Title: Scelestial: Steiner Tree Based Single-Cell Lineage Tree
Inference
Description: Scelestial infers a lineage tree from single-cell DNA mutation matrix.
It generates a tree with approximately maximum parsimony through
a Steiner tree approximation algorithm.
Author: Mohammad Hadi Foroughmand Araabi [aut, cre],
Sama Goliaei [aut, ctb],
Alice McHardy [ctb]
Maintainer: Mohammad Hadi Foroughmand Araabi <foroughmand@gmail.com>
Diff between RScelestial versions 1.0.3 dated 2021-12-09 and 1.0.4 dated 2023-11-30
DESCRIPTION | 14 MD5 | 23 NEWS.md | 4 R/scelestial.R | 2 build/vignette.rds |binary inst/WORDLIST |only inst/doc/RScelestial-vignette.R | 5 inst/doc/RScelestial-vignette.Rmd | 3 inst/doc/RScelestial-vignette.html | 882 ++++++++++++++++++++++--------------- man/scelestial.Rd | 2 src/scelestial.cc | 23 src/scelestial.h | 156 +++++- vignettes/RScelestial-vignette.Rmd | 3 13 files changed, 731 insertions(+), 386 deletions(-)
Title: Frictionless Standards
Description: A "tabular-data-resource" (<https://specs.frictionlessdata.io/tabular-data-resource/>) is a simple format to describe a singular tabular data resource such as a CSV file. It includes support both for metadata such as author and title and a schema to describe the data, for example the types of the fields/columns in the data. Create a tabular-data-resource by providing a data.frame and specifying metadata. Write and read tabular-data-resources to and from disk.
Author: Cole Brokamp [aut, cre, cph]
Maintainer: Cole Brokamp <cole@colebrokamp.com>
Diff between fr versions 0.5.0 dated 2023-11-22 and 0.5.1 dated 2023-11-30
DESCRIPTION | 6 ++-- MD5 | 32 ++++++++++++------------- NEWS.md | 4 +++ R/fr-package.R | 2 - R/fr_tdr.R | 2 - R/update_field.R | 4 +-- inst/doc/creating_a_tabular-data-resource.html | 2 - inst/doc/read_fr_tdr.R | 4 +-- inst/doc/read_fr_tdr.Rmd | 4 +-- inst/doc/read_fr_tdr.html | 6 ++-- man/as_fr_tdr.Rd | 2 - man/update_field.Rd | 2 - tests/testthat/test-fr_field.R | 1 tests/testthat/test-fr_schema.R | 1 tests/testthat/test-fr_tdr.R | 1 tests/testthat/test-write_fr_tdr.R | 1 vignettes/read_fr_tdr.Rmd | 4 +-- 17 files changed, 43 insertions(+), 35 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl],
Mikko Korpela [aut, cph, trl],
Franco Biondi [aut, cph],
Filipe Campelo [aut, cph],
Pierre Merian [aut, cph],
Fares Qeadan [aut, cph],
Christian Zang [aut, cph],
Allan Buras [ctb],
Alice Cecile [ctb],
Manfred Mudelsee [...truncated...]
Maintainer: Andy Bunn <bunna@wwu.edu>
Diff between dplR versions 1.7.5 dated 2023-08-30 and 1.7.6 dated 2023-11-30
ChangeLog | 15 +++++++++++++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/detrend.series.Rd | 2 +- man/read.compact.Rd | 14 ++++++++++++++ src/rcompact.c | 4 ++-- 6 files changed, 40 insertions(+), 11 deletions(-)
Title: Modern Database Engine for Multi-Modal Data via Sparse and Dense
Multidimensional Arrays
Description: The modern database 'TileDB' introduces a powerful on-disk
format for multi-modal data based on 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 0.21.1 dated 2023-09-27 and 0.22.0 dated 2023-11-30
DESCRIPTION | 19 MD5 | 92 + NAMESPACE | 8 NEWS.md | 84 + R/Array.R | 35 R/ArraySchema.R | 28 R/ArraySchemaEvolution.R | 58 + R/Attribute.R | 26 R/BatchedQuery.R | 4 R/Query.R | 2 R/QueryCondition.R | 84 + R/RcppExports.R | 40 R/TileDBArray.R | 30 R/VFS.R | 90 + README.md | 8 build/vignette.rds |binary configure | 75 + configure.ac | 15 inst/config.log |only inst/config.status |only inst/include/tiledb.h | 16 inst/tinytest/test_aggregates.R |only inst/tinytest/test_arrayschemaevolution.R | 79 + inst/tinytest/test_arrayschemaevolution_arrow.R |only inst/tinytest/test_arrowio.R | 3 inst/tinytest/test_dataframe.R | 2 inst/tinytest/test_ordered.R | 15 inst/tinytest/test_querycondition.R | 101 ++ inst/tinytest/test_tiledbarray.R | 4 inst/tinytest/test_vfs.R | 19 man/parse_query_condition.Rd | 17 man/tiledb_array_apply_aggregate.Rd |only man/tiledb_array_delete_fragments.Rd | 9 man/tiledb_array_schema_evolution_add_enumeration_empty.Rd |only man/tiledb_array_schema_evolution_extend_enumeration.Rd |only man/tiledb_array_schema_set_enumeration_empty.Rd |only man/tiledb_query_condition_create.Rd |only man/tiledb_vfs_copy_file.Rd |only man/tiledb_vfs_read.Rd | 4 man/tiledb_vfs_serialize.Rd |only man/tiledb_vfs_unserialize.Rd |only src/Makevars.win | 2 src/RcppExports.cpp | 145 ++ src/arrowio.cpp | 60 + src/libtiledb.cpp | 323 ++++++ src/nanoarrow.c | 634 +++++++++---- src/nanoarrow.h | 530 +++++++++- tools/buildTileDB.sh | 22 tools/ci/valgrind/installDependencies.sh | 1 tools/fetchTileDBLib.R | 2 tools/fetchTileDBSrc.R | 46 tools/tiledbVersion.txt | 4 tools/winlibs.R | 2 53 files changed, 2300 insertions(+), 438 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between rjags versions 4-14 dated 2023-04-23 and 4-15 dated 2023-11-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/parallel.cc | 6 ++---- 3 files changed, 8 insertions(+), 10 deletions(-)
Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. It is based on an input/output system, where the
output random variable (RV) Y is a non-linearly transformed version of an input
RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
The transformed RV Y has a Lambert W x F distribution. This package contains
functions to model and analyze skewed, heavy-tailed data the Lambert Way:
simulate random samples, estimate parameters, compute quantiles, and plot/
print results nicely. The most useful function is 'Gaussianize',
which works similarly to 'scale', but actually makes the data Gaussian.
A do-it-yourself toolkit allows users to define their own Lambert W x
'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg [aut, cre]
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.6.9 dated 2023-10-30 and 0.6.9-1 dated 2023-11-30
DESCRIPTION | 8 MD5 | 10 NEWS.md | 4 R/RcppExports.R | 2 inst/doc/lambertw-overview.html | 431 +++++++++++++++------------------------- src/RcppExports.cpp | 8 6 files changed, 185 insertions(+), 278 deletions(-)
Title: Workflow for Cluster Randomised Trials with Spillover
Description: Design, workflow and statistical analysis of Cluster Randomised Trials of (health) interventions where there may be geographical contamination between the arms (see <https://thomasasmith.github.io/index.html>).
Author: Thomas Smith [aut, cre, cph] ,
Lea Multerer [ctb],
Mariah Silkey [ctb]
Maintainer: Thomas Smith <Thomas-a.Smith@unibas.ch>
Diff between CRTspat versions 1.0.0 dated 2023-10-16 and 1.1.0 dated 2023-11-30
CRTspat-1.0.0/CRTspat/inst/doc/CRTspat.Rmd |only CRTspat-1.0.0/CRTspat/inst/doc/CRTspat.html |only CRTspat-1.0.0/CRTspat/vignettes/CRTspat.Rmd |only CRTspat-1.0.0/CRTspat/vignettes/CRTspat.Rmd.orig |only CRTspat-1.0.0/CRTspat/vignettes/workflow.svg |only CRTspat-1.1.0/CRTspat/DESCRIPTION | 8 CRTspat-1.1.0/CRTspat/MD5 | 102 CRTspat-1.1.0/CRTspat/NEWS.md | 5 CRTspat-1.1.0/CRTspat/R/CRTsp.R |only CRTspat-1.1.0/CRTspat/R/analyseCRT.R | 158 CRTspat-1.1.0/CRTspat/R/designCRT.R | 217 - CRTspat-1.1.0/CRTspat/R/plotCRT.R | 7 CRTspat-1.1.0/CRTspat/R/utils.R | 317 - CRTspat-1.1.0/CRTspat/README.md | 33 CRTspat-1.1.0/CRTspat/build/vignette.rds |binary CRTspat-1.1.0/CRTspat/inst/doc/Usecase1.Rmd | 17 CRTspat-1.1.0/CRTspat/inst/doc/Usecase1.html | 24 CRTspat-1.1.0/CRTspat/inst/doc/Usecase2.Rmd | 3 CRTspat-1.1.0/CRTspat/inst/doc/Usecase2.html | 3 CRTspat-1.1.0/CRTspat/inst/doc/Usecase3.Rmd | 14 CRTspat-1.1.0/CRTspat/inst/doc/Usecase3.html | 14 CRTspat-1.1.0/CRTspat/inst/doc/Usecase4.Rmd | 45 CRTspat-1.1.0/CRTspat/inst/doc/Usecase4.html | 59 CRTspat-1.1.0/CRTspat/inst/doc/Usecase5.Rmd | 11 CRTspat-1.1.0/CRTspat/inst/doc/Usecase5.html | 11 CRTspat-1.1.0/CRTspat/inst/doc/Usecase6.Rmd | 1 CRTspat-1.1.0/CRTspat/inst/doc/Usecase6.html | 1 CRTspat-1.1.0/CRTspat/inst/doc/Usecase7.Rmd | 6 CRTspat-1.1.0/CRTspat/inst/doc/Usecase7.html | 6 CRTspat-1.1.0/CRTspat/inst/doc/Usecase8.Rmd | 2 CRTspat-1.1.0/CRTspat/inst/doc/Usecase8.html | 2 CRTspat-1.1.0/CRTspat/inst/extdata/exampleCRT.txt | 3710 +++++++++--------- CRTspat-1.1.0/CRTspat/inst/extdata/example_design.txt | 4 CRTspat-1.1.0/CRTspat/man/CRTanalysis.Rd | 16 CRTspat-1.1.0/CRTspat/man/CRTpower.Rd | 61 CRTspat-1.1.0/CRTspat/man/CRTsp.Rd | 2 CRTspat-1.1.0/CRTspat/man/CRTspat-package.Rd | 2 CRTspat-1.1.0/CRTspat/man/figures/manual.pdf |binary CRTspat-1.1.0/CRTspat/man/randomizeCRT.Rd | 2 CRTspat-1.1.0/CRTspat/man/specify_clusters.Rd | 8 CRTspat-1.1.0/CRTspat/man/summary.CRTsp.Rd | 2 CRTspat-1.1.0/CRTspat/tests/testthat/tests1_2.R | 2 CRTspat-1.1.0/CRTspat/vignettes/Usecase1.Rmd | 17 CRTspat-1.1.0/CRTspat/vignettes/Usecase2.Rmd | 3 CRTspat-1.1.0/CRTspat/vignettes/Usecase3.Rmd | 14 CRTspat-1.1.0/CRTspat/vignettes/Usecase3.Rmd.orig | 12 CRTspat-1.1.0/CRTspat/vignettes/Usecase4.Rmd | 45 CRTspat-1.1.0/CRTspat/vignettes/Usecase4.Rmd.orig | 45 CRTspat-1.1.0/CRTspat/vignettes/Usecase5.Rmd | 11 CRTspat-1.1.0/CRTspat/vignettes/Usecase6.Rmd | 1 CRTspat-1.1.0/CRTspat/vignettes/Usecase7.Rmd | 6 CRTspat-1.1.0/CRTspat/vignettes/Usecase7.Rmd.orig | 6 CRTspat-1.1.0/CRTspat/vignettes/Usecase8.Rmd | 2 CRTspat-1.1.0/CRTspat/vignettes/Usecase8.Rmd.orig | 2 CRTspat-1.1.0/CRTspat/vignettes/runVignette.R | 1 55 files changed, 2427 insertions(+), 2613 deletions(-)
Title: Visualize Draws from the Prior and Posterior Distributions
Description: Interactive visualization for Bayesian prior and posterior distributions.
