Title: Tables so Beautifully Fine-Tuned You Will Believe It's Magic
Description: The introduction of the 'broom' package has made converting model
objects into data frames as simple as a single function. While the 'broom'
package focuses on providing tidy data frames that can be used in advanced
analysis, it deliberately stops short of providing functionality for reporting
models in publication-ready tables. 'pixiedust' provides this functionality with
a programming interface intended to be similar to 'ggplot2's system of layers
with fine tuned control over each cell of the table. Options for output include
printing to the console and to the common markdown formats (markdown, HTML, and
LaTeX). With a little 'pixiedust' (and happy thoughts) tables can really fly.
Author: Benjamin Nutter [aut, cre],
David Kretch [ctb]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between pixiedust versions 0.9.1 dated 2021-01-15 and 0.9.4 dated 2023-10-09
DESCRIPTION | 9 MD5 | 24 R/pixiedust-pkg.R | 4 R/print_dust_latex.R | 2 R/print_dust_latex_hhline.R | 2 R/sanitize_latex.R | 2 README.md | 204 +- build/vignette.rds |binary inst/doc/advancedMagic.html | 3850 +++++++++++++++++++++++--------------------- inst/doc/pixiedust.html | 2543 +++++++++++++++-------------- inst/doc/sprinkles.html | 2706 +++++++++++++++--------------- man/pixiedust.Rd | 19 man/sanitize_latex.Rd | 2 13 files changed, 4945 insertions(+), 4422 deletions(-)
Title: Set of Tools to Data Analysis using Generalized Linear Models
Description: Set of tools to the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial and random-clumped binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) Zero-inflated and zero-altered regression models to deal with zero-excess in count data; (6) generalized estimating equations for cluster correlated data.
Author: Luis Hernando Vanegas [aut, cre],
Luz Marina Rondon [aut],
Gilberto A. Paula [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between glmtoolbox versions 0.1.8 dated 2023-08-15 and 0.1.9 dated 2023-10-09
DESCRIPTION | 8 - MD5 | 31 +++-- NAMESPACE | 6 + R/data.R | 33 +++++ R/geeglm.R | 3 R/glms.R | 259 +++++++++++++++++++++++++++++++++++++++++++-- R/overglm3.R | 65 +++++------ data/rabbits.rda |only data/skincancer.rda |binary man/BoxTidwell.Rd |only man/BoxTidwell.glm.Rd |only man/BoxTidwell.lm.Rd |only man/FisherScoring.Rd | 2 man/anova.overglm.Rd | 25 +--- man/anova.zeroinflation.Rd | 20 +-- man/gvif.glm.Rd | 2 man/rabbits.Rd |only man/skincancer.Rd | 5 man/vdtest.glm.Rd | 2 19 files changed, 370 insertions(+), 91 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.1.3 dated 2021-10-04 and 1.2.0 dated 2023-10-09
phylopath-1.1.3/phylopath/vignettes/binary_models.md |only phylopath-1.1.3/phylopath/vignettes/intro_to_phylopath.md |only phylopath-1.2.0/phylopath/DESCRIPTION | 15 phylopath-1.2.0/phylopath/MD5 | 40 phylopath-1.2.0/phylopath/NEWS.md | 18 phylopath-1.2.0/phylopath/R/phylopath.R | 55 - phylopath-1.2.0/phylopath/R/print_and_plot.R | 13 phylopath-1.2.0/phylopath/build/vignette.rds |binary phylopath-1.2.0/phylopath/inst/CITATION | 47 - phylopath-1.2.0/phylopath/inst/doc/binary_models.R | 2 phylopath-1.2.0/phylopath/inst/doc/binary_models.Rmd | 29 phylopath-1.2.0/phylopath/inst/doc/binary_models.html | 466 ++++++++-- phylopath-1.2.0/phylopath/inst/doc/intro_to_phylopath.R | 20 phylopath-1.2.0/phylopath/inst/doc/intro_to_phylopath.Rmd | 4 phylopath-1.2.0/phylopath/inst/doc/intro_to_phylopath.html | 561 ++++++++++--- phylopath-1.2.0/phylopath/man/average.Rd | 5 phylopath-1.2.0/phylopath/man/best.Rd | 5 phylopath-1.2.0/phylopath/man/choice.Rd | 5 phylopath-1.2.0/phylopath/man/figures |only phylopath-1.2.0/phylopath/man/phylo_path.Rd | 15 phylopath-1.2.0/phylopath/vignettes/binary_models.Rmd | 29 phylopath-1.2.0/phylopath/vignettes/intro_to_phylopath.Rmd | 4 22 files changed, 989 insertions(+), 344 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between V8 versions 4.3.3 dated 2023-07-18 and 4.4.0 dated 2023-10-09
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS | 8 ++++++++ build/partial.rdb |binary inst/doc/npm.R | 2 +- inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.R | 16 ++++++---------- inst/doc/v8_intro.Rmd | 11 ++--------- inst/doc/v8_intro.html | 15 +++++---------- inst/js/wasm-feature-detect.js | 2 +- src/Makevars.win | 11 +++++++++-- tools/winlibs.R | 32 ++++++++++++++++++-------------- vignettes/v8_intro.Rmd | 11 ++--------- 13 files changed, 69 insertions(+), 73 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut, cre],
Brian Ripley [trl]
Maintainer: Beth Atkinson <atkinson@mayo.edu>
Diff between rpart versions 4.1.19 dated 2022-10-21 and 4.1.21 dated 2023-10-09
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/pred.rpart.R | 2 +- README.md | 2 +- build/vignette.rds |binary data/solder.rda |binary inst/doc/longintro.pdf |binary inst/doc/usercode.pdf |binary man/labels.rpart.Rd | 2 +- man/rpart-internal.Rd | 4 ++++ 10 files changed, 20 insertions(+), 16 deletions(-)
Title: Convenience Functions for Psychology
Description: Make your workflow faster and easier. Easily customizable
plots (via 'ggplot2'), nice APA tables (following the style of the
*American Psychological Association*) exportable to Word (via
'flextable'), easily run statistical tests or check assumptions, and
automatize various other tasks.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between rempsyc versions 0.1.6 dated 2023-09-13 and 0.1.7 dated 2023-10-09
rempsyc-0.1.6/rempsyc/vignettes/images/blog_assumptions/assumptions1.png |only rempsyc-0.1.6/rempsyc/vignettes/images/blog_assumptions/assumptions2.png |only rempsyc-0.1.6/rempsyc/vignettes/images/blog_assumptions/assumptions2_edited.png |only rempsyc-0.1.7/rempsyc/DESCRIPTION | 10 rempsyc-0.1.7/rempsyc/MD5 | 86 rempsyc-0.1.7/rempsyc/NEWS.md | 849 ++-- rempsyc-0.1.7/rempsyc/R/global_variables.R | 18 rempsyc-0.1.7/rempsyc/R/nice_randomize.R | 198 - rempsyc-0.1.7/rempsyc/R/nice_reverse.R | 66 rempsyc-0.1.7/rempsyc/R/nice_t_test.R | 368 +- rempsyc-0.1.7/rempsyc/R/nice_table.R | 1815 +++++----- rempsyc-0.1.7/rempsyc/R/rcompanion_groupwiseMean.R | 632 +-- rempsyc-0.1.7/rempsyc/R/scale_mad.R | 64 rempsyc-0.1.7/rempsyc/R/winsorize_mad.R | 70 rempsyc-0.1.7/rempsyc/R/zzz.R | 16 rempsyc-0.1.7/rempsyc/build/vignette.rds |binary rempsyc-0.1.7/rempsyc/inst/CITATION | 28 rempsyc-0.1.7/rempsyc/inst/WORDLIST | 2 rempsyc-0.1.7/rempsyc/inst/doc/assumptions.R | 14 rempsyc-0.1.7/rempsyc/inst/doc/assumptions.html | 10 rempsyc-0.1.7/rempsyc/inst/doc/circles.R | 4 rempsyc-0.1.7/rempsyc/inst/doc/contrasts.R | 12 rempsyc-0.1.7/rempsyc/inst/doc/contrasts.html | 4 rempsyc-0.1.7/rempsyc/inst/doc/moderation.R | 2 rempsyc-0.1.7/rempsyc/inst/doc/moderation.html | 20 rempsyc-0.1.7/rempsyc/inst/doc/randomize.R | 2 rempsyc-0.1.7/rempsyc/inst/doc/scatter.R | 2 rempsyc-0.1.7/rempsyc/inst/doc/t-test.R | 4 rempsyc-0.1.7/rempsyc/inst/doc/t-test.html | 16 rempsyc-0.1.7/rempsyc/inst/doc/table.R | 10 rempsyc-0.1.7/rempsyc/inst/doc/table.Rmd | 10 rempsyc-0.1.7/rempsyc/inst/doc/table.html | 67 rempsyc-0.1.7/rempsyc/inst/doc/violin.R | 6 rempsyc-0.1.7/rempsyc/man/install_if_not_installed.Rd | 28 rempsyc-0.1.7/rempsyc/man/nice_t_test.Rd | 4 rempsyc-0.1.7/rempsyc/man/rempsyc-package.Rd | 50 rempsyc-0.1.7/rempsyc/man/winsorize_mad.Rd | 84 rempsyc-0.1.7/rempsyc/tests/testthat/_snaps/best_duplicate.md | 4 rempsyc-0.1.7/rempsyc/tests/testthat/_snaps/nice_contrasts.md | 216 - rempsyc-0.1.7/rempsyc/tests/testthat/_snaps/nice_lm_contrasts.md | 144 rempsyc-0.1.7/rempsyc/tests/testthat/_snaps/nice_t_test.md | 45 rempsyc-0.1.7/rempsyc/tests/testthat/test-best_duplicate.R | 18 rempsyc-0.1.7/rempsyc/tests/testthat/test-nice_t_test.R | 101 rempsyc-0.1.7/rempsyc/vignettes/images/blog_assumptions/assumptions1.PNG |only rempsyc-0.1.7/rempsyc/vignettes/images/blog_assumptions/assumptions2.PNG |only rempsyc-0.1.7/rempsyc/vignettes/images/blog_assumptions/assumptions2_edited.PNG |only rempsyc-0.1.7/rempsyc/vignettes/table.Rmd | 10 47 files changed, 2562 insertions(+), 2547 deletions(-)
Title: Phase II Single-Arm Two-Stage Designs with Time-to-Event
Outcomes
Description: Two-stage design for single-arm phase II
trials with time-to-event endpoints (e.g., clinical trials on
immunotherapies among cancer patients) can be calculated using this package.
Two notable advantages of the package: 1) It provides flexible choices from
three design methods (optimal, minmax, and admissible), and 2) the power of
the design is more accurately calculated using the exact variance in the
one-sample log-rank test. The package can be used for 1) planning the sample
sizes and other design parameters, and 2) conducting the interim and final
analyses for the Go/No-go decisions. More details about the design method
can be found in: Wu, J, Chen L, Wei J, Weiss H, Chauhan A. (2020).
<doi:10.1002/pst.1983>.
Author: Xiaomeng Yuan [aut, cre],
Haitao Pan [aut],
Jianrong Wu [aut]
Maintainer: Xiaomeng Yuan <xiaomeng.yuan@stjude.org>
Diff between OneArm2stage versions 1.1.5 dated 2022-12-01 and 1.2.1 dated 2023-10-09
OneArm2stage-1.1.5/OneArm2stage/R/Optimal.KJ.c1.r |only OneArm2stage-1.1.5/OneArm2stage/R/Optimal.rKJ.c1.r |only OneArm2stage-1.1.5/OneArm2stage/R/Sim_KJ.R |only OneArm2stage-1.1.5/OneArm2stage/R/Sim_rKJ.R |only OneArm2stage-1.1.5/OneArm2stage/R/sysdata.rda |only OneArm2stage-1.1.5/OneArm2stage/man/Optimal.KJ.Rd |only OneArm2stage-1.1.5/OneArm2stage/man/Optimal.rKJ.Rd |only OneArm2stage-1.1.5/OneArm2stage/man/Sim_KJ.Rd |only OneArm2stage-1.1.5/OneArm2stage/man/Sim_rKJ.Rd |only OneArm2stage-1.2.1/OneArm2stage/DESCRIPTION | 31 OneArm2stage-1.2.1/OneArm2stage/MD5 | 37 OneArm2stage-1.2.1/OneArm2stage/NAMESPACE | 6 OneArm2stage-1.2.1/OneArm2stage/NEWS.md | 19 OneArm2stage-1.2.1/OneArm2stage/R/FitDat.r | 24 OneArm2stage-1.2.1/OneArm2stage/R/LRT.r | 52 OneArm2stage-1.2.1/OneArm2stage/R/Sim.R |only OneArm2stage-1.2.1/OneArm2stage/R/phase2.TTE_052520231531.r |only OneArm2stage-1.2.1/OneArm2stage/inst/doc/OneArm2stage.R | 260 +- OneArm2stage-1.2.1/OneArm2stage/inst/doc/OneArm2stage.Rmd | 387 ++- OneArm2stage-1.2.1/OneArm2stage/inst/doc/OneArm2stage.html | 1167 ++++++++---- OneArm2stage-1.2.1/OneArm2stage/inst/extdata/d4.csv |only OneArm2stage-1.2.1/OneArm2stage/inst/extdata/d4_t1.csv |only OneArm2stage-1.2.1/OneArm2stage/man/FitDat.Rd | 24 OneArm2stage-1.2.1/OneArm2stage/man/LRT.Rd | 33 OneArm2stage-1.2.1/OneArm2stage/man/Sim.Rd |only OneArm2stage-1.2.1/OneArm2stage/man/phase2.TTE.Rd |only OneArm2stage-1.2.1/OneArm2stage/vignettes/OneArm2stage.Rmd | 387 ++- 27 files changed, 1519 insertions(+), 908 deletions(-)
