Title: Format BibTeX Entries and Files
Description: Format BibTeX entries and files in an opinionated way.
Author: Wenjie Wang [aut, cre]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between formatBibtex versions 0.1.0 dated 2023-02-03 and 0.1.1 dated 2025-03-03
formatBibtex-0.1.0/formatBibtex/R/zzz.R |only formatBibtex-0.1.1/formatBibtex/DESCRIPTION | 11 +- formatBibtex-0.1.1/formatBibtex/MD5 | 26 +++--- formatBibtex-0.1.1/formatBibtex/NAMESPACE | 2 formatBibtex-0.1.1/formatBibtex/NEWS.md |only formatBibtex-0.1.1/formatBibtex/R/bibtex.R | 12 +-- formatBibtex-0.1.1/formatBibtex/R/default_options.R |only formatBibtex-0.1.1/formatBibtex/R/format_string.R | 39 +++++++--- formatBibtex-0.1.1/formatBibtex/R/misc.R | 5 + formatBibtex-0.1.1/formatBibtex/README.md | 6 - formatBibtex-0.1.1/formatBibtex/inst/CITATION | 4 - formatBibtex-0.1.1/formatBibtex/inst/examples/ex-bibtex.R | 24 ++---- formatBibtex-0.1.1/formatBibtex/inst/examples/ex-format_string.R | 12 +-- formatBibtex-0.1.1/formatBibtex/man/format_bibtex_entry.Rd | 28 +++---- formatBibtex-0.1.1/formatBibtex/man/format_options.Rd |only formatBibtex-0.1.1/formatBibtex/man/format_string.Rd | 27 +++--- 16 files changed, 108 insertions(+), 88 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [ctb],
Ching Ching Lau [ [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 0.98 dated 2024-09-19 and 1.0.5 dated 2025-03-03
dartR.base-0.98/dartR.base/R/gl.prop.shared.r |only dartR.base-0.98/dartR.base/R/gl2svdquartets.r |only dartR.base-0.98/dartR.base/man/gl2svdquartets.Rd |only dartR.base-1.0.5/dartR.base/DESCRIPTION | 16 dartR.base-1.0.5/dartR.base/MD5 | 230 +-- dartR.base-1.0.5/dartR.base/NAMESPACE | 18 dartR.base-1.0.5/dartR.base/R/gl.compliance.check.r | 12 dartR.base-1.0.5/dartR.base/R/gl.diagnostics.hwe.r | 10 dartR.base-1.0.5/dartR.base/R/gl.dist.phylo.r | 20 dartR.base-1.0.5/dartR.base/R/gl.dist.pop.r | 71 - dartR.base-1.0.5/dartR.base/R/gl.drop.ind.r | 24 dartR.base-1.0.5/dartR.base/R/gl.drop.pop.r | 61 dartR.base-1.0.5/dartR.base/R/gl.filter.excess.het.r |only dartR.base-1.0.5/dartR.base/R/gl.filter.hwe.r | 5 dartR.base-1.0.5/dartR.base/R/gl.filter.monomorphs.r | 3 dartR.base-1.0.5/dartR.base/R/gl.filter.rdepth.r | 20 dartR.base-1.0.5/dartR.base/R/gl.filter.reproducibility.r | 28 dartR.base-1.0.5/dartR.base/R/gl.filter.secondaries.r | 21 dartR.base-1.0.5/dartR.base/R/gl.join.r | 346 +++-- dartR.base-1.0.5/dartR.base/R/gl.keep.ind.r | 32 dartR.base-1.0.5/dartR.base/R/gl.keep.pop.r | 51 dartR.base-1.0.5/dartR.base/R/gl.load.r | 26 dartR.base-1.0.5/dartR.base/R/gl.map.interactive.r | 75 - dartR.base-1.0.5/dartR.base/R/gl.pcoa.r | 186 ++ dartR.base-1.0.5/dartR.base/R/gl.propShared.r |only dartR.base-1.0.5/dartR.base/R/gl.read.PLINK.r | 1 dartR.base-1.0.5/dartR.base/R/gl.read.csv.r | 17 dartR.base-1.0.5/dartR.base/R/gl.read.dart.r | 3 dartR.base-1.0.5/dartR.base/R/gl.read.vcf.r | 15 dartR.base-1.0.5/dartR.base/R/gl.report.allelerich.r |only dartR.base-1.0.5/dartR.base/R/gl.report.allna.r | 8 dartR.base-1.0.5/dartR.base/R/gl.report.bases.r | 2 dartR.base-1.0.5/dartR.base/R/gl.report.callrate.r | 50 dartR.base-1.0.5/dartR.base/R/gl.report.diversity.r | 98 - dartR.base-1.0.5/dartR.base/R/gl.report.excess.het.r |only dartR.base-1.0.5/dartR.base/R/gl.report.heterozygosity.r | 18 dartR.base-1.0.5/dartR.base/R/gl.report.hwe.r | 5 dartR.base-1.0.5/dartR.base/R/gl.report.ld.map.r | 11 dartR.base-1.0.5/dartR.base/R/gl.report.maf.r | 6 dartR.base-1.0.5/dartR.base/R/gl.report.pa.r | 135 + dartR.base-1.0.5/dartR.base/R/gl.report.polyploid_heterozygosity.r | 24 dartR.base-1.0.5/dartR.base/R/gl.report.reproducibility.r | 31 dartR.base-1.0.5/dartR.base/R/gl.report.shannon.r |only dartR.base-1.0.5/dartR.base/R/gl.save.r | 5 dartR.base-1.0.5/dartR.base/R/gl.sort.r | 78 - dartR.base-1.0.5/dartR.base/R/gl.subsample.ind.r | 145 +- dartR.base-1.0.5/dartR.base/R/gl.subsample.loc.r | 84 - dartR.base-1.0.5/dartR.base/R/gl.tree.fitch.r | 7 dartR.base-1.0.5/dartR.base/R/gl.tree.nj.r | 37 dartR.base-1.0.5/dartR.base/R/gl2bpp.r | 101 + dartR.base-1.0.5/dartR.base/R/gl2fasta.r | 21 dartR.base-1.0.5/dartR.base/R/gl2genepop.r | 4 dartR.base-1.0.5/dartR.base/R/gl2paup.parsimony.r |only dartR.base-1.0.5/dartR.base/R/gl2paup.svdquartets.r |only dartR.base-1.0.5/dartR.base/R/utils.check.datatype.R | 4 dartR.base-1.0.5/dartR.base/R/utils.collapse.matrix.r |only dartR.base-1.0.5/dartR.base/R/utils.dart2genlight.r | 56 dartR.base-1.0.5/dartR.base/R/utils.het.report.r | 16 dartR.base-1.0.5/dartR.base/R/utils.read.dart.r | 14 dartR.base-1.0.5/dartR.base/R/utils.read.ped.r | 15 dartR.base-1.0.5/dartR.base/man/gl.alf.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.allele.freq.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.dist.phylo.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.dist.pop.Rd | 10 dartR.base-1.0.5/dartR.base/man/gl.filter.excess.het.Rd |only dartR.base-1.0.5/dartR.base/man/gl.filter.hwe.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.join.Rd | 21 dartR.base-1.0.5/dartR.base/man/gl.load.Rd | 13 dartR.base-1.0.5/dartR.base/man/gl.map.interactive.Rd | 31 dartR.base-1.0.5/dartR.base/man/gl.prop.shared.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.read.csv.Rd | 6 dartR.base-1.0.5/dartR.base/man/gl.read.vcf.Rd | 14 dartR.base-1.0.5/dartR.base/man/gl.report.allelerich.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.allna.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.bases.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.report.basics.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.callrate.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.report.diversity.Rd | 26 dartR.base-1.0.5/dartR.base/man/gl.report.excess.het.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.hamming.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.heterozygosity.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.report.hwe.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.report.ld.map.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl.report.locmetric.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.maf.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.overshoot.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.pa.Rd | 39 dartR.base-1.0.5/dartR.base/man/gl.report.polyploid_heterozygosity.Rd | 684 ++++------ dartR.base-1.0.5/dartR.base/man/gl.report.rdepth.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.reproducibility.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.secondaries.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.shannon.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.taglength.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.sort.Rd | 42 dartR.base-1.0.5/dartR.base/man/gl.subsample.ind.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.subsample.loc.Rd | 8 dartR.base-1.0.5/dartR.base/man/gl.tree.fitch.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.tree.nj.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl2bpp.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl2genepop.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl2paup.parsimony.Rd |only dartR.base-1.0.5/dartR.base/man/gl2paup.svdquartets.Rd |only dartR.base-1.0.5/dartR.base/man/utils.check.datatype.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.collapse.matrix.Rd |only dartR.base-1.0.5/dartR.base/man/utils.dart2genlight.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.dist.binary.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.flag.start.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.hamming.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.het.pop.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.impute.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.is.fixed.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.jackknife.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.n.var.invariant.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.plot.save.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.read.fasta.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.read.ped.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.avgpic.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.callrate.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhets.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhomref.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhomsnp.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.maf.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.reset.flags.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.transpose.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.vcfr2genlight.polyploid.Rd | 1 125 files changed, 2112 insertions(+), 1143 deletions(-)
Title: Load and Process Passive Acoustic Data
Description: Tools for loading and processing passive acoustic data. Read in data
that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite
processing functions, and export data for reports or external modeling tools. Parameter
calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>,
Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)
<doi:10.1121/1.3479549>.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Emily Griffiths [ctb],
Michael Oswald [ctb],
Simone Baumann-Pickering [ctb],
Julie Oswald [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMpal versions 1.2.1 dated 2024-07-11 and 1.4.4 dated 2025-03-03
DESCRIPTION | 8 - MD5 | 58 ++++----- NAMESPACE | 10 + NEWS.md | 41 ++++++ R/PAMpalSettings.R | 7 - R/addFunction.R | 16 ++ R/addRecordings.R | 41 ++++-- R/calculateAverageSpectra.R | 5 R/calculateEchoDepth.R | 242 ++++++++++++++++++++++++++++++++------- R/calculateICI.R | 38 +++--- R/calculateModuleData.R | 51 -------- R/getClipData.R | 2 R/getDetectorData.R | 4 R/plotGram.R | 15 +- R/processPgDetections.R | 170 +++++++++++++++++++-------- R/runDepthReview.R | 124 +++++++++++++++---- R/runIciReview.R |only R/setSpecies.R | 7 - R/standardClickCalcs.R | 6 R/updateFiles.R | 22 +++ R/utils.R | 4 R/wavUtils.R | 2 man/PAMpalSettings.Rd | 3 man/addFunction.Rd | 4 man/addRecordings.Rd | 7 + man/calculateEchoDepth.Rd | 10 + man/calculateICI.Rd | 6 man/getDetectorData.Rd | 4 man/processPgDetections.Rd | 14 +- man/runIciReview.Rd |only tests/testthat/test-processPps.R | 28 +++- 31 files changed, 681 insertions(+), 268 deletions(-)
Title: Influential Cases in Structural Equation Modeling
Description: Sensitivity analysis in structural equation modeling using
influence measures and diagnostic plots. Support leave-one-out casewise
sensitivity analysis presented by Pek and MacCallum (2011)
<doi:10.1080/00273171.2011.561068> and approximate casewise influence
using scores and casewise likelihood.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semfindr versions 0.1.8 dated 2024-04-08 and 0.1.9 dated 2025-03-03
DESCRIPTION | 11 - MD5 | 63 +++++---- NEWS.md | 50 +++++++ R/approx_check.R | 11 - R/est_change_plot.R | 4 R/est_change_raw_user.R | 46 +++++-- R/generic_index_plot.R | 6 R/influence_plot.R | 4 R/lavaan_rerun.R | 60 +++++++-- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/casewise_scores.html | 14 +- inst/doc/selecting_cases.html | 8 - inst/doc/semfindr.R | 40 +++--- inst/doc/semfindr.Rmd | 2 inst/doc/semfindr.html | 38 ++--- inst/doc/user_id.R | 2 inst/doc/user_id.html | 8 - man/approx_check.Rd | 8 - man/est_change_plot.Rd | 4 man/index_plot.Rd | 2 man/influence_plot.Rd | 4 man/lavaan_rerun.Rd | 17 ++ man/pars_id_to_lorg.Rd | 6 man/semfindr-package.Rd | 2 man/user_change_raw.Rd | 22 ++- tests/testthat/test-approx_check.R | 2 tests/testthat/test-est_change_raw_loo_single_user_function.R | 64 ++++++++++ tests/testthat/test-lavaan_rerun_parallel.R |only vignettes/articles/user_fun-1.png |only vignettes/articles/user_fun2-1.png |only vignettes/articles/user_function.Rmd |only vignettes/articles/user_function.Rmd.original |only vignettes/semfindr.Rmd | 2 35 files changed, 354 insertions(+), 148 deletions(-)
Title: Convert Among Citation Formats
Description: Converts among many citation formats, including 'BibTeX',
'Citeproc', 'Codemeta', 'RDF XML', 'RIS', 'Schema.org', and
'Citation File Format'. A low level 'R6' class is provided, as well
as stand-alone functions for each citation format for both read
and write.
