExpressions.R | 4 R/generateDesign.R | 16 +- R/getBounds.R | 4 R/getParamNr.R | 2 R/getParamSet.R | 2 R/getRequiredParamNames.R | 2 R/getRequirements.R | 2 R/hasExpression.R | 2 R/renderOptPathPlot.R | 2 R/renderOptPathPlot_helpers.R | 2 R/renderOptPathPlot_workers.R | 48 +++---- R/zzz.R | 1 man/OptPath.Rd | 2 man/addOptPathEl.Rd | 2 man/evaluateParamExpressions.Rd | 4 man/getOptPathBestIndex.Rd | 2 man/getOptPathDOB.Rd | 2 man/getOptPathEOL.Rd | 2 man/getOptPathEl.Rd | 2 man/getOptPathErrorMessages.Rd | 2 man/getOptPathExecTimes.Rd | 2 man/getOptPathLength.Rd | 2 man/getOptPathParetoFront.Rd | 2 man/getOptPathX.Rd | 2 man/getOptPathY.Rd | 2 man/getParamNr.Rd | 2 man/getParamSet.Rd | 2 man/getRequirements.Rd | 2 man/hasExpression.Rd | 2 man/sampleValue.Rd | 2 man/sampleValues.Rd | 2 man/setOptPathElDOB.Rd | 2 man/setOptPathElEOL.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_LearnerParam.R | 2 tests/testthat/test_OptPath.R | 2 tests/testthat/test_Param.R | 2 tests/testthat/test_ParamSet.R | 6 tests/testthat/test_cnames.R | 2 tests/testthat/test_convertDiscrete.R | 3 tests/testthat/test_convertParamSetToIrace.R | 18 +- tests/testthat/test_dfRowToList.R | 3 tests/testthat/test_dropParams.R | 2 tests/testthat/test_evaluateParamExpressions.R | 2 tests/testthat/test_filterParams.R | 2 tests/testthat/test_forbidden.R | 3 tests/testthat/test_generateDesign.R | 2 tests/testthat/test_generateDesignOfDefaults.R | 11 - tests/testthat/test_generateGridDesign.R | 2 tests/testthat/test_generateRandomDesign.R | 2 tests/testthat/test_getDefaults.R | 2 tests/testthat/test_getParamNr.R | 2 tests/testthat/test_getParamTypeCounts.R | 2 tests/testthat/test_getParamTypes.R | 2 tests/testthat/test_getRequiredParamNames.R | 2 tests/testthat/test_getRequirements.R | 2 tests/testthat/test_hasExpression.R | 2 tests/testthat/test_hasFiniteBoxConstraints.R | 2 tests/testthat/test_hasIsType.R | 2 tests/testthat/test_hasRequires.R | 2 tests/testthat/test_isFeasible.R | 2 tests/testthat/test_isSpecialValue.R | 2 tests/testthat/test_isVector.R | 2 tests/testthat/test_paramValueToString.R | 2 tests/testthat/test_plotEAF.R | 4 tests/testthat/test_plotYTrace.R | 12 - tests/testthat/test_renderOptPathPlot.R | 17 +- tests/testthat/test_repairPoint.R | 2 tests/testthat/test_sample.R | 2 tests/testthat/test_trafo.R | 2 tests/testthat/test_updateParVals.R | 4 78 files changed, 216 insertions(+), 268 deletions(-)
Title: Mediation with External Summary Statistic Information
Description: Fits the MESSI, hard constraint, and unconstrained models in Boss
et al. (2023) <doi:10.48550/arXiv.2306.17347> for mediation analyses with external
summary-level information on the total effect.
Author: Jonathan Boss [aut],
Bhramar Mukherjee [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between messi versions 0.1.1 dated 2023-07-13 and 0.1.2 dated 2025-01-09
DESCRIPTION | 17 - MD5 | 8 R/main_function.R | 506 +++++++++++++++++++++++++++++++----------------------- README.md | 12 - man/messi.Rd | 14 - 5 files changed, 323 insertions(+), 234 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>; L [...truncated...]
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Jan Linnenbrink [aut],
Fabian Schumacher [aut],
Philipp Otto [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Jakub Nowosad [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 1.0.2 dated 2024-06-14 and 1.0.3 dated 2025-01-09
DESCRIPTION | 16 ++++--- MD5 | 79 +++++++++++++++++++------------------- NEWS.md | 3 + R/CreateSpacetimeFolds.R | 8 ++- R/aoa.R | 27 ++++++++---- R/bss.R | 20 ++++----- R/errorProfiles.R | 2 R/ffs.R | 20 ++++----- R/geodist.R | 31 ++++++++------ R/global_validation.R | 4 - R/knndm.R | 37 +++++++++-------- R/nndm.R | 8 +-- R/trainDI.R | 36 +++++++++++------ README.md | 4 + build/partial.rdb |binary build/vignette.rds |binary data/cookfarm.rda |binary data/splotdata.rda |binary inst/doc/cast01-CAST-intro.R | 13 +++++- inst/doc/cast01-CAST-intro.Rmd | 19 ++++++--- inst/doc/cast01-CAST-intro.html | 68 ++++++++++++++++++-------------- inst/doc/cast02-plotgeodist.Rmd | 4 + inst/doc/cast02-plotgeodist.html | 22 +++++----- inst/doc/cast03-CV.html | 6 +- inst/doc/cast04-AOA-tutorial.Rmd | 2 inst/doc/cast04-AOA-tutorial.html | 20 ++++----- inst/doc/cast05-parallel.html | 4 - man/CreateSpacetimeFolds.Rd | 8 ++- man/aoa.Rd | 12 +++++ man/bss.Rd | 20 ++++----- man/errorProfiles.Rd | 2 man/ffs.Rd | 20 ++++----- man/figures/logo.png |only man/geodist.Rd | 5 +- man/global_validation.Rd | 4 - man/knndm.Rd | 5 +- man/nndm.Rd | 7 ++- man/trainDI.Rd | 8 +++ vignettes/cast01-CAST-intro.Rmd | 19 ++++++--- vignettes/cast02-plotgeodist.Rmd | 4 + vignettes/cast04-AOA-tutorial.Rmd | 2 41 files changed, 338 insertions(+), 231 deletions(-)
Title: Corbae-Ouliaris Frequency Domain Filtering
Description: Corbae-Ouliaris frequency domain filtering. According to
Corbae and Ouliaris (2006) <doi:10.1017/CBO9781139164863.008>,
this is a solution for extracting cycles from time series, like
business cycles etc. when filtering. This method is valid for both
stationary and non-stationary time series.
Author: Christos Adam [aut, cre]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between corbouli versions 0.1.3 dated 2024-11-20 and 0.1.4 dated 2025-01-09
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ README.md | 37 +++++++++++++++++++++++-------------- inst/doc/Introduction.Rmd | 11 +++++++---- inst/doc/Introduction.html | 7 ++++--- man/corbae_ouliaris.Rd | 6 +++--- man/dftse.Rd | 6 +++--- vignettes/Introduction.Rmd | 11 +++++++---- 9 files changed, 67 insertions(+), 44 deletions(-)
Title: Combinatorial Efficient Global Optimization
Description: Model building, surrogate model
based optimization and Efficient Global Optimization in combinatorial
or mixed search spaces.
Author: Martin Zaefferer [aut, cre]
Maintainer: Martin Zaefferer <mzaefferer@gmail.com>
Diff between CEGO versions 2.4.3 dated 2024-01-27 and 2.4.4 dated 2025-01-09
DESCRIPTION | 20 ++++++++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 1 - NEWS | 19 ++++++++++++------- R/cegoPackage.R | 4 ++-- R/optimEA.R | 34 +++++++++++++++++----------------- man/mutationSelfAdapt.Rd | 9 ++++----- man/optimEA.Rd | 2 +- man/selfAdapt.Rd | 3 --- 9 files changed, 56 insertions(+), 52 deletions(-)
Title: Air Quality Evaluation
Description: Developed for use by those tasked with the routine detection,
characterisation and quantification of discrete changes in air quality
time-series, such as identifying the impacts of air quality policy
interventions. The main functions use signal isolation then
break-point/segment (BP/S) methods based on 'strucchange' and 'segmented'
methods to detect and quantify change events (Ropkins & Tate, 2021,
<doi:10.1016/j.scitotenv.2020.142374>).
Author: Karl Ropkins [aut, cre] ,
Anthony Walker [aut] ,
James Tate [aut]
Maintainer: Karl Ropkins <k.ropkins@its.leeds.ac.uk>
Diff between AQEval versions 0.5.7 dated 2024-04-03 and 0.6.0 dated 2025-01-09
AQEval-0.5.7/AQEval/man/AQEval.Rd |only AQEval-0.6.0/AQEval/DESCRIPTION | 35 +++---- AQEval-0.6.0/AQEval/MD5 | 42 ++++---- AQEval-0.6.0/AQEval/NAMESPACE | 5 + AQEval-0.6.0/AQEval/NEWS.md | 5 + AQEval-0.6.0/AQEval/R/AQEval-package.R | 20 +++- AQEval-0.6.0/AQEval/R/AQEval.data.R | 4 AQEval-0.6.0/AQEval/R/aqe.generics.R |only AQEval-0.6.0/AQEval/R/aqe.misc.R | 3 AQEval-0.6.0/AQEval/R/calculate.stats.R | 139 ++++++++++++++++++++++++++--- AQEval-0.6.0/AQEval/R/find.breaks.R | 8 + AQEval-0.6.0/AQEval/R/find.near.R | 48 +++++++--- AQEval-0.6.0/AQEval/R/isolate.signal.R | 18 ++- AQEval-0.6.0/AQEval/R/quantify.breaks.R | 12 +- AQEval-0.6.0/AQEval/build/partial.rdb |binary AQEval-0.6.0/AQEval/inst/CITATION | 4 AQEval-0.6.0/AQEval/man/AQEval-package.Rd |only AQEval-0.6.0/AQEval/man/AQEval.data.Rd | 4 AQEval-0.6.0/AQEval/man/aqeval.generics.Rd |only AQEval-0.6.0/AQEval/man/calculate.stats.Rd | 7 + AQEval-0.6.0/AQEval/man/find.breaks.Rd | 8 + AQEval-0.6.0/AQEval/man/find.near.Rd | 2 AQEval-0.6.0/AQEval/man/isolate.signal.Rd | 18 ++- AQEval-0.6.0/AQEval/man/quantify.breaks.Rd | 12 +- 24 files changed, 293 insertions(+), 101 deletions(-)
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 0.3.8 dated 2024-11-17 and 0.3.9 dated 2025-01-09
DESCRIPTION | 6 MD5 | 34 ++- R/All.R | 134 ++++++--------- R/FlowAnalysis.R | 195 +++++++++++++++++++++- R/GISfuncs.R | 3 R/GetData.R | 408 ++++++++++++++++++++++++++++++++++++++--------- R/RainfallAnalysis.R |only man/AMplot.Rd | 14 + man/AnnualStat.Rd | 8 man/Bootstrap.Rd | 6 man/DDFExtract.Rd |only man/DesHydro.Rd | 12 - man/FlowDurationCurve.Rd | 14 + man/FlowSplit.Rd |only man/GetDataEA_QH.Rd | 24 +- man/GetDataEA_Rain.Rd | 17 + man/GetDataNRFA.Rd | 2 man/GetDataSEPA_QH.Rd |only man/GetDataSEPA_Rain.Rd | 13 - man/HydroPlot.Rd | 10 - 20 files changed, 675 insertions(+), 225 deletions(-)
Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette.
'tinycodet' primarily focuses on 4 aspects.
1) Safer decimal (in)equality testing,
standard-evaluated alternatives to with() and aes(),
and other functions for safer coding.
2) A new package import system,
that attempts to combine the benefits of using a package without attaching it,
with the benefits of attaching a package.
3) Extending the string manipulation capabilities of the 'stringi' R package.
4) Reducing repetitive code.
Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between tinycodet versions 0.5.3 dated 2024-07-21 and 0.5.4 dated 2025-01-09
tinycodet-0.5.3/tinycodet/src/rcpp_stri_locate_ith.cpp |only tinycodet-0.5.4/tinycodet/DESCRIPTION | 6 tinycodet-0.5.4/tinycodet/MD5 | 47 +++---- tinycodet-0.5.4/tinycodet/NEWS.md | 4 tinycodet-0.5.4/tinycodet/R/RcppExports.R | 24 --- tinycodet-0.5.4/tinycodet/R/aaa0_tinycodet_help.R | 2 tinycodet-0.5.4/tinycodet/R/aaa1_tinycodet_safer.R | 4 tinycodet-0.5.4/tinycodet/R/aaa3_tinycodet_strings.R | 21 +-- tinycodet-0.5.4/tinycodet/R/str_search.R | 13 +- tinycodet-0.5.4/tinycodet/R/str_subset_ops.R | 26 ++-- tinycodet-0.5.4/tinycodet/R/strcut.R | 10 - tinycodet-0.5.4/tinycodet/R/stri_locate_ith.R | 12 - tinycodet-0.5.4/tinycodet/R/tinycodetWrappers.R | 15 ++ tinycodet-0.5.4/tinycodet/inst/examples/str_subset_ops.R | 8 - tinycodet-0.5.4/tinycodet/inst/tinytest/strings/test-stri_locate_ith_general.R | 27 +++- tinycodet-0.5.4/tinycodet/inst/tinytest/strings/test-stri_locate_ith_internal.R | 18 -- tinycodet-0.5.4/tinycodet/inst/tinytest/test-internal.R | 9 - tinycodet-0.5.4/tinycodet/man/aaa0_tinycodet_help.Rd | 2 tinycodet-0.5.4/tinycodet/man/aaa1_tinycodet_safer.Rd | 4 tinycodet-0.5.4/tinycodet/man/aaa3_tinycodet_strings.Rd | 21 +-- tinycodet-0.5.4/tinycodet/man/str_search.Rd | 3 tinycodet-0.5.4/tinycodet/man/str_subset_ops.Rd | 38 +++--- tinycodet-0.5.4/tinycodet/man/stri_locate_ith.Rd | 2 tinycodet-0.5.4/tinycodet/src/C_do_stri_locate_ith0.c |only tinycodet-0.5.4/tinycodet/src/C_do_stri_locate_ith1.c |only tinycodet-0.5.4/tinycodet/src/RcppExports.cpp | 62 +--------- 26 files changed, 157 insertions(+), 221 deletions(-)
Title: Sun Position and Daylight Calculations
Description: Compute the position of the sun, and local solar time using Meeus'
formulae. Compute day and/or night length using different
twilight definitions or arbitrary sun elevation angles. This package is
part of the 'r4photobiology' suite, Aphalo, P. J. (2015)
<doi:10.19232/uv4pb.2015.1.14>. Algorithms from Meeus (1998, ISBN:0943396611).
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between SunCalcMeeus versions 0.1.1 dated 2024-12-11 and 0.1.2 dated 2025-01-09
DESCRIPTION | 9 +-- MD5 | 19 ++++--- NAMESPACE | 1 NEWS.md | 21 ++++++-- R/sun_irrad_et.r |only README.md | 16 ++++-- inst/doc/userguide-0-r4p-introduction.html | 2 inst/doc/userguide-1-astronomy.html | 54 ++++++++++---------- man/irrad_extraterrestrial.Rd |only tests/testthat/test_irrad_extraterrestrial.R |only tests/testthat/test_sun_times.R | 70 +++++++++++++++++++++++---- tests/testthat/test_utilities.R | 47 ++++++++++++------ 12 files changed, 168 insertions(+), 71 deletions(-)
Title: Efficient Estimation Under Staggered Treatment Timing
Description: Efficiently estimates treatment effects in settings with randomized staggered rollouts, using tools
proposed by Roth and Sant'Anna (2023) <doi:10.48550/arXiv.2102.01291>.
Author: Jonathan Roth [aut],
Pedro H.C. Sant'Anna [aut, cre]
Maintainer: Pedro H.C. Sant'Anna <pedrohcgs@gmail.com>
Diff between staggered versions 1.2.1 dated 2024-09-24 and 1.2.2 dated 2025-01-09
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/balance_checks.R | 10 ++++++++++ R/compute_efficient_estimator_and_se.R | 32 +++++++++++++++++++++++++++++++- R/create_A0_lists.R | 4 ++-- README.md | 10 +++++----- build/partial.rdb |binary man/balance_checks.Rd | 10 ++++++++++ man/staggered.Rd | 10 ++++++++++ man/staggered_cs.Rd | 10 ++++++++++ man/staggered_sa.Rd | 10 ++++++++++ 11 files changed, 102 insertions(+), 22 deletions(-)
Title: Manipulate 'JDemetra+' Workspaces
Description: Set of tools to manipulate the 'JDemetra+' workspaces.
Based on the 'RJDemetra' package (which interfaces with version 2 of the 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks).
This package provides access to additional workspace manipulation functions such as metadata manipulation, raw paths and wrangling of several workspaces simultaneously.
These additional functionalities are useful as part of a CVS data production chain.
Author: Tanguy Barthelemy [aut, cre, art],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjdworkspace versions 1.1.7 dated 2024-05-21 and 1.1.8 dated 2025-01-09
DESCRIPTION | 11 +++--- MD5 | 27 ++++++++--------- NEWS.md | 31 ++++++++++++++++++- R/manip_sa_item.R | 15 +++++---- R/metadata.R | 24 ++++++++------- R/replace_series.R | 73 +++++++++++++++++++++++++++------------------- R/transfer_series.R | 12 +++---- R/update_path.R | 30 ++++++------------ R/utils.R | 2 - README.md | 48 +++++++++++++----------------- man/figures/logo.png |binary man/figures/logo.svg |only man/get_comment.Rd | 3 + man/manipulate_sa_item.Rd | 11 ++++-- man/replace_series.Rd | 4 +- 15 files changed, 168 insertions(+), 123 deletions(-)
Title: Enhanced 'PAM50' Subtyping of Breast Cancer
Description: Accurate classification of breast cancer tumors based on gene expression data is not a trivial task, and it lacks standard practices.The 'PAM50' classifier, which uses 50 gene centroid correlation distances to classify tumors, faces challenges with balancing estrogen receptor (ER) status and gene centering. The 'PCAPAM50' package leverages principal component analysis and iterative 'PAM50' calls to create a gene expression-based ER-balanced subset for gene centering, avoiding the use of protein expression-based ER data resulting into an enhanced Breast Cancer subtyping.
Author: Praveen-Kumar Raj-Kumar [aut, cre, cph],
Boyi Chen [aut],
Ming-Wen Hu [aut],
Tyler Hohenstein [aut],
Jianfang Liu [aut],
Craig D. Shriver [aut],
Xiaoying Lin [aut, cph],
Hai Hu [aut, cph]
Maintainer: Praveen-Kumar Raj-Kumar <p.rajkumar@wriwindber.org>
Diff between PCAPAM50 versions 1.0.2 dated 2024-11-23 and 1.0.3 dated 2025-01-09
PCAPAM50-1.0.2/PCAPAM50/vignettes/Plots/PC1_misclassified_cases.png |only PCAPAM50-1.0.3/PCAPAM50/DESCRIPTION | 6 - PCAPAM50-1.0.3/PCAPAM50/MD5 | 26 ++-- PCAPAM50-1.0.3/PCAPAM50/NEWS.md | 11 +- PCAPAM50-1.0.3/PCAPAM50/R/functions_PCA-PAM50.R | 55 +++++++--- PCAPAM50-1.0.3/PCAPAM50/build/vignette.rds |binary PCAPAM50-1.0.3/PCAPAM50/inst/PAM50/bioclassifier_R/subtypePrediction_distributed_PNmodified.R | 6 - PCAPAM50-1.0.3/PCAPAM50/inst/doc/PCAPAM50_vignette.R | 10 - PCAPAM50-1.0.3/PCAPAM50/inst/doc/PCAPAM50_vignette.Rmd | 12 +- PCAPAM50-1.0.3/PCAPAM50/inst/doc/PCAPAM50_vignette.html | 14 +- PCAPAM50-1.0.3/PCAPAM50/vignettes/PCAPAM50_vignette.Rmd | 12 +- PCAPAM50-1.0.3/PCAPAM50/vignettes/Plots/Ihc.Mdns_PAM50_normalized_heatmap.pdf |binary PCAPAM50-1.0.3/PCAPAM50/vignettes/Plots/PC1_discordance_cases.png |only PCAPAM50-1.0.3/PCAPAM50/vignettes/Plots/PC1ihc.Mdns_PAM50_normalized_heatmap.pdf |binary PCAPAM50-1.0.3/PCAPAM50/vignettes/Plots/PCAPAM50.Mdns_PAM50_normalized_heatmap.pdf |binary 15 files changed, 96 insertions(+), 56 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.10 dated 2024-12-13 and 5.2.11 dated 2025-01-09
DESCRIPTION | 6 MD5 | 522 +++---- NAMESPACE | 1094 ++++++++-------- R/apis.R | 68 - R/audio.R | 368 ++--- R/cache.R | 326 ++-- R/chatgpt.R | 937 ++++++------- R/checks.R | 334 ++-- R/clusters.R | 694 +++++----- R/colour_palettes.R | 394 ++--- R/confidence.R | 172 +- R/correlations.R | 1116 ++++++++-------- R/cran.R | 176 +- R/credentials.R | 196 +- R/crossbrand.R | 682 +++++----- R/crossbrand2.R | 936 ++++++------- R/crosstab.R | 202 +-- R/currency.R | 146 +- R/dalex_explainers.R | 436 +++--- R/dataframe_str.R | 462 +++--- R/datasets.R | 160 +- R/dim_reduction.R | 336 ++--- R/distribution.R | 950 +++++++------- R/dropbox.R | 246 +-- R/encoding.R | 44 R/facebook.R | 1528 +++++++++++----------- R/family.R | 104 - R/forecasting.R | 710 +++++----- R/frequencies.R | 1724 ++++++++++++------------- R/gemini.R | 166 +- R/geodata.R | 524 +++---- R/google_analytics.R | 130 - R/google_sheets.R | 258 +-- R/google_trends.R | 380 ++--- R/hubspot.R | 398 ++--- R/hubspot_f1.R | 502 +++---- R/lares.R | 306 ++-- R/lasso.R | 264 +-- R/linkedin.R | 114 - R/logo.R | 98 - R/mails.R | 190 +- R/maze.R | 668 ++++----- R/missings.R | 260 +-- R/model_functions.R | 1956 ++++++++++++++--------------- R/model_metrics.R | 1232 +++++++++--------- R/model_plots.R | 2928 +++++++++++++++++++++---------------------- R/model_predict.R | 328 ++-- R/model_preprocessing.R | 490 +++---- R/numble.R | 54 R/object_detection.R | 120 - R/onehotencoding.R | 1052 +++++++-------- R/other_functions.R | 2262 ++++++++++++++++----------------- R/other_plots.R | 548 ++++---- R/outliers.R | 358 ++--- R/plot_scales.R | 224 +-- R/querieSQL.R | 64 R/robyn.R | 1304 ++++++++++--------- R/rtistry.R | 96 - R/scrabble.R | 996 +++++++------- R/shapley.R | 538 ++++---- R/shiny.R | 2 R/slack.R | 92 - R/statusbar.R | 158 +- R/stocks.R | 3016 ++++++++++++++++++++++----------------------- R/sudoku.R | 178 +- R/surveys.R | 84 - R/text_mining.R | 1124 ++++++++-------- R/theme_lares.R | 820 ++++++------ R/tictoc.R | 188 +- R/trees.R | 298 ++-- R/twitter.R | 56 R/typeform.R | 98 - R/update.R | 74 - R/wordle.R | 596 ++++---- R/wrangling.R | 1745 +++++++++++++------------- R/x2y.R | 736 +++++----- R/zzz.R | 198 +- README.md | 146 +- inst/_pkgdown.yml | 20 inst/docs/config.yml | 28 inst/docs/stocksReport.Rmd | 160 +- man/ROC.Rd | 132 - man/autoline.Rd | 154 +- man/balance_data.Rd | 126 - man/bind_files.Rd | 114 - man/bring_api.Rd | 154 +- man/cache_write.Rd | 160 +- man/categ_reducer.Rd | 172 +- man/checks.Rd | 256 +-- man/chr2num.Rd | 142 +- man/ci_lower.Rd | 74 - man/ci_var.Rd | 72 - man/clean_text.Rd | 214 +-- man/clusterKmeans.Rd | 236 +-- man/clusterOptimalK.Rd | 116 - man/clusterVisualK.Rd | 86 - man/conf_mat.Rd | 144 +- man/corr.Rd | 208 +-- man/corr_cross.Rd | 218 +-- man/corr_var.Rd | 230 +-- man/cran_logs.Rd | 74 - man/crosstab.Rd | 146 +- man/dalex_local.Rd | 64 man/dalex_residuals.Rd | 48 man/dalex_variable.Rd | 88 - man/date_cuts.Rd | 102 - man/date_feats.Rd | 206 +-- man/db_download.Rd | 212 +-- man/db_upload.Rd | 174 +- man/df_str.Rd | 122 - man/dfr.Rd | 70 - man/dft.Rd | 98 - man/dist2d.Rd | 70 - man/distr.Rd | 268 +-- man/errors.Rd | 132 - man/etf_sector.Rd | 68 - man/export_plot.Rd | 180 +- man/export_results.Rd | 196 +- man/fb_accounts.Rd | 144 +- man/fb_ads.Rd | 174 +- man/fb_creatives.Rd | 134 - man/fb_insights.Rd | 294 ++-- man/fb_process.Rd | 114 - man/fb_report_check.Rd | 150 +- man/fb_rf.Rd | 306 ++-- man/fb_token.Rd | 116 - man/file_name.Rd | 156 +- man/filesGD.Rd | 86 - man/files_functions.Rd | 148 +- man/filterdata.Rd | 246 +-- man/font_exists.Rd | 138 +- man/forecast_arima.Rd | 162 +- man/formatColoured.Rd | 144 +- man/format_string.Rd | 324 ++-- man/freqs.Rd | 272 ++-- man/freqs_df.Rd | 178 +- man/freqs_list.Rd | 258 +-- man/freqs_plot.Rd | 180 +- man/gain_lift.Rd | 142 +- man/gemini_ask.Rd | 199 +- man/get_credentials.Rd | 268 +-- man/get_currency.Rd | 88 - man/get_mp3.Rd | 174 +- man/get_tweets.Rd | 68 - man/gg_fill_customs.Rd | 162 +- man/glued.Rd | 192 +- man/google_sheets.Rd | 174 +- man/google_trends.Rd | 106 - man/gpt_ask.Rd | 353 ++--- man/gpt_prompter.Rd | 276 ++-- man/grepl_letters.Rd | 68 - man/grepm.Rd | 158 +- man/h2o_automl.Rd | 426 +++--- man/h2o_explainer.Rd | 140 +- man/h2o_results.Rd | 142 +- man/h2o_selectmodel.Rd | 154 +- man/h2o_shap.Rd | 154 +- man/haveInternet.Rd | 118 - man/holidays.Rd | 176 +- man/image_metadata.Rd | 112 - man/importxlsx.Rd | 114 - man/impute.Rd | 140 +- man/install_recommended.Rd | 38 man/ip_data.Rd | 156 +- man/iter_seeds.Rd | 84 - man/json2vector.Rd | 122 - man/lares-exports.Rd | 18 man/lares.Rd | 44 man/lares_logo.Rd | 36 man/lares_pal.Rd | 114 - man/lasso_vars.Rd | 188 +- man/left_right.Rd | 106 - man/li_auth.Rd | 88 - man/li_profile.Rd | 78 - man/list_cats.Rd | 134 - man/listfiles.Rd | 152 +- man/loglossBinary.Rd | 58 man/mail_send.Rd | 218 +-- man/markdown2df.Rd | 120 - man/maze_solve.Rd | 182 +- man/missingness.Rd | 140 +- man/model_metrics.Rd | 248 +-- man/model_preprocess.Rd | 230 +-- man/move_files.Rd | 120 - man/mplot_conf.Rd | 180 +- man/mplot_cuts.Rd | 134 - man/mplot_cuts_error.Rd | 128 - man/mplot_density.Rd | 138 +- man/mplot_full.Rd | 188 +- man/mplot_gain.Rd | 192 +- man/mplot_importance.Rd | 164 +- man/mplot_lineal.Rd | 118 - man/mplot_metrics.Rd | 104 - man/mplot_response.Rd | 186 +- man/mplot_roc.Rd | 174 +- man/mplot_splits.Rd | 158 +- man/mplot_topcats.Rd | 98 - man/msplit.Rd | 172 +- man/myip.Rd | 116 - man/ngrams.Rd | 98 - man/noPlot.Rd | 82 - man/normalize.Rd | 105 - man/num_abbr.Rd | 114 - man/ohe_commas.Rd | 140 +- man/ohse.Rd | 248 +-- man/outlier_turkey.Rd | 60 man/outlier_zscore.Rd | 68 - man/outlier_zscore_plot.Rd | 86 - man/plot_cats.Rd | 72 - man/plot_chord.Rd | 110 - man/plot_df.Rd | 72 - man/plot_nums.Rd | 80 - man/plot_palette.Rd | 82 - man/plot_survey.Rd | 74 - man/plot_timeline.Rd | 182 +- man/prophesize.Rd | 104 - man/quants.Rd | 132 - man/queryDB.Rd | 72 - man/queryGA.Rd | 160 +- man/quiet.Rd | 118 - man/read.file.Rd | 128 - man/reduce_pca.Rd | 128 - man/reduce_tsne.Rd | 102 - man/remove_stopwords.Rd | 82 - man/replaceall.Rd | 182 +- man/replacefactor.Rd | 114 - man/robyn_crossmmm.Rd | 250 +-- man/robyn_hypsbuilder.Rd | 124 - man/robyn_modelselector.Rd | 168 +- man/robyn_performance.Rd | 133 + man/rtistry_sphere.Rd | 36 man/scale_x_comma.Rd | 208 +-- man/scrabble.Rd | 318 ++-- man/sentimentBreakdown.Rd | 110 - man/seq_surnames.Rd | 60 man/shap_var.Rd | 118 - man/slackSend.Rd | 124 - man/spread_list.Rd | 82 - man/statusbar.Rd | 182 +- man/stocks_hist.Rd | 170 +- man/stocks_report.Rd | 334 ++-- man/sudoku_solver.Rd | 96 - man/target_set.Rd | 56 man/textCloud.Rd | 112 - man/textFeats.Rd | 134 - man/textTokenizer.Rd | 204 +-- man/theme_lares.Rd | 210 +-- man/tic.Rd | 200 +- man/topics_rake.Rd | 72 - man/tree_var.Rd | 254 +-- man/trim_mp3.Rd | 72 - man/try_require.Rd | 148 +- man/updateLares.Rd | 130 - man/vector2text.Rd | 132 - man/warnifnot.Rd | 118 - man/weighted_value.Rd | 102 - man/what_size.Rd | 146 +- man/winsorize.Rd | 64 man/wordle.Rd | 156 +- man/x2y.Rd | 256 +-- man/year_month.Rd | 110 - man/zerovar.Rd | 98 - 262 files changed, 35077 insertions(+), 34977 deletions(-)
Title: Statistical Modelling for Plant Size Distributions
Description: Developed for the following tasks. 1 ) Computing the probability density function,
cumulative distribution function, random generation, and estimating the parameters
of the eleven mixture models. 2 ) Point estimation of the parameters of two -
parameter Weibull distribution using twelve methods and three - parameter Weibull
distribution using nine methods. 3 ) The Bayesian inference for the three -
parameter Weibull distribution. 4 ) Estimating parameters of the three - parameter
Birnbaum - Saunders, generalized exponential, and Weibull distributions fitted to
grouped data using three methods including approximated maximum likelihood,
expectation maximization, and maximum likelihood. 5 ) Estimating the parameters
of the gamma, log-normal, and Weibull mixture models fitted to the grouped data
through the EM algorithm, 6 ) Estimating parameters of the nonlinear height curve
fitted to the height - diameter observation, 7 ) Estimating parameters, computing
probability density function, cum [...truncated...]
Author: Mahdi Teimouri [aut, cre, cph, ctb]
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>
Diff between ForestFit versions 2.2.3 dated 2023-02-28 and 2.4.3 dated 2025-01-09
DESCRIPTION | 19 ++++--- MD5 | 33 +++++++----- NAMESPACE | 37 +++++++++++--- R/ForestFit.R | 120 +++++++++++++++++++++++++++++++++++++---------- man/djsb.Rd | 11 ++-- man/djsbb.Rd |only man/fitJSB.Rd | 2 man/fitWeibull.Rd | 2 man/fitbayesJSB.Rd | 2 man/fitbayesWeibull.Rd | 2 man/fitgrouped1.Rd | 2 man/fitgrouped2.Rd | 2 man/fitgsm.Rd | 2 man/fitmixture.Rd | 2 man/fitmixturegrouped.Rd | 2 man/rjsb.Rd | 3 - man/rjsbb.Rd |only man/rmixture.Rd | 9 +++ man/rmvnorm.Rd |only 19 files changed, 180 insertions(+), 70 deletions(-)
Title: Stratified Evaluation of Subgroup Classification Accuracy
Description: Enables simultaneous statistical inference for the accuracy of multiple classifiers in multiple subgroups (strata). For instance, allows to perform multiple comparisons in diagnostic accuracy studies with co-primary endpoints sensitivity and specificity (Westphal M, Zapf A. Statistical inference for diagnostic test accuracy studies with multiple comparisons. Statistical Methods in Medical Research. 2024;0(0). <doi:10.1177/09622802241236933>).
