Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb, cph],
Julian Gi [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.0-6 dated 2023-01-26 and 3.1-0 dated 2023-03-13
DESCRIPTION | 17 +--- MD5 | 84 ++++++++++---------- NAMESPACE | 2 NEWS | 44 ++++++++++ R/FGmultiInhom.R | 12 +- R/Gmulti.R | 6 - R/Jinhom.R | 6 - R/Jmulti.R | 6 - R/Kmulti.R | 6 - R/Kmulti.inhom.R | 6 - R/bw.abram.R | 16 ++- R/bw.optim.R | 6 - R/dclftest.R | 6 - R/densityAdaptiveKernel.R | 24 +++-- R/envelope.R | 4 R/kernels.R | 66 ++++++++++++---- R/localKcross.R | 6 - R/pcf.R | 114 ++-------------------------- R/pcfFromK.R |only R/pcfinhom.R | 12 +- R/pcfmulti.R | 6 - R/pcfmulti.inhom.R | 29 +++---- R/plot.fv.R | 40 +++++++-- R/resolve.lambda.R | 57 ++++++-------- R/rhohat.R | 8 + R/smooth.ppp.R | 6 - R/transect.R | 3 inst/CITATION | 98 +++++++++--------------- inst/doc/packagesizes.txt | 1 man/Finhom.Rd | 9 +- man/FmultiInhom.Rd | 20 +++- man/Jinhom.Rd | 12 +- man/bits.test.Rd | 3 man/bw.abram.Rd | 157 +++------------------------------------ man/bw.abram.ppp.Rd |only man/densityAdaptiveKernel.Rd | 6 - man/dg.test.Rd | 3 man/kernel.moment.Rd | 16 +++ man/macros/defns.Rd | 3 man/pcf.ppp.Rd | 9 +- man/pcfcross.inhom.Rd | 32 +++++-- man/pcfdot.inhom.Rd | 35 +++++--- man/pcfinhom.Rd | 26 +++++- man/spatstat.explore-internal.Rd | 5 - 44 files changed, 494 insertions(+), 533 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See
Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.1.6 dated 2022-05-10 and 1.1.7 dated 2023-03-13
DESCRIPTION | 8 +- MD5 | 50 +++++++-------- NAMESPACE | 3 NEWS.md | 5 + R/classes_methods.r | 127 +++++++++++++++++++++++++++++++++++++-- R/fun.r | 6 + R/multivariate.stat.r | 29 ++++++-- R/mvBM.r | 10 +-- R/mvEB.r | 15 ++-- R/mvgls.dfa.r | 9 ++ R/mvgls.pca.r | 3 R/mvgls.r | 3 R/mvols.r | 2 R/penalized.r | 61 +++++++++++++++--- R/zzz.r | 2 inst/CITATION | 6 - inst/doc/How_to_use_mvMORPH.Rmd | 3 inst/doc/How_to_use_mvMORPH.pdf |binary inst/doc/tutorial_mvMORPH.pdf |binary man/EIC.Rd | 2 man/mvMORPH-package.Rd | 4 - man/mvgls.Rd | 3 man/mvols.Rd | 4 - man/predict.mvgls.Rd | 2 man/pruning.Rd | 2 vignettes/How_to_use_mvMORPH.Rmd | 3 26 files changed, 278 insertions(+), 84 deletions(-)
Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'RTF',
'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'.
'R Markdown', 'Quarto' and the package 'officer' can be used to produce
the result files. The syntax is the same for the user regardless of
the type of output to be produced. A set of functions allows the
creation, definition of cell arrangement, addition of headers or
footers, formatting and definition of cell content with text and
or images. The package also offers a set of high-level functions
that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] ,
Titouan Robert [ctb],
Michael Barrowman [ctb] ,
Atsushi Yasumoto [ctb] ,
Paul Julian [ctb] ,
Sean Browning [ctb] , [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.8.6 dated 2023-02-23 and 0.9.0 dated 2023-03-13
flextable-0.8.6/flextable/man/reexports.Rd |only flextable-0.9.0/flextable/DESCRIPTION | 8 flextable-0.9.0/flextable/MD5 | 86 ++-- flextable-0.9.0/flextable/NAMESPACE | 17 flextable-0.9.0/flextable/NEWS.md | 18 flextable-0.9.0/flextable/R/as_flextable.tabular.R | 86 ++-- flextable-0.9.0/flextable/R/as_flextable_tabulator.R | 5 flextable-0.9.0/flextable/R/augment_rows.R | 15 flextable-0.9.0/flextable/R/body_add_flextable.R | 2 flextable-0.9.0/flextable/R/captions.R | 38 + flextable-0.9.0/flextable/R/docx_str.R | 2 flextable-0.9.0/flextable/R/formatters.R | 318 ++++++++-------- flextable-0.9.0/flextable/R/html_str.R | 69 +++ flextable-0.9.0/flextable/R/latex-borders.R | 1 flextable-0.9.0/flextable/R/pptx_str.R | 2 flextable-0.9.0/flextable/R/printers.R | 165 +++++--- flextable-0.9.0/flextable/R/rtf_str.R | 18 flextable-0.9.0/flextable/R/styles.R | 47 +- flextable-0.9.0/flextable/README.md | 8 flextable-0.9.0/flextable/man/as_flextable.tabular.Rd | 6 flextable-0.9.0/flextable/man/as_raster.Rd | 1 flextable-0.9.0/flextable/man/colformat_char.Rd | 3 flextable-0.9.0/flextable/man/colformat_date.Rd | 6 flextable-0.9.0/flextable/man/colformat_datetime.Rd | 6 flextable-0.9.0/flextable/man/colformat_double.Rd | 6 flextable-0.9.0/flextable/man/colformat_image.Rd | 10 flextable-0.9.0/flextable/man/colformat_num.Rd | 10 flextable-0.9.0/flextable/man/df_printer.Rd | 1 flextable-0.9.0/flextable/man/flextable_to_rmd.Rd | 1 flextable-0.9.0/flextable/man/font.Rd | 16 flextable-0.9.0/flextable/man/gen_grob.Rd | 1 flextable-0.9.0/flextable/man/htmltools_value.Rd | 11 flextable-0.9.0/flextable/man/knit_print.flextable.Rd | 1 flextable-0.9.0/flextable/man/plot.flextable.Rd | 1 flextable-0.9.0/flextable/man/print.flextable.Rd | 1 flextable-0.9.0/flextable/man/save_as_docx.Rd | 4 flextable-0.9.0/flextable/man/save_as_html.Rd | 8 flextable-0.9.0/flextable/man/save_as_image.Rd | 4 flextable-0.9.0/flextable/man/save_as_pptx.Rd | 4 flextable-0.9.0/flextable/man/save_as_rtf.Rd |only flextable-0.9.0/flextable/man/set_formatter.Rd | 31 - flextable-0.9.0/flextable/man/set_header_labels.Rd | 4 flextable-0.9.0/flextable/man/to_html.flextable.Rd | 5 flextable-0.9.0/flextable/tests/testthat/test-borders.R | 10 flextable-0.9.0/flextable/tests/testthat/test-headers.R | 6 45 files changed, 709 insertions(+), 353 deletions(-)
Title: Interpolation of Data with Variable Spatial Support
Description: Geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.
Author: Jon Olav Skoien [aut, cre],
Qingyun Duan [ctb]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between rtop versions 0.5-14 dated 2018-04-06 and 0.6-2 dated 2023-03-13
DESCRIPTION | 19 ++- MD5 | 55 +++++---- NAMESPACE | 9 + R/checkVario.R | 2 R/discAreas.R | 82 ++++++++++++-- R/fitVariogram.R | 14 -- R/gDist.r | 14 ++ R/krige.R | 4 R/rtop.R | 62 ++++++---- R/rtopKrige.R | 39 ++++-- R/rtopSim.R | 27 ++++ R/rtopVario.R | 12 ++ R/rtopVred.R | 6 - R/rtopread.R | 234 ++++++++++++++++++++--------------------- R/sceua.R | 44 ++++--- R/varMat.R | 48 ++++++-- inst/CITATION | 17 +- man/checkVario.Rd | 15 +- man/createRtopObject.Rd | 36 ++---- man/gDist.Rd | 10 + man/plot.rtopVariogramCloud.Rd | 133 ++++++++++++----------- man/rtop-package.Rd | 15 +- man/rtopFitVariogram.Rd | 16 ++ man/rtopKrige.Rd | 14 +- man/rtopSim.Rd | 34 +++-- man/sceua.Rd | 10 + tests/rtop.R | 15 +- tests/rtop.rout.save |only tests/rtop_sf.R |only tests/rtop_sf.Rout.save |only 30 files changed, 610 insertions(+), 376 deletions(-)
Title: Social Ranking Solutions for Power Relations on Coalitions
Description: The notion of power index has been widely used in literature to evaluate the influence of individual players (e.g., voters, political parties, nations, stockholders, etc.) involved in a collective decision situation like an electoral system, a parliament, a council, a management board, etc., where players may form coalitions. Traditionally this ranking is determined through numerical evaluation. More often than not however only ordinal data between coalitions is known. The package 'socialranking' offers a set of solutions to rank players based on a transitive ranking between coalitions, including through CP-Majority, ordinal Banzhaf or lexicographic excellence solution summarized by Tahar Allouche, Bruno Escoffier, Stefano Moretti and Meltem Öztürk (2020, <doi:10.24963/ijcai.2020/3>).
