Title: Makes 'R' Easier for Everyone
Description: A meta-package that aims to make 'R' easier for everyone,
especially programmers who have a background in 'SAS®' software.
This set of packages brings many useful concepts to 'R', including
data libraries, data dictionaries, formats
and format catalogs, a data step, and a traceable log. The 'flagship'
package is a reporting package that can output in text, rich text, 'PDF',
'HTML', and 'DOCX' file formats.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between sassy versions 1.0.8 dated 2022-08-10 and 1.1.0 dated 2022-11-28
sassy-1.0.8/sassy/inst/extdata/DA.csv |only sassy-1.0.8/sassy/man/images/ae4.png |only sassy-1.0.8/sassy/man/images/archive |only sassy-1.0.8/sassy/man/images/listing2.png |only sassy-1.0.8/sassy/man/images/sassy1.png |only sassy-1.1.0/sassy/DESCRIPTION | 14 - sassy-1.1.0/sassy/MD5 | 116 +++++++------- sassy-1.1.0/sassy/NEWS.md | 12 + sassy-1.1.0/sassy/R/sassy.R | 2 sassy-1.1.0/sassy/build/vignette.rds |binary sassy-1.1.0/sassy/inst/doc/sassy-ae.Rmd | 18 -- sassy-1.1.0/sassy/inst/doc/sassy-ae.html | 39 ++-- sassy-1.1.0/sassy/inst/doc/sassy-dm.R | 4 sassy-1.1.0/sassy/inst/doc/sassy-dm.Rmd | 17 -- sassy-1.1.0/sassy/inst/doc/sassy-dm.html | 36 ++-- sassy-1.1.0/sassy/inst/doc/sassy-ds.R |only sassy-1.1.0/sassy/inst/doc/sassy-ds.Rmd |only sassy-1.1.0/sassy/inst/doc/sassy-ds.html |only sassy-1.1.0/sassy/inst/doc/sassy-faq.Rmd | 9 - sassy-1.1.0/sassy/inst/doc/sassy-faq.html | 5 sassy-1.1.0/sassy/inst/doc/sassy-figure.R | 2 sassy-1.1.0/sassy/inst/doc/sassy-figure.Rmd | 13 - sassy-1.1.0/sassy/inst/doc/sassy-figure.html | 32 ++-- sassy-1.1.0/sassy/inst/doc/sassy-figureby.Rmd | 11 - sassy-1.1.0/sassy/inst/doc/sassy-figureby.html | 31 ++- sassy-1.1.0/sassy/inst/doc/sassy-forest.R |only sassy-1.1.0/sassy/inst/doc/sassy-forest.Rmd |only sassy-1.1.0/sassy/inst/doc/sassy-forest.html |only sassy-1.1.0/sassy/inst/doc/sassy-listing.Rmd | 10 - sassy-1.1.0/sassy/inst/doc/sassy-listing.html | 30 ++- sassy-1.1.0/sassy/inst/doc/sassy-pfigure.R |only sassy-1.1.0/sassy/inst/doc/sassy-pfigure.Rmd |only sassy-1.1.0/sassy/inst/doc/sassy-pfigure.html |only sassy-1.1.0/sassy/inst/doc/sassy-plisting.R |only sassy-1.1.0/sassy/inst/doc/sassy-plisting.Rmd |only sassy-1.1.0/sassy/inst/doc/sassy-plisting.html |only sassy-1.1.0/sassy/inst/doc/sassy-profile.R | 12 - sassy-1.1.0/sassy/inst/doc/sassy-profile.Rmd | 27 ++- sassy-1.1.0/sassy/inst/doc/sassy-profile.html | 41 +++-- sassy-1.1.0/sassy/inst/doc/sassy-survival.Rmd | 8 - sassy-1.1.0/sassy/inst/doc/sassy-survival.html | 25 ++- sassy-1.1.0/sassy/inst/doc/sassy-vs.R | 3 sassy-1.1.0/sassy/inst/doc/sassy-vs.Rmd | 16 -- sassy-1.1.0/sassy/inst/doc/sassy-vs.html | 199 ++++++++++++------------- sassy-1.1.0/sassy/inst/doc/sassy.Rmd | 29 +++ sassy-1.1.0/sassy/inst/doc/sassy.html | 15 + sassy-1.1.0/sassy/man/images/disposition.png |only sassy-1.1.0/sassy/man/images/forest.png |only sassy-1.1.0/sassy/man/images/logo_blue.png |binary sassy-1.1.0/sassy/man/images/pfigure.png |only sassy-1.1.0/sassy/man/images/plisting.png |only sassy-1.1.0/sassy/man/sassy.Rd | 2 sassy-1.1.0/sassy/vignettes/sassy-ae.Rmd | 18 -- sassy-1.1.0/sassy/vignettes/sassy-dm.Rmd | 17 -- sassy-1.1.0/sassy/vignettes/sassy-ds.Rmd |only sassy-1.1.0/sassy/vignettes/sassy-faq.Rmd | 9 - sassy-1.1.0/sassy/vignettes/sassy-figure.Rmd | 13 - sassy-1.1.0/sassy/vignettes/sassy-figureby.Rmd | 11 - sassy-1.1.0/sassy/vignettes/sassy-forest.Rmd |only sassy-1.1.0/sassy/vignettes/sassy-listing.Rmd | 10 - sassy-1.1.0/sassy/vignettes/sassy-pfigure.Rmd |only sassy-1.1.0/sassy/vignettes/sassy-plisting.Rmd |only sassy-1.1.0/sassy/vignettes/sassy-profile.Rmd | 27 ++- sassy-1.1.0/sassy/vignettes/sassy-survival.Rmd | 8 - sassy-1.1.0/sassy/vignettes/sassy-vs.Rmd | 16 -- sassy-1.1.0/sassy/vignettes/sassy.Rmd | 29 +++ 66 files changed, 521 insertions(+), 415 deletions(-)
Title: Sparse Group Lasso
Description: Efficient implementation of sparse group lasso with optional
bound constraints on the coefficients. It supports the use of a sparse
design matrix as well as returning coefficient estimates in a sparse
matrix. Furthermore, it correctly calculates the degrees of freedom to
allow for information criteria rather than cross-validation with very
large data. Finally, the interface to compiled code avoids unnecessary
copies and allows for the use of long integers.
Author: Daniel J. McDonald [aut, cre],
Xiaoxuan Liang [aut],
Anibal Solon Heinsfeld [aut],
Aaron Cohen [aut],
Yi Yang [ctb],
Hui Zou [ctb],
Jerome Friedman [ctb],
Trevor Hastie [ctb],
Rob Tibshirani [ctb],
Balasubramanian Narasimhan [ctb],
Kenneth Tay [ctb], [...truncated...]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between sparsegl versions 0.5.0 dated 2022-09-22 and 1.0.0 dated 2022-11-28
sparsegl-0.5.0/sparsegl/R/zzz.R |only sparsegl-0.5.0/sparsegl/man/print.sparsegl.Rd |only sparsegl-1.0.0/sparsegl/DESCRIPTION | 42 sparsegl-1.0.0/sparsegl/MD5 | 92 - sparsegl-1.0.0/sparsegl/NAMESPACE | 23 sparsegl-1.0.0/sparsegl/NEWS.md | 6 sparsegl-1.0.0/sparsegl/R/calc_gamma.R | 78 + sparsegl-1.0.0/sparsegl/R/cv.R | 267 +++-- sparsegl-1.0.0/sparsegl/R/cv.sparsegl-methods.R | 135 ++ sparsegl-1.0.0/sparsegl/R/data.R | 55 - sparsegl-1.0.0/sparsegl/R/estimate_risk.R | 15 sparsegl-1.0.0/sparsegl/R/glmnet-utilities.R | 219 ++-- sparsegl-1.0.0/sparsegl/R/imports.R | 6 sparsegl-1.0.0/sparsegl/R/norms.R | 10 sparsegl-1.0.0/sparsegl/R/plot.cv.sparsegl.R | 52 - sparsegl-1.0.0/sparsegl/R/plot.sparsegl.R | 117 +- sparsegl-1.0.0/sparsegl/R/sgl_irwls.R |only sparsegl-1.0.0/sparsegl/R/sgl_logit.R | 15 sparsegl-1.0.0/sparsegl/R/sgl_ls.R | 18 sparsegl-1.0.0/sparsegl/R/sparsegl-methods.R | 184 ++- sparsegl-1.0.0/sparsegl/R/sparsegl.R | 186 ++- sparsegl-1.0.0/sparsegl/README.md | 18 sparsegl-1.0.0/sparsegl/build/partial.rdb |binary sparsegl-1.0.0/sparsegl/build/vignette.rds |binary sparsegl-1.0.0/sparsegl/data/trust_experts.rda |binary sparsegl-1.0.0/sparsegl/inst/doc/sparsegl.R | 55 - sparsegl-1.0.0/sparsegl/inst/doc/sparsegl.Rmd | 256 ++--- sparsegl-1.0.0/sparsegl/inst/doc/sparsegl.html | 494 ++++------ sparsegl-1.0.0/sparsegl/man/coef.cv.sparsegl.Rd | 10 sparsegl-1.0.0/sparsegl/man/coef.sparsegl.Rd | 7 sparsegl-1.0.0/sparsegl/man/cv.sparsegl.Rd | 49 sparsegl-1.0.0/sparsegl/man/figures/README-minimal-ex-1.png |binary sparsegl-1.0.0/sparsegl/man/grouped_sp_norm.Rd | 10 sparsegl-1.0.0/sparsegl/man/make_irls_warmup.Rd |only sparsegl-1.0.0/sparsegl/man/plot.cv.sparsegl.Rd | 9 sparsegl-1.0.0/sparsegl/man/plot.sparsegl.Rd | 7 sparsegl-1.0.0/sparsegl/man/predict.cv.sparsegl.Rd | 30 sparsegl-1.0.0/sparsegl/man/predict.sparsegl.Rd | 20 sparsegl-1.0.0/sparsegl/man/sparsegl.Rd | 70 - sparsegl-1.0.0/sparsegl/man/trust_experts.Rd | 55 - sparsegl-1.0.0/sparsegl/src/Makevars | 5 sparsegl-1.0.0/sparsegl/src/sparsegl_init.c | 158 +++ sparsegl-1.0.0/sparsegl/src/wsgl.f90 |only sparsegl-1.0.0/sparsegl/tests/testthat/test-cv.R |only sparsegl-1.0.0/sparsegl/tests/testthat/test-irwls.R |only sparsegl-1.0.0/sparsegl/tests/testthat/test-irwls_comparisons.R |only sparsegl-1.0.0/sparsegl/tests/testthat/test-methods.R |only sparsegl-1.0.0/sparsegl/tests/testthat/test-predict.R | 12 sparsegl-1.0.0/sparsegl/tests/testthat/test-sgl_irwls.R |only sparsegl-1.0.0/sparsegl/tests/testthat/test-sparsegl_comparisons.R | 16 sparsegl-1.0.0/sparsegl/tests/testthat/test-sparsegl_params.R | 18 sparsegl-1.0.0/sparsegl/vignettes/sparsegl.Rmd | 256 ++--- 52 files changed, 1858 insertions(+), 1217 deletions(-)
Title: Sparse Arrays and Multivariate Polynomials
Description: Sparse arrays interpreted as multivariate polynomials. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.10848>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between spray versions 1.0-20 dated 2022-07-05 and 1.0-22 dated 2022-11-28
DESCRIPTION | 8 ++--- MD5 | 33 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 5 +++ R/spray.R | 7 +++-- README.md | 2 - build/spray.pdf |binary build/vignette.rds |binary inst/CITATION |only inst/doc/spray.R | 44 ++++++++++++++++++++++---------- inst/doc/spray.Rnw | 68 ++++++++++++++++++++++++++++++++++++++------------ inst/doc/spray.pdf |binary man/nterms.Rd | 17 +++++++++++- man/spraycross.Rd | 2 - man/zero.Rd | 70 +++++++++++++++++++++++++++++----------------------- src/spray_ops.cpp | 6 +--- vignettes/spray.Rnw | 68 ++++++++++++++++++++++++++++++++++++++------------ vignettes/spray.bib | 26 ++++++++++++++----- 18 files changed, 244 insertions(+), 113 deletions(-)
Title: Wrappers for 'GDAL' Utilities Executables
Description: R's 'sf' package ships with self-contained 'GDAL'
executables, including a bare bones interface to several
'GDAL'-related utility programs collectively known as the 'GDAL
utilities'. For each of those utilities, this package provides an
R wrapper whose formal arguments closely mirror those of the
'GDAL' command line interface. The utilities operate on data
stored in files and typically write their output to other
files. Therefore, to process data stored in any of R's more common
spatial formats (i.e. those supported by the 'sp', 'sf', and
'raster' packages), first write them to disk, then process them
with the package's wrapper functions before reading the outputted
results back into R. GDAL function arguments introduced in GDAL
version 3.5.2 or earlier are supported.
