Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Description: A set of tools for empirical analysis of diversity (a number
and frequency of different types in a population) and similarity
(a number and frequency of shared types in two populations) in
biological or ecological systems.
Author: Christoph Sadee [aut],
Maciej Pietrzak [aut, cre],
Michal Seweryn [aut],
Cankun Wang [aut],
Grzegorz Rempala [aut]
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>
Diff between divo versions 1.0.1 dated 2019-12-16 and 1.0.2 dated 2025-02-15
DESCRIPTION | 38 +++++++++++++++++++++++++++++++------- MD5 | 22 +++++++++++----------- build/vignette.rds |binary inst/doc/divo-Manual.Rnw | 3 ++- inst/doc/divo-Manual.pdf |binary inst/doc/divo-Vignette.Rnw | 4 ++-- inst/doc/divo-Vignette.pdf |binary man/TCR.Data.Rd | 24 ++++++++++++++++-------- man/li.Rd | 32 ++++++++++++++++++++++++-------- src/OL_read.c | 1 + vignettes/divo-Manual.Rnw | 3 ++- vignettes/divo-Vignette.Rnw | 4 ++-- 12 files changed, 91 insertions(+), 40 deletions(-)
Title: Fixing Data Made Easy for Statistical Analysis
Description: A set of functions that facilitate basic data manipulation and cleaning for statistical analysis including functions for finding and fixing duplicate rows and columns, missing values, outliers, and special characters in column and row names and functions for checking data consistency, distribution, quality, reliability, and structure.
Author: Ambu Vijayan [aut, cre] ,
J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>
Diff between fixr versions 0.1.0 dated 2023-04-20 and 0.2.0 dated 2025-02-15
fixr-0.1.0/fixr/man/find_duplicate_cols.Rd |only fixr-0.2.0/fixr/DESCRIPTION | 14 ++--- fixr-0.2.0/fixr/MD5 | 8 +-- fixr-0.2.0/fixr/NAMESPACE | 1 fixr-0.2.0/fixr/NEWS.md |only fixr-0.2.0/fixr/R/find_duplicate_cols.R | 75 +++++++++++------------------ 6 files changed, 40 insertions(+), 58 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.1.0 dated 2024-10-19 and 2.2 dated 2025-02-15
aqp-2.1.0/aqp/R/profile_compare.R |only aqp-2.1.0/aqp/man/profile_compare.Rd |only aqp-2.1.0/aqp/tests/testthat/test-profile_compare.R |only aqp-2.2/aqp/DESCRIPTION | 16 aqp-2.2/aqp/MD5 | 196 +-- aqp-2.2/aqp/NAMESPACE | 13 aqp-2.2/aqp/NEWS.md | 11 aqp-2.2/aqp/R/NCSP.R | 7 aqp-2.2/aqp/R/SoilProfileCollection-coercion.R | 6 aqp-2.2/aqp/R/SoilProfileCollection-methods.R | 3 aqp-2.2/aqp/R/SoilProfileCollection-slice-methods.R | 1 aqp-2.2/aqp/R/accumulateDepths.R | 3 aqp-2.2/aqp/R/accuracy_uncertainty.R | 23 aqp-2.2/aqp/R/addBracket.R | 14 aqp-2.2/aqp/R/aggregateColor.R | 72 - aqp-2.2/aqp/R/aggregateColorPlot.R |only aqp-2.2/aqp/R/aqp-package.R | 15 aqp-2.2/aqp/R/colorChart.R | 124 +- aqp-2.2/aqp/R/colorContrast.R | 5 aqp-2.2/aqp/R/colorContrastPlot.R | 5 aqp-2.2/aqp/R/colorQuantiles.R | 12 aqp-2.2/aqp/R/combine.R | 133 +- aqp-2.2/aqp/R/data-documentation.R | 43 aqp-2.2/aqp/R/dice.R | 2 aqp-2.2/aqp/R/equivalentMunsellChips.R | 1 aqp-2.2/aqp/R/evalGenHz.R | 20 aqp-2.2/aqp/R/generalize.hz.R | 14 aqp-2.2/aqp/R/huePositionCircle.R | 15 aqp-2.2/aqp/R/hzTransitionProbabilities.R | 35 aqp-2.2/aqp/R/invertLabelColor.R | 2 aqp-2.2/aqp/R/munsell2rgb.R | 10 aqp-2.2/aqp/R/parseMunsell.R | 5 aqp-2.2/aqp/R/plotMultipleSPC.R | 2 aqp-2.2/aqp/R/plotProfileDendrogram.R |only aqp-2.2/aqp/R/plotSPC.R | 27 aqp-2.2/aqp/R/plot_distance_graph.R | 2 aqp-2.2/aqp/R/previewColors.R | 7 aqp-2.2/aqp/R/quickSPC.R | 15 aqp-2.2/aqp/R/random_profile.R | 9 aqp-2.2/aqp/R/segment.R | 2 aqp-2.2/aqp/R/slab.R | 1 aqp-2.2/aqp/R/soilColorSignature.R | 6 aqp-2.2/aqp/R/soilPalette.R | 14 aqp-2.2/aqp/R/spec2Munsell.R | 42 aqp-2.2/aqp/R/texture.R | 235 ++-- aqp-2.2/aqp/build/partial.rdb |binary aqp-2.2/aqp/build/vignette.rds |binary aqp-2.2/aqp/data/wilson2022.rda |binary aqp-2.2/aqp/demo/aqp.R | 2 aqp-2.2/aqp/inst/WORDLIST | 2 aqp-2.2/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 256 ++-- aqp-2.2/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 144 +- aqp-2.2/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 294 ++--- aqp-2.2/aqp/inst/doc/Munsell-color-conversion.R | 2 aqp-2.2/aqp/inst/doc/Munsell-color-conversion.Rmd | 2 aqp-2.2/aqp/inst/doc/Munsell-color-conversion.html | 2 aqp-2.2/aqp/inst/doc/NCSP.R | 10 aqp-2.2/aqp/inst/doc/NCSP.Rmd | 14 aqp-2.2/aqp/inst/doc/NCSP.html | 57 - aqp-2.2/aqp/inst/doc/aqp-overview.R | 2 aqp-2.2/aqp/inst/doc/aqp-overview.Rmd | 2 aqp-2.2/aqp/inst/doc/label-placement.R | 94 - aqp-2.2/aqp/inst/doc/label-placement.Rmd | 11 aqp-2.2/aqp/inst/doc/label-placement.html | 521 ++++------ aqp-2.2/aqp/inst/doc/missing-data.R | 6 aqp-2.2/aqp/inst/doc/missing-data.Rmd | 8 aqp-2.2/aqp/inst/doc/missing-data.html | 38 aqp-2.2/aqp/inst/doc/new-in-aqp-2.R | 2 aqp-2.2/aqp/inst/doc/new-in-aqp-2.Rmd | 2 aqp-2.2/aqp/man/accumulateDepths.Rd | 3 aqp-2.2/aqp/man/addDiagnosticBracket.Rd | 2 aqp-2.2/aqp/man/aggregateColor.Rd | 58 - aqp-2.2/aqp/man/aggregateColorPlot.Rd |only aqp-2.2/aqp/man/colorChart.Rd | 112 +- aqp-2.2/aqp/man/evalGenHZ.Rd | 7 aqp-2.2/aqp/man/generalize.hz.Rd | 7 aqp-2.2/aqp/man/hzTransitionProbabilities.Rd | 35 aqp-2.2/aqp/man/jacobs2000.Rd | 13 aqp-2.2/aqp/man/munsell2rgb.Rd | 6 aqp-2.2/aqp/man/parseMunsell.Rd | 4 aqp-2.2/aqp/man/plotMultipleSPC.Rd | 2 aqp-2.2/aqp/man/plotProfileDendrogram.Rd |only aqp-2.2/aqp/man/plot_distance_graph.Rd | 2 aqp-2.2/aqp/man/previewColors.Rd | 2 aqp-2.2/aqp/man/random_profile.Rd | 7 aqp-2.2/aqp/man/soilPalette.Rd | 3 aqp-2.2/aqp/man/soilTextureColorPal.Rd | 70 - aqp-2.2/aqp/man/sp3.Rd | 2 aqp-2.2/aqp/man/spec2Munsell.Rd | 44 aqp-2.2/aqp/man/wilson2022.Rd | 148 +- aqp-2.2/aqp/tests/testthat/Rplots.pdf |binary aqp-2.2/aqp/tests/testthat/test-DT-tbl.R | 6 aqp-2.2/aqp/tests/testthat/test-aggregateColor.R | 2 aqp-2.2/aqp/tests/testthat/test-color-signature.R | 6 aqp-2.2/aqp/tests/testthat/test-genhz.R | 1 aqp-2.2/aqp/tests/testthat/test-plotProfileDendrogram.R |only aqp-2.2/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 144 +- aqp-2.2/aqp/vignettes/Munsell-color-conversion.Rmd | 2 aqp-2.2/aqp/vignettes/NCSP.Rmd | 14 aqp-2.2/aqp/vignettes/aqp-overview.Rmd | 2 aqp-2.2/aqp/vignettes/label-placement.Rmd | 11 aqp-2.2/aqp/vignettes/missing-data.Rmd | 8 aqp-2.2/aqp/vignettes/new-in-aqp-2.Rmd | 2 103 files changed, 1551 insertions(+), 1813 deletions(-)
Title: Bifurcation Analysis of Ordinary Differential Equation Systems
Description: Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary
differential equations. The package allows for computation of equilibrium curves as a function of
a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along
these curves, and computation of curves representing these transcritical, saddle-node and hopf
bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization
of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve
continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995;
ISBN: 0-387-94418-4).