Title: Modelling Pathways and Movement Potential Within a Landscape
Description: Calculates cost surfaces based on slope to be used when modelling pathways and movement potential within a landscape (Lewis, 2021) <doi:10.1007/s10816-021-09522-w>.
Author: Joseph Lewis [aut, cre]
Maintainer: Joseph Lewis <josephlewis1992@gmail.com>
Diff between leastcostpath versions 1.8.7 dated 2022-06-03 and 2.0.12 dated 2023-10-09
leastcostpath-1.8.7/leastcostpath/R/apply_cost.R |only leastcostpath-1.8.7/leastcostpath/R/calculate_slope.R |only leastcostpath-1.8.7/leastcostpath/R/cost_matrix.R |only leastcostpath-1.8.7/leastcostpath/R/create_CCP_lcps.R |only leastcostpath-1.8.7/leastcostpath/R/create_banded_lcps.R |only leastcostpath-1.8.7/leastcostpath/R/create_barrier_cs.R |only leastcostpath-1.8.7/leastcostpath/R/create_feature_cs.R |only leastcostpath-1.8.7/leastcostpath/R/create_lcp_network.R |only leastcostpath-1.8.7/leastcostpath/R/create_stochastic_lcp.R |only leastcostpath-1.8.7/leastcostpath/R/create_traversal_cs.R |only leastcostpath-1.8.7/leastcostpath/R/create_wide_lcp.R |only leastcostpath-1.8.7/leastcostpath/R/neighbours.R |only leastcostpath-1.8.7/leastcostpath/R/transitions.R |only leastcostpath-1.8.7/leastcostpath/R/validate_lcp.R |only leastcostpath-1.8.7/leastcostpath/R/wide_path_matrix.R |only leastcostpath-1.8.7/leastcostpath/build |only leastcostpath-1.8.7/leastcostpath/inst/doc |only leastcostpath-1.8.7/leastcostpath/man/apply_cost.Rd |only leastcostpath-1.8.7/leastcostpath/man/calculate_slope.Rd |only leastcostpath-1.8.7/leastcostpath/man/cost_matrix.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_CCP_lcps.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_banded_lcps.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_barrier_cs.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_feature_cs.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_lcp_network.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_stochastic_lcp.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_traversal_cs.Rd |only leastcostpath-1.8.7/leastcostpath/man/create_wide_lcp.Rd |only leastcostpath-1.8.7/leastcostpath/man/neighbours_32.Rd |only leastcostpath-1.8.7/leastcostpath/man/neighbours_48.Rd |only leastcostpath-1.8.7/leastcostpath/man/validate_lcp.Rd |only leastcostpath-1.8.7/leastcostpath/man/wide_path_matrix.Rd |only leastcostpath-1.8.7/leastcostpath/vignettes |only leastcostpath-2.0.12/leastcostpath/DESCRIPTION | 18 leastcostpath-2.0.12/leastcostpath/MD5 | 112 +-- leastcostpath-2.0.12/leastcostpath/NAMESPACE | 40 - leastcostpath-2.0.12/leastcostpath/NEWS.md | 239 +----- leastcostpath-2.0.12/leastcostpath/R/PDI_validation.R | 169 +--- leastcostpath-2.0.12/leastcostpath/R/add_dem_error.R | 144 +-- leastcostpath-2.0.12/leastcostpath/R/add_global_stochasticity.R |only leastcostpath-2.0.12/leastcostpath/R/buffer_validation.R |only leastcostpath-2.0.12/leastcostpath/R/calculate_distance.R |only leastcostpath-2.0.12/leastcostpath/R/check_locations.R | 90 +- leastcostpath-2.0.12/leastcostpath/R/cost.R | 362 ++++++---- leastcostpath-2.0.12/leastcostpath/R/create_FETE_lcps.R | 206 ++--- leastcostpath-2.0.12/leastcostpath/R/create_accum_cost.R |only leastcostpath-2.0.12/leastcostpath/R/create_cost_corridor.R | 127 +-- leastcostpath-2.0.12/leastcostpath/R/create_cs.R |only leastcostpath-2.0.12/leastcostpath/R/create_distance_cs.R | 122 +-- leastcostpath-2.0.12/leastcostpath/R/create_lcp.R | 172 ++-- leastcostpath-2.0.12/leastcostpath/R/create_lcp_density.R | 125 +-- leastcostpath-2.0.12/leastcostpath/R/create_slope_cs.R | 264 ++++--- leastcostpath-2.0.12/leastcostpath/R/crop_cs.R | 114 --- leastcostpath-2.0.12/leastcostpath/R/force_isotropy.R | 64 - leastcostpath-2.0.12/leastcostpath/R/get_coordinates.R |only leastcostpath-2.0.12/leastcostpath/R/neighbourhood.R |only leastcostpath-2.0.12/leastcostpath/R/rasterise.R |only leastcostpath-2.0.12/leastcostpath/R/replace_values.R |only leastcostpath-2.0.12/leastcostpath/R/update_values.R |only leastcostpath-2.0.12/leastcostpath/README.md | 196 ----- leastcostpath-2.0.12/leastcostpath/inst/extdata |only leastcostpath-2.0.12/leastcostpath/man/PDI_validation.Rd | 50 - leastcostpath-2.0.12/leastcostpath/man/add_dem_error.Rd | 43 - leastcostpath-2.0.12/leastcostpath/man/add_global_stochasticity.Rd |only leastcostpath-2.0.12/leastcostpath/man/buffer_validation.Rd |only leastcostpath-2.0.12/leastcostpath/man/calculate_distance.Rd |only leastcostpath-2.0.12/leastcostpath/man/check_locations.Rd | 66 + leastcostpath-2.0.12/leastcostpath/man/create_FETE_lcps.Rd | 92 +- leastcostpath-2.0.12/leastcostpath/man/create_accum_cost.Rd |only leastcostpath-2.0.12/leastcostpath/man/create_cost_corridor.Rd | 31 leastcostpath-2.0.12/leastcostpath/man/create_cs.Rd |only leastcostpath-2.0.12/leastcostpath/man/create_distance_cs.Rd | 22 leastcostpath-2.0.12/leastcostpath/man/create_lcp.Rd | 42 - leastcostpath-2.0.12/leastcostpath/man/create_lcp_density.Rd | 38 - leastcostpath-2.0.12/leastcostpath/man/create_slope_cs.Rd | 73 +- leastcostpath-2.0.12/leastcostpath/man/crop_cs.Rd | 36 leastcostpath-2.0.12/leastcostpath/man/force_isotropy.Rd | 29 leastcostpath-2.0.12/leastcostpath/man/get_coordinates.Rd |only leastcostpath-2.0.12/leastcostpath/man/neighbourhood.Rd |only leastcostpath-2.0.12/leastcostpath/man/plot.conductanceMatrix.Rd |only leastcostpath-2.0.12/leastcostpath/man/rasterise.Rd |only leastcostpath-2.0.12/leastcostpath/man/replace_values.Rd |only leastcostpath-2.0.12/leastcostpath/man/update_values.Rd |only 83 files changed, 1402 insertions(+), 1684 deletions(-)
Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel, with contributions by Felix Ernst, Neal Fultz, Colin
Gillespie, Christoph Stepper, Thomas Leeper, Mark van der Loo, Jan Gorecki,
Joey Reid, Arne Johannes Holmin, and others.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.2.3 dated 2022-04-13 and 0.2.4 dated 2023-10-09
ChangeLog | 83 +++++++++++++++ DESCRIPTION | 17 +-- MD5 | 51 +++++---- R/archivePackages.R | 35 +++--- R/insertPackage.R | 5 R/pruneRepo.R | 75 +++++++------- README.md | 12 +- build/vignette.rds |binary inst/NEWS.Rd | 14 ++ inst/doc/CombiningDratAndTravis.html | 50 +++++++-- inst/doc/CombiningDratAndTravis.md | 2 inst/doc/DratFAQ.html | 153 ++++++++++++++++++++++------- inst/doc/DratFAQ.md | 2 inst/doc/DratForPackageAuthors.html | 137 ++++++++++++++++++++------ inst/doc/DratForPackageAuthors.md | 2 inst/doc/DratForPackageUsers.html | 62 ++++++++--- inst/doc/DratStepByStep.html | 182 ++++++++++++++++++++++++++--------- inst/doc/WhyDrat.html | 81 +++++++++++---- inst/extdata/big-sur-x86_64 |only inst/extdata/src/bar_1.1.tar.gz |only man/archivePackages.Rd | 22 ++-- man/pruneRepo.Rd | 41 ++++--- tests/skeleton_git2r.R | 22 ++++ tests/testArmBinary.R | 2 tests/testBig-sur-x86_64Binary.R |only vignettes/CombiningDratAndTravis.md | 2 vignettes/DratFAQ.md | 2 vignettes/DratForPackageAuthors.md | 2 28 files changed, 768 insertions(+), 288 deletions(-)
Title: Efficient Inference on High-Dimensional Linear Model with
Missing Outcomes
Description: A statistically and computationally efficient debiasing method for conducting valid inference on the high-dimensional linear regression function with missing outcomes.
The reference paper is Zhang, Giessing, and Chen (2023) <arXiv:2309.06429>.
Author: Yikun Zhang [aut, cre] ,
Alexander Giessing [aut] ,
Yen-Chi Chen [aut]
Maintainer: Yikun Zhang <yikunzhang@foxmail.com>
Diff between DebiasInfer versions 0.1 dated 2023-09-14 and 0.2 dated 2023-10-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.10/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.0.0 dated 2023-08-11 and 1.1.0 dated 2023-10-09
DESCRIPTION | 10 MD5 | 67 ++--- NAMESPACE | 3 NEWS.md | 28 +- R/CFdatum.R | 14 - R/CFfactor.R |only R/CFformat.R | 152 +---------- R/CFparse.R | 21 - R/CFtime.R | 75 +++-- R/CFutils.R | 70 ++--- R/zzz.R | 17 - README.md | 44 ++- TODO | 6 build/vignette.rds |binary inst/doc/CFtime.R | 116 +++----- inst/doc/CFtime.Rmd | 366 +++++++++++---------------- inst/doc/CFtime.html | 480 +++++++++++++++++------------------- inst/doc/Processing.R |only inst/doc/Processing.Rmd |only inst/doc/Processing.html |only man/CFfactor.Rd | 11 man/CFfactor_coverage.Rd |only man/CFfactor_units.Rd |only man/CFmonth_days.Rd | 7 man/CFproperties.Rd | 10 man/CFrange.Rd | 2 man/CFtime-class.Rd | 2 man/CFtime-package.Rd | 8 man/CFtime.Rd | 19 - man/CFtimestamp.Rd | 13 man/equals-CFtime-CFtime-method.Rd | 2 man/plus-CFtime-CFtime-method.Rd | 2 man/plus-CFtime-numeric-method.Rd | 8 tests/testthat/test-CFformat.R | 97 ++++++- tests/testthat/test-CFtime.R | 10 tests/testthat/test-parse_deparse.R | 16 - vignettes/CFtime.Rmd | 366 +++++++++++---------------- vignettes/Processing.Rmd |only 38 files changed, 986 insertions(+), 1056 deletions(-)
Title: Download Data from Bundesbank
Description: Download data from the time-series
databases of the Bundesbank, the German central
bank. See the overview at the Bundesbank website
(<https://www.bundesbank.de/en/statistics/time-series-databases>)
for available series. The package provides only a
single function, getSeries(), which supports both
traditional and real-time datasets; it will also
download meta data if available. Downloaded data
can automatically be arranged in various formats,
such as data frames or 'zoo' series. The data
may optionally be cached, so as to avoid repeated
downloads of the same series.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between bundesbank versions 0.1-9 dated 2019-05-17 and 0.1-11 dated 2023-10-09
ChangeLog | 18 +++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 8 +++---- NEWS | 20 +++++++++++++++++ man/getSeries.Rd | 62 ++++++++++++++++++++++++++++++++----------------------- 5 files changed, 83 insertions(+), 33 deletions(-)
Title: Tools for Causal Inference with Possibly Invalid Instrumental