Author: Max Westphal [aut, cre]
Maintainer: Max Westphal <dev@maxwestphal.io>
Diff between cases versions 0.1.1 dated 2023-05-18 and 0.2.0 dated 2025-01-09
cases-0.1.1/cases/R/test_bootstrap.R |only cases-0.1.1/cases/man/complete_results.Rd |only cases-0.2.0/cases/DESCRIPTION | 21 cases-0.2.0/cases/MD5 | 133 +- cases-0.2.0/cases/NAMESPACE | 2 cases-0.2.0/cases/NEWS.md |only cases-0.2.0/cases/R/argmin.R | 26 cases-0.2.0/cases/R/bootstrap_functions.R |only cases-0.2.0/cases/R/cases.R | 29 cases-0.2.0/cases/R/categorize.R | 64 - cases-0.2.0/cases/R/compare.R | 44 cases-0.2.0/cases/R/cormat.R | 30 cases-0.2.0/cases/R/data.R | 8 cases-0.2.0/cases/R/define_contrast.R | 57 cases-0.2.0/cases/R/draw_data_lfc.R | 104 - cases-0.2.0/cases/R/draw_data_prb.R | 37 cases-0.2.0/cases/R/draw_data_roc.R | 167 +- cases-0.2.0/cases/R/evaluate.R | 119 - cases-0.2.0/cases/R/evaluate_bonferroni.R | 75 - cases-0.2.0/cases/R/evaluate_bootstrap.R | 54 cases-0.2.0/cases/R/evaluate_maxt.R | 132 +- cases-0.2.0/cases/R/evaluate_mbeta.R | 174 +- cases-0.2.0/cases/R/evaluate_none.R | 94 - cases-0.2.0/cases/R/generate_instance.R | 167 +- cases-0.2.0/cases/R/global_variables.R |only cases-0.2.0/cases/R/helpers.R | 38 cases-0.2.0/cases/R/moments.R | 68 - cases-0.2.0/cases/R/preproc.R | 22 cases-0.2.0/cases/R/print.R | 19 cases-0.2.0/cases/R/process_instance.R | 101 - cases-0.2.0/cases/R/stats.R | 58 cases-0.2.0/cases/R/stats2results.R | 136 +- cases-0.2.0/cases/R/transformation.R | 63 - cases-0.2.0/cases/R/visualize.R | 131 +- cases-0.2.0/cases/README.md | 40 cases-0.2.0/cases/build/vignette.rds |binary cases-0.2.0/cases/inst/doc/example_wdbc.R | 76 - cases-0.2.0/cases/inst/doc/example_wdbc.Rmd | 80 - cases-0.2.0/cases/inst/doc/example_wdbc.html | 870 +++++++------- cases-0.2.0/cases/inst/doc/package_overview.R | 48 cases-0.2.0/cases/inst/doc/package_overview.Rmd | 50 cases-0.2.0/cases/inst/doc/package_overview.html | 781 +++++------- cases-0.2.0/cases/man/cases.Rd | 56 cases-0.2.0/cases/man/categorize.Rd | 88 - cases-0.2.0/cases/man/compare.Rd | 72 - cases-0.2.0/cases/man/cormat_ar1.Rd | 45 cases-0.2.0/cases/man/cormat_equi.Rd | 45 cases-0.2.0/cases/man/data_wdbc.Rd | 66 - cases-0.2.0/cases/man/define_contrast.Rd | 20 cases-0.2.0/cases/man/draw_data.Rd | 82 - cases-0.2.0/cases/man/draw_data_lfc.Rd | 115 - cases-0.2.0/cases/man/draw_data_prb.Rd | 42 cases-0.2.0/cases/man/draw_data_roc.Rd | 121 - cases-0.2.0/cases/man/evaluate.Rd | 49 cases-0.2.0/cases/man/generate_instance_lfc.Rd | 130 +- cases-0.2.0/cases/man/generate_instance_roc.Rd | 136 +- cases-0.2.0/cases/man/pipe.Rd | 40 cases-0.2.0/cases/man/process_instance.Rd | 127 +- cases-0.2.0/cases/man/visualize.Rd | 12 cases-0.2.0/cases/tests/testthat/test-argmin.R | 4 cases-0.2.0/cases/tests/testthat/test-categorize.R | 7 cases-0.2.0/cases/tests/testthat/test-compare.R | 24 cases-0.2.0/cases/tests/testthat/test-cormat.R | 14 cases-0.2.0/cases/tests/testthat/test-define_contrast.R |only cases-0.2.0/cases/tests/testthat/test-evaluate.R | 154 ++ cases-0.2.0/cases/tests/testthat/test-generate_data_lfc.R | 3 cases-0.2.0/cases/tests/testthat/test-generate_data_roc.R | 3 cases-0.2.0/cases/tests/testthat/test-sim_functions.R |only cases-0.2.0/cases/tests/testthat/test-visualize.R | 16 cases-0.2.0/cases/vignettes/example_wdbc.Rmd | 80 - cases-0.2.0/cases/vignettes/package_overview.Rmd | 50 71 files changed, 3018 insertions(+), 2701 deletions(-)
Title: A Two-Stage Estimation Approach to Cox Regression Using M-Spline
Function
Description: Implements a two-stage estimation approach for Cox
regression using five-parameter M-spline functions to model the baseline hazard. It allows
for flexible hazard shapes and model selection based on log-likelihood criteria.
Author: Ren Teranishi [aut, cre]
Maintainer: Ren Teranishi <ren.teranishi1227@gmail.com>
Diff between splineCox versions 0.0.1 dated 2024-12-18 and 0.0.2 dated 2025-01-09
DESCRIPTION | 6 +- MD5 | 20 +++---- NEWS.md | 6 ++ R/splineCoxreg1.R | 74 +++++++++++++++++------------ R/splineCoxreg2.R | 31 ++++++------ inst/doc/splineCox-introduction.R | 18 ++++++- inst/doc/splineCox-introduction.Rmd | 43 +++++++++++++---- inst/doc/splineCox-introduction.html | 88 +++++++++++++++++++++++++++++------ man/splineCox.reg1.Rd | 14 +++-- man/splineCox.reg2.Rd | 16 +++--- vignettes/splineCox-introduction.Rmd | 43 +++++++++++++---- 11 files changed, 253 insertions(+), 106 deletions(-)
Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>, the beta method based on signal detection theory by Li and Chen (2024) <DOI:10.1111/bmsp.12371> and Q-matrix validation based on relative fit index by Chen et la. (2013) <DOI:10.1111/j.1745-3984.2012.00185.x>. Different research methods and iterative procedures during Q-matrix validating are avai [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 1.1.0 dated 2025-01-07 and 1.1.1 dated 2025-01-09
Qval-1.1.0/Qval/tests/test.JSS.R |only Qval-1.1.1/Qval/DESCRIPTION | 8 ++-- Qval-1.1.1/Qval/MD5 | 25 ++++++------ Qval-1.1.1/Qval/NEWS.md | 5 ++ Qval-1.1.1/Qval/R/GDI.R | 60 ++++++++++++++++++++++-------- Qval-1.1.1/Qval/R/Hull.R | 68 +++++++++++++++++----------------- Qval-1.1.1/Qval/R/MLR-B.R | 20 +++++----- Qval-1.1.1/Qval/R/Wald.R | 18 +++++---- Qval-1.1.1/Qval/R/beta.R | 75 +++++++++++++++++++++++++++----------- Qval-1.1.1/Qval/R/validation.R | 30 +++++++++++++-- Qval-1.1.1/Qval/man/validation.Rd | 10 +++-- Qval-1.1.1/Qval/tests/building.R | 1 Qval-1.1.1/Qval/tests/demo.R | 8 ++-- Qval-1.1.1/Qval/tests/repeat.R | 9 ++-- 14 files changed, 216 insertions(+), 121 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear
programming (MILP). It provides a flexible interface for building and
solving conservation planning problems. Once built, conservation planning
problems can be solved using a variety of commercial and open-source exact
algorithm solvers. By using exact algorithm solvers, solutions can be
generated that are guaranteed to be optimal (or within a pre-specified
optimality gap). Furthermore, conservation problems can be constructed to
optimize the spatial allocation of different management actions or zones,
meaning that conservation practitioners can identify solutions that benefit
multiple stakeholders. To solve large-scale or complex conservation
planning problems, users should install the Gurobi optimization software
(available from <https://www.gurobi.com/>) and the 'gurobi' R package (see
Gurobi Installation Guide vignette for details). Users can also install the
IBM CPLEX software (<https://www.ibm.com/products [...truncated...]
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Brandon P M Edwards [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph R Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 8.0.4 dated 2024-06-05 and 8.0.6 dated 2025-01-09
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Title: Simulating Nonhomogeneous Poisson Point Processes
Description: Simulates events from one dimensional nonhomogeneous Poisson point processes (NHPPPs) as per Trikalinos and Sereda (2024, <doi:10.48550/arXiv.2402.00358> and 2024, <doi:10.1371/journal.pone.0311311>). Functions are based on three algorithms that provably sample from a target NHPPP: the time-transformation of a homogeneous Poisson process (of intensity one) via the inverse of the integrated intensity function (Cinlar E, "Theory of stochastic processes" (1975, ISBN:0486497996)); the generation of a Poisson number of order statistics from a fixed density function; and the thinning of a majorizing NHPPP via an acceptance-rejection scheme (Lewis PAW, Shedler, GS (1979) <doi:10.1002/nav.3800260304>).
Author: Thomas Trikalinos [aut, cre, cph]
,
Yuliia Sereda [aut]
Maintainer: Thomas Trikalinos <thomas_trikalinos@brown.edu>
Diff between nhppp versions 1.0.0 dated 2024-10-23 and 1.0.2 dated 2025-01-09
DESCRIPTION | 8 - MD5 | 40 ++++---- NEWS.md | 12 ++ R/get_step_majorizer.R | 7 + inst/CITATION | 24 ++++ inst/doc/Log_linear_times.html | 4 inst/doc/Simple_des_model_cancer_natural_Hx.R | 4 inst/doc/Simple_des_model_cancer_natural_Hx.Rmd | 4 inst/doc/Simple_des_model_cancer_natural_Hx.html | 112 +++++++++++------------ man/get_step_majorizer.Rd | 1 man/nhppp-package.Rd | 2 src/RcppExports.cpp | 6 - src/nhppp.h | 7 + src/rztpois.cpp | 12 ++ src/step_regular_inverse.cpp | 4 src/vdraw_intensity_step_regular.cpp | 12 -- src/vdraw_sc_step_regular.cpp | 2 src/vdraw_sc_step_regular2.cpp | 2 src/vztdraw_sc_step_regular2.cpp | 3 tests/testthat/test-get_step_majorizer.R | 3 vignettes/Simple_des_model_cancer_natural_Hx.Rmd | 4 21 files changed, 157 insertions(+), 116 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.10.1 dated 2024-12-10 and 0.11.0 dated 2025-01-09
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Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R.
It further includes fast functions for common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data.
It is well integrated with base R classes, 'dplyr'/' [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.0.18 dated 2024-11-23 and 2.0.19 dated 2025-01-09
DESCRIPTION | 13 ++--- MD5 | 37 +++++++++------- NEWS.md | 14 +++++- R/join.R | 6 +- build/vignette.rds |binary inst/doc/collapse_documentation.Rmd | 3 + inst/doc/collapse_documentation.html | 7 ++- inst/doc/collapse_for_tidyverse_users.html | 4 - inst/doc/collapse_object_handling.html | 4 - inst/doc/developing_with_collapse.Rmd |only inst/doc/developing_with_collapse.html |only man/collap.Rd | 2 src/data.table_rbindlist.c | 26 +++++++---- src/fbstats.cpp | 4 - src/kit_dup.c | 64 ++++++++++++++++------------- src/match.c | 46 +++++++++++++++++++- tests/testthat/test-join.R | 5 ++ tests/testthat/test-misc.R | 9 ++++ tests/testthat/test-miscellaneous-issues.R | 7 +++ vignettes/collapse_documentation.Rmd | 3 + vignettes/developing_with_collapse.Rmd |only 21 files changed, 176 insertions(+), 78 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science:
modeling of loss distributions; risk theory and ruin theory;
simulation of compound models, discrete mixtures and compound
hierarchical models; credibility theory. Support for many additional
probability distributions to model insurance loss size and
frequency: 23 continuous heavy tailed distributions; the
Poisson-inverse Gaussian discrete distribution; zero-truncated and
zero-modified extensions of the standard discrete distributions.
Support for phase-type distributions commonly used to compute ruin
probabilities. Main reference: <doi:10.18637/jss.v025.i07>.
Implementation of the Feller-Pareto family of distributions:
<doi:10.18637/jss.v103.i06>.