Author: Scott Chamberlain [aut] ,
Brenton M. Wiernik [aut, cre] ,
Thierry Onkelinx [ctb]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between handlr versions 0.3.0 dated 2020-10-15 and 0.3.1 dated 2025-03-03
DESCRIPTION | 27 ++++--- MD5 | 66 ++++++++--------- NEWS.md | 9 ++ R/a_types.R | 2 R/cff_reader.R | 76 +++++++++++++------- R/cff_writer.R | 64 +++++++++++----- R/codemeta_reader.R | 12 +-- R/codemeta_writer.R | 16 ++-- R/doi_utils.R | 17 ++-- R/handlr-package.r | 20 ++--- R/schema_org_writer.R | 34 ++++---- R/translations.R | 12 +-- README.md | 75 ++++++++----------- inst/extdata/bib-many.bib | 4 - inst/extdata/citation_1.2.0.cff |only inst/extdata/citation_1.2.0_project.cff |only inst/extdata/citeproc-many.json | 2 inst/extdata/citeproc2.json | 2 inst/extdata/codemeta-many.json | 36 ++++----- inst/extdata/codemeta.json | 18 ++-- inst/extdata/crosscite.json | 4 - inst/extdata/crossref.bib | 4 - inst/extdata/crossref.ris | 2 inst/extdata/elsevier.ris | 2 man/HandlrClient.Rd | 36 ++++----- man/cff_reader.Rd | 14 ++- man/cff_reference_types.Rd | 2 man/cff_writer.Rd | 20 ++++- man/codemeta_writer.Rd | 2 man/handl.Rd | 6 + man/handlr-package.Rd | 12 ++- man/schema_org_writer.Rd | 2 tests/testthat/test-cff_reader.R | 121 +++++++++++++++++++++++++++++--- tests/testthat/test-cff_writer.R | 70 +++++++++++++++++- tests/testthat/test-client.R | 3 35 files changed, 528 insertions(+), 264 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Davis Vaughan [aut, cre] ,
Jim Hester [aut] ,
Romain Francois [aut] ,
Benjamin Kietzman [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between cpp11 versions 0.5.1 dated 2024-12-04 and 0.5.2 dated 2025-03-03
DESCRIPTION | 6 - MD5 | 24 +++--- NEWS.md | 4 + inst/doc/FAQ.R | 6 + inst/doc/FAQ.html | 6 - inst/doc/cpp11.Rmd | 2 inst/doc/cpp11.html | 25 +++--- inst/doc/motivations.R | 148 +++++++++++++++++++-------------------- inst/doc/motivations.html | 99 ++++++++++++++++---------- inst/include/cpp11/R.hpp | 2 inst/include/cpp11/named_arg.hpp | 2 inst/include/fmt/format.h | 4 - vignettes/cpp11.Rmd | 2 13 files changed, 180 insertions(+), 150 deletions(-)
Title: Output Space-Filling Design
Description: Methods to generate a design in the input space that sequentially fills the output space of a black-box function. The output space-filling designs are helpful in inverse design or feature-based modeling problems.
See Wang, Shangkun, Adam P. Generale, Surya R. Kalidindi, and V. Roshan Joseph. (2024), Sequential designs for filling output spaces, Technometrics, 66, 65–76. for details. This work is supported by U.S. National Foundation grant CMMI-1921646.
Author: Shangkun Wang [aut, cre],
Roshan Joseph [aut]
Maintainer: Shangkun Wang <sk_wang@gatech.edu>
Diff between OSFD versions 3.0 dated 2025-01-15 and 3.1 dated 2025-03-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/OSFD.cpp | 11 ++++++++--- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Machine Learning Experiments
Description: Provides 'R6' objects to perform parallelized hyperparameter
optimization and cross-validation. Hyperparameter optimization can be
performed with Bayesian optimization (via 'ParBayesianOptimization'
<https://cran.r-project.org/package=ParBayesianOptimization>) and grid
search. The optimized hyperparameters can be validated using k-fold
cross-validation. Alternatively, hyperparameter optimization and
validation can be performed with nested cross-validation. While
'mlexperiments' focuses on core wrappers for machine learning
experiments, additional learner algorithms can be supplemented by
inheriting from the provided learner base class.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlexperiments versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 108 +-- NAMESPACE | 38 - R/MLTuneParameters.R | 410 ++++++------ R/cv_helper_base.R | 14 R/cv_performance.R | 390 ++++++------ R/cv_predictions.R | 282 ++++---- R/learner_lm.R | 4 R/optimizer_class_base.R | 84 +- R/optimizer_class_bayesian.R | 70 +- R/optimizer_helper_base.R | 102 +-- R/utils_handle_cat_vars.R | 66 +- R/utils_method_params_refactor.R | 22 R/utils_metrics.R | 472 +++++++------- R/utils_validate_fold_equality.R | 260 ++++---- R/zzz.R | 40 - build/vignette.rds |binary inst/doc/mlexperiments_knn_binary.html | 5 inst/doc/mlexperiments_knn_multiclass.html | 5 inst/doc/mlexperiments_knn_multiclass.qmd | 1 inst/doc/mlexperiments_rpart_binary.html | 7 inst/doc/mlexperiments_rpart_multiclass.html | 5 inst/doc/mlexperiments_rpart_multiclass.qmd | 1 inst/doc/mlexperiments_rpart_regression.R | 6 inst/doc/mlexperiments_rpart_regression.html | 23 inst/doc/mlexperiments_rpart_regression.qmd | 6 inst/doc/mlexperiments_starter.R | 262 ++++---- inst/doc/mlexperiments_starter.html | 7 inst/doc/mlexperiments_starter.qmd | 1 man/LearnerGlm.Rd | 210 +++--- man/LearnerKnn.Rd | 242 +++---- man/LearnerLm.Rd | 210 +++--- man/LearnerRpart.Rd | 272 ++++---- man/MLBase.Rd | 132 ++-- man/MLCrossValidation.Rd | 716 +++++++++++----------- man/MLExperimentsBase.Rd | 208 +++--- man/MLLearnerBase.Rd | 792 ++++++++++++------------- man/MLNestedCV.Rd | 852 +++++++++++++-------------- man/MLTuneParameters.Rd | 584 +++++++++--------- man/handle_cat_vars.Rd | 66 +- man/metric_types_helper.Rd | 94 +- man/performance.Rd | 216 +++--- man/predictions.Rd | 168 ++--- man/validate_fold_equality.Rd | 186 ++--- tests/testthat.R | 3 tests/testthat/test-fold_equality.R | 194 +++--- tests/testthat/test-glm_predictions.R | 438 ++++++------- tests/testthat/test-knn.R | 602 +++++++++---------- tests/testthat/test-lints.R | 26 tests/testthat/test-lm.R | 73 ++ tests/testthat/test-rpart_regression.R | 502 +++++++-------- vignettes/mlexperiments_knn_multiclass.qmd | 1 vignettes/mlexperiments_rpart_multiclass.qmd | 1 vignettes/mlexperiments_rpart_regression.qmd | 6 vignettes/mlexperiments_starter.qmd | 1 55 files changed, 4787 insertions(+), 4709 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.9.0 dated 2025-02-19 and 1.9.1 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ build/vignette.rds |binary inst/doc/json-aaquickstart.html | 2 +- inst/doc/json-mapping.pdf |binary tests/testthat/test-fromJSON-datasets.R | 6 +++--- 7 files changed, 16 insertions(+), 13 deletions(-)
Title: Toolkit for HLA Immunogenomics
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Author: Livia Tran [aut],
Ryan Nickens [aut],
Leamon Crooms IV [aut],
Derek Pappas [aut],
Vinh Luu [ctb],
Josh Bredeweg [ctb],
Steven Mack [aut, cre]
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Diff between HLAtools versions 1.3.0 dated 2024-11-14 and 1.4.0 dated 2025-03-03
DESCRIPTION | 8 MD5 | 115 ++++---- NAMESPACE | 3 NEWS.md | 19 + R/AlleleTrim.R | 16 - R/BDtoPyPop.R | 4 R/GIANT.R | 29 +- R/GLStoUNI.R | 4 R/GLupdater.R | 590 ++++++++++++++++++++---------------------- R/SearchandBuildAlignments.R | 26 + R/ThirdPartyFunctions.R | 3 R/VersionValidation.R | 8 R/accessoryFunctions.R | 51 ++- R/atlasMaker.R | 2 R/buildGazeteer.R | 2 R/compareSequences.R | 2 R/data.R | 4 R/locusValidator.R | 2 R/relRisk.R | 2 README.md | 40 +- build/vignette.rds |binary data/HLAatlas.rda |binary data/HLAgazeteer.rda |binary data/alleleListHistory.rda |binary data/fragmentFeatureNames.rda |binary inst/doc/HLAtools.Rmd | 22 + inst/doc/HLAtools.html | 43 ++- man/GIANT.Rd | 4 man/GLSC.ex.Rd | 2 man/GLV.Rd | 4 man/GLV2.Rd | 4 man/GLVhelper.Rd | 4 man/GLupdate.Rd | 34 -- man/GLvalidate.Rd | 6 man/HLAatlas.Rd | 2 man/alignmentSearch.Rd | 12 man/atlasMaker.Rd | 2 man/compareSequences.Rd | 2 man/convertAny.Rd | 6 man/countSpaces.Rd | 3 man/customAlign.Rd | 10 man/formatHead.Rd | 6 man/getAlignmentNames.Rd | 2 man/getField.Rd | 2 man/multiAlign.Rd | 2 man/multiTranslateGLstring.Rd |only man/multiUpdateGL.Rd | 23 - man/parseAlignmentHead.Rd | 2 man/redec.Rd | 2 man/relRisk.Rd | 2 man/repoVersion.Rd | 4 man/squashVersion.Rd | 4 man/translateAllele.Rd |only man/translateGLstring.Rd |only man/uniAlign.Rd | 2 man/updateGL.Rd | 29 -- man/validateAllele.Rd | 4 man/validateLocus.Rd | 2 man/verifyAllele.Rd | 16 - vignettes/HLAtools.Rmd | 22 + 60 files changed, 660 insertions(+), 554 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.6 dated 2025-02-10 and 3.6.7 dated 2025-03-03
DESCRIPTION | 8 MD5 | 93 - NEWS.md | 11 inst/doc/ConditionalErrorSpending.R | 4 inst/doc/ConditionalErrorSpending.Rmd | 4 inst/doc/ConditionalErrorSpending.html | 1367 +++++++++++++++-- inst/doc/ConditionalPowerPlot.R | 4 inst/doc/ConditionalPowerPlot.Rmd | 4 inst/doc/ConditionalPowerPlot.html | 607 +++++++ inst/doc/GentleIntroductionToGSD.R | 4 inst/doc/GentleIntroductionToGSD.Rmd | 4 inst/doc/GentleIntroductionToGSD.html | 2 inst/doc/PoissonMixtureModel.R | 4 inst/doc/PoissonMixtureModel.Rmd | 4 inst/doc/PoissonMixtureModel.html | 1818 ++++++++++++++++++++++- inst/doc/SpendingFunctionOverview.R | 4 inst/doc/SpendingFunctionOverview.Rmd | 4 inst/doc/SurvivalOverview.R | 4 inst/doc/SurvivalOverview.Rmd | 4 inst/doc/SurvivalOverview.html | 651 ++++++++ inst/doc/VaccineEfficacy.R | 4 inst/doc/VaccineEfficacy.Rmd | 4 inst/doc/VaccineEfficacy.html | 442 ++--- inst/doc/binomialSPRTExample.R | 4 inst/doc/binomialSPRTExample.Rmd | 4 inst/doc/binomialSPRTExample.html | 1763 ++++++++++++++++++++-- inst/doc/gsDesignPackageOverview.R | 4 inst/doc/gsDesignPackageOverview.Rmd | 4 inst/doc/gsDesignPackageOverview.html | 512 ++++++ inst/doc/gsSurvBasicExamples.R | 4 inst/doc/gsSurvBasicExamples.Rmd | 4 inst/doc/gsSurvBasicExamples.html | 1224 +++++++++++++-- inst/doc/nNormal.R | 4 inst/doc/nNormal.Rmd | 4 inst/doc/nNormal.html | 328 ++++ inst/doc/toInteger.html | 2 tests/testthat/test-independent-test-toInteger.R |only vignettes/ConditionalErrorSpending.Rmd | 4 vignettes/ConditionalPowerPlot.Rmd | 4 vignettes/GentleIntroductionToGSD.Rmd | 4 vignettes/PoissonMixtureModel.Rmd | 4 vignettes/SpendingFunctionOverview.Rmd | 4 vignettes/SurvivalOverview.Rmd | 4 vignettes/VaccineEfficacy.Rmd | 4 vignettes/binomialSPRTExample.Rmd | 4 vignettes/gsDesignPackageOverview.Rmd | 4 vignettes/gsSurvBasicExamples.Rmd | 4 vignettes/nNormal.Rmd | 4 48 files changed, 8066 insertions(+), 894 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.2.0 dated 2023-12-06 and 0.3.0 dated 2025-03-03