Author: Felix Fritz [aut, cre],
Jochen Staudacher [aut, cph, ths],
Moretti Stefano [aut, cph, ths]
Maintainer: Felix Fritz <felix.fritz@dauphine.eu>
Diff between socialranking versions 0.1.2 dated 2022-10-27 and 1.0.0 dated 2023-03-13
socialranking-0.1.2/socialranking/R/helpers.R |only socialranking-0.1.2/socialranking/R/powerRelation.R |only socialranking-0.1.2/socialranking/R/rankingBoilerplate.R |only socialranking-0.1.2/socialranking/build/socialranking.pdf |only socialranking-0.1.2/socialranking/man/PowerRelation.default.Rd |only socialranking-0.1.2/socialranking/man/SocialRankingSolution.Rd |only socialranking-0.1.2/socialranking/man/SocialRankingSolution.default.Rd |only socialranking-0.1.2/socialranking/man/socialranking.Rd |only socialranking-0.1.2/socialranking/tests/testthat/test-doRanking.R |only socialranking-0.1.2/socialranking/tests/testthat/test-equivalenceClassIndex.R |only socialranking-0.1.2/socialranking/tests/testthat/test-newPowerRelation.R |only socialranking-1.0.0/socialranking/DESCRIPTION | 16 socialranking-1.0.0/socialranking/MD5 | 154 - socialranking-1.0.0/socialranking/NAMESPACE | 26 socialranking-1.0.0/socialranking/NEWS.md | 24 socialranking-1.0.0/socialranking/R/PowerRelation.R |only socialranking-1.0.0/socialranking/R/SocialRanking.R |only socialranking-1.0.0/socialranking/R/appendMissingCoalitions.R |only socialranking-1.0.0/socialranking/R/asPowerRelation.R |only socialranking-1.0.0/socialranking/R/banzhaf.R | 80 socialranking-1.0.0/socialranking/R/copeland.R | 51 socialranking-1.0.0/socialranking/R/cpmajority.R | 84 socialranking-1.0.0/socialranking/R/createPowerset.R |only socialranking-1.0.0/socialranking/R/cumulative.R | 29 socialranking-1.0.0/socialranking/R/docs.R | 10 socialranking-1.0.0/socialranking/R/dominance.R | 21 socialranking-1.0.0/socialranking/R/generator.R |only socialranking-1.0.0/socialranking/R/kramerSimpson.R | 47 socialranking-1.0.0/socialranking/R/lexcel.R | 89 socialranking-1.0.0/socialranking/R/lexcel1.R |only socialranking-1.0.0/socialranking/R/makePowerRelationMonotonic.R |only socialranking-1.0.0/socialranking/R/pipes.R | 104 socialranking-1.0.0/socialranking/R/relation.R | 66 socialranking-1.0.0/socialranking/R/transitiveClosure.R | 58 socialranking-1.0.0/socialranking/README.md | 42 socialranking-1.0.0/socialranking/build/partial.rdb |binary socialranking-1.0.0/socialranking/build/vignette.rds |binary socialranking-1.0.0/socialranking/inst/doc/socialranking.R | 222 + socialranking-1.0.0/socialranking/inst/doc/socialranking.Rmd | 422 ++- socialranking-1.0.0/socialranking/inst/doc/socialranking.html | 1177 +++++----- socialranking-1.0.0/socialranking/inst/doc/socialranking_pdf.R | 222 + socialranking-1.0.0/socialranking/inst/doc/socialranking_pdf.Rmd | 422 ++- socialranking-1.0.0/socialranking/inst/doc/socialranking_pdf.pdf |binary socialranking-1.0.0/socialranking/man/L1Scores.Rd |only socialranking-1.0.0/socialranking/man/PowerRelation.Rd | 161 + socialranking-1.0.0/socialranking/man/SocialRanking.Rd |only socialranking-1.0.0/socialranking/man/appendMissingCoalitions.Rd |only socialranking-1.0.0/socialranking/man/as.PowerRelation.Rd |only socialranking-1.0.0/socialranking/man/coalitionsAreIndifferent.Rd | 39 socialranking-1.0.0/socialranking/man/copelandScores.Rd | 49 socialranking-1.0.0/socialranking/man/cpMajorityComparison.Rd | 65 socialranking-1.0.0/socialranking/man/createPowerset.Rd | 69 socialranking-1.0.0/socialranking/man/cumulativeScores.Rd | 34 socialranking-1.0.0/socialranking/man/doRanking.Rd | 133 - socialranking-1.0.0/socialranking/man/dominates.Rd | 25 socialranking-1.0.0/socialranking/man/elementLookup.Rd |only socialranking-1.0.0/socialranking/man/equivalenceClassIndex.Rd | 51 socialranking-1.0.0/socialranking/man/generateNextPartition.Rd |only socialranking-1.0.0/socialranking/man/kramerSimpsonScores.Rd | 55 socialranking-1.0.0/socialranking/man/lexcelScores.Rd | 83 socialranking-1.0.0/socialranking/man/makePowerRelationMonotonic.Rd |only socialranking-1.0.0/socialranking/man/newPowerRelation.Rd | 136 - socialranking-1.0.0/socialranking/man/newPowerRelationFromString.Rd | 52 socialranking-1.0.0/socialranking/man/ordinalBanzhafScores.Rd | 50 socialranking-1.0.0/socialranking/man/powerRelationGenerator.Rd |only socialranking-1.0.0/socialranking/man/powerRelationMatrix.Rd | 27 socialranking-1.0.0/socialranking/man/socialrankingpackage.Rd |only socialranking-1.0.0/socialranking/man/testRelation.Rd | 10 socialranking-1.0.0/socialranking/man/transitiveClosure.Rd | 27 socialranking-1.0.0/socialranking/tests/testthat/test-PowerRelation.R |only socialranking-1.0.0/socialranking/tests/testthat/test-SocialRanking.R |only socialranking-1.0.0/socialranking/tests/testthat/test-copeland.R | 44 socialranking-1.0.0/socialranking/tests/testthat/test-cpMajorityComparison.R | 84 socialranking-1.0.0/socialranking/tests/testthat/test-createPowerset.R | 74 socialranking-1.0.0/socialranking/tests/testthat/test-cumulative.R | 29 socialranking-1.0.0/socialranking/tests/testthat/test-dominance.R | 6 socialranking-1.0.0/socialranking/tests/testthat/test-generator.R |only socialranking-1.0.0/socialranking/tests/testthat/test-kramerSimpson.R | 36 socialranking-1.0.0/socialranking/tests/testthat/test-lexcel.R | 36 socialranking-1.0.0/socialranking/tests/testthat/test-lexcel1.R |only socialranking-1.0.0/socialranking/tests/testthat/test-makeMonotonic.R |only socialranking-1.0.0/socialranking/tests/testthat/test-makeTotal.R |only socialranking-1.0.0/socialranking/tests/testthat/test-ordinalBanzhaf.R | 61 socialranking-1.0.0/socialranking/tests/testthat/test-pipes.R | 2 socialranking-1.0.0/socialranking/tests/testthat/test-relationRelationRelation.R | 83 socialranking-1.0.0/socialranking/tests/testthat/test-releaseBullets.R |only socialranking-1.0.0/socialranking/tests/testthat/test-transitiveClosure.R | 63 socialranking-1.0.0/socialranking/vignettes/media/altupanddown.jpg |binary socialranking-1.0.0/socialranking/vignettes/media/altupanddown.png |only socialranking-1.0.0/socialranking/vignettes/socialranking.Rmd | 422 ++- socialranking-1.0.0/socialranking/vignettes/socialranking_pdf.Rmd | 422 ++- socialranking-1.0.0/socialranking/vignettes/styles.css | 6 socialranking-1.0.0/socialranking/vignettes/tables/functionTable.html | 5 socialranking-1.0.0/socialranking/vignettes/tables/functionTable.tex | 3 socialranking-1.0.0/socialranking/vignettes/tables/prObject.html | 17 socialranking-1.0.0/socialranking/vignettes/tables/prObject.tex | 6 96 files changed, 3429 insertions(+), 2402 deletions(-)
Title: Predicting Ethnic Group from Names
Description: Implementation of the race/ethnicity prediction method, described
in "rethnicity: An R package for predicting ethnicity from names"
by Fangzhou Xie (2022) <doi:10.1016/j.softx.2021.100965> and
"Rethnicity: Predicting Ethnicity from Names" by Fangzhou Xie (2021) <arXiv:2109.09228>.
Author: Fangzhou Xie [aut, cre]
Maintainer: Fangzhou Xie <fangzhou.xie@rutgers.edu>
Diff between rethnicity versions 0.2.3 dated 2022-05-31 and 0.2.4 dated 2023-03-13
DESCRIPTION | 11 +-- MD5 | 18 ++--- NEWS.md | 26 ++++++- R/zzz.R | 27 +++----- README.md | 24 +++++-- build/vignette.rds |binary inst/doc/advanced_usage.html | 140 +++++++++++++++++++++--------------------- inst/doc/introduction.html | 142 ++++++++++++++++++++++--------------------- src/Makevars | 2 src/Makevars.win | 2 10 files changed, 214 insertions(+), 178 deletions(-)
Title: A Toolbox for the Multi-Criteria Minimum Spanning Tree Problem
Description: Algorithms to approximate the Pareto-front of multi-criteria minimum spanning tree problems.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between mcMST versions 1.0.1 dated 2017-09-18 and 1.1.1 dated 2023-03-13
mcMST-1.0.1/mcMST/R/graph.R |only mcMST-1.0.1/mcMST/R/plotGraph.R |only mcMST-1.0.1/mcMST/inst/doc/Generation.R |only mcMST-1.0.1/mcMST/inst/doc/Generation.Rmd |only mcMST-1.0.1/mcMST/inst/doc/Generation.html |only mcMST-1.0.1/mcMST/man/addCenters.Rd |only mcMST-1.0.1/mcMST/man/addCoordinates.Rd |only mcMST-1.0.1/mcMST/man/addWeights.Rd |only mcMST-1.0.1/mcMST/man/coordGenerators.Rd |only mcMST-1.0.1/mcMST/man/mcGP.Rd |only mcMST-1.0.1/mcMST/man/plot.mcGP.Rd |only mcMST-1.0.1/mcMST/tests/testthat/Rplots.pdf |only mcMST-1.0.1/mcMST/tests/testthat/test_generators.R |only mcMST-1.0.1/mcMST/vignettes/Generation.Rmd |only mcMST-1.1.1/mcMST/DESCRIPTION | 19 mcMST-1.1.1/mcMST/LICENSE | 2 mcMST-1.1.1/mcMST/MD5 | 123 +- mcMST-1.1.1/mcMST/NAMESPACE | 37 mcMST-1.1.1/mcMST/NEWS | 21 mcMST-1.1.1/mcMST/NEWS.md | 19 mcMST-1.1.1/mcMST/R/checks.R |only mcMST-1.1.1/mcMST/R/computeSimilarityMatrix.R |only mcMST-1.1.1/mcMST/R/emoa_operators.R | 300 +++++-- mcMST-1.1.1/mcMST/R/enumerators.R | 2 mcMST-1.1.1/mcMST/R/genRandomSpanningTrees.R |only mcMST-1.1.1/mcMST/R/generators.R | 17 mcMST-1.1.1/mcMST/R/getExactFront.R | 50 - mcMST-1.1.1/mcMST/R/getExtremeSolutions.R |only mcMST-1.1.1/mcMST/R/getNumberOfSpanningTrees.R |only mcMST-1.1.1/mcMST/R/getRandomSpanningTree.R |only mcMST-1.1.1/mcMST/R/getReferencePoint.R | 8 mcMST-1.1.1/mcMST/R/getWeight.R | 45 - mcMST-1.1.1/mcMST/R/helpers.R |only mcMST-1.1.1/mcMST/R/mcMST-package.R | 5 mcMST-1.1.1/mcMST/R/mcMSTEmoaBG.R | 16 mcMST-1.1.1/mcMST/R/mcMSTEmoaZhou.R | 4 mcMST-1.1.1/mcMST/R/mcMSTPrim.R | 40 mcMST-1.1.1/mcMST/R/metrics.R |only mcMST-1.1.1/mcMST/R/plotEdgeFrequency.R |only mcMST-1.1.1/mcMST/R/plotEdges.R |only mcMST-1.1.1/mcMST/R/transformations.R | 49 + mcMST-1.1.1/mcMST/R/zzz.R | 8 mcMST-1.1.1/mcMST/build/vignette.rds |binary mcMST-1.1.1/mcMST/inst/doc/introduction.R | 17 mcMST-1.1.1/mcMST/inst/doc/introduction.Rmd | 19 mcMST-1.1.1/mcMST/inst/doc/introduction.html | 414 ++++++++-- mcMST-1.1.1/mcMST/man/charVecToEdgelist.Rd |only mcMST-1.1.1/mcMST/man/computeSimilarityMatrix.Rd |only mcMST-1.1.1/mcMST/man/edgeListToCharVec.Rd | 12 mcMST-1.1.1/mcMST/man/genRandomMCGP.Rd | 10 mcMST-1.1.1/mcMST/man/genRandomSpanningTree.Rd |only mcMST-1.1.1/mcMST/man/genRandomSpanningTrees.Rd |only mcMST-1.1.1/mcMST/man/getCommonSubtrees.Rd |only mcMST-1.1.1/mcMST/man/getExactFront.Rd | 8 mcMST-1.1.1/mcMST/man/getExtremeSolutions.Rd |only mcMST-1.1.1/mcMST/man/getNumberOfSpanningTrees.Rd |only mcMST-1.1.1/mcMST/man/getRandomSpanningTree.Rd |only mcMST-1.1.1/mcMST/man/getWeight.Rd | 13 mcMST-1.1.1/mcMST/man/mcMST-package.Rd | 5 mcMST-1.1.1/mcMST/man/mcMSTEmoaBG.Rd | 30 mcMST-1.1.1/mcMST/man/mcMSTEmoaZhou.Rd | 27 mcMST-1.1.1/mcMST/man/mcMSTPrim.Rd | 13 mcMST-1.1.1/mcMST/man/mutEdgeExchange.Rd | 13 mcMST-1.1.1/mcMST/man/mutKEdgeExchange.Rd |only mcMST-1.1.1/mcMST/man/mutSubforestMST.Rd |only mcMST-1.1.1/mcMST/man/mutSubgraphMST.Rd | 28 mcMST-1.1.1/mcMST/man/mutUniformPruefer.Rd | 8 mcMST-1.1.1/mcMST/man/nodelistToEdgelist.Rd |only mcMST-1.1.1/mcMST/man/permutationToCharVec.Rd | 12 mcMST-1.1.1/mcMST/man/permutationToEdgelist.Rd | 12 mcMST-1.1.1/mcMST/man/plotEdgeFrequency.Rd |only mcMST-1.1.1/mcMST/man/plotEdges.Rd |only mcMST-1.1.1/mcMST/man/prueferToCharVec.Rd | 12 mcMST-1.1.1/mcMST/man/prueferToEdgeList.Rd | 12 mcMST-1.1.1/mcMST/man/sampleWeights.Rd |only mcMST-1.1.1/mcMST/man/scalarizeWeights.Rd |only mcMST-1.1.1/mcMST/man/similarity_metrics.Rd |only mcMST-1.1.1/mcMST/tests/testthat/test_algorithms.R | 61 + mcMST-1.1.1/mcMST/tests/testthat/test_enumerators.R | 12 mcMST-1.1.1/mcMST/tests/testthat/test_genRandomSpanningTree.R |only mcMST-1.1.1/mcMST/tests/testthat/test_helpers.R |only mcMST-1.1.1/mcMST/tests/testthat/test_measures.R |only mcMST-1.1.1/mcMST/tests/testthat/test_transformations.R | 25 mcMST-1.1.1/mcMST/vignettes/introduction.Rmd | 19 84 files changed, 1163 insertions(+), 384 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis.
