Title: Hierarchical Partitioning of Adjusted R2 and Explained Deviance
for Generalized Additive Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of gam()in 'mgcv' package, applying the algorithm in this paper: Lai(2024) <doi:10.1016/j.pld.2024.06.002>.
Author: Jiangshan Lai [aut, cre] ,
Jing Tang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between gam.hp versions 0.0-2 dated 2024-07-25 and 0.0-3 dated 2024-12-15
DESCRIPTION | 10 - MD5 | 11 +- R/gam.hp.r | 267 +++++++++++++++++++++++++++++++++++++++++++++-------- R/permu.gamhp.r | 120 +++++++++-------------- R/zzz.R |only man/gam.hp.Rd | 7 + man/permu.gamhp.Rd | 8 + 7 files changed, 302 insertions(+), 121 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 5.8 dated 2024-04-11 and 5.8-1 dated 2024-12-15
DESCRIPTION | 12 MD5 | 50 NAMESPACE | 1 NEWS | 4336 +++++++++++++++++++++++++++++++++++++++- R/ace.R | 9 R/cophenetic.phylo.R | 11 R/plot.phylo.R | 92 R/read.nexus.R | 24 R/scales.R | 151 - R/summary.phylo.R | 17 R/write.nexus.R | 8 R/write.phyloXML.R |only R/write.tree.R | 4 build/partial.rdb |binary build/vignette.rds |binary data/carnivora.csv.gz |binary inst/doc/DrawingPhylogenies.pdf |binary inst/doc/MoranI.pdf |binary inst/doc/RandomTopologies.pdf |binary man/axisPhylo.Rd | 9 man/cophenetic.phylo.Rd | 6 man/getAnnotationsGenBank.Rd | 2 man/image.DNAbin.Rd | 2 man/kronoviz.Rd | 11 man/write.nexus.Rd | 6 man/write.phyloXML.Rd |only man/write.tree.Rd | 15 27 files changed, 4592 insertions(+), 174 deletions(-)
Title: Hacks for 'ggplot2'
Description: A 'ggplot2' extension that does a variety of little
helpful things. The package extends 'ggplot2' facets through
customisation, by setting individual scales per panel, resizing panels
and providing nested facets. Also allows multiple colour and fill
scales per plot. Also hosts a smaller collection of stats, geoms and axis
guides.
Author: Teun van den Brand [aut, cre]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between ggh4x versions 0.2.8 dated 2024-01-23 and 0.3.0 dated 2024-12-15
ggh4x-0.2.8/ggh4x/inst/doc/PositionGuides.R |only ggh4x-0.2.8/ggh4x/inst/doc/PositionGuides.Rmd |only ggh4x-0.2.8/ggh4x/inst/doc/PositionGuides.html |only ggh4x-0.2.8/ggh4x/tests/testthat/_snaps/guide_axis_manual |only ggh4x-0.2.8/ggh4x/tests/testthat/_snaps/guide_axis_manual.md |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_logticks.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_manual.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_minor.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_nested.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_scalebar.