fwb-0.2.0/fwb/build/fwb.pdf |only fwb-0.3.0/fwb/DESCRIPTION | 16 fwb-0.3.0/fwb/MD5 | 53 +- fwb-0.3.0/fwb/NAMESPACE | 1 fwb-0.3.0/fwb/NEWS.md | 26 + fwb-0.3.0/fwb/R/fwb.R | 323 ++++++++++++---- fwb-0.3.0/fwb/R/fwb.ci.R | 130 ++++-- fwb-0.3.0/fwb/R/plot.fwb.R | 12 fwb-0.3.0/fwb/R/set_fwb_wtype.R | 8 fwb-0.3.0/fwb/R/summary.fwb.R | 83 ++-- fwb-0.3.0/fwb/R/utils.R | 287 ++++++++------ fwb-0.3.0/fwb/R/vcovFWB.R | 145 +++++-- fwb-0.3.0/fwb/README.md | 61 +-- fwb-0.3.0/fwb/build/stage23.rdb |binary fwb-0.3.0/fwb/build/vignette.rds |only fwb-0.3.0/fwb/inst |only fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-10-1.png |binary fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-5-1.png |binary fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-9-1.png |binary fwb-0.3.0/fwb/man/fwb-package.Rd | 1 fwb-0.3.0/fwb/man/fwb.Rd | 36 + fwb-0.3.0/fwb/man/fwb.ci.Rd | 5 fwb-0.3.0/fwb/man/get_ci.Rd | 2 fwb-0.3.0/fwb/man/set_fwb_wtype.Rd | 8 fwb-0.3.0/fwb/man/summary.fwb.Rd | 17 fwb-0.3.0/fwb/man/vcovFWB.Rd | 40 + fwb-0.3.0/fwb/tests |only fwb-0.3.0/fwb/vignettes |only 28 files changed, 871 insertions(+), 383 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.5.0 dated 2025-01-15 and 1.5.1 dated 2025-03-03
DESCRIPTION | 9 MD5 | 50 ++-- NEWS.md | 7 R/CFCalendar.R | 9 R/CFCalendarProleptic.R | 2 R/CFCalendarStandard.R | 4 R/CFCalendarUTC.R | 22 +- R/CFtime.R | 113 +++++----- R/api.R | 16 - R/deprecated.R | 4 README.md | 133 +++++------- TODO | 5 inst/doc/CFtime.R | 63 +++--- inst/doc/CFtime.Rmd | 79 +++---- inst/doc/CFtime.html | 263 ++++++++++++++++++------- inst/doc/Processing.R | 74 +++---- inst/doc/Processing.Rmd | 116 +++++------ inst/doc/Processing.html | 376 +++++++++++++++++++++++------------- man/CFCalendar.Rd | 2 man/CFTime.Rd | 30 +- tests/testthat/test-CFformat.R | 17 + tests/testthat/test-CFtime.R | 31 +- tests/testthat/test-functions.R | 16 + tests/testthat/test-parse_deparse.R | 44 ++++ vignettes/CFtime.Rmd | 79 +++---- vignettes/Processing.Rmd | 116 +++++------ 26 files changed, 1005 insertions(+), 675 deletions(-)
Title: R6-Based ML Survival Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners for survival analysis. The package
provides R6-based survival learners for the following algorithms:
'glmnet' <https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'rpart'
<https://CRAN.R-project.org/package=rpart>. These can be used directly
with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlsurvlrnrs versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 52 +-- NAMESPACE | 24 - R/learner_surv_coxph_cox.R | 316 +++++++++++----------- R/surv_c_index.R | 54 +-- R/zzz.R | 50 +-- build/vignette.rds |binary inst/doc/mlsurvlrnrs_glmnet_survival.html | 5 inst/doc/mlsurvlrnrs_ranger_survival.html | 5 inst/doc/mlsurvlrnrs_rpart_survival.html | 5 inst/doc/mlsurvlrnrs_xgboost_survival_aft.html | 5 inst/doc/mlsurvlrnrs_xgboost_survival_cox.html | 5 man/LearnerSurvCoxPHCox.Rd | 284 +++++++++---------- man/LearnerSurvGlmnetCox.Rd | 308 ++++++++++----------- man/LearnerSurvRangerCox.Rd | 314 +++++++++++----------- man/LearnerSurvRpartCox.Rd | 342 ++++++++++++------------ man/LearnerSurvXgboostAft.Rd | 356 ++++++++++++------------- man/LearnerSurvXgboostCox.Rd | 348 ++++++++++++------------ man/c_index.Rd | 66 ++-- tests/testthat.R | 27 + tests/testthat/test-lints.R | 26 - tests/testthat/test-surv_coxph_cox.R | 128 ++++---- tests/testthat/test-surv_glmnet_cox.R | 214 +++++++-------- tests/testthat/test-surv_ranger_cox.R | 236 ++++++++-------- tests/testthat/test-surv_rpart_cox.R | 230 ++++++++-------- tests/testthat/test-surv_xgboost_aft.R | 248 ++++++++--------- tests/testthat/test-surv_xgboost_cox.R | 246 ++++++++--------- 27 files changed, 1951 insertions(+), 1953 deletions(-)
Title: (Kernel) Isotope Niche Estimation
Description: Applies methods used to estimate animal homerange, but
instead of geospatial coordinates, we use isotopic coordinates. The estimation
methods include: 1) 2-dimensional bivariate normal kernel utilization density
estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon
estimator, all applied to stable isotope data. Additionally, functions to
determine niche area, polygon overlap between groups and levels (confidence
contours) and plotting capabilities.
Author: Shannon E Albeke [aut, cre]
Maintainer: Shannon E Albeke <salbeke@uwyo.edu>
Diff between rKIN versions 1.0.3 dated 2025-02-14 and 1.0.4 dated 2025-03-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/getColors.R | 17 ++++++----------- 3 files changed, 12 insertions(+), 17 deletions(-)
Title: Color-Based Image Segmentation
Description: Automatic, semi-automatic, and manual functions for
generating color maps from images. The idea is to simplify
the colors of an image according to a metric that is useful for
the user, using deterministic methods whenever possible.
Many images will be clustered well using the out-of-the-box
functions, but the package also includes a toolbox of functions
for making manual adjustments (layer merging/isolation, blurring,
fitting to provided color clusters or those from another image, etc).
Also includes export methods for other color/pattern analysis packages
(pavo, patternize, colordistance).
Author: Hannah Weller [aut, cre]
Maintainer: Hannah Weller <hannahiweller@gmail.com>
Diff between recolorize versions 0.1.0 dated 2021-12-07 and 0.2.0 dated 2025-03-03
DESCRIPTION | 15 MD5 | 200 ++--- NAMESPACE | 3 NEWS.md | 9 R/absorbLayer.R | 60 + R/apply_imager_operation.R | 10 R/assignPixels.R | 4 R/backgroundCondition.R | 2 R/backgroundIndex.R | 14 R/blurImage.R | 16 R/brick_to_array.R | 11 R/cimgConversions.R | 2 R/colorClusters.R | 70 + R/colorResiduals.R | 6 R/editLayers.R | 28 R/imDist.R | 20 R/imposeColors.R | 5 R/medianColors.R |only R/mergeLayers.R | 31 R/pixelAssignMatrix.R | 4 R/plotColorPalette.R | 4 R/plotImageArray.R | 4 R/plot_recolorize.R | 6 R/raster_array_conversions.R | 4 R/readImage.R | 17 R/recluster.R | 22 R/recolorImage.R | 4 R/recolorize-package.R |only R/recolorize.R | 27 R/recolorize2.R | 8 R/recolorizeVector.R | 19 R/recolorize_adjacency.R | 1 R/reorder_colors.R |only R/rerun_recolorize.R | 2 R/splitByColor.R | 19 R/thresholdRecolor.R | 6 R/wernerColor.R | 16 README.md | 113 ++ build/vignette.rds |binary inst/doc/Introduction.R | 223 ++--- inst/doc/Introduction.Rmd | 11 inst/doc/Introduction.html | 1166 ++++++++++++++++-------------- inst/doc/step00_prep.R | 79 +- inst/doc/step00_prep.Rmd | 1 inst/doc/step00_prep.html | 715 ++++++++++-------- inst/doc/step01_loading.R | 83 +- inst/doc/step01_loading.Rmd | 1 inst/doc/step01_loading.html | 835 +++++++++++---------- inst/doc/step02_initial_cluster.R | 253 +++--- inst/doc/step02_initial_cluster.Rmd | 1 inst/doc/step02_initial_cluster.html | 1095 ++++++++++++++++------------ inst/doc/step03_refinement.R | 79 +- inst/doc/step03_refinement.Rmd | 1 inst/doc/step03_refinement.html | 848 +++++++++++---------- inst/doc/step04_manual_tweak.R | 82 +- inst/doc/step04_manual_tweak.Rmd | 6 inst/doc/step04_manual_tweak.html | 858 +++++++++++----------- inst/doc/step05_visualization_export.R | 139 +-- inst/doc/step05_visualization_export.Rmd | 1 inst/doc/step05_visualization_export.html | 965 +++++++++++++----------- inst/extdata/msc/corbetti_vector.rds |binary man/absorbLayer.Rd | 9 man/apply_imager_operation.Rd | 10 man/array_to_RasterStack.Rd | 2 man/array_to_cimg.Rd | 2 man/assignPixels.Rd | 4 man/backgroundCondition.Rd | 2 man/backgroundIndex.Rd | 6 man/blurImage.Rd | 14 man/col2col.Rd | 7 man/colorClusters.Rd | 14 man/colorClustersHist.Rd | 12 man/colorClustersKMeans.Rd | 6 man/colorResiduals.Rd | 6 man/editLayer.Rd | 12 man/editLayers.Rd | 12 man/figures |only man/imDist.Rd | 10 man/imHeatmap.Rd | 6 man/imposeColors.Rd | 5 man/match_colors.Rd |only man/medianColors.Rd |only man/mergeLayers.Rd | 12 man/pixelAssignMatrix.Rd | 4 man/plot.recolorize.Rd | 6 man/plotColorPalette.Rd | 4 man/plotImageArray.Rd | 4 man/readImage.Rd | 2 man/recluster.Rd | 20 man/recoloredImage.Rd | 2 man/recolorize-package.Rd |only man/recolorize.Rd | 14 man/recolorize2.Rd | 8 man/reorder_colors.Rd |only man/splitByColor.Rd | 14 man/thresholdRecolor.Rd | 2 man/wernerColor.Rd | 10 vignettes/Introduction.Rmd | 11 vignettes/step00_prep.Rmd | 1 vignettes/step01_loading.Rmd | 1 vignettes/step02_initial_cluster.Rmd | 1 vignettes/step03_refinement.Rmd | 1 vignettes/step04_manual_tweak.Rmd | 6 vignettes/step05_visualization_export.Rmd | 1 104 files changed, 4692 insertions(+), 3795 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Isaac Gravestock [aut, cre],
Craig Gower-Page [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between rbmi versions 1.4.0 dated 2025-02-07 and 1.4.1 dated 2025-03-03
DESCRIPTION | 16 +++++----- MD5 | 24 ++++++++-------- NEWS.md | 5 +++ R/utilities.R | 26 ++++++++++------- build/vignette.rds |binary inst/doc/advanced.html | 2 - inst/doc/quickstart.html | 50 +++++++++++++++++----------------- inst/stan/MMRM.stan | 2 - man/rbmi-package.Rd | 4 +- man/rbmi-settings.Rd | 10 ++++++ tests/testthat.R | 5 +++ tests/testthat/test-reproducibility.R | 5 +++ tests/testthat/test-utilities.R | 10 +++--- 13 files changed, 95 insertions(+), 64 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.3.7 dated 2024-10-03 and 2.0.0 dated 2025-03-03
DESCRIPTION | 8 MD5 | 81 +++--- NAMESPACE | 6 NEWS.md | 12 R/class_plot.R | 407 +++++++++++++++++++++++++++++-- R/class_print.R | 20 + R/class_summary.R | 11 R/data_countryside.R |only R/obs_shape.R | 9 R/sar_countryside.R |only R/sar_habitat.R | 67 ++--- README.md | 102 +++---- build/vignette.rds |binary data/countryside.rda |only inst/doc/sars-r-package.Rmd | 23 + inst/doc/sars-r-package.html | 155 ++--------- man/coleman.Rd | 108 ++++---- man/countryside.Rd |only man/countryside_extrap.Rd |only man/display_sars_models.Rd | 56 ++-- man/figures/README-unnamed-chunk-5-1.png |binary man/gdm.Rd | 356 +++++++++++++-------------- man/lin_pow.Rd | 144 +++++----- man/plot.habitat.Rd | 213 ++++++++++++++-- man/sar_countryside.Rd |only man/sar_habitat.Rd | 335 ++++++++++++------------- man/sar_linear.Rd | 148 +++++------ man/sar_logistic.Rd | 194 +++++++------- man/sar_multi.Rd | 142 +++++----- tests/testthat.R | 10 tests/testthat/Rplots.pdf |only tests/testthat/test_coleman.R | 2 tests/testthat/test_countryside.R |only tests/testthat/test_fit_collection.R | 6 tests/testthat/test_gdm.R | 12 tests/testthat/test_habitat.R |only tests/testthat/test_lin_pow.R | 14 - tests/testthat/test_loga.R | 4 tests/testthat/test_monod.R | 1 tests/testthat/test_multi.R | 52 +++ tests/testthat/test_power.R | 13 tests/testthat/test_pred.R | 2 tests/testthat/test_sar_linear.R | 6 tests/testthat/test_thresholds.R | 32 ++ tests/testthat/test_weibull3.R | 22 + vignettes/sars-r-package.Rmd | 23 + 46 files changed, 1734 insertions(+), 1062 deletions(-)
Title: Rating and Evaluating Texts Using Large Language Models
Description: Generates ratings and psycholinguistic metrics for textual stimuli using large language models.