b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534.
c) Tsagris M. (2015). A novel, divergence based, regression for compositional data. Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444.
d) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Stat [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 6.1 dated 2023-01-08 and 6.2 dated 2023-03-13
Compositional-6.1/Compositional/R/mixreg.R |only Compositional-6.2/Compositional/DESCRIPTION | 15 +- Compositional-6.2/Compositional/MD5 | 81 +++++------ Compositional-6.2/Compositional/NAMESPACE | 2 Compositional-6.2/Compositional/R/alfa.contour.R | 35 ---- Compositional-6.2/Compositional/R/alfa.pcr.R | 3 Compositional-6.2/Compositional/R/alfareg.tune.R | 2 Compositional-6.2/Compositional/R/beta.reg.R | 8 - Compositional-6.2/Compositional/R/bivt.contour.R | 37 ----- Compositional-6.2/Compositional/R/compnorm.contour.R | 37 ----- Compositional-6.2/Compositional/R/diri.contour.R | 36 ---- Compositional-6.2/Compositional/R/diri.est.R | 16 +- Compositional-6.2/Compositional/R/diri.reg3.R |only Compositional-6.2/Compositional/R/fd.contour.R | 37 ----- Compositional-6.2/Compositional/R/folded.contour.R | 37 ----- Compositional-6.2/Compositional/R/gendiri.contour.R | 3 Compositional-6.2/Compositional/R/js.compreg.R | 22 +- Compositional-6.2/Compositional/R/kent.contour.R | 2 Compositional-6.2/Compositional/R/kl.compreg.R | 2 Compositional-6.2/Compositional/R/makefolds.R | 6 Compositional-6.2/Compositional/R/mix.compnorm.contour.R | 4 Compositional-6.2/Compositional/R/mixdiri.contour.R | 37 ----- Compositional-6.2/Compositional/R/ols.compreg.R | 22 +- Compositional-6.2/Compositional/R/skewnorm.contour.R | 2 Compositional-6.2/Compositional/R/symkl.compreg.R | 20 +- Compositional-6.2/Compositional/R/tv.compreg.R | 22 +- Compositional-6.2/Compositional/R/zad.est.R | 6 Compositional-6.2/Compositional/R/zadr.R | 56 +++++-- Compositional-6.2/Compositional/R/zadr2.R |only Compositional-6.2/Compositional/man/Compositional-package.Rd | 4 Compositional-6.2/Compositional/man/acor.Rd | 6 Compositional-6.2/Compositional/man/acor.tune.Rd | 18 +- Compositional-6.2/Compositional/man/cv.lasso.klcompreg.Rd | 3 Compositional-6.2/Compositional/man/diri.reg.Rd | 18 +- Compositional-6.2/Compositional/man/kl.alfapcr.Rd | 4 Compositional-6.2/Compositional/man/kl.compreg.Rd | 8 - Compositional-6.2/Compositional/man/klalfapcr.tune.Rd | 8 - Compositional-6.2/Compositional/man/lasso.klcompreg.Rd | 5 Compositional-6.2/Compositional/man/lassocoef.plot.Rd | 5 Compositional-6.2/Compositional/man/lc.glm.Rd | 2 Compositional-6.2/Compositional/man/lc.reg.Rd | 4 Compositional-6.2/Compositional/man/lc.reg2.Rd | 23 +-- Compositional-6.2/Compositional/man/zadr.Rd | 25 +-- 43 files changed, 229 insertions(+), 454 deletions(-)
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.18.0 dated 2023-01-19 and 0.19.0 dated 2023-03-13
DESCRIPTION | 6 - MD5 | 71 +++++++++--------- NEWS.md | 40 ++++++++++ R/Config.R | 3 R/Metadata.R | 14 +-- R/QueryCondition.R | 28 +++++-- R/RcppExports.R | 16 +++- R/Stats.R | 36 ++++----- R/TileDBArray.R | 26 +++--- R/Utils.R | 76 +++++++++++++++++++ configure | 37 +++++++-- configure.ac | 16 +++- inst/config.log | 128 +++++++++++++++++++++++++++++++++ inst/config.status | 11 +- inst/include/tiledb.h | 7 + inst/sampledata/legacy_validity.tar.gz |only inst/sampledata/legacy_write.tar.gz |only inst/scripts |only inst/tinytest/test_config.R | 9 ++ inst/tinytest/test_query.R | 7 + inst/tinytest/test_querycondition.R | 26 ++++++ inst/tinytest/test_tiledbarray.R | 70 ++++++++++++++++++ man/parse_query_condition.Rd | 3 man/tiledb_dim.Rd | 12 +-- man/tiledb_get_all_metadata.Rd | 8 +- man/tiledb_get_metadata.Rd | 2 man/tiledb_num_metadata.Rd | 2 man/tiledb_put_metadata.Rd | 2 man/tiledb_stats_dump.Rd | 4 - man/tiledb_stats_raw_dump.Rd | 13 +-- man/tiledb_stats_raw_get.Rd | 2 src/Makevars.in | 2 src/Makevars.win | 2 src/RcppExports.cpp | 48 +++++++++--- src/batched.cpp | 5 - src/libtiledb.cpp | 83 ++++++++++++++------- src/shmem.cpp | 2 tools/tiledbVersion.txt | 4 - 38 files changed, 643 insertions(+), 178 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Luedecke [aut, cre] ,
Alexander Bartel [ctb] ,
Carsten Schwemmer [ctb],
Chuck Powell [ctb] ,
Amir Djalovski [ctb],
Johannes Titz [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.12 dated 2022-11-19 and 2.8.13 dated 2023-03-13
DESCRIPTION | 8 +-- MD5 | 94 ++++++++++++++++++------------------ NEWS.md | 6 ++ R/S3-methods.R | 40 +++++++-------- R/plot_gpt.R | 21 ++++---- R/plot_likert.R | 8 +-- R/plot_models.R | 8 +++ R/tab_model.R | 36 ++++++++----- R/tidiers.R | 2 R/utils.R | 3 + README.md | 4 - inst/doc/blackwhitefigures.html | 4 - inst/doc/custplot.html | 4 - inst/doc/plot_interactions.R | 1 inst/doc/plot_interactions.Rmd | 1 inst/doc/plot_interactions.html | 24 ++++----- inst/doc/plot_likert_scales.R | 1 inst/doc/plot_likert_scales.Rmd | 1 inst/doc/plot_likert_scales.html | 16 +++--- inst/doc/plot_marginal_effects.R | 3 - inst/doc/plot_marginal_effects.Rmd | 1 inst/doc/plot_marginal_effects.html | 22 ++++---- inst/doc/plot_model_estimates.R | 1 inst/doc/plot_model_estimates.Rmd | 1 inst/doc/plot_model_estimates.html | 6 +- inst/doc/sjtitemanalysis.html | 4 - inst/doc/tab_bayes.R | 2 inst/doc/tab_bayes.html | 24 ++++----- inst/doc/tab_mixed.R | 2 inst/doc/tab_mixed.html | 12 ++-- inst/doc/tab_model_estimates.html | 4 - inst/doc/tab_model_robust.R | 2 inst/doc/table_css.html | 4 - man/plot_gpt.Rd | 21 ++++---- man/plot_likert.Rd | 2 man/tab_corr.Rd | 2 man/tab_df.Rd | 2 man/tab_fa.Rd | 2 man/tab_itemscale.Rd | 2 man/tab_model.Rd | 2 man/tab_pca.Rd | 2 man/tab_stackfrq.Rd | 2 man/tab_xtab.Rd | 2 man/view_df.Rd | 2 vignettes/plot_interactions.Rmd | 1 vignettes/plot_likert_scales.Rmd | 1 vignettes/plot_marginal_effects.Rmd | 1 vignettes/plot_model_estimates.Rmd | 1 48 files changed, 228 insertions(+), 187 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.
Author: Peter Bourke [aut, cre],
Geert van Geest [aut],
Roeland Voorrips [ctb],
Yanlin Liao [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.1.2 dated 2021-03-09 and 1.1.3 dated 2023-03-13
polymapR-1.1.2/polymapR/man/merge_marker_assignments.Rd |only polymapR-1.1.3/polymapR/DESCRIPTION | 12 polymapR-1.1.3/polymapR/MD5 | 47 - polymapR-1.1.3/polymapR/NAMESPACE | 1 polymapR-1.1.3/polymapR/R/aiding_functions.R | 122 +++ polymapR-1.1.3/polymapR/R/exported_functions.R | 339 ++++------ polymapR-1.1.3/polymapR/inst/doc/Vignette_genotype_probabilities.Rmd | 4 polymapR-1.1.3/polymapR/inst/doc/Vignette_genotype_probabilities.html | 34 - polymapR-1.1.3/polymapR/inst/doc/Vignette_polymapR.R | 11 polymapR-1.1.3/polymapR/inst/doc/Vignette_polymapR.Rmd | 24 polymapR-1.1.3/polymapR/inst/doc/Vignette_polymapR.html | 54 + polymapR-1.1.3/polymapR/man/checkF1.Rd | 2 polymapR-1.1.3/polymapR/man/check_maxP.Rd | 2 polymapR-1.1.3/polymapR/man/cluster_SN_markers.Rd | 2 polymapR-1.1.3/polymapR/man/convert_updog.Rd | 12 polymapR-1.1.3/polymapR/man/finish_linkage_analysis.Rd | 16 polymapR-1.1.3/polymapR/man/gp_overview.Rd | 2 polymapR-1.1.3/polymapR/man/homologue_lg_assignment.Rd | 2 polymapR-1.1.3/polymapR/man/linkage.Rd | 9 polymapR-1.1.3/polymapR/man/linkage.gp.Rd | 2 polymapR-1.1.3/polymapR/man/marker_data_summary.Rd | 9 polymapR-1.1.3/polymapR/man/screen_for_duplicate_individuals.gp.Rd | 2 polymapR-1.1.3/polymapR/vignettes/Vignette_genotype_probabilities.Rmd | 4 polymapR-1.1.3/polymapR/vignettes/Vignette_polymapR.Rmd | 24 polymapR-1.1.3/polymapR/vignettes/bibliography.bib | 10 25 files changed, 479 insertions(+), 267 deletions(-)
Title: Joint Models of Survival and Multivariate Longitudinal Data
Description: Fit joint models of survival and multivariate longitudinal data. The longitudinal
data is specified by generalised linear mixed models. The joint models are fit via maximum
likelihood using an approximate expectation maximisation algorithm.