Author: Joshua O'Brien
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between gdalUtilities versions 1.2.1 dated 2022-04-19 and 1.2.2 dated 2022-11-28
DESCRIPTION | 16 ++++----- MD5 | 52 ++++++++++++++++--------------- NAMESPACE | 2 + NEWS.md | 19 +++++++++++ R/gdal_grid.R | 2 - R/gdal_rasterize.R | 2 - R/gdal_translate.R | 12 +++---- R/gdalbuildvrt.R | 7 ++-- R/gdaldem.R | 2 - R/gdalinfo.R | 17 ++++++---- R/gdalmdiminfo.R |only R/gdalmdimtranslate.R |only R/gdalwarp.R | 23 +++++++------ R/nearblack.R | 2 - R/ogr2ogr.R | 32 ++++++++++--------- R/zzz.R | 78 ++++++++++++++++++++++++++++++++++++----------- README.md | 53 ++++++++++++------------------- build/partial.rdb |binary man/gdal_grid.Rd | 5 +-- man/gdal_rasterize.Rd | 2 - man/gdal_translate.Rd | 11 +++--- man/gdalbuildvrt.Rd | 7 +++- man/gdaldem.Rd | 2 - man/gdalinfo.Rd | 9 ++++- man/gdalmdiminfo.Rd |only man/gdalmdimtranslate.Rd |only man/gdalwarp.Rd | 15 ++++++--- man/nearblack.Rd | 2 - man/ogr2ogr.Rd | 33 ++++++++++++------- 29 files changed, 249 insertions(+), 156 deletions(-)
Title: Linear and Nonlinear Autoregressive Distributed Lag Models:
General-to-Specific Approach
Description: Estimate the linear and nonlinear autoregressive distributed lag (ARDL & NARDL) models and the corresponding error correction models, and test for longrun and short-run asymmetric. The general-to-specific approach is also available in estimating the ARDL and NARDL models. The Pesaran, Shin & Smith (2001) (<doi:10.1002/jae.616>) bounds test for level relationships is also provided. The 'ardl.nardl' package also performs short-run and longrun symmetric restrictions available at Shin et al. (2014) <doi:10.1007/978-1-4899-8008-3_9> and their corresponding tests.
Author: Eric I. Otoakhia [aut, cre]
Maintainer: Eric I. Otoakhia <otoakhiai@gmail.com>
Diff between ardl.nardl versions 1.1.0 dated 2022-11-23 and 1.2.0 dated 2022-11-28
DESCRIPTION | 8 +-- MD5 | 17 ++++--- NAMESPACE | 2 NEWS |only R/auto_case_ardl.R |only R/gets_ardl_uecm.R | 38 +++------------- R/gets_nardl_uecm.R | 108 ++++++++++++++++++---------------------------- R/nardl_auto_case.R |only R/rename_model.R | 13 +---- man/ardl.nardl-package.Rd | 24 +++++++++- man/auto_case_ardl.Rd |only man/nardl_auto_case.Rd |only 12 files changed, 93 insertions(+), 117 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.8.9 dated 2022-06-03 and 1.9.2 dated 2022-11-28
DESCRIPTION | 8 - MD5 | 18 +- build/vignette.rds |binary inst/doc/haplostats.pdf |binary man/haplo.design.Rd | 8 - man/haplo.glm.Rd | 17 +- src/haplo.stats_init.c | 4 src/haplo_em_pin.c | 17 -- src/haplo_em_pin.h | 40 ----- src/seqhap.c | 325 ++++++++++++++++++++++-------------------------- 10 files changed, 185 insertions(+), 252 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.8.0 dated 2022-09-15 and 1.9.0 dated 2022-11-28
TreeTools-1.8.0/TreeTools/man/SingleTaxonTree.Rd |only TreeTools-1.9.0/TreeTools/DESCRIPTION | 10 TreeTools-1.9.0/TreeTools/MD5 | 126 ++++---- TreeTools-1.9.0/TreeTools/NAMESPACE | 6 TreeTools-1.9.0/TreeTools/NEWS.md | 25 + TreeTools-1.9.0/TreeTools/R/DropTip.R | 94 +++--- TreeTools-1.9.0/TreeTools/R/ImposeConstraint.R | 10 TreeTools-1.9.0/TreeTools/R/ReadTntTree.R | 10 TreeTools-1.9.0/TreeTools/R/SplitFunctions.R | 12 TreeTools-1.9.0/TreeTools/R/Splits.R | 59 ++-- TreeTools-1.9.0/TreeTools/R/TreeNumber.R | 18 - TreeTools-1.9.0/TreeTools/R/as.matrix.R |only TreeTools-1.9.0/TreeTools/R/parse_files.R | 41 ++ TreeTools-1.9.0/TreeTools/R/phylo.R | 24 + TreeTools-1.9.0/TreeTools/R/tree_generation.R | 18 - TreeTools-1.9.0/TreeTools/R/tree_write.R | 2 TreeTools-1.9.0/TreeTools/build/partial.rdb |binary TreeTools-1.9.0/TreeTools/build/vignette.rds |binary TreeTools-1.9.0/TreeTools/inst/doc/filesystem-navigation.html | 128 ++++---- TreeTools-1.9.0/TreeTools/inst/doc/load-data.html | 146 +++++----- TreeTools-1.9.0/TreeTools/inst/doc/load-trees.Rmd | 2 TreeTools-1.9.0/TreeTools/inst/doc/load-trees.html | 130 ++++---- TreeTools-1.9.0/TreeTools/inst/extdata/tests/encoding.nex |only TreeTools-1.9.0/TreeTools/inst/extdata/tests/taxon-notes.nex |only TreeTools-1.9.0/TreeTools/inst/include/TreeTools/SplitList.h | 7 TreeTools-1.9.0/TreeTools/inst/include/TreeTools/renumber_tree.h | 4 TreeTools-1.9.0/TreeTools/man/AddTip.Rd | 4 TreeTools-1.9.0/TreeTools/man/CollapseNode.Rd | 4 TreeTools-1.9.0/TreeTools/man/CompatibleSplits.Rd | 3 TreeTools-1.9.0/TreeTools/man/ConsensusWithout.Rd | 4 TreeTools-1.9.0/TreeTools/man/ConstrainedNJ.Rd | 10 TreeTools-1.9.0/TreeTools/man/DropTip.Rd | 28 + TreeTools-1.9.0/TreeTools/man/EnforceOutgroup.Rd | 4 TreeTools-1.9.0/TreeTools/man/GenerateTree.Rd | 4 TreeTools-1.9.0/TreeTools/man/ImposeConstraint.Rd | 10 TreeTools-1.9.0/TreeTools/man/KeptPaths.Rd | 4 TreeTools-1.9.0/TreeTools/man/KeptVerts.Rd | 4 TreeTools-1.9.0/TreeTools/man/LeafLabelInterchange.Rd | 4 TreeTools-1.9.0/TreeTools/man/MakeTreeBinary.Rd | 4 TreeTools-1.9.0/TreeTools/man/NJTree.Rd | 4 TreeTools-1.9.0/TreeTools/man/ReadCharacters.Rd | 2 TreeTools-1.9.0/TreeTools/man/Renumber.Rd | 4 TreeTools-1.9.0/TreeTools/man/RenumberTips.Rd | 4 TreeTools-1.9.0/TreeTools/man/Reorder.Rd | 4 TreeTools-1.9.0/TreeTools/man/RootTree.Rd | 4 TreeTools-1.9.0/TreeTools/man/SortTree.Rd | 4 TreeTools-1.9.0/TreeTools/man/Splits.Rd | 2 TreeTools-1.9.0/TreeTools/man/Subtree.Rd | 4 TreeTools-1.9.0/TreeTools/man/TreeNumber.Rd | 2 TreeTools-1.9.0/TreeTools/man/TrivialTree.Rd |only TreeTools-1.9.0/TreeTools/src/RcppExports.cpp | 12 TreeTools-1.9.0/TreeTools/src/as_newick.cpp | 39 ++ TreeTools-1.9.0/TreeTools/src/int_to_tree.cpp | 33 +- TreeTools-1.9.0/TreeTools/src/minimum_spanning_tree.cpp | 3 TreeTools-1.9.0/TreeTools/src/splits.cpp | 13 TreeTools-1.9.0/TreeTools/src/tips_in_splits.cpp | 4 TreeTools-1.9.0/TreeTools/tests/testthat/test-DropTip.R | 11 TreeTools-1.9.0/TreeTools/tests/testthat/test-ImposeConstraint.R | 5 TreeTools-1.9.0/TreeTools/tests/testthat/test-SplitFunctions.R | 1 TreeTools-1.9.0/TreeTools/tests/testthat/test-Splits.R | 41 ++ TreeTools-1.9.0/TreeTools/tests/testthat/test-as.matrix.R |only TreeTools-1.9.0/TreeTools/tests/testthat/test-int_to_tree.cpp.R | 35 +- TreeTools-1.9.0/TreeTools/tests/testthat/test-mst.R | 2 TreeTools-1.9.0/TreeTools/tests/testthat/test-parsers.R | 31 +- TreeTools-1.9.0/TreeTools/tests/testthat/test-splits.cpp.R | 6 TreeTools-1.9.0/TreeTools/tests/testthat/test-tree_generation.R | 1 TreeTools-1.9.0/TreeTools/vignettes/load-trees.Rmd | 2 67 files changed, 773 insertions(+), 459 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Seqinr includes
utilities for sequence data management under the ACNUC system
described in Gouy, M. et al. (1984) Nucleic Acids Res.
12:121-127 <doi:10.1093/nar/12.1Part1.121>.
Author: Delphine Charif [aut],
Olivier Clerc [ctb],
Carolin Frank [ctb],
Jean R. Lobry [aut, cph],
Anamaria Necsulea [ctb],
Leonor Palmeira [ctb],
Simon Penel [cre],
Guy Perriere [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 4.2-16 dated 2022-05-19 and 4.2-23 dated 2022-11-28
DESCRIPTION | 12 ++-- MD5 | 124 ++++++++++++++++++++++++------------------------ build/partial.rdb |binary data/AnoukResult.RData |binary data/ECH.RData |binary data/EXP.RData |binary data/JLO.RData |binary data/SEQINR.UTIL.RData |binary data/aacost.RData |binary data/aaindex.RData |binary data/caitab.RData |binary data/chargaff.RData |binary data/clustal.RData |binary data/dinucl.RData |binary data/ec999.RData |binary data/fasta.RData |binary data/gcO2.rda |binary data/gcT.rda |binary data/gs500liz.RData |binary data/identifiler.RData |binary data/kaksTorture.RData |binary data/m16j.RData |binary data/mase.RData |binary data/msf.RData |binary data/pK.RData |binary data/phylip.RData |binary data/prochlo.RData |binary data/revaligntest.RData |binary data/sysdata.rda |binary data/toyaa.RData |binary data/toycodon.RData |binary data/waterabs.RData |binary man/ECH.Rd | 5 - man/GC.Rd | 2 man/JLO.Rd | 5 - man/aaindex.Rd | 10 +-- man/acnucopen.Rd | 18 +++--- man/autosocket.Rd | 2 man/cai.Rd | 8 +-- man/caitab.Rd | 14 ++--- man/choosebank.Rd | 38 +++++++------- man/countfreelists.Rd | 10 +-- man/countsubseqs.Rd | 4 - man/getliststate.Rd | 6 +- man/gfrag.Rd | 10 +-- man/ghelp.Rd | 4 - man/isenum.Rd | 12 ++-- man/kaks.Rd | 24 ++++----- man/knowndbs.Rd | 16 +++--- man/modifylist.Rd | 12 ++-- man/pK.Rd | 6 +- man/plot.SeqAcnucWeb.Rd | 10 +-- man/prettyseq.Rd | 8 +-- man/query.Rd | 34 ++++++------- man/read.abif.Rd | 18 +++--- man/read.alignment.Rd | 101 +++++++++++++++++++-------------------- man/read.fasta.Rd | 38 +++++++------- man/readfirstrec.Rd | 12 ++-- man/readsmj.Rd | 10 +-- man/residuecount.Rd | 4 - man/savelist.Rd | 8 +-- man/setlistname.Rd | 4 - src/util.c | 22 ++++---- 63 files changed, 304 insertions(+), 307 deletions(-)
Title: Creates Statistical Reports
Description: Contains functions to create regulatory-style statistical reports.
Originally designed to create tables, listings, and figures for the
pharmaceutical, biotechnology, and medical device industries, these
reports are generalized enough that they could be used in any industry.
Generates text, rich-text, PDF, HTML, and Microsoft Word file formats.
The package specializes
in printing wide and long tables with automatic page wrapping and splitting.
Reports can be produced with a minimum of function calls, and without
relying on other table packages. The package supports titles, footnotes,
page header, page footers, spanning headers, page by variables,
and automatic page numbering.
Author: David Bosak [aut, cre],
Kevin Kramer [ctb],
Duong Tran [ctb],
Raphael Huang [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between reporter versions 1.3.7 dated 2022-10-07 and 1.3.8 dated 2022-11-28
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reporter-1.3.8/reporter/tests/testthat/test-rtf.R | 65 reporter-1.3.8/reporter/tests/testthat/test-rtf2.R | 666 +++++++++- reporter-1.3.8/reporter/tests/testthat/test-styles.R | 36 reporter-1.3.8/reporter/vignettes/reporter-styles.Rmd | 119 + reporter-1.3.8/reporter/vignettes/reporter.Rmd | 5 137 files changed, 2650 insertions(+), 412 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa <minatonakazawa@gmail.com>
Maintainer: Minato Nakazawa <minatonakazawa@gmail.com>
Diff between fmsb versions 0.7.3 dated 2022-03-01 and 0.7.4 dated 2022-11-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 5 +++++ R/demogjpn.R | 19 +++++++++++++------ build/partial.rdb |binary man/Jfert.Rd | 42 +++++++++++++++++++++++------------------- man/Jlife.Rd | 13 ++++++++----- man/PrefYLL2015.Rd | 3 +-- man/WhipplesIndex.Rd | 2 +- 9 files changed, 63 insertions(+), 45 deletions(-)
Title: Change Metrics for Species Geographic Ranges
Description: Facilitates workflows to reproducibly transform estimates of species’ distributions into metrics relevant for conservation. For example, combining predictions from species distribution models with other maps of environmental data to characterize the proportion of a species’ range that is under protection, calculating metrics used under the IUCN Criteria A and B guidelines (Area of Occupancy and Extent of Occurrence), and calculating more general metrics such as taxonomic and phylogenetic diversity, as well as endemism. Also facilitates temporal comparisons among biodiversity metrics to inform efforts towards complementarity and consideration of future scenarios in conservation decisions. 'changeRangeR' also provides tools to determine the effects of modeling decisions through sensitivity tests.
Author: Peter J. Galante [aut],
Samuel Chang [aut],
Andrea Paz [aut],
Jamie M. Kass [aut],
Matthew Aiello-Lammens [aut],
Beth Gerstner [aut],
Bethany Johnson [aut],
Cory Merow [aut],
Elkin Noguera-Urbano [aut],
Gonzalo E. Pinilla-Buitrago [aut],
Dan Rosauer [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
Diff between changeRangeR versions 1.0.0 dated 2022-11-21 and 1.0.1 dated 2022-11-28
changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/WDPA_COL_olinguito_simp.dbf |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/WDPA_COL_olinguito_simp.prj |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/WDPA_COL_olinguito_simp.shp |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/WDPA_COL_olinguito_simp.shx |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/vn/VN_NRs_simp.dbf |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/vn/VN_NRs_simp.prj |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/vn/VN_NRs_simp.shp |only changeRangeR-1.0.0/changeRangeR/inst/extdata/DemoData/shapefiles/vn/VN_NRs_simp.shx |only changeRangeR-1.0.1/changeRangeR/DESCRIPTION | 8 +- changeRangeR-1.0.1/changeRangeR/MD5 | 34 ++++------ changeRangeR-1.0.1/changeRangeR/R/ratioOverlap.R | 18 ++--- changeRangeR-1.0.1/changeRangeR/build/partial.rdb |binary changeRangeR-1.0.1/changeRangeR/build/vignette.rds |binary changeRangeR-1.0.1/changeRangeR/inst/doc/BiodivMetrics.R | 4 - changeRangeR-1.0.1/changeRangeR/inst/doc/BiodivMetrics.Rmd | 4 - changeRangeR-1.0.1/changeRangeR/inst/doc/BiodivMetrics.pdf |binary changeRangeR-1.0.1/changeRangeR/inst/doc/singleSpeciesMetrics.R | 4 - changeRangeR-1.0.1/changeRangeR/inst/doc/singleSpeciesMetrics.Rmd | 4 - changeRangeR-1.0.1/changeRangeR/inst/doc/singleSpeciesMetrics.pdf |binary changeRangeR-1.0.1/changeRangeR/inst/extdata/DemoData/shapefiles/WDPA_COL_olinguito_simp.rds |only changeRangeR-1.0.1/changeRangeR/inst/extdata/DemoData/shapefiles/vn/VN_NRs_simp.rds |only changeRangeR-1.0.1/changeRangeR/vignettes/BiodivMetrics.Rmd | 4 - changeRangeR-1.0.1/changeRangeR/vignettes/singleSpeciesMetrics.Rmd | 4 - 23 files changed, 39 insertions(+), 45 deletions(-)
Title: Clustering of Sites with Species Data
Description: Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.
Author: Sebastian Schmidtlein [aut, cre]
,
Jason Collison [aut],
Robin Pfannendoerfer [aut],
Lubomir Tichy [ctb]
Maintainer: Sebastian Schmidtlein <schmidtlein@kit.edu>
Diff between isopam versions 1.0.0 dated 2022-11-19 and 1.1.0 dated 2022-11-28
DESCRIPTION | 14 ++-- MD5 | 18 ++--- NAMESPACE | 6 + R/isopam.R | 191 ++++++++++++++++++++++++++++++++++++++++++--------------- R/isopamp.R | 170 +++++++++++++++++++++++++++++++++----------------- R/isotab.R | 56 +++++++++------- inst/CITATION | 11 ++- man/andechs.rd | 20 ++--- man/isopam.Rd | 53 +++++++++------ man/isotab.Rd | 14 +++- 10 files changed, 368 insertions(+), 185 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6.9 dated 2021-09-27 and 1.7 dated 2022-11-28
DESCRIPTION | 10 MD5 | 64 NAMESPACE | 274 - R/boot.R | 743 ++--- R/hmm.R | 4 R/msm.R | 60 R/mstate.R | 118 R/optim.R | 494 +-- R/outputs.R | 116 R/pearson.R | 1348 ++++----- R/phase.R | 430 +-- R/simul.R | 738 ++--- R/utils.R | 46 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 38 inst/NEWS | 2509 +++++++++--------- inst/doc/msm-manual.pdf |binary man/MatrixExp.Rd | 178 - man/hmm-dists.Rd | 426 +-- man/msm.Rd | 1996 +++++++------- man/msm2Surv.Rd | 274 - man/pexp.Rd | 157 - man/plot.msm.Rd | 4 man/pmatrix.msm.Rd | 262 - man/prevalence.msm.Rd | 404 +- man/simmulti.msm.Rd | 3 man/viterbi.msm.Rd | 106 src/lik.c | 251 - tests/testthat/test_models.r | 3 tests/testthat/test_models_hmm.r | 318 +- tests/testthat/test_utils.r | 266 - tests/testthat/test_viterbi.R |only vignettes/msm-manual.Rnw | 5406 +++++++++++++++++++-------------------- 34 files changed, 8564 insertions(+), 8482 deletions(-)
Title: Utility Functions for Forest Inventory Estimation and Analysis
Description: A set of tools for data wrangling, spatial data analysis,
statistical modeling (including direct, model-assisted, photo-based, and
small area tools), and USDA Forest Service data base tools. These tools are
aimed to help Foresters, Analysts, and Scientists extract and perform
analyses on USDA Forest Service data.
Author: Tracey Frescino [aut],
Chris Toney [aut],
Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTAutils versions 1.1.3 dated 2022-08-06 and 1.1.4 dated 2022-11-28
DESCRIPTION | 10 +- MD5 | 27 +++-- NAMESPACE | 7 + R/DBinternal.R | 243 +++++++++++++++++++++++++++++++++++++++++++++----- R/checks.R | 4 R/cool_functions.R | 26 ++++- R/eval_options.R |only R/getadjfactorDWM.R |only R/getadjfactorP2VEG.R |only R/getadjfactorVOL.R |only R/pcheck.functions.R | 73 ++++++++++++--- R/strat_collapse.R | 7 + R/xy_options.R |only R/zzz.R | 2 man/eval_options.Rd |only man/internal_desc.Rd | 78 +++++++++++++++- man/pcheck_desc.Rd | 5 - man/xy_options.Rd |only 18 files changed, 421 insertions(+), 61 deletions(-)
Title: Create Interactive Web Maps of Air Pollution Data
Description: Combine the air quality data analysis methods of 'openair'
with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library.
Functionality includes plotting site maps, "directional analysis"
figures such as polar plots, and air mass trajectories.
Author: Jack Davison [cre, aut],
David Carslaw [aut]
Maintainer: Jack Davison <davison.jack.jd@gmail.com>
Diff between openairmaps versions 0.5.1 dated 2022-10-20 and 0.6.0 dated 2022-11-28
DESCRIPTION | 10 MD5 | 65 ++-- NAMESPACE | 1 NEWS.md | 36 ++ R/addPolarMarkers.R | 17 - R/addTrajPaths.R | 1 R/annulusMap.R | 108 +++--- R/buildPopup.R |only R/freqMap.R | 137 ++++---- R/networkMap.R | 731 ++++++++++++++++++++++++++------------------- R/percentileMap.R | 102 ++---- R/polarMap.R | 84 +++-- R/polar_data.R | 2 R/pollroseMap.R | 113 +++--- R/quickTextHTML.R | 3 R/trajLevelMap.R | 19 - R/trajMap.R | 26 - R/utils-map.R | 61 ++- R/windroseMap.R | 112 +++--- README.md | 24 - man/addPolarMarkers.Rd | 4 man/annulusMap.Rd | 153 ++++++++- man/buildPopup.Rd |only man/figures/logo.png |only man/freqMap.Rd | 106 ++++-- man/networkMap.Rd | 48 ++ man/openairmaps-package.Rd | 2 man/percentileMap.Rd | 90 ++++- man/polarMap.Rd | 231 +++++++++++++- man/polar_data.Rd | 2 man/pollroseMap.Rd | 69 +++- man/quickTextHTML.Rd | 1 man/trajLevelMap.Rd | 8 man/trajMap.Rd | 27 - man/windroseMap.Rd | 143 +++++++- 35 files changed, 1677 insertions(+), 859 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Author: Robert J. Hijmans [cre, aut] ,
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ct [...truncated...]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.6-3 dated 2022-09-18 and 3.6-11 dated 2022-11-28
DESCRIPTION | 10 MD5 | 52 - NEWS | 2 R/AAAClasses.R | 3 R/AAgeneric_functions.R | 2 R/coerce.R | 23 R/coverPolygons.R | 3 R/extractPolygons.R | 8 R/factor.R | 8 R/fasterize.R | 1 R/projectRaster.R | 12 R/raster.R | 4 R/rasterFromFile.R | 14 R/rasterFromGDAL.R | 12 R/readCells.R | 11 R/readCellsGDAL.R | 1 R/readRasterBrick.R | 11 R/readRasterLayer.R | 8 R/update.R | 4 R/writeRaster.R | 19 R/writeStartStopGDAL.R | 10 build/partial.rdb |binary inst/external/rlogo.grd | 18 man/getData.Rd | 4 src/geodesic.c | 1715 +++++++++++++++++++++++++++--------------------- src/geodesic.h | 777 +++++++++++---------- src/memory.cpp | 2 27 files changed, 1514 insertions(+), 1220 deletions(-)
Title: Cubature over Polygonal Domains
Description: Numerical integration of continuously differentiable
functions f(x,y) over simple closed polygonal domains.
The following cubature methods are implemented:
product Gauss cubature (Sommariva and Vianello, 2007,
<doi:10.1007/s10543-007-0131-2>),
the simple two-dimensional midpoint rule
(wrapping 'spatstat.geom' functions),
adaptive cubature for radially symmetric functions via line
integrate() along the polygon boundary (Meyer and Held, 2014,
<doi:10.1214/14-AOAS743>, Supplement B),
and integration of the bivariate Gaussian density based on
polygon triangulation.
For simple integration along the axes, the 'cubature' package
is more appropriate.
Author: Sebastian Meyer [aut, cre, trl]
,
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between polyCub versions 0.8.0 dated 2021-01-26 and 0.8.1 dated 2022-11-28
DESCRIPTION | 10 MD5 | 38 +-- NEWS.md | 6 R/circleCub.R | 9 R/plotpolyf.R | 2 R/polyCub.exact.Gauss.R | 10 R/sfg2gpc.R | 15 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/polyCub.R | 4 inst/doc/polyCub.Rmd | 18 + inst/doc/polyCub.html | 468 +++++++++++++++++++++++++++------------------ man/circleCub.Gauss.Rd | 9 man/plotpolyf.Rd | 2 man/polyCub.exact.Gauss.Rd | 14 - man/polyCub.iso.Rd | 3 man/polyCub.midpoint.Rd | 3 man/sfg2gpc.Rd | 15 - tests/test-polyCub.R | 6 vignettes/polyCub.Rmd | 18 + 20 files changed, 395 insertions(+), 255 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.5.7 dated 2022-09-16 and 0.6.0 dated 2022-11-28
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Title: Longitudinal Dataframes into Arrays for Machine Learning
Training
Description: An easy tool to transform 2D longitudinal data into 3D arrays suitable for
Long short-term memory neural networks training. The array output can be
used by the 'keras' package. Long short-term memory neural networks are described
in: Hochreiter, S., & Schmidhuber, J. (1997) <doi:10.1162/neco.1997.9.8.1735>.
Author: Luis Garcez [aut, cre, cph]
Maintainer: Luis Garcez <luisgarcez1@gmail.com>
Diff between long2lstmarray versions 0.0.1 dated 2022-07-18 and 0.2.0 dated 2022-11-28
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
More information about long2lstmarray at CRAN
Permanent link
Title: Minimal Examples of Using Rust Code in R
Description: Template R package with minimal setup to use Rust code in R without
hacks or frameworks. Includes basic examples of importing cargo dependencies,
spawning threads and passing numbers or strings from Rust to R. The GitHub
repository for this package has more details and also explains how to set up
CI. This project was first presented at 'Erum2018' to showcase R-Rust integration
<https://jeroen.github.io/erum2018/>; for a real world use-case, see the
'gifski' package on 'CRAN'.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between hellorust versions 1.0.0 dated 2022-11-21 and 1.0.1 dated 2022-11-28
DESCRIPTION | 18 +++++++++++------- LICENSE | 2 +- MD5 | 6 ++++-- tests |only 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Modeling Species Distributions in Three Dimensions
Description: Facilitates modeling species' ecological niches and
geographic distributions based on occurrences and environments that
have a vertical as well as horizontal component, and projecting models
into three-dimensional geographic space. Working in three dimensions is
useful in an aquatic context when the organisms one wishes to model can
be found across a wide range of depths in the water column. The package
also contains functions to automatically generate marine training
model training regions using machine learning, and interpolate and smooth
patchily sampled environmental rasters using thin plate splines.
Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA (2016) <doi:10.1038/ncomms11484>.
Nychka D, Furrer R, Paige J, Sain S (2021) <doi:10.5065/D6W957CT>.
Pateiro-Lopez B, Rodriguez-Casal A (2022) <https://CRAN.R-project.org/package=alphahull>.
Author: Hannah L. Owens [aut, cre] ,
Carsten Rahbek [aut]
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between voluModel versions 0.1.7 dated 2022-11-17 and 0.1.8 dated 2022-11-28
DESCRIPTION | 16 MD5 | 72 ++-- NAMESPACE | 10 NEWS.md | 6 R/BackgroundSamplingFunctions.R | 123 +++--- R/marineBackground.R | 137 +++---- inst/CITATION | 2 inst/doc/a_Introduction.R | 6 inst/doc/a_Introduction.Rmd | 6 inst/doc/a_Introduction.html | 32 + inst/doc/b_RasterProcessing.R | 3 inst/doc/b_RasterProcessing.Rmd | 3 inst/doc/b_RasterProcessing.html | 13 inst/doc/c_DataSampling.R | 124 +++---- inst/doc/c_DataSampling.Rmd | 168 +++++---- inst/doc/c_DataSampling.html | 389 +++++++++++----------- inst/doc/d_Visualization.R | 10 inst/doc/d_Visualization.Rmd | 13 inst/doc/d_Visualization.html | 149 +++----- inst/doc/e_GLMWorkflow.R | 10 inst/doc/e_GLMWorkflow.Rmd | 10 inst/doc/e_GLMWorkflow.html | 50 +- inst/extdata/backgroundSamplingRegions.rds |binary man/mSampling2D.Rd | 18 - man/mSampling3D.Rd | 28 - man/marineBackground.Rd | 4 tests/testthat/test-BackgroundSamplingFunctions.R | 112 ++---- tests/testthat/test-marineBackground.R | 40 -- vignettes/PointsAndTrainingRegion.png |binary vignettes/a_Introduction.Rmd | 6 vignettes/alphaHullDemonstration-1.png |binary vignettes/b_RasterProcessing.Rmd | 3 vignettes/c_DataSampling.Rmd | 168 +++++---- vignettes/clipToOceanDemo-1.png |binary vignettes/d_Visualization.Rmd | 13 vignettes/e_GLMWorkflow.Rmd | 10 vignettes/meridianWrapDemo-1.png |binary 37 files changed, 894 insertions(+), 860 deletions(-)
Title: R Access to Mass-Spec Data
Description: R-based access to mass-spectrometry (MS) data. While many packages
exist to process MS data, many of these make it difficult to
access the underlying mass-to-charge ratio (m/z), intensity, and
retention time of the files
themselves. This package is designed to format MS data in a tidy fashion and
allows the user perform the plotting and analysis.
Author: William Kumler [aut, cre, cph],
Ricardo Cunha [ctb],
Ethan Bass [ctb]
Maintainer: William Kumler <wkumler@uw.edu>
Diff between RaMS versions 1.0.0 dated 2021-03-22 and 1.3.0 dated 2022-11-28
RaMS-1.0.0/RaMS/tests/testthat/helper-load.R |only RaMS-1.3.0/RaMS/DESCRIPTION | 26 RaMS-1.3.0/RaMS/MD5 | 100 + RaMS-1.3.0/RaMS/NAMESPACE | 29 RaMS-1.3.0/RaMS/NEWS.md | 26 RaMS-1.3.0/RaMS/R/RaMS-package.R |only RaMS-1.3.0/RaMS/R/grabMSdataCode.R | 237 +++ RaMS-1.3.0/RaMS/R/grabMzmlFunctions.R | 298 ++++ RaMS-1.3.0/RaMS/R/grabMzxmlFunctions.R | 171 ++ RaMS-1.3.0/RaMS/R/minifyMSFunctions.R |only RaMS-1.3.0/RaMS/R/tmzMLFunctions.R |only RaMS-1.3.0/RaMS/README.md | 100 - RaMS-1.3.0/RaMS/build/vignette.rds |binary RaMS-1.3.0/RaMS/inst/doc/Intro-to-RaMS.R | 28 RaMS-1.3.0/RaMS/inst/doc/Intro-to-RaMS.Rmd | 83 - RaMS-1.3.0/RaMS/inst/doc/Intro-to-RaMS.html | 969 +++++++++++----- RaMS-1.3.0/RaMS/inst/doc/Intro-to-tmzML.R |only RaMS-1.3.0/RaMS/inst/doc/Intro-to-tmzML.Rmd |only RaMS-1.3.0/RaMS/inst/doc/Intro-to-tmzML.html |only RaMS-1.3.0/RaMS/inst/doc/Minifying-files-with-RaMS.R |only RaMS-1.3.0/RaMS/inst/doc/Minifying-files-with-RaMS.Rmd |only RaMS-1.3.0/RaMS/inst/doc/Minifying-files-with-RaMS.html |only RaMS-1.3.0/RaMS/inst/doc/RaMS-and-friends.R | 15 RaMS-1.3.0/RaMS/inst/doc/RaMS-and-friends.Rmd | 15 RaMS-1.3.0/RaMS/inst/doc/RaMS-and-friends.html | 493 ++++++-- RaMS-1.3.0/RaMS/inst/extdata/DDApos_2.mzML.gz |binary RaMS-1.3.0/RaMS/inst/extdata/DDApos_2.mzXML.gz |binary RaMS-1.3.0/RaMS/inst/extdata/LB12HL_AB.mzML.gz |binary RaMS-1.3.0/RaMS/inst/extdata/LB12HL_AB.mzXML.gz |binary RaMS-1.3.0/RaMS/inst/extdata/LB12HL_CD.mzML.gz |binary RaMS-1.3.0/RaMS/inst/extdata/LB12HL_EF.mzML.gz |binary RaMS-1.3.0/RaMS/inst/extdata/uv_test_mini.mzML.gz |only RaMS-1.3.0/RaMS/inst/extdata/wk_chrom.mzML.gz |only RaMS-1.3.0/RaMS/man/RaMS-package.Rd |only RaMS-1.3.0/RaMS/man/cash-.msdata_connection.Rd |only RaMS-1.3.0/RaMS/man/figures/README-isoexampleplot-1.png |binary RaMS-1.3.0/RaMS/man/figures/README-plotfragdata-1.png |binary RaMS-1.3.0/RaMS/man/figures/README-showbaseplot-1.png |binary RaMS-1.3.0/RaMS/man/figures/README-showggplot-1.png |binary RaMS-1.3.0/RaMS/man/getEncoded.Rd |only RaMS-1.3.0/RaMS/man/giveEncoding.Rd |only RaMS-1.3.0/RaMS/man/grabAccessionData.Rd |only RaMS-1.3.0/RaMS/man/grabMSdata.Rd | 208 +-- RaMS-1.3.0/RaMS/man/grabMzmlDAD.Rd |only RaMS-1.3.0/RaMS/man/grabMzmlData.Rd | 194 +-- RaMS-1.3.0/RaMS/man/grabMzmlMS1.Rd | 57 RaMS-1.3.0/RaMS/man/grabMzxmlData.Rd | 181 +- RaMS-1.3.0/RaMS/man/grabMzxmlMS1.Rd | 57 RaMS-1.3.0/RaMS/man/minifyMSdata.Rd |only RaMS-1.3.0/RaMS/man/minifyMzml.Rd |only RaMS-1.3.0/RaMS/man/minifyMzxml.Rd |only RaMS-1.3.0/RaMS/man/msdata_connection.Rd |only RaMS-1.3.0/RaMS/man/node2dt.Rd |only RaMS-1.3.0/RaMS/man/print.msdata_connection.Rd |only RaMS-1.3.0/RaMS/man/reexports.Rd |only RaMS-1.3.0/RaMS/man/sub-.msdata_connection.Rd |only RaMS-1.3.0/RaMS/man/tmzmlMaker.Rd |only RaMS-1.3.0/RaMS/tests/testthat/setup-load.R |only RaMS-1.3.0/RaMS/tests/testthat/test_DAD.R |only RaMS-1.3.0/RaMS/tests/testthat/test_chroms.R |only RaMS-1.3.0/RaMS/tests/testthat/test_errors_n_messes.R | 26 RaMS-1.3.0/RaMS/tests/testthat/test_minify.R |only RaMS-1.3.0/RaMS/tests/testthat/test_prefilter.R |only RaMS-1.3.0/RaMS/tests/testthat/test_tmzML_things.R |only RaMS-1.3.0/RaMS/vignettes/Intro-to-RaMS.Rmd | 83 - RaMS-1.3.0/RaMS/vignettes/Intro-to-tmzML.Rmd |only RaMS-1.3.0/RaMS/vignettes/Minifying-files-with-RaMS.Rmd |only RaMS-1.3.0/RaMS/vignettes/RaMS-and-friends.Rmd | 15 RaMS-1.3.0/RaMS/vignettes/figures |only 69 files changed, 2392 insertions(+), 1019 deletions(-)
Title: Visualizing Class Specific Heterogeneous Tendencies in
Categorical Data
Description: Performing multiple-class cluster correspondence analysis(MCCCA). The main functions are create.MCCCAdata() to create a list to be applied to MCCCA, MCCCA() to apply MCCCA, and plot.mccca() for visualizing MCCCA result. Methods used in the
package refers to Mariko Takagishi and Michel van de Velden (2022)<doi:10.1080/10618600.2022.2035737>.
Author: Mariko Takagishi [aut, cre]
Maintainer: Mariko Takagishi <m.takagishi0728@gmail.com>
Diff between mccca versions 0.1.1 dated 2022-09-07 and 1.1.0 dated 2022-11-28
mccca-0.1.1/mccca/R/updateB.MCCCA.func.R |only mccca-1.1.0/mccca/DESCRIPTION | 9 mccca-1.1.0/mccca/MD5 | 32 ++- mccca-1.1.0/mccca/NAMESPACE | 4 mccca-1.1.0/mccca/R/MCCCA.func.R | 231 +++++++++++++++-------- mccca-1.1.0/mccca/R/RcppExports.R |only mccca-1.1.0/mccca/R/dummy.ed.func.R | 43 +++- mccca-1.1.0/mccca/R/generate.cate.func.R | 2 mccca-1.1.0/mccca/R/plot.MCCCA.func.R | 6 mccca-1.1.0/mccca/R/split.data.byext.comb.func.R | 5 mccca-1.1.0/mccca/R/updateUG.MCCCA.func.R | 18 + mccca-1.1.0/mccca/R/various.func.R | 50 ---- mccca-1.1.0/mccca/man/MCCCA.Rd | 2 mccca-1.1.0/mccca/man/mccca-package.Rd |only mccca-1.1.0/mccca/src |only 15 files changed, 243 insertions(+), 159 deletions(-)
Title: A Fast and Lightweight Logging System for R, Based on 'log4j'
Description: The log4r package is meant to provide a fast, lightweight,
object-oriented approach to logging in R based on the widely-emulated
'log4j' system and etymology.