It enables users to evaluate idioms and other language materials by combining context, prompts, and stimulus inputs.
It supports multiple LLM APIs (such as 'OpenAI', 'DeepSeek', 'Anthropic', 'Cohere', 'Google PaLM', and 'Ollama')
by allowing users to switch models with a single parameter. In addition to generating numeric ratings,
'chatRater' provides functions for obtaining detailed psycholinguistic metrics including word frequency (with optional corpus input),
lexical coverage (with customizable vocabulary size and test basis), Zipf metric, Levenshtein distance, and semantic transparency.
Author: Shiyang Zheng [aut, cre]
Maintainer: Shiyang Zheng <Shiyang.Zheng@nottingham.ac.uk>
Diff between chatRater versions 1.0.0 dated 2025-02-17 and 1.1.0 dated 2025-03-03
DESCRIPTION | 20 - MD5 | 19 NAMESPACE | 9 R/chatRater.R | 762 +++++++++++++++++++++++++++++++-------- README.md | 70 +++ man/chatRater-package.Rd |only man/generate_ratings.Rd | 51 +- man/generate_ratings_for_all.Rd | 47 +- man/get_levenshtein_d.Rd |only man/get_lexical_coverage.Rd |only man/get_semantic_transparency.Rd |only man/get_word_frequency.Rd |only man/get_zipf_metric.Rd |only man/llm_api_call.Rd |only 14 files changed, 763 insertions(+), 215 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson [aut, cre]
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 3.1.1 dated 2022-11-05 and 3.1.2 dated 2025-03-03
DESCRIPTION | 17 - MD5 | 42 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BHSBVAR.Rnw | 1 inst/doc/BHSBVAR.pdf |binary man/BHSBVAR-package.Rd | 50 ++--- man/BH_SBVAR.Rd | 372 ++++++++++++++++++++--------------------- man/Dist_Plots.Rd | 268 ++++++++++++++--------------- man/FEVD_Plots.Rd | 292 ++++++++++++++++---------------- man/HD_Plots.Rd | 308 ++++++++++++++++----------------- man/IRF_Plots.Rd | 274 +++++++++++++++--------------- man/USLMData.Rd | 54 ++--- src/BHSBVAR.cpp | 2 src/Makevars | 12 - src/Makevars.win | 12 - vignettes/BHSBVAR.Rnw | 1 vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/FEVD_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary 22 files changed, 842 insertions(+), 863 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Facilitate the evaluation of forecasts in a convenient
framework based on data.table. It allows user to to check their forecasts
and diagnose issues, to visualise forecasts and missing data, to transform
data before scoring, to handle missing forecasts, to aggregate scores, and
to visualise the results of the evaluation. The package mostly focuses on
the evaluation of probabilistic forecasts and allows evaluating several
different forecast types and input formats. Find more information about the
package in the Vignettes as well as in the accompanying paper,
<doi:10.48550/arXiv.2205.07090>.
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Toshiaki Asakura [ctb] ,
James Mba Azam [ctb] ,
Sebastian Funk [aut],
Michael Chirico [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 2.0.0 dated 2024-10-31 and 2.1.0 dated 2025-03-03
scoringutils-2.0.0/scoringutils/R/z-packageStartupMessage.R |only scoringutils-2.1.0/scoringutils/DESCRIPTION | 34 scoringutils-2.1.0/scoringutils/MD5 | 148 +-- scoringutils-2.1.0/scoringutils/NAMESPACE | 13 scoringutils-2.1.0/scoringutils/NEWS.md | 78 - scoringutils-2.1.0/scoringutils/R/class-forecast-binary.R | 29 scoringutils-2.1.0/scoringutils/R/class-forecast-nominal.R | 50 - scoringutils-2.1.0/scoringutils/R/class-forecast-ordinal.R |only scoringutils-2.1.0/scoringutils/R/class-forecast-point.R | 11 scoringutils-2.1.0/scoringutils/R/class-forecast-quantile.R | 18 scoringutils-2.1.0/scoringutils/R/class-forecast-sample.R | 42 scoringutils-2.1.0/scoringutils/R/class-forecast.R | 30 scoringutils-2.1.0/scoringutils/R/documentation-templates.R | 15 scoringutils-2.1.0/scoringutils/R/get-forecast-type.R | 9 scoringutils-2.1.0/scoringutils/R/get-pit-histogram.R | 6 scoringutils-2.1.0/scoringutils/R/helper-quantile-interval-range.R | 3 scoringutils-2.1.0/scoringutils/R/metrics-nominal.R | 76 + scoringutils-2.1.0/scoringutils/R/metrics-ordinal.R |only scoringutils-2.1.0/scoringutils/R/metrics-quantile.R | 11 scoringutils-2.1.0/scoringutils/R/metrics-sample.R | 24 scoringutils-2.1.0/scoringutils/R/score.R | 2 scoringutils-2.1.0/scoringutils/README.md | 7 scoringutils-2.1.0/scoringutils/build/partial.rdb |binary scoringutils-2.1.0/scoringutils/build/vignette.rds |binary scoringutils-2.1.0/scoringutils/data/example_ordinal.rda |only scoringutils-2.1.0/scoringutils/inst/create-example-data.R | 14 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-functions.html | 5 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.R | 478 +++++----- scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.Rmd | 10 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.html | 9 scoringutils-2.1.0/scoringutils/inst/doc/scoring-rules.Rmd | 6 scoringutils-2.1.0/scoringutils/inst/doc/scoring-rules.html | 15 scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.Rmd | 23 scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.aux | 70 - scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.log | 228 ++-- scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.tex | 85 + scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/calibration-plots-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/correlation-plot-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/coverage-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/pairwise-plot-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/pit-plots-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/plot-forecast-counts-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/score-heatmap-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/wis-components-1.pdf |binary scoringutils-2.1.0/scoringutils/man/as_forecast_binary.Rd | 12 scoringutils-2.1.0/scoringutils/man/as_forecast_generic.Rd | 15 scoringutils-2.1.0/scoringutils/man/as_forecast_nominal.Rd | 15 scoringutils-2.1.0/scoringutils/man/as_forecast_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/as_forecast_point.Rd | 4 scoringutils-2.1.0/scoringutils/man/as_forecast_quantile.Rd | 4 scoringutils-2.1.0/scoringutils/man/as_forecast_sample.Rd | 15 scoringutils-2.1.0/scoringutils/man/assert_input_categorical.Rd |only scoringutils-2.1.0/scoringutils/man/assert_input_nominal.Rd | 26 scoringutils-2.1.0/scoringutils/man/assert_input_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/example_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/figures/metrics-ordinal.png |only scoringutils-2.1.0/scoringutils/man/figures/workflow.png |binary scoringutils-2.1.0/scoringutils/man/get_metrics.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_binary.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_nominal.Rd | 3 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_point.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_quantile.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_sample.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.scores.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_pit_histogram.Rd | 6 scoringutils-2.1.0/scoringutils/man/illustration-input-metric-ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/is_forecast.Rd | 8 scoringutils-2.1.0/scoringutils/man/logs_sample.Rd | 2 scoringutils-2.1.0/scoringutils/man/rps_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/score.Rd | 8 scoringutils-2.1.0/scoringutils/man/scoring-functions-binary.Rd | 2 scoringutils-2.1.0/scoringutils/man/scoring-functions-nominal.Rd | 31 scoringutils-2.1.0/scoringutils/tests/testthat/setup.R | 2 scoringutils-2.1.0/scoringutils/tests/testthat/test-class-forecast-ordinal.R |only scoringutils-2.1.0/scoringutils/tests/testthat/test-class-forecast-quantile.R | 19 scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-nominal.R | 14 scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-ordinal.R |only scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-sample.R | 10 scoringutils-2.1.0/scoringutils/vignettes/Deprecated-visualisations.Rmd | 10 scoringutils-2.1.0/scoringutils/vignettes/scoring-rules.Rmd | 6 82 files changed, 1004 insertions(+), 763 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Patrick J. Breheny [aut, cre] ,
Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.2.0 dated 2025-02-18 and 4.2.1 dated 2025-03-03
plmmr-4.2.0/plmmr/tests/tinytest.R |only plmmr-4.2.1/plmmr/DESCRIPTION | 8 ++++---- plmmr-4.2.1/plmmr/MD5 | 14 +++++++------- plmmr-4.2.1/plmmr/NEWS.md | 4 ++++ plmmr-4.2.1/plmmr/build/partial.rdb |binary plmmr-4.2.1/plmmr/build/vignette.rds |binary plmmr-4.2.1/plmmr/inst/doc/getting-started.html | 10 +++++----- plmmr-4.2.1/plmmr/src/plmm_init.c | 9 ++++++--- plmmr-4.2.1/plmmr/tests/test.R |only 9 files changed, 26 insertions(+), 19 deletions(-)
Title: Generates Expectations for 'testthat' Unit Testing
Description: Helps systematize and ease the process of
building unit tests with the 'testthat' package by providing
tools for generating expectations.
Author: Ludvig Renbo Olsen [aut, cre] ,
R. Mark Sharp [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between xpectr versions 0.4.3 dated 2022-11-18 and 0.4.4 dated 2025-03-03
xpectr-0.4.3/xpectr/build/xpectr.pdf |only xpectr-0.4.3/xpectr/man/xpectr.Rd |only xpectr-0.4.4/xpectr/DESCRIPTION | 13 xpectr-0.4.4/xpectr/MD5 | 38 xpectr-0.4.4/xpectr/NEWS.md | 8 xpectr-0.4.4/xpectr/R/create_expectations.R | 2 xpectr-0.4.4/xpectr/R/do_if.R | 9 xpectr-0.4.4/xpectr/R/element_descriptors.R | 20 xpectr-0.4.4/xpectr/R/package_info.R | 4 xpectr-0.4.4/xpectr/R/strip.R | 1 xpectr-0.4.4/xpectr/R/strip_side_effect_messages.R | 10 xpectr-0.4.4/xpectr/README.md | 135 - xpectr-0.4.4/xpectr/build/stage23.rdb |only xpectr-0.4.4/xpectr/build/vignette.rds |binary xpectr-0.4.4/xpectr/inst/doc/readme.R | 986 ++++---- xpectr-0.4.4/xpectr/inst/doc/readme.Rmd | 2 xpectr-0.4.4/xpectr/inst/doc/readme.html | 1204 +++++----- xpectr-0.4.4/xpectr/man/stop_if.Rd | 9 xpectr-0.4.4/xpectr/man/strip_msg.Rd | 10 xpectr-0.4.4/xpectr/man/xpectr-package.Rd |only xpectr-0.4.4/xpectr/tests/testthat/test_capture_side_effects.R | 3 xpectr-0.4.4/xpectr/vignettes/readme.Rmd | 2 22 files changed, 1247 insertions(+), 1209 deletions(-)
Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics.