This package facilitates an animated transition between prior and posterior distributions.
Additionally, it splits the distribution into bars based on the provided 'breaks,' displaying
the probability for each region. If no 'breaks' are provided, it defaults to zero.
Author: Ignacio Martinez [aut, cre],
Linus Marco [aut],
Dan Thal [aut]
Maintainer: Ignacio Martinez <ignacio@protonmail.com>
Diff between vizdraws versions 1.2 dated 2022-02-04 and 1.3 dated 2023-11-30
DESCRIPTION | 28 ++-- MD5 | 24 +-- NEWS.md | 5 R/dataframeToD3.R | 2 R/vizdraws.R | 8 + README.md | 13 -- build/vignette.rds |binary inst/doc/introduction.R | 2 inst/doc/introduction.html | 82 +++++++----- inst/doc/shiny-example.R | 2 inst/doc/shiny-example.html | 141 ++++++++++++---------- inst/htmlwidgets/lib/vizdraws/vizdraws-general.js | 34 ++--- man/vizdraws.Rd | 6 13 files changed, 194 insertions(+), 153 deletions(-)
Title: Simulate Agricultural Production and Evolution of Pesticide
Resistance
Description: Simulates individual-based models of agricultural pest management
and the evolution of pesticide resistance. Management occurs on a spatially
explicit landscape that is divided into an arbitrary number of farms that
can grow one of up to 10 crops and apply one of up to 10 pesticides. Pest
genomes are modelled in a way that allows for any number of pest traits with
an arbitrary covariance structure that is constructed using an evolutionary
algorithm in the mine_gmatrix() function. Simulations are then run using the
run_farm_sim() function. This package thereby allows for highly mechanistic
social-ecological models of the evolution of pesticide resistance under
different types of crop rotation and pesticide application regimes.
Author: A. Bradley Duthie [aut, cre] ,
Rose McKeon [aut, ctr],
Rosie Mangan [ctr],
Luc Bussiére [ctr],
Matthew Tinsley [ctr]
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>
Diff between resevol versions 0.3.0.1 dated 2022-07-13 and 0.3.4.0 dated 2023-11-30
DESCRIPTION | 8 MD5 | 100 +- NAMESPACE | 2 NEWS.md | 35 R/gmatrices.R | 10 R/initialise.R | 159 ++-- R/landscape.R | 1 R/sim_farming.R | 117 ++- R/stress_test.R |only README.md | 2 build/vignette.rds |binary inst/advanced_eg.rda |only inst/doc/advanced_techniques.R |only inst/doc/advanced_techniques.Rmd |only inst/doc/advanced_techniques.html |only inst/doc/evolutionary_algorithm.R | 4 inst/doc/evolutionary_algorithm.Rmd | 27 inst/doc/evolutionary_algorithm.html | 476 ++++--------- inst/doc/resevol.R | 436 +++++++----- inst/doc/resevol.Rmd | 933 +++++++++++++++---------- inst/doc/resevol.html | 1270 ++++++++++------------------------- inst/landscape_eg.csv |only inst/last_time_step.csv |only inst/last_time_step_sim1.csv |only inst/last_time_step_sim2.csv |only inst/new_network.rda |only inst/population_data.csv |only inst/population_data_sim1.csv |only inst/population_data_sim2.csv |only inst/resevol.bib |only inst/sim.rda |only man/initialise_inds.Rd | 6 man/make_landscape.Rd | 1 man/mg_n1.Rd | 2 man/mg_n2.Rd | 2 man/mg_n3.Rd | 2 man/mg_n4.Rd | 2 man/mg_n5.Rd | 2 man/mg_v1.Rd | 2 man/mg_v2.Rd | 2 man/mg_v3.Rd | 2 man/mg_v4.Rd | 2 man/mg_v5.Rd | 2 man/run_farm_sim.Rd | 42 + man/stress_test.Rd |only src/land_change.c | 102 ++ src/land_change.h | 5 src/mine_gmatrix.c | 4 src/movement.c | 46 + src/parents.c | 17 src/reproduction.c | 2 src/resevol_init.c | 4 src/sim_farming.c | 21 src/statistics.c | 2 tests/testthat/test-initialise.R | 75 ++ tests/testthat/test-sim_farming.R | 227 ++++++ tests/testthat/test-stress.R |only vignettes/advanced_techniques.Rmd |only vignettes/evolutionary_algorithm.Rmd | 27 vignettes/resevol.Rmd | 933 +++++++++++++++---------- 60 files changed, 2874 insertions(+), 2240 deletions(-)
Title: Modelling of Extreme Values
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes [Dombry, Engelke and Oesting (2016) <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] ,
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut],
Scott D. Grimshaw [aut],
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb],
Raphael Huser [aut]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 1.15 dated 2023-04-20 and 1.16 dated 2023-11-30
DESCRIPTION | 7 MD5 | 174 - NAMESPACE | 2 NEWS.md | 15 R/RcppExports.R | 59 R/Wdiag.R | 26 R/automrl.R | 6 R/bias.R | 7 R/coefvariation.R | 14 R/datasets.R | 98 R/egp.R | 90 R/gp.R | 18 R/mgplikelihoods.R | 177 - R/multivar.R | 6 R/packageImports.R | 2 R/penultimate.R | 11 R/profile.R | 5043 ++++++++++++++++++++++++++--------------- R/rgparp.R | 156 - R/rmev.R | 148 - R/rparpcs.R | 127 - R/specdens.R | 1 R/tailindex.R |only R/threshold.R | 67 R/univdist.R | 132 - R/vartymetric.R | 10 build/partial.rdb |binary build/vignette.rds |binary data/frwind.rda |only data/nutrients.rda |only data/pandemics.rda |only inst/doc/mev-vignette.pdf |binary inst/include/mev_RcppExports.h | 20 man/PickandsXU.Rd |only man/W.diag.Rd | 26 man/angextrapo.Rd | 6 man/automrl.Rd | 6 man/clikmgp.Rd | 2 man/cvselect.Rd | 14 man/dot-fit.gpd.rob.Rd | 4 man/dot-gev.postpred.Rd | 5 man/dot-gpd_2D_fit.Rd | 2 man/dot-mvasym.check.Rd | 6 man/dot-rPBrownResnick.Rd | 2 man/dot-rPHuslerReiss.Rd | 2 man/dot-rPSmith.Rd | 2 man/dot-rPbilog.Rd | 2 man/dot-rPdir.Rd | 2 man/dot-rPdirmix.Rd | 2 man/dot-rPexstud.Rd | 6 man/dot-rPlog.Rd | 2 man/dot-rPneglog.Rd | 2 man/dot-rPsite.Rd | 10 man/dot-rdirspec.Rd | 2 man/dot-rexstudspec.Rd | 6 man/dot-rhrspec.Rd | 2 man/dot-rmevA1.Rd | 6 man/dot-rmevA2.Rd | 6 man/dot-rmevasy.Rd | 6 man/dot-rmevspec_cpp.Rd | 6 man/dot-wecdf.Rd | 2 man/egp2.fit.Rd | 2 man/expme.Rd | 2 man/fit.extgp.Rd | 2 man/frwind.Rd |only man/gev.Rd | 22 man/gev.pll.Rd | 38 man/gev.tem.Rd | 20 man/gevN.Rd | 12 man/gevr.Rd | 14 man/gpd.Rd | 22 man/gpd.ll.Rd | 2 man/gpd.pll.Rd | 42 man/gpd.tem.Rd | 20 man/gpdN.Rd | 12 man/gpde.Rd | 16 man/gpdr.Rd | 16 man/nutrients.Rd |only man/pandemics.Rd |only man/pp.Rd | 6 man/rgparp.Rd | 16 man/rlarg.Rd | 6 man/rmev.Rd | 8 man/rmevspec.Rd | 7 man/rparp.Rd | 18 man/rparpcs.Rd | 32 man/smith.penult.Rd | 11 man/tem.corr.Rd | 4 man/tstab.gpd.Rd | 9 man/vmetric.diag.Rd | 10 src/Makevars | 2 src/RcppExports.cpp | 150 - src/sampling.cpp | 115 92 files changed, 4647 insertions(+), 2544 deletions(-)
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP
<doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors'
package in the 'Monolix' installation, as described at the following url
<https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>.
When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
Chart Data instead of exporting it from the 'Monolix' gui.
Author: Amine Gassem [aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Matthew Fidler [aut, cre] ,
Seid Hamzic [aut],
Benjami [...truncated...]