Author: Andre M. de Roos [aut, cre]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>
Diff between deBif versions 0.1.8 dated 2023-12-04 and 0.1.9 dated 2025-02-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 +++++++- R/bif1parplot.R | 22 +++++++++++----------- build/vignette.rds |binary 5 files changed, 26 insertions(+), 20 deletions(-)
Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency,
all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut],
Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>
Diff between TDAvec versions 0.1.3 dated 2022-10-31 and 0.1.4 dated 2025-02-15
TDAvec-0.1.3/TDAvec/NEWS.md |only TDAvec-0.1.3/TDAvec/man/computeECC.Rd |only TDAvec-0.1.3/TDAvec/man/computeNL.Rd |only TDAvec-0.1.3/TDAvec/man/computePES.Rd |only TDAvec-0.1.3/TDAvec/man/computePI.Rd |only TDAvec-0.1.3/TDAvec/man/computePL.Rd |only TDAvec-0.1.3/TDAvec/man/computePS.Rd |only TDAvec-0.1.3/TDAvec/man/computeVAB.Rd |only TDAvec-0.1.3/TDAvec/man/computeVPB.Rd |only TDAvec-0.1.3/TDAvec/src/ECC.cpp |only TDAvec-0.1.3/TDAvec/src/NL.cpp |only TDAvec-0.1.3/TDAvec/src/PES.cpp |only TDAvec-0.1.3/TDAvec/src/PI.cpp |only TDAvec-0.1.3/TDAvec/src/PL.cpp |only TDAvec-0.1.3/TDAvec/src/PS.cpp |only TDAvec-0.1.3/TDAvec/src/VAB.cpp |only TDAvec-0.1.3/TDAvec/src/VPB.cpp |only TDAvec-0.1.4/TDAvec/DESCRIPTION | 37 - TDAvec-0.1.4/TDAvec/MD5 | 66 + TDAvec-0.1.4/TDAvec/NAMESPACE | 7 TDAvec-0.1.4/TDAvec/R/RcppExports.R | 56 + TDAvec-0.1.4/TDAvec/README.md | 57 - TDAvec-0.1.4/TDAvec/build/vignette.rds |binary TDAvec-0.1.4/TDAvec/inst/doc/TDAvec_vignette.R | 115 --- TDAvec-0.1.4/TDAvec/inst/doc/TDAvec_vignette.Rmd | 206 ++--- TDAvec-0.1.4/TDAvec/inst/doc/TDAvec_vignette.html | 581 +++++++--------- TDAvec-0.1.4/TDAvec/man/computeAlgebraicFunctions.Rd |only TDAvec-0.1.4/TDAvec/man/computeBettiCurve.Rd |only TDAvec-0.1.4/TDAvec/man/computeComplexPolynomial.Rd |only TDAvec-0.1.4/TDAvec/man/computeEulerCharacteristic.Rd |only TDAvec-0.1.4/TDAvec/man/computeLimits.Rd |only TDAvec-0.1.4/TDAvec/man/computeNormalizedLife.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceBlock.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceImage.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceLandscape.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistenceSilhouette.Rd |only TDAvec-0.1.4/TDAvec/man/computePersistentEntropy.Rd |only TDAvec-0.1.4/TDAvec/man/computeStats.Rd |only TDAvec-0.1.4/TDAvec/man/computeTemplateFunction.Rd |only TDAvec-0.1.4/TDAvec/man/computeTropicalCoordinates.Rd |only TDAvec-0.1.4/TDAvec/src/AlgebraicFunctions.cpp |only TDAvec-0.1.4/TDAvec/src/BettiCurve.cpp |only TDAvec-0.1.4/TDAvec/src/ComplexPolynomial.cpp |only TDAvec-0.1.4/TDAvec/src/EulerCharacteristic.cpp |only TDAvec-0.1.4/TDAvec/src/Limits.cpp |only TDAvec-0.1.4/TDAvec/src/Makevars |only TDAvec-0.1.4/TDAvec/src/NormalizedLife.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceBlock.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceImage.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceLandscape.cpp |only TDAvec-0.1.4/TDAvec/src/PersistenceSilhouette.cpp |only TDAvec-0.1.4/TDAvec/src/PersistentEntropy.cpp |only TDAvec-0.1.4/TDAvec/src/RcppExports.cpp | 235 ++++-- TDAvec-0.1.4/TDAvec/src/Stats.cpp |only TDAvec-0.1.4/TDAvec/src/TemplateFunction.cpp |only TDAvec-0.1.4/TDAvec/src/TropicalCoordinates.cpp |only TDAvec-0.1.4/TDAvec/vignettes/TDAvec_vignette.Rmd | 206 ++--- 57 files changed, 718 insertions(+), 848 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.12 dated 2024-12-19 and 1.13 dated 2025-02-15