These can be used to run survival models under a frequentist (based on maximum likelihood)
or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian
Monte Carlo). To run the Bayesian models, the user needs to install additional modules
(packages), i.e. 'survHEinla' and 'survHEhmc'. These can be installed using
'remotes::install_github' from their GitHub repositories:
(<https://github.com/giabaio/survHEhmc> and <https://github.com/giabaio/survHEinla/>
respectively). 'survHEinla' is based on the package INLA, which is available for download at
<https://inla.r-inla-download.org/R/stable/>. The user can specify a set of parametric models
using a common notation and select the preferred mode of inference. The results can also be
post-processed to produce probabilistic sensitivity analysis and can be used to export the
output to an Excel file (e.g. for a Markov model, [...truncated...]
Author: Gianluca Baio [aut, cre],
Andrea Berardi [ctb],
Philip Cooney [ctb],
Andrew Jones [ctb],
Nathan Green [ctb]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between survHE versions 2.0.2 dated 2024-10-04 and 2.0.3 dated 2025-03-03
survHE-2.0.2/survHE/inst |only survHE-2.0.3/survHE/DESCRIPTION | 12 ++-- survHE-2.0.3/survHE/MD5 | 17 +++--- survHE-2.0.3/survHE/NEWS.md | 64 ++++++++++++++++++++++++-- survHE-2.0.3/survHE/R/make.transition.probs.R | 2 survHE-2.0.3/survHE/R/psa.plot.R | 6 +- survHE-2.0.3/survHE/R/utils_plot_survHE.R | 6 +- survHE-2.0.3/survHE/R/write.surv.R | 2 survHE-2.0.3/survHE/README.md | 4 + survHE-2.0.3/survHE/build/partial.rdb |binary 10 files changed, 86 insertions(+), 27 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.7.1). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.7.1.1.1 dated 2025-02-10 and 0.7.1.1.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ inst/include/vinecopulib/misc/nlohmann_json.hpp | 4 ++-- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Realistic Quantitative Structure Models
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Author: Aidan Morales [aut, cre, cph] ,
David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
Diff between rTwig versions 1.3.0 dated 2024-11-21 and 1.4.0 dated 2025-03-03
rTwig-1.3.0/rTwig/R/import_qsm.R |only rTwig-1.3.0/rTwig/R/qsm_summary.R |only rTwig-1.3.0/rTwig/R/standardize_qsm.R |only rTwig-1.3.0/rTwig/man/standardize_qsm.Rd |only rTwig-1.4.0/rTwig/DESCRIPTION | 6 rTwig-1.4.0/rTwig/MD5 | 115 +-- rTwig-1.4.0/rTwig/NAMESPACE | 5 rTwig-1.4.0/rTwig/NEWS.md | 424 ++++++------ rTwig-1.4.0/rTwig/R/RcppExports.R | 73 ++ rTwig-1.4.0/rTwig/R/box_dimension.R | 12 rTwig-1.4.0/rTwig/R/cluster_cloud.R | 18 rTwig-1.4.0/rTwig/R/correct_radii.R | 5 rTwig-1.4.0/rTwig/R/export_mat.R | 4 rTwig-1.4.0/rTwig/R/export_mesh.R | 353 +++++++--- rTwig-1.4.0/rTwig/R/import_leaves.R |only rTwig-1.4.0/rTwig/R/import_treeqsm.R |only rTwig-1.4.0/rTwig/R/plot_qsm.R | 466 ++++++++++--- rTwig-1.4.0/rTwig/R/prune_qsm.R | 37 - rTwig-1.4.0/rTwig/R/run_rtwig.R | 73 +- rTwig-1.4.0/rTwig/R/smooth_qsm.R | 5 rTwig-1.4.0/rTwig/R/standardise_qsm.R |only rTwig-1.4.0/rTwig/R/summarise_qsm.R |only rTwig-1.4.0/rTwig/R/tools.R | 13 rTwig-1.4.0/rTwig/R/tree_metrics.R | 298 ++++++-- rTwig-1.4.0/rTwig/R/twigs.R | 21 rTwig-1.4.0/rTwig/R/update_cylinders.R | 7 rTwig-1.4.0/rTwig/README.md | 15 rTwig-1.4.0/rTwig/build/partial.rdb |binary rTwig-1.4.0/rTwig/data/twigs_index.rda |only rTwig-1.4.0/rTwig/inst/REFERENCES.bib | 50 + rTwig-1.4.0/rTwig/inst/doc/Dictionary.Rmd | 272 +++++++ rTwig-1.4.0/rTwig/inst/doc/Dictionary.html | 328 +++++++++ rTwig-1.4.0/rTwig/inst/doc/Metrics.html | 6 rTwig-1.4.0/rTwig/inst/doc/Overview.R | 10 rTwig-1.4.0/rTwig/inst/doc/Overview.Rmd | 16 rTwig-1.4.0/rTwig/inst/doc/Overview.html | 39 - rTwig-1.4.0/rTwig/inst/doc/Twigs.R | 49 + rTwig-1.4.0/rTwig/inst/doc/Twigs.Rmd | 73 ++ rTwig-1.4.0/rTwig/inst/doc/Twigs.html | 97 ++ rTwig-1.4.0/rTwig/inst/doc/Validation.html | 770 +++++++++++----------- rTwig-1.4.0/rTwig/inst/include/helper_functions.h | 1 rTwig-1.4.0/rTwig/man/box_dimension.Rd | 9 rTwig-1.4.0/rTwig/man/cluster_cloud.Rd | 6 rTwig-1.4.0/rTwig/man/correct_radii.Rd | 5 rTwig-1.4.0/rTwig/man/export_mat.Rd | 4 rTwig-1.4.0/rTwig/man/export_mesh.Rd | 93 ++ rTwig-1.4.0/rTwig/man/import_leaves.Rd |only rTwig-1.4.0/rTwig/man/import_qsm.Rd | 26 rTwig-1.4.0/rTwig/man/import_treeqsm.Rd |only rTwig-1.4.0/rTwig/man/plot_qsm.Rd | 113 ++- rTwig-1.4.0/rTwig/man/prune_qsm.Rd | 24 rTwig-1.4.0/rTwig/man/qsm_summary.Rd | 28 rTwig-1.4.0/rTwig/man/run_rtwig.Rd | 24 rTwig-1.4.0/rTwig/man/smooth_qsm.Rd | 5 rTwig-1.4.0/rTwig/man/standardise_qsm.Rd |only rTwig-1.4.0/rTwig/man/summarise_qsm.Rd |only rTwig-1.4.0/rTwig/man/tree_metrics.Rd | 15 rTwig-1.4.0/rTwig/man/twigs.Rd | 4 rTwig-1.4.0/rTwig/man/twigs_index.Rd |only rTwig-1.4.0/rTwig/man/update_cylinders.Rd | 7 rTwig-1.4.0/rTwig/src/RcppExports.cpp | 65 + rTwig-1.4.0/rTwig/src/helper_functions.cpp | 67 + rTwig-1.4.0/rTwig/src/io.cpp |only rTwig-1.4.0/rTwig/vignettes/Dictionary.Rmd | 272 +++++++ rTwig-1.4.0/rTwig/vignettes/Overview.Rmd | 16 rTwig-1.4.0/rTwig/vignettes/Twigs.Rmd | 73 ++ 66 files changed, 3363 insertions(+), 1154 deletions(-)
Title: Rearranging Data
Description: Arrange data by a set of methods. Use rearrangers to reorder
data points and mutators to change their values. From basic utilities,
to centering the greatest value, to swirling in 3-dimensional space,
'rearrr' enables creativity when plotting and experimenting with data.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between rearrr versions 0.3.4 dated 2024-02-07 and 0.3.5 dated 2025-03-03
rearrr-0.3.4/rearrr/build/rearrr.pdf |only rearrr-0.3.5/rearrr/DESCRIPTION | 13 - rearrr-0.3.5/rearrr/MD5 | 37 +-- rearrr-0.3.5/rearrr/NEWS.md | 6 rearrr-0.3.5/rearrr/R/transfer_centroids.R | 2 rearrr-0.3.5/rearrr/README.md | 111 +++++----- rearrr-0.3.5/rearrr/build/stage23.rdb |only rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-11-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-14-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-16-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-19-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-21-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-27-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-29-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-31-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-33-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-35-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-6-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-9-1.png |binary rearrr-0.3.5/rearrr/man/figures/rearrr_square_logo_242x225_259dpi.png |only rearrr-0.3.5/rearrr/tests/testthat/test_n_fn.R | 24 -- 21 files changed, 92 insertions(+), 101 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.5.0 dated 2024-12-19 and 1.5.1-1 dated 2025-03-03
DESCRIPTION | 11 MD5 | 72 +++-- NEWS.md | 43 +++ R/GMAT.R | 2 R/GMAT2test.R | 2 R/GMATtest.R | 4 R/NLR.R | 612 +++++++++++++++++++------------------------------- R/ORD.R | 2 R/difNLR-package.R | 31 +- R/difNLR.R | 77 +++--- R/difORD.R | 5 R/estimNLR.R | 4 R/formulaNLR.R | 10 R/genNLR.R | 2 R/private.R | 2 README.md | 48 ++- build/partial.rdb |binary man/GMAT.Rd | 2 man/GMAT2test.Rd | 2 man/GMATtest.Rd | 4 man/NLR.Rd | 6 man/ORD.Rd | 2 man/coef.difNLR.Rd | 5 man/difNLR-package.Rd | 31 +- man/difNLR.Rd | 2 man/difORD.Rd | 5 man/estimNLR.Rd | 2 man/genNLR.Rd | 2 tests |only 29 files changed, 478 insertions(+), 512 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem. References: Makowski et al. (2020) <doi:10.21105/joss.02306>.
Author: Dominique Makowski [aut, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Remi Theriault [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.6 dated 2024-10-26 and 0.8.7 dated 2025-03-03
correlation-0.8.6/correlation/tests/testthat/_snaps/as.list.md |only correlation-0.8.6/correlation/tests/testthat/test-as.list.R |only correlation-0.8.7/correlation/DESCRIPTION | 12 correlation-0.8.7/correlation/MD5 | 56 +-- correlation-0.8.7/correlation/NEWS.md | 10 correlation-0.8.7/correlation/R/cor_sort.R | 90 ++++- correlation-0.8.7/correlation/R/cormatrix_to_excel.R | 22 - correlation-0.8.7/correlation/R/correlation.R | 82 ++-- correlation-0.8.7/correlation/R/display.R | 3 correlation-0.8.7/correlation/R/methods_format.R | 25 + correlation-0.8.7/correlation/R/methods_print.R | 10 correlation-0.8.7/correlation/README.md | 49 +- correlation-0.8.7/correlation/inst/doc/multilevel.R | 42 +- correlation-0.8.7/correlation/inst/doc/multilevel.html | 64 ++- correlation-0.8.7/correlation/inst/doc/types.R | 154 ++++---- correlation-0.8.7/correlation/inst/doc/types.html | 175 +++++----- correlation-0.8.7/correlation/man/correlation-package.Rd | 12 correlation-0.8.7/correlation/man/correlation.Rd | 21 - correlation-0.8.7/correlation/man/display.easycormatrix.Rd | 3 correlation-0.8.7/correlation/man/figures/README-12-1.png |binary correlation-0.8.7/correlation/man/figures/README-7-1.png |binary correlation-0.8.7/correlation/man/figures/README-corr-1.png |binary correlation-0.8.7/correlation/tests/testthat/_snaps/as_list.md |only correlation-0.8.7/correlation/tests/testthat/_snaps/display_print_dataframe.md | 54 --- correlation-0.8.7/correlation/tests/testthat/_snaps/display_print_matrix.md | 27 - correlation-0.8.7/correlation/tests/testthat/_snaps/methods.md | 14 correlation-0.8.7/correlation/tests/testthat/_snaps/windows |only correlation-0.8.7/correlation/tests/testthat/test-as_list.R |only correlation-0.8.7/correlation/tests/testthat/test-cor_sort.R |only correlation-0.8.7/correlation/tests/testthat/test-correlation.R | 13 correlation-0.8.7/correlation/tests/testthat/test-display_print_dataframe.R | 12 correlation-0.8.7/correlation/tests/testthat/test-display_print_matrix.R | 21 - 32 files changed, 543 insertions(+), 428 deletions(-)
Title: Topic Inference to Identify Tissue Architecture in Multiplexed
Images
Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see <https://xiyupeng.github.io/SpaTopic/>.