Variables
Description: Two stage curvature identification with machine learning for causal
inference in settings when instrumental variable regression is not suitable
because of potentially invalid instrumental variables. Based on Guo and
Buehlmann (2022) "Two Stage Curvature Identification with Machine Learning:
Causal Inference with Possibly Invalid Instrumental Variables"
<arXiv:2203.12808>. The vignette is available in Carl, Emmenegger, Bühlmann and Guo (2023)
"TSCI: two stage curvature identification for causal inference with
invalid instruments" <arXiv:2304.00513>.
Author: David Carl [aut, cre] ,
Corinne Emmenegger [aut] ,
Wei Yuan [aut],
Mengchu Zheng [aut],
Zijian Guo [aut]
Maintainer: David Carl <david.carl@phd.unibocconi.it>
Diff between TSCI versions 3.0.0 dated 2023-05-31 and 3.0.4 dated 2023-10-09
DESCRIPTION | 6 +- MD5 | 42 +++++++++--------- R/get_forest_hatmatrix.R | 8 ++- R/get_l2boost_hatmatrix.R | 27 ++++++++---- R/tsci_boosting.R | 64 ++-------------------------- R/tsci_forest.R | 73 ++++++-------------------------- R/tsci_poly.R | 48 --------------------- R/tsci_secondstage.R | 54 +----------------------- man/coef.tsci.Rd | 48 ++++++++++----------- man/confint.tsci.Rd | 52 +++++++++++------------ man/print.summary.tsci.Rd | 36 ++++++++-------- man/print.tsci.Rd | 36 ++++++++-------- man/summary.tsci.Rd | 74 ++++++++++++++++----------------- man/tsci_boosting.Rd | 61 +-------------------------- man/tsci_forest.Rd | 69 +++++------------------------- man/tsci_poly.Rd | 48 --------------------- man/tsci_secondstage.Rd | 54 +----------------------- tests/testthat/df_tsci_functions.rds |binary tests/testthat/test-tsci_boosting.R | 4 + tests/testthat/test-tsci_forest.R | 4 + tests/testthat/test-tsci_poly.R | 4 + tests/testthat/test-tsci_secondstage.R | 3 - 22 files changed, 230 insertions(+), 585 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehr [...truncated...]
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.9.7 dated 2023-07-05 and 1.9.8 dated 2023-10-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 8 ++++++++ inst/doc/QuickReferenceGuide.html | 4 ++-- src/getpval.f | 4 ++-- src/util.f | 9 +++++---- 6 files changed, 26 insertions(+), 17 deletions(-)
Title: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry
Description: Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.
Author: Antonio Profico [aut, cre],
Luca Bondioli [aut],
Pasquale Raia [aut],
Julien Claude [ctb],
Paul O'Higgins [aut],
Damiano Marchi [aut]
Maintainer: Antonio Profico <antonio.profico@gmail.com>
Diff between morphomap versions 1.4 dated 2023-02-01 and 1.5 dated 2023-10-09
morphomap-1.4/morphomap/R/morphomapRaster.R |only morphomap-1.4/morphomap/man/morphomapRaster.Rd |only morphomap-1.5/morphomap/DESCRIPTION | 13 ++++++------- morphomap-1.5/morphomap/MD5 | 10 ++++------ morphomap-1.5/morphomap/NAMESPACE | 5 ----- morphomap-1.5/morphomap/R/morphomap.R | 2 -- morphomap-1.5/morphomap/R/morphomapPCA.R | 2 +- 7 files changed, 11 insertions(+), 21 deletions(-)
Title: Miscellaneous Useful Functions Including LaTeX Tables, Kalman
Filtering, QQplots with Simulation-Based Confidence Intervals
and Development Tools
Description: Implementing various things including functions for LaTeX tables,
the Kalman filter, QQ-plots with simulation-based confidence intervals, web scraping, development tools, relative risk and odds
ratio.