openxlsx2-1.12/openxlsx2/man/figures/badge.png |only openxlsx2-1.12/openxlsx2/man/figures/badge.svg |only openxlsx2-1.13/openxlsx2/DESCRIPTION | 6 openxlsx2-1.13/openxlsx2/LICENSE | 2 openxlsx2-1.13/openxlsx2/MD5 | 181 openxlsx2-1.13/openxlsx2/NAMESPACE | 1 openxlsx2-1.13/openxlsx2/NEWS.md | 30 openxlsx2-1.13/openxlsx2/R/RcppExports.R | 12 openxlsx2-1.13/openxlsx2/R/asserts.R | 11 openxlsx2-1.13/openxlsx2/R/baseXML.R | 24 openxlsx2-1.13/openxlsx2/R/class-comment.R | 4 openxlsx2-1.13/openxlsx2/R/class-sheet-data.R | 13 openxlsx2-1.13/openxlsx2/R/class-workbook-wrappers.R | 5 openxlsx2-1.13/openxlsx2/R/class-workbook.R | 542 openxlsx2-1.13/openxlsx2/R/class-worksheet.R | 10 openxlsx2-1.13/openxlsx2/R/converters.R | 2 openxlsx2-1.13/openxlsx2/R/helper-functions.R | 399 openxlsx2-1.13/openxlsx2/R/openxlsx2-package.R | 2 openxlsx2-1.13/openxlsx2/R/pugixml.R | 6 openxlsx2-1.13/openxlsx2/R/read.R | 23 openxlsx2-1.13/openxlsx2/R/utils.R | 28 openxlsx2-1.13/openxlsx2/R/wb_functions.R | 76 openxlsx2-1.13/openxlsx2/R/wb_load.R | 50 openxlsx2-1.13/openxlsx2/R/wb_styles.R | 523 openxlsx2-1.13/openxlsx2/R/write.R | 61 openxlsx2-1.13/openxlsx2/R/write_xlsx.R | 31 openxlsx2-1.13/openxlsx2/R/xl_open.R | 7 openxlsx2-1.13/openxlsx2/README.md | 6 openxlsx2-1.13/openxlsx2/build/vignette.rds |binary openxlsx2-1.13/openxlsx2/inst/AUTHORS | 5 openxlsx2-1.13/openxlsx2/inst/WORDLIST | 138 openxlsx2-1.13/openxlsx2/inst/doc/conditional-formatting.R | 34 openxlsx2-1.13/openxlsx2/inst/doc/conditional-formatting.Rmd | 40 openxlsx2-1.13/openxlsx2/inst/doc/conditional-formatting.html | 118 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_charts_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_charts_manual.html | 5 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_formulas_manual.R | 2 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_formulas_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_formulas_manual.html | 12 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_read_to_df.Rmd | 4 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_read_to_df.html | 4 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_style_manual.R | 8 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 8 openxlsx2-1.13/openxlsx2/inst/doc/openxlsx2_style_manual.html | 235 openxlsx2-1.13/openxlsx2/inst/extdata/hex_icon.R |only openxlsx2-1.13/openxlsx2/inst/include/pugixml/pugiconfig.hpp | 11 openxlsx2-1.13/openxlsx2/inst/include/pugixml/pugixml.cpp | 829 - openxlsx2-1.13/openxlsx2/inst/include/pugixml/pugixml.hpp | 121 openxlsx2-1.13/openxlsx2/man/create_border.Rd | 50 openxlsx2-1.13/openxlsx2/man/create_cell_style.Rd | 67 openxlsx2-1.13/openxlsx2/man/create_dxfs_style.Rd | 7 openxlsx2-1.13/openxlsx2/man/create_fill.Rd | 31 openxlsx2-1.13/openxlsx2/man/create_font.Rd | 48 openxlsx2-1.13/openxlsx2/man/create_numfmt.Rd | 17 openxlsx2-1.13/openxlsx2/man/create_shape.Rd |only openxlsx2-1.13/openxlsx2/man/dims_helper.Rd | 2 openxlsx2-1.13/openxlsx2/man/figures/logo.png |only openxlsx2-1.13/openxlsx2/man/fmt_txt.Rd | 5 openxlsx2-1.13/openxlsx2/man/openxlsx2-package.Rd | 2 openxlsx2-1.13/openxlsx2/man/wb_add_border.Rd | 3 openxlsx2-1.13/openxlsx2/man/wb_add_formula.Rd | 2 openxlsx2-1.13/openxlsx2/man/wb_dims.Rd | 2 openxlsx2-1.13/openxlsx2/man/write_xlsx.Rd | 8 openxlsx2-1.13/openxlsx2/man/xl_open.Rd | 4 openxlsx2-1.13/openxlsx2/src/RcppExports.cpp | 35 openxlsx2-1.13/openxlsx2/src/helper_functions.cpp | 352 openxlsx2-1.13/openxlsx2/src/load_workbook.cpp | 115 openxlsx2-1.13/openxlsx2/src/openxlsx2.h | 192 openxlsx2-1.13/openxlsx2/src/openxlsx2_types.h | 94 openxlsx2-1.13/openxlsx2/src/pugi.cpp | 212 openxlsx2-1.13/openxlsx2/src/strings_xml.cpp | 36 openxlsx2-1.13/openxlsx2/src/styles_xml.cpp | 312 openxlsx2-1.13/openxlsx2/src/write_file.cpp | 175 openxlsx2-1.13/openxlsx2/src/xlsb.cpp | 6789 +++++----- openxlsx2-1.13/openxlsx2/src/xlsb_defines.h | 1866 +- openxlsx2-1.13/openxlsx2/src/xlsb_funs.h | 2166 +-- openxlsx2-1.13/openxlsx2/tests/testthat/test-class-workbook.R | 4 openxlsx2-1.13/openxlsx2/tests/testthat/test-conditional_formatting.R | 4 openxlsx2-1.13/openxlsx2/tests/testthat/test-date_time_conversion.R | 4 openxlsx2-1.13/openxlsx2/tests/testthat/test-formulas.R | 42 