Author: Xiyu Peng [aut, cre]
Maintainer: Xiyu Peng <pansypeng124@gmail.com>
Diff between SpaTopic versions 1.1.0 dated 2024-04-22 and 1.2.0 dated 2025-03-03
SpaTopic-1.1.0/SpaTopic/man/gibbs.res-class.Rd |only SpaTopic-1.2.0/SpaTopic/DESCRIPTION | 10 SpaTopic-1.2.0/SpaTopic/MD5 | 38 SpaTopic-1.2.0/SpaTopic/NAMESPACE | 3 SpaTopic-1.2.0/SpaTopic/NEWS.md | 5 SpaTopic-1.2.0/SpaTopic/R/Gibbs_sampler.R | 981 ++++++++++--------- SpaTopic-1.2.0/SpaTopic/R/RcppExports.R | 46 SpaTopic-1.2.0/SpaTopic/R/SpaTopic-package.R | 27 SpaTopic-1.2.0/SpaTopic/R/class.R | 10 SpaTopic-1.2.0/SpaTopic/R/prepare_SpaTopic_input.R | 28 SpaTopic-1.2.0/SpaTopic/README.md | 209 +--- SpaTopic-1.2.0/SpaTopic/build/vignette.rds |binary SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.R | 41 SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.Rmd | 145 +- SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.html | 672 ++++++++----- SpaTopic-1.2.0/SpaTopic/man/SpaTopic-Package.Rd | 34 SpaTopic-1.2.0/SpaTopic/man/SpaTopic-class.Rd |only SpaTopic-1.2.0/SpaTopic/man/SpaTopic_inference.Rd | 4 SpaTopic-1.2.0/SpaTopic/man/print.SpaTopic.Rd |only SpaTopic-1.2.0/SpaTopic/man/spatopic_message.Rd |only SpaTopic-1.2.0/SpaTopic/src/Makevars | 4 SpaTopic-1.2.0/SpaTopic/vignettes/Intro_SpaTopic.Rmd | 145 +- 22 files changed, 1388 insertions(+), 1014 deletions(-)
Title: A Collection of Loss Functions for Assessing Point Forecasts
Description: Implements multiple consistent scoring functions
(Gneiting T (2011) <doi:10.1198/jasa.2011.r10138>) for assessing point
forecasts and point predictions. Detailed documentation of scoring
functions' properties is included for facilitating interpretation of
results.
Author: Hristos Tyralis [aut, cre] ,
Georgia Papacharalampous [aut]
Maintainer: Hristos Tyralis <montchrister@gmail.com>
Diff between scoringfunctions versions 1.0 dated 2024-12-01 and 1.1 dated 2025-03-03
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++++++----- NAMESPACE | 5 +++++ R/meanlog_if.R |only R/serrexp_sf.R |only R/serrlog_sf.R |only R/serrpower_sf.R |only R/serrsq_sf.R |only build/partial.rdb |binary man/mean_if.Rd | 4 ++-- man/meanlog_if.Rd |only man/scoringfunctions-package.Rd | 14 ++++++++++++-- man/serrexp_sf.Rd |only man/serrlog_sf.Rd |only man/serrpower_sf.Rd |only man/serrsq_sf.Rd |only 16 files changed, 39 insertions(+), 14 deletions(-)
More information about scoringfunctions at CRAN
Permanent link
Title: Calculate Bark Beetle Phenology Using Different Models
Description: Calculate the bark beetle phenology based on raster data or
point-related data. There are multiple models implemented for two bark
beetle species. The models can be customized and their submodels (onset of
infestation, beetle development, diapause initiation, mortality) can be
combined. The following models are available in the package:
PHENIPS-Clim (first-time release in this package),
PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>,
RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>,
CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>,
BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>,
Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>,
Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>.
The package may be expanded by models for other bark beetle species in the
future.
Author: Jakob Jentschke [aut, cre],
FVA BW, Abt. Waldschutz [cph, fnd]
Maintainer: Jakob Jentschke <jakob.jentschke@forst.bwl.de>
Diff between barrks versions 1.0.1 dated 2024-11-04 and 1.1.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 68 ++--- NEWS.md | 32 ++ R/model-joensson.R | 10 R/model-lange.R | 6 R/model-phenips-clim.R | 73 ++++- R/model-phenips.R | 21 + R/phenology-results.R | 12 R/phenology.R | 5 R/plot-development-diagram.R | 69 ++++- R/utils-log.R | 86 +++--- R/utils-model-functions.R | 272 ++++++++++++---------- build/partial.rdb |binary inst/doc/bso.html | 10 inst/doc/model-comparison.html | 33 +- inst/doc/model-customization.html | 12 inst/doc/stations.html | 4 inst/doc/storage.html | 4 inst/tinytest/data/test-data-phenips-clim.rda |binary inst/tinytest/data/test-data-spring-mortality.rda |binary inst/tinytest/storage-test.R | 72 ++--- inst/tinytest/test-model-phenips-clim.R | 25 +- inst/tinytest/test-models-min.R | 46 +-- inst/tinytest/test-spring-mortality.R | 5 inst/tinytest/test-storage-chapy.R | 36 +- inst/tinytest/test-storage-combine.R | 48 +-- inst/tinytest/test-storage-joensson.R | 36 +- inst/tinytest/test-storage-lange.R | 36 +- inst/tinytest/test-storage-phenips-clim.R | 36 +- inst/tinytest/test-storage-phenips.R | 36 +- inst/tinytest/test-storage-rity.R | 36 +- man/get_generations.Rd | 10 man/model.joensson.customize.Rd | 4 man/model.phenips_clim.customize.Rd | 12 tests/tinytest.R | 12 35 files changed, 671 insertions(+), 502 deletions(-)
Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be
challenging, both because these models are typically built for
extrapolating outside the original region represented by training data
and due to potential spatially structured errors, with "hot spots" of
higher than expected error clustered geographically due to spatial
structure in the underlying data. Methods are provided for assessing
models fit to spatial data, including approaches for measuring the
spatial structure of model errors, assessing model predictions at
multiple spatial scales, and evaluating where predictions can be made
safely. Methods are particularly useful for models fit using the
'tidymodels' framework. Methods include Moran's I ('Moran' (1950)
<doi:10.2307/2332142>), Geary's C ('Geary' (1954)
<doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from
'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement
m [...truncated...]
Author: Michael Mahoney [aut, cre] ,
Lucas Johnson [ctb] ,
Virgilio Gomez-Rubio [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/571>),
Jakub Nowosad [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between waywiser versions 0.6.1 dated 2025-02-16 and 0.6.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/multi-scale-assessment.R | 6 +++++- inst/doc/multi-scale-assessment.Rmd | 6 +++++- inst/doc/multi-scale-assessment.html | 8 ++++++-- vignettes/multi-scale-assessment.Rmd | 6 +++++- 7 files changed, 34 insertions(+), 14 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.1.0 dated 2025-02-10 and 0.3.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 R/globals.R | 2 R/readARS.R | 49 - README.md | 36 inst/extdata/ADAE.csv | 2384 +++++++++++++++++++++++++------------------------- man/ARS_example.Rd | 44 man/readARS.Rd | 3 9 files changed, 1275 insertions(+), 1269 deletions(-)
Title: A Mini-Dictionary for 'R', 'shiny' and 'rmarkdown' Documents
Description: Despite the predominant use of R for data manipulation and various robust statistical calculations, in recent years, more people from various disciplines are beginning to use R for other purposes. In doing this seemlessly, further tools are needed users to easily and freely write in R for all kinds of purposes. The r2dictionary introduces a means for users to directly search for definitions of terms within the R environment.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2dictionary versions 0.2 dated 2023-07-16 and 0.3 dated 2025-03-03
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/complete.dic |binary inst/doc/simple_samples.html | 4 ++-- man/defineSelected.Rd | 2 +- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting
text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering
of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further
processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between pdftools versions 3.4.1 dated 2024-09-20 and 3.5.0 dated 2025-03-03
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 42 ++++++++++++++++++++++++------------------ 4 files changed, 39 insertions(+), 30 deletions(-)
Title: Exact Matching and Matching-Adjusted Indirect Comparison (MAIC)
Description: The second version (0.2.0) contains implementation for exact matching which is an alternative to propensity score matching (see Glimm & Yau (2025)). The initial version (0.1.2) contains a collection of easy-to-implement tools for checking whether a MAIC can be conducted, as well as an alternative way of calculating weights (see Glimm & Yau (2021) <doi:10.1002/pst.2210>.)
Author: Lillian Yau [aut, cre],
Ekkehard Glimm [aut],
Xinlei Deng [aut]
Maintainer: Lillian Yau <maicChecks@gmail.com>
Diff between maicChecks versions 0.1.2 dated 2022-01-04 and 0.2.0 dated 2025-03-03
DESCRIPTION | 28 ++++-- MD5 | 51 +++++++----- NAMESPACE | 19 ++-- R/eAD.R | 40 +++++---- R/eIPD.R | 40 +++++---- R/exmLP.2ipd.R |only R/exmWt.2ipd.R |only R/maicChecks-package.R |only R/maicLP.R | 73 ++++++++++++------ R/maicMD.R | 184 +++++++++++++++++++++++++-------------------- R/maicPCA.R | 186 ++++++++++++++++++++++++++-------------------- R/maicT2Test.R | 82 +++++++++++--------- R/maicWt.R | 102 +++++++++++++++---------- R/maxessWt.R | 92 +++++++++++++--------- R/sim110.R |only README.md |only build |only data/eAD.txt | 8 - data/eIPD.txt | 86 ++++++++++----------- data/sim110.rda |only man/eAD.Rd | 47 ++++++----- man/eIPD.Rd | 45 ++++++----- man/exmLP.2ipd.Rd |only man/exmWt.2ipd.Rd |only man/maicChecks-package.Rd |only man/maicLP.Rd | 60 +++++++------- man/maicMD.Rd | 66 +++++++++------- man/maicPCA.Rd | 78 +++++++++---------- man/maicT2Test.Rd | 66 ++++++++-------- man/maicWt.Rd | 67 ++++++++-------- man/maxessWt.Rd | 57 +++++++------- man/sim110.Rd |only 32 files changed, 832 insertions(+), 645 deletions(-)
Title: Generate Simulated Sawn Timber Strength Grading Data
Description: Tools for generating simulated sawn timber
strength grading data with a main focus on statistical simulation based on
covariance matrices. Simulation data
for Norway spruce sawn timber from Austria and reference values of means and
standard deviations of grade determining properties from literature
for a number of European countries are provided, as well.
Author: Andreas Weidenhiller [cre, aut]
,
Anton Wegscheider [aut]
Maintainer: Andreas Weidenhiller <a.weidenhiller@holzforschung.at>
Diff between WoodSimulatR versions 0.6.1 dated 2023-12-04 and 0.6.2 dated 2025-03-03
DESCRIPTION | 10 MD5 | 42 NEWS.md | 113 +- R/data.r | 4 R/stat_sim_dataset.r | 945 ++++++++++----------- R/statistical_simulation.r | 1296 ++++++++++++++--------------- R/subsample_data.r | 436 ++++----- README.md | 7 build/vignette.rds |binary inst/doc/woodsimulatr_basics.Rmd | 1072 +++++++++++------------ inst/doc/woodsimulatr_basics.html | 11 man/gdp_data.Rd | 2 man/get_subsample_definitions.Rd | 6 man/get_transform_names.Rd | 6 man/simbase.Rd | 2 man/simbase_covar.Rd | 12 man/simbase_labeler.Rd | 2 man/simbase_list.Rd | 12 man/simulate_conditionally.Rd | 2 man/simulate_conditionally.simbase_list.Rd | 6 man/simulate_dataset.Rd | 28 vignettes/woodsimulatr_basics.Rmd | 1072 +++++++++++------------ 22 files changed, 2546 insertions(+), 2540 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.7 dated 2025-02-10 and 0.3.8 dated 2025-03-03
DESCRIPTION | 6 +- MD5 | 18 +++---- NEWS.md | 4 + R/gg_scatter.R | 2 R/locus.R | 7 ++ inst/doc/locuszoomr.R | 104 ++++++++++++++++++++++++++++++++++--------- inst/doc/locuszoomr.Rmd | 113 ++++++++++++++++++++++++++++++++++++++--------- inst/doc/locuszoomr.html | 53 +++++++--------------- man/locus.Rd | 5 +- vignettes/locuszoomr.Rmd | 113 ++++++++++++++++++++++++++++++++++++++--------- 10 files changed, 311 insertions(+), 114 deletions(-)
Title: 'ade4' Tcl/Tk Graphical User Interface
Description: A Tcl/Tk GUI for some basic functions in the 'ade4' package.