Author: Vincent Goulet [cre, aut],
Sebastien Auclair [ctb],
Christophe Dutang [aut],
Walter Garcia-Fontes [ctb],
Nicholas Langevin [ctb],
Xavier Milhaud [ctb],
Tommy Ouellet [ctb],
Alexandre Parent [ctb],
Mathieu Pigeon [aut],
Louis-Philippe Pouliot [ctb],
J [...truncated...]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 3.3-4 dated 2023-11-08 and 3.3-5 dated 2025-01-09
DESCRIPTION | 8 +++--- MD5 | 54 +++++++++++++++++++++---------------------- R/cm.R | 4 ++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 29 ++++++++++++++++++++++- inst/doc/actuar.pdf |binary inst/doc/coverage.pdf |binary inst/doc/credibility.R | 2 - inst/doc/credibility.Rnw | 2 - inst/doc/credibility.pdf |binary inst/doc/distributions.Rnw | 4 +-- inst/doc/distributions.pdf |binary inst/doc/modeling.Rnw | 10 +++---- inst/doc/modeling.pdf |binary inst/doc/risk.pdf |binary inst/doc/simulation.pdf |binary man/InverseGaussian.Rd | 2 - man/Logarithmic.Rd | 2 - man/ZeroTruncatedPoisson.Rd | 2 - man/betaint.Rd | 7 ++--- man/cm.Rd | 3 ++ vignettes/Makefile | 6 ++-- vignettes/actuar.bib | 13 ++++------ vignettes/credibility.Rnw | 2 - vignettes/distributions.Rnw | 4 +-- vignettes/modeling.Rnw | 10 +++---- vignettes/share/preamble.tex | 33 +++++++++++--------------- 28 files changed, 111 insertions(+), 86 deletions(-)
Title: Fitting Bayesian and MLE Football Models
Description: This is the first package allowing for the estimation,
visualization and prediction of the most well-known
football models: double Poisson, bivariate Poisson,
Skellam, student_t, diagonal-inflated bivariate Poisson, and
zero-inflated Skellam. The package allows Hamiltonian
Monte Carlo (HMC) estimation through the underlying Stan
environment and Maximum Likelihood estimation (MLE, for
'static' models only). The model construction relies on
the most well-known football references, such as
Dixon and Coles (1997) <doi:10.1111/1467-9876.00065>,
Karlis and Ntzoufras (2003) <doi:10.1111/1467-9884.00366> and
Egidi, Pauli and Torelli (2018) <doi:10.1177/1471082X18798414>.
Author: Leonardo Egidi [aut, cre],
Roberto Macrì Demartino [aut],
Vasilis Palaskas. [aut]
Maintainer: Leonardo Egidi <legidi@units.it>
Diff between footBayes versions 0.2.0 dated 2023-08-31 and 1.0.0 dated 2025-01-09
footBayes-0.2.0/footBayes/build |only footBayes-0.2.0/footBayes/inst/doc |only footBayes-0.2.0/footBayes/vignettes |only footBayes-1.0.0/footBayes/DESCRIPTION | 31 footBayes-1.0.0/footBayes/MD5 | 103 footBayes-1.0.0/footBayes/NAMESPACE | 24 footBayes-1.0.0/footBayes/NEWS.md | 6 footBayes-1.0.0/footBayes/R/btd_foot.R |only footBayes-1.0.0/footBayes/R/compare_foot.R |only footBayes-1.0.0/footBayes/R/foot_abilities.R | 970 ++-- footBayes-1.0.0/footBayes/R/foot_prob.R | 647 +-- footBayes-1.0.0/footBayes/R/foot_rank.R | 959 ++-- footBayes-1.0.0/footBayes/R/foot_round_robin.R | 107 footBayes-1.0.0/footBayes/R/globals.R | 3 footBayes-1.0.0/footBayes/R/italy.R | 34 footBayes-1.0.0/footBayes/R/mle_foot.R | 141 footBayes-1.0.0/footBayes/R/plot_btdPosterior.R |only footBayes-1.0.0/footBayes/R/plot_logStrength.R |only footBayes-1.0.0/footBayes/R/pp_foot.R | 191 footBayes-1.0.0/footBayes/R/print_fun_foot.R |only footBayes-1.0.0/footBayes/R/stan_foot.R | 4468 ++------------------- footBayes-1.0.0/footBayes/R/utils_foot.R |only footBayes-1.0.0/footBayes/inst/precompiled |only footBayes-1.0.0/footBayes/inst/stan |only footBayes-1.0.0/footBayes/man/btd_foot.Rd |only footBayes-1.0.0/footBayes/man/compare_foot.Rd |only footBayes-1.0.0/footBayes/man/england.Rd | 62 footBayes-1.0.0/footBayes/man/foot_abilities.Rd | 42 footBayes-1.0.0/footBayes/man/foot_prob.Rd | 30 footBayes-1.0.0/footBayes/man/foot_rank.Rd | 30 footBayes-1.0.0/footBayes/man/foot_round_robin.Rd | 25 footBayes-1.0.0/footBayes/man/italy.Rd | 54 footBayes-1.0.0/footBayes/man/plot_btdPosterior.Rd |only footBayes-1.0.0/footBayes/man/plot_logStrength.Rd |only footBayes-1.0.0/footBayes/man/pp_foot.Rd | 23 footBayes-1.0.0/footBayes/man/print.btdFoot.Rd |only footBayes-1.0.0/footBayes/man/print.compareFoot.Rd |only footBayes-1.0.0/footBayes/man/print.stanFoot.Rd |only footBayes-1.0.0/footBayes/man/stan_foot.Rd | 211 footBayes-1.0.0/footBayes/tests/testthat.R | 65 40 files changed, 2610 insertions(+), 5616 deletions(-)
Title: Import Gaze Data for EyeLink Eye Tracker
Description: Import gaze data from edf files generated by
the SR Research <https://www.sr-research.com/> EyeLink eye tracker. Gaze data,
both recorded events and samples, is imported per trial. The package allows to extract
events of interest, such as saccades, blinks, etc. as well as
recorded variables and custom events (areas of interest, triggers) into separate tables.
The package requires EDF API library that can be obtained at <https://www.sr-research.com/support/>.
Author: Alexander Pastukhov [aut, cre]
Maintainer: Alexander Pastukhov <pastukhov.alexander@gmail.com>
Diff between eyelinkReader versions 1.0.2 dated 2024-10-08 and 1.0.3 dated 2025-01-09
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md | 4 ++++ README.md | 2 +- build/vignette.rds |binary inst/cpp/edf_interface.cpp | 8 ++++---- man/figures |only 7 files changed, 19 insertions(+), 14 deletions(-)
More information about VARcpDetectOnline at CRAN
Permanent link
Title: Concept Drift Detection Methods for Stream Data
Description: A system designed for detecting concept drift in streaming datasets. It offers a comprehensive suite of statistical methods to detect concept drift, including methods for monitoring changes in data distributions
over time. The package supports several tests, such as Drift Detection Method (DDM), Early Drift Detection Method (EDDM), Hoeffding Drift Detection Methods (HDDM_A, HDDM_W), Kolmogorov-Smirnov test-based Windowing (KSWIN)
and Page Hinkley (PH) tests. The methods implemented in this package are based on established research and have been demonstrated to be effective in real-time data analysis. For more details on the methods,
please check to the following sources. Kobylińska et al. (2023) <doi:10.48550/arXiv.2308.11446>, S. Kullback & R.A. Leibler (1951) <doi:10.1214/aoms/1177729694>, Gama et al. (2004) <doi:10.1007/978-3-540-28645-5_29>, Baena-Garcia et al. (2006) <https://www.researchgate.net/publication/245999704_Early_Drift_Detection_Method>,
Fría [...truncated...]
Author: Ugur Dar [aut, cre],
Mustafa Cavus [ctb, ths]
Maintainer: Ugur Dar <ugurdarr@gmail.com>
Diff between datadriftR versions 0.0.1 dated 2024-06-13 and 1.0.0 dated 2025-01-09
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++++--- NAMESPACE | 5 +++++ R/KLDivergence.R |only R/ProfileDifference.R |only README.md | 7 +++++++ man/KLDivergence.Rd |only man/ProfileDifference.Rd |only 8 files changed, 25 insertions(+), 9 deletions(-)
Title: The Calibration Simplex
Description: Generates the calibration simplex (a generalization of the reliability diagram) for three-category probability forecasts, as proposed by Wilks (2013) <doi:10.1175/WAF-D-13-00027.1>.
Author: Johannes Resin [aut, cre]
Maintainer: Johannes Resin <johannes.resin@h-its.org>
Diff between CalSim versions 0.5.2 dated 2021-03-25 and 0.5.4 dated 2025-01-09
DESCRIPTION | 19 +++++++----- MD5 | 24 +++++++-------- NAMESPACE | 3 + NEWS.md | 52 +++++++++++++++++---------------- R/calibration_simplex.R | 4 +- R/calibration_simplex.default.R | 10 +++--- R/error.calibration_simplex.R | 2 + R/make_forecasts.calibration_simplex.R | 2 + R/plot.calibration_simplex.R | 28 ++++++----------- R/rel_freq.calibration_simplex.R | 2 + README.md | 10 +++--- man/calibration_simplex.Rd | 8 ++--- man/plot.calibration_simplex.Rd | 12 +++++-- 13 files changed, 96 insertions(+), 80 deletions(-)
Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre],
Juliane Schmachtenberg [ctb],
Swenja Wagner [ctb],
Patricia Scheil [ctb],
Tom Waschischek [ctb],
Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 1.1.1 dated 2024-03-11 and 1.1.2 dated 2025-01-09
PTXQC-1.1.1/PTXQC/R/PTXQC.R |only PTXQC-1.1.2/PTXQC/DESCRIPTION | 48 +++- PTXQC-1.1.2/PTXQC/MD5 | 72 +++--- PTXQC-1.1.2/PTXQC/NAMESPACE | 1 PTXQC-1.1.2/PTXQC/NEWS | 5 PTXQC-1.1.2/PTXQC/R/FilenameMapper.R | 13 - PTXQC-1.1.2/PTXQC/R/MQDataReader.R | 16 + PTXQC-1.1.2/PTXQC/R/PTXQC-package.R | 1 PTXQC-1.1.2/PTXQC/R/createReport.R | 4 PTXQC-1.1.2/PTXQC/R/fcn_MQ.R | 8 PTXQC-1.1.2/PTXQC/R/fcn_MQalign.R | 2 PTXQC-1.1.2/PTXQC/R/fcn_PCA.R | 28 +- PTXQC-1.1.2/PTXQC/R/fcn_QCHeat.R | 6 PTXQC-1.1.2/PTXQC/R/fcn_miscGGplot.R | 8 PTXQC-1.1.2/PTXQC/R/fcn_plots.R | 100 ++++----- PTXQC-1.1.2/PTXQC/R/mzQC.R | 25 ++ PTXQC-1.1.2/PTXQC/R/plot_peptideMods.R | 2 PTXQC-1.1.2/PTXQC/R/qcMetric.R | 36 ++- PTXQC-1.1.2/PTXQC/R/qcMetric_EVD.R | 35 +-- PTXQC-1.1.2/PTXQC/R/qcMetric_MSMS.R | 6 PTXQC-1.1.2/PTXQC/R/qcMetric_MSMSScans.R | 2 PTXQC-1.1.2/PTXQC/R/qcMetric_SM.R | 2 PTXQC-1.1.2/PTXQC/README.md | 2 PTXQC-1.1.2/PTXQC/inst/doc/PTXQC-Basic_Guide_for_R_users.html | 4 PTXQC-1.1.2/PTXQC/inst/doc/PTXQC-CustomizeReport.html | 4 PTXQC-1.1.2/PTXQC/inst/doc/PTXQC-DragNDrop.html | 4 PTXQC-1.1.2/PTXQC/inst/doc/PTXQC-FAQ.html | 4 PTXQC-1.1.2/PTXQC/inst/doc/PTXQC-Input_And_Output_Data.html | 4 PTXQC-1.1.2/PTXQC/inst/doc/PTXQC-ListOfMetrics.html | 5 PTXQC-1.1.2/PTXQC/man/PTXQC-package.Rd | 105 +++++----- PTXQC-1.1.2/PTXQC/man/QCMetaFilenames.Rd | 4 PTXQC-1.1.2/PTXQC/man/getMetaFilenames.Rd |only PTXQC-1.1.2/PTXQC/man/getPCA.Rd | 8 PTXQC-1.1.2/PTXQC/man/modsToTable.Rd | 54 ++--- PTXQC-1.1.2/PTXQC/man/modsToTableByRaw.Rd | 74 +++---- PTXQC-1.1.2/PTXQC/man/plot_MBRgain.Rd | 14 - PTXQC-1.1.2/PTXQC/man/plot_peptideMods.Rd | 68 +++--- PTXQC-1.1.2/PTXQC/man/qcMetric-class.Rd | 29 ++ 38 files changed, 467 insertions(+), 336 deletions(-)
More information about pacta.multi.loanbook at CRAN
Permanent link
Title: Machine Learning in 'shiny' with 'mlr3'
Description: A web-based graphical user interface to provide the basic steps of a machine learning workflow. It uses the functionalities of the 'mlr3' framework.