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-guide_axis_truncated.R |only ggh4x-0.2.8/ggh4x/tests/testthat/test-scale_dendrogram.R |only ggh4x-0.2.8/ggh4x/vignettes/PositionGuides.Rmd |only ggh4x-0.3.0/ggh4x/DESCRIPTION | 37 ggh4x-0.3.0/ggh4x/MD5 | 199 ++-- ggh4x-0.3.0/ggh4x/NAMESPACE | 6 ggh4x-0.3.0/ggh4x/NEWS.md | 41 ggh4x-0.3.0/ggh4x/R/at_panel.R |only ggh4x-0.3.0/ggh4x/R/coord_axes_inside.R | 59 - ggh4x-0.3.0/ggh4x/R/facet_grid2.R | 15 ggh4x-0.3.0/ggh4x/R/facet_manual.R | 6 ggh4x-0.3.0/ggh4x/R/facet_nested.R | 4 ggh4x-0.3.0/ggh4x/R/facet_nested_wrap.R | 4 ggh4x-0.3.0/ggh4x/R/facet_wrap2.R | 46 - ggh4x-0.3.0/ggh4x/R/geom_outline_point.R | 2 ggh4x-0.3.0/ggh4x/R/geom_text_aimed.R | 2 ggh4x-0.3.0/ggh4x/R/guide_axis_logticks.R | 28 ggh4x-0.3.0/ggh4x/R/guide_axis_manual.R | 18 ggh4x-0.3.0/ggh4x/R/guide_axis_minor.R | 21 ggh4x-0.3.0/ggh4x/R/guide_axis_nested.R | 25 ggh4x-0.3.0/ggh4x/R/guide_axis_scalebar.R | 16 ggh4x-0.3.0/ggh4x/R/guide_axis_truncated.R | 21 ggh4x-0.3.0/ggh4x/R/guide_axis_utils.R | 6 ggh4x-0.3.0/ggh4x/R/guide_dendrogram.R | 14 ggh4x-0.3.0/ggh4x/R/guide_stringlegend.R | 420 +--------- ggh4x-0.3.0/ggh4x/R/help_secondary.R | 20 ggh4x-0.3.0/ggh4x/R/scale_dendrogram.R | 22 ggh4x-0.3.0/ggh4x/R/stat_difference.R | 2 ggh4x-0.3.0/ggh4x/R/stat_theodensity.R | 2 ggh4x-0.3.0/ggh4x/R/strip_tag.R |only ggh4x-0.3.0/ggh4x/R/strip_vanilla.R | 30 ggh4x-0.3.0/ggh4x/R/themes.R | 35 ggh4x-0.3.0/ggh4x/R/utils.R | 42 - ggh4x-0.3.0/ggh4x/README.md | 22 ggh4x-0.3.0/ggh4x/build/vignette.rds |binary ggh4x-0.3.0/ggh4x/inst/doc/Facets.R | 34 ggh4x-0.3.0/ggh4x/inst/doc/Facets.Rmd | 14 ggh4x-0.3.0/ggh4x/inst/doc/Facets.html | 96 +- ggh4x-0.3.0/ggh4x/inst/doc/Miscellaneous.R | 13 ggh4x-0.3.0/ggh4x/inst/doc/Miscellaneous.Rmd | 16 ggh4x-0.3.0/ggh4x/inst/doc/Miscellaneous.html | 190 ++-- ggh4x-0.3.0/ggh4x/inst/doc/Statistics.R | 2 ggh4x-0.3.0/ggh4x/inst/doc/Statistics.html | 56 - ggh4x-0.3.0/ggh4x/inst/doc/ggh4x.R | 2 ggh4x-0.3.0/ggh4x/inst/doc/ggh4x.Rmd | 4 ggh4x-0.3.0/ggh4x/inst/doc/ggh4x.html | 10 ggh4x-0.3.0/ggh4x/man/at_panel.Rd |only ggh4x-0.3.0/ggh4x/man/coord_axes_inside.Rd | 9 ggh4x-0.3.0/ggh4x/man/facet_grid2.Rd | 15 ggh4x-0.3.0/ggh4x/man/facet_manual.Rd | 14 ggh4x-0.3.0/ggh4x/man/facet_nested.Rd | 2 ggh4x-0.3.0/ggh4x/man/facet_nested_wrap.Rd | 2 ggh4x-0.3.0/ggh4x/man/facet_wrap2.Rd | 16 ggh4x-0.3.0/ggh4x/man/figures/README-facets-1.png |binary ggh4x-0.3.0/ggh4x/man/figures/lifecycle-deprecated.svg | 22 ggh4x-0.3.0/ggh4x/man/figures/lifecycle-experimental.svg | 22 ggh4x-0.3.0/ggh4x/man/figures/lifecycle-stable.svg | 30 ggh4x-0.3.0/ggh4x/man/figures/lifecycle-superseded.svg | 22 ggh4x-0.3.0/ggh4x/man/geom_box.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_outline_point.Rd | 83 + ggh4x-0.3.0/ggh4x/man/geom_pointpath.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_polygonraster.