Bernhardt (2015) <doi:10.1016/j.csda.2014.11.011>.
Author: James Murray [aut, cre]
Maintainer: James Murray <j.murray7@ncl.ac.uk>
Diff between gmvjoint versions 0.1.0 dated 2022-12-07 and 0.2.0 dated 2023-03-13
DESCRIPTION | 9 - MD5 | 80 ++++++++------ NAMESPACE | 28 ++++ NEWS.md | 8 + R/EMUpdate.R | 50 ++++---- R/PBC.R | 13 +- R/ROC.R |only R/RcppExports.R | 42 ++++++- R/bootAUC.R |only R/condb.R |only R/dynPred-draws.R |only R/dynPred-prepare.R |only R/dynPred.R |only R/fitted.R |only R/inits.R | 28 +++- R/joint.R | 149 ++++++++++++++++---------- R/joint.object.R | 10 + R/loglik.R | 115 +++++++++++++++++++- R/misc.R | 85 ++++++++++++-- R/rfixef.R | 5 R/simData.R | 18 ++- R/survmod.R | 251 ++++++++++++++++++++++---------------------- R/vcov.R | 88 +++++++++------ README.md | 28 +++- build/partial.rdb |binary man/PBC.Rd | 11 + man/ROC.Rd |only man/anova.joint.Rd |only man/bootAUC.Rd |only man/bootAUCdiff.Rd |only man/cond.ranefs.Rd |only man/dynPred.Rd |only man/fitted.joint.Rd |only man/joint.Rd | 58 +++++++--- man/joint.object.Rd | 10 + man/logLik.joint.Rd | 4 man/parseCoxph.Rd | 30 +++-- man/plot.ROC.joint.Rd |only man/plot.dynPred.Rd |only man/plot.residuals.joint.Rd |only man/ranef.joint.Rd | 5 man/residuals.joint.Rd |only man/simData.Rd | 6 + man/vcov.joint.Rd | 23 +++- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 154 ++++++++++++++++++++++---- src/dynpreds.cpp |only src/funs.cpp | 239 +++++++++++++++++++++++++---------------- src/init.c | 20 ++- src/vech2mat.cpp |only 51 files changed, 1083 insertions(+), 488 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories
(also known as a Sankey diagram), flow charts by extending the grid package,
a method for variable selection based on the SVD, Bézier lines with arrows
complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 3.0.1 dated 2022-11-19 and 3.0.2 dated 2023-03-13
Gmisc-3.0.1/Gmisc/tests/testthat/Rplots.pdf |only Gmisc-3.0.2/Gmisc/DESCRIPTION | 8 ++++---- Gmisc-3.0.2/Gmisc/MD5 | 15 +++++++-------- Gmisc-3.0.2/Gmisc/R/mergeDesc_S3_fns.R | 17 +++++++++-------- Gmisc-3.0.2/Gmisc/inst/doc/Descriptives.html | 4 ++-- Gmisc-3.0.2/Gmisc/inst/doc/Grid-based_flowcharts.html | 2 +- Gmisc-3.0.2/Gmisc/inst/doc/Transition-class.html | 4 ++-- Gmisc-3.0.2/Gmisc/inst/doc/transitionPlot.html | 4 ++-- Gmisc-3.0.2/Gmisc/man/htmlTable_latex.Rd | 4 ++-- 9 files changed, 29 insertions(+), 29 deletions(-)
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis spec [...truncated...]
Author: Jeffrey Dick [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 1.4.3 dated 2022-02-21 and 2.0.0 dated 2023-03-13
CHNOSZ-1.4.3/CHNOSZ/R/EOSregress.R |only CHNOSZ-1.4.3/CHNOSZ/R/findit.R |only CHNOSZ-1.4.3/CHNOSZ/R/objective.R |only CHNOSZ-1.4.3/CHNOSZ/R/revisit.R |only CHNOSZ-1.4.3/CHNOSZ/demo/adenine.R |only CHNOSZ-1.4.3/CHNOSZ/demo/findit.R |only CHNOSZ-1.4.3/CHNOSZ/demo/zinc.R |only CHNOSZ-1.4.3/CHNOSZ/inst/doc/eos-regress.R |only CHNOSZ-1.4.3/CHNOSZ/inst/doc/eos-regress.Rmd |only CHNOSZ-1.4.3/CHNOSZ/inst/doc/eos-regress.html |only CHNOSZ-1.4.3/CHNOSZ/inst/extdata/OBIGT/biotic_aq.csv |only CHNOSZ-1.4.3/CHNOSZ/inst/tinytest/test-EOSregress.R |only CHNOSZ-1.4.3/CHNOSZ/inst/tinytest/test-findit.R |only CHNOSZ-1.4.3/CHNOSZ/inst/tinytest/test-objective.R |only CHNOSZ-1.4.3/CHNOSZ/inst/tinytest/test-revisit.R |only CHNOSZ-1.4.3/CHNOSZ/man/EOSregress.Rd |only CHNOSZ-1.4.3/CHNOSZ/man/eos.Rd |only CHNOSZ-1.4.3/CHNOSZ/man/findit.Rd |only CHNOSZ-1.4.3/CHNOSZ/man/objective.Rd |only CHNOSZ-1.4.3/CHNOSZ/man/revisit.Rd |only CHNOSZ-1.4.3/CHNOSZ/vignettes/eos-regress.Rmd |only CHNOSZ-2.0.0/CHNOSZ/DESCRIPTION | 10 CHNOSZ-2.0.0/CHNOSZ/MD5 | 442 +- CHNOSZ-2.0.0/CHNOSZ/NAMESPACE | 29 CHNOSZ-2.0.0/CHNOSZ/R/AD.R | 18 CHNOSZ-2.0.0/CHNOSZ/R/Berman.R | 13 CHNOSZ-2.0.0/CHNOSZ/R/DEW.R | 16 CHNOSZ-2.0.0/CHNOSZ/R/IAPWS95.R | 41 CHNOSZ-2.0.0/CHNOSZ/R/NaCl.R | 132 CHNOSZ-2.0.0/CHNOSZ/R/add.OBIGT.R | 126 CHNOSZ-2.0.0/CHNOSZ/R/add.protein.R | 107 CHNOSZ-2.0.0/CHNOSZ/R/affinity.R | 101 CHNOSZ-2.0.0/CHNOSZ/R/buffer.R | 59 CHNOSZ-2.0.0/CHNOSZ/R/cgl.R | 78 CHNOSZ-2.0.0/CHNOSZ/R/diagram.R | 386 +- CHNOSZ-2.0.0/CHNOSZ/R/equilibrate.R | 212 - CHNOSZ-2.0.0/CHNOSZ/R/examples.R | 49 CHNOSZ-2.0.0/CHNOSZ/R/hkf.R | 122 CHNOSZ-2.0.0/CHNOSZ/R/info.R | 145 CHNOSZ-2.0.0/CHNOSZ/R/ionize.aa.R | 58 CHNOSZ-2.0.0/CHNOSZ/R/logB.to.OBIGT.R |only CHNOSZ-2.0.0/CHNOSZ/R/makeup.R | 162 CHNOSZ-2.0.0/CHNOSZ/R/mix.R | 8 CHNOSZ-2.0.0/CHNOSZ/R/mosaic.R | 110 CHNOSZ-2.0.0/CHNOSZ/R/nonideal.R | 101 CHNOSZ-2.0.0/CHNOSZ/R/palply.R | 8 CHNOSZ-2.0.0/CHNOSZ/R/protein.info.R | 139 CHNOSZ-2.0.0/CHNOSZ/R/rank.affinity.R |only 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CHNOSZ-2.0.0/CHNOSZ/R/water.R | 209 - CHNOSZ-2.0.0/CHNOSZ/R/zzz.R | 14 CHNOSZ-2.0.0/CHNOSZ/build/partial.rdb |binary CHNOSZ-2.0.0/CHNOSZ/build/vignette.rds |binary CHNOSZ-2.0.0/CHNOSZ/demo/00Index | 6 CHNOSZ-2.0.0/CHNOSZ/demo/AD.R | 2 CHNOSZ-2.0.0/CHNOSZ/demo/DEW.R | 164 CHNOSZ-2.0.0/CHNOSZ/demo/E_coli.R | 8 CHNOSZ-2.0.0/CHNOSZ/demo/NaCl.R | 14 CHNOSZ-2.0.0/CHNOSZ/demo/ORP.R | 181 - CHNOSZ-2.0.0/CHNOSZ/demo/Shh.R | 144 CHNOSZ-2.0.0/CHNOSZ/demo/TCA.R | 48 CHNOSZ-2.0.0/CHNOSZ/demo/affinity.R | 91 CHNOSZ-2.0.0/CHNOSZ/demo/aluminum.R | 62 CHNOSZ-2.0.0/CHNOSZ/demo/arsenic.R | 22 CHNOSZ-2.0.0/CHNOSZ/demo/buffer.R | 28 CHNOSZ-2.0.0/CHNOSZ/demo/carboxylase.R | 131 CHNOSZ-2.0.0/CHNOSZ/demo/comproportionation.R | 11 CHNOSZ-2.0.0/CHNOSZ/demo/contour.R | 4 CHNOSZ-2.0.0/CHNOSZ/demo/copper.R | 71 CHNOSZ-2.0.0/CHNOSZ/demo/dehydration.R | 62 CHNOSZ-2.0.0/CHNOSZ/demo/density.R | 90 CHNOSZ-2.0.0/CHNOSZ/demo/glycinate.R | 28 CHNOSZ-2.0.0/CHNOSZ/demo/gold.R | 16 CHNOSZ-2.0.0/CHNOSZ/demo/ionize.R | 14 CHNOSZ-2.0.0/CHNOSZ/demo/lambda.R | 90 CHNOSZ-2.0.0/CHNOSZ/demo/minsol.R |only CHNOSZ-2.0.0/CHNOSZ/demo/potassium.R | 32 CHNOSZ-2.0.0/CHNOSZ/demo/protbuff.R | 40 CHNOSZ-2.0.0/CHNOSZ/demo/protein.equil.R | 21 CHNOSZ-2.0.0/CHNOSZ/demo/rank.affinity.R |only CHNOSZ-2.0.0/CHNOSZ/demo/saturation.R | 10 CHNOSZ-2.0.0/CHNOSZ/demo/solubility.R | 12 CHNOSZ-2.0.0/CHNOSZ/demo/sources.R | 18 CHNOSZ-2.0.0/CHNOSZ/demo/sphalerite.R | 24 CHNOSZ-2.0.0/CHNOSZ/demo/yttrium.R |only CHNOSZ-2.0.0/CHNOSZ/inst/CHECKLIST | 36 CHNOSZ-2.0.0/CHNOSZ/inst/NEWS.Rd | 232 + CHNOSZ-2.0.0/CHNOSZ/inst/TODO | 10 CHNOSZ-2.0.0/CHNOSZ/inst/doc/OBIGT.R | 3 CHNOSZ-2.0.0/CHNOSZ/inst/doc/OBIGT.Rmd | 20 CHNOSZ-2.0.0/CHNOSZ/inst/doc/OBIGT.bib | 146 CHNOSZ-2.0.0/CHNOSZ/inst/doc/OBIGT.html | 117 CHNOSZ-2.0.0/CHNOSZ/inst/doc/anintro.R | 179 - CHNOSZ-2.0.0/CHNOSZ/inst/doc/anintro.Rmd | 309 - CHNOSZ-2.0.0/CHNOSZ/inst/doc/anintro.html | 598 +-- CHNOSZ-2.0.0/CHNOSZ/inst/doc/custom_data.R |only CHNOSZ-2.0.0/CHNOSZ/inst/doc/custom_data.Rmd |only CHNOSZ-2.0.0/CHNOSZ/inst/doc/custom_data.html |only CHNOSZ-2.0.0/CHNOSZ/inst/doc/equilibrium.html | 23 CHNOSZ-2.0.0/CHNOSZ/inst/doc/mklinks.sh | 179 - CHNOSZ-2.0.0/CHNOSZ/inst/doc/multi-metal.R | 171 CHNOSZ-2.0.0/CHNOSZ/inst/doc/multi-metal.Rmd | 101 CHNOSZ-2.0.0/CHNOSZ/inst/doc/multi-metal.html | 1109 +++--- CHNOSZ-2.0.0/CHNOSZ/inst/extdata/Berman/testing/BA96_OBIGT.csv | 42 CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/AD.csv | 50 CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/AS04.csv | 8 CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv | 186 - CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/DEW.csv | 422 +- CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/GEMSFIT.csv | 86 CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/H2O_aq.csv | 8 CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv | 346 - CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/SUPCRT92.csv | 356 +- CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv | 1763 ++++------ CHNOSZ-2.0.0/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv | 307 - 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CHNOSZ-2.0.0/CHNOSZ/vignettes/OBIGT.bib | 146 CHNOSZ-2.0.0/CHNOSZ/vignettes/anintro.Rmd | 309 - CHNOSZ-2.0.0/CHNOSZ/vignettes/custom_data.Rmd |only CHNOSZ-2.0.0/CHNOSZ/vignettes/mklinks.sh | 179 - CHNOSZ-2.0.0/CHNOSZ/vignettes/multi-metal.Rmd | 101 CHNOSZ-2.0.0/CHNOSZ/vignettes/vig.bib | 159 243 files changed, 10772 insertions(+), 10696 deletions(-)
Title: Partitioning Beta Diversity into Turnover and Nestedness
Components
Description: Functions to compute pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.