Author: Laurens Tetzlaff [aut, cre],
Gero Szepannek [aut],
Alexander Frahm [aut],
Dominic Henning [aut],
Jakob Steinbrink [aut]
Maintainer: Laurens Tetzlaff <laurens.tetzlaff@outlook.de>
Diff between mlr3shiny versions 0.3.0 dated 2023-09-30 and 0.5.0 dated 2025-01-09
mlr3shiny-0.3.0/mlr3shiny/inst/mlr3shiny/tests/shinytest/basic_test-expected |only mlr3shiny-0.3.0/mlr3shiny/inst/mlr3shiny/tests/shinytest/basic_test.R |only mlr3shiny-0.5.0/mlr3shiny/DESCRIPTION | 34 ++ mlr3shiny-0.5.0/mlr3shiny/MD5 | 36 +-- mlr3shiny-0.5.0/mlr3shiny/NEWS.md | 20 + mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/global.R | 5 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_benchmarking.R | 38 ++- mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_explain.R | 10 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_learner.R | 118 ++++++---- mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_predict.R | 87 +++++++ mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_resample.R | 2 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_task.R | 84 +++++++ mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/server/server_trainEvaluate.R | 2 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/tests/shinytest/Basic_test-expected |only mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/tests/shinytest/Basic_test.R |only mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/ui.R | 10 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/ui/ui_benchmarking.R | 2 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/ui/ui_predict.R | 9 mlr3shiny-0.5.0/mlr3shiny/inst/mlr3shiny/ui/ui_task.R | 7 mlr3shiny-0.5.0/mlr3shiny/tests/testthat/test-launchMlr3Shiny.R | 2 20 files changed, 367 insertions(+), 99 deletions(-)
Title: Correct Mass Isotopologue Distribution Vectors
Description: In metabolic flux experiments tracer molecules (often glucose
containing labelled carbon) are incorporated in compounds measured
using mass spectrometry. The mass isotopologue distributions of these
compounds needs to be corrected for natural abundance of labelled
carbon and other effects, which are specific on the compound and
ionization technique applied. This package provides functions to
correct such effects in gas chromatography atmospheric pressure
chemical ionization mass spectrometry analyses.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between CorMID versions 0.2.1 dated 2024-10-02 and 0.3.1 dated 2025-01-09
DESCRIPTION | 15 ++-- MD5 | 64 +++++++++-------- NAMESPACE | 2 R/CalcTheoreticalMDV.R | 2 R/CorMID.R | 43 ++++++----- R/CountChemicalElements.R | 6 + R/FitMID.R | 44 ++++++++--- R/RcppExports.R |only R/data.R | 6 + R/getMID.R | 22 +++-- R/recMID.R | 13 ++- R/utils.R | 81 +++++++++++++++++++--- README.md | 38 +++++++--- data/known_frags.rda |only inst/doc/CorMID.R | 18 ++-- inst/doc/CorMID.Rmd | 18 ++-- inst/doc/CorMID.html | 34 ++++----- man/CalcTheoreticalMDV.Rd | 2 man/CountChemicalElements.Rd | 2 man/getMID.Rd | 2 man/known_frags.Rd |only man/recMID.Rd | 7 + src |only tests/testthat/_snaps/CorMID/cormid-plot-alt.svg | 2 tests/testthat/_snaps/CorMID/cormid-plot.svg | 4 - tests/testthat/_snaps/recMID/recmid-plot-alt.svg | 21 +++-- tests/testthat/_snaps/recMID/recmid-plot-alt2.svg | 53 +++++++------- tests/testthat/_snaps/recMID/recmid-plot.svg | 53 +++++++------- tests/testthat/test-CalcTheoreticalMDV.R | 3 tests/testthat/test-CorMID.R | 20 ++--- tests/testthat/test-FitMID.R | 10 +- tests/testthat/test-calc_mid_error.R | 15 ++-- tests/testthat/test-recMID.R | 20 ++--- vignettes/CorMID.Rmd | 18 ++-- 34 files changed, 394 insertions(+), 244 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.3.0 dated 2024-12-16 and 2.3.1 dated 2025-01-09
DESCRIPTION | 6 ++-- MD5 | 64 +++++++++++++++++++++---------------------- NEWS | 4 ++ R/base64.R | 3 ++ configure | 2 - inst/doc/bignum.html | 32 ++++++++++----------- inst/doc/crypto_hashing.html | 4 +- inst/doc/keys.html | 48 ++++++++++++++++---------------- inst/doc/secure_rng.html | 18 ++++++------ src/Makevars.in | 2 - src/Makevars.win | 2 - src/aes.c | 8 ++--- src/base64.c | 13 ++++++-- src/bignum.c | 20 ++++++------- src/cert.c | 32 ++++++++++----------- src/diffie.c | 2 - src/envelope.c | 14 ++++----- src/hash.c | 24 ++++++++-------- src/info.c | 10 +++--- src/keygen.c | 14 ++++----- src/keys.c | 14 ++++----- src/openssh.c | 36 ++++++++++++------------ src/password.c | 20 ++++++------- src/pem.c | 20 ++++++------- src/pkcs12.c | 14 ++++----- src/pkcs7.c | 18 ++++++------ src/rand.c | 4 +- src/rsa.c | 8 ++--- src/signing.c | 8 ++--- src/ssl.c | 14 ++++----- src/stream.c | 34 +++++++++++----------- src/write.c | 16 +++++----- src/x25519.c | 10 +++--- 33 files changed, 275 insertions(+), 263 deletions(-)
Title: Practical Multilevel Modeling
Description: Convenience functions and datasets to be used with Practical Multilevel Modeling using R. The package includes functions for calculating group means, group mean centered variables, and displaying some basic missing data information. A function for computing robust standard errors for linear mixed models based on Liang and Zeger (1986) <doi:10.1093/biomet/73.1.13> and Bell and 'McCaffrey' (2002) <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2002002/article/9058-eng.pdf?st=NxMjN1YZ> is included as well as a function for checking for level-one homoskedasticity (Raudenbush & Bryk, 2002, ISBN:076191904X).
Author: Francis Huang [aut, cre]
Maintainer: Francis Huang <flhuang2000@yahoo.com>
Diff between MLMusingR versions 0.3.2 dated 2024-01-27 and 0.4.0 dated 2025-01-09
DESCRIPTION | 12 +-- MD5 | 27 +++++-- NAMESPACE | 15 ++++ NEWS.md | 5 + R/Htest.R | 5 - R/helper.R | 175 +++++++++++++++++++++++++++++++++++++++++++++++++++ R/lrtPV.R |only R/mixPV.R |only R/robust_mixed.R | 2 R/wscale.R |only build |only man/Htest.Rd | 5 - man/lrtPV.Rd |only man/mixPV.Rd |only man/pool_pv.Rd |only man/robust_mixed.Rd | 2 man/summary.mixPV.Rd |only man/summary_all.Rd |only man/tidy.mixPV.Rd |only man/wscale.Rd |only 20 files changed, 226 insertions(+), 22 deletions(-)
Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods
with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling
conventions.
Author: Oleg Sklyar [aut],
Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Mike Smith [ctb],
Duncan Murdoch [ctb],
Karline Soetaert [ctb] ,
Johannes Ranke [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between inline versions 0.3.20 dated 2024-11-10 and 0.3.21 dated 2025-01-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/cfunction.R | 14 ++++++++++---- build/partial.rdb |binary inst/NEWS.Rd | 9 +++------ 5 files changed, 21 insertions(+), 18 deletions(-)
Title: Decomposition of Seats-to-Votes Distortions
Description: Analyses districted electoral systems of any magnitude by computing district-party conversion ratios and seats-to-votes deviations, decomposing the sources of deviation. Traditional indexes are also computed.
References:
Kedar, O., Harsgor, L. and Sheinerman, R.A. (2016). <doi:10.1111/ajps.12225>.
Penades, A and Pavia, J.M. (2025) ''The decomposition of seats-to-votes distortion in elections: mean, variance, malapportionment and participation''.
Acknowledgements:
The authors wish to thank Consellería de Educación, Cultura, Universidades y Empleo, Generalitat Valenciana (grant CIACO/2023/031) for supporting this research.
Author: Alberto Penades [aut] ,
Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between ElectDecomp versions 0.0.1-1 dated 2024-07-26 and 0.0.1-8 dated 2025-01-09
DESCRIPTION | 17 ++++++++---- MD5 | 18 ++++++++++--- NAMESPACE | 4 +++ NEWS.md |only R/distortion.R | 56 ++++++++++++++++++++++++++---------------- R/inequality.R |only R/malapportionment_index.R |only R/plot.R |only R/traditional_indexes.R |only build |only man/distortion.Rd | 35 +++++++++++++++++--------- man/inequality.Rd |only man/malapportionment_index.Rd |only man/plot.ElectDecomp.Rd |only man/traditional_indexes.Rd |only 15 files changed, 87 insertions(+), 43 deletions(-)
Title: Interactive Scatter Plot and Volcano Plot Labels
Description: Interactive labelling of scatter plots, volcano plots and
Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover
over points to see where specific points are located and click points
on/off to easily label them. Labels can be dragged around the plot to place
them optimally. Plots can be exported directly to PDF for publication. For
plots with large numbers of points, points can optionally be rasterized as a
bitmap, while all other elements (axes, text, labels & lines) are preserved
as vector objects. This can dramatically reduce file size for plots with
millions of points such as Manhattan plots, and is ideal for publication.
Author: Myles Lewis [aut, cre] ,
Katriona Goldmann [aut] ,
Cankut Cubuk [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between easylabel versions 0.2.8 dated 2024-03-08 and 0.3.2 dated 2025-01-09
DESCRIPTION | 22 + MD5 | 30 +- NAMESPACE | 15 + NEWS.md | 10 R/easyManhattan.R | 2 R/easylabel.R | 494 +++++++++++--------------------------------- R/loadlabel.R |only R/utils.R |only README.md | 3 build/vignette.rds |binary inst/doc/easylabel.Rmd | 23 ++ inst/doc/easylabel.html | 123 ++++++---- man/easylabel.Rd | 30 +- man/loadlabel.Rd |only man/summary.easylab.Rd |only vignettes/easylabel.Rmd | 23 ++ vignettes/locus.png |binary vignettes/plotly_output.png |binary 18 files changed, 336 insertions(+), 439 deletions(-)
Title: Experimental Evaluation of Algorithm-Assisted Human
Decision-Making
Description: Provides statistical methods for analyzing experimental
evaluation of the causal impacts of algorithmic recommendations
on human decisions developed by Imai, Jiang, Greiner, Halen, and
Shin (2023) <doi:10.1093/jrsssa/qnad010> and Ben-Michael, Greiner,
Huang, Imai, Jiang, and Shin (2024) <doi:10.48550/arXiv.2403.12108>.
The data used for this paper, and made available here, are interim,
based on only half of the observations in the study and (for those
observations) only half of the study follow-up period. We use them
only to illustrate methods, not to draw substantive conclusions.