Author: Jean Thioulouse [aut] ,
Stephane Dray [aut] ,
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4TkGUI versions 0.3-1 dated 2020-12-03 and 0.3.3 dated 2025-03-03
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 10 +++++----- NAMESPACE | 30 +++++++++++++++++++++++++++++- R/choose.R | 10 +++++----- R/ordiClust.R | 14 +++++++------- inst/CITATION | 41 +++++++++++++++++------------------------ 6 files changed, 82 insertions(+), 50 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.1.1 dated 2024-09-08 and 2.2.0 dated 2025-03-03
DESCRIPTION | 14 +++--- MD5 | 27 ++++++------ NEWS.md | 15 ++++++ R/launchApp.R | 2 R/realisedCoeffs.R | 49 ++++++++++++---------- README.md | 17 +++---- build/partial.rdb |binary inst/shiny/R/plot-functions.R | 2 inst/shiny/R/saveData.R | 8 +-- inst/shiny/app.R | 28 +++++++----- inst/shiny/www/custom.css | 2 inst/shiny/www/scripts.js |only man/figures/README-ibdsim2-example-distplot-1.png |binary man/ibdsim2-package.Rd | 2 man/realised.Rd | 11 +++- 15 files changed, 103 insertions(+), 74 deletions(-)
Title: The Echelon Analysis and the Detection of Spatial Clusters using
Echelon Scan Method
Description: Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Author: Fumio Ishioka [aut, cre]
Maintainer: Fumio Ishioka <fishioka@okayama-u.ac.jp>
Diff between echelon versions 0.2.0 dated 2024-02-08 and 0.3.0 dated 2025-03-03
echelon-0.2.0/echelon/R/e.monte.bin.r |only echelon-0.2.0/echelon/R/e.monte.poi.r |only echelon-0.2.0/echelon/R/e.scan.pop.r |only echelon-0.2.0/echelon/man/e.cluster.decision.Rd |only echelon-0.2.0/echelon/man/e.cluster.dendrogram.Rd |only echelon-0.2.0/echelon/man/e.cluster.map.Rd |only echelon-0.2.0/echelon/man/e.dendrogram.Rd |only echelon-0.2.0/echelon/man/e.dendrogram.axis.Rd |only echelon-0.2.0/echelon/man/e.main.Rd |only echelon-0.2.0/echelon/man/e.monte.bin.Rd |only echelon-0.2.0/echelon/man/e.monte.poi.Rd |only echelon-0.2.0/echelon/man/e.profile.Rd |only echelon-0.2.0/echelon/man/e.scan.Rd |only echelon-0.2.0/echelon/man/e.scan.pop.Rd |only echelon-0.2.0/echelon/man/nlimb.Rd |only echelon-0.3.0/echelon/DESCRIPTION | 23 - echelon-0.3.0/echelon/MD5 | 53 -- echelon-0.3.0/echelon/NAMESPACE | 4 echelon-0.3.0/echelon/NEWS.md | 4 echelon-0.3.0/echelon/R/RcppExports.R |only echelon-0.3.0/echelon/R/e.cluster.decision.r | 49 +- echelon-0.3.0/echelon/R/e.cluster.dendrogram.r | 154 +++--- echelon-0.3.0/echelon/R/e.cluster.map.r | 81 +-- echelon-0.3.0/echelon/R/e.dendrogram.axis.r | 74 +-- echelon-0.3.0/echelon/R/e.dendrogram.r | 163 +++---- echelon-0.3.0/echelon/R/e.echebin.r | 480 ++++++++++----------- echelon-0.3.0/echelon/R/e.echelon.r | 357 +++++++-------- echelon-0.3.0/echelon/R/e.echepoi.r | 502 +++++++++++----------- echelon-0.3.0/echelon/R/e.profile.r | 226 ++++----- echelon-0.3.0/echelon/R/e.scan.r | 335 +++++++++----- echelon-0.3.0/echelon/R/e_main.monte.r |only echelon-0.3.0/echelon/R/e_main.r | 342 +++++++------- echelon-0.3.0/echelon/man/echebin.Rd | 34 - echelon-0.3.0/echelon/man/echelon.Rd | 56 +- echelon-0.3.0/echelon/man/echepoi.Rd | 34 - echelon-0.3.0/echelon/src |only 36 files changed, 1543 insertions(+), 1428 deletions(-)
More information about IndexNumberTools at CRAN
Permanent link
More information about maths.genealogy at CRAN
Permanent link
More information about Certara.ModelResults at CRAN
Permanent link
Title: Data on Base and Recommended Packages for Current and Previous
Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 4.4.2.0 dated 2024-11-11 and 4.4.3.0 dated 2025-03-03
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 5 +++ README.md | 48 ++++++++++++++++--------------- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary 8 files changed, 41 insertions(+), 34 deletions(-)
Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.3 dated 2024-09-18 and 0.0.4 dated 2025-03-03
DESCRIPTION | 12 ++++---- MD5 | 13 +++++---- R/CausalNetwork.R |only R/RGM.R | 42 ++++++++++++++++++++---------- README.md | 7 +---- man/RGM.Rd | 38 +++++++++++++++++---------- man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary 8 files changed, 69 insertions(+), 43 deletions(-)
Title: Latent Space-Based Transfer Learning
Description: Implements transfer learning methods for low-rank matrix
estimation. These methods leverage similarity in the latent row and column
spaces between the source and target populations to improve estimation in
the target population. The methods include the LatEnt spAce-based tRaNsfer
lEaRning (LEARNER) method and the direct projection LEARNER (D-LEARNER)
method described by McGrath et al. (2024) <doi:10.48550/arXiv.2412.20605>.
Author: Sean McGrath [aut, cre] ,
Ryan ODea [aut],
Cenhao Zhu [aut],
Rui Duan [aut]
Maintainer: Sean McGrath <sean.mcgrath514@gmail.com>
Diff between learner versions 0.1.0 dated 2025-01-08 and 1.0.0 dated 2025-03-03
learner-0.1.0/learner/R/cv_learner.R |only learner-1.0.0/learner/DESCRIPTION | 14 + learner-1.0.0/learner/MD5 | 26 +- learner-1.0.0/learner/NAMESPACE | 5 learner-1.0.0/learner/NEWS.md | 11 + learner-1.0.0/learner/R/RcppExports.R |only learner-1.0.0/learner/R/dlearner.R | 5 learner-1.0.0/learner/R/globals.R | 11 + learner-1.0.0/learner/R/learner-package.R |only learner-1.0.0/learner/R/learner.R | 205 ++++++++++------------- learner-1.0.0/learner/README.md | 11 + learner-1.0.0/learner/man/cv.learner.Rd | 5 learner-1.0.0/learner/src |only learner-1.0.0/learner/tests/testthat/test-main.R | 85 +++++++++ 14 files changed, 240 insertions(+), 138 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks API. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both CPU and GPU devices.
Author: Tomasz Kalinowski [aut, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
Posit Software, PBC [cph, fnd],
Google [cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigri [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between keras3 versions 1.2.0 dated 2024-09-05 and 1.3.0 dated 2025-03-03
DESCRIPTION | 10 MD5 | 1203 ++++++------- NAMESPACE | 72 NEWS.md | 165 + R/Layer.R | 11 R/Loss.R | 9 R/activations.R | 282 +++ R/applications.R | 8 R/callbacks.R | 26 R/config.R | 75 R/image-utils.R | 2 R/initializers.R | 53 R/install.R | 238 ++ R/layers-attention.R | 25 R/layers-backend-wrappers.R | 2 R/layers-convolutional.R | 2 R/layers-core.R | 4 R/layers-normalization.R | 2 R/layers-preprocessing.R | 1092 +++++++++++ R/layers-rnn.R | 29 R/losses.R | 272 ++ R/metrics.R | 217 ++ R/model-creation.R | 122 + R/model-persistence.R | 211 ++ R/model-training.R | 136 - R/module-tethers.R | 20 R/ops-linalg.R | 4 R/ops-nn.R | 440 ++++ R/ops-numpy.R | 460 ++++ R/ops.R | 59 R/optimizers.R | 6 R/package.R | 28 R/r-utils.R | 16 R/random.R | 214 +- R/reexports.R | 5 R/s3-methods.R | 30 R/utils.R | 18 build/vignette.rds |binary inst/doc/custom_train_step_in_tensorflow.Rmd | 29 inst/doc/custom_train_step_in_tensorflow.html | 29 inst/doc/distribution.Rmd | 20 inst/doc/distribution.html | 20 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man/op_shape.Rd | 29 man/op_sigmoid.Rd | 41 man/op_sign.Rd | 45 man/op_silu.Rd | 41 man/op_sin.Rd | 45 man/op_sinh.Rd | 45 man/op_size.Rd | 45 man/op_slice.Rd | 29 man/op_slice_update.Rd | 29 man/op_slogdet.Rd | 29 man/op_soft_shrink.Rd |only man/op_softmax.Rd | 41 man/op_softplus.Rd | 41 man/op_softsign.Rd | 41 man/op_solve.Rd | 32 man/op_solve_triangular.Rd | 31 man/op_sort.Rd | 45 man/op_sparse_categorical_crossentropy.Rd | 41 man/op_sparse_plus.Rd |only man/op_sparsemax.Rd |only man/op_split.Rd | 45 man/op_sqrt.Rd | 45 man/op_square.Rd | 45 man/op_squareplus.Rd |only man/op_squeeze.Rd | 45 man/op_stack.Rd | 45 man/op_std.Rd | 45 man/op_stft.Rd | 30 man/op_stop_gradient.Rd | 29 man/op_subtract.Rd | 45 man/op_sum.Rd | 45 man/op_svd.Rd | 29 man/op_swapaxes.Rd | 45 man/op_switch.Rd | 33 man/op_take.Rd | 45 man/op_take_along_axis.Rd | 45 man/op_tan.Rd | 45 man/op_tanh.Rd | 45 man/op_tanh_shrink.Rd |only man/op_tensordot.Rd | 45 man/op_threshold.Rd |only man/op_tile.Rd | 45 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| 10 man/set_state_tree.Rd |only man/summary.keras.src.models.model.Model.Rd | 2 man/use_backend.Rd | 21 tests/testthat/helper-utils.R | 9 tests/testthat/test-activations.R | 13 tests/testthat/test-layer-text_vectorization.R | 6 tests/testthat/test-layers-preprocessing.R | 1 vignettes/custom_train_step_in_tensorflow.Rmd | 29 vignettes/distribution.Rmd | 20 vignettes/functional_api.Rmd | 10 vignettes/getting_started.Rmd | 2 vignettes/intro_to_keras_for_engineers.Rmd | 26 vignettes/making_new_layers_and_models_via_subclassing.Rmd | 13 vignettes/sequential_model.Rmd | 7 vignettes/training_with_built_in_methods.Rmd | 78 vignettes/transfer_learning.Rmd | 10 vignettes/transfer_learning/unnamed-chunk-17-1.png |binary vignettes/writing_a_custom_training_loop_in_tensorflow.Rmd | 42 635 files changed, 17475 insertions(+), 1546 deletions(-)
Title: Regression Models for Event History Outcomes
Description: A user friendly, easy to understand way of doing event
history regression for marginal estimands of interest,
including the cumulative incidence and the restricted mean
survival, using the pseudo observation framework for
estimation. For a review of the methodology, see Andersen and
Pohar Perme (2010) <doi:10.1177/0962280209105020> or Sachs
and Gabriel (2022) <doi:10.18637/jss.v102.i09>. The
interface uses the well known formulation of a generalized
linear model and allows for features including plotting of
residuals, the use of sampling weights, and corrected
variance estimation.