Maintainer: Matthew Fidler <matt.fidler@novartis.com>
Diff between ggPMX versions 1.2.10 dated 2023-06-16 and 1.2.11 dated 2023-11-30
ggPMX-1.2.10/ggPMX/man/plot_pmx_gpar_real.Rd |only ggPMX-1.2.10/ggPMX/tests/testthat/_snaps |only ggPMX-1.2.11/ggPMX/DESCRIPTION | 18 ggPMX-1.2.11/ggPMX/MD5 | 191 ggPMX-1.2.11/ggPMX/NAMESPACE | 1 ggPMX-1.2.11/ggPMX/NEWS.md | 9 ggPMX-1.2.11/ggPMX/R/ggPMX-options.R | 2 ggPMX-1.2.11/ggPMX/R/ggPMX-package.R | 2 ggPMX-1.2.11/ggPMX/R/param_table.R | 2 ggPMX-1.2.11/ggPMX/R/plot-base.R | 29 ggPMX-1.2.11/ggPMX/R/plot-density.R | 24 ggPMX-1.2.11/ggPMX/R/plot-distribution.R | 22 ggPMX-1.2.11/ggPMX/R/plot-eta-cov.R | 6 ggPMX-1.2.11/ggPMX/R/plot-qq.R | 12 ggPMX-1.2.11/ggPMX/R/plot-residual.R | 14 ggPMX-1.2.11/ggPMX/R/plot-vpc.R | 76 ggPMX-1.2.11/ggPMX/R/pmx-reader.R | 42 ggPMX-1.2.11/ggPMX/R/pmxClass.R | 12 ggPMX-1.2.11/ggPMX/R/pmx_read_nm_model.R | 98 ggPMX-1.2.11/ggPMX/R/read_extfile.R | 74 ggPMX-1.2.11/ggPMX/build/vignette.rds |binary ggPMX-1.2.11/ggPMX/inst/doc/ggPMX-guide.R | 40 ggPMX-1.2.11/ggPMX/inst/doc/ggPMX-guide.Rmd | 144 ggPMX-1.2.11/ggPMX/inst/doc/ggPMX-guide.pdf |binary ggPMX-1.2.11/ggPMX/man/distrib.Rd | 20 ggPMX-1.2.11/ggPMX/man/eta_cov.Rd | 8 ggPMX-1.2.11/ggPMX/man/eta_pairs.Rd | 2 ggPMX-1.2.11/ggPMX/man/ggPMX.Rd | 36 ggPMX-1.2.11/ggPMX/man/individual.Rd | 2 ggPMX-1.2.11/ggPMX/man/param_table.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.Rd | 4 ggPMX-1.2.11/ggPMX/man/plot_pmx.distrib.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.eta_cov.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.eta_pairs.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.individual.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.pmx_dens.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.pmx_gpar.Rd |only ggPMX-1.2.11/ggPMX/man/plot_pmx.pmx_qq.Rd | 2 ggPMX-1.2.11/ggPMX/man/plot_pmx.residual.Rd | 2 ggPMX-1.2.11/ggPMX/man/pmxOptions.Rd | 2 ggPMX-1.2.11/ggPMX/man/pmx_dens.Rd | 24 ggPMX-1.2.11/ggPMX/man/pmx_qq.Rd | 12 ggPMX-1.2.11/ggPMX/man/pmx_read_nm_model.Rd | 18 ggPMX-1.2.11/ggPMX/man/pmx_settings.Rd | 2 ggPMX-1.2.11/ggPMX/man/pmx_vpc_ci.Rd | 16 ggPMX-1.2.11/ggPMX/man/pmx_vpc_pi.Rd | 28 ggPMX-1.2.11/ggPMX/man/read_extfile.Rd | 6 ggPMX-1.2.11/ggPMX/man/residual.Rd | 14 ggPMX-1.2.11/ggPMX/man/set_plot.Rd | 8 ggPMX-1.2.11/ggPMX/tests/testthat.R | 3 ggPMX-1.2.11/ggPMX/tests/testthat/helper-skip.R |only ggPMX-1.2.11/ggPMX/tests/testthat/helper-update_plots.R | 3 ggPMX-1.2.11/ggPMX/tests/testthat/test-2023table.R |only ggPMX-1.2.11/ggPMX/tests/testthat/test-assertions.R | 873 ++-- ggPMX-1.2.11/ggPMX/tests/testthat/test-config.R | 663 +-- ggPMX-1.2.11/ggPMX/tests/testthat/test-ggforce-facet-paginate.R | 92 ggPMX-1.2.11/ggPMX/tests/testthat/test-gpar.R | 355 - ggPMX-1.2.11/ggPMX/tests/testthat/test-nlmixr.R | 2 ggPMX-1.2.11/ggPMX/tests/testthat/test-nonmem_reader.R | 361 - ggPMX-1.2.11/ggPMX/tests/testthat/test-param_table.R | 205 ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-base.R | 120 ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-defaults.R | 47 ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-density.R | 315 - ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-distribution.R | 653 +-- ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-eta-pairs.R | 79 ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-individual.R | 651 +-- ggPMX-1.2.11/ggPMX/tests/testthat/test-plot-residual.R | 697 +-- ggPMX-1.2.11/ggPMX/tests/testthat/test-plot.R | 179 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-all-compute.R | 105 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-all-plots.R | 451 +- ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-plot-eta-cov.R | 175 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-plot-vpc.R | 437 +- ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-plots-distribution.R | 27 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-plots-scatter.R | 569 +- ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-post_load.R | 151 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-report.R | 819 +-- ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx-vpc-bin.R | 43 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmxClass.R | 2089 +++++----- ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_filter.R | 23 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_list_nm_tables.R | 311 - ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_manual_import.R | 151 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_nlmixr.R | 6 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_options.R | 127 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_read_nm_files.R | 139 ggPMX-1.2.11/ggPMX/tests/testthat/test-pmx_update.R | 209 - ggPMX-1.2.11/ggPMX/tests/testthat/test-reader.R | 562 +- ggPMX-1.2.11/ggPMX/tests/testthat/test-shrinkage.R | 69 ggPMX-1.2.11/ggPMX/tests/testthat/test-utils.R | 808 +-- ggPMX-1.2.11/ggPMX/tests/testthat/test-vdiff.R | 190 ggPMX-1.2.11/ggPMX/tests/testthat/warfarin_PD_project.zip |only ggPMX-1.2.11/ggPMX/vignettes/ggPMX-guide.Rmd | 144 91 files changed, 7035 insertions(+), 6904 deletions(-)
Title: Seamless Multicollinearity Management
Description: System for seamless management of multicollinearity in data frames
with numeric and/or categorical variables for statistical analysis and
machine learning modeling. The package combines bivariate correlation
(Pearson, Spearman, and Cramer's V) with variance inflation factor analysis,
target encoding to transform categorical variables into numeric (Micci-Barreca, D. 2001
<DOI:10.1145/507533.507538>), and a flexible
feature prioritization method, to deliver a comprehensive
multicollinearity management tool covering a wide range of use cases.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 1.0.1 dated 2023-10-24 and 1.1.0 dated 2023-11-30
collinear-1.0.1/collinear/man/f_rf_deviance.Rd |only collinear-1.0.1/collinear/tests/testthat/testthat-problems.rds |only collinear-1.1.0/collinear/DESCRIPTION | 21 collinear-1.1.0/collinear/LICENSE |only collinear-1.1.0/collinear/MD5 | 74 collinear-1.1.0/collinear/NAMESPACE | 9 collinear-1.1.0/collinear/NEWS.md | 47 collinear-1.1.0/collinear/R/collinear.R | 4 collinear-1.1.0/collinear/R/cor_df.R | 7 collinear-1.1.0/collinear/R/cor_select.R | 30 collinear-1.1.0/collinear/R/data.R | 51 collinear-1.1.0/collinear/R/globals.R | 3 collinear-1.1.0/collinear/R/identify.R | 1 collinear-1.1.0/collinear/R/preference_order.R | 534 +++++ collinear-1.1.0/collinear/R/target_encoding_lab.R | 77 collinear-1.1.0/collinear/R/target_encoding_methods.R | 181 + collinear-1.1.0/collinear/R/vif_df.R | 18 collinear-1.1.0/collinear/R/vif_select.R | 4 collinear-1.1.0/collinear/README.md | 981 +++++----- collinear-1.1.0/collinear/build/partial.rdb |binary collinear-1.1.0/collinear/data/toy.rda |only collinear-1.1.0/collinear/data/vi.rda |binary collinear-1.1.0/collinear/inst |only collinear-1.1.0/collinear/man/auc_score.Rd |only collinear-1.1.0/collinear/man/collinear-package.Rd | 2 collinear-1.1.0/collinear/man/collinear.Rd | 4 collinear-1.1.0/collinear/man/cor_select.Rd | 4 collinear-1.1.0/collinear/man/f_gam_auc_balanced.Rd |only collinear-1.1.0/collinear/man/f_gam_auc_unbalanced.Rd |only collinear-1.1.0/collinear/man/f_logistic_auc_balanced.Rd |only collinear-1.1.0/collinear/man/f_logistic_auc_unbalanced.Rd |only collinear-1.1.0/collinear/man/f_rf_auc_balanced.Rd |only collinear-1.1.0/collinear/man/f_rf_auc_unbalanced.Rd |only collinear-1.1.0/collinear/man/f_rf_rsquared.Rd |only collinear-1.1.0/collinear/man/internal.Rd |only collinear-1.1.0/collinear/man/preference_order.Rd | 13 collinear-1.1.0/collinear/man/target_encoding_lab.Rd | 19 collinear-1.1.0/collinear/man/target_encoding_methods.Rd | 16 collinear-1.1.0/collinear/man/toy.Rd |only collinear-1.1.0/collinear/man/vi.Rd | 2 collinear-1.1.0/collinear/tests/testthat/test-auc_score.R |only collinear-1.1.0/collinear/tests/testthat/test-case_weights.R |only collinear-1.1.0/collinear/tests/testthat/test-preference_order.R | 55 collinear-1.1.0/collinear/tests/testthat/test-target_encoding_lab.R | 1 collinear-1.1.0/collinear/tests/testthat/test-target_encoding_methods.R | 27 collinear-1.1.0/collinear/tests/testthat/test-vif_df.R | 5 46 files changed, 1503 insertions(+), 687 deletions(-)
Title: Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Description: Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Author: Carsten F. Dormann [aut, cre] ,
Jochen Fruend [aut] ,
Bernd Gruber [aut] ,
Stephen Beckett [ctb] ,
Mariano Devoto [ctb] ,
Gabriel M.F. Felix [ctb] ,
Jose M. Iriondo [ctb] ,
Tore Opsahl [ctb] ,
Rafael B.P. Pinheiro [ctb] ,
Rouven Strauss [ctb],
Diego [...truncated...]
Maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between bipartite versions 2.18 dated 2022-10-18 and 2.19 dated 2023-11-30
DESCRIPTION | 16 ++++----- MD5 | 36 ++++++++++----------- R/computeModules.R | 15 ++++---- R/czvalues.R | 2 - R/drawModules.R | 72 +++++++++++++++++++++--------------------- R/nestedness.R | 1 R/r2dexternal.R | 13 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 ++++++------ inst/doc/Intro2bipartite.R | 4 +- inst/doc/Intro2bipartite.Rnw | 8 ++-- inst/doc/Intro2bipartite.pdf |binary man/bipartite-package.Rd | 13 +++++-- man/r2dexternal.Rd | 2 + man/versionlog.Rd | 4 +- man/wine.rd | 2 - src/identifyModules.cc | 18 +++++----- vignettes/Intro2bipartite.Rnw | 8 ++-- 19 files changed, 125 insertions(+), 111 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2023) <doi:10.1093/jrsssc/qlad102>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 2.1-4 dated 2023-08-28 and 2.1-5 dated 2023-11-30
DESCRIPTION | 10 MD5 | 19 R/BayesSUR.R | 6 README.md |only build/vignette.rds |binary configure | 1484 ++++++++++++++++++++++++++++----------------- data/exampleGDSC.rda |binary inst/CITATION | 23 man/BayesSUR.Rd | 6 src/distr.cpp | 2 vignettes/BayesSUR-RE.Rmd |only vignettes/BayesSUR-RE.html |only 12 files changed, 989 insertions(+), 561 deletions(-)
Title: Poisson-Tweedie Exponential Family Models
Description: Simulation of models Poisson-Tweedie.
Author: David Pechel Cactcha, Laure Pauline Fotso and Celestin C
Kokonendji
Maintainer: David Pechel Cactcha <davidpechel@uy1.uninet.cm>
Diff between poistweedie versions 1.0.1 dated 2021-01-27 and 1.0.2 dated 2023-11-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/dpt2.R | 2 +- R/dptp.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Probabilities for Bivariate Normal Distribution
Description: Computes probabilities of the bivariate normal distribution
in a vectorized R function (Drezner & Wesolowsky, 1990,
<doi:10.1080/00949659008811236>).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between pbv versions 0.4-22 dated 2020-05-11 and 0.5-47 dated 2023-11-30
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/RcppExports.R | 4 ++-- README.md | 10 ++++------ build/partial.rdb |binary inst/CITATION | 5 +++-- inst/NEWS | 10 ++++++++-- man/pbvnorm.Rd | 6 +++--- src/RcppExports.cpp | 19 ++++++++++++------- 9 files changed, 46 insertions(+), 36 deletions(-)
Title: Read Hierarchical Fixed Width Files
Description: Read hierarchical fixed width files like those commonly used by
many census data providers. Also allows for reading of data in chunks,
and reading 'gzipped' files without storing the full file in memory.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Mark Padgham [ctb],
Hadley Wickham [ctb] ,
Jim Hester [ctb] ,
Romain Francois [ctb] ,
R Core Team [ctb] ,
RStudio [cph, fnd] ,
Jukka Jylaenki [ctb, cph] ,
Mikkel Joergensen [ctb, cph] [...truncated...]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between hipread versions 0.2.3 dated 2022-09-30 and 0.2.4 dated 2023-11-30
DESCRIPTION | 9 +++--- MD5 | 7 +++-- NEWS.md | 45 ++++++++++++++++++---------------- src/column.cpp | 2 - tests/testthat/test-coltype-warning.R |only 5 files changed, 33 insertions(+), 30 deletions(-)
Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded
'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] ,
Danny Smith [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between haven versions 2.5.3 dated 2023-06-30 and 2.5.4 dated 2023-11-30
DESCRIPTION | 10 +++++----- LICENSE | 4 ++-- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/semantics.R | 2 +- inst/doc/semantics.html | 38 +++++++++++++++++++------------------- man/figures/logo.png |binary man/haven-package.Rd | 2 +- src/DfReader.cpp | 2 +- src/cpp11.cpp | 6 +++--- 11 files changed, 46 insertions(+), 42 deletions(-)
Title: Your Friendly Solution to Managing Browser Cookies
Description: A convenient tool to store and format browser cookies and use them
in 'HTTP' requests (for example, through 'httr2', 'httr' or 'curl').