Author: Sooahn Shin [aut, cre] ,
Zhichao Jiang [aut],
Kosuke Imai [aut]
Maintainer: Sooahn Shin <sooahnshin@g.harvard.edu>
Diff between aihuman versions 0.1.0 dated 2023-03-02 and 1.0.0 dated 2025-01-09
DESCRIPTION | 16 MD5 | 171 +- NAMESPACE | 126 + NEWS.md | 11 R/ability_agreement.R |only R/ability_ai.R |only R/ability_compute_bounds.R |only R/ability_compute_nuisance_functions.R |only R/ability_compute_stats.R |only R/ability_human.R |only R/ability_human_override.R |only R/ability_preference.R |only R/apce.R | 562 ++++---- R/crt.R | 352 ++--- R/data.R | 169 ++ R/frequentist.R | 410 +++--- R/frequentist_re.R | 465 ++++--- R/mcmc.R | 180 +- R/plot_apce.R | 162 +- R/plot_decision.R | 417 +++--- R/plot_fairness.R | 265 ++- R/plot_itt.R | 308 ++-- R/plot_optimaldecision.R | 334 ++--- R/plot_principal.R | 158 +- R/plot_utility.R | 210 +-- R/sysdata.rda |only README.md | 115 + build/partial.rdb |binary build/vignette.rds |binary data/FTAdata.rda |binary data/HearingDate.rda |binary data/NCAdata.rda |binary data/NVCAdata.rda |binary data/PSAdata.rda |binary inst/CITATION |only inst/doc/ability.R |only inst/doc/ability.Rmd |only inst/doc/ability.html |only inst/doc/aihuman.R | 1853 +++++++++++++++------------ inst/doc/aihuman.Rmd | 1237 ++++++++++-------- inst/doc/aihuman.html | 2188 +++++++++++++++++---------------- man/APCEsummary.Rd | 19 man/APCEsummaryipw.Rd | 46 man/A_llama.Rd |only man/AiEvalmcmc.Rd | 2 man/BootstrapAPCEipw.Rd | 3 man/BootstrapAPCEipwRE.Rd | 34 man/BootstrapAPCEipwREparallel.Rd | 29 man/CalAPCE.Rd | 17 man/CalAPCEipw.Rd | 2 man/CalAPCEipwRE.Rd | 28 man/CalAPCEparallel.Rd | 23 man/CalDIMsubgroup.Rd | 6 man/CalDelta.Rd | 16 man/CalFairness.Rd | 14 man/CalOptimalDecision.Rd | 14 man/CalPS.Rd | 14 man/FTAdata.Rd | 10 man/HearingDate.Rd | 4 man/NCAdata.Rd | 10 man/NVCAdata.Rd | 10 man/PSAdata.Rd | 8 man/PlotAPCE.Rd | 26 man/PlotDIMdecisions.Rd | 16 man/PlotDIMoutcomes.Rd | 12 man/PlotFairness.Rd | 22 man/PlotOptimalDecision.Rd | 12 man/PlotPS.Rd | 16 man/PlotSpilloverCRTpower.Rd | 8 man/PlotStackedBar.Rd | 20 man/PlotStackedBarDMF.Rd | 10 man/PlotUtilityDiff.Rd | 12 man/PlotUtilityDiffCI.Rd | 14 man/SpilloverCRTpower.Rd | 8 man/TestMonotonicityRE.Rd | 26 man/compute_bounds_aipw.Rd |only man/compute_nuisance_functions.Rd |only man/compute_nuisance_functions_ai.Rd |only man/compute_stats.Rd |only man/compute_stats_agreement.Rd |only man/compute_stats_aipw.Rd |only man/compute_stats_subgroup.Rd |only man/crossfit.Rd |only man/figures/README-example-1.png |binary man/figures/README-example2-1.png |only man/figures/README-example2-2.png |only man/nca_follow_policy.Rd |only man/nca_follow_policy_dec.Rd |only man/nca_provide_policy.Rd |only man/nca_provide_policy_dec.Rd |only man/nuis_func.Rd |only man/nuis_func_ai.Rd |only man/plot_agreement.Rd |only man/plot_diff_ai_aipw.Rd |only man/plot_diff_human.Rd |only man/plot_diff_human_aipw.Rd |only man/plot_diff_subgroup.Rd |only man/plot_preference.Rd |only man/synth.Rd | 2 man/table_agreement.Rd |only man/vis_agreement.Rd |only man/vis_diff_ai.Rd |only man/vis_diff_human.Rd |only man/vis_diff_subgroup.Rd |only man/vis_preference.Rd |only src/AiEvalProbit_ordinal.cpp | 3 vignettes/ability.Rmd |only vignettes/aihuman.Rmd | 1237 ++++++++++-------- 108 files changed, 6460 insertions(+), 5002 deletions(-)
Title: Search and Query CRAN R Packages
Description: Search CRAN metadata about packages by keyword, popularity,
recent activity, package name and more. Uses the 'R-hub' search
server, see <https://r-pkg.org> and the CRAN metadata database, that
contains information about CRAN packages. Note that this is _not_ a
CRAN project.
Author: Gabor Csardi [aut, cre],
Maelle Salmon [aut] ,
R Consortium [fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgsearch versions 3.1.3 dated 2023-12-10 and 3.1.4 dated 2025-01-09
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 5 R/advanced_search.R | 6 R/api.R | 32 +-- R/http.R | 26 ++- R/utils.R | 18 +- README.md | 450 ++++++++++++++++++++++++++-------------------------- 8 files changed, 300 insertions(+), 259 deletions(-)
Title: Multinomial Goodness-of-Fit Tests
Description: Computes exact p-values for multinomial goodness-of-fit tests based on multiple test statistics, namely, Pearson's chi-square, the log-likelihood ratio and the probability mass statistic. Implements the algorithm detailed in Resin (2023) <doi:10.1080/10618600.2022.2102026>. Estimates based on the classical asymptotic chi-square approximation or Monte-Carlo simulation can also be computed.
Author: Johannes Resin [aut, cre]
Maintainer: Johannes Resin <johannes.resin@h-its.org>
Diff between ExactMultinom versions 0.1.1 dated 2020-09-04 and 0.1.3 dated 2025-01-09
DESCRIPTION | 19 +++++++++------ MD5 | 16 ++++++------ NAMESPACE | 1 NEWS.md | 12 ++++++++- R/multinom.test.R | 58 ++++++++++++++++++++++++++-------------------- README.md | 2 - man/multinom.test.Rd | 24 +++++++++---------- src/RcppExports.cpp | 5 ++++ src/multinom_test.cpp | 62 ++++++++++++++++++++++++++------------------------ 9 files changed, 115 insertions(+), 84 deletions(-)
Title: Drug Repurposing in Cancer via a Subpathway Crosstalk Network
Description: A systematic biology tool was developed to repurpose drugs via a subpathway crosstalk network. The operation modes include 1) calculating centrality scores of SPs in the context of gene expression data to reflect the influence of SP crosstalk, 2) evaluating drug-disease reverse association based on disease- and drug-induced SPs weighted by the SP crosstalk, 3) identifying cancer candidate drugs through perturbation analysis. There are also several functions used to visualize the results.
Author: Junwei Han [aut, cre, cph],
Jiashuo Wu [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between DRviaSPCN versions 0.1.4 dated 2024-01-12 and 0.1.5 dated 2025-01-09
DRviaSPCN-0.1.4/DRviaSPCN/R/DRviaSPCN-package.R |only DRviaSPCN-0.1.4/DRviaSPCN/R/getMolecularFm.R |only DRviaSPCN-0.1.4/DRviaSPCN/man/DRviaSPCN-package.Rd |only DRviaSPCN-0.1.4/DRviaSPCN/man/getMolecularFm.Rd |only DRviaSPCN-0.1.5/DRviaSPCN/DESCRIPTION | 11 - DRviaSPCN-0.1.5/DRviaSPCN/MD5 | 18 +- DRviaSPCN-0.1.5/DRviaSPCN/NAMESPACE | 3 DRviaSPCN-0.1.5/DRviaSPCN/build/vignette.rds |binary DRviaSPCN-0.1.5/DRviaSPCN/inst/doc/DRviaSPCN.R | 76 ++++------- DRviaSPCN-0.1.5/DRviaSPCN/inst/doc/DRviaSPCN.Rmd | 28 ---- DRviaSPCN-0.1.5/DRviaSPCN/inst/doc/DRviaSPCN.html | 137 ++++++++------------- DRviaSPCN-0.1.5/DRviaSPCN/vignettes/DRviaSPCN.Rmd | 28 ---- 12 files changed, 108 insertions(+), 193 deletions(-)
Title: Multivariate Tools for Compositional Data Analysis
Description: Provides functions for multivariate analysis with compositional data. Includes a function for doing compositional canonical correlation analysis. This analysis requires two data matrices of compositions, which can be adequately transformed and used as entries in a specialized program for canonical correlation analysis, that is able to deal with singular covariance matrices. The methodology is described in Graffelman et al. (2017) <doi:10.1101/144584>. Functions for log-ratio principal component analysis with condition number computations and log-ratio discriminant analysis have been added to the package.
Author: Jan Graffelman [aut, cre]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between ToolsForCoDa versions 1.0.9 dated 2024-09-01 and 1.1.0 dated 2025-01-09
DESCRIPTION | 8 - MD5 | 14 +- R/lrlda.R | 313 +++++++++++++++++++++++---------------------- R/lrpca.R | 18 +- inst/doc/ToolsForCoDa.R | 7 + inst/doc/ToolsForCoDa.Rmd | 9 + inst/doc/ToolsForCoDa.html | 21 ++- vignettes/ToolsForCoDa.Rmd | 9 + 8 files changed, 221 insertions(+), 178 deletions(-)
Title: Robust Non-Linear Regression using AIC Scores
Description: Non-linear least squares regression with the Levenberg-Marquardt algorithm using multiple starting values for increasing the chance that the minimum found is the global minimum.
Author: Daniel Padfield [aut, cre],
Granville Matheson [aut],
Francis Windram [aut]
Maintainer: Daniel Padfield <d.padfield@exeter.ac.uk>
Diff between nls.multstart versions 1.3.0 dated 2023-08-15 and 2.0.0 dated 2025-01-09
DESCRIPTION | 19 ++++-- MD5 | 14 ++-- NEWS.md | 7 ++ R/nls_multstart.R | 101 +++++++++++++++++++++-------------- README.md | 71 ++++++++++++++++++++---- inst/image/README-confint_plot-1.png |binary man/nls_multstart.Rd | 28 ++++++--- tests/testthat/test-nls_multstart.R | 12 ++++ 8 files changed, 177 insertions(+), 75 deletions(-)
Title: Robust Analytical Methods for Evaluating Educational
Interventions using Randomised Controlled Trials Designs
Description: Analysing data from evaluations of educational interventions using a randomised controlled trial design. Various analytical tools to perform sensitivity analysis using different methods are supported (e.g. frequentist models with bootstrapping and permutations options, Bayesian models). The included commands can be used for simple randomised trials, cluster randomised trials and multisite trials. The methods can also be used more widely beyond education trials. This package can be used to evaluate other intervention designs using Frequentist and Bayesian multilevel models.