Author: Andres Baselga [aut, cre],
David Orme [aut],
Sebastien Villeger [aut],
Julien De Bortoli [aut],
Fabien Leprieur [aut],
Maxime Logez [aut],
Sara Martinez-Santalla [aut],
Ramiro Martin-Devasa [aut],
Carola Gomez-Rodriguez [aut],
Rosa M. Crujeiras [aut] [...truncated...]
Maintainer: Andres Baselga <andres.baselga@usc.es>
Diff between betapart versions 1.5.6 dated 2022-04-06 and 1.6 dated 2023-03-13
DESCRIPTION | 35 +- MD5 | 33 +- NAMESPACE | 3 NEWS.md | 54 +-- R/decay-functions.R | 500 ++++++++++++++++++++----------- R/phylo.betapart.core.r | 2 data/ceram.n.txt | 3 data/ceram.s.txt | 32 - data/coords.n.txt |only data/coords.s.txt |only man/betapart-package.Rd | 14 man/boot.coefs.decay.Rd | 47 +- man/ceram.n.Rd | 2 man/coords.n.Rd |only man/coords.s.Rd |only man/decay.model.Rd | 91 +++-- man/functional.beta.pair.Rd | 2 man/functional.betapart.core.pairwise.Rd | 2 man/plot.decay.Rd | 49 +-- man/zdep.Rd |only 20 files changed, 540 insertions(+), 329 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Veronique Bachelier [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between antaresRead versions 2.4.2 dated 2023-02-14 and 2.5.0 dated 2023-03-13
DESCRIPTION | 8 MD5 | 41 ++-- NAMESPACE | 4 NEWS.md | 25 ++ R/aggregateResult.R | 306 +++++++++++++++++--------------- R/digest.R |only R/getGeographicTrimming.R | 2 R/h5_antaresReadH5.R | 2 R/h5_setSimulationPathH5.R | 2 R/h5_writeH5ByYear.R | 2 R/importOutput.R | 158 ++++++++++++++++ R/readAntares.R | 12 + R/zzz.R | 5 inst/doc/antaresH5.html | 4 inst/doc/antaresRead.html | 4 inst/test_v8/test_case_study_v8.tar.gz |binary inst/testdata/antares-test-study.tar.gz |binary man/dot-getOptionsH5.Rd |only man/dot-h5ReadAntares.Rd |only man/dot-writeAntaresH5Fun.Rd |only man/mergeDigests.Rd |only man/readAntares.Rd | 3 man/readDigestFile.Rd |only man/writeDigest.Rd |only tests/testthat/test-digest.R |only tests/testthat/test-readAntares_bc.R |only 26 files changed, 408 insertions(+), 170 deletions(-)
Title: Interface to 'Altair'
Description: Interface to 'Altair' <https://altair-viz.github.io>, which itself
is a 'Python' interface to 'Vega-Lite' <https://vega.github.io/vega-lite/>.
This package uses the 'Reticulate' framework
<https://rstudio.github.io/reticulate/> to manage the interface between R
and 'Python'.
Author: Ian Lyttle [aut, cre] ,
Haley Jeppson [aut],
Altair Developers [aut],
Alicia Schep [ctb] ,
Jake Vanderplas [ctb] ,
Brian Granger [ctb]
Maintainer: Ian Lyttle <ijlyttle@me.com>
Diff between altair versions 4.2.1 dated 2022-02-14 and 4.2.2 dated 2023-03-13
DESCRIPTION | 12 - MD5 | 16 - NEWS.md | 6 R/utils-jupyterlab.R | 4 README.md | 115 ++++++------- man/alt.Rd | 2 man/repr_text.altair.vegalite.v4.api.TopLevelMixin.Rd | 2 man/repr_vegalite4.altair.vegalite.v4.api.TopLevelMixin.Rd | 2 man/vegawidgetOutput.Rd | 8 9 files changed, 82 insertions(+), 85 deletions(-)
Title: Robust Bayesian T-Test
Description: An implementation of Bayesian model-averaged t-test that allows
users to draw inference about the presence vs absence of the effect,
heterogeneity of variances, and outliers. The 'RoBTT' packages estimates model
ensembles of models created as a combination of the competing hypotheses and uses
Bayesian model-averaging to combine the models using posterior model probabilities.
Users can obtain the model-averaged posterior distributions and inclusion Bayes
factors which account for the uncertainty in the data generating process
(Maier et al., 2022, <doi:10.31234/osf.io/d5zwc>).
Users can define a wide range of informative priors for all parameters
of interest. The package provides convenient functions for summary, visualizations,
and fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBTT versions 1.0.0 dated 2022-09-20 and 1.0.1 dated 2023-03-13
RoBTT-1.0.0/RoBTT/cleanup |only RoBTT-1.0.0/RoBTT/cleanup.win |only RoBTT-1.0.0/RoBTT/inst/include/meta_header.hpp |only RoBTT-1.0.0/RoBTT/src/Modules.cpp |only RoBTT-1.0.0/RoBTT/src/RoBTT-win.def |only RoBTT-1.0.0/RoBTT/src/init.cpp |only RoBTT-1.0.0/RoBTT/src/stan_files/beta.stan |only RoBTT-1.0.0/RoBTT/src/stan_files/chunks |only RoBTT-1.0.0/RoBTT/src/stan_files/gamma.stan |only RoBTT-1.0.0/RoBTT/src/stan_files/lognormal.stan |only RoBTT-1.0.0/RoBTT/src/stan_files/normal.stan |only RoBTT-1.0.0/RoBTT/src/stan_files/t.stan |only RoBTT-1.0.0/RoBTT/tools |only RoBTT-1.0.1/RoBTT/DESCRIPTION | 6 RoBTT-1.0.1/RoBTT/MD5 | 64 +++++--- RoBTT-1.0.1/RoBTT/NAMESPACE | 2 RoBTT-1.0.1/RoBTT/NEWS.md |only RoBTT-1.0.1/RoBTT/R/RoBTT-package.R | 2 RoBTT-1.0.1/RoBTT/R/stanmodels.R | 60 +++----- RoBTT-1.0.1/RoBTT/R/utilities.R | 1 RoBTT-1.0.1/RoBTT/R/zzz.R | 7 RoBTT-1.0.1/RoBTT/build/partial.rdb |binary RoBTT-1.0.1/RoBTT/build/vignette.rds |binary RoBTT-1.0.1/RoBTT/configure |only RoBTT-1.0.1/RoBTT/configure.win |only RoBTT-1.0.1/RoBTT/inst/doc/Introduction_to_RoBTT.html | 133 ++++++++---------- RoBTT-1.0.1/RoBTT/inst/include/stan_meta_header.hpp |only RoBTT-1.0.1/RoBTT/inst/stan |only RoBTT-1.0.1/RoBTT/src/Makevars | 27 --- RoBTT-1.0.1/RoBTT/src/Makevars.win | 25 --- RoBTT-1.0.1/RoBTT/src/RcppExports.cpp |only RoBTT-1.0.1/RoBTT/src/stanExports_beta.cc |only RoBTT-1.0.1/RoBTT/src/stanExports_beta.h |only RoBTT-1.0.1/RoBTT/src/stanExports_gamma.cc |only RoBTT-1.0.1/RoBTT/src/stanExports_gamma.h |only RoBTT-1.0.1/RoBTT/src/stanExports_lognormal.cc |only RoBTT-1.0.1/RoBTT/src/stanExports_lognormal.h |only RoBTT-1.0.1/RoBTT/src/stanExports_normal.cc |only RoBTT-1.0.1/RoBTT/src/stanExports_normal.h |only RoBTT-1.0.1/RoBTT/src/stanExports_t.cc |only RoBTT-1.0.1/RoBTT/src/stanExports_t.h |only RoBTT-1.0.1/RoBTT/src/stan_files/beta.hpp |only RoBTT-1.0.1/RoBTT/src/stan_files/gamma.hpp |only RoBTT-1.0.1/RoBTT/src/stan_files/lognormal.hpp |only RoBTT-1.0.1/RoBTT/src/stan_files/normal.hpp |only RoBTT-1.0.1/RoBTT/src/stan_files/t.hpp |only 46 files changed, 147 insertions(+), 180 deletions(-)
Title: Robust Bayesian Survival Analysis
Description: A framework for estimating ensembles of parametric survival models
with different parametric families. The RoBSA framework uses Bayesian
model-averaging to combine the competing parametric survival models into
a model ensemble, weights the posterior parameter distributions based on
posterior model probabilities and uses Bayes factors to test for the
presence or absence of the individual predictors or preference for a
parametric family (Bartoš, Aust & Haaf, 2021, <doi:10.48550/arXiv.2112.08311>).
The user can define a wide range of informative priors for all parameters
of interest. The package provides convenient functions for summary, visualizations,
fit diagnostics, and prior distribution calibration.