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_rectmargin.Rd | 63 + ggh4x-0.3.0/ggh4x/man/geom_text_aimed.Rd | 82 + ggh4x-0.3.0/ggh4x/man/ggh4x_extensions.Rd | 9 ggh4x-0.3.0/ggh4x/man/guide_axis_logticks.Rd | 32 ggh4x-0.3.0/ggh4x/man/guide_axis_manual.Rd | 21 ggh4x-0.3.0/ggh4x/man/guide_axis_minor.Rd | 26 ggh4x-0.3.0/ggh4x/man/guide_axis_nested.Rd | 29 ggh4x-0.3.0/ggh4x/man/guide_axis_scalebar.Rd | 8 ggh4x-0.3.0/ggh4x/man/guide_axis_truncated.Rd | 21 ggh4x-0.3.0/ggh4x/man/guide_dendro.Rd | 11 ggh4x-0.3.0/ggh4x/man/guide_stringlegend.Rd | 79 - ggh4x-0.3.0/ggh4x/man/help_secondary.Rd | 6 ggh4x-0.3.0/ggh4x/man/scale_dendrogram.Rd | 14 ggh4x-0.3.0/ggh4x/man/scale_x_manual.Rd | 8 ggh4x-0.3.0/ggh4x/man/stat_difference.Rd | 67 + ggh4x-0.3.0/ggh4x/man/stat_funxy.Rd | 62 + ggh4x-0.3.0/ggh4x/man/stat_rle.Rd | 47 - ggh4x-0.3.0/ggh4x/man/stat_rollingkernel.Rd | 47 - ggh4x-0.3.0/ggh4x/man/stat_theodensity.Rd | 51 - ggh4x-0.3.0/ggh4x/man/strip_nested.Rd | 1 ggh4x-0.3.0/ggh4x/man/strip_split.Rd | 1 ggh4x-0.3.0/ggh4x/man/strip_tag.Rd |only ggh4x-0.3.0/ggh4x/man/strip_themed.Rd | 1 ggh4x-0.3.0/ggh4x/man/strip_vanilla.Rd | 1 ggh4x-0.3.0/ggh4x/man/theme_extensions.Rd | 35 ggh4x-0.3.0/ggh4x/tests/testthat/Rplots.pdf |binary ggh4x-0.3.0/ggh4x/tests/testthat/_snaps/facetted_pos_scales.md | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-facet_grid2.R | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-facet_nested.R | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-facet_wrap2.R | 8 ggh4x-0.3.0/ggh4x/tests/testthat/test-guide_axis_deprecated.R |only ggh4x-0.3.0/ggh4x/tests/testthat/test-guide_stringlegend.R | 17 ggh4x-0.3.0/ggh4x/tests/testthat/test-stat_theodensity.R | 2 ggh4x-0.3.0/ggh4x/tests/testthat/test-strip_tag.R |only ggh4x-0.3.0/ggh4x/tests/testthat/test-utils.R | 6 ggh4x-0.3.0/ggh4x/vignettes/Facets.Rmd | 14 ggh4x-0.3.0/ggh4x/vignettes/Miscellaneous.Rmd | 16 ggh4x-0.3.0/ggh4x/vignettes/ggh4x.Rmd | 4 110 files changed, 1579 insertions(+), 1244 deletions(-)
Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in psychological research and teaching. Keng
currently has a built-in dataset depress, and could (1) scale a vector; (2) compute the cut-off
values of Pearson's r with known sample size; (3) test the significance and compute the post-hoc
power for Pearson's r with known sample size; (4) conduct prior power analysis and plan the
sample size for Pearson's r; (5) compare lm()'s fitted outputs using R-squared, f_squared,
post-hoc power, and PRE (Proportional Reduction in Error, also called partial R-squared or
partial Eta-squared); (6) calculate PRE from partial correlation, Cohen's f, or f_squared;
(7) conduct prior power analysis and plan the sample size for one or a set of predictors in
regression analysis; (8) conduct post-hoc power analysis for one or a set of predictors in
regression analysis with known sample size.