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
Diff between miscFuncs versions 1.5-4 dated 2023-06-07 and 1.5-5 dated 2023-10-09
DESCRIPTION | 13 +++++++------ MD5 | 12 +++++++----- NAMESPACE | 6 ++++++ R/qqCI.R |only R/zzz.R | 6 +++--- build/vignette.rds |binary inst/doc/miscFuncs.pdf |binary man/qqci.Rd |only 8 files changed, 23 insertions(+), 14 deletions(-)
Title: Generalized Correlations, Causal Paths and Portfolio Selection
Description: Function gmcmtx0() computes a more reliable (general)
correlation matrix. Since causal paths from data are important for all sciences, the
package provides many sophisticated functions. causeSummBlk() and causeSum2Blk()
give easy-to-interpret causal paths. Let Z denote control variables and compare
two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X, Z)+e2. Our criterion Cr1
says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent"
than in Y, and the causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These
inequalities between many absolute values are quantified by four orders of
stochastic dominance. Our third criterion Cr3, for the causal path X to Y,
requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|.
The function parcorVec() reports generalized partials between the first
variable and all others. The package provides several R functions including
get0outliers() for outlier detection, bigfp() for numerical int [...truncated...]
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.2.5 dated 2023-10-07 and 1.2.6 dated 2023-10-09
DESCRIPTION | 29 ++++++------ MD5 | 84 ++++++++++++++++++------------------- NEWS | 3 + R/GcRsqYX.R | 2 R/bigfp.R | 2 R/canonRho.R | 10 +++- R/causeSum2Panel.R | 43 +++++++++--------- R/causeSummBlk.R | 10 ++-- R/causeSummary2.R | 38 ++++++++-------- R/causeSummary2NoP.R | 36 +++++++-------- R/compPortfo.R | 2 R/comp_portfo2.R | 2 R/depMeas.R | 4 - R/exactSdMtx.R | 41 +++++++++++++----- R/get0outliers.R | 2 R/gmcmtx0.R | 18 ++++--- R/outOFsamp.R | 6 +- R/pillar3D.R | 16 +++---- R/prelec2.R | 2 R/stochdom2.R | 14 +++--- R/wtdpapb.R | 2 inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary inst/doc/generalCorr-vignette5.pdf |binary man/GcRsqYX.Rd | 2 man/bigfp.Rd | 2 man/canonRho.Rd | 10 +++- man/causeSum2Panel.Rd | 43 +++++++++--------- man/causeSummBlk.Rd | 10 ++-- man/causeSummary2.Rd | 38 ++++++++-------- man/causeSummary2NoP.Rd | 36 +++++++-------- man/compPortfo.Rd | 2 man/comp_portfo2.Rd | 2 man/depMeas.Rd | 4 - man/exactSdMtx.Rd | 42 +++++++++++++----- man/get0outliers.Rd | 4 - man/gmcmtx0.Rd | 18 ++++--- man/outOFsamp.Rd | 6 +- man/pillar3D.Rd | 16 +++---- man/prelec2.Rd | 2 man/stochdom2.Rd | 14 +++--- man/wtdpapb.Rd | 2 43 files changed, 348 insertions(+), 271 deletions(-)
Title: Download and Extract Data from US EPA's ECOTOX Database
Description: The US EPA ECOTOX database is a freely available database
with a treasure of aquatic and terrestrial ecotoxicological data.
As the online search interface doesn't come with an API, this
package provides the means to easily access and search the database
in R. To this end, all raw tables are downloaded from the EPA website
and stored in a local SQLite database.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ECOTOXr versions 1.0.3 dated 2023-08-21 and 1.0.5 dated 2023-10-09
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 14 + R/cas_handlers.r | 7 R/init.r | 64 ++++-- R/online.r | 67 ++++-- build/partial.rdb |binary man/ECOTOