Title: Network-Based Regularization for Generalized Linear Models
Description: Network-based regularization has achieved success in variable selection for
high-dimensional biological data due to its ability to incorporate correlations among
genomic features. This package provides procedures of network-based variable selection
for generalized linear models (Ren et al. (2017) <doi:10.1186/s12863-017-0495-5> and
Ren et al.(2019) <doi:10.1002/gepi.22194>). Continuous, binary, and survival response
are supported. Robust network-based methods are available for continuous and survival
responses.
Author: Jie Ren, Luann C. Jung, Yinhao Du, Cen Wu, Yu Jiang, Junhao Liu
Maintainer: Jie Ren <jieren@ksu.edu>
Diff between regnet versions 1.0.0 dated 2022-08-18 and 1.0.1 dated 2024-02-21
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- R/regnet-package.R | 3 + R/regnet.R | 16 ++++---- README.md | 92 ++++++++++++++++++++++++-------------------------- build/partial.rdb |binary man/regnet-package.Rd | 11 +++++ man/regnet.Rd | 16 ++++---- src/Makevars | 6 +-- src/Makevars.win | 6 +-- 10 files changed, 94 insertions(+), 82 deletions(-)
Title: These Functions Fetch and Extract Text Content from Specified
Web Pages
Description: The 'scrapeR' package utilizes functions that fetch and extract text content from specified web pages. It handles HTTP errors and parses HTML efficiently. The package can handle hundreds of websites at a time using the scrapeR_in_batches() command.
Author: Mathieu Dubeau [aut, cre, cph]
Maintainer: Mathieu Dubeau <mdubeau20@gmail.com>
Diff between scrapeR versions 0.1.7 dated 2023-11-23 and 0.1.8 dated 2024-02-21
DESCRIPTION | 8 +++---- LICENSE | 2 - MD5 | 10 ++++----- NAMESPACE | 1 R/scrapeR.R | 48 +++++++++++++++++++++++++++++++++------------- man/scrapeR_in_batches.Rd | 17 ++++++++-------- 6 files changed, 55 insertions(+), 31 deletions(-)
Title: Parse and Render Molecular Structures in 3D
Description: Downloads and parses 'SDF' (Structural Description Format) and 'PDB' (Protein Database) files for 3D rendering.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between raymolecule versions 0.5.0 dated 2022-03-21 and 0.5.3 dated 2024-02-21
DESCRIPTION | 16 ++++++++++------ MD5 | 26 +++++++++++++++----------- NAMESPACE | 1 + R/convert_color.R |only R/generate_atom_scene.R | 7 ++++--- R/generate_bond_scene.R | 1 + R/generate_full_scene.R | 9 +++++---- R/get_molecule.R | 17 +++++++++++------ R/render_model.R | 17 ++++++++++++----- R/run_documentation.R |only R/util.R | 1 - man/convert_color.Rd |only man/generate_bond_scene.Rd | 4 ++-- man/get_molecule.Rd | 17 +++++++++++------ man/onb_from_w.Rd | 3 --- man/run_documentation.Rd |only 16 files changed, 72 insertions(+), 47 deletions(-)
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 0.9.0 dated 2024-02-08 and 0.9.1 dated 2024-02-21
DESCRIPTION | 6 +- MD5 | 45 ++++++++-------- NEWS.md | 10 +++ R/interface.R | 75 ++++++++++++++++++++-------- R/tspop.R | 12 +++- R/visualization.R | 22 +++++--- R/zzz.R | 2 inst/doc/vignette-01-tutorial.html | 10 +-- inst/doc/vignette-02-grid-model.html | 12 ++-- inst/doc/vignette-04-nonspatial-models.R | 10 +++ inst/doc/vignette-04-nonspatial-models.Rmd | 16 +++++ inst/doc/vignette-04-nonspatial-models.html | 23 +++++++- inst/doc/vignette-05-tree-sequences.html | 14 ++--- inst/doc/vignette-06-locations.html | 4 - inst/doc/vignette-07-backends.html | 4 - inst/doc/vignette-08-nonslendr-tskit.html | 4 - inst/doc/vignette-09-paper.html | 16 ++--- inst/doc/vignette-10-tracts.html | 2 man/clear_env.Rd | 7 +- man/get_env.Rd |only man/plot_model.Rd | 3 + man/ts_tracts.Rd | 12 ++++ tests/testthat/test-tspop.R | 15 ++++- vignettes/vignette-04-nonspatial-models.Rmd | 16 +++++ 24 files changed, 241 insertions(+), 99 deletions(-)
Title: Phylogenetic ANalyses of DiversificAtion
Description: Implements macroevolutionary analyses on phylogenetic trees. See
Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011)
<DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>,
Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>,
Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>,
Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>,
Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>,
Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>,
Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewi [...truncated...]
Author: Helene Morlon [aut, cre, cph],
Eric Lewitus [aut, cph],
Fabien Condamine [aut, cph],
Marc Manceau [aut, cph],
Julien Clavel [aut, cph],
Jonathan Drury [aut, cph],
Olivier Billaud [aut, cph],
Odile Maliet [aut, cph],
Leandro Aristide [aut, cph],
Benoi [...truncated...]
Maintainer: Helene Morlon <helene.morlon@bio.ens.psl.eu>
Diff between RPANDA versions 2.2 dated 2022-10-24 and 2.3 dated 2024-02-21
DESCRIPTION | 29 +- MD5 | 118 ++++++-- NAMESPACE | 32 +- R/CreateBioGeoB_Object_subclade.R | 26 - R/CreateClassObject.R | 64 ++-- R/CreateGeoObject_BioGeoBEARS.R | 63 +++- R/add.gts.R |only R/all_comb_models.R |only R/apply_prob_dtt.R |only R/div.models.R |only R/div.rates.R |only R/extract.clade.ln.R |only R/fitTipData.R | 5 R/fit_ClaDS.R | 2 R/fit_bd_backbone.R |only R/fit_bd_backbone_c.R |only R/fit_t_comp.R | 447 ++++++++++++++++++++++---------- R/fit_t_comp_subgroup.R | 172 +++++++++++- R/fit_t_env.R | 21 - R/fit_t_env_ou.R |only R/fit_t_pl.R | 5 R/fit_t_standard.R | 121 +++++--- R/get.branching.nodes.R |only R/get.comb.shift.R |only R/get.node.ages.R |only R/get.sampling.fractions.R |only R/globals.R |only R/likelihood_bd_backbone.R |only R/likelihood_subgroup_model.R | 14 - R/likelihood_t_env.R | 10 R/make.simmap.BGB.R |only R/misc_functions.R | 384 ++++++++++++++++++++++++++++ R/paleodiv.R |only R/phylosignal_network.R | 4 R/plot.fit_t_env.ou.R |only R/plot_BipartiteEvol.R | 26 - R/plot_phylo_comb.R |only R/plot_prob_dtt.R | 140 ++++++---- R/remove.model.R |only R/shift.estimates.R |only R/sim_ClaDS.R | 4 R/sim_t_comp.R | 2 R/sim_t_env_ou.R |only R/sim_t_tworegime.R | 2 R/simul.comb.shift.R |only R/subtree.R |only R/utils.R | 503 +++++++++++++++++++++++++++++++++++++ README.md | 8 data/Anolis.data.rda |binary data/Cetacea.rda |binary data/datalist | 2 data/shifts_cetacea.rda |only data/taxo_cetacea.rda |only inst/CITATION | 4 man/CreateClassObject.Rd | 7 man/CreateGeoObject_BioGeoBEARS.Rd | 14 - man/RPANDA-package.Rd | 9 man/add.gts.Rd |only man/apply_prob_dtt.Rd |only man/div.models.Rd |only man/div.rates.Rd |only man/fit_bd_backbone.Rd |only man/fit_bd_backbone_c.Rd |only man/fit_t_comp.Rd | 23 + man/fit_t_comp_subgroup.Rd | 98 +++++-- man/fit_t_env.Rd | 6 man/fit_t_env_ou.Rd |only man/fit_t_standard.Rd | 4 man/get.comb.shift.Rd |only man/get.sampling.fractions.Rd |only man/likelihood_bd_backbone.Rd |only man/likelihood_subgroup_model.Rd | 6 man/lines.fit_t_env.ou.Rd |only man/paleodiv.Rd |only man/plot.fit_t_env.ou.Rd |only man/plot_phylo_comb.Rd |only man/plot_prob_dtt.Rd | 11 man/remove.model.Rd |only man/shift.estimates.Rd |only man/shifts_cetacea.Rd |only man/sim_t_env_ou.Rd |only man/simul.comb.shift.Rd |only man/taxo_cetacea.Rd |only 83 files changed, 1916 insertions(+), 470 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [ctb] ,
Xintong Li [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 0.6.0 dated 2024-02-08 and 0.6.1 dated 2024-02-21
DESCRIPTION | 6 +- MD5 | 19 ++++---- NAMESPACE | 2 R/formattedTables.R | 2 R/reexports-omopgenerics.R |only R/tidyTables.R | 2 inst/doc/addCohortIntersections.html | 4 - inst/doc/addPatientCharacteristics.html | 4 - man/reexports.Rd |only tests/testthat/test-class.R |only tests/testthat/test-summariseCharacteristics.R | 6 +- tests/testthat/test-summariseResult.R | 56 ++++++++++++------------- 12 files changed, 53 insertions(+), 48 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services. Data are discovered from
National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.14 dated 2023-10-05 and 2.7.15 dated 2024-02-21
DESCRIPTION | 12 +- MD5 | 81 +++++++------ NAMESPACE | 2 NEWS | 6 + R/AAA.R | 22 +++ R/citations.R |only R/constructNWISURL.R | 2 R/dataRetrievals-package.R | 5 R/importWQP.R | 2 R/readNWISdata.R | 4 R/readNWISqw.R | 5 R/readNWISunit.R | 14 +- R/readWQPdata.R | 4 R/readWQPqw.R | 136 ----------------------- R/whatNWISdata.R | 14 +- R/whatNWISsites.R | 4 R/whatWQPdata.R | 31 ----- R/whatWQPsites.R | 90 +-------------- build/vignette.rds |binary inst/CITATION | 6 - inst/doc/dataRetrieval.R | 60 +++++++--- inst/doc/dataRetrieval.Rmd | 188 +++++++++++++++++++++++++++---- inst/doc/dataRetrieval.html | 253 +++++++++++++++++++++++++++++++------------ inst/doc/qwdata_changes.Rmd | 11 + inst/doc/qwdata_changes.html | 35 +++-- man/constructNWISURL.Rd | 2 man/create_NWIS_bib.Rd |only man/create_WQP_bib.Rd |only man/dataRetrieval.Rd | 11 + man/readNWISdata.Rd | 4 man/readNWISgwl.Rd | 2 man/readNWISstat.Rd | 4 man/readNWISuse.Rd | 2 man/readNWISuv.Rd | 6 - man/readWQPdata.Rd | 2 man/readWQPqw.Rd | 130 ---------------------- man/readWQPsummary.Rd | 2 man/whatNWISdata.Rd | 4 man/whatNWISsites.Rd | 4 man/whatWQPdata.Rd | 29 ---- man/wqpSpecials.Rd | 84 -------------- vignettes/dataRetrieval.Rmd | 188 +++++++++++++++++++++++++++---- vignettes/qwdata_changes.Rmd | 11 + 43 files changed, 751 insertions(+), 721 deletions(-)
Title: The T-LARS Algorithm: Early-Terminated Forward Variable
Selection
Description: Computes the solution path of the Terminating-LARS (T-LARS) algorithm. The T-LARS algorithm
is a major building block of the T-Rex selector (see R package 'TRexSelector').
The package is based on the papers Machkour, Muma, and Palomar (2022) <arXiv:2110.06048>, Efron, Hastie, Johnstone,
and Tibshirani (2004) <doi:10.1214/009053604000000067>, and Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>.
Author: Jasin Machkour [aut, cre],
Simon Tien [aut],
Daniel P. Palomar [aut],
Michael Muma [aut]
Maintainer: Jasin Machkour <jasin.machkour@tu-darmstadt.de>
Diff between tlars versions 0.0.1 dated 2022-07-15 and 1.0.0 dated 2024-02-21
DESCRIPTION | 14 MD5 | 28 NEWS.md | 8 README.md | 30 build/vignette.rds |binary inst/CITATION | 46 inst/doc/tlars_variable_selection.R | 20 inst/doc/tlars_variable_selection.Rmd | 32 inst/doc/tlars_variable_selection.html | 2049 ++++++++++++++++++---- man/figures/README-full_solution_path-1.png |binary man/figures/README-terminated_solution_path-1.png |binary src/Makevars | 1 src/Makevars.win | 1 vignettes/refs.bib | 7 vignettes/tlars_variable_selection.Rmd | 32 15 files changed, 1819 insertions(+), 449 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.3 dated 2023-09-19 and 1.0.4 dated 2024-02-21
renv-1.0.3/renv/R/mran.R |only renv-1.0.3/renv/inst/repos/src/contrib/renv_1.0.3.tar.gz |only renv-1.0.4/renv/DESCRIPTION | 8 renv-1.0.4/renv/LICENSE | 2 renv-1.0.4/renv/MD5 | 259 +++++----- renv-1.0.4/renv/NEWS.md | 88 +++ renv-1.0.4/renv/R/activate.R | 1 renv-1.0.4/renv/R/available-packages.R | 80 ++- renv-1.0.4/renv/R/bioconductor.R | 2 renv-1.0.4/renv/R/cache.R | 22 renv-1.0.4/renv/R/call.R | 13 renv-1.0.4/renv/R/consent.R | 1 renv-1.0.4/renv/R/dcf.R | 6 renv-1.0.4/renv/R/defer.R | 11 renv-1.0.4/renv/R/dependencies.R | 42 + renv-1.0.4/renv/R/description.R | 22 renv-1.0.4/renv/R/download.R | 68 ++ renv-1.0.4/renv/R/dynamic.R | 13 renv-1.0.4/renv/R/embed.R | 7 renv-1.0.4/renv/R/extsoft.R | 8 renv-1.0.4/renv/R/files.R | 22 renv-1.0.4/renv/R/http.R | 8 renv-1.0.4/renv/R/hydrate.R | 24 - renv-1.0.4/renv/R/init.R | 60 +- renv-1.0.4/renv/R/install.R | 52 +- renv-1.0.4/renv/R/json-read.R | 14 renv-1.0.4/renv/R/knitr.R | 2 renv-1.0.4/renv/R/libpaths.R | 16 renv-1.0.4/renv/R/load.R | 36 + renv-1.0.4/renv/R/lock.R | 10 renv-1.0.4/renv/R/lockfile-api.R | 2 renv-1.0.4/renv/R/lockfile-write.R | 25 - renv-1.0.4/renv/R/lockfile.R | 4 renv-1.0.4/renv/R/mapping.R |only renv-1.0.4/renv/R/metadata.R | 10 renv-1.0.4/renv/R/options.R | 4 renv-1.0.4/renv/R/p3m.R |only renv-1.0.4/renv/R/package.R | 70 ++ renv-1.0.4/renv/R/pak.R | 6 renv-1.0.4/renv/R/paths.R | 5 renv-1.0.4/renv/R/pip.R | 18 renv-1.0.4/renv/R/ppm.R | 73 ++- renv-1.0.4/renv/R/pretty.R | 8 renv-1.0.4/renv/R/project.R | 39 - renv-1.0.4/renv/R/python-virtualenv.R | 9 renv-1.0.4/renv/R/r.R | 4 renv-1.0.4/renv/R/record.R | 23 renv-1.0.4/renv/R/records.R | 64 +- renv-1.0.4/renv/R/remotes.R | 16 renv-1.0.4/renv/R/report.R | 8 renv-1.0.4/renv/R/repos.R | 24 - renv-1.0.4/renv/R/restore.R | 10 renv-1.0.4/renv/R/retrieve.R | 100 +++- renv-1.0.4/renv/R/roxygen.R | 7 renv-1.0.4/renv/R/run.R | 7 renv-1.0.4/renv/R/scope.R | 10 renv-1.0.4/renv/R/shims.R | 25 - renv-1.0.4/renv/R/snapshot-auto.R | 15 renv-1.0.4/renv/R/snapshot.R | 107 +++- renv-1.0.4/renv/R/status.R | 111 +++- renv-1.0.4/renv/R/tar.R | 11 renv-1.0.4/renv/R/truthy.R | 24 - renv-1.0.4/renv/R/update.R | 10 renv-1.0.4/renv/R/upgrade.R | 5 renv-1.0.4/renv/R/utils.R | 50 +- renv-1.0.4/renv/R/watchdog-server.R | 13 renv-1.0.4/renv/R/watchdog.R | 13 renv-1.0.4/renv/R/zzz.R | 2 renv-1.0.4/renv/build/vignette.rds |binary renv-1.0.4/renv/inst/config.yml | 2 renv-1.0.4/renv/inst/doc/ci.Rmd | 6 renv-1.0.4/renv/inst/doc/ci.html | 5 renv-1.0.4/renv/inst/doc/package-install.Rmd | 30 + renv-1.0.4/renv/inst/doc/package-install.html | 36 + renv-1.0.4/renv/inst/doc/packages.Rmd | 42 + renv-1.0.4/renv/inst/doc/packages.html | 41 + renv-1.0.4/renv/inst/doc/renv.Rmd | 4 renv-1.0.4/renv/inst/doc/renv.html | 12 renv-1.0.4/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.0.4/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.0.4/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.0.4/renv/inst/repos/src/contrib/renv_1.0.4.tar.gz |only renv-1.0.4/renv/inst/resources/activate.R | 37 + renv-1.0.4/renv/man/activate.Rd | 5 renv-1.0.4/renv/man/config.Rd | 2 renv-1.0.4/renv/man/hydrate.Rd | 2 renv-1.0.4/renv/man/init.Rd | 5 renv-1.0.4/renv/man/install.Rd | 12 renv-1.0.4/renv/man/load.Rd | 5 renv-1.0.4/renv/man/paths.Rd | 1 renv-1.0.4/renv/man/restore.Rd | 2 renv-1.0.4/renv/man/status.Rd | 19 renv-1.0.4/renv/tests/testthat/_snaps/bootstrap.md | 20 renv-1.0.4/renv/tests/testthat/_snaps/dots.md | 5 renv-1.0.4/renv/tests/testthat/_snaps/lockfile-read.md | 5 renv-1.0.4/renv/tests/testthat/_snaps/preflight.md | 5 renv-1.0.4/renv/tests/testthat/_snaps/repair.md | 5 renv-1.0.4/renv/tests/testthat/_snaps/snapshot.md | 10 renv-1.0.4/renv/tests/testthat/_snaps/status.md | 45 + renv-1.0.4/renv/tests/testthat/helper-scope.R | 8 renv-1.0.4/renv/tests/testthat/helper-setup.R | 11 renv-1.0.4/renv/tests/testthat/packages/jamie |only renv-1.0.4/renv/tests/testthat/packages/kevin |only renv-1.0.4/renv/tests/testthat/packages/packrat/DESCRIPTION | 2 renv-1.0.4/renv/tests/testthat/packages/packrat/README |only renv-1.0.4/renv/tests/testthat/packages/phone |only renv-1.0.4/renv/tests/testthat/resources/chunk-eval.Rmd |only renv-1.0.4/renv/tests/testthat/resources/import.R | 12 renv-1.0.4/renv/tests/testthat/test-autoload.R | 6 renv-1.0.4/renv/tests/testthat/test-available-packages.R | 2 renv-1.0.4/renv/tests/testthat/test-call.R | 5 renv-1.0.4/renv/tests/testthat/test-dependencies.R | 50 ++ renv-1.0.4/renv/tests/testthat/test-files.R | 20 renv-1.0.4/renv/tests/testthat/test-http.R |only renv-1.0.4/renv/tests/testthat/test-init.R | 9 renv-1.0.4/renv/tests/testthat/test-install.R | 87 +++ renv-1.0.4/renv/tests/testthat/test-json.R | 34 + renv-1.0.4/renv/tests/testthat/test-lock.R | 4 renv-1.0.4/renv/tests/testthat/test-migrate.R | 14 renv-1.0.4/renv/tests/testthat/test-mran.R | 15 renv-1.0.4/renv/tests/testthat/test-ppm.R | 287 +++++++++++- renv-1.0.4/renv/tests/testthat/test-profile.R | 4 renv-1.0.4/renv/tests/testthat/test-profiles.R | 2 renv-1.0.4/renv/tests/testthat/test-python.R | 13 renv-1.0.4/renv/tests/testthat/test-records.R | 2 renv-1.0.4/renv/tests/testthat/test-repos.R | 13 renv-1.0.4/renv/tests/testthat/test-restore.R | 31 + renv-1.0.4/renv/tests/testthat/test-settings.R | 7 renv-1.0.4/renv/tests/testthat/test-snapshot.R | 5 renv-1.0.4/renv/tests/testthat/test-socket.R | 5 renv-1.0.4/renv/tests/testthat/test-status.R | 43 + renv-1.0.4/renv/tests/testthat/test-utils.R | 28 - renv-1.0.4/renv/vignettes/ci.Rmd | 6 renv-1.0.4/renv/vignettes/package-install.Rmd | 30 + renv-1.0.4/renv/vignettes/packages.Rmd | 42 + renv-1.0.4/renv/vignettes/renv.Rmd | 4 136 files changed, 2289 insertions(+), 708 deletions(-)
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] ,
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.2-13 dated 2023-05-22 and 0.2-14 dated 2024-02-21
DESCRIPTION | 16 +++++++++------- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 1 + NEWS.md | 30 ++++++++++++++++-------------- R/perimeter.R | 19 ++++++++++++++++--- configure | 43 ++++++++++++------------------------------- configure.ac | 41 +++++++++++------------------------------ man/perimeter.Rd | 3 +++ src/Makevars.ucrt | 21 ++++++++++++++++----- src/lwgeom.cpp | 4 ++-- src/postgis_config.h | 2 +- tests/geod.R | 4 ++-- tests/geod.Rout.save | 20 +++++--------------- tests/perimeter.R | 2 +- tests/perimeter.Rout.save | 12 ++++++------ tests/testthat.Rout.save | 11 ++++------- 16 files changed, 120 insertions(+), 139 deletions(-)
Title: Tools for 2D and 3D Plots of Single and Multi-Objective
Linear/Integer Programming Models
Description: Make 2D and 3D plots of linear programming (LP),
integer linear programming (ILP), or mixed integer linear programming (MILP) models
with up to three objectives. Plots of both the solution and criterion space are possible.
For instance the non-dominated (Pareto) set for bi-objective LP/ILP/MILP programming models
(see vignettes for an overview). The package also contains an function for checking if a point
is inside the convex hull.
Author: Lars Relund Nielsen [aut, cre]
Maintainer: Lars Relund Nielsen <lars@relund.dk>
Diff between gMOIP versions 1.5.0 dated 2023-05-26 and 1.5.2 dated 2024-02-21
DESCRIPTION | 10 MD5 | 52 +-- NEWS.md | 8 R/hull.R | 2 R/ndset.R | 577 +++++++++++++++++++++++--------------- R/plot.R | 2 build/vignette.rds |binary inst/doc/bi-objective_2x.R | 4 inst/doc/bi-objective_2x.html | 186 ++++++------ inst/doc/bi-objective_3x_ex1.R | 4 inst/doc/bi-objective_3x_ex1.html | 132 ++++---- inst/doc/intro.R | 10 inst/doc/intro.html | 342 +++++++++++----------- inst/doc/polytope_2d.R | 4 inst/doc/polytope_2d.html | 472 +++++++++++++++---------------- inst/doc/polytope_3d_ex1.R | 4 inst/doc/polytope_3d_ex1.html | 64 ++-- inst/doc/tri-objective.R | 14 inst/doc/tri-objective.Rmd | 6 inst/doc/tri-objective.html | 214 +++++++------- man/addNDSet.Rd | 6 man/classifyNDSet.Rd | 28 + man/genNDSet.Rd | 54 ++- man/genSample.Rd | 43 ++ man/inHull.Rd | 2 man/plotRectangle3D.Rd | 2 vignettes/tri-objective.Rmd | 6 27 files changed, 1238 insertions(+), 1010 deletions(-)
Title: Fast Relative Comparisons of Floating Point Numbers in 'C++'
Description: Compare double-precision floating point vectors using
relative differences. All equality operations are calculated using
'cpp11'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cppdoubles versions 0.1.1 dated 2023-11-10 and 0.2.0 dated 2024-02-21
cppdoubles-0.1.1/cppdoubles/src/cpp_doubles.cpp |only cppdoubles-0.2.0/cppdoubles/DESCRIPTION | 6 cppdoubles-0.2.0/cppdoubles/LICENSE | 4 cppdoubles-0.2.0/cppdoubles/MD5 | 30 - cppdoubles-0.2.0/cppdoubles/NAMESPACE | 31 - cppdoubles-0.2.0/cppdoubles/NEWS.md | 7 cppdoubles-0.2.0/cppdoubles/R/all_equal.R |only cppdoubles-0.2.0/cppdoubles/R/cpp11.R | 4 cppdoubles-0.2.0/cppdoubles/R/cppdoubles-package.R | 8 cppdoubles-0.2.0/cppdoubles/R/zzz.R | 6 cppdoubles-0.2.0/cppdoubles/README.md | 55 ++ cppdoubles-0.2.0/cppdoubles/man/all_equal.Rd |only cppdoubles-0.2.0/cppdoubles/man/diff.Rd | 46 +- cppdoubles-0.2.0/cppdoubles/man/doubles.Rd | 282 +++++++------- cppdoubles-0.2.0/cppdoubles/src/cpp11.cpp | 20 cppdoubles-0.2.0/cppdoubles/src/doubles.cpp |only cppdoubles-0.2.0/cppdoubles/tests/testthat.R | 24 - cppdoubles-0.2.0/cppdoubles/tests/testthat/test-doubles.R | 4 18 files changed, 297 insertions(+), 230 deletions(-)
Title: Randomization-Based Inference
Description: Randomization-Based Inference for customized experiments.
Computes Fisher-Exact P-Values alongside null randomization
distributions. Retrieves counternull sets and generates counternull
distributions. Computes Fisher Intervals and Fisher-Adjusted P-Values.
Package includes visualization of randomization distributions and Fisher
Intervals. Users can input custom test statistics and their own methods for
randomization.
Rosenthal and Rubin (1994) <doi:10.1111/j.1467-9280.1994.tb00281.x>.
Author: Mabene Yasmine [aut, cre],
Bind Marie [aut],
Harvard University [cph]
Maintainer: Mabene Yasmine <ymabene@stanford.edu>
Diff between Counternull versions 0.2.0 dated 2023-08-27 and 0.2.1 dated 2024-02-21
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 3 +++ R/create_fisher_interval.R | 16 ++++++++++++++-- R/find_counternull_values.R | 28 ++++++++++++++++++++++------ R/find_counternull_values_int.R | 6 ++++-- inst/doc/counternull_vignette.html | 10 +++++----- man/create_fisher_interval.Rd | 6 +++++- man/find_counternull_values.Rd | 6 +++++- tests/testthat/test-counternull_values.R | 9 +++++++++ tests/testthat/test-fisher.R | 8 ++++++++ 11 files changed, 88 insertions(+), 30 deletions(-)
Title: Ridge-Type Penalized Estimation of a Potpourri of Models
Description: The name of the package is derived from the French, 'pour' ridge, and provides functionality for ridge-type estimation of a potpourri of models. Currently, this estimation concerns that of various Gaussian graphical models from different study designs. Among others it considers the regular Gaussian graphical model and a mixture of such models. The porridge-package implements the estimation of the former either from i) data with replicated observations by penalized loglikelihood maximization using the regular ridge penalty on the parameters (van Wieringen, Chen, 2021) or ii) from non-replicated data by means of either a ridge estimator with multiple shrinkage targets (as presented in van Wieringen et al. 2020, <doi:10.1016/j.jmva.2020.104621>) or the generalized ridge estimator that allows for both the inclusion of quantitative and qualitative prior information on the precision matrix via element-wise penalization and shrinkage (van Wieringen, 2019, <doi:10.1080/10618600.2019.1 [...truncated...]
Author: Wessel N. van Wieringen [aut, cre]
,
Mehran Aflakparast [ctb]
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between porridge versions 0.3.2 dated 2023-10-15 and 0.3.3 dated 2024-02-21
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/porridge-package.Rd | 4 +--- 3 files changed, 8 insertions(+), 10 deletions(-)
Title: Tools to Create, Use, and Convert ecocomDP Data
Description: Work with the Ecological Community Data Design Pattern. 'ecocomDP'
is a flexible data model for harmonizing ecological community surveys, in a
research question agnostic format, from source data published across
repositories, and with methods that keep the derived data up-to-date as the
underlying sources change. Described in O'Brien et al. (2021),
<doi:10.1016/j.ecoinf.2021.101374>.
Author: Colin Smith [aut, cre, cph] ,
Eric Sokol [aut] ,
Margaret O'Brien [aut] ,
Matt Bitters [ctb],
Melissa Chen [ctb],
Savannah Gonzales [ctb],
Matt Helmus [ctb],
Brendan Hobart [ctb],
Ruvi Jaimes [ctb],
Lara Janson [ctb],
Marta Jarzyna [ctb],
Michael Jus [...truncated...]
Maintainer: Colin Smith <colin.smith@wisc.edu>
Diff between ecocomDP versions 1.2.2 dated 2023-06-19 and 1.3.1 dated 2024-02-21
DESCRIPTION | 8 - MD5 | 57 +++---- NEWS.md | 14 + R/map_neon.ecocomdp.10003.001.001.R | 58 ++++--- R/map_neon.ecocomdp.10022.001.001.R | 232 ++++++++++++++++++------------ R/map_neon.ecocomdp.10043.001.001.R | 155 ++++++++++++++++---- R/map_neon.ecocomdp.10072.001.001.R | 167 +++++++++++---------- R/map_neon.ecocomdp.10093.001.001.R | 49 ++++-- R/map_neon.ecocomdp.20107.001.001.R | 212 ++++++++++++++++++--------- R/map_neon.ecocomdp.20120.001.001.R | 145 +++++++++++------- R/map_neon.ecocomdp.20166.001.001.R | 74 +++++++-- R/map_neon.ecocomdp.20219.001.001.R | 7 R/plot_taxa.R | 275 ++++++++++++++++++++++++------------ R/search_data.R | 5 R/utilities.R | 2 R/zzz.R | 5 README.md | 2 build/vignette.rds |binary inst/doc/convert.R | 2 inst/doc/create.R | 2 inst/doc/model_overview.R | 2 inst/doc/shared_practices_create.R | 2 inst/doc/use.R | 12 - inst/doc/use.html | 6 man/figures |only man/plot_sample_space_time.Rd | 13 + man/plot_sites.Rd | 4 man/plot_taxa_rank.Rd | 2 man/plot_taxa_sample_time.Rd | 1 man/search_data.Rd | 5 30 files changed, 987 insertions(+), 531 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [ctb]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.2.2 dated 2023-11-07 and 0.3.0 dated 2024-02-21
altdoc-0.2.2/altdoc/R/build.R |only altdoc-0.2.2/altdoc/R/preview.R |only altdoc-0.2.2/altdoc/R/reference.R |only altdoc-0.2.2/altdoc/R/reformat.R |only altdoc-0.2.2/altdoc/R/update.R |only altdoc-0.2.2/altdoc/R/use.R |only altdoc-0.2.2/altdoc/R/utils-rmd.R |only altdoc-0.2.2/altdoc/R/utils-yaml.R |only altdoc-0.2.2/altdoc/R/vignettes.R |only altdoc-0.2.2/altdoc/inst/docsify/README.md |only altdoc-0.2.2/altdoc/inst/docsify/_sidebar.md |only altdoc-0.2.2/altdoc/inst/docsify/index.html |only altdoc-0.2.2/altdoc/inst/docute/README.md |only altdoc-0.2.2/altdoc/inst/docute/index.html |only altdoc-0.2.2/altdoc/inst/misc |only altdoc-0.2.2/altdoc/man/init.Rd |only altdoc-0.2.2/altdoc/man/preview.Rd |only altdoc-0.2.2/altdoc/man/update_docs.Rd |only altdoc-0.2.2/altdoc/tests/testthat/test-rd2md.R |only altdoc-0.2.2/altdoc/tests/testthat/test-reformat.R |only altdoc-0.2.2/altdoc/tests/testthat/test-update_docs.R |only altdoc-0.2.2/altdoc/tests/testthat/test-use_docsify.R |only altdoc-0.2.2/altdoc/tests/testthat/test-use_docute.R |only altdoc-0.2.2/altdoc/tests/testthat/test-use_mkdocs.R |only altdoc-0.2.2/altdoc/tests/testthat/test-utils-yaml.R |only altdoc-0.2.2/altdoc/tests/testthat/test-vignettes.R |only altdoc-0.3.0/altdoc/DESCRIPTION | 47 + altdoc-0.3.0/altdoc/MD5 | 123 +++- altdoc-0.3.0/altdoc/NAMESPACE | 9 altdoc-0.3.0/altdoc/NEWS.md | 86 +++ altdoc-0.3.0/altdoc/R/altdoc_variables.R |only altdoc-0.3.0/altdoc/R/check.R | 81 +-- altdoc-0.3.0/altdoc/R/freeze.R |only altdoc-0.3.0/altdoc/R/import_man.R |only altdoc-0.3.0/altdoc/R/import_misc.R |only altdoc-0.3.0/altdoc/R/import_readme.R |only altdoc-0.3.0/altdoc/R/import_vignettes.R |only altdoc-0.3.0/altdoc/R/preview_docs.R |only altdoc-0.3.0/altdoc/R/qmd2md.R |only altdoc-0.3.0/altdoc/R/rd2qmd.R |only altdoc-0.3.0/altdoc/R/render_docs.R |only altdoc-0.3.0/altdoc/R/settings.R |only altdoc-0.3.0/altdoc/R/settings_docsify.R |only altdoc-0.3.0/altdoc/R/settings_docute.R |only altdoc-0.3.0/altdoc/R/settings_mkdocs.R |only altdoc-0.3.0/altdoc/R/settings_quarto_website.R |only altdoc-0.3.0/altdoc/R/setup_docs.R |only altdoc-0.3.0/altdoc/R/setup_github_actions.R |only altdoc-0.3.0/altdoc/R/utils.R | 247 +++------ altdoc-0.3.0/altdoc/README.md | 251 +++++++--- altdoc-0.3.0/altdoc/build |only altdoc-0.3.0/altdoc/inst/WORDLIST | 27 - altdoc-0.3.0/altdoc/inst/doc |only altdoc-0.3.0/altdoc/inst/docsify/docsify.html |only altdoc-0.3.0/altdoc/inst/docsify/docsify.md |only altdoc-0.3.0/altdoc/inst/docute/docute.html |only altdoc-0.3.0/altdoc/inst/gha |only altdoc-0.3.0/altdoc/inst/mkdocs |only altdoc-0.3.0/altdoc/inst/preamble |only altdoc-0.3.0/altdoc/inst/quarto_website |only altdoc-0.3.0/altdoc/man/figures |only altdoc-0.3.0/altdoc/man/preview_docs.Rd |only altdoc-0.3.0/altdoc/man/render_docs.Rd |only altdoc-0.3.0/altdoc/man/setup_docs.Rd |only altdoc-0.3.0/altdoc/man/setup_github_actions.Rd |only altdoc-0.3.0/altdoc/tests/spelling.R | 9 altdoc-0.3.0/altdoc/tests/testthat/DESCRIPTION |only altdoc-0.3.0/altdoc/tests/testthat/_snaps |only altdoc-0.3.0/altdoc/tests/testthat/examples/examples-man/between.Rd | 9 altdoc-0.3.0/altdoc/tests/testthat/examples/examples-man/is-internal.Rd |only altdoc-0.3.0/altdoc/tests/testthat/examples/examples-man/should-fail.Rd |only altdoc-0.3.0/altdoc/tests/testthat/examples/examples-qmd |only altdoc-0.3.0/altdoc/tests/testthat/examples/examples-vignettes/with-figure.Rmd | 2 altdoc-0.3.0/altdoc/tests/testthat/examples/testpkg.altdoc |only altdoc-0.3.0/altdoc/tests/testthat/helper.R | 32 - altdoc-0.3.0/altdoc/tests/testthat/test-check_md_structure.R |only altdoc-0.3.0/altdoc/tests/testthat/test-freeze.R |only altdoc-0.3.0/altdoc/tests/testthat/test-import_man.R |only altdoc-0.3.0/altdoc/tests/testthat/test-parallel.R |only altdoc-0.3.0/altdoc/tests/testthat/test-preview_docs.R |only altdoc-0.3.0/altdoc/tests/testthat/test-qmd2md.R |only altdoc-0.3.0/altdoc/tests/testthat/test-rd2qmd.R |only altdoc-0.3.0/altdoc/tests/testthat/test-render_docs.R |only altdoc-0.3.0/altdoc/tests/testthat/test-settings.R |only altdoc-0.3.0/altdoc/tests/testthat/test-setup_docs.R |only altdoc-0.3.0/altdoc/tests/testthat/test-setup_github_actions.R |only altdoc-0.3.0/altdoc/tests/testthat/test-update.R |only altdoc-0.3.0/altdoc/tests/testthat/test-utils.R | 84 +-- altdoc-0.3.0/altdoc/vignettes |only 89 files changed, 584 insertions(+), 423 deletions(-)
Title: Robust Land-Use Optimization
Description: Robust multi-criteria land-allocation optimization that explicitly accounts for the uncertainty of the indicators in the objective function. Solves the problem of allocating scarce land to various land-use options with regard to multiple, coequal indicators. The method aims to find the land allocation that represents the indicator composition with the best possible trade-off under uncertainty. optimLanduse includes the actual optimization procedure as described by Knoke et al. (2016) <doi:10.1038/ncomms11877> and the post-hoc calculation of the portfolio performance as presented by Gosling et al. (2020) <doi:10.1016/j.jenvman.2020.110248>.
Author: Kai Husmann [aut, cre] ,
Volker von Gross [aut] ,
Jasper Fuchs [aut] ,
Kai Boedeker [aut] ,
Carola Paul [aut] ,
Thomas Knoke [aut] ,
Goettingen University - Forest Economics and Sustainable Land-use
Planning [cph, fnd],
TUM School of Life Sciences - Fo [...truncated...]
Maintainer: Kai Husmann <kai.husmann@uni-goettingen.de>
Diff between optimLanduse versions 1.2.0 dated 2023-08-31 and 1.2.1 dated 2024-02-21
DESCRIPTION | 18 +++++++++++++++--- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 21 insertions(+), 5 deletions(-)
Title: Label Data Frames, Variables, and Values
Description: Create and use data frame labels for data frame objects (frame labels), their columns (name labels), and individual values of a column (value labels). Value labels include one-to-one and many-to-one labels for nominal and ordinal variables, as well as numerical range-based value labels for continuous variables. Convert value-labeled variables so each value is replaced by its corresponding value label. Add values-converted-to-labels columns to a value-labeled data frame while preserving parent columns. Filter and subset a value-labeled data frame using labels, while returning results in terms of values. Overlay labels in place of values in common R commands to increase interpretability. Generate tables of value frequencies, with categories expressed as raw values or as labels. Access data frames that show value-to-label mappings for easy reference.
Author: Robert Hartman [aut, cre],
The MITRE Corporation [cph]
Maintainer: Robert Hartman <rohartman@gmail.com>
Diff between labelr versions 0.1.2 dated 2024-01-23 and 0.1.3 dated 2024-02-21
labelr-0.1.2/labelr/inst/doc/labelr-getting-started.R |only labelr-0.1.2/labelr/inst/doc/labelr-getting-started.Rmd |only labelr-0.1.2/labelr/inst/doc/labelr-getting-started.html |only labelr-0.1.2/labelr/vignettes/labelr-getting-started.Rmd |only labelr-0.1.3/labelr/DESCRIPTION | 9 labelr-0.1.3/labelr/MD5 | 127 +++--- labelr-0.1.3/labelr/NAMESPACE | 221 ++++++----- labelr-0.1.3/labelr/NEWS.md |only labelr-0.1.3/labelr/R/add1m1.R | 11 labelr-0.1.3/labelr/R/add_lab_col1.R |only labelr-0.1.3/labelr/R/add_lab_cols.R | 109 ++--- labelr-0.1.3/labelr/R/add_lab_dumm1.R |only labelr-0.1.3/labelr/R/add_lab_dummies.R |only labelr-0.1.3/labelr/R/add_name_labs.R | 6 labelr-0.1.3/labelr/R/add_quant1.R | 18 labelr-0.1.3/labelr/R/add_quant_labs.R | 7 labelr-0.1.3/labelr/R/add_val1.R | 10 labelr-0.1.3/labelr/R/all_quant_labs.R |only labelr-0.1.3/labelr/R/as_base_data_frame.R | 2 labelr-0.1.3/labelr/R/axis_lab.R |only labelr-0.1.3/labelr/R/check_irregular.R | 4 labelr-0.1.3/labelr/R/clean_data_atts.R | 7 labelr-0.1.3/labelr/R/convert_labs.R | 23 + labelr-0.1.3/labelr/R/drop_name_labs.R | 5 labelr-0.1.3/labelr/R/drop_val1.R | 10 labelr-0.1.3/labelr/R/factor_to_lab_int.R |only labelr-0.1.3/labelr/R/flab.R | 47 +- labelr-0.1.3/labelr/R/greml.R | 45 +- labelr-0.1.3/labelr/R/gremlr.R | 44 +- labelr-0.1.3/labelr/R/has_decv.R | 4 labelr-0.1.3/labelr/R/is_numable.R | 4 labelr-0.1.3/labelr/R/lab_int_to_factor.R |only labelr-0.1.3/labelr/R/make_demo_data.R | 15 labelr-0.1.3/labelr/R/restore_factor_info.R | 3 labelr-0.1.3/labelr/R/sbrac.R | 2 labelr-0.1.3/labelr/R/sdrop.R | 4 labelr-0.1.3/labelr/R/sfilter.R | 2 labelr-0.1.3/labelr/R/slab.R | 58 +- labelr-0.1.3/labelr/R/somel.R | 4 labelr-0.1.3/labelr/R/ssort.R | 9 labelr-0.1.3/labelr/R/tabl.R | 292 +++++++++------ labelr-0.1.3/labelr/R/use_val_lab1.R |only labelr-0.1.3/labelr/R/use_val_labs.R | 77 +-- labelr-0.1.3/labelr/R/val_labs_vec.R | 11 labelr-0.1.3/labelr/README.md | 98 +---- labelr-0.1.3/labelr/build/vignette.rds |binary labelr-0.1.3/labelr/inst/doc/labelr-introduction.R |only labelr-0.1.3/labelr/inst/doc/labelr-introduction.Rmd |only labelr-0.1.3/labelr/inst/doc/labelr-introduction.html |only labelr-0.1.3/labelr/inst/doc/labelr-special-topics.R |only labelr-0.1.3/labelr/inst/doc/labelr-special-topics.Rmd |only labelr-0.1.3/labelr/inst/doc/labelr-special-topics.html |only labelr-0.1.3/labelr/man/add_lab_col1.Rd |only labelr-0.1.3/labelr/man/add_lab_cols.Rd | 69 +-- labelr-0.1.3/labelr/man/add_lab_dumm1.Rd |only labelr-0.1.3/labelr/man/add_lab_dummies.Rd |only labelr-0.1.3/labelr/man/all_quant_labs.Rd |only labelr-0.1.3/labelr/man/as_base_data_frame.Rd | 2 labelr-0.1.3/labelr/man/axis_lab.Rd |only labelr-0.1.3/labelr/man/check_irregular.Rd | 4 labelr-0.1.3/labelr/man/convert_labs.Rd | 4 labelr-0.1.3/labelr/man/factor_to_lab_int.Rd |only labelr-0.1.3/labelr/man/flab.Rd | 47 +- labelr-0.1.3/labelr/man/greml.Rd | 42 +- labelr-0.1.3/labelr/man/gremlr.Rd | 42 +- labelr-0.1.3/labelr/man/has_decv.Rd | 4 labelr-0.1.3/labelr/man/is_numable.Rd | 4 labelr-0.1.3/labelr/man/lab_int_to_factor.Rd |only labelr-0.1.3/labelr/man/make_demo_data.Rd | 15 labelr-0.1.3/labelr/man/restore_factor_info.Rd | 3 labelr-0.1.3/labelr/man/sdrop.Rd | 4 labelr-0.1.3/labelr/man/slab.Rd | 56 +- labelr-0.1.3/labelr/man/somel.Rd | 2 labelr-0.1.3/labelr/man/tabl.Rd | 144 +++---- labelr-0.1.3/labelr/man/use_val_lab1.Rd |only labelr-0.1.3/labelr/man/use_val_labs.Rd | 40 -- labelr-0.1.3/labelr/man/val_labs_vec.Rd | 124 +++--- labelr-0.1.3/labelr/vignettes/labelr-introduction.Rmd |only labelr-0.1.3/labelr/vignettes/labelr-special-topics.Rmd |only 79 files changed, 1014 insertions(+), 880 deletions(-)
Title: Journal Abbreviations for BibTeX Documents
Description: Since the reference management software (such as 'Zotero', 'Mendeley') exports Bib file journal abbreviation is not detailed enough, the 'journalabbr' package only abbreviates the journal field of Bib file, and then outputs a new Bib file for generating reference format with journal abbreviation on other software (such as 'texstudio'). The abbreviation table is from 'JabRef'. At the same time, 'Shiny' application is provided to generate 'thebibliography', a reference format that can be directly used for latex paper writing based on 'Rmd' files.
Author: ShuCai Zou [aut, cre],
Yu Chen [aut]
Maintainer: ShuCai Zou <zscmoyujian@163.com>
Diff between journalabbr versions 0.4.0 dated 2022-08-09 and 0.4.3 dated 2024-02-21
journalabbr-0.4.0/journalabbr/tests/testthat/test-roxytest-testexamples-add_abbrtable.R |only journalabbr-0.4.0/journalabbr/tests/testthat/test-roxytest-testexamples-read_bib2dt.R |only journalabbr-0.4.0/journalabbr/tests/testthat/test-roxytest-testexamples-replace_field.R |only journalabbr-0.4.3/journalabbr/DESCRIPTION | 26 +++--- journalabbr-0.4.3/journalabbr/MD5 | 38 +++++----- journalabbr-0.4.3/journalabbr/NAMESPACE | 2 journalabbr-0.4.3/journalabbr/NEWS.md | 28 +++++++ journalabbr-0.4.3/journalabbr/R/add_abbrtable.R | 5 - journalabbr-0.4.3/journalabbr/R/journalabbr-package.R | 2 journalabbr-0.4.3/journalabbr/R/read_bib2dt.R | 9 -- journalabbr-0.4.3/journalabbr/R/replace_field.R | 5 - journalabbr-0.4.3/journalabbr/R/sysdata.rda |binary journalabbr-0.4.3/journalabbr/README.md | 23 +++++- journalabbr-0.4.3/journalabbr/inst/extdata/myabbr.csv | 11 +- journalabbr-0.4.3/journalabbr/inst/shiny-examples/appckwx/app.R | 2 journalabbr-0.4.3/journalabbr/man/abbr_bib.Rd | 4 - journalabbr-0.4.3/journalabbr/man/add_abbrtable.Rd | 2 journalabbr-0.4.3/journalabbr/man/read_bib2dt.Rd | 2 journalabbr-0.4.3/journalabbr/man/replace_field.Rd | 2 journalabbr-0.4.3/journalabbr/tests/testthat.R | 4 - journalabbr-0.4.3/journalabbr/tests/testthat/test-add_abbrtable.R |only journalabbr-0.4.3/journalabbr/tests/testthat/test-read_bib2dt.R |only journalabbr-0.4.3/journalabbr/tests/testthat/test-replace_field.R |only 23 files changed, 103 insertions(+), 62 deletions(-)
Title: DCC Models with GARCH and GARCH-MIDAS Specifications in the
Univariate Step, RiskMetrics, Moving Covariance and Scalar and
Diagonal BEKK Models
Description: Estimates a variety of Dynamic Conditional Correlation (DCC) models. More in detail, the 'dccmidas' package allows the estimation of the corrected DCC (cDCC) of Aielli (2013) <doi:10.1080/07350015.2013.771027>, the DCC-MIDAS of Colacito et al. (2011) <doi:10.1016/j.jeconom.2011.02.013>, the Asymmetric DCC of Cappiello et al. <doi:10.1093/jjfinec/nbl005>, and the Dynamic Equicorrelation (DECO) of Engle and Kelly (2012) <doi:10.1080/07350015.2011.652048>. 'dccmidas' offers the possibility of including standard GARCH <doi:10.1016/0304-4076(86)90063-1>, GARCH-MIDAS <doi:10.1162/REST_a_00300> and Double Asymmetric GARCH-MIDAS <doi:10.1016/j.econmod.2018.07.025> models in the univariate estimation. Moreover, also the scalar and diagonal BEKK <doi:10.1017/S0266466600009063> models can be estimated. Finally, the package calculates also the var-cov matrix under two non-parametric models: the Moving Covariance and the RiskMetrics specifications.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vcandila@unisa.it>
Diff between dccmidas versions 0.1.0 dated 2021-03-15 and 0.1.2 dated 2024-02-21
dccmidas-0.1.0/dccmidas/man/moving_cov_est.Rd |only dccmidas-0.1.0/dccmidas/man/riskmetrics_est.Rd |only dccmidas-0.1.2/dccmidas/DESCRIPTION | 24 dccmidas-0.1.2/dccmidas/MD5 | 48 dccmidas-0.1.2/dccmidas/NEWS.md |only dccmidas-0.1.2/dccmidas/R/data.R | 6 dccmidas-0.1.2/dccmidas/R/functions.R | 1524 +++++++++++++++++++++++-- dccmidas-0.1.2/dccmidas/build/partial.rdb |binary dccmidas-0.1.2/dccmidas/inst/CITATION | 6 dccmidas-0.1.2/dccmidas/inst/REFERENCES.bib | 25 dccmidas-0.1.2/dccmidas/man/a_dcc_mat_est.Rd | 8 dccmidas-0.1.2/dccmidas/man/bekk_fit.Rd |only dccmidas-0.1.2/dccmidas/man/cov_eval.Rd | 11 dccmidas-0.1.2/dccmidas/man/dBEKK_loglik.Rd |only dccmidas-0.1.2/dccmidas/man/dBEKK_mat_est.Rd |only dccmidas-0.1.2/dccmidas/man/dcc_fit.Rd | 24 dccmidas-0.1.2/dccmidas/man/dcc_mat_est.Rd | 8 dccmidas-0.1.2/dccmidas/man/deco_mat_est.Rd | 8 dccmidas-0.1.2/dccmidas/man/ftse100.Rd | 2 dccmidas-0.1.2/dccmidas/man/moving_cov.Rd |only dccmidas-0.1.2/dccmidas/man/nasdaq.Rd | 2 dccmidas-0.1.2/dccmidas/man/plot_dccmidas.Rd | 11 dccmidas-0.1.2/dccmidas/man/riskmetrics_mat.Rd |only dccmidas-0.1.2/dccmidas/man/sBEKK_loglik.Rd |only dccmidas-0.1.2/dccmidas/man/sBEKK_mat_est.Rd |only dccmidas-0.1.2/dccmidas/man/sp500.Rd | 2 dccmidas-0.1.2/dccmidas/src/Makevars | 1 dccmidas-0.1.2/dccmidas/src/Makevars.win | 1 dccmidas-0.1.2/dccmidas/src/RcppExports.cpp | 5 dccmidas-0.1.2/dccmidas/src/invf.cpp | 2 30 files changed, 1554 insertions(+), 164 deletions(-)
Title: Computation of Variance-Based Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to fourth-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol' indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis. An overview of the package can be found in Puy et al. (2022) <doi:10.18637/jss.v102.i05>.
Author: Arnald Puy [aut, cre] ,
Bertrand Ioos [ctb] ,
Gilles Pujol [ctb] ,
RStudio [cph]
Maintainer: Arnald Puy <arnald.puy@pm.me>
Diff between sensobol versions 1.1.4 dated 2023-04-06 and 1.1.5 dated 2024-02-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 11 ++++------- inst/doc/sensobol.pdf |binary 7 files changed, 19 insertions(+), 16 deletions(-)
Title: Working with netCDF for Essential Biodiversity Variables
Description: The concept of Essential Biodiversity Variables (EBV, <https://geobon.org/ebvs/what-are-ebvs/>)
comes with a data structure based on the Network Common Data Form (netCDF).
The 'ebvcube' 'R' package provides functionality to easily create, access and
visualise this data. The EBV netCDFs can be downloaded from the EBV Data
Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
Author: Luise Quoss [aut, cre] ,
Nestor Fernandez [aut] ,
Christian Langer [aut] ,
Jose Valdez [aut] ,
Henrique Miguel Pereira [aut]
Maintainer: Luise Quoss <luise.quoss@idiv.de>
Diff between ebvcube versions 0.1.6 dated 2023-10-11 and 0.1.7 dated 2024-02-21
DESCRIPTION | 14 - MD5 | 53 +-- NEWS.md | 14 - R/ebv_add_data.R | 14 - R/ebv_attribute.R | 2 R/ebv_create.R | 22 - R/ebv_download.R | 70 ++++- R/ebv_map.R | 6 R/ebv_read.R | 6 R/ebv_read_bb.R | 6 R/ebv_read_shp.R | 4 R/ebv_utils.R | 194 +++++++++++++- README.md | 6 inst/CITATION | 34 +- inst/docs/ebvcube_0.1.7.pdf |only inst/extdata/baisero_spepop_id5_20220405_v1_empty.nc |binary inst/extdata/martins_comcom_subset.nc |binary inst/extdata/metadata.json | 4 inst/extdata/test.nc |binary inst/extdata/testdata/cSAR-iDiv.json | 4 inst/extdata/testdata/pereira_csar_bes_sim_20220830_4d.nc |binary inst/extdata/testdata/test.nc |binary inst/extdata/testdata/test_att.nc |binary inst/extdata/testdata/test_create.nc |binary man/ebv_add_data.Rd | 6 man/ebv_download.Rd | 16 - man/ebv_read_bb.Rd | 2 tests/testthat/test-ebv_properties.R | 2 28 files changed, 372 insertions(+), 107 deletions(-)
Title: Calculating Spatial Risk
Description: Methods for spatial risk calculations. It offers an efficient approach to determine the sum of all observations within a
circle of a certain radius. This might be beneficial for insurers who are required (by a recent European Commission regulation) to determine
the maximum value of insured fire risk policies of all buildings that are partly or fully located within a circle of a radius of 200m. See
Church (1974) <doi:10.1007/BF01942293> for a description of the problem.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between spatialrisk versions 0.7.0 dated 2021-11-10 and 0.7.1 dated 2024-02-21
spatialrisk-0.7.0/spatialrisk/R/gh_grid_search.R |only spatialrisk-0.7.0/spatialrisk/R/map_tmap.R |only spatialrisk-0.7.0/spatialrisk/R/nlchoropleth.R |only spatialrisk-0.7.0/spatialrisk/man/choropleth_sf.Rd |only spatialrisk-0.7.0/spatialrisk/man/choropleth_tmap.Rd |only spatialrisk-0.7.1/spatialrisk/DESCRIPTION | 13 spatialrisk-0.7.1/spatialrisk/MD5 | 93 +-- spatialrisk-0.7.1/spatialrisk/NAMESPACE | 42 + spatialrisk-0.7.1/spatialrisk/NEWS.md | 4 spatialrisk-0.7.1/spatialrisk/R/Groningen.R | 6 spatialrisk-0.7.1/spatialrisk/R/choropleth.R | 31 - spatialrisk-0.7.1/spatialrisk/R/concentration.R | 40 + spatialrisk-0.7.1/spatialrisk/R/haversine.R | 20 spatialrisk-0.7.1/spatialrisk/R/highest_concentration.R | 253 ++++++---- spatialrisk-0.7.1/spatialrisk/R/insurance.R | 6 spatialrisk-0.7.1/spatialrisk/R/knmi_historic.R | 59 +- spatialrisk-0.7.1/spatialrisk/R/kriging.R | 45 + spatialrisk-0.7.1/spatialrisk/R/map_ggplot2.R | 45 + spatialrisk-0.7.1/spatialrisk/R/nl_gemeente.R | 52 +- spatialrisk-0.7.1/spatialrisk/R/plot_points.R | 27 - spatialrisk-0.7.1/spatialrisk/R/points_in_circle.R | 24 spatialrisk-0.7.1/spatialrisk/R/points_to_polygon.R | 62 +- spatialrisk-0.7.1/spatialrisk/R/smooth_sphere.R | 45 + spatialrisk-0.7.1/spatialrisk/R/utils.R | 35 + spatialrisk-0.7.1/spatialrisk/R/zzz.R | 2 spatialrisk-0.7.1/spatialrisk/man/Groningen.Rd | 6 spatialrisk-0.7.1/spatialrisk/man/choropleth.Rd | 15 spatialrisk-0.7.1/spatialrisk/man/choropleth_ggplot2.Rd | 11 spatialrisk-0.7.1/spatialrisk/man/concentration.Rd | 21 spatialrisk-0.7.1/spatialrisk/man/haversine.Rd | 14 spatialrisk-0.7.1/spatialrisk/man/highest_concentration.Rd | 137 +---- spatialrisk-0.7.1/spatialrisk/man/insurance.Rd | 7 spatialrisk-0.7.1/spatialrisk/man/interpolate_krige.Rd | 23 spatialrisk-0.7.1/spatialrisk/man/interpolate_spline.Rd | 27 - spatialrisk-0.7.1/spatialrisk/man/knmi_historic_data.Rd | 10 spatialrisk-0.7.1/spatialrisk/man/knmi_stations.Rd | 3 spatialrisk-0.7.1/spatialrisk/man/neighborhood_gh_search.Rd | 60 -- spatialrisk-0.7.1/spatialrisk/man/nl_corop.Rd | 9 spatialrisk-0.7.1/spatialrisk/man/nl_gemeente.Rd | 5 spatialrisk-0.7.1/spatialrisk/man/nl_postcode2.Rd | 9 spatialrisk-0.7.1/spatialrisk/man/nl_postcode3.Rd | 9 spatialrisk-0.7.1/spatialrisk/man/nl_postcode4.Rd | 16 spatialrisk-0.7.1/spatialrisk/man/nl_provincie.Rd | 3 spatialrisk-0.7.1/spatialrisk/man/plot.Rd | 38 - spatialrisk-0.7.1/spatialrisk/man/plot.concentration.Rd | 29 - spatialrisk-0.7.1/spatialrisk/man/plot_points.Rd | 5 spatialrisk-0.7.1/spatialrisk/man/points_in_circle.Rd | 18 spatialrisk-0.7.1/spatialrisk/man/points_to_polygon.Rd | 15 spatialrisk-0.7.1/spatialrisk/tests/testthat/test_concentration.R | 30 - spatialrisk-0.7.1/spatialrisk/tests/testthat/test_pointsincircle.R | 9 50 files changed, 835 insertions(+), 598 deletions(-)
Title: Cryptographic Hash and Extendable-Output Functions
Description: SHA-256, SHA-3 cryptographic hash and SHAKE256 extendable-output
functions (XOF). The SHA-3 Secure Hash Standard was published by the
National Institute of Standards and Technology (NIST) in 2015 at
<doi:10.6028/NIST.FIPS.202>. The SHA-256 Secure Hash Standard was published
by NIST in 2002 at
<https://csrc.nist.gov/publications/fips/fips180-2/fips180-2.pdf>. Fast and
memory-efficient implementation using the core algorithms from 'Mbed TLS'
under the Trusted Firmware Project
<https://www.trustedfirmware.org/projects/mbed-tls/>.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 0.2.0 dated 2024-02-01 and 0.3.0 dated 2024-02-21
DESCRIPTION | 19 + MD5 | 23 +- NAMESPACE | 2 NEWS.md | 5 R/base.R | 54 +++-- README.md | 48 ++-- man/secretbase-package.Rd | 11 - man/sha256.Rd |only man/sha3.Rd | 15 - src/init.c | 2 src/secret.c | 458 ++++++++++++++++++++++++++++++++++++++++++---- src/secret.h | 24 ++ tests/tests.R | 24 ++ 13 files changed, 569 insertions(+), 116 deletions(-)
Title: Estimation, Variable Selection and Prediction for Functional
Semiparametric Models
Description: Routines for estimation or simultaneous estimation and variable selection of several functional semiparametric models with scalar response, such as the functional single-index model, the semi-functional partial linear model or the semi-functional partial linear single-index model. In addition, it includes algorithms for dealing with scalar covariates with linear effect coming from the discretization of a curve in the cases of the linear model, the multi-functional partial linear model and the multi-functional partial linear single-index model.