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2024.11.25 dated 2024-11-24 and 2024.12.15 dated 2024-12-15
DESCRIPTION | 32 +++-- MD5 | 67 ++++++----- NAMESPACE | 3 NEWS.md | 16 +- R/Scale.R | 119 ++++++++++---------- R/calc_PRE.R | 21 ++- R/compare_lm.R | 71 +++++++----- R/cut_r.R | 15 +- R/data.R | 2 R/plot.Keng_power.R |only R/power_lm.R | 230 +++++++++++++++++++++++++-------------- R/power_r.R |only R/print.Keng_power.R |only R/test_r.R | 147 ++++++++++++++++-------- README.md | 49 +++++--- inst/doc/PRE.html | 57 +++++---- inst/doc/PartialRegression.html | 38 +++--- inst/doc/PlanSampleSize.R | 19 +++ inst/doc/PlanSampleSize.Rmd | 76 +++++++----- inst/doc/PlanSampleSize.html | 127 +++++++++++++-------- man/Scale.Rd | 4 man/calc_PRE.Rd | 2 man/compare_lm.Rd | 55 +++++---- man/cut_r.Rd | 10 - man/depress.Rd | 2 man/plot.Keng_power.Rd |only man/power_lm.Rd | 88 +++++++++++--- man/power_r.Rd |only man/print.Keng_power.Rd |only man/test_r.Rd | 68 +++++++---- tests/testthat/test-Scale.R | 4 tests/testthat/test-calc_PRE.R | 19 +++ tests/testthat/test-compare_lm.R | 36 +++++- tests/testthat/test-cut_r.R | 4 tests/testthat/test-power_lm.R | 47 +++++++ tests/testthat/test-power_r.R |only tests/testthat/test-test_r.R | 10 + vignettes/PlanSampleSize.Rmd | 76 +++++++----- 38 files changed, 976 insertions(+), 538 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels
(Autonomous Communities, Provinces, Municipalities) based on the
'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco>
and 'CartoBase SIANE' from 'Instituto Geografico Nacional'
<https://www.ign.es/>. It also provides a 'leaflet' plugin and the
ability of downloading and processing static tiles.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.9.2 dated 2024-08-26 and 0.10.0 dated 2024-12-15
DESCRIPTION | 21 + MD5 | 46 ++-- NEWS.md | 7 R/esp_get_comarca.R | 345 +++++++++++++++++--------------- R/esp_get_prov.R | 9 R/sysdata.rda |binary R/utils_siane.R | 4 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary data/esp_codelist.rda |binary data/esp_munic.sf.rda |binary data/esp_nuts.sf.rda |binary data/esp_tiles_providers.rda |binary data/leaflet.providersESP.df.rda |binary data/pobmun19.rda |binary inst/WORDLIST | 10 inst/schemaorg.json | 4 man/esp_get_comarca.Rd | 59 +++-- man/mapSpain-package.Rd | 2 tests/testthat/test-esp_getTiles.R | 4 tests/testthat/test-esp_get_comarca.R | 8 tests/testthat/test-esp_get_munic.R | 1 tests/testthat/test-esp_make_provider.R | 4 24 files changed, 309 insertions(+), 221 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.10.0 dated 2024-10-29 and 1.11.0 dated 2024-12-15