Author: Johannes B. Gruber [aut, cre]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between cookiemonster versions 0.0.2 dated 2023-11-13 and 0.0.3 dated 2023-11-30
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 4 ++++ R/set.r | 6 +++--- R/utils.r |only inst/WORDLIST | 5 +---- inst/doc/cookies.R | 2 +- inst/doc/cookies.html | 4 ++-- tests/testthat/test-get.R | 30 ++++++++++++++++++++++++++++++ tests/testthat/test-set.R | 1 + 10 files changed, 54 insertions(+), 21 deletions(-)
Title: Computer Algebra
Description: Computer algebra via the 'SymPy' library (<https://www.sympy.org/>).
This makes it possible to solve equations symbolically,
find symbolic integrals, symbolic sums and other important quantities.
Author: Mikkel Meyer Andersen [aut, cre, cph],
Soeren Hoejsgaard [aut, cph]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between caracas versions 2.1.0 dated 2023-10-17 and 2.1.1 dated 2023-11-30
DESCRIPTION | 6 +-- MD5 | 37 ++++++++++---------- NAMESPACE | 7 +++ NEWS.md | 8 ++++ R/Ops_math.R | 2 + R/expr_to_fun.R | 11 +++++ R/lin_alg_advanced.R | 72 ++++++++++++++++++++++++++++++++++++++- R/matrix_scaled.R | 47 ++++++++++++++++++++++--- R/output.R | 29 ++++++++------- R/parse_python.R | 39 ++++++++++++++++++++- R/sym_symbol.R | 2 + R/vector.R | 47 +++++++++++++++++++++++++ inst/doc/a11-linear-algebra.html | 2 - inst/doc/a21-ar-ssm.html | 2 - inst/doc/a91-sympy-object.html | 52 ++++++++++++++-------------- man/as_expr.Rd | 18 +++++++++ man/as_func.Rd | 10 +++++ man/cumsum.caracas_symbol.Rd |only man/do_la.Rd | 18 +++++++++ man/linalg.Rd | 12 ++++++ 20 files changed, 352 insertions(+), 69 deletions(-)
Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and
Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate
frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it
to estimate process completion times and encoding plus motor execution times next to the process probabilities
of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs
sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in
the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the
possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Henrik Singmann [ctb],
Jean Marie Linhart [ctb],
Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 1.0-0 dated 2022-04-10 and 1.0-1 dated 2023-11-30
DESCRIPTION | 10 MD5 | 22 R/SBC_fit_rtmpt.R | 2 R/get_infofile.R | 2 R/set_params.R | 8 R/set_resps.R | 2 build/vignette.rds |binary inst/CITATION | 14 inst/doc/rtmpt_guideline.html | 1212 +++++++++++++++++++++++++----------------- src/Makevars | 2 src/Makevars.win | 2 src/main.cpp | 2 12 files changed, 773 insertions(+), 505 deletions(-)
Title: R Bindings to 'hiredis'
Description: A 'hiredis' wrapper that includes support for
transactions, pipelining, blocking subscription, serialisation of
all keys and values, 'Redis' error handling with R errors.
Includes an automatically generated 'R6' interface to the full
'hiredis' API. Generated functions are faithful to the
'hiredis' documentation while attempting to match R's argument
semantics. Serialisation must be explicitly done by the user, but
both binary and text-mode serialisation is supported.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between redux versions 1.1.3 dated 2022-01-12 and 1.1.4 dated 2023-11-30
redux-1.1.3/redux/inst/doc/low_level.Rmd |only redux-1.1.3/redux/inst/doc/low_level.html |only redux-1.1.3/redux/src/connection.c.gcov |only redux-1.1.3/redux/src/connection.gcda |only redux-1.1.3/redux/src/connection.gcno |only redux-1.1.3/redux/src/conversions.c.gcov |only redux-1.1.3/redux/src/conversions.gcda |only redux-1.1.3/redux/src/conversions.gcno |only redux-1.1.3/redux/src/registration.c.gcov |only redux-1.1.3/redux/src/registration.gcda |only redux-1.1.3/redux/src/registration.gcno |only redux-1.1.3/redux/src/subscribe.c.gcov |only redux-1.1.3/redux/src/subscribe.gcda |only redux-1.1.3/redux/src/subscribe.gcno |only redux-1.1.3/redux/vignettes/low_level.Rmd |only redux-1.1.4/redux/DESCRIPTION | 6 +- redux-1.1.4/redux/MD5 | 31 ++--------- redux-1.1.4/redux/NEWS.md | 9 ++- redux-1.1.4/redux/README.md | 4 - redux-1.1.4/redux/build/vignette.rds |binary redux-1.1.4/redux/inst/doc/redux.html | 14 +++- redux-1.1.4/redux/src/conversions.c | 2 redux-1.1.4/redux/tests/testthat/test-conversions.R | 4 + redux-1.1.4/redux/tests/testthat/test-zzz-commands-generic.R | 4 + 24 files changed, 38 insertions(+), 36 deletions(-)
Title: Examples using 'RcppClassic' to Interface R and C++
Description: The 'Rcpp' package contains a C++ library that facilitates the
integration of R and C++ in various ways via a rich API. This API was
preceded by an earlier version which has been deprecated since 2010 (but is
still supported to provide backwards compatibility in the package
'RcppClassic'). This package 'RcppClassicExamples' provides usage examples for
the older, deprecated API. There is also a corresponding package
'RcppExamples' with examples for the newer, current API which we
strongly recommend as the basis for all new development.
Author: Dirk Eddelbuettel and Romain Francois, based on code written
during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppClassicExamples versions 0.1.2 dated 2018-03-15 and 0.1.3 dated 2023-11-30
ChangeLog | 28 ++++++++++++++++++++++++++++ DESCRIPTION | 12 +++++++----- MD5 | 22 +++++++++++----------- inst/NEWS.Rd | 9 ++++++++- src/Makevars | 3 +-- src/Makevars.win | 5 +---- src/classicRcppDateExample.cpp | 7 +++---- src/classicRcppExample.cpp | 7 +++---- src/classicRcppMatrixExample.cpp | 7 +++---- src/classicRcppParamsExample.cpp | 7 +++---- src/classicRcppStringVectorExample.cpp | 9 ++++----- src/classicRcppVectorExample.cpp | 7 +++---- 12 files changed, 75 insertions(+), 48 deletions(-)
More information about RcppClassicExamples at CRAN
Permanent link
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of sparse and dense matrix classes,
including general, symmetric, triangular, and diagonal matrices
with numeric, logical, or pattern entries. Efficient methods for
operating on such matrices, often wrapping the 'BLAS', 'LAPACK',
and 'SuiteSparse' libraries.
Author: Douglas Bates [aut] ,
Martin Maechler [aut, cre] ,
Mikael Jagan [aut] ,
Timothy A. Davis [ctb] )),
Jens Oehlschlaegel [ctb] ),
Jason Riedy [ctb] and onenormest, Copyright: Regents of the
University of California),
R Core Team [ctb]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.6-3 dated 2023-11-14 and 1.6-4 dated 2023-11-30
DESCRIPTION | 8 - MD5 | 40 ++--- R/zzz.R | 2 build/Matrix.pdf |binary build/stage23.rdb |binary inst/NEWS.Rd | 17 ++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/Matrix/cholmod-utils.h | 4 inst/include/Matrix/remap.h | 19 +- inst/include/Matrix/stubs.c | 25 +++ inst/include/Matrix/version.h | 4 src/chm_common.c | 282 +++++++++++++++++++++++++++++++++--- src/chm_common.h | 24 +-- src/init.c | 5 src/t_Csparse_subassign.c | 4 src/utils-R.c | 18 +- src/version.h | 4 21 files changed, 373 insertions(+), 83 deletions(-)
Title: Occurrence Data Cleaning
Description: Flags and checks occurrence data that are in Darwin Core
format. The package includes generic functions and data as well as
some that are specific to bees. This package is meant to build upon
and be complimentary to other excellent occurrence cleaning packages,
including 'bdc' and 'CoordinateCleaner'. This package uses datasets
from several sources and particularly from the Discover Life Website,
created by Ascher and Pickering (2020). For further information,
please see the original publication and package website. Publication
- Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package
website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.
Author: James B. Dorey [aut, cre, cph]
,
Robert L. O'Reilly [aut] ,
Silas Bossert [aut] ,
Erica E. Fischer [aut]
Maintainer: James B. Dorey <jbdorey@me.com>
Diff between BeeBDC versions 1.0.1 dated 2023-10-09 and 1.0.2 dated 2023-11-30
DESCRIPTION | 6 ++--- MD5 | 32 ++++++++++++++--------------- NEWS.md | 10 +++++++++ R/atlasDownloader.R | 50 +++++++++++++++++++++------------------------- R/beesChecklist.R | 10 ++++++--- R/beesTaxonomy.R | 9 ++++++-- R/countryOutliers.R | 6 +++-- R/nameSplitR.R | 12 +++++++++-- R/plotFlagSummary.R | 39 +++++++++++++++++++++++++++-------- R/taxoMergeR.R | 27 +++++++++++++++--------- README.md | 10 ++++++--- inst/CITATION | 4 +-- inst/doc/BeeBDC_main.html | 20 +++++++++--------- man/beesChecklist.Rd | 4 +++ man/beesTaxonomy.Rd | 7 ++++-- man/countryOutlieRs.Rd | 6 +++-- man/plotFlagSummary.Rd | 16 +++++++++++++- 17 files changed, 174 insertions(+), 94 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables.
An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables.
'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects).
The usual term to describe this model selection process is structure discovery.
The core functionality is concerned with model selection - deter [...truncated...]
Author: Matteo Delucchi [aut, cre] ,
Reinhard Furrer [aut] ,
Gilles Kratzer [aut] ,
Fraser Iain Lewis [aut] ,
Marta Pittavino [ctb] ,
Kalina Cherneva [ctb]
Maintainer: Matteo Delucchi <matteo.delucchi@math.uzh.ch>
Diff between abn versions 3.0.3 dated 2023-11-03 and 3.0.4 dated 2023-11-30
ChangeLog | 4 ++++ DESCRIPTION | 11 ++++++----- MD5 | 30 +++++++++++++++--------------- R/calc_node_inla_glmm.R | 2 -- README.md | 10 ++++++---- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- src/node_binomial_marginals_rv.c | 15 ++++++++++----- src/node_binomial_rv.c | 21 ++++++++++++--------- src/node_binomial_rv_inner.c | 8 +++++--- src/node_gaussian_marginals_rv.c | 12 +++++++++--- src/node_gaussian_rv.c | 34 ++++++++++++++++++++++++---------- src/node_gaussian_rv_inner.c | 28 ++++++++++++++-------------- src/node_poisson_marginals_rv.c | 10 ++++++++-- src/node_poisson_rv.c | 18 +++++++++++++----- 16 files changed, 136 insertions(+), 87 deletions(-)
Title: Copula-Based Mixed Regression Models
Description: Estimation of 2-level factor copula-based regression models for clustered data where the response variable can be either discrete or continuous.