Author: German Aneiros [aut],
Silvia Novo [aut, cre]
Maintainer: Silvia Novo <snovo@est-econ.uc3m.es>
Diff between fsemipar versions 1.0 dated 2023-01-23 and 1.0.1 dated 2024-02-21
DESCRIPTION | 15 +++------- MD5 | 60 ++++++++++++++++++++--------------------- R/IASSMR.kNN.fit.R | 2 - R/PVS.fit.R | 5 ++- R/PVS.kernel.fit.R | 4 +- R/fsim.kNN.R | 2 - R/fsim.kernel.fit.fixedtheta.R | 48 ++++++++++++++++++-------------- R/sfpl.kernel.fit.R | 3 -- build/partial.rdb |binary man/FASSMR.kNN.fit.Rd | 32 ++++++++++----------- man/FASSMR.kernel.fit.Rd | 34 +++++++++++------------ man/IASSMR.kNN.fit.Rd | 54 ++++++++++++++++++------------------ man/IASSMR.kernel.fit.Rd | 58 +++++++++++++++++++-------------------- man/PVS.fit.Rd | 59 +++++++++++++++++++++------------------- man/PVS.kNN.fit.Rd | 50 +++++++++++++++++----------------- man/PVS.kernel.fit.Rd | 54 ++++++++++++++++++------------------ man/fsemipar-package.Rd | 10 ------ man/fsim.kNN.fit.Rd | 4 +- man/fsim.kNN.test.Rd | 2 - man/fsim.kernel.fit.Rd | 2 - man/lm.pels.fit.Rd | 6 ++-- man/plot.classes.Rd | 2 - man/predict.fsim.Rd | 2 - man/predict.lm.Rd | 2 - man/predict.sfpl.Rd | 2 - man/predict.sfplsim.FASSMR.Rd | 4 +- man/print.summary.mfplsim.Rd | 2 - man/sfpl.kNN.fit.Rd | 14 ++++----- man/sfpl.kernel.fit.Rd | 16 +++++----- man/sfplsim.kNN.fit.Rd | 24 ++++++++-------- man/sfplsim.kernel.fit.Rd | 16 +++++----- 31 files changed, 292 insertions(+), 296 deletions(-)
Title: Create Maps and Visualize Data in 2D and 3D
Description: Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayshader versions 0.35.7 dated 2023-06-13 and 0.37.3 dated 2024-02-21
DESCRIPTION | 24 +-- MD5 | 251 ++++++++++++++++---------------- NAMESPACE | 5 R/add_overlay.R | 12 + R/add_shadow.R | 8 - R/add_water.R | 4 R/ambient_shade.R | 8 - R/calculate_normal.R | 4 R/colorspace_functions.R | 10 - R/constant_shade.R | 10 - R/convert_path_to_animation_coords.R | 4 R/convert_rgl_to_raymesh.R |only R/generate_altitude_overlay.R | 6 R/generate_compass_overlay.R | 31 ++- R/generate_contour_overlay.R | 27 ++- R/generate_label_overlay.R | 22 +- R/generate_line_overlay.R | 20 +- R/generate_point_overlay.R | 14 + R/generate_polygon_overlay.R | 23 ++ R/generate_scalebar_overlay.R | 29 ++- R/generate_surface.R | 8 - R/generate_waterline_overlay.R | 29 ++- R/get_ids_with_labels.R | 8 - R/get_interpolated_points_path.R | 4 R/get_polygon_data_value.R |only R/height_shade.R | 6 R/lamb_shade.R | 8 - R/make_base.R | 96 +++++++----- R/make_base_triangulated.R | 2 R/make_lines.R | 45 +++-- R/make_water.R | 37 ++-- R/make_waterlines.R | 10 + R/plot_3d.R | 45 +++-- R/plot_gg.R | 34 ++-- R/plot_map.R | 12 - R/raster_to_matrix.R | 2 R/ray_shade.R | 8 - R/render_beveled_polygons.R |only R/render_buildings.R |only R/render_camera.R | 15 + R/render_clouds.R | 33 +--- R/render_compass.R | 16 +- R/render_contours.R | 49 ++++-- R/render_depth.R | 30 ++- R/render_floating_overlay.R | 2 R/render_highquality.R | 136 +++++++++-------- R/render_label.R | 14 - R/render_multipolygonz.R | 2 R/render_obj.R | 36 +++- R/render_path.R | 61 ++++--- R/render_points.R | 10 - R/render_polygons.R | 31 ++- R/render_raymesh.R |only R/render_resize_window.R | 6 R/render_scalebar.R | 16 +- R/render_snapshot.R | 32 ++-- R/render_snapshot_software.R | 45 ++--- R/render_tree.R | 25 ++- R/render_water.R | 8 - R/resize_matrix.R | 10 - R/save_3dprint.R | 8 - R/save_multipolygonz_to_obj.R | 17 +- R/save_obj.R | 6 R/texture_shade.R | 12 - R/transform_into_heightmap_coords.R | 21 +- R/transform_sf_to_raycoords.R |only R/utils.R | 20 +- R/zzz.R | 2 man/add_overlay.Rd | 8 - man/add_shadow.Rd | 8 - man/add_water.Rd | 4 man/ambient_shade.Rd | 6 man/calculate_normal.Rd | 4 man/cloud_shade.Rd | 4 man/constant_shade.Rd | 8 - man/convert_path_to_animation_coords.Rd | 4 man/convert_rgl_to_raymesh.Rd |only man/darken_color.Rd | 2 man/gen_fractal_perlin.Rd | 3 man/generate_altitude_overlay.Rd | 6 man/generate_base_shape.Rd | 3 man/generate_cloud_layer.Rd | 3 man/generate_compass_overlay.Rd | 26 ++- man/generate_contour_overlay.Rd | 16 +- man/generate_label_overlay.Rd | 16 +- man/generate_line_overlay.Rd | 12 + man/generate_point_overlay.Rd | 8 - man/generate_polygon_overlay.Rd | 14 + man/generate_scalebar_overlay.Rd | 24 +-- man/generate_waterline_overlay.Rd | 32 ++-- man/get_polygon_data_value.Rd |only man/height_shade.Rd | 6 man/lamb_shade.Rd | 8 - man/make_base_triangulated.Rd | 3 man/plot_3d.Rd | 23 +- man/plot_gg.Rd | 28 +-- man/plot_map.Rd | 8 - man/raster_to_matrix.Rd | 2 man/ray_shade.Rd | 8 - man/raymarch_cloud_layer.Rd | 3 man/reduce_matrix_size.Rd | 2 man/render_beveled_polygons.Rd |only man/render_buildings.Rd |only man/render_camera.Rd | 12 - man/render_clouds.Rd | 24 +-- man/render_compass.Rd | 16 +- man/render_contours.Rd | 12 - man/render_depth.Rd | 23 +- man/render_floating_overlay.Rd | 2 man/render_highquality.Rd | 50 ++++-- man/render_label.Rd | 14 - man/render_multipolygonz.Rd | 2 man/render_obj.Rd | 24 ++- man/render_path.Rd | 20 +- man/render_points.Rd | 10 - man/render_polygons.Rd | 18 +- man/render_raymesh.Rd |only man/render_resize_window.Rd | 6 man/render_scalebar.Rd | 16 +- man/render_snapshot.Rd | 29 +-- man/render_snapshot_software.Rd | 13 - man/render_tree.Rd | 17 +- man/render_water.Rd | 8 - man/resize_matrix.Rd | 8 - man/run_documentation.Rd | 9 - man/save_3dprint.Rd | 8 - man/save_obj.Rd | 6 man/texture_shade.Rd | 12 - man/transform_into_heightmap_coords.Rd | 3 man/transform_points_custom_crs.Rd |only man/transform_points_into_raycoords.Rd |only man/transform_polygon_custom_crs.Rd |only man/transform_polygon_into_raycoords.Rd |only src/make_base_cpp.cpp | 48 +++++- 134 files changed, 1284 insertions(+), 957 deletions(-)
Title: Access Open Target Genetics
Description: Interact seamlessly with Open Target Genetics' GraphQL endpoint to query and retrieve tidy data tables, facilitating the analysis of genetic data. For more information about the Open Target Genetics API(<https://genetics.opentargets.org/api>).
Author: Amir Feizi [aut, cre],
Kamalika Ray [aut]
Maintainer: Amir Feizi <afeizi@gmail.com>
Diff between otargen versions 1.1.0 dated 2023-12-12 and 1.1.1 dated 2024-02-21
otargen-1.1.0/otargen/man/get_genes.Rd |only otargen-1.1.1/otargen/DESCRIPTION | 7 - otargen-1.1.1/otargen/MD5 | 26 ++-- otargen-1.1.1/otargen/NAMESPACE | 2 otargen-1.1.1/otargen/NEWS.md | 29 ++++ otargen-1.1.1/otargen/R/getLociGenes.R | 2 otargen-1.1.1/otargen/R/pheWAS.R | 1 otargen-1.1.1/otargen/R/plot_l2g.R | 13 +- otargen-1.1.1/otargen/R/plot_manhattan.R | 1 otargen-1.1.1/otargen/R/plot_phewas.R | 1 otargen-1.1.1/otargen/README.md | 90 ++++----------- otargen-1.1.1/otargen/man/getLociGenes.Rd |only otargen-1.1.1/otargen/man/plot_l2g.Rd | 8 + otargen-1.1.1/otargen/tests/testthat/test-getLociGenes.R | 4 otargen-1.1.1/otargen/tests/testthat/test-plot_l2g.R | 1 15 files changed, 89 insertions(+), 96 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.1.4 dated 2024-01-09 and 0.1.5 dated 2024-02-21
NMdata-0.1.4/NMdata/tests/testthat/testReference/NMreadExt_01.rds |only NMdata-0.1.4/NMdata/tests/testthat/testReference/NMreadExt_03.rds |only NMdata-0.1.4/NMdata/tests/testthat/testReference/NMreadExt_04.rds |only NMdata-0.1.5/NMdata/DESCRIPTION | 6 NMdata-0.1.5/NMdata/MD5 | 48 ++-- NMdata-0.1.5/NMdata/NEWS.md | 34 +++ NMdata-0.1.5/NMdata/R/NMdataConf.R | 98 ++++++++-- NMdata-0.1.5/NMdata/R/NMorderColumns.R | 33 +-- NMdata-0.1.5/NMdata/R/NMreadExt.R | 58 ++++- NMdata-0.1.5/NMdata/R/NMreadParsText.R | 37 +++ NMdata-0.1.5/NMdata/R/addTableStep.R | 1 NMdata-0.1.5/NMdata/R/egdt.R | 4 NMdata-0.1.5/NMdata/R/flagsCount.R | 9 NMdata-0.1.5/NMdata/man/NMdataConf.Rd | 14 + NMdata-0.1.5/NMdata/man/NMorderColumns.Rd | 23 +- NMdata-0.1.5/NMdata/man/NMreadExt.Rd | 49 ++++- NMdata-0.1.5/NMdata/man/NMreadParsText.Rd | 11 + NMdata-0.1.5/NMdata/man/egdt.Rd | 4 NMdata-0.1.5/NMdata/tests/testthat/testReference/NMdataConf_01.rds |binary NMdata-0.1.5/NMdata/tests/testthat/testReference/NMdataConf_02.rds |binary NMdata-0.1.5/NMdata/tests/testthat/testReference/NMreadExt_02.rds |binary NMdata-0.1.5/NMdata/tests/testthat/testReference/NMreadExt_06.rds |only NMdata-0.1.5/NMdata/tests/testthat/testReference/NMreadParText_02.rds |only NMdata-0.1.5/NMdata/tests/testthat/testReference/NMreadParText_03.rds |only NMdata-0.1.5/NMdata/tests/testthat/test_NMdataConf.R | 18 + NMdata-0.1.5/NMdata/tests/testthat/test_NMreadExt.R | 21 ++ NMdata-0.1.5/NMdata/tests/testthat/test_NMreadParText.R |only NMdata-0.1.5/NMdata/tests/testthat/test_NMreadTab.R | 1 NMdata-0.1.5/NMdata/tests/testthat/test_flagsCount.R |only 29 files changed, 373 insertions(+), 96 deletions(-)
Title: Cluster Adjusted t Statistic Applications
Description: Simulation results detailed in Esarey and Menger (2019) <doi:10.1017/psrm.2017.42>
demonstrate that cluster adjusted t statistics (CATs) are an effective method
for correcting standard errors in scenarios with a small number of clusters.
The 'mmiCATs' package offers a suite of tools for working with CATs. The
mmiCATs() function initiates a 'shiny' web application, facilitating
the analysis of data utilizing CATs, as implemented in the cluster.im.glm()
function from the 'clusterSEs' package. Additionally, the pwr_func_lmer()
function is designed to simplify the process of conducting simulations to
compare mixed effects models with CATs models. For educational purposes, the
CloseCATs() function launches a 'shiny' application card game, aimed at enhancing
users' understanding of the conditions under which CATs should be preferred
over random intercept models.
Author: Mackson Ncube [aut, cre],
mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Diff between mmiCATs versions 0.1.0 dated 2024-02-16 and 0.1.1 dated 2024-02-21
DESCRIPTION | 8 LICENSE | 4 MD5 | 18 R/CloseCATs.R | 598 ++++++++++++++++---------------- R/cluster_im_glmrob.R | 304 ++++++++-------- R/cluster_im_lmRob.R | 278 +++++++------- R/pwr_func_lmer.R | 496 +++++++++++++------------- tests/testthat/test-cc_game_mgmt.R | 14 tests/testthat/test-cluster_im_glmrob.R | 222 +++++------ tests/testthat/test-cluster_im_lmRob.R | 254 +++++++------ 10 files changed, 1110 insertions(+), 1086 deletions(-)
Title: Compositional Data Analysis for Microbiome Studies
Description: Functions for microbiome data analysis that take into account its compositional nature. Performs variable selection through penalized regression for both, cross-sectional and longitudinal studies, and for binary and continuous outcomes.