Author: John Myles White [aut, cph],
Kenton White [ctb],
Kirill Mueller [ctb],
Aaron Jacobs [aut, cre]
Maintainer: Aaron Jacobs <atheriel@gmail.com>
Diff between log4r versions 0.4.2 dated 2021-11-04 and 0.4.3 dated 2022-11-28
DESCRIPTION | 6 MD5 | 22 - NEWS.md | 5 build/vignette.rds |binary inst/doc/logging-beyond-local-files.Rmd | 2 inst/doc/logging-beyond-local-files.html | 376 +++++++++++++++++++++------ inst/doc/performance.Rmd | 2 inst/doc/performance.html | 426 +++++++++++++++++++++++-------- inst/doc/structured-logging.html | 359 ++++++++++++++++++++------ src/logfmt.c | 2 vignettes/logging-beyond-local-files.Rmd | 2 vignettes/performance.Rmd | 2 12 files changed, 939 insertions(+), 265 deletions(-)
Title: Rendering Math to HTML, 'MathML', or R-Documentation Format
Description: Convert latex math expressions to HTML and 'MathML' for use in
markdown documents or package manual pages. The rendering is done in
R using the V8 engine (i.e. server-side), which eliminates the need
for embedding the 'MathJax' library into your web pages. In addition
a 'math-to-rd' wrapper is provided to automatically render beautiful
math in R documentation files.
Author: Jeroen Ooms [aut, cre] ,
Khan Academy and other contributors [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between katex versions 1.4.0 dated 2022-02-08 and 1.4.1 dated 2022-11-28
katex-1.4.0/katex/inst/js/katex-0.15.2.min.js |only katex-1.4.1/katex/DESCRIPTION | 16 +- katex-1.4.1/katex/MD5 | 23 ++- katex-1.4.1/katex/NEWS | 4 katex-1.4.1/katex/R/katex.R | 8 - katex-1.4.1/katex/R/rd.R | 8 + katex-1.4.1/katex/build/partial.rdb |binary katex-1.4.1/katex/build/vignette.rds |binary katex-1.4.1/katex/inst/doc/katex-tests.html | 150 +++++++++++++++----------- katex-1.4.1/katex/inst/js/bindings.js | 4 katex-1.4.1/katex/inst/js/katex-0.16.3.min.js |only katex-1.4.1/katex/man/figures |only katex-1.4.1/katex/man/katex.Rd | 2 katex-1.4.1/katex/man/math_to_rd.Rd | 12 +- 14 files changed, 135 insertions(+), 92 deletions(-)
Title: Statistical Modelling in Action with R
Description: Datasets and functions for the book "Modélisation statistique par la pratique avec R", F. Bertrand, E. Claeys and M. Maumy-Bertrand (2019, ISBN:9782100793525, Dunod, Paris). The first chapter of the book is dedicated to an introduction to the R statistical software. The second chapter deals with correlation analysis: Pearson, Spearman and Kendall simple, multiple and partial correlation coefficients. New wrapper functions for permutation tests or bootstrap of matrices of correlation are provided with the package. The third chapter is dedicated to data exploration with factorial analyses (PCA, CA, MCA, MDA) and clustering. The fourth chapter is dedicated to regression analysis: fitting and model diagnostics are detailed. The exercises focus on covariance analysis, logistic regression, Poisson regression, two-way analysis of variance for fixed or random factors. Various example datasets are shipped with the package: for instance on pokemon, world of warcraft, house tasks or food nutritio [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Emmanuelle Claeys [aut],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between ModStatR versions 1.3.1 dated 2021-03-14 and 1.3.2 dated 2022-11-28
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/datasets.R | 2 +- data/data_event.RData |binary man/polypes.Rd | 2 +- 6 files changed, 23 insertions(+), 15 deletions(-)
Title: Genomic Regression Workbench
Description: Workbench for testing genomic regression accuracy on
(optionally noisy) phenotypes.
Author: Nelson Nazzicari & Filippo Biscarini
Maintainer: Nelson Nazzicari <nelson.nazzicari@gmail.com>
Diff between GROAN versions 1.3.0 dated 2022-08-26 and 1.3.1 dated 2022-11-28
DESCRIPTION | 8 +++--- MD5 | 13 +++++---- NEWS | 4 +++ build/partial.rdb |binary inst/CITATION |only inst/doc/GROAN.vignette.Rmd | 12 ++++----- inst/doc/GROAN.vignette.html | 57 +++++++++++++++++++++---------------------- vignettes/GROAN.vignette.Rmd | 12 ++++----- 8 files changed, 56 insertions(+), 50 deletions(-)
Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [ctb, ctr],
Tim Schreier [ctb, ctr],
Luis Winckelman [ctb, ctr],
Quirin Stier [ctb, ctr],
Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between GeneralizedUmatrix versions 1.2.4 dated 2022-05-25 and 1.2.5 dated 2022-11-28
GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/DefaultColorSequence.R |only GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/DESCRIPTION | 8 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/MD5 | 53 ++--- GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/R/GeneratePmatrix.R | 3 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/build/partial.rdb |binary GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/inst/doc/GeneralizedUmatrix.html | 11 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/CalcUstarmatrix.Rd | 10 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/Chainlink.Rd | 1 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/Delta3DWeightsC.Rd | 4 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/EsomNeuronsAsList.Rd | 11 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/ExtendToroidalUmatrix.Rd | 106 +++++----- GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/GeneralizedUmatrix.Rd | 35 +-- GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/GeneratePmatrix.Rd | 2 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/ListAsEsomNeurons.Rd | 13 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/LowLand.Rd | 14 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/NormalizeUmatrix.Rd | 10 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/ReduceToLowLand.Rd | 12 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/TopviewTopographicMap.Rd | 36 +-- GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/Uheights4Data.Rd | 4 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/UmatrixColormap.Rd | 7 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/UniqueBestMatchingUnits.Rd | 4 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/XYcoords2LinesColumns.Rd | 21 + GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/addRowWiseC.Rd | 8 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/plotTopographicMap.Rd | 67 +++--- GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/sESOM4BMUs.Rd | 15 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/setdiffMatrix.Rd | 14 - GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/trainstepC.Rd | 4 GeneralizedUmatrix-1.2.5/GeneralizedUmatrix/man/upscaleUmatrix.Rd | 26 +- 28 files changed, 259 insertions(+), 240 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: Create Constraints for Small Test Assembly Problems
Description: Provides simple functions to create constraints for small test assembly problems
(e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently,
'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from
any mainstream repository; see <https://www.gurobi.com/downloads/>.
Author: Benjamin Becker [aut, cre],
Dries Debeer [aut]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatATA versions 1.1.0 dated 2022-09-26 and 1.1.1 dated 2022-11-28
DESCRIPTION | 8 MD5 | 20 NEWS.md | 8 R/acrossFormsConstraint.R | 4 build/eatATA.pdf | 1486 ++++++++++++++++++------------------- build/partial.rdb |binary inst/doc/minimal_example.html | 18 inst/doc/overview.html | 18 inst/doc/use_case_pilot_study.html | 18 man/acrossFormsConstraint.Rd | 4 tests/testthat/test_useSolver.R | 26 11 files changed, 816 insertions(+), 794 deletions(-)
Title: Algorithms for Routing and Solving the Traffic Assignment
Problem
Description: Calculation of distances, shortest paths and isochrones on weighted graphs using several variants of Dijkstra algorithm.
Proposed algorithms are unidirectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>),
bidirectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) <https://archive.siam.org/meetings/alenex05/papers/03agoldberg.pdf>),
A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) <doi:10.1109/TSSC.1968.300136>),
new bidirectional A* (Pijls & Post (2009) <https://repub.eur.nl/pub/16100/ei2009-10.pdf>),
Contraction hierarchies (R. Geisberger, P. Sanders, D. Schultes and D. Delling (2008) <doi:10.1007/978-3-540-68552-4_24>),
PHAST (D. Delling, A.Goldberg, A. Nowatzyk, R. Werneck (2011) <doi:10.1016/j.jpdc.2012.02.007>).
Algorithms for solving the traffic assignment problem are All-or-Nothing assignment,
Method of Successive Averages,
Frank-Wolfe algorithm (M. Fukushima (1984) <doi:10.1016/0191-2615(84 [...truncated...]