Author: Pavel Krupskii [aut, ctb, cph],
Bouchra R. Nasri [aut, ctb, cph],
Bruno N Remillard [aut, cre, cph]
Maintainer: Bruno N Remillard <bruno.remillard@hec.ca>
Diff between CopulaGAMM versions 0.3.0 dated 2023-06-07 and 0.4.1 dated 2023-11-30
CopulaGAMM-0.3.0/CopulaGAMM/data/poisson.rda |only CopulaGAMM-0.3.0/CopulaGAMM/man/poisson.Rd |only CopulaGAMM-0.4.1/CopulaGAMM/DESCRIPTION | 6 +- CopulaGAMM-0.4.1/CopulaGAMM/MD5 | 40 ++++++------- CopulaGAMM-0.4.1/CopulaGAMM/R/EstContinuous.R | 21 +++++-- CopulaGAMM-0.4.1/CopulaGAMM/R/EstDiscrete.R | 63 +++++++++++++++------ CopulaGAMM-0.4.1/CopulaGAMM/R/MAP.continuous.R | 18 ++++-- CopulaGAMM-0.4.1/CopulaGAMM/R/MAP.discrete.R | 23 +++++-- CopulaGAMM-0.4.1/CopulaGAMM/R/SimGenCluster.R | 19 ++++-- CopulaGAMM-0.4.1/CopulaGAMM/R/coplik.R | 29 +++++++-- CopulaGAMM-0.4.1/CopulaGAMM/R/invfunc.R | 21 ++++--- CopulaGAMM-0.4.1/CopulaGAMM/R/margins.R | 4 - CopulaGAMM-0.4.1/CopulaGAMM/R/predictDiscrete.R | 19 +++++- CopulaGAMM-0.4.1/CopulaGAMM/R/qcond.R | 37 ++++++++---- CopulaGAMM-0.4.1/CopulaGAMM/data/out.poisson.rda |binary CopulaGAMM-0.4.1/CopulaGAMM/data/sim.poisson.rda |only CopulaGAMM-0.4.1/CopulaGAMM/man/EstDiscrete.Rd | 23 ++++--- CopulaGAMM-0.4.1/CopulaGAMM/man/MAP.discrete.Rd | 4 - CopulaGAMM-0.4.1/CopulaGAMM/man/SimGenCluster.Rd | 2 CopulaGAMM-0.4.1/CopulaGAMM/man/invfunc.Rd | 4 + CopulaGAMM-0.4.1/CopulaGAMM/man/multinomcpdf.Rd | 4 - CopulaGAMM-0.4.1/CopulaGAMM/man/predictDiscrete.Rd | 3 - CopulaGAMM-0.4.1/CopulaGAMM/man/sim.poisson.Rd |only 23 files changed, 228 insertions(+), 112 deletions(-)
Title: Bootstrapping the ARDL Tests for Cointegration
Description: The bootstrap ARDL tests for cointegration is the main functionality of this package. It also acts as a wrapper of the most commond ARDL testing procedures for cointegration: the bound tests of Pesaran, Shin and Smith (PSS; 2001 - <doi:10.1002/jae.616>) and the asymptotic test on the independent variables of Sam, McNown and Goh (SMG: 2019 - <doi:10.1016/j.econmod.2018.11.001>). Bootstrap and bound tests are performed under both the conditional and unconditional ARDL models.
Author: Gianmarco Vacca, Stefano Bertelli
Maintainer: Gianmarco Vacca <gianmarco.vacca@unicatt.it>
Diff between bootCT versions 1.1.1 dated 2022-09-27 and 2.0.0 dated 2023-11-30
bootCT-1.1.1/bootCT/R/gen_boot_ardl.R |only bootCT-1.1.1/bootCT/R/ger_macro.R |only bootCT-1.1.1/bootCT/man/gen_boot_ardl.Rd |only bootCT-2.0.0/bootCT/DESCRIPTION | 12 bootCT-2.0.0/bootCT/MD5 | 35 +- bootCT-2.0.0/bootCT/NAMESPACE | 10 bootCT-2.0.0/bootCT/R/RcppExports.R | 2 bootCT-2.0.0/bootCT/R/boot_ardl.R | 507 ++++++++++++++++-------------- bootCT-2.0.0/bootCT/R/sim_vecm_ardl.R | 148 ++++---- bootCT-2.0.0/bootCT/R/smk_crit.R | 2 bootCT-2.0.0/bootCT/R/summary_bootCT.R | 324 ++++++++++++++----- bootCT-2.0.0/bootCT/R/sysdata.rda |binary bootCT-2.0.0/bootCT/data/ita_macro.rda |only bootCT-2.0.0/bootCT/man/boot_ardl.Rd | 57 ++- bootCT-2.0.0/bootCT/man/ger_macro.Rd | 56 +-- bootCT-2.0.0/bootCT/man/ita_macro.Rd |only bootCT-2.0.0/bootCT/man/sim_vecm_ardl.Rd | 46 +- bootCT-2.0.0/bootCT/man/summary.bootCT.Rd | 4 bootCT-2.0.0/bootCT/src/Makevars | 11 bootCT-2.0.0/bootCT/src/Makevars.win | 11 bootCT-2.0.0/bootCT/src/boot_ardl_c.cpp | 27 - 21 files changed, 746 insertions(+), 506 deletions(-)
Title: Easily Install and Load 'tesselle' Packages
Description: Easy install and load key packages from the 'tesselle' suite
in a single step. The 'tesselle' suite is a collection of packages for
research and teaching in archaeology. These packages focus on
quantitative analysis methods developed for archaeology. The
'tesselle' packages are designed to work seamlessly together and to
complement general-purpose and other specialized statistical packages.
These packages can be used to explore and analyze common data types in
archaeology: count data, compositional data and chronological data.
Learn more about 'tesselle' at <https://www.tesselle.org>.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tesselle versions 1.3.0 dated 2023-10-18 and 1.4.0 dated 2023-11-30
DESCRIPTION | 19 ++++++++++++------- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/attach.R | 2 +- R/tesselle-package.R | 5 +++-- README.md | 16 ++++++++-------- man/tesselle-package.Rd | 2 +- 7 files changed, 38 insertions(+), 25 deletions(-)
Title: Antigenic Cartography Macros
Description: A toolkit for making antigenic maps from immunological assay data,
in order to quantify and visualize antigenic differences between different
pathogen strains as described in
Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World
Health Organization influenza vaccine strain selection process. Additional
functions allow for the diagnostic evaluation of antigenic maps and an
interactive viewer is provided to explore antigenic relationships amongst
several strains and incorporate the visualization of associated genetic
information.
Author: Sam Wilks [aut, cre]
Maintainer: Sam Wilks <sw463@cam.ac.uk>
Diff between Racmacs versions 1.2.8 dated 2023-11-23 and 1.2.9 dated 2023-11-30
DESCRIPTION | 8 MD5 | 38 +-- NEWS.md | 372 ++++++++++++++++---------------- inst/doc/adding-sequences.R | 3 inst/doc/adding-sequences.Rmd | 3 inst/doc/adding-sequences.html | 10 inst/doc/comparing-maps.R | 3 inst/doc/comparing-maps.Rmd | 3 inst/doc/comparing-maps.html | 16 - inst/doc/making-a-map-from-scratch.R | 3 inst/doc/making-a-map-from-scratch.Rmd | 3 inst/doc/making-a-map-from-scratch.html | 10 src/ac_titers.cpp | 2 src/utils_error.cpp | 4 src/utils_progress.h | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-view_map.R | 3 vignettes/adding-sequences.Rmd | 3 vignettes/comparing-maps.Rmd | 3 vignettes/making-a-map-from-scratch.Rmd | 3 20 files changed, 253 insertions(+), 239 deletions(-)
Title: A Simple Author Handler for Scientific Writing
Description: Handles and formats author information in scientific writing
in 'R Markdown' and 'Quarto'. 'plume' provides easy-to-use and
flexible tools for injecting author metadata in 'YAML' headers as well
as generating author and contribution lists (among others) as strings
from tabular data.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between plume versions 0.1.0 dated 2023-10-06 and 0.2.0 dated 2023-11-30
plume-0.1.0/plume/LICENSE.note |only plume-0.1.0/plume/R/strings.R |only plume-0.1.0/plume/inst/doc/using-credit-roles.R |only plume-0.1.0/plume/inst/doc/using-credit-roles.Rmd |only plume-0.1.0/plume/inst/doc/using-credit-roles.html |only plume-0.1.0/plume/man/StatusSetterQuarto.Rd |only plume-0.1.0/plume/vignettes/using-credit-roles.Rmd |only plume-0.2.0/plume/DESCRIPTION | 23 plume-0.2.0/plume/MD5 | 142 - plume-0.2.0/plume/NAMESPACE | 17 plume-0.2.0/plume/NEWS.md | 70 plume-0.2.0/plume/R/aaa.R | 29 plume-0.2.0/plume/R/als.R | 10 plume-0.2.0/plume/R/checkers.R | 47 plume-0.2.0/plume/R/context-binder.R | 15 plume-0.2.0/plume/R/context-selectors.R |only plume-0.2.0/plume/R/credit_roles.R |only plume-0.2.0/plume/R/data-encyclopedists.R | 8 plume-0.2.0/plume/R/enumerate.R | 2 plume-0.2.0/plume/R/plm-template.R | 60 plume-0.2.0/plume/R/plume-handler.R | 82 plume-0.2.0/plume/R/plume-package.R | 13 plume-0.2.0/plume/R/plume-quarto.R | 34 plume-0.2.0/plume/R/plume.R | 56 plume-0.2.0/plume/R/sequential.R | 6 plume-0.2.0/plume/R/set-default-names.R | 5 plume-0.2.0/plume/R/status-setter.R | 178 - plume-0.2.0/plume/R/utils-list.R | 4 plume-0.2.0/plume/R/utils-tbl.R | 35 plume-0.2.0/plume/R/utils.R | 71 plume-0.2.0/plume/R/yaml.R | 7 plume-0.2.0/plume/README.md | 58 plume-0.2.0/plume/build/vignette.rds |binary plume-0.2.0/plume/data/encyclopedists.rda |binary plume-0.2.0/plume/data/encyclopedists_fr.rda |binary plume-0.2.0/plume/inst/doc/plume.R | 138 - plume-0.2.0/plume/inst/doc/plume.Rmd | 200 - plume-0.2.0/plume/inst/doc/plume.html | 1319 ++++++---- plume-0.2.0/plume/inst/doc/working-in-other-languages.html | 14 plume-0.2.0/plume/man/Plume.Rd | 28 plume-0.2.0/plume/man/PlumeHandler.Rd | 11 plume-0.2.0/plume/man/PlumeQuarto.Rd | 31 plume-0.2.0/plume/man/StatusSetter.Rd | 16 plume-0.2.0/plume/man/StatusSetterPlume.Rd |only plume-0.2.0/plume/man/StatusSetterPlumeQuarto.Rd |only plume-0.2.0/plume/man/credit_roles.Rd |only plume-0.2.0/plume/man/encyclopedists.Rd | 8 plume-0.2.0/plume/man/enumerate.Rd | 2 plume-0.2.0/plume/man/everyone.Rd | 23 plume-0.2.0/plume/man/figures |only plume-0.2.0/plume/man/plm_template.Rd | 18 plume-0.2.0/plume/man/plume-package.Rd | 5 plume-0.2.0/plume/man/sequential.Rd | 3 plume-0.2.0/plume/man/set_default_names.Rd | 2 plume-0.2.0/plume/tests/testthat/_snaps/credit-roles.md |only plume-0.2.0/plume/tests/testthat/_snaps/get-contact-details.md | 22 plume-0.2.0/plume/tests/testthat/_snaps/get-contributions.md | 20 plume-0.2.0/plume/tests/testthat/_snaps/initialize.md | 95 plume-0.2.0/plume/tests/testthat/_snaps/plm-template.md | 21 plume-0.2.0/plume/tests/testthat/_snaps/set-default-names.md | 19 plume-0.2.0/plume/tests/testthat/_snaps/set-main-contributors.md |only plume-0.2.0/plume/tests/testthat/_snaps/set-status.md | 63 plume-0.2.0/plume/tests/testthat/_snaps/to-yaml.md | 68 plume-0.2.0/plume/tests/testthat/helper-plume.R | 46 plume-0.2.0/plume/tests/testthat/test-credit-roles.R |only plume-0.2.0/plume/tests/testthat/test-get-author-list.R | 27 plume-0.2.0/plume/tests/testthat/test-get-contact-details.R | 31 plume-0.2.0/plume/tests/testthat/test-get-contributions.R | 106 plume-0.2.0/plume/tests/testthat/test-get-footnotes.R | 34 plume-0.2.0/plume/tests/testthat/test-get-orcids.R | 4 plume-0.2.0/plume/tests/testthat/test-initialize.R | 149 - plume-0.2.0/plume/tests/testthat/test-plm-template.R | 44 plume-0.2.0/plume/tests/testthat/test-set-default-names.R | 6 plume-0.2.0/plume/tests/testthat/test-set-main-contributors.R |only plume-0.2.0/plume/tests/testthat/test-set-status.R | 55 plume-0.2.0/plume/tests/testthat/test-to-yaml.R | 47 plume-0.2.0/plume/vignettes/plume.Rmd | 200 - 77 files changed, 2540 insertions(+), 1307 deletions(-)
Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept
analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23>
and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It
provides functions to load and save a formal context, extract its
concept lattice and implications. In addition, one can use the
implications to compute semantic closures of fuzzy sets and, thus,
build recommendation systems.