Author: Malu Calle [aut] ,
Toni Susin [aut, cre] ,
Meritxell Pujolassos [aut]
Maintainer: Toni Susin <toni.susin@upc.edu>
Diff between coda4microbiome versions 0.2.2 dated 2024-01-26 and 0.2.3 dated 2024-02-21
DESCRIPTION | 6 +-- MD5 | 8 ++--- R/coda4microbiome_functions.R | 42 +++++++++++++++++++++------ R/coda4microbiome_longitudinal_functions.R | 44 ++++++++++++++++++++++------- R/coda_coxnet.R | 31 ++++++++++++++------ 5 files changed, 95 insertions(+), 36 deletions(-)
More information about coda4microbiome at CRAN
Permanent link
Title: Bootstrap Methods for Various Network Estimation Routines
Description: Bootstrap methods to assess accuracy and stability of estimated network structures
and centrality indices <doi:10.3758/s13428-017-0862-1>. Allows for flexible
specification of any undirected network estimation procedure in R, and offers
default sets for various estimation routines.
Author: Sacha Epskamp [aut, cre],
Eiko I. Fried [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between bootnet versions 1.5.6 dated 2023-10-04 and 1.6 dated 2024-02-21
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NEWS | 3 + R/defaultFunctions.R | 78 ++++++++++++++++++++++++++++++++-------- R/plotMethod.R | 1 man/estimateNetwork.Rd | 95 ++++++++++++++++++++++++++----------------------- 6 files changed, 128 insertions(+), 67 deletions(-)
Title: Fast Generation of High-Dimensional Random Vectors
Description: Simulate multivariate data with arbitrary marginal distributions.
'bigsimr' is a package for simulating high-dimensional multivariate data with
a target correlation and arbitrary marginal distributions via Gaussian copula.
It utilizes the Julia package 'Bigsimr.jl' for its core routines.
Author: Alex Knudson [aut, cre],
Grant Schissler [aut],
Duc Tran [ctb]
Maintainer: Alex Knudson <alexk.706@gmail.com>
Diff between bigsimr versions 0.11.2 dated 2021-09-11 and 0.12.0 dated 2024-02-21
DESCRIPTION | 33 ++-- MD5 | 20 +- NAMESPACE | 8 - R/bigsimr.R | 93 ++++++------- R/distributions.R | 51 ++----- README.md | 292 +++++++++++++++++++++--------------------- inst/COPYRIGHTS | 42 +++--- man/bigsimr_setup.Rd | 62 +++----- man/distributions_setup.Rd | 48 ++---- tests/testthat.R | 8 - tests/testthat/test-bigsimr.R | 44 ------ 11 files changed, 311 insertions(+), 390 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-25 0.2.1
2022-08-07 0.2.0
2022-03-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-28 1.0.5
2023-03-27 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-04 0.4.0
2024-01-14 0.3.2
2023-12-08 0.3.1
2023-12-02 0.3.0
2023-11-03 0.2.0
2023-10-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-05 0.3.2
2024-01-31 0.3.1
2023-11-08 0.3.0
2023-09-29 0.2.7
2023-03-31 0.2.6
2023-01-23 0.2.5
2022-12-04 0.2.4
2022-09-02 0.2.3
2022-08-24 0.2.2
2022-01-04 0.2.1
2021-10-06 0.1.4
2021-08-12 0.1.3
2021-08-10 0.1.2
2021-06-30 0.1.1
2021-06-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-15 1.2.1
2023-12-13 1.2.0
2023-10-12 1.1.1
2023-02-14 1.1.0
2022-07-07 1.0.3
2022-05-02 1.0.2
2022-04-07 1.0.1
2022-03-14 1.0.0
2021-06-16 0.3.0
2021-03-13 0.2.0
2021-02-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-08 1.1.3
2022-11-06 1.1.2
2022-08-11 1.1.1
2022-07-22 1.1.0
2021-11-12 1.0.0
2021-05-25 0.1.1
2021-05-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-06 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-05 1.0.4
2024-01-31 1.0.3
2024-01-14 1.0.2
2023-11-08 1.0.1
2023-11-04 1.0.0
2023-09-27 0.3.3
2023-03-25 0.3.2
2023-03-05 0.3.1
2023-01-22 0.3.0
2022-12-02 0.2.0
2022-09-02 0.1.1
2022-08-23 0.1.0
Title: Alternative Time Series Analysis
Description: Contains some tools for testing, analyzing time series data and
fitting popular time series models such as ARIMA, Moving Average and Holt
Winters, etc. Most functions also provide nice and clear outputs like SAS
does, such as identify, estimate and forecast, which are the same statements
in PROC ARIMA in SAS.
Author: Debin Qiu
Maintainer: Debin Qiu <debinqiu@uga.edu>
Diff between aTSA versions 3.1.2 dated 2015-07-08 and 3.1.2.1 dated 2024-02-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/trendtest.R | 4 ++-- man/trend.test.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Compact Package Representations
Description: A tool, grammar, and standard to represent and exchange
R package source code as text files. Converts one or more source
packages to a text file and restores the package structures from the file.
Author: Nan Xiao [aut, cre] ,
Yilong Zhang [aut],
Keaven Anderson [aut],
Amin Shirazi [ctb],
Jeff Cheng [ctb],
Danfeng Fu [ctb],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Nan Xiao <nan.xiao1@merck.com>
Diff between pkglite versions 0.2.1 dated 2022-08-28 and 0.2.2 dated 2024-02-21
DESCRIPTION | 24 MD5 | 204 NAMESPACE | 80 NEWS.md | 83 R/collate.R | 445 - R/collection.R | 517 - R/dictionary.R | 371 R/pack.R | 655 - R/pkglite-package.R | 39 R/spec.R | 267 R/templates.R | 501 - R/unpack.R | 661 - R/utils-cli.R | 487 - R/utils.R | 263 README.md | 148 build/vignette.rds |binary inst/CITATION |only inst/doc/filecollection.R | 64 inst/doc/filecollection.Rmd | 164 inst/doc/filecollection.html | 598 - inst/doc/filespec.R | 90 inst/doc/filespec.Rmd | 244 inst/doc/filespec.html | 710 - inst/doc/format.R | 12 inst/doc/format.Rmd | 184 inst/doc/format.html | 374 inst/doc/pkglite.R | 150 inst/doc/pkglite.Rmd | 344 inst/doc/pkglite.html | 694 - inst/examples/pkg1/DESCRIPTION | 32 inst/examples/pkg1/NAMESPACE | 6 inst/examples/pkg1/NEWS.md | 10 inst/examples/pkg1/R/data.R | 12 inst/examples/pkg1/R/hello.R | 22 inst/examples/pkg1/R/pkg1-package.R | 4 inst/examples/pkg1/README.md | 6 inst/examples/pkg1/inst/extdata/dataset.tsv | 202 inst/examples/pkg1/man/dataset.Rd | 32 inst/examples/pkg1/man/hello_world.Rd | 34 inst/examples/pkg1/man/pkg1-package.Rd | 36 inst/examples/pkg1/vignettes/example.bib | 16 inst/examples/pkg1/vignettes/pkg1.Rmd | 44 inst/examples/pkg2/DESCRIPTION | 32 inst/examples/pkg2/NAMESPACE | 6 inst/examples/pkg2/NEWS.md | 10 inst/examples/pkg2/R/data.R | 12 inst/examples/pkg2/R/hello.R | 22 inst/examples/pkg2/R/pkg2-package.R | 4 inst/examples/pkg2/README.md | 6 inst/examples/pkg2/inst/extdata/dataset.tsv | 202 inst/examples/pkg2/man/dataset.Rd | 32 inst/examples/pkg2/man/hello_world.Rd | 34 inst/examples/pkg2/man/pkg2-package.Rd | 36 inst/examples/pkg2/vignettes/example.bib | 16 inst/examples/pkg2/vignettes/pkg2.Rmd | 44 inst/logo/logo.R | 26 man/collate.Rd | 80 man/ext_binary.Rd | 60 man/ext_text.Rd | 60 man/file_auto.Rd | 72 man/file_default.Rd | 58 man/file_ectd.Rd | 60 man/file_name_patterns.Rd | 62 man/file_spec.Rd | 114 man/file_spec_templates.Rd | 114 man/is_file_collection.Rd | 66 man/is_file_spec.Rd | 72 man/merge.file_collection.Rd | 84 man/pack.Rd | 118 man/pipe.Rd | 34 man/pkglite-package.Rd | 79 man/print.file_collection.Rd | 68 man/print.file_spec.Rd | 74 man/prune.Rd | 78 man/remove_content.Rd | 96 man/sanitize.Rd | 72 man/sanitize_file_collection.Rd | 66 man/unpack.Rd | 138 man/verify_ascii.Rd | 84 tests/testthat.R | 8 tests/testthat/_snaps/independent_test_pack/fc_to_text1.txt | 2156 ++-- tests/testthat/_snaps/independent_test_pack/fc_to_text2.txt | 2156 ++-- tests/testthat/_snaps/independent_test_pack/file_to_vec.txt | 2156 ++-- tests/testthat/_snaps/independent_test_pack/pack.txt | 4318 +++++----- tests/testthat/_snaps/independent_test_pack/read_file_text1.txt | 32 tests/testthat/_snaps/independent_test_pack/read_file_text2.txt | 6 tests/testthat/_snaps/independent_test_pack/read_file_text3.txt | 10 tests/testthat/_snaps/independent_test_pack/read_file_text4.txt | 6 tests/testthat/_snaps/independent_test_pack/read_file_text5.txt | 12 tests/testthat/helper.R |only tests/testthat/test-independent-test_dictionary.R | 278 tests/testthat/test-independent-test_file_spec.R | 122 tests/testthat/test-independent-test_templates.R | 1148 +- tests/testthat/test-independent-test_utils.R | 122 tests/testthat/test-independent-test_utils_cli.R | 56 tests/testthat/test-independent_test_collate.R | 258 tests/testthat/test-independent_test_collection.R | 318 tests/testthat/test-independent_test_pack.R | 146 tests/testthat/test-independent_test_unpack.R | 201 vignettes/custom.css | 80 vignettes/filecollection.Rmd | 164 vignettes/filespec.Rmd | 244 vignettes/format.Rmd | 184 vignettes/pkglite.Rmd | 344 104 files changed, 12693 insertions(+), 12952 deletions(-)