Author: Frantisek Bartos [aut, cre] ,
Julia M. Haaf [ths] ,
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBSA versions 1.0.0 dated 2022-05-27 and 1.0.1 dated 2023-03-13
DESCRIPTION | 16 - MD5 | 82 ++++---- NAMESPACE | 2 NEWS.md | 6 R/RoBSA-package.R | 2 R/main.R | 3 R/plot.R | 23 +- R/utilities.R | 6 R/zzz.R | 5 build/partial.rdb |binary man/RoBSA-package.Rd | 70 +++---- man/RoBSA.Rd | 331 +++++++++++++++++------------------ man/RoBSA_control.Rd | 142 +++++++-------- man/calibrate_meta_analytic.Rd | 82 ++++---- man/calibrate_quartiles.Rd | 108 +++++------ man/check_RoBSA.Rd | 40 ++-- man/check_setup.Rd | 275 ++++++++++++++--------------- man/contr.orthonormal.Rd | 60 +++--- man/default_prior.Rd | 78 ++++---- man/diagnostics.Rd | 186 +++++++++---------- man/exp-aft.Rd | 130 ++++++------- man/extract_flexsurv.Rd | 42 ++-- man/gamma-aft.Rd | 134 +++++++------- man/is.RoBSA.Rd | 34 +-- man/llogis-aft.Rd | 134 +++++++------- man/lnorm-aft.Rd | 134 +++++++------- man/plot.RoBSA.Rd | 194 ++++++++++---------- man/plot_models.Rd | 182 +++++++++---------- man/plot_prediction.Rd | 268 ++++++++++++++-------------- man/predict.RoBSA.Rd | 126 ++++++------- man/print.RoBSA.Rd | 44 ++-- man/print.summary.RoBSA.Rd | 44 ++-- man/prior.Rd | 170 ++++++++--------- man/prior_factor.Rd | 178 +++++++++--------- man/prior_informed.Rd | 138 +++++++------- man/prior_informed_medicine_names.Rd | 38 ++-- man/prior_none.Rd | 80 ++++---- man/summary.RoBSA.Rd | 246 +++++++++++++------------- man/update.RoBSA.Rd | 297 +++++++++++++++---------------- man/weibull-aft.Rd | 134 +++++++------- src/Makevars.ucrt | 192 ++++++++++---------- src/Makevars.win | 2 42 files changed, 2234 insertions(+), 2224 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2021,
<doi:10.31234/osf.io/kvsp7>; Maier, Bartoš & Wagenmakers, in press,
<doi:10.31234/osf.io/u4cns>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 2.3.1 dated 2022-07-16 and 2.3.2 dated 2023-03-13
DESCRIPTION | 13 +- MD5 | 36 +++--- NAMESPACE | 2 NEWS.md | 5 R/RoBMA-package.R | 2 R/diagnostics.R | 34 +++++- R/utilities.R | 6 - R/zzz.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/CustomEnsembles.html | 173 ++++++++++++++++---------------- inst/doc/MedicineBMA.html | 146 ++++++++++++++------------- inst/doc/ReproducingBMA.html | 146 ++++++++++++++------------- man/Anderson2010.Rd | 52 ++++----- man/Bem2011.Rd | 54 +++++----- man/Poulsen2006.Rd | 56 +++++----- man/RoBMA.Rd | 4 man/check_setup.Rd | 224 +++++++++++++++++++++--------------------- man/prior_informed.Rd | 138 ++++++++++++------------- 19 files changed, 573 insertions(+), 523 deletions(-)
Title: Datasets and Functions for the Class "Modelling and Data
Analysis for Pharmaceutical Sciences"
Description: Provides datasets and functions for the class "Modelling and Data Analysis for Pharmaceutical Sciences".
The datasets can be used to present various methods of data analysis and statistical modeling.
Functions for data visualization are also implemented.
Author: Lionel Voirol [aut, cre],
Stephane Guerrier [aut],
Yuming Zhang [aut],
Luca Insolia [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between idarps versions 0.0.1 dated 2023-01-27 and 0.0.2 dated 2023-03-13
DESCRIPTION | 16 ++++++++++------ MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/document_data.R | 8 ++++---- README.md | 28 +++++++++++++++++++++++++++- data/codex.RData |binary man/codex.Rd | 4 ++-- man/cortisol.Rd | 2 +- man/reading.Rd | 2 +- 9 files changed, 57 insertions(+), 23 deletions(-)
Title: Tools for Modelling of Animal Flight Performance
Description: Allows estimation and modelling of flight costs in animal (vertebrate) flight,
implementing the aerodynamic power model described in Klein Heerenbrink et al.
(2015) <doi:10.1098/rspa.2014.0952>. Taking inspiration from the program
'Flight', developed by Colin Pennycuick (Pennycuick (2008) "Modelling the flying
bird". Amsterdam: Elsevier. ISBN 0-19-857721-4), flight performance is estimated
based on basic morphological measurements such as body mass, wingspan and wing
area. 'afpt' can be used to make predictions on how animals should adjust their
flight behaviour and wingbeat kinematics to varying flight conditions.
Author: Marco KleinHeerenbrink [aut, cre]
,
Anders Hedenstroem [fnd]
Maintainer: Marco KleinHeerenbrink <Marco.KleinHeerenbrink@biology.ox.ac.uk>
Diff between afpt versions 1.1.0.2 dated 2022-05-30 and 1.1.0.3 dated 2023-03-13
DESCRIPTION | 12 +-- MD5 | 10 +- inst/doc/afpt-aerodynamic-model.html | 133 +++++++++++++++++------------------ inst/doc/afpt-basic-usage.html | 133 +++++++++++++++++------------------ inst/doc/afpt-multiple-birds.html | 133 +++++++++++++++++------------------ tests/testthat/Rplots.pdf |binary 6 files changed, 209 insertions(+), 212 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location
of the species (as a point pattern) is needed together with environmental conditions
(as a categorical raster). To test for significance habitat associations, one of
the two components is randomized. Methods are mainly based on Plotkin et al. (2000)
<doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Zeke Marshall [ctb] ,
Thomas Etherington [ctb] ,
Janosch Heinermann [ctb]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between shar versions 2.0.2 dated 2022-11-16 and 2.0.3 dated 2023-03-13
DESCRIPTION | 15 MD5 | 40 - NEWS.md | 4 R/reconstruct_pattern.R | 17 R/reconstruct_pattern_cluster.R | 20 R/reconstruct_pattern_hetero.R | 20 R/reconstruct_pattern_homo.R | 19 R/reconstruct_pattern_marks.R | 29 build/vignette.rds |binary inst/CITATION | 26 inst/doc/get_started.R | 92 +- inst/doc/get_started.html | 998 ++++++++++++------------- man/reconstruct_pattern.Rd | 4 man/reconstruct_pattern_cluster.Rd | 4 man/reconstruct_pattern_hetero.Rd | 4 man/reconstruct_pattern_homo.Rd | 4 man/reconstruct_pattern_marks.Rd | 4 man/shar.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-reconstruct_pattern.R | 4 tests/testthat/test-reconstruct_pattern_homo.R | 2 21 files changed, 685 insertions(+), 622 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Description: Bayesian geostatistical modeling of Gaussian processes using a
reparameterized and marginalized posterior sampling (RAMPS) algorithm
designed to lower autocorrelation in MCMC samples. Package performance is
tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between ramps versions 0.6.17 dated 2022-08-24 and 0.6.18 dated 2023-03-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/utils.R | 15 +++++++-------- 3 files changed, 13 insertions(+), 14 deletions(-)
Title: Partial LeAst Squares for Multiomic Analysis
Description: Contains tools for supervised analyses of incomplete, overlapping
multiomics datasets. Applies partial least squares in multiple steps to find
models that predict survival outcomes. See Yamaguchi et al. (2023)
<doi:10.1101/2023.03.10.532096>.
Author: Kevin R. Coombes [cre, aut],
Kyoko Yamaguchi [aut],
Salma Abdelbaky [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between plasma versions 0.9.21 dated 2022-12-06 and 1.0.0 dated 2023-03-13
plasma-0.9.21/plasma/inst/bib/theory.Rmd |only plasma-0.9.21/plasma/inst/bib/theory.pdf |only plasma-1.0.0/plasma/DESCRIPTION | 11 plasma-1.0.0/plasma/MD5 | 37 plasma-1.0.0/plasma/R/04-extend.R | 41 plasma-1.0.0/plasma/R/05-interpret.R | 21 plasma-1.0.0/plasma/R/06-weights.R | 12 plasma-1.0.0/plasma/build/vignette.rds |binary plasma-1.0.0/plasma/data/mirESCA.rda |binary plasma-1.0.0/plasma/data/tfESCA.rda |binary plasma-1.0.0/plasma/inst/GeneLists/ClinicalCont1.txt |only plasma-1.0.0/plasma/inst/GeneLists/allGenes.txt | 189 +- plasma-1.0.0/plasma/inst/GeneLists/finalGenes.txt | 135 - plasma-1.0.0/plasma/inst/TGOUT/ClinicalCont1.tsv |only plasma-1.0.0/plasma/inst/TGOUT/allGenes.tsv | 640 +++---- plasma-1.0.0/plasma/inst/TGOUT/finalGenes.tsv | 635 +++---- plasma-1.0.0/plasma/inst/bib/interpret.Rmd | 151 - plasma-1.0.0/plasma/inst/bib/plasma.Rmd | 66 plasma-1.0.0/plasma/inst/bib/plasma.bib | 1540 +++++++++---------- plasma-1.0.0/plasma/inst/bib/plasma.log |only plasma-1.0.0/plasma/inst/doc/interpret.pdf |binary plasma-1.0.0/plasma/inst/doc/plasma.pdf |binary 22 files changed, 1817 insertions(+), 1661 deletions(-)
More information about greencrab.toolkit at CRAN
Permanent link
Title: Modular Cohort-Building Framework for Analytical Dashboards
Description: You can easily add advanced cohort-building component
to your analytical dashboard or simple 'Shiny' app.
Then you can instantly start building cohorts using multiple
filters of different types, filtering datasets, and filtering steps.
Filters can be complex and data-specific, and together
with multiple filtering steps you can use complex filtering rules.
The cohort-building sidebar panel allows you to easily
work with filters, add and remove filtering steps.
It helps you with handling missing values during filtering,
and provides instant filtering feedback with filter feedback plots.
The GUI panel is not only compatible with native shiny
bookmarking, but also provides reproducible R code.
Author: Krystian Igras [cre, aut],
Kamil Wais [aut],
Adam Forys [ctb]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between shinyCohortBuilder versions 0.1 dated 2022-06-23 and 0.2.0 dated 2023-03-13
DESCRIPTION | 18 - MD5 | 53 +-- NEWS.md | 9 R/actions.R | 47 +-- R/app.R | 38 +- R/cb_layer.R | 11 R/control_utils.R |only R/filter_discrete.R | 53 ++- R/filter_discrete_text.R | 2 R/filter_multi_discrete.R | 95 ++++-- R/renders.R | 68 +++- R/shinyCohortBuilder-package.R | 3 R/source_tblist.R | 12 README.md | 18 - build/vignette.rds |binary inst/doc/custom-gui-layer.html | 453 ++++++++++++++++++++++------- inst/doc/gui-filter-layer.html | 608 ++++++++++++++++++++++++++++++--------- inst/doc/package-options.html | 241 ++++++++++++++- inst/doc/shinyCohortBuilder.Rmd | 4 inst/doc/shinyCohortBuilder.html | 526 ++++++++++++++++++++++++++------- inst/doc/updating-source.html | 366 ++++++++++++++++++----- inst/www/scb.css | 33 +- inst/www/scb.min.css | 2 man/cb_ui.Rd | 9 man/demo_app.Rd | 14 man/gui.Rd | 6 man/keep_na_input.Rd | 18 + vignettes/shinyCohortBuilder.Rmd | 4 28 files changed, 2119 insertions(+), 592 deletions(-)
More information about shinyCohortBuilder at CRAN
Permanent link
Title: Population Downscaling Using Areal Interpolation
Description: Given a
set of source zone polygons such as
census tracts or city blocks alongside with population counts and a
target zone of incogruent yet superimposed polygon features (such as
individual buildings) populR transforms population counts from the
former to the latter using Areal Interpolation methods.