Author: Domingo Lopez Rodriguez [aut, cre]
,
Angel Mora [aut],
Jesus Dominguez [aut],
Ana Villalon [aut],
Ian Johnson [ctb]
Maintainer: Domingo Lopez Rodriguez <dominlopez@uma.es>
Diff between fcaR versions 1.2.1 dated 2023-04-27 and 1.2.2 dated 2023-11-30
fcaR-1.2.1/fcaR/man/fcaR.Rd |only fcaR-1.2.2/fcaR/DESCRIPTION | 20 - fcaR-1.2.2/fcaR/MD5 | 57 ++-- fcaR-1.2.2/fcaR/NAMESPACE | 1 fcaR-1.2.2/fcaR/NEWS.md | 12 + fcaR-1.2.2/fcaR/R/Rsimplification.R | 49 ++-- fcaR-1.2.2/fcaR/R/fcaR-package.R | 8 fcaR-1.2.2/fcaR/R/formal_context.R | 53 ++-- fcaR-1.2.2/fcaR/R/implication_set.R | 4 fcaR-1.2.2/fcaR/R/options.R | 2 fcaR-1.2.2/fcaR/R/plot_context.R | 43 +++ fcaR-1.2.2/fcaR/R/scaling.R | 26 +- fcaR-1.2.2/fcaR/README.md | 12 - fcaR-1.2.2/fcaR/inst/doc/arules.R | 2 fcaR-1.2.2/fcaR/inst/doc/concept_lattice.R | 2 fcaR-1.2.2/fcaR/inst/doc/concept_lattice.html | 4 fcaR-1.2.2/fcaR/inst/doc/conceptual-scaling.R | 2 fcaR-1.2.2/fcaR/inst/doc/conceptual-scaling.html | 213 ++++++++++-------- fcaR-1.2.2/fcaR/inst/doc/extending_equivalence.R | 2 fcaR-1.2.2/fcaR/inst/doc/extending_equivalence.html | 18 - fcaR-1.2.2/fcaR/inst/doc/implications.R | 2 fcaR-1.2.2/fcaR/inst/doc/implications.html | 10 fcaR-1.2.2/fcaR/man/FormalContext.Rd | 2 fcaR-1.2.2/fcaR/man/fcaR-package.Rd |only fcaR-1.2.2/fcaR/man/fcaR_options.Rd | 2 fcaR-1.2.2/fcaR/src/nextclosure.cpp | 13 - fcaR-1.2.2/fcaR/tests/testthat/Rplots.pdf |binary fcaR-1.2.2/fcaR/tests/testthat/test-concept_lattice.R | 50 +++- fcaR-1.2.2/fcaR/tests/testthat/test-formal_context.R | 73 ++++++ fcaR-1.2.2/fcaR/tests/testthat/test-implication_set.R | 17 + fcaR-1.2.2/fcaR/tests/testthat/test.tex |only 31 files changed, 465 insertions(+), 234 deletions(-)
Title: Easily Access and Maintain Time-Based Versioned Data
(Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time.
More specifically, the package facilitates type-2 history for data-warehouses and provides a number
of Quality of life improvements for working on SQL databases with R.
For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut] ,
Marcus Munch Gruenewald [aut, cre]
Maintainer: Marcus Munch Gruenewald <mmgr@ssi.dk>
Diff between SCDB versions 0.2 dated 2023-09-26 and 0.2.1 dated 2023-11-30
SCDB-0.2.1/SCDB/DESCRIPTION | 24 SCDB-0.2.1/SCDB/MD5 | 130 - SCDB-0.2.1/SCDB/NAMESPACE | 11 SCDB-0.2.1/SCDB/NEWS.md | 16 SCDB-0.2.1/SCDB/R/Logger.R | 36 SCDB-0.2.1/SCDB/R/SCDB-package.R | 18 SCDB-0.2.1/SCDB/R/connection.R | 14 SCDB-0.2.1/SCDB/R/create_table.R | 3 SCDB-0.2.1/SCDB/R/db_joins.R | 568 ++-- SCDB-0.2.1/SCDB/R/db_manipulating_functions.R | 54 SCDB-0.2.1/SCDB/R/db_timestamps.R | 81 SCDB-0.2.1/SCDB/R/digest_to_checksum.R | 172 - SCDB-0.2.1/SCDB/R/get_schema.R | 80 SCDB-0.2.1/SCDB/R/get_table.R | 85 SCDB-0.2.1/SCDB/R/helpers.R | 236 - SCDB-0.2.1/SCDB/README.md | 4 SCDB-0.2.1/SCDB/build/vignette.rds |binary SCDB-0.2.1/SCDB/inst/WORDLIST | 2 SCDB-0.2.1/SCDB/inst/doc/basic-principles.R |only SCDB-0.2.1/SCDB/inst/doc/basic-principles.Rmd |only SCDB-0.2.1/SCDB/inst/doc/basic-principles.html |only SCDB-0.2.1/SCDB/inst/doc/slowly-changing-dimension.R |only SCDB-0.2.1/SCDB/inst/doc/slowly-changing-dimension.Rmd |only SCDB-0.2.1/SCDB/inst/doc/slowly-changing-dimension.html |only SCDB-0.2.1/SCDB/man/Logger.Rd | 11 SCDB-0.2.1/SCDB/man/SCDB-package.Rd | 4 SCDB-0.2.1/SCDB/man/close_connection.Rd | 44 SCDB-0.2.1/SCDB/man/create_logs_if_missing.Rd | 3 SCDB-0.2.1/SCDB/man/create_table.Rd | 64 SCDB-0.2.1/SCDB/man/db_timestamp.Rd | 67 SCDB-0.2.1/SCDB/man/digest_to_checksum.Rd | 54 SCDB-0.2.1/SCDB/man/figures/SCDB-logo.svg | 1216 ++++------ SCDB-0.2.1/SCDB/man/figures/logo.png |binary SCDB-0.2.1/SCDB/man/filter_keys.Rd | 82 SCDB-0.2.1/SCDB/man/get_connection.Rd | 116 SCDB-0.2.1/SCDB/man/get_schema.Rd | 8 SCDB-0.2.1/SCDB/man/get_table.Rd | 4 SCDB-0.2.1/SCDB/man/get_tables.Rd | 52 SCDB-0.2.1/SCDB/man/grapes-notin-grapes.Rd | 48 SCDB-0.2.1/SCDB/man/id.Rd | 5 SCDB-0.2.1/SCDB/man/interlace_sql.Rd | 25 SCDB-0.2.1/SCDB/man/is.historical.Rd | 56 SCDB-0.2.1/SCDB/man/joins.Rd | 206 - SCDB-0.2.1/SCDB/man/nrow.Rd | 50 SCDB-0.2.1/SCDB/man/schema_exists.Rd | 54 SCDB-0.2.1/SCDB/man/slice_time.Rd | 82 SCDB-0.2.1/SCDB/man/table_exists.Rd | 6 SCDB-0.2.1/SCDB/man/unite.tbl_dbi.Rd | 94 SCDB-0.2.1/SCDB/man/update_snapshot.Rd | 118 SCDB-0.2.1/SCDB/tests/spelling.R | 6 SCDB-0.2.1/SCDB/tests/testthat.R | 26 SCDB-0.2.1/SCDB/tests/testthat/setup.R | 8 SCDB-0.2.1/SCDB/tests/testthat/test-Logger.R | 27 SCDB-0.2.1/SCDB/tests/testthat/test-connection.R | 26 SCDB-0.2.1/SCDB/tests/testthat/test-create_table.R | 40 SCDB-0.2.1/SCDB/tests/testthat/test-db_functions.R | 8 SCDB-0.2.1/SCDB/tests/testthat/test-db_joins.R | 270 +- SCDB-0.2.1/SCDB/tests/testthat/test-db_manipulating_functions.R | 366 +-- SCDB-0.2.1/SCDB/tests/testthat/test-db_timestamp.R | 40 SCDB-0.2.1/SCDB/tests/testthat/test-get_schema.R | 4 SCDB-0.2.1/SCDB/tests/testthat/test-get_table.R | 15 SCDB-0.2.1/SCDB/tests/testthat/test-helpers.R | 24 SCDB-0.2.1/SCDB/tests/testthat/test-non_ascii.R | 82 SCDB-0.2.1/SCDB/tests/testthat/test-rd-files.R |only SCDB-0.2.1/SCDB/tests/testthat/test-update_snapshot.R | 2 SCDB-0.2.1/SCDB/vignettes/basic-principles.Rmd |only SCDB-0.2.1/SCDB/vignettes/references.bib |only SCDB-0.2.1/SCDB/vignettes/slowly-changing-dimension.Rmd |only SCDB-0.2/SCDB/inst/doc/basic_principles.R |only SCDB-0.2/SCDB/inst/doc/basic_principles.Rmd |only SCDB-0.2/SCDB/inst/doc/basic_principles.html |only SCDB-0.2/SCDB/tests/testthat/test-examples.R |only SCDB-0.2/SCDB/tests/testthat/test-return.R |only SCDB-0.2/SCDB/vignettes/basic_principles.Rmd |only 74 files changed, 2591 insertions(+), 2356 deletions(-)
Title: Consensus Pathway Analysis
Description: Provides a set of functions to perform pathway analysis and meta analysis from multiple gene expression datasets, as well as visualization of the results. The package is a wrapper of the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu, Z. (2012) <https://CRAN.R-project.org/package=CePa>.