Author: Vincent Larmet
Maintainer: Vincent Larmet <larmet.vincent@gmail.com>
Diff between cppRouting versions 2.0 dated 2020-01-07 and 3.0 dated 2022-11-28
cppRouting-2.0/cppRouting/inst/CITATION |only cppRouting-2.0/cppRouting/inst/doc/cpprouting.R |only cppRouting-2.0/cppRouting/inst/doc/cpprouting.Rmd |only cppRouting-2.0/cppRouting/inst/doc/cpprouting.html |only cppRouting-2.0/cppRouting/man/cppRouting-package.Rd |only cppRouting-2.0/cppRouting/src/Astar.cpp |only cppRouting-2.0/cppRouting/src/Astar_path.cpp |only cppRouting-2.0/cppRouting/src/bidir.cpp |only cppRouting-2.0/cppRouting/src/bidir_astar2.cpp |only cppRouting-2.0/cppRouting/src/bidir_astar_path.cpp |only cppRouting-2.0/cppRouting/src/bidir_mat3.cpp |only cppRouting-2.0/cppRouting/src/bidir_mod3.cpp |only cppRouting-2.0/cppRouting/src/bidir_mod_path.cpp |only cppRouting-2.0/cppRouting/src/bidir_path.cpp |only cppRouting-2.0/cppRouting/src/contract_ED4.cpp |only cppRouting-2.0/cppRouting/src/detour.cpp |only cppRouting-2.0/cppRouting/src/dijkstra_early_stop.cpp |only cppRouting-2.0/cppRouting/src/dijkstra_early_stop_path.cpp |only cppRouting-2.0/cppRouting/src/dijkstra_mat.cpp |only cppRouting-2.0/cppRouting/src/dijkstra_multi_path.cpp |only cppRouting-2.0/cppRouting/src/duplicated.cpp |only cppRouting-2.0/cppRouting/src/functions_one_to_all_ED4.cpp |only cppRouting-2.0/cppRouting/src/functions_one_to_all_ED4.h |only cppRouting-2.0/cppRouting/src/isochrone.cpp |only cppRouting-2.0/cppRouting/src/isochrone_multi.cpp |only cppRouting-2.0/cppRouting/src/par_NBA.cpp |only cppRouting-2.0/cppRouting/src/par_astar.cpp |only cppRouting-2.0/cppRouting/src/par_bidir2.cpp |only cppRouting-2.0/cppRouting/src/par_bidir_mat2.cpp |only cppRouting-2.0/cppRouting/src/par_bidir_mod.cpp |only cppRouting-2.0/cppRouting/src/par_dijkstra.cpp |only cppRouting-2.0/cppRouting/src/par_dijkstra_mat.cpp |only cppRouting-2.0/cppRouting/src/phast3.cpp |only cppRouting-2.0/cppRouting/src/phast_par.cpp |only cppRouting-2.0/cppRouting/src/simp.cpp |only cppRouting-2.0/cppRouting/src/simp.h |only cppRouting-2.0/cppRouting/src/simplify5.cpp |only cppRouting-2.0/cppRouting/vignettes/cpprouting.Rmd |only cppRouting-3.0/cppRouting/DESCRIPTION | 25 cppRouting-3.0/cppRouting/MD5 | 124 +- cppRouting-3.0/cppRouting/NAMESPACE | 4 cppRouting-3.0/cppRouting/NEWS.md | 18 cppRouting-3.0/cppRouting/R/RcppExports.R | 112 -- cppRouting-3.0/cppRouting/R/assign_traffic.R |only cppRouting-3.0/cppRouting/R/contract.R | 32 cppRouting-3.0/cppRouting/R/get_aon.R |only cppRouting-3.0/cppRouting/R/get_detour.R | 67 - cppRouting-3.0/cppRouting/R/get_distance_mat.R | 218 ++-- cppRouting-3.0/cppRouting/R/get_distance_pair.R | 236 +++- cppRouting-3.0/cppRouting/R/get_isochrone.R | 70 - cppRouting-3.0/cppRouting/R/get_multi_paths.R | 78 - cppRouting-3.0/cppRouting/R/get_path_pair.R | 140 +- cppRouting-3.0/cppRouting/R/graphs.R | 123 +- cppRouting-3.0/cppRouting/R/simplify.R | 80 - cppRouting-3.0/cppRouting/R/to_df.R | 16 cppRouting-3.0/cppRouting/build/vignette.rds |binary cppRouting-3.0/cppRouting/inst/doc/cppRouting.R |only cppRouting-3.0/cppRouting/inst/doc/cppRouting.Rmd |only cppRouting-3.0/cppRouting/inst/doc/cppRouting.html |only cppRouting-3.0/cppRouting/man/assign_traffic.Rd |only cppRouting-3.0/cppRouting/man/cpp_contract.Rd | 75 - cppRouting-3.0/cppRouting/man/cpp_simplify.Rd | 149 +-- cppRouting-3.0/cppRouting/man/get_aon.Rd |only cppRouting-3.0/cppRouting/man/get_detour.Rd | 159 +-- cppRouting-3.0/cppRouting/man/get_distance_matrix.Rd | 131 +- cppRouting-3.0/cppRouting/man/get_distance_pair.Rd | 159 +-- cppRouting-3.0/cppRouting/man/get_isochrone.Rd | 109 +- cppRouting-3.0/cppRouting/man/get_multi_paths.Rd | 109 +- cppRouting-3.0/cppRouting/man/get_path_pair.Rd | 157 +-- cppRouting-3.0/cppRouting/man/makegraph.Rd | 125 +- cppRouting-3.0/cppRouting/man/to_df.Rd | 62 - cppRouting-3.0/cppRouting/src/Makevars |only cppRouting-3.0/cppRouting/src/Makevars.win |only cppRouting-3.0/cppRouting/src/RcppExports.cpp | 645 +++++-------- cppRouting-3.0/cppRouting/src/aggc.cpp |only cppRouting-3.0/cppRouting/src/aggc.h |only cppRouting-3.0/cppRouting/src/aon.cpp |only cppRouting-3.0/cppRouting/src/aon.h |only cppRouting-3.0/cppRouting/src/bush.cpp |only cppRouting-3.0/cppRouting/src/bush.h |only cppRouting-3.0/cppRouting/src/cgraph.cpp |only cppRouting-3.0/cppRouting/src/cgraph.h |only cppRouting-3.0/cppRouting/src/contract.cpp |only cppRouting-3.0/cppRouting/src/distance_mat.cpp |only cppRouting-3.0/cppRouting/src/distance_mat.h |only cppRouting-3.0/cppRouting/src/distance_pair.cpp |only cppRouting-3.0/cppRouting/src/distance_pair.h |only cppRouting-3.0/cppRouting/src/graph.cpp |only cppRouting-3.0/cppRouting/src/graph.h |only cppRouting-3.0/cppRouting/src/path_mat.cpp |only cppRouting-3.0/cppRouting/src/path_mat.h |only cppRouting-3.0/cppRouting/src/path_pair.cpp |only cppRouting-3.0/cppRouting/src/path_pair.h |only cppRouting-3.0/cppRouting/src/simplify.cpp |only cppRouting-3.0/cppRouting/src/stall.cpp |only cppRouting-3.0/cppRouting/src/stall.h |only cppRouting-3.0/cppRouting/src/traffic.cpp |only cppRouting-3.0/cppRouting/src/wrapper.cpp |only cppRouting-3.0/cppRouting/vignettes/cppRouting.Rmd |only 99 files changed, 1696 insertions(+), 1527 deletions(-)
Title: Experimental Data of Cascade Experiments in Genomics
Description: These experimental expression data (5 leukemic 'CLL' B-lymphocyte of aggressive form from 'GSE39411', <doi:10.1073/pnas.1211130110>), after B-cell receptor stimulation, are used as examples by packages such as the 'Cascade' one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between CascadeData versions 1.3 dated 2021-03-19 and 1.4 dated 2022-11-28
CascadeData-1.3/CascadeData/NEWS |only CascadeData-1.4/CascadeData/DESCRIPTION | 17 +++++++++-------- CascadeData-1.4/CascadeData/MD5 | 13 ++++++------- CascadeData-1.4/CascadeData/NEWS.md | 4 ++++ CascadeData-1.4/CascadeData/R/CascadeData-package.R | 2 +- CascadeData-1.4/CascadeData/README.md | 2 +- CascadeData-1.4/CascadeData/build/partial.rdb |binary CascadeData-1.4/CascadeData/man/CascadeData-package.Rd | 2 +- 8 files changed, 22 insertions(+), 18 deletions(-)
Title: Selection, Reverse-Engineering and Prediction in Cascade
Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between Cascade versions 2.0 dated 2021-03-19 and 2.1 dated 2022-11-28
Cascade-2.0/Cascade/NEWS |only Cascade-2.1/Cascade/DESCRIPTION | 22 +-- Cascade-2.1/Cascade/MD5 | 35 ++-- Cascade-2.1/Cascade/NAMESPACE | 1 Cascade-2.1/Cascade/NEWS.md | 6 Cascade-2.1/Cascade/R/Cascade-package.R | 7 Cascade-2.1/Cascade/R/micro_array.R | 8 - Cascade-2.1/Cascade/R/network.R | 8 - Cascade-2.1/Cascade/README.md | 117 ++++++++++++++-- Cascade-2.1/Cascade/build/vignette.rds |binary Cascade-2.1/Cascade/inst/CITATION | 4 Cascade-2.1/Cascade/man/evolution-network-method.Rd | 8 - Cascade-2.1/Cascade/man/geneSelection.Rd | 2 Cascade-2.1/Cascade/man/head-micro_array-method.Rd | 2 Cascade-2.1/Cascade/man/inference-micro_array-method.Rd | 4 Cascade-2.1/Cascade/man/micro_array-class.Rd | 2 Cascade-2.1/Cascade/man/micropredict-class.Rd | 2 Cascade-2.1/Cascade/man/network-class.Rd | 2 Cascade-2.1/Cascade/man/plot-methods.Rd | 4 19 files changed, 170 insertions(+), 64 deletions(-)
Title: Initiation à La Statistique Avec R
Description: Datasets and functions for the book "Initiation à la Statistique avec R", F. Bertrand and M. Maumy-Bertrand (2022, ISBN:978-2100782826 Dunod, 4ème edition).
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between BioStatR versions 3.1.2 dated 2021-03-14 and 4.0.0 dated 2022-11-28
DESCRIPTION | 20 ++++++++++---------- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 4 ++++ R/binom.ci.R | 4 ++-- R/cvar.R | 4 ++-- R/eta2.R | 4 ++-- R/gg_qqplot.R | 4 ++-- R/panel.hist.R | 4 ++-- R/plotcdf2.R | 4 ++-- R/poi.ci.R | 4 ++-- demo/Chapitre1.R | 33 +++++++++++++++++++++++++++------ demo/Chapitre2.R | 29 +++++++++++++++-------------- man/binom.ci.Rd | 4 ++-- man/cvar.Rd | 4 ++-- man/eta2.Rd | 4 ++-- man/gg_qqplot.Rd | 4 ++-- man/panel.hist.Rd | 4 ++-- man/plotcdf2.Rd | 4 ++-- man/poi.ci.Rd | 4 ++-- 19 files changed, 102 insertions(+), 76 deletions(-)
Title: 'ASReml-R' Genomics Tools
Description: Presents a series of molecular and genetic routines in the R
environment with the aim of assisting in analytical pipelines before
and after the use of 'asreml' or another library to perform analyses such
as Genomic Selection or Genome-Wide Association Analyses.
Methods and examples are described in Gezan, Oliveira, Galli, and Murray (2022)
<https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/ASRgenomics_Manual.pdf>.
Author: Salvador Gezan [aut, cre],
Darren Murray [aut],
Amanda Avelar de Oliveira [aut],
Giovanni Galli [aut],
VSN International [cph]
Maintainer: Salvador Gezan <salvador.gezan@vsni.co.uk>
Diff between ASRgenomics versions 1.1.2 dated 2022-11-22 and 1.1.3 dated 2022-11-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 11 +++++++++++ R/match_G2A.R | 11 ++++++----- tests/testthat/test-internal.R | 10 +++++----- 5 files changed, 29 insertions(+), 17 deletions(-)
Title: Document Conversion to 'PDF' or 'PNG'
Description: Functions to convert 'Microsoft Word' or 'Microsoft PowerPoint'
documents to 'PDF' format and also for converting them into a thumbnail.