Author: Marios Batsaris
Maintainer: Marios Batsaris <m.batsaris@aegean.gr>
Diff between populR versions 0.2.0 dated 2023-01-12 and 0.2.1 dated 2023-03-13
DESCRIPTION | 12 MD5 | 23 - R/pp_ancillary.R | 14 R/pp_compare.R | 13 R/pp_estimate.R | 35 + R/pp_vgi.R | 22 - R/utils.R | 13 README.md |only inst/doc/areal-interpolation-comparison.Rmd | 10 inst/doc/areal-interpolation-comparison.html | 560 ++++++++++++++++++++------- man/pp_compare.Rd | 4 man/pp_vgi.Rd | 10 vignettes/areal-interpolation-comparison.Rmd | 10 13 files changed, 531 insertions(+), 195 deletions(-)
Title: Biodiversity Data Cleaning
Description: It brings together several aspects of biodiversity
data-cleaning in one place. 'bdc' is organized in thematic modules
related to different biodiversity dimensions, including 1) Merge
datasets: standardization and integration of different datasets; 2)
Pre-filter: flagging and removal of invalid or non-interpretable
information, followed by data amendments; 3) Taxonomy: cleaning,
parsing, and harmonization of scientific names from several taxonomic
groups against taxonomic databases locally stored through the
application of exact and partial matching algorithms; 4) Space:
flagging of erroneous, suspect, and low-precision geographic
coordinates; and 5) Time: flagging and, whenever possible, correction
of inconsistent collection date. In addition, it contains
features to visualize, document, and report data quality – which is
essential for making data quality assessment transparent and
reproducible. The reference for the methodology is Bruno et al. (2022)
<doi:10.1111/2041-210X.13868> [...truncated...]
Author: Bruno Ribeiro [aut, cre] ,
Santiago Velazco [aut] ,
Karlo Guidoni-Martins [aut] ,
Geiziane Tessarolo [aut] ,
Lucas Jardim [aut] ,
Steven Bachman [ctb] ,
Rafael Loyola [ctb]
Maintainer: Bruno Ribeiro <ribeiro.brr@gmail.com>
Diff between bdc versions 1.1.2 dated 2022-08-18 and 1.1.4 dated 2023-03-13
bdc-1.1.2/bdc/R/bdc_extract_cntr_names.R |only bdc-1.1.2/bdc/inst/extdata/countries_names/wiki_country_names.txt |only bdc-1.1.4/bdc/DESCRIPTION | 17 bdc-1.1.4/bdc/MD5 | 53 bdc-1.1.4/bdc/NAMESPACE | 3 bdc-1.1.4/bdc/NEWS.md | 25 bdc-1.1.4/bdc/R/bdc_coord_trans.R | 1 bdc-1.1.4/bdc/R/bdc_coordinates_country_inconsistent.R | 17 bdc-1.1.4/bdc/R/bdc_correct_coordinates.R | 1 bdc-1.1.4/bdc/R/bdc_country_from_coordinates.R | 13 bdc-1.1.4/bdc/R/bdc_country_standardized.R | 32 bdc-1.1.4/bdc/R/bdc_filter_name.R | 4 bdc-1.1.4/bdc/R/bdc_get_world_map.R | 55 bdc-1.1.4/bdc/R/bdc_query_names_taxadb.R | 50 bdc-1.1.4/bdc/R/bdc_standardize_country.R | 74 bdc-1.1.4/bdc/R/bdc_standardize_datasets.R | 6 bdc-1.1.4/bdc/R/bdc_stdz_cntr.R |only bdc-1.1.4/bdc/inst/doc/integrate_datasets.html | 743 +++++----- bdc-1.1.4/bdc/inst/doc/prefilter.html | 630 ++++---- bdc-1.1.4/bdc/inst/doc/space.html | 630 ++++---- bdc-1.1.4/bdc/inst/doc/taxonomy.html | 638 ++++---- bdc-1.1.4/bdc/inst/doc/time.html | 634 ++++---- bdc-1.1.4/bdc/inst/extdata/countries_names/country_names.txt |only bdc-1.1.4/bdc/inst/extdata/countries_names/reword-countries.csv |only bdc-1.1.4/bdc/inst/extdata/outpus_vignettes/04_Report_time.csv | 14 bdc-1.1.4/bdc/man/bdc_country_standardized.Rd | 4 bdc-1.1.4/bdc/tests/testthat/test-bdc_get_world_map.R | 2 bdc-1.1.4/bdc/tests/testthat/test-bdc_query_names_taxadb.R | 83 + bdc-1.1.4/bdc/tests/testthat/test-bdc_standardize_country.R | 13 bdc-1.1.4/bdc/tests/testthat/test-bdc_standardize_datasets.R | 25 30 files changed, 1986 insertions(+), 1781 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
Kasper Klitgaard Berthelsen [ctb],
Ya-Mei Chang [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.1-3 dated 2023-01-25 and 3.1-4 dated 2023-03-13
DESCRIPTION | 12 ++--- MD5 | 36 ++++++++-------- NAMESPACE | 3 + NEWS | 36 +++++++++++++--- R/clusterinfo.R | 14 +++--- R/rclusterBKBC.R | 33 +++++++++------ R/rmhmodel.R | 56 ++++++++++++++++---------- R/truncpois.R | 17 +++++++ inst/CITATION | 98 ++++++++++++++++++---------------------------- inst/doc/packagesizes.txt | 1 man/clusterfield.Rd | 18 ++++---- man/clusterkernel.Rd | 7 ++- man/clusterradius.Rd | 12 ----- man/macros/defns.Rd | 3 - man/rLGCP.Rd | 30 ++++++++------ man/rMosaicField.Rd | 10 +--- man/rMosaicSet.Rd | 9 ---- man/rPSNCP.Rd | 19 +++++++- man/recipEnzpois.Rd |only man/rpoistrunc.Rd |only 20 files changed, 234 insertions(+), 180 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Gruen <dominic.gruen@gmail.com>
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.2.9 dated 2023-03-01 and 0.3.0 dated 2023-03-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/RaceID.R | 5 +++-- R/VarID_functions.R | 7 ++++++- inst/doc/RaceID.html | 8 ++++---- man/plotsymbolsmap.Rd | 5 ++++- 6 files changed, 26 insertions(+), 17 deletions(-)
Title: Building and Training Neural Networks
Description: Building and training custom neural networks in the typical R syntax. The 'torch' package is used for numerical calculations, which allows for training on CPU as well as on a graphics card.
Author: Christian Amesoeder [aut, cre],
Maximilian Pichler [aut]
Maintainer: Christian Amesoeder <Christian.Amesoeder@informatik.uni-regensburg.de>
Diff between cito versions 1.0.0 dated 2022-08-11 and 1.0.1 dated 2023-03-13
DESCRIPTION | 21 MD5 | 100 +-- NEWS.md |only R/ALE.R | 326 ++++++----- R/PDP.R | 66 +- R/cito.R | 9 R/continue_training.R | 204 +++--- R/dnn.R | 824 ++++++++++++++-------------- R/lr_scheduler.R | 293 +++++---- R/model.R | 296 ++++------ R/optimizer.R | 4 R/plot.R | 132 ++-- R/training.R | 325 ++++++----- R/utils.R | 273 ++++----- README.md | 75 -- build/vignette.rds |binary inst/doc/Introduction_to_cito.R | 6 inst/doc/Introduction_to_cito.Rmd | 589 +++++++++----------- inst/doc/Introduction_to_cito.html | 208 +++---- inst/examples/ALE-example.R | 18 inst/examples/PDP-example.R | 18 inst/examples/analyze_training-example.R | 42 - inst/examples/coef.citodnn-example.R | 32 - inst/examples/config_lr_scheduler-example.R | 28 inst/examples/config_optimizer-example.R | 28 inst/examples/continue_training-example.R | 32 - inst/examples/dnn-example.R | 106 ++- inst/examples/plot.citodnn-example.R | 24 inst/examples/predict.citodnn-example.R | 34 - inst/examples/print.citodnn-example.R | 26 man/ALE.Rd | 117 ++- man/PDP.Rd | 13 man/analyze_training.Rd | 2 man/cito.Rd | 77 +- man/coef.citodnn.Rd | 2 man/config_lr_scheduler.Rd | 101 +-- man/config_optimizer.Rd | 106 +-- man/continue_training.Rd | 2 man/dnn.Rd | 63 +- man/plot.citodnn.Rd | 2 man/predict.citodnn.Rd | 14 man/print.citodnn.Rd | 2 man/print.summary.citodnn.Rd | 38 - man/residuals.citodnn.Rd | 38 - man/summary.citodnn.Rd | 50 - tests/testthat.R | 9 tests/testthat/Rplots.pdf |binary tests/testthat/test-dnn.R | 272 ++++++--- tests/testthat/test-examples.R | 4 tests/testthat/test-xAI.R | 129 +++- tests/testthat/utils.R |only vignettes/Introduction_to_cito.Rmd | 589 +++++++++----------- 52 files changed, 3134 insertions(+), 2635 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results [...truncated...]
Author: Emmanuel Paradis [aut, cre, cph]
,
Simon Blomberg [aut, cph] ,
Ben Bolker [aut, cph] ,
Joseph Brown [aut, cph] ,
Santiago Claramunt [aut, cph] ,
Julien Claude [aut, cph] ,
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph] [...truncated...]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.7 dated 2023-02-16 and 5.7-1 dated 2023-03-13
DESCRIPTION | 11 ++- MD5 | 34 ++++++------ NEWS | 1 R/rtt.R | 2 inst/doc/DrawingPhylogenies.pdf |binary inst/doc/MoranI.pdf |binary inst/doc/RandomTopologies.pdf |binary man/ape-internal.Rd | 1 man/as.bitsplits.Rd | 2 man/bind.tree.Rd | 12 ++-- man/compar.lynch.Rd | 7 -- man/dnds.Rd | 5 + man/pic.Rd | 7 -- man/plot.phylo.Rd | 7 -- man/read.caic.Rd | 11 ++- man/read.dna.Rd | 113 ++++++++++++++++++++++++++-------------- man/read.tree.Rd | 16 +++-- src/tree_build.c | 34 ++++++------ 18 files changed, 152 insertions(+), 111 deletions(-)
Title: Convert Files to Parquet Format
Description: Collection of functions to get files in parquet format.
Parquet is a columnar storage file format <https://parquet.apache.org/>.
The files to convert can be of several formats
("csv", "RData", "rds", "RSQLite",
"json", "ndjson", "SAS", "SPSS"...).
Author: Damien Dotta [aut, cre]
Maintainer: Damien Dotta <damien.dotta@live.fr>
Diff between parquetize versions 0.5.3 dated 2023-02-20 and 0.5.4 dated 2023-03-13
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/json_to_parquet.R | 12 ++++++------ R/table_to_parquet.R | 10 +++++----- R/utilities.R | 9 +++------ README.md | 1 + tests/testthat/_snaps/table_to_parquet.md | 8 ++++---- tests/testthat/output/test_data.parquet |binary tests/testthat/test-bychunk.R | 6 +++--- tests/testthat/test-table_to_parquet.R | 8 ++++---- 10 files changed, 38 insertions(+), 40 deletions(-)
Title: Nature Inspired Colours
Description: Color palettes based on nature inspired colours in "Sri Lanka".