Author: Germaine Uwimpuhwe [aut, cre],
Qing Zhang [aut],
Akansha Singh [aut],
Dimitris Vallis [aut],
Jochen Einbeck [aut],
Steve Higgins [aut],
ZhiMin Xiao [aut],
Ewoud De Troyer [aut],
Adetayo Kasim [aut]
Maintainer: Germaine Uwimpuhwe <germaine.uwimpuhwe@durham.ac.uk>
Diff between eefAnalytics versions 1.1.4 dated 2024-12-17 and 1.1.5 dated 2025-01-09
eefAnalytics-1.1.4/eefAnalytics/inst/jags/CRT.txt |only eefAnalytics-1.1.4/eefAnalytics/inst/jags/MLM_UNC.txt |only eefAnalytics-1.1.4/eefAnalytics/inst/jags/MST-DW-PF24GQEJ.txt |only eefAnalytics-1.1.4/eefAnalytics/inst/jags/MST.txt |only eefAnalytics-1.1.4/eefAnalytics/inst/jags/OLS_UNC.txt |only eefAnalytics-1.1.4/eefAnalytics/inst/jags/SRT.txt |only eefAnalytics-1.1.5/eefAnalytics/DESCRIPTION | 6 +- eefAnalytics-1.1.5/eefAnalytics/MD5 | 24 +++------- eefAnalytics-1.1.5/eefAnalytics/NEWS.md | 6 +- eefAnalytics-1.1.5/eefAnalytics/R/crtBayes.R | 11 ++-- eefAnalytics-1.1.5/eefAnalytics/R/mstBayes.R | 11 ++-- eefAnalytics-1.1.5/eefAnalytics/R/plotfunctions.R | 5 +- eefAnalytics-1.1.5/eefAnalytics/R/srtBayes.R | 16 +++++- eefAnalytics-1.1.5/eefAnalytics/inst/doc/eefAnalytics.Rmd | 2 eefAnalytics-1.1.5/eefAnalytics/inst/doc/eefAnalytics.html | 2 eefAnalytics-1.1.5/eefAnalytics/vignettes/eefAnalytics.Rmd | 2 16 files changed, 48 insertions(+), 37 deletions(-)
Title: Multivariate Hypothesis Tests
Description: Hypothesis tests for multivariate data. Tests for one and two mean vectors, multivariate analysis of variance, tests for one, two or more covariance matrices. References include: Mardia K.V., Kent J.T. and Bibby J.M. (1979). Multivariate Analysis. ISBN: 978-0124712522. London: Academic Press.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between mvhtests versions 1.0 dated 2023-10-20 and 1.1 dated 2025-01-09
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/hotel1T2.R | 5 ++--- R/hotel2T2.R | 3 +-- R/james.R | 3 +-- man/el.test1.Rd | 2 +- man/mvhtests-package.Rd | 4 ++-- 7 files changed, 18 insertions(+), 20 deletions(-)
Title: Composite Indicators Functions
Description: A collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, 'Vidoli' and 'Fusco' and 'Mazziotta' <doi:10.1007/s11205-014-0710-y>, 'Mazziotta' and 'Pareto' (2016) <doi:10.1007/s11205-015-0998-2>, 'Van Puyenbroeck and 'Rogge' <doi:10.1016/j.ejor.2016.07.038> and other authors.
Author: Francesco Vidoli [aut, cre],
Elisa Fusco [aut]
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 3.1 dated 2024-03-25 and 3.2 dated 2025-01-09
DESCRIPTION | 20 ++++++++++++++------ MD5 | 10 +++++----- NEWS | 6 ++++++ R/ci_ampi.R | 10 +++++----- build/vignette.rds |binary man/ci_ampi.Rd | 2 +- 6 files changed, 31 insertions(+), 17 deletions(-)
Title: Permutation Conditional Random Tests
Description: It provides functions to perform permutation conditional random one-sample and two-samples t-tests in a multivariate framework.
Author: Angela Andreella [aut, cre]
Maintainer: Angela Andreella <angela.andreella@unitn.it>
Diff between pecora versions 0.1.1 dated 2021-11-05 and 0.1.2 dated 2025-01-09
DESCRIPTION | 12 ++-- MD5 | 22 ++++---- NAMESPACE | 20 +++---- NEWS.md | 8 +++ R/RcppExports.R | 22 ++++---- R/oneSample.R | 94 +++++++++++++++++------------------ R/pecora-package.R | 68 ++++++++++++------------- R/t2p.R | 12 ++-- R/twoSamples.R | 140 ++++++++++++++++++++++++++--------------------------- R/utils.R | 16 +++--- README.md | 40 +++++++-------- src/Makevars.win | 1 12 files changed, 231 insertions(+), 224 deletions(-)
Title: Location Identify Tool
Description: Determine the sea area where the fishing boat operates.
The latitude and longitude of geographic coordinates are used to match oceanic areas and economic sea areas.
You can plot the distribution map with dotplot() function.
Please refer to Flanders Marine Institute (2020) <doi:10.14284/403>.
Author: shiao chih hao [aut, cre, ctb],
chang shu ting [aut, ctb],
wang shyh jiun [aut, ctb]
Maintainer: shiao chih hao <chihhao@ofdc.org.tw>
Diff between oceanic versions 0.1.7 dated 2024-06-10 and 0.1.8 dated 2025-01-09
oceanic-0.1.7/oceanic/R/idfoutliers.R |only oceanic-0.1.7/oceanic/data/port.rda |only oceanic-0.1.7/oceanic/man/idfoutliers.Rd |only oceanic-0.1.7/oceanic/man/port.Rd |only oceanic-0.1.8/oceanic/DESCRIPTION | 14 +++++----- oceanic-0.1.8/oceanic/MD5 | 18 ++++++------- oceanic-0.1.8/oceanic/NAMESPACE | 33 +++++++++++------------- oceanic-0.1.8/oceanic/R/data.R | 4 +-- oceanic-0.1.8/oceanic/R/idfeez.R | 41 +++++++++++++++---------------- oceanic-0.1.8/oceanic/R/idfocean.R | 39 ++++++++++++++--------------- oceanic-0.1.8/oceanic/R/idfport.R | 20 +++++++++------ oceanic-0.1.8/oceanic/data/port_sf.rda |only oceanic-0.1.8/oceanic/man/port_sf.Rd |only 13 files changed, 84 insertions(+), 85 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.4.0 dated 2024-12-07 and 0.5.0 dated 2025-01-09
DESCRIPTION | 14 - MD5 | 28 +-- NAMESPACE | 2 R/chordplot.R | 2 R/lineplot.R | 68 +++++++- R/piechart.R | 6 R/sankeyplot.R | 393 +++++++++++++++++++++++++++++++++++------------- man/LinePlot.Rd | 18 ++ man/LinePlotAtomic.Rd | 13 + man/LinePlotGrouped.Rd | 13 + man/LinePlotSingle.Rd | 13 + man/PieChart.Rd | 5 man/PieChartAtomic.Rd | 3 man/SankeyPlotAtomic.Rd | 122 ++++++++++++-- man/sankeyplot.Rd | 277 ++++++++++++++++++++++++++++----- 15 files changed, 780 insertions(+), 197 deletions(-)
Title: Retrieving Oral Opioid Information
Description: Provides details such as Morphine Equivalent Dose (MED),
brand name and opioid content which are calculated of all oral opioids
authorized for sale by Health Canada and the FDA based on their Drug Identification Number (DIN) or National Drug Code (NDC).
MEDs are calculated based on recommendations by Canadian Institute for Health Information (CIHI) and Von Korff et al (2008)
and information obtained from Health Canada's Drug Product Database's monthly data dump or FDA Daily database for Canadian and US databases respectively.
Please note in no way should output from this package be a substitute for medical advise.
All medications should only be consumed on prescription from a licensed healthcare provider.
Author: Ankona Banerjee [aut, cre] ,
Erik Stricker [aut]
Maintainer: Ankona Banerjee <asb426@mail.usask.ca>
Diff between OralOpioids versions 2.0.2 dated 2024-01-10 and 2.0.4 dated 2025-01-09
OralOpioids-2.0.2/OralOpioids/inst/doc/OralOpioid.html |only OralOpioids-2.0.2/OralOpioids/inst/download/2024-01-02_HealthCanada_Opioid_Table.xlsx |only OralOpioids-2.0.2/OralOpioids/inst/download/2024-01-08_FDA_Opioid_Table.xlsx |only OralOpioids-2.0.4/OralOpioids/DESCRIPTION | 8 OralOpioids-2.0.4/OralOpioids/MD5 | 22 OralOpioids-2.0.4/OralOpioids/NAMESPACE | 3 OralOpioids-2.0.4/OralOpioids/NEWS.md | 6 OralOpioids-2.0.4/OralOpioids/R/OralOpioids.R | 1678 +++++----- OralOpioids-2.0.4/OralOpioids/build/vignette.rds |binary OralOpioids-2.0.4/OralOpioids/inst/doc/OralOpioid.Rmd | 2 OralOpioids-2.0.4/OralOpioids/inst/doc/OralOpioid.pdf |only OralOpioids-2.0.4/OralOpioids/inst/download/2025-01-02_HealthCanada_Opioid_Table.xlsx |only OralOpioids-2.0.4/OralOpioids/inst/download/2025-01-03_FDA_Opioid_Table.xlsx |only OralOpioids-2.0.4/OralOpioids/inst/download/2025-01-08_FDA_Opioid_Table.xlsx |only OralOpioids-2.0.4/OralOpioids/vignettes/OralOpioid.Rmd | 2 OralOpioids-2.0.4/OralOpioids/vignettes/OralOpioid.html |only 16 files changed, 913 insertions(+), 808 deletions(-)
Title: Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, K-Nearest Neighbors, Penalized Regression (L1/L2), and Bayesian Additive Regression Trees. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Author: Alireza S. Mahani [aut, cre],
Mansour T.A. Sharabiani [aut]
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between EnsembleBase versions 1.0.2 dated 2016-09-13 and 1.0.4 dated 2025-01-09
ChangeLog | 40 - DESCRIPTION | 20 MD5 | 70 - NAMESPACE | 174 ++-- R/aaa.R | 42 - R/baselearners.R | 1160 +++++++++++++++--------------- R/integrators.R | 54 - R/regression_bart.R | 124 +-- R/regression_gbm.R | 86 +- R/regression_knn.R | 86 +- R/regression_nnet.R | 118 +-- R/regression_penreg.R | 118 +-- R/regression_rf.R | 100 +- R/regression_svm.R | 86 +- R/utils.R | 88 +- man/ALL.Regression.Config-class.Rd | 152 +-- man/ALL.Regression.FitObj-class.Rd | 106 +- man/BaseLearner.Batch.FitObj-class.Rd | 78 +- man/BaseLearner.CV.Batch.FitObj-class.Rd | 78 +- man/BaseLearner.CV.FitObj-class.Rd | 70 - man/BaseLearner.Config-class.Rd | 62 - man/BaseLearner.Fit-methods.Rd | 118 +-- man/BaseLearner.FitObj-class.Rd | 66 - man/Instance-class.Rd | 86 +- man/OptionalInteger-class.Rd | 54 - man/Regression.Batch.Fit.Rd | 114 +- man/Regression.CV.Batch.Fit.Rd | 148 +-- man/Regression.CV.Fit.Rd | 110 +- man/Regression.Integrator.Config-class.Rd | 78 +- man/Regression.Integrator.Fit-methods.Rd | 50 - man/RegressionEstObj-class.Rd | 50 - man/RegressionSelectPred-class.Rd | 46 - man/generate.partition.Rd | 76 - man/make.configs.Rd | 140 +-- man/servo.Rd | 48 - man/validate-methods.Rd | 45 - 36 files changed, 2077 insertions(+), 2064 deletions(-)
Title: Bayesian Mixture Survival Models using Additive
Mixture-of-Weibull Hazards, with Lasso Shrinkage and
Stratification
Description: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and
Stratification. As a Bayesian dynamic survival model, it relaxes the proportional-hazard assumption. Lasso shrinkage controls
overfitting, given the increase in the number of free parameters in the model due to presence of two Weibull components
in the hazard function.
Author: Alireza S. Mahani [aut, cre],
Mansour T.A. Sharabiani [aut]
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between BayesMixSurv versions 0.9.1 dated 2016-09-08 and 0.9.3 dated 2025-01-09
ChangeLog | 11 DESCRIPTION | 20 MD5 | 26 NAMESPACE | 34 - R/BayesMixSurv.R | 1418 +++++++++++++++++++++---------------------- R/Sample.R | 294 ++++---- R/SliceSampler.R | 362 +++++----- R/utils.R | 140 ++-- R/zzz.R | 12 man/BayesMixSurv.Rd | 194 ++--- man/BayesMixSurv_CrossVal.Rd | 132 ++-- man/plot_BayesMixSurv.Rd | 66 +- man/predict_BayesMixSurv.Rd | 116 +-- man/summary_BayesMixSurv.Rd | 92 +- 14 files changed, 1464 insertions(+), 1453 deletions(-)