In order to work, 'LibreOffice' must be installed on the machine and
or 'Microsoft Word'. If the latter is available,
it can be used to produce PDF documents identical to the originals,
otherwise, 'LibreOffice' is used. A function is also provided to update
all fields and table of contents of a Word document using 'Microsoft Word'.
Author: David Gohel [aut, cre],
ArData [cph],
David Hajage [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between doconv versions 0.1.4 dated 2022-08-19 and 0.2.0 dated 2022-11-28
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 3 +++ R/expect_snapshot_doc.R |only man/expect_snapshot_doc.Rd |only 5 files changed, 12 insertions(+), 7 deletions(-)
More information about qualitycontrol at CRAN
Permanent link
Title: Compute and Illustrate the Multiple Facets of Functional
Diversity
Description: Computing functional traits-based distances between pairs of
species for species gathered in assemblages allowing to build several
functional spaces. The package allows to compute functional diversity
indices assessing the distribution of species (and of their dominance) in a
given functional space for each assemblage and the overlap between
assemblages in a given functional space, see: Chao et al. (2018)
<doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>,
Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al.
(2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009)
<doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included.
Visit the 'mFD' website for more information, documentation and examples.
Author: Camille Magneville [aut, cre, cph]
,
Nicolas Loiseau [aut] ,
Camille Albouy [aut] ,
Nicolas Casajus [aut] ,
Thomas Claverie [aut] ,
Arthur Escalas [aut] ,
Fabien Leprieur [aut] ,
Eva Maire [aut] ,
David Mouillot [aut] ,
Sebastien Villeger [aut]
Maintainer: Camille Magneville <camille.magneville@gmail.com>
Diff between mFD versions 1.0.2 dated 2022-11-08 and 1.0.3 dated 2022-11-28
DESCRIPTION | 6 MD5 | 34 - NEWS.md | 7 R/beta_ind_computation.R | 2 R/cont_tr_fspace.R | 2 R/plot_alpha_indices.R | 8 inst/doc/Compute_and_interpret_quality_of_functional_spaces.html | 4 inst/doc/Compute_functional_hill_indices.html | 4 inst/doc/Continuous_traits_framework.html | 142 ++-- inst/doc/Customised_plots.html | 4 inst/doc/How_to_deal_with_Functional_Entities.Rmd | 2 inst/doc/How_to_deal_with_Functional_Entities.html | 6 inst/doc/mFD_general_workflow.R | 77 +- inst/doc/mFD_general_workflow.Rmd | 40 - inst/doc/mFD_general_workflow.html | 309 ---------- man/beta.fd.multidim.Rd | 2 vignettes/How_to_deal_with_Functional_Entities.Rmd | 2 vignettes/mFD_general_workflow.Rmd | 40 - 18 files changed, 189 insertions(+), 502 deletions(-)
Title: Package of the German Book "Statistik mit R und RStudio" by
Joerg grosse Schlarmann
Description: All datasets and functions used in the german book "Statistik mit R und RStudio" by Joerg grosse Schlarmann.
You can read it online at <https://www.produnis.de/R/> .
Author: Joerg grosse Schlarmann
Maintainer: Joerg grosse Schlarmann <schlarmann@produnis.de>
Diff between jgsbook versions 1.0 dated 2022-05-13 and 1.0.1 dated 2022-11-28
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE | 1 + NEWS.md | 4 ++++ R/functions.R | 27 ++++++++++++++++++++++++--- man/lon.lat.osm.Rd |only 6 files changed, 40 insertions(+), 13 deletions(-)
Title: Draw Histograms and Restricted Cubic Splines (RCS)
Description: You can use this function to easily draw a combined histogram and restricted cubic spline.
The function draws the graph through 'ggplot2'. RCS fitting requires the use of the rcs() function of the 'rms' package.
Can fit cox regression, logistic regression. This method was described by Per Kragh (2003) <doi:10.1002/sim.1497>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>
Diff between ggrcs versions 0.2.4 dated 2022-09-02 and 0.2.6 dated 2022-11-28
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- R/ggrcs.R | 6 +++--- R/predata.ols.R |only man/predata.ols.Rd |only 5 files changed, 10 insertions(+), 8 deletions(-)
Title: Ranked Voting Election Audits with Dirichlet-Trees
Description: Perform ballot-polling Bayesian audits for ranked voting elections
using Dirichlet-tree prior distributions. Everest et al. (2022)
<arXiv:2206.14605>, <arXiv:2209.03881>.
Author: Floyd Everest [aut, cre, cph] ,
Damjan Vukcevic [aut]
Maintainer: Floyd Everest <me@floydeverest.com>
Diff between elections.dtree versions 1.0.3 dated 2022-11-17 and 1.1.0 dated 2022-11-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 8 +++++++- R/dtree.R | 22 ++++++++++++++++++++-- build/partial.rdb |binary inst/WORDLIST | 17 +++++++++++++++++ man/dirichlet_tree.Rd | 4 ++++ man/sample_posterior.Rd | 4 ++++ src/R_tree.cpp | 3 ++- src/R_tree.h | 4 ++-- src/dirichlet_tree.h | 15 +++++++++++---- tests/testthat/test-posterior.R | 16 ++++++++++++++++ 12 files changed, 98 insertions(+), 25 deletions(-)
More information about elections.dtree at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-12 0.1.9
2022-06-26 0.1.8
2022-04-26 0.1.7
2022-03-14 0.1.6
2022-02-11 0.1.5
2022-01-17 0.1.4
Title: Binary R server
Description: Rserve acts as a socket server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for popular languages such as C/C++ and Java, allowing
any application to use facilities of R without the need of
linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client
is included in this package as well.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-10 dated 2021-11-25 and 1.8-11 dated 2022-11-28
DESCRIPTION | 6 - MD5 | 76 +++++++-------- NEWS | 28 +++++ R/conn.R | 16 ++- R/zzz.R | 3 inst/java/REngine.jar |binary inst/java/Rserve.jar |binary man/Rserve.eval.Rd | 42 +++++++- src/RSserver.c | 4 src/RSserver.h | 19 ++- src/Rserv.c | 177 ++++++++++++++++++++----------------- src/Rsrv.h | 38 +++---- src/client/cxx/Rsrv.h | 38 +++---- src/client/java/JRI/JRIEngine.java | 38 +++---- src/client/java/REXPReference.java | 2 src/client/java/REngine.java | 2 src/client/java/Rserve/Makefile | 2 src/client/java/Rserve/Rserve.jar |binary src/http.c | 18 +++ src/ioc.c | 10 +- src/md5.c | 20 +--- src/md5.h | 8 - src/proxy/chandler.c | 2 src/proxy/chandler.h | 2 src/proxy/http.c | 8 - src/proxy/server.c | 20 ++-- src/proxy/server.h | 23 ++-- src/proxy/tls.c | 42 ++++++++ src/proxy/tls.h | 10 +- src/proxy/websockets.c | 162 +++++++++++++++++++++------------ src/session.c | 4 src/session.h | 2 src/standalone.c | 11 +- src/tls.c | 12 +- src/tls.h | 2 src/ulog.c | 14 +- src/ulog.h | 8 - src/utils.c | 49 ++++++++-- src/websockets.c | 162 +++++++++++++++++++++------------ 39 files changed, 669 insertions(+), 411 deletions(-)
Title: Public Key Infrastucture for R Based on the X.509 Standard
Description: Public Key Infrastucture functions such as verifying certificates, RSA encription and signing which can be used to build PKI infrastructure and perform cryptographic tasks.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between PKI versions 0.1-11 dated 2022-03-16 and 0.1-12 dated 2022-11-28
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS | 5 +++++ src/asn1.c | 20 ++++++++++---------- src/init.c | 2 +- src/pem.c | 21 ++++++++++++--------- src/pgp.c | 4 +++- src/pki-x509.c | 42 ++++++++++++++++++++++-------------------- src/pki.h | 28 ++++++++++++++++++++++++---- src/register.c | 2 +- src/tools.c | 7 ++++--- 11 files changed, 95 insertions(+), 62 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available
from several federated data sources (mainly sources maintained by the
US Federal government). Currently, the package enables extraction from
seven datasets: The National Elevation Dataset digital elevation
models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset
(USGS); The Soil Survey Geographic (SSURGO) database from the National
Cooperative Soil Survey (NCSS), which is led by the Natural Resources
Conservation Service (NRCS) under the USDA; the Global Historical
Climatology Network (GHCN), coordinated by National Climatic Data
Center at NOAA; the Daymet gridded estimates of daily weather
parameters for North America, version 3, available from the Oak Ridge
National Laboratory's Distributed Active Archive Center (DAAC); the
International Tree Ring Data Bank; and the National Land Cover
Database (NLCD).
Author: R. Kyle Bocinsky [aut, cre, cph],
Dylan Beaudette [ctb],
Scott Chamberlain [ctb, rev],
Jeffrey Hollister [ctb],
Julia Gustavsen [rev]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 3.0.0 dated 2022-10-11 and 3.0.1 dated 2022-11-28
DESCRIPTION | 12 +-- MD5 | 36 +++++----- NEWS.md | 96 +++++++++++++++------------- R/DAYMET_FUNCTIONS.R | 16 +++- R/NASS_FUNCTIONS.R | 47 +++++++++++-- R/NLCD_FUNCTIONS.R | 14 ++-- R/UTILITY_FUNCTIONS.R | 51 ++++++++------ README.md | 17 ++++ man/figures/README-DAYMET-1.png |binary man/figures/README-GHCN-precipitation-1.png |binary man/figures/README-GHCN-temperature-1.png |binary man/figures/README-NASS-CDL-1.png |binary man/figures/README-NED-1.png |binary man/figures/README-NHD-1.png |binary man/figures/README-NLCD-1.png |binary man/figures/README-SSURGO-1.png |binary man/figures/README-SSURGO-area-1.png |binary man/get_daymet.Rd | 2 man/get_nlcd.Rd | 2 19 files changed, 186 insertions(+), 107 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-01 1.7.0
2015-02-09 1.6.3
2014-11-04 1.6.0
2014-09-26 1.5-0
2014-09-11 1.4-1
2014-02-04 1.4-0
2013-09-27 1.2-3
2013-07-25 1.1-3
2013-05-29 1.1-0
2013-04-26 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-03 0.1.1
2021-05-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-16 0.1.0