openxlsx2-1.13/openxlsx2/tests/testthat/test-helper-functions.R | 30 openxlsx2-1.13/openxlsx2/tests/testthat/test-pugi_cpp.R | 20 openxlsx2-1.13/openxlsx2/tests/testthat/test-read_from_created_wb.R | 11 openxlsx2-1.13/openxlsx2/tests/testthat/test-read_xlsb.R | 37 openxlsx2-1.13/openxlsx2/tests/testthat/test-save.R | 53 openxlsx2-1.13/openxlsx2/tests/testthat/test-utils.R | 13 openxlsx2-1.13/openxlsx2/tests/testthat/test-wb_functions.R | 6 openxlsx2-1.13/openxlsx2/tests/testthat/test-wb_styles.R | 6 openxlsx2-1.13/openxlsx2/tests/testthat/test-write.R | 50 openxlsx2-1.13/openxlsx2/vignettes/conditional-formatting.Rmd | 40 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_charts_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_formulas_manual.Rmd | 2 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_read_to_df.Rmd | 4 openxlsx2-1.13/openxlsx2/vignettes/openxlsx2_style_manual.Rmd | 8 94 files changed, 8938 insertions(+), 7623 deletions(-)
Title: Pattern Causality Algorithm
Description: A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.
Author: Stavros Stavroglou [aut] ,
Athanasios Pantelous [aut] ,
Hui Wang [aut, cre]
Maintainer: Hui Wang <huiw1128@gmail.com>
Diff between patterncausality versions 0.2.0 dated 2025-01-09 and 0.2.1 dated 2025-02-15
DESCRIPTION | 6 MD5 | 56 +++---- R/PC.Mk.II.Full.Details.R | 3 R/PC.Mk.II.Lightweight.R | 3 R/natureOfCausality.R | 13 + R/optimalParametersSearch.R | 5 R/pcAccuracy.R | 7 R/pcCV.R | 71 ++++++--- R/pcCrossMatrix.R | 10 - R/pcMatrix.R | 9 - R/pc_full_details_utils.R | 5 R/pc_lightweight_utils.R | 69 ++++---- R/signatureSpace.R | 22 ++ README.md | 81 +++++++--- inst/doc/advanced.html | 20 +- inst/doc/dynamic.html | 6 inst/doc/matrix.html | 6 inst/doc/patterncausality.R | 6 inst/doc/patterncausality.Rmd | 32 +++- inst/doc/patterncausality.html | 53 +++++- inst/doc/series.html | 318 ++++++++++++++++++++--------------------- man/optimalParametersSearch.Rd | 3 man/pcAccuracy.Rd | 3 man/pcCrossMatrix.Rd | 3 man/pcCrossValidation.Rd | 5 man/pcFullDetails.Rd | 3 man/pcLightweight.Rd | 3 man/pcMatrix.Rd | 3 vignettes/patterncausality.Rmd | 32 +++- 29 files changed, 517 insertions(+), 339 deletions(-)
More information about patterncausality at CRAN
Permanent link
Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph]
,
Azka Ubaidillah [aut] ,
Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>
Diff between sae.projection versions 0.1.0 dated 2024-12-19 and 0.1.1 dated 2025-02-15
DESCRIPTION | 14 +++-- MD5 | 18 +++++-- NAMESPACE | 6 ++ R/Projection_rf.R |only R/Projection_rf_CorrectedBias.R |only R/data.R | 88 +++++++++++++++++++++++++++++++++++++ R/projection.R | 10 +++- data/df_susenas_mar2020.rda |only data/df_susenas_sep2020.rda |only man/Projection_rf.Rd |only man/Projection_rf_CorrectedBias.Rd |only man/df_susenas_mar2020.Rd |only man/df_susenas_sep2020.Rd |only man/projection.Rd | 12 ++--- 14 files changed, 129 insertions(+), 19 deletions(-)
More information about sae.projection at CRAN
Permanent link
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.14.4 dated 2025-01-21 and 0.15.2 dated 2025-02-15
rix-0.14.4/rix/inst/doc/e-interactive-use.R |only rix-0.14.4/rix/inst/doc/e-interactive-use.Rmd |only rix-0.14.4/rix/inst/doc/e-interactive-use.html |only rix-0.14.4/rix/vignettes/e-interactive-use.Rmd |only rix-0.15.2/rix/DESCRIPTION | 6 rix-0.15.2/rix/MD5 | 166 ++-- rix-0.15.2/rix/NAMESPACE | 2 rix-0.15.2/rix/NEWS.md | 42 + rix-0.15.2/rix/R/fetchers.R | 371 +++++++++- rix-0.15.2/rix/R/ga_cachix.R | 6 rix-0.15.2/rix/R/make_launcher.R |only rix-0.15.2/rix/R/nix_build.R | 10 rix-0.15.2/rix/R/nix_build_helpers.R | 2 rix-0.15.2/rix/R/nix_hash.R | 32 rix-0.15.2/rix/R/renv_helpers.R | 2 rix-0.15.2/rix/R/rix.R | 174 +++- rix-0.15.2/rix/R/rix_helpers.R | 49 - rix-0.15.2/rix/R/rix_init.R | 44 - rix-0.15.2/rix/R/setup_cachix.R | 11 rix-0.15.2/rix/R/tar_nix_ga.R | 6 