Author: Thiyanga S. Talagala [aut, cre]
,
Janith C. Wanniarachchi [aut],
Udeshi Salgado [ctb]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Diff between nic versions 0.0.1 dated 2022-01-27 and 0.0.2 dated 2023-03-13
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- build/vignette.rds |binary inst/doc/color-palette-demo.R | 3 ++- inst/doc/color-palette-demo.Rmd | 3 ++- inst/doc/color-palette-demo.html | 29 +++++++++++++++-------------- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary vignettes/color-palette-demo.Rmd | 3 ++- 11 files changed, 36 insertions(+), 32 deletions(-)
Title: Morphological and Structural Features of Medicinal Leaves
Description: Contains a dataset of morphological and structural features of 'Medicinal LEAves (MedLEA)'. The features of each species is recorded by manually viewing the medicinal plant repository available at (<http://www.instituteofayurveda.org/plants/>). You can also download repository of leaf images of 1099 medicinal plants in Sri Lanka.
Author: Jayani P. G. Lakshika [aut, cph],
Thiyanga S. Talagala [aut, ths, cre, cph]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Diff between MedLEA versions 1.0.1 dated 2021-04-10 and 1.0.2 dated 2023-03-13
DESCRIPTION | 12 MD5 | 16 README.md | 18 build/vignette.rds |binary inst/doc/MedLEA.R | 6 inst/doc/MedLEA.Rmd | 6 inst/doc/MedLEA.html | 2551 +------------------------------------- man/figures/README-example3-1.png |binary vignettes/MedLEA.Rmd | 6 9 files changed, 113 insertions(+), 2502 deletions(-)
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Data in Sri
Lanka
Description: Provides a daily counts of the Coronavirus (COVID19) cases by districts and country. Data source: Epidemiological Unit, Ministry of Health, Sri Lanka <https://www.epid.gov.lk/web/>.
Author: Thiyanga S. Talagala [aut, cre]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Diff between covid19srilanka versions 1.0.0 dated 2021-12-16 and 1.1.0 dated 2023-03-13
DESCRIPTION | 9 ++++----- MD5 | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-)
More information about covid19srilanka at CRAN
Permanent link
Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data.
Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU),
and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters
can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized
in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>,
Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>,
Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>,
Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, Samozino P. and Peyrot N., et al (2022)
<doi: 10.1111/sms.14097>, and Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanovic [aut, cre],
Jason D. Vescovi [dtc]
Maintainer: Mladen Jovanovic <coach.mladen.jovanovic@gmail.com>
Diff between shorts versions 2.3.0 dated 2022-10-29 and 2.4.0 dated 2023-03-13
DESCRIPTION | 9 +- MD5 | 53 +++++++------ NAMESPACE | 1 NEWS.md | 10 ++ R/convert-FV.R | 2 R/find-optimal-distance.R | 3 R/make-FV-profile.R | 2 R/model-radar-gun.R | 22 +++++ R/model-tether.R | 22 +++++ R/model-timing-gates.R | 33 +++++++- R/optimal-functions.R | 1 R/predict-functions.R | 10 +- R/probe-functions.R | 1 R/shorts-S3.R | 25 ++++++ README.md | 114 +++++++++++++++++++++++------- inst/CITATION | 33 ++++---- man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-16-1.png |only man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-22-1.png |binary man/figures/README-unnamed-chunk-23-1.png |only man/figures/README-unnamed-chunk-24-1.png |binary man/figures/README-unnamed-chunk-25-1.png |only man/figures/README-unnamed-chunk-26-1.png |only man/find_optimal_distance.Rd | 3 man/fitted.shorts_model.Rd |only man/model_radar_gun.Rd | 3 man/model_tether.Rd | 3 man/model_timing_gates.Rd | 5 + man/predict.shorts_model.Rd | 6 - 30 files changed, 269 insertions(+), 92 deletions(-)
Title: R as a Plotting Engine
Description: Generate basic charts either by custom applications, or from a small script launched from the system console, or within the R console. Two ASCII text files are necessary:
(1) The graph parameters file, which name is passed to the function 'rplotengine()'.
The user can specify the titles, choose the type of the graph, graph output formats
(e.g. png, eps), proportion of the X-axis and Y-axis, position of the legend,
whether to show or not a grid at the background, etc.
(2) The data to be plotted, which name is specified as a parameter ('data_filename')
in the previous file. This data file has a tabulated format, with a single character
(e.g. tab) between each column. Optionally, the file could include data columns for
showing confidence intervals.
Author: Pedro-Pablo Garrido Abenza [aut, cre]
Maintainer: Pedro-Pablo Garrido Abenza <pgarrido@umh.es>
Diff between rplotengine versions 1.0-8 dated 2022-04-06 and 1.0-9 dated 2023-03-13
DESCRIPTION | 8 +-- MD5 | 11 ++--- NAMESPACE | 2 R/rplotengine.R | 100 +++++++++++++++++++++++++++-------------------- inst/extdata/mygraph.arg | 4 - man/figures/mygraph.eps |only man/rplotengine.Rd | 6 +- 7 files changed, 74 insertions(+), 57 deletions(-)
Title: Utilities for Graphical Rendering and Fonts Management
Description: Tools are provided to compute metrics of
formatted strings and to check the availability of a font.
Another set of functions is provided to support the collection
of fonts from 'Google Fonts' in a cache. Their use is simple within
'R Markdown' documents and 'shiny' applications but also with graphic
productions generated with the 'ggiraph', 'ragg' and 'svglite' packages
or with tabular productions from the 'flextable' package.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.3.1 dated 2023-02-17 and 0.3.2 dated 2023-03-13
DESCRIPTION | 6 +++--- MD5 | 25 +++++++++++++------------ NAMESPACE | 1 + NEWS | 12 ++++++++++++ R/font-caching.R | 2 ++ R/fonts.R | 19 +++++++++++++++++++ man/addGFontHtmlDependency.Rd | 1 + man/fonts_cache_dir.Rd | 1 + man/gfontHtmlDependency.Rd | 1 + man/install_gfont_script.Rd | 1 + man/installed_gfonts.Rd |only man/liberationsansHtmlDependency.Rd | 1 + man/register_gfont.Rd | 1 + man/register_liberationsans.Rd | 1 + 14 files changed, 57 insertions(+), 15 deletions(-)
Title: Tool for Stability Indices Calculation
Description: Tools to calculate stability indices with parametric,
non-parametric and probabilistic approaches. The basic data format requirement for 'toolStability' is a data frame with 3 columns including numeric trait values, genotype,and environmental labels. Output format of each function is the dataframe with chosen stability index for each genotype.
Function "table_stability" offers the summary table of all stability indices in this package.
This R package toolStability is part of the main publication:
Wang, Casadebaig and Chen (2023) <doi:10.1007/s00122-023-04264-7>.
Analysis pipeline for main publication can be found on github: <https://github.com/Illustratien/Wang_2023_TAAG/tree/V1.0.0>.
Sample dataset in this package is derived from another publication:
Casadebaig P, Zheng B, Chapman S et al. (2016) <doi:10.1371/journal.pone.0146385>.
For detailed documentation of dataset, please see on Zenodo <doi:10.5281/zenodo.4729636>.
Indices used in this package are from:
Dö [...truncated...]
Author: Tien-Cheng Wang [aut, cre],
Tsu-Wei Chen [com]
Maintainer: Tien-Cheng Wang <wangtien@student.hu-berlin.de>
Diff between toolStability versions 0.1.1 dated 2022-01-12 and 0.1.2 dated 2023-03-13
DESCRIPTION | 54 ++++--- MD5 | 28 +-- NAMESPACE | 1 NEWS.md | 12 + R/ecovalence.R | 6 README.md | 314 +++++++++++++------------------------------ build/partial.rdb |binary inst/CITATION | 29 --- inst/REFERENCES.bib | 8 + inst/doc/toolStability.R | 7 inst/doc/toolStability.Rmd | 111 +++++++-------- inst/doc/toolStability.pdf |binary man/toolStability-package.Rd | 9 - vignettes/REFERENCES.bib | 8 + vignettes/toolStability.Rmd | 111 +++++++-------- 15 files changed, 295 insertions(+), 403 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.60-16 dated 2022-10-18 and 0.60-17 dated 2023-03-13
CHANGELOG | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/np.plot.R | 10 +++++++++- R/zzz.R | 2 +- build/vignette.rds |binary data/cps71.rda |binary inst/CITATION | 6 +++--- inst/doc/entropy_np.pdf |binary inst/doc/np.pdf |binary inst/doc/np_faq.Rnw | 14 +++++++++++++- inst/doc/np_faq.pdf |binary vignettes/np_faq.Rnw | 14 +++++++++++++- 13 files changed, 63 insertions(+), 23 deletions(-)
Title: Regression Models for Meta Signal Detection Theory
Description: Regression methods for the meta-SDT model. The package implements methods for cognitive experiments of metacognition as described in Kristensen, S. B., Sandberg, K., & Bibby, B. M. (2020). Regression methods for metacognitive sensitivity. Journal of Mathematical Psychology, 94. <doi:10.1016/j.jmp.2019.102297>.
Author: Simon Bang Kristensen [aut, cre],
Kristian Sandberg [aut],
Bo Martin Bibby [aut]
Maintainer: Simon Bang Kristensen <simonbk@ph.au.dk>
Diff between metaSDTreg versions 0.2.1 dated 2020-10-14 and 0.2.2 dated 2023-03-13
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- data/simMetaData.rda |binary 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre]
,
Grigorios Papageorgiou [aut],
Pedro Miranda Afonso [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.3-0 dated 2022-09-09 and 0.4-0 dated 2023-03-13
DESCRIPTION | 8 MD5 | 30 +- NAMESPACE | 10 NEWS.md | 16 + R/accuracy_measures.R | 601 ++++++++++++++++++++++++++++++++++++++++++++------ R/basic_methods.R | 209 ++++++++++++++++- R/help_functions.R | 83 +++++- R/jm.R | 4 R/predict_funs.R | 39 ++- README.md | 1 man/JMbayes2.Rd | 4 man/accuracy.Rd | 39 ++- man/jm.Rd | 8 man/predict.Rd | 18 + src/Makevars | 1 src/Makevars.win | 1 16 files changed, 940 insertions(+), 132 deletions(-)
Title: Generalized Linear Mixed Models using Adaptive Gaussian
Quadrature
Description: Fits generalized linear mixed models for a single grouping factor under
maximum likelihood approximating the integrals over the random effects with an
adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995)
<doi:10.1080/10618600.1995.10474663>.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between GLMMadaptive versions 0.8-5 dated 2022-02-07 and 0.8-8 dated 2023-03-13
DESCRIPTION | 8 MD5 | 12 - NAMESPACE | 3 R/methods.R | 28 ++ build/vignette.rds |binary inst/doc/GLMMadaptive.html | 500 ++++++++++++++++++++++++++++++++++++--------- man/GLMMadaptive.Rd | 4 7 files changed, 444 insertions(+), 111 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Theresa Burkard [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 0.4.0 dated 2023-03-08 and 0.4.1 dated 2023-03-13
DrugExposureDiagnostics-0.4.0/DrugExposureDiagnostics/man/dropTables.Rd |only DrugExposureDiagnostics-0.4.0/DrugExposureDiagnostics/tests/testthat/test-DropTables.R |only DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/DESCRIPTION | 10 +- DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/MD5 | 13 +-- DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/NEWS.md |only DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/R/executeChecks.R | 2 DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/R/utils.R | 41 ---------- DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/inst/doc/Introduction_to_DrugExposureDiagnostics.html | 4 DrugExposureDiagnostics-0.4.1/DrugExposureDiagnostics/inst/doc/Summary_of_checks.html | 6 - 9 files changed, 17 insertions(+), 59 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-12 0.0.5
2023-03-08 0.0.4
2023-03-07 0.0.3
2023-02-20 0.0.2