Author: Ha Nguyen [aut, cre],
Zeynab Maghsoudi [aut],
Phi Hung Bya [aut],
Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006@auburn.edu>
Diff between RCPA versions 0.1.2 dated 2023-11-21 and 0.2.1 dated 2023-11-30
DESCRIPTION | 10 MD5 | 46 +-- NAMESPACE | 5 R/DE-analysis.R | 11 R/GEO-download.R | 584 +++++++++++++++++++++++----------------------- R/annotation.R | 57 +++- R/common-de.R | 2 R/common-sigPath.R | 2 R/geneset-analysis.R | 1 R/genesets.R | 35 ++ R/pathway-analysis.R | 4 R/plot-KEGG-map.R | 2 R/utils.R | 34 ++ inst/doc/RCPA.R | 36 ++ inst/doc/RCPA.Rmd | 81 ++++-- inst/doc/RCPA.html | 71 +++-- man/downloadGEO.Rd | 27 -- man/getCommonDEGenes.Rd | 2 man/getCommonPathways.Rd | 2 man/loadData.Rd | 1 man/processAffymetrix.Rd |only man/processAgilent.Rd |only man/runDEAnalysis.Rd | 11 man/runGeneSetAnalysis.Rd | 1 vignettes/RCPA.Rmd | 81 ++++-- 25 files changed, 670 insertions(+), 436 deletions(-)
Title: Interface allowing R to use OpenCL
Description: This package provides an interface to OpenCL, allowing R to leverage computing power of GPUs and other HPC accelerator devices.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Aaron Puchert <aaronpuchert@alice-dsl.net>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between OpenCL versions 0.2-2 dated 2021-07-24 and 0.2-9 dated 2023-11-30
DESCRIPTION | 8 +- INSTALL | 52 ++++++++++++++++- MD5 | 44 ++++++++------- NAMESPACE | 9 ++- NEWS | 57 +++++++++++++++++++ R/clBuffer.R | 63 ++++++++++++++------- R/clLocal.R |only R/ocl.R | 56 ++++++++++++------- configure.win | 26 +++++++- man/clBuffer.Rd | 33 ++++++++--- man/clLocal.Rd |only man/oclDevices.Rd | 3 - man/oclMemLimits.Rd |only man/oclRun.Rd | 18 +++--- src/Makevars | 14 ++++ src/buffer.c | 142 ++++++++++++++++++++++++++++++++++++++++--------- src/c.h | 4 + src/ocl.c | 111 +++++++++++++++++++++++++++++++------- src/ocl.h | 7 ++ src/oclerr.c |only src/reg.c | 3 + src/wrap.c | 118 +++++++++++++++++++++++++++++++++++++++- tests/buffer.R | 26 +++++++- tests/buffer.Rout.save | 48 +++++++++++++--- tests/kernel.Rout.save | 14 +--- 25 files changed, 688 insertions(+), 168 deletions(-)
Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn'
package implements an efficient data structure for storing medical
records, and provides a set of functions for data extraction,
manipulation and analysis.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Ben Gilat [aut],
Netta Mendelson-Cohen [ctb],
Rami Jaschek [ctb],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between naryn versions 2.6.23 dated 2023-08-17 and 2.6.25 dated 2023-11-30
DESCRIPTION | 6 +++--- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 10 ++++++++++ R/extract.R | 3 ++- R/filter.R | 4 ++-- R/track-vars.R | 5 +++-- R/vtrack.R | 6 +----- README.md | 1 + inst/WORDLIST | 1 + man/emr_cor.Rd | 3 ++- man/emr_dist.Rd | 3 ++- man/emr_extract.Rd | 3 ++- man/emr_filter.name.Rd | 2 +- man/emr_quantiles.Rd | 3 ++- man/emr_screen.Rd | 3 ++- man/emr_summary.Rd | 3 ++- man/emr_track.create.Rd | 3 ++- man/emr_vtrack.name.Rd | 2 +- src/naryn.cpp | 6 +++--- tests/spelling.R | 9 +++------ tests/testthat/test-vtrack.R | 6 ++++-- 21 files changed, 69 insertions(+), 53 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph]
,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Julien Ruffault [ctb],
Francois Pimont [ctb] ,
Herve Cochard [ctb] ,
Aitor Amezte [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 3.1.4 dated 2023-08-29 and 3.2.0 dated 2023-11-30
DESCRIPTION | 8 - MD5 | 71 +++++------ R/RcppExports.R | 16 ++ R/defaultControl.R | 8 - R/droughtStress.R | 10 - R/extractSubdaily.R | 18 -- R/fordyn.R | 25 +++- R/forest.R | 9 - R/hydraulics_vulnerabilityCurvePlot.R | 201 +++++++++++++++++++++------------ R/plot.spwb.R | 52 ++++---- R/plot.spwb_day.R | 100 +++++++++------- R/plot_internals.R | 25 +++- R/regeneration.R | 142 ++++++++++++++++++----- build/partial.rdb |binary data/SpParamsDefinition.rda |binary data/SpParamsMED.rda |binary man/defaultControl.Rd | 5 man/droughtStress.Rd | 10 - man/extractSubdaily.Rd | 2 man/forest.Rd | 8 - man/hydraulics_conductancefunctions.Rd | 3 man/hydraulics_supplyfunctions.Rd | 3 man/plot.spwb.Rd | 50 ++++---- man/plot.spwb_day.Rd | 83 ++++++------- man/regeneration.Rd | 45 +++++-- man/sureau_ecos.Rd | 10 + src/RcppExports.cpp | 111 ++++++++++-------- src/inner_cochard.cpp | 71 +++++++---- src/inner_sperry.cpp | 35 +++++ src/modelInput.cpp | 12 - src/paramutils.cpp | 43 ++++++- src/spwb.cpp | 27 ++-- src/transpiration_advanced.cpp | 5 tests/testthat/Rplots.pdf |only tests/testthat/test_post_processing.R | 3 tests/testthat/test_pre_processing.R | 6 tests/testthat/test_spwb.R | 6 37 files changed, 798 insertions(+), 425 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre]
,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 6.1.1 dated 2023-10-13 and 6.1.3 dated 2023-11-30
DESCRIPTION | 8 MD5 | 33 +- NAMESPACE | 2 NEWS.md | 27 ++ R/RcppExports.R | 111 ++++++++ R/datamanag.R | 86 ++++-- R/popdyn.R | 2 build/vignette.rds |binary man/create_lM.Rd | 14 - man/ltre3.Rd | 2 man/markov_run.Rd |only man/mpm_create.Rd | 4 src/DataManagement.cpp | 57 +--- src/ExtraFunctions.cpp | 12 src/MatsNProj.cpp | 532 ++++++++++++++++++++++++++------------- src/PopChar.cpp | 659 ++++++++++++++++++++++++------------------------- src/PopDyn2.cpp | 21 + src/RcppExports.cpp | 15 + 18 files changed, 987 insertions(+), 598 deletions(-)
Title: An R Package for Factor Model Asset Pricing
Description: Functions for evaluating and testing asset pricing models, including
estimation and testing of factor risk premia, selection of "strong" risk
factors (factors having nonzero population correlation with test asset
returns), heteroskedasticity and autocorrelation robust covariance matrix
estimation and testing for model misspecification and identification.
The functions for estimating and testing factor risk
premia implement the Fama-MachBeth (1973) <doi:10.1086/260061> two-pass
approach, the misspecification-robust approaches of Kan-Robotti-Shanken (2013)
<doi:10.1111/jofi.12035>, and the approaches based on tradable factor risk
premia of Quaini-Trojani-Yuan (2023) <doi:10.2139/ssrn.4574683>. The
functions for selecting the "strong" risk factors are based on the Oracle
estimator of Quaini-Trojani-Yuan (2023) <doi:10.2139/ssrn.4574683> and the
factor screening procedure of Gospodinov-Kan-Robotti (2014) <doi:10.2139/ssrn.2579821>.
The functions for evaluating [...truncated...]
Author: Alberto Quaini [aut, cre, cph]
Maintainer: Alberto Quaini <alberto91quaini@gmail.com>
Diff between intrinsicFRP versions 1.0.0 dated 2023-09-18 and 2.0.0 dated 2023-11-30
intrinsicFRP-1.0.0/intrinsicFRP/R/identification_test.R |only intrinsicFRP-1.0.0/intrinsicFRP/R/misspecification_test.R |only intrinsicFRP-1.0.0/intrinsicFRP/man/HJMisspecificationTest.Rd |only intrinsicFRP-1.0.0/intrinsicFRP/src/hac_standard_errors.cpp |only intrinsicFRP-1.0.0/intrinsicFRP/src/hac_standard_errors.h |only intrinsicFRP-1.0.0/intrinsicFRP/src/identification_test.cpp |only intrinsicFRP-1.0.0/intrinsicFRP/src/misspecification_tests.cpp |only intrinsicFRP-1.0.0/intrinsicFRP/src/misspecification_tests.h |only intrinsicFRP-1.0.0/intrinsicFRP/tests/testthat/test-identification_test.R |only intrinsicFRP-1.0.0/intrinsicFRP/tests/testthat/test-misspecification_test.R |only intrinsicFRP-2.0.0/intrinsicFRP/DESCRIPTION | 47 intrinsicFRP-2.0.0/intrinsicFRP/MD5 | 93 + intrinsicFRP-2.0.0/intrinsicFRP/NAMESPACE | 5 intrinsicFRP-2.0.0/intrinsicFRP/NEWS.md | 8 intrinsicFRP-2.0.0/intrinsicFRP/R/RcppExports.R | 494 ---------- intrinsicFRP-2.0.0/intrinsicFRP/R/data.R | 2 intrinsicFRP-2.0.0/intrinsicFRP/R/frp.R | 81 + intrinsicFRP-2.0.0/intrinsicFRP/R/gkr_factor_screening.R |only intrinsicFRP-2.0.0/intrinsicFRP/R/hac_covariance.R |only intrinsicFRP-2.0.0/intrinsicFRP/R/identification_tests.R |only intrinsicFRP-2.0.0/intrinsicFRP/R/misspecification_distance.R |only intrinsicFRP-2.0.0/intrinsicFRP/R/oracle_tfrp.R | 222 ++-- intrinsicFRP-2.0.0/intrinsicFRP/R/tfrp.R | 46 intrinsicFRP-2.0.0/intrinsicFRP/R/utils.R | 2 intrinsicFRP-2.0.0/intrinsicFRP/README.md | 479 ++++++++- intrinsicFRP-2.0.0/intrinsicFRP/man/ChenFang2019BetaRankTest.Rd | 55 - intrinsicFRP-2.0.0/intrinsicFRP/man/FRP.Rd | 74 + intrinsicFRP-2.0.0/intrinsicFRP/man/GKRFactorScreening.Rd |only intrinsicFRP-2.0.0/intrinsicFRP/man/HACcovariance.Rd |only intrinsicFRP-2.0.0/intrinsicFRP/man/HJMisspecificationDistance.Rd |only intrinsicFRP-2.0.0/intrinsicFRP/man/IterativeKleibergenPaap2006BetaRankTest.Rd |only intrinsicFRP-2.0.0/intrinsicFRP/man/OracleTFRP.Rd | 138 +- intrinsicFRP-2.0.0/intrinsicFRP/man/TFRP.Rd | 46 intrinsicFRP-2.0.0/intrinsicFRP/man/factors.Rd | 2 intrinsicFRP-2.0.0/intrinsicFRP/src/RcppExports.cpp | 137 +- intrinsicFRP-2.0.0/intrinsicFRP/src/adaptive_weights.cpp | 41 intrinsicFRP-2.0.0/intrinsicFRP/src/adaptive_weights.h | 32 intrinsicFRP-2.0.0/intrinsicFRP/src/frp.cpp | 288 +++-- intrinsicFRP-2.0.0/intrinsicFRP/src/frp.h | 216 +--- intrinsicFRP-2.0.0/intrinsicFRP/src/gkr_factor_screening.cpp |only intrinsicFRP-2.0.0/intrinsicFRP/src/gkr_factor_screening.h |only intrinsicFRP-2.0.0/intrinsicFRP/src/hac_covariance.cpp |only intrinsicFRP-2.0.0/intrinsicFRP/src/hac_covariance.h |only intrinsicFRP-2.0.0/intrinsicFRP/src/hj_misspecification_distance.cpp |only intrinsicFRP-2.0.0/intrinsicFRP/src/hj_misspecification_distance.h |only intrinsicFRP-2.0.0/intrinsicFRP/src/identification_tests.cpp |only intrinsicFRP-2.0.0/intrinsicFRP/src/identification_tests.h | 117 +- intrinsicFRP-2.0.0/intrinsicFRP/src/oracle_tfrp.cpp | 310 ++++-- intrinsicFRP-2.0.0/intrinsicFRP/src/oracle_tfrp.h | 385 +++---- intrinsicFRP-2.0.0/intrinsicFRP/src/tfrp.cpp | 54 - intrinsicFRP-2.0.0/intrinsicFRP/src/tfrp.h | 107 -- intrinsicFRP-2.0.0/intrinsicFRP/src/tuning.cpp | 278 ++--- intrinsicFRP-2.0.0/intrinsicFRP/src/tuning.h | 21 intrinsicFRP-2.0.0/intrinsicFRP/src/utils.cpp |only intrinsicFRP-2.0.0/intrinsicFRP/src/utils.h |only intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/Rplots.pdf |binary intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-frp.R | 32 intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-gkr_factor_screening.R |only intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-hac_covariance.R |only intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-identification_tests.R |only intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-misspecification_distance.R |only intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-oracle_tfrp.R | 127 ++ intrinsicFRP-2.0.0/intrinsicFRP/tests/testthat/test-tfrp.R | 29 63 files changed, 2223 insertions(+), 1745 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions. This package implements the
following distributions: Bernoulli, beta-binomial, beta-negative
binomial, beta prime, Bhattacharjee, Birnbaum-Saunders,
bivariate normal, bivariate Poisson, categorical, Dirichlet,
Dirichlet-multinomial, discrete gamma, discrete Laplace,
discrete normal, discrete uniform, discrete Weibull, Frechet,
gamma-Poisson, generalized extreme value, Gompertz,
generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t,
Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy,
Laplace, location-scale t, logarithmic, Lomax, multivariate
hypergeometric, multinomial, negative hypergeometric,
non-standard beta, normal mixture, Poisson mixture, Pareto,
power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam,
slash, triangular, truncated binomial, truncated normal,
truncated Poisson, Tukey lambda, Wald, zero-inflated binomial,
zer [...truncated...]