Author: Michael C Sachs [aut, cre],
Erin E Gabriel [aut],
Morten Overgaard [ctb] ,
Thomas A Gerds [ctb] ,
Terry Therneau [ctb]
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between eventglm versions 1.2.2 dated 2022-04-26 and 1.4.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 51 NAMESPACE | 1 NEWS.md | 125 +- R/event-model-fit.R | 1121 ++++++++++---------- R/eventglm-package.R | 37 R/pseudo-modules.R | 127 ++ R/pseudoglm-methods.R | 2 R/utils.R | 526 ++++----- README.md | 84 - build/vignette.rds |binary inst/doc/example-analysis.R | 513 ++++----- inst/doc/example-analysis.Rmd | 784 +++++++------- inst/doc/example-analysis.html | 2044 +++++++++++++++++++++---------------- inst/doc/extenstions.R | 188 +-- inst/doc/extenstions.Rmd | 6 inst/doc/extenstions.html | 933 ++++++++++------ inst/doc/stata-sas-comparason.R | 26 inst/doc/stata-sas-comparason.html | 1162 ++++++++++++--------- man/cumincglm.Rd | 11 man/eventglm.Rd | 25 man/pseudo_infjack.Rd |only man/rmeanglm.Rd | 13 src/loo.c | 67 + tests/testthat/test-model-fit.R | 556 ++++++---- vignettes/example-analysis.Rmd | 784 +++++++------- vignettes/extenstions.Rmd | 6 27 files changed, 5242 insertions(+), 3960 deletions(-)
Title: Computes Statistics from Discrimination Experimental Data
Description: In discrimination experiments candidates are sent on the same test (e.g. job, house rental) and one examines whether they receive the same outcome. The number of non negative answers are first examined in details looking for outcome differences. Then various statistics are computed. This package can also be used for analyzing the results from random experiments.
Author: Emmanuel Duguet [aut, cre] ,
David Gray [ctb] ,
Loic du Parquet [dtc],
Yannick L'Horty [ctb] ,
Remi Le Gall [dtc] ,
Noam Leandri [dtc],
Pascale Petit [ctb] ,
Florent Sari [ctb]
Maintainer: Emmanuel Duguet <emmanuel.duguet@u-pec.fr>
Diff between callback versions 0.1.1 dated 2024-07-13 and 0.1.3 dated 2025-03-03
callback-0.1.1/callback/R/callback_graph.R |only callback-0.1.1/callback/inst/doc/getting-started.R |only callback-0.1.1/callback/inst/doc/getting-started.Rmd |only callback-0.1.1/callback/inst/doc/getting-started.html |only callback-0.1.1/callback/man/g_prop.Rd |only callback-0.1.1/callback/man/graph.Rd |only callback-0.1.1/callback/man/graph.stat_ecs.Rd |only callback-0.1.1/callback/man/graph.stat_glob.Rd |only callback-0.1.1/callback/man/graph.stat_mcr.Rd |only callback-0.1.1/callback/man/graph.stat_tcs.Rd |only callback-0.1.1/callback/man/print.stat_count.Rd |only callback-0.1.1/callback/man/print.stat_ecs.Rd |only callback-0.1.1/callback/man/print.stat_glob.Rd |only callback-0.1.1/callback/man/print.stat_prop.Rd |only callback-0.1.1/callback/man/stat_count.Rd |only callback-0.1.1/callback/man/stat_glob.Rd |only callback-0.1.1/callback/vignettes/getting-started.Rmd |only callback-0.1.3/callback/DESCRIPTION | 51 callback-0.1.3/callback/MD5 | 101 callback-0.1.3/callback/NAMESPACE | 30 callback-0.1.3/callback/R/callback.R | 421 - callback-0.1.3/callback/R/callback_comp.R |only callback-0.1.3/callback/R/callback_data.R | 964 ++-- callback-0.1.3/callback/R/callback_misc.R | 2 callback-0.1.3/callback/R/callback_plot.R |only callback-0.1.3/callback/R/callback_print.R | 471 - callback-0.1.3/callback/R/callback_reg.R |only callback-0.1.3/callback/R/callback_stat.R | 2409 +++++----- callback-0.1.3/callback/R/callback_summary.R |only callback-0.1.3/callback/build/vignette.rds |binary callback-0.1.3/callback/data/train1.RData |only callback-0.1.3/callback/data/train2.RData |only callback-0.1.3/callback/inst/doc/callback-components-models.R |only callback-0.1.3/callback/inst/doc/callback-components-models.Rmd |only callback-0.1.3/callback/inst/doc/callback-components-models.html |only callback-0.1.3/callback/inst/doc/callback-presentation.R |only callback-0.1.3/callback/inst/doc/callback-presentation.Rmd |only callback-0.1.3/callback/inst/doc/callback-presentation.html |only callback-0.1.3/callback/man/address1.Rd | 26 callback-0.1.3/callback/man/callback.Rd | 42 callback-0.1.3/callback/man/callback_comp.Rd |only callback-0.1.3/callback/man/g_difp.Rd | 20 callback-0.1.3/callback/man/g_ecs.Rd | 20 callback-0.1.3/callback/man/g_mcr.Rd |only callback-0.1.3/callback/man/g_raw.Rd |only callback-0.1.3/callback/man/g_tcs.Rd | 10 callback-0.1.3/callback/man/gender1.Rd | 42 callback-0.1.3/callback/man/gender2.Rd | 34 callback-0.1.3/callback/man/gender3.Rd | 34 callback-0.1.3/callback/man/gender4.Rd | 34 callback-0.1.3/callback/man/inter1.Rd | 36 callback-0.1.3/callback/man/labour1.Rd | 18 callback-0.1.3/callback/man/labour2.Rd | 18 callback-0.1.3/callback/man/mobility1.Rd | 35 callback-0.1.3/callback/man/origin1.Rd | 52 callback-0.1.3/callback/man/origin2.Rd | 56 callback-0.1.3/callback/man/plot.callback_stat.Rd |only callback-0.1.3/callback/man/print.callback.Rd | 2 callback-0.1.3/callback/man/print.callback_comp.Rd |only callback-0.1.3/callback/man/print.callback_reg.Rd |only callback-0.1.3/callback/man/print.callback_stat.Rd |only callback-0.1.3/callback/man/print.stat_paired.Rd |only callback-0.1.3/callback/man/reg.Rd |only callback-0.1.3/callback/man/reg.callback_comp.Rd |only callback-0.1.3/callback/man/reg_als.Rd |only callback-0.1.3/callback/man/stat_ecs.Rd | 119 callback-0.1.3/callback/man/stat_mcr.Rd | 111 callback-0.1.3/callback/man/stat_paired.Rd |only callback-0.1.3/callback/man/stat_raw.Rd |only callback-0.1.3/callback/man/stat_tcs.Rd | 129 callback-0.1.3/callback/man/summary.callback_reg.Rd |only callback-0.1.3/callback/man/train1.Rd |only callback-0.1.3/callback/man/train2.Rd |only callback-0.1.3/callback/vignettes/callback-components-models.Rmd |only callback-0.1.3/callback/vignettes/callback-presentation.Rmd |only 75 files changed, 2692 insertions(+), 2595 deletions(-)
Title: CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation
Description: Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. [...truncated...]
Author: Xiao Zhang [aut, cre],
Wei Liu [aut],
Jin Liu [aut]
Maintainer: Xiao Zhang <zhangxiao1994@cuhk.edu.cn>
Diff between CAESAR.Suite versions 0.1.0 dated 2024-09-16 and 0.2.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 16 - R/CAESAR_enrich_pathway.R | 22 +- R/caesar_annotation.R | 20 + R/caesar_enrichscore.R | 20 + README.md | 1 build/vignette.rds |binary inst/doc/STMOB.html | 374 ++++++++++++++++++----------------- inst/doc/XeniumBC.html | 479 +++++++++++++++++++++++----------------------- 9 files changed, 499 insertions(+), 439 deletions(-)
Title: Streamlines the Process of Fitting Areal Spatial Models
Description: Helpers for addressing the issue of disconnected spatial units.
It allows for convenient adding and removal of neighbourhood connectivity between areal units prior to modelling, with the visual aid of maps.
Post-modelling, it reduces the human workload for extracting, tidying and mapping predictions from areal models.
Author: Kevin Horan [aut, cre, cph] ,
Katarina Domijan [aut, ths] ,
Chris Brunsdon [aut, ths]
Maintainer: Kevin Horan <kevin.horan.2021@mumail.ie>
Diff between sfislands versions 1.1.0 dated 2025-03-01 and 1.1.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: Matching Methods for Causal Inference with Time-Series
Cross-Sectional Data
Description: Implements a set of methodological tools
that enable researchers to apply matching methods to
time-series cross-sectional data. Imai, Kim, and Wang
(2023) <http://web.mit.edu/insong/www/pdf/tscs.pdf>
proposes a nonparametric generalization of the
difference-in-differences estimator, which does not rely
on the linearity assumption as often done in
practice. Researchers first select a method of matching
each treated observation for a given unit in a
particular time period with control observations from
other units in the same time period that have a similar
treatment and covariate history. These methods include
standard matching methods based on propensity score and
Mahalanobis distance, as well as weighting methods. Once
matching and refinement is done,
treatment effects can be estimated with
standard errors. The package also offers diagnostics for researchers to assess the quality
of their results.
Author: In Song Kim [aut, cre],
Adam Rauh [aut],
Erik Wang [aut],
Kosuke Imai [aut]
Maintainer: In Song Kim <insong@mit.edu>
Diff between PanelMatch versions 2.2.0 dated 2024-06-04 and 3.0.0 dated 2025-03-03
PanelMatch-2.2.0/PanelMatch/R/balance_scatter.R |only PanelMatch-2.2.0/PanelMatch/inst/doc/matched_set_objects.R |only PanelMatch-2.2.0/PanelMatch/inst/doc/matched_set_objects.Rmd |only PanelMatch-2.2.0/PanelMatch/inst/doc/matched_set_objects.html |only PanelMatch-2.2.0/PanelMatch/inst/doc/using_panelmatch.R |only PanelMatch-2.2.0/PanelMatch/inst/doc/using_panelmatch.Rmd |only PanelMatch-2.2.0/PanelMatch/inst/doc/using_panelmatch.pdf |only PanelMatch-2.2.0/PanelMatch/man/balance_scatter.Rd |only PanelMatch-2.2.0/PanelMatch/vignettes/matched_set_objects.Rmd |only PanelMatch-2.2.0/PanelMatch/vignettes/using_panelmatch.Rmd |only PanelMatch-3.0.0/PanelMatch/DESCRIPTION | 8 PanelMatch-3.0.0/PanelMatch/MD5 | 144 + PanelMatch-3.0.0/PanelMatch/NAMESPACE | 21 PanelMatch-3.0.0/PanelMatch/R/DisplayTreatment.R | 82 PanelMatch-3.0.0/PanelMatch/R/PanelBalance.R |only PanelMatch-3.0.0/PanelMatch/R/PanelData.R |only PanelMatch-3.0.0/PanelMatch/R/PanelEstimate.R | 93 - PanelMatch-3.0.0/PanelMatch/R/PanelEstimateObject.R | 139 + PanelMatch-3.0.0/PanelMatch/R/PanelMatch-package.R | 7 PanelMatch-3.0.0/PanelMatch/R/PanelMatch.R | 174 -- PanelMatch-3.0.0/PanelMatch/R/PanelMatchObject.R |only PanelMatch-3.0.0/PanelMatch/R/bootstrap_placebo.R | 5 PanelMatch-3.0.0/PanelMatch/R/calculate_estimates.R | 10 PanelMatch-3.0.0/PanelMatch/R/calculate_placebo_estimates.R | 7 PanelMatch-3.0.0/PanelMatch/R/data.R | 2 PanelMatch-3.0.0/PanelMatch/R/data_preprocessing.R | 17 PanelMatch-3.0.0/PanelMatch/R/do_exact_matching.R | 2 PanelMatch-3.0.0/PanelMatch/R/enforce_lead_restrictions.R | 1 PanelMatch-3.0.0/PanelMatch/R/estimation_components.R | 6 PanelMatch-3.0.0/PanelMatch/R/get_covariate_balance.R | 225 +- PanelMatch-3.0.0/PanelMatch/R/get_set_treatment_effects.R | 31 PanelMatch-3.0.0/PanelMatch/R/handle_moderating_variable.R | 3 PanelMatch-3.0.0/PanelMatch/R/listwise_delete.R | 74 PanelMatch-3.0.0/PanelMatch/R/matched_set_helpers.r | 10 PanelMatch-3.0.0/PanelMatch/R/matched_set_obj.R | 330 ++- PanelMatch-3.0.0/PanelMatch/R/perform_refinement.R | 55 PanelMatch-3.0.0/PanelMatch/R/placebo_test.R | 97 - 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