microeco-1.10.0/microeco/inst/extdata/Tax4Fun_0.3.1.tar.gz |only microeco-1.11.0/microeco/DESCRIPTION | 6 microeco-1.11.0/microeco/MD5 | 33 - microeco-1.11.0/microeco/R/microtable.R | 32 - microeco-1.11.0/microeco/R/trans_abund.R | 48 ++ microeco-1.11.0/microeco/R/trans_alpha.R | 35 + microeco-1.11.0/microeco/R/trans_diff.R | 51 ++ microeco-1.11.0/microeco/R/trans_env.R | 248 +++++-------- microeco-1.11.0/microeco/R/trans_func.R | 68 --- microeco-1.11.0/microeco/R/trans_network.R | 104 +++-- microeco-1.11.0/microeco/R/utility.R | 3 microeco-1.11.0/microeco/man/microtable.Rd | 6 microeco-1.11.0/microeco/man/trans_abund.Rd | 9 microeco-1.11.0/microeco/man/trans_alpha.Rd | 19 microeco-1.11.0/microeco/man/trans_diff.Rd | 8 microeco-1.11.0/microeco/man/trans_env.Rd | 28 - microeco-1.11.0/microeco/man/trans_func.Rd | 25 - microeco-1.11.0/microeco/man/trans_network.Rd | 6 18 files changed, 379 insertions(+), 350 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 3.0.2 dated 2024-10-30 and 3.0.3 dated 2024-12-15
DESCRIPTION | 6 MD5 | 133 ++++++++----- NAMESPACE | 29 ++ NEWS.md | 32 +++ R/build.R | 11 - R/d.R | 181 +++++++++++++++++- R/dfIni.R | 234 +++++++++++++----------- R/elu.R |only R/err-foceiBase.R | 10 - R/et.R | 66 +++--- R/gelu.R |only R/lrelu.R |only R/parseFuns.R | 107 ++++++----- R/prelu.R |only R/relu.R |only R/rudfui.R | 33 +++ R/rxode2_md5.R | 2 R/rxrandomui.R | 340 +++++++++++++---------------------- R/selu.R |only R/softplus.R |only R/swish.R |only R/symengine.R | 142 +++++++++++++- R/utils.R | 31 +++ build/partial.rdb |binary build/vignette.rds |binary data/rxReservedKeywords.rda |binary data/rxResidualError.rda |binary data/rxSyntaxFunctions.rda |binary inst/doc/rxode2-syntax.html | 26 +- inst/include/rxode2_model_shared.c | 59 ++++++ inst/include/rxode2_model_shared.h | 6 inst/include/rxode2parseHandleEvid.h | 5 inst/include/rxode2parseVer.h | 4 inst/include/rxode2ptr.h | 5 inst/tools/workaround.R | 25 +- man/ELU.Rd |only man/GELU.Rd |only man/PReLU.Rd |only man/ReLU.Rd |only man/SELU.Rd |only man/Swish.Rd |only man/dELU.Rd |only man/dGELU.Rd |only man/dPReLU.Rd |only man/dReLU.Rd |only man/dSELU.Rd |only man/dSwish.Rd |only man/dlReLU.Rd |only man/dot-uiArg.Rd |only man/dsoftplus.Rd |only man/lReLU.Rd |only man/linMod.Rd | 1 man/rxUdfUiControl.Rd |only man/rxUdfUiData.Rd | 1 man/rxUdfUiEst.Rd | 1 man/rxUdfUiIniLhs.Rd | 1 man/rxUdfUiMv.Rd | 1 man/rxUdfUiNum.Rd | 1 man/rxUdfUiParsing.Rd | 1 man/softplus.Rd |only src/Makevars.in | 2 src/codegen.c | 4 src/codegen2.h | 28 ++ src/genModelVars.h | 60 +++++- src/init.c | 69 ++++++- src/parseCmtProperties.h | 10 - src/parseDdt.h | 7 src/parseFuns.h | 7 src/parseFunsDosing.h | 59 ++++-- src/parseVars.h | 1 src/rx2api.c | 4 src/rx2api.h | 3 src/tran.c | 3 src/tran.h | 31 ++- src/utilc.c | 256 ++++++++++++++++++++++++++ tests/testthat/test-activation.R |only tests/testthat/test-dsl.R | 78 +++++++- tests/testthat/test-et.R | 17 + tests/testthat/test-logit.R | 33 +++ tests/testthat/test-tad.R | 56 +++++ tests/testthat/test-transit.R | 32 +++ 81 files changed, 1701 insertions(+), 553 deletions(-)