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Diff between extraDistr versions 1.9.1 dated 2020-09-07 and 1.10.0 dated 2023-11-30
extraDistr-1.10.0/extraDistr/DESCRIPTION | 18 extraDistr-1.10.0/extraDistr/MD5 | 26 extraDistr-1.10.0/extraDistr/NEWS.md | 5 extraDistr-1.10.0/extraDistr/R/RcppExports.R | 2 extraDistr-1.10.0/extraDistr/R/extraDistr-package.R | 20 extraDistr-1.10.0/extraDistr/R/gompertz-distribution.R | 13 extraDistr-1.10.0/extraDistr/R/negative-hypergeometric-distribution.R | 46 - extraDistr-1.10.0/extraDistr/man/Gompertz.Rd | 2 extraDistr-1.10.0/extraDistr/man/NegHyper.Rd | 6 extraDistr-1.10.0/extraDistr/man/extraDistr-package.Rd |only extraDistr-1.10.0/extraDistr/src/RcppExports.cpp | 373 +++++----- extraDistr-1.10.0/extraDistr/src/gpd-distribution.cpp | 281 ++++--- extraDistr-1.10.0/extraDistr/tests/testthat/test-non-negative.R | 31 extraDistr-1.10.0/extraDistr/tests/testthat/test_vectorization.R | 18 extraDistr-1.9.1/extraDistr/man/extraDistr.Rd |only 15 files changed, 433 insertions(+), 408 deletions(-)
Title: 'ARDECO' Dataset
Description: A set of functions to access the 'ARDECO' (Annual Regional Database
of the European Commission) data directly from the official ARDECO public
repository through the exploitation of the 'ARDECO' APIs.
The APIs are completely transparent to the user and the provided functions
provide a direct access to the 'ARDECO' data.
The 'ARDECO' database is a collection of variables related to demography,
employment, labour market, domestic product, capital formation.
Each variable can be exposed in one or more units of measure as well as
refers to total values plus economic sectors.
The description of the 'ARDECO' database can be found at the following URL
<https://urban.jrc.ec.europa.eu/ardeco>.
Author: European Commission
Maintainer: European Commission <carmelo.attardo@ec.europa.eu>
Diff between ARDECO versions 0.1.0 dated 2023-11-28 and 0.1.1 dated 2023-11-30
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS | 2 ++ R/get_variable_list.R | 30 ++++++++++++++++++++++++++++++ README.md |only 5 files changed, 39 insertions(+), 6 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.2 dated 2023-06-29 and 0.6.3 dated 2023-11-30
DESCRIPTION | 8 - MD5 | 24 +-- NEWS.md | 13 + R/RcppExports.R | 2 R/checks.R | 6 R/cl.R | 12 - R/region_matrix.R | 45 ++++-- README.md | 8 - inst/doc/vignette.html | 4 src/RcppExports.cpp | 134 ++++++++++---------- src/addons.cpp | 15 +- tests/testthat/test_get_region_matrix.R | 15 ++ tests/testthat/test_region_matrix_to_struc_matrix.R |only tests/testthat/test_struc_values.R |only 14 files changed, 170 insertions(+), 116 deletions(-)
Title: Survival Distributions with Piece-Wise Constant Hazards
Description: Density, distribution function, ... hazard function, cumulative hazard function, survival function for survival distributions with piece-wise constant hazards and multiple states.
Author: Tobias Fellinger [aut, cre] ,
Florian Klinglmueller [aut]
Maintainer: Tobias Fellinger <tobias.fellinger@ages.at>
Diff between miniPCH versions 0.3.0 dated 2023-11-07 and 0.3.1 dated 2023-11-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/RcppExports.cpp | 12 ++++++------ 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.
Author: David Bolin [cre, aut] ,
Finn Lindgren [aut] ,
Suen Man Ho [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.5.7 dated 2023-10-23 and 2.5.8 dated 2023-11-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/RngStream.c | 4 ++-- src/integration.cpp | 13 ++++++++----- src/qinv.cpp | 3 ++- 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Optimal Transport Weights for Causal Inference
Description: Uses optimal transport distances to find probabilistic
matching estimators for causal inference.
These methods are described in Dunipace, Eric (2021) <arXiv:2109.01991>.
The package will build the weights, estimate treatment effects, and
calculate confidence intervals via the methods described in the paper.
The package also supports several other methods as described in the help
files.
Author: Eric Dunipace [aut, cre]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between causalOT versions 1.0 dated 2023-11-28 and 1.0.1 dated 2023-11-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ R/utils.R | 3 ++- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing
Parents
Description: Parentage assignment package.
Parentage assignment is performed based on observed average Mendelian transmission probability distributions or Exclusion.
The main functions of this package are the function APIS_2n(), APIS_3n and launch_APIShiny(), which perform parentage assignment.
Author: Julien Roche [aut, cre],
Ronan Griot [aut],
Mathieu Besson [aut],
Francois Allal [aut],
Marc Vandeputte [aut],
Jonathan D'Ambrosio [aut],
Romain Morvezin [aut],
Florence Phocas [aut],
Sophie Brard-Fudulea [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <jjm.roche@gmail.com>
Diff between APIS versions 2.0.3 dated 2023-11-23 and 2.0.4 dated 2023-11-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/function_simulate_offspring.R | 8 ++++---- src/calculate_likelihood.c | 38 +++++++++++++++++++------------------- 4 files changed, 29 insertions(+), 29 deletions(-)
Title: Statistical Modeling of Animal Movements
Description: Animal movement models including Moving-Resting Process
with Embedded Brownian Motion
(Yan et al., 2014, <doi:10.1007/s10144-013-0428-8>;
Pozdnyakov et al., 2017, <doi:10.1007/s11009-017-9547-6>),
Brownian Motion with Measurement Error
(Pozdnyakov et al., 2014, <doi:10.1890/13-0532.1>),
Moving-Resting-Handling Process with Embedded Brownian Motion
(Pozdnyakov et al., 2020, <doi:10.1007/s11009-020-09774-1>),
Moving-Resting Process with Measurement Error
(Hu et al., 2021, <doi:10.1111/2041-210X.13694>),
Moving-Moving Process with two Embedded Brownian Motions.
Author: Chaoran Hu [aut, cre],
Vladimir Pozdnyakov [aut],
Jun Yan [aut]
Maintainer: Chaoran Hu <chaoran.hu@uconn.edu>
Diff between smam versions 0.7.0 dated 2023-08-21 and 0.7.1 dated 2023-11-30
DESCRIPTION | 8 +- MD5 | 12 ++-- NEWS.md | 6 ++ configure | 18 +++--- configure.ac | 2 inst/CITATION | 4 - src/RcppExports.cpp | 154 ++++++++++++++++++++++++++-------------------------- 7 files changed, 105 insertions(+), 99 deletions(-)
More information about historicalborrowlong at CRAN
Permanent link
Title: Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library
containing many standard implementations of neural networks. This
package wraps the SNNS functionality to make it available from
within R. Using the 'RSNNS' low-level interface, all of the
algorithmic functionality and flexibility of SNNS can be accessed.
Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and
learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir [aut, cre, cph],
Jose M. Benitez [ths],
Andreas Zell [ctb] ,
Niels Mache [ctb] ,
Guenter Mamier [ctb] ,
Michael Vogt [ctb] ,
Sven Doering [ctb] ,
Ralf Huebner [ctb] ,
Kai-Uwe Herrmann [ctb] ,
Tobias Soyez [ctb] ,
Michael Schmalzl [ctb [...truncated...]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between RSNNS versions 0.4-16 dated 2023-05-09 and 0.4-17 dated 2023-11-30
ChangeLog | 5 +++ DESCRIPTION | 8 ++--- MD5 | 66 +++++++++++++++++++++---------------------- R/RSNNS-package.R | 7 +--- R/SnnsRObjectFactory.R | 2 - R/art1.R | 2 - R/art2.R | 2 - R/artmap.R | 2 - R/assoz.R | 2 - R/dlvq.R | 2 - R/elman.R | 2 - R/jordan.R | 2 - R/mlp.R | 2 - R/rbf.R | 2 - R/rbfDDA.R | 2 - R/reg_class.R | 2 - R/som.R | 2 - inst/CITATION | 4 -- man/RSNNS-package.Rd | 7 +--- man/SnnsR-class.Rd | 2 - man/analyzeClassification.Rd | 2 - man/art1.Rd | 2 - man/art2.Rd | 2 - man/artmap.Rd | 2 - man/assoz.Rd | 2 - man/dlvq.Rd | 2 - man/elman.Rd | 2 - man/jordan.Rd | 2 - man/mlp.Rd | 2 - man/rbf.Rd | 2 - man/rbfDDA.Rd | 2 - man/som.Rd | 2 - src/SnnsCLibGenericR_util.c | 2 - src/tacoma_learn.cpp | 6 +-- 34 files changed, 79 insertions(+), 78 deletions(-)
Title: Open Source Geometry Engine ('GEOS') R API
Description: Provides an R API to the Open Source Geometry Engine
('GEOS') library (<https://libgeos.org/>) and a vector format
with which to efficiently store 'GEOS' geometries. High-performance functions
to extract information from, calculate relationships between, and
transform geometries are provided. Finally, facilities to import
and export geometry vectors to other spatial formats are provided.
Author: Dewey Dunnington [aut, cre] ,
Edzer Pebesma [aut]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between geos versions 0.2.3 dated 2023-05-31 and 0.2.4 dated 2023-11-30
DESCRIPTION | 6 MD5 | 38 +-- NEWS.md | 4 src/geoarrow-imports.h | 2 src/geos-basic-strtree.c | 42 +-- src/geos-binary-atomic.c | 460 ++++++++++++++++++++----------------------- src/geos-binary-geometry.c | 183 ++++++++--------- src/geos-common.c | 42 ++- src/geos-common.h | 43 ++-- src/geos-geometry.c | 1 src/geos-io.c | 77 +++---- src/geos-make.c | 124 +++++------ src/geos-polygonize.c | 88 +++----- src/geos-segment.c | 49 +--- src/geos-strtree.c | 362 ++++++++++++++++------------------ src/geos-unary-atomic.c | 218 ++++++++------------ src/geos-unary-geometry.c | 473 +++++++++++++++++++++------------------------ src/handle-geos.c | 70 +++--- src/init.c | 397 +++++++++++++++++++------------------ tests/testthat/Rplots.pdf |binary 20 files changed, 1286 insertions(+), 1393 deletions(-)