rix-0.15.2/rix/R/with_nix.R | 16 rix-0.15.2/rix/README.md | 40 - rix-0.15.2/rix/build/vignette.rds |binary rix-0.15.2/rix/inst/doc/a-getting-started.R | 6 rix-0.15.2/rix/inst/doc/a-getting-started.Rmd | 14 rix-0.15.2/rix/inst/doc/a-getting-started.html | 10 rix-0.15.2/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.R | 4 rix-0.15.2/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd | 4 rix-0.15.2/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.html | 4 rix-0.15.2/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.Rmd | 21 rix-0.15.2/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.html | 21 rix-0.15.2/rix/inst/doc/c-using-rix-to-build-project-specific-environments.R | 2 rix-0.15.2/rix/inst/doc/c-using-rix-to-build-project-specific-environments.Rmd | 8 rix-0.15.2/rix/inst/doc/c-using-rix-to-build-project-specific-environments.html | 8 rix-0.15.2/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.R | 8 rix-0.15.2/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.Rmd | 10 rix-0.15.2/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.html | 8 rix-0.15.2/rix/inst/doc/d2-installing-system-tools-and-texlive-packages-in-a-nix-environment.R | 8 rix-0.15.2/rix/inst/doc/d2-installing-system-tools-and-texlive-packages-in-a-nix-environment.Rmd | 10 rix-0.15.2/rix/inst/doc/d2-installing-system-tools-and-texlive-packages-in-a-nix-environment.html | 8 rix-0.15.2/rix/inst/doc/e-configuring-ide.R |only rix-0.15.2/rix/inst/doc/e-configuring-ide.Rmd |only rix-0.15.2/rix/inst/doc/e-configuring-ide.html |only rix-0.15.2/rix/inst/doc/z-advanced-topic-building-an-environment-for-literate-programming.R | 6 rix-0.15.2/rix/inst/doc/z-advanced-topic-building-an-environment-for-literate-programming.Rmd | 6 rix-0.15.2/rix/inst/doc/z-advanced-topic-building-an-environment-for-literate-programming.html | 6 rix-0.15.2/rix/inst/doc/z-advanced-topic-handling-packages-with-remote-dependencies.R | 2 rix-0.15.2/rix/inst/doc/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd | 291 ++++--- rix-0.15.2/rix/inst/doc/z-advanced-topic-handling-packages-with-remote-dependencies.html | 249 ++++-- rix-0.15.2/rix/inst/doc/z-advanced-topic-reproducible-analytical-pipelines-with-nix.R | 4 rix-0.15.2/rix/inst/doc/z-advanced-topic-reproducible-analytical-pipelines-with-nix.Rmd | 4 rix-0.15.2/rix/inst/doc/z-advanced-topic-reproducible-analytical-pipelines-with-nix.html | 4 rix-0.15.2/rix/inst/doc/z-advanced-topic-running-r-or-shell-code-in-nix-from-r.R | 2 rix-0.15.2/rix/inst/doc/z-advanced-topic-running-r-or-shell-code-in-nix-from-r.Rmd | 2 rix-0.15.2/rix/inst/doc/z-advanced-topic-running-r-or-shell-code-in-nix-from-r.html | 2 rix-0.15.2/rix/inst/doc/z-advanced-topic-using-nix-inside-docker.R | 4 rix-0.15.2/rix/inst/doc/z-advanced-topic-using-nix-inside-docker.Rmd | 4 rix-0.15.2/rix/inst/doc/z-advanced-topic-using-nix-inside-docker.html | 4 rix-0.15.2/rix/inst/extdata/available_df.csv | 5 rix-0.15.2/rix/inst/extdata/default.nix | 27 rix-0.15.2/rix/inst/extdata/result |only rix-0.15.2/rix/man/make_launcher.Rd |only rix-0.15.2/rix/man/renv2nix.Rd | 35 rix-0.15.2/rix/man/renv_lock_r_ver.Rd | 3 rix-0.15.2/rix/man/rix.Rd | 106 +- rix-0.15.2/rix/tests/testthat/_snaps/make_launcher |only rix-0.15.2/rix/tests/testthat/_snaps/renv_helpers/default_datathin.nix | 2 rix-0.15.2/rix/tests/testthat/_snaps/rix/code_default.nix | 3 rix-0.15.2/rix/tests/testthat/_snaps/rix/codium_default.nix |only rix-0.15.2/rix/tests/testthat/_snaps/rix/dups-entries_default.nix |only rix-0.15.2/rix/tests/testthat/_snaps/rix/positron_default.nix |only rix-0.15.2/rix/tests/testthat/_snaps/rix/skip-dups-entries_default.nix |only rix-0.15.2/rix/tests/testthat/_snaps/rix_init/append_Rprofile.txt | 15 rix-0.15.2/rix/tests/testthat/_snaps/rix_init/golden_Rprofile.txt | 15 rix-0.15.2/rix/tests/testthat/test-fetchers.R | 217 +++++ rix-0.15.2/rix/tests/testthat/test-get_sri_hash_deps.R | 33 rix-0.15.2/rix/tests/testthat/test-make_launcher.R |only rix-0.15.2/rix/tests/testthat/test-renv_helpers.R | 21 rix-0.15.2/rix/tests/testthat/test-rix.R | 121 ++- rix-0.15.2/rix/tests/testthat/testdata/default-nix_samples |only rix-0.15.2/rix/tests/testthat/testdata/remote-pkgs |only rix-0.15.2/rix/vignettes/a-getting-started.Rmd | 14 rix-0.15.2/rix/vignettes/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd | 4 rix-0.15.2/rix/vignettes/b2-setting-up-and-using-rix-on-macos.Rmd | 21 rix-0.15.2/rix/vignettes/c-using-rix-to-build-project-specific-environments.Rmd | 8 rix-0.15.2/rix/vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd | 10 rix-0.15.2/rix/vignettes/d2-installing-system-tools-and-texlive-packages-in-a-nix-environment.Rmd | 10 rix-0.15.2/rix/vignettes/e-configuring-ide.Rmd |only rix-0.15.2/rix/vignettes/z-advanced-topic-building-an-environment-for-literate-programming.Rmd | 6 rix-0.15.2/rix/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd | 291 ++++--- rix-0.15.2/rix/vignettes/z-advanced-topic-reproducible-analytical-pipelines-with-nix.Rmd | 4 rix-0.15.2/rix/vignettes/z-advanced-topic-running-r-or-shell-code-in-nix-from-r.Rmd | 2 rix-0.15.2/rix/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd | 4 93 files changed, 1876 insertions(+), 824 deletions(-)
Title: Interact with Data Type Registries and Create Machine-Readable
Data
Description: You can load a schema from a DTR (data type registry) as an R
object. Use this schema to write your data in JSON-LD (JavaScript
Object Notation for Linked Data) format to make it machine readable.
Author: Olga Lezhnina [aut, cre] ,
Manuel Prinz [aut] ,
Markus Stocker [aut] ,
Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Olga Lezhnina <olga.lezhnina@tib.eu>
Diff between dtreg versions 1.1.0 dated 2024-12-02 and 1.1.1 dated 2025-02-15
DESCRIPTION | 7 MD5 | 62 +-- NEWS.md | 6 R/helpers.R | 4 R/load_datatype.R | 2 R/to_jsonld.R | 6 README.md | 18 inst/doc/dtreg.R | 200 +++++---- inst/doc/dtreg.Rmd | 274 ++++++++----- inst/doc/dtreg.html | 362 +++++++++++------- inst/extdata/ePIC-21-T11909-286991b26f02d58ee490.json | 2 inst/extdata/ePIC-21-T11909-37182ecfb4474942e255.json | 2 inst/extdata/ePIC-21-T11909-3f64a93eef69d721518f.json | 2 inst/extdata/ePIC-21-T11909-437807f8d1a81b5138a3.json | 2 inst/extdata/ePIC-21-T11909-5b66cb584b974b186f37.json | 2 inst/extdata/ePIC-21-T11909-5e782e67e70d0b2a022a.json | 2 inst/extdata/ePIC-21-T11909-6e3e29ce3ba5a0b9abfe.json | 2 inst/extdata/ePIC-21-T11909-abef9f1c0d48853f3e51.json | 2 inst/extdata/ePIC-21-T11909-b9335ce2c99ed87735a6.json | 2 inst/extdata/ePIC-21-T11909-c6b413ba96ba477b5dca.json | 2 inst/extdata/ePIC-21-T11909-c6e19df3b52ab8d855a9.json | 2 inst/extdata/ePIC-21-T11909-feeb33ad3e4440682a4d.json |only man/load_datatype.Rd | 2 man/show_fields.Rd | 4 man/to_jsonld.Rd | 4 tests/testthat/helper-mocked.R |only tests/testthat/test-extract_epic.R | 23 - tests/testthat/test-extract_orkg.R | 3 tests/testthat/test-helpers.R | 6 tests/testthat/test-load_datatype.R | 5 tests/testthat/test-request_dtr.R | 8 tests/testthat/test-to_jsonld.R | 7 vignettes/dtreg.Rmd | 274 ++++++++----- 33 files changed, 763 insertions(+), 536 deletions(-)
Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rolog versions 0.9.18 dated 2024-07-09 and 0.9.20 dated 2025-02-15
rolog-0.9.18/rolog/tests |only rolog-0.9.20/rolog/DESCRIPTION | 12 rolog-0.9.20/rolog/MD5 | 18 rolog-0.9.20/rolog/NEWS.md | 9 rolog-0.9.20/rolog/README.md | 111 +---- rolog-0.9.20/rolog/build/vignette.rds |binary rolog-0.9.20/rolog/inst/doc/rolog.html | 717 ++++++++++++++++----------------- rolog-0.9.20/rolog/src/Makevars | 4 rolog-0.9.20/rolog/src/Makevars.win | 2 rolog-0.9.20/rolog/src/crolog.cpp | 153 ++++++- 10 files changed, 571 insertions(+), 455 deletions(-)
Title: ICESat-2 Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begu [...truncated...]
Author: Lampros Mouselimis [aut, cre] ,
OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between IceSat2R versions 1.0.6 dated 2024-08-17 and 1.0.7 dated 2025-02-15
DESCRIPTION | 10 +-- MD5 | 28 ++++---- NEWS.md | 7 ++ R/mission_orbits.R | 34 ++++++++++ README.md | 13 ++-- build/vignette.rds |binary data/RGT_cycle_14.rda |binary data/ne_10m_glaciated_areas.rda |binary inst/data_files/technical_specs_urls.csv | 60 +++++++++---------- inst/doc/IceSat-2_Atlas_products_PDF.pdf |binary inst/doc/IceSat-2_Mission_Orbits_PDF.pdf |binary inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.pdf |binary tests/testthat/test-API_utils.R | 8 ++ tests/testthat/test-get_Atlas_data.R | 10 ++- tests/testthat/test-mission_orbits.R | 17 +++-- 15 files changed, 122 insertions(+), 65 deletions(-)
Title: Flexible Parametric Cure Models
Description: Flexible parametric mixture and non-mixture cure models for time-to-event data.
Author: Jordan Amdahl [aut, cre]
Maintainer: Jordan Amdahl <jrdnmdhl@gmail.com>
Diff between flexsurvcure versions 1.3.1 dated 2022-11-01 and 1.3.3 dated 2025-02-15
DESCRIPTION | 10 +- MD5 | 18 ++-- NEWS.md | 6 + R/flexsurvcure.R | 12 +- R/mixture.r | 2 R/nonmixture.R | 4 build/vignette.rds |binary inst/doc/flexsurvcure.R | 10 +- inst/doc/flexsurvcure.html | 198 +++++++++++++++++++++++---------------------- man/flexsurvcure.Rd | 10 +- 10 files changed, 141 insertions(+), 129 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0.1 dated 2024-12-08 and 1.0.2 dated 2025-02-15
DESCRIPTION | 9 +- MD5 | 16 ++-- NAMESPACE | 4 + R/Cluster.R | 158 ++++++++++++++++++++++--------------------- R/MapperAlgo.R | 92 ++++++++++++++++--------- README.md | 33 ++++++-- man/MapperAlgo.Rd | 10 +- man/figures/Performance1.png |only man/figures/Performance2.png |only man/perform_clustering.Rd | 3 10 files changed, 189 insertions(+), 136 deletions(-)
Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph],
Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>
Diff between r2redux versions 1.0.17 dated 2023-11-28 and 1.0.18 dated 2025-02-15
r2redux-1.0.17/r2redux/tests |only r2redux-1.0.18/r2redux/DESCRIPTION | 6 +++--- r2redux-1.0.18/r2redux/MD5 | 6 ++---- r2redux-1.0.18/r2redux/R/r_diff.r | 14 +++++--------- 4 files changed, 10 insertions(+), 16 deletions(-)
Title: Estimates OIPP and OIZTNB Regression Models
Description: Estimates one-inflated positive Poisson (OIPP) and
one-inflated zero-truncated negative binomial (OIZTNB) regression
models. A suite of ancillary statistical tools are also provided,
including: estimation of positive Poisson (PP) and zero-truncated
negative binomial (ZTNB) models; marginal effects and their standard
errors; diagnostic likelihood ratio and Wald tests; plotting;
predicted counts and expected responses; and random variate
generation. The models and tools, as well as four applications, are
shown in Godwin, R. T. (2024). "One-inflated zero-truncated count
regression models" arXiv preprint <doi:10.48550/arXiv.2402.02272>.
Author: Ryan T. Godwin [aut, cre]
Maintainer: Ryan T. Godwin <ryan.godwin@umanitoba.ca>
Diff between oneinfl versions 1.0.0 dated 2025-02-06 and 1.0.1 dated 2025-02-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/dEdq_nb.R | 5 +++-- R/dEdq_pois.R | 5 +++-- R/margins.R | 10 +++++----- R/summary-oneinfl.R | 4 ++-- 7 files changed, 29 insertions(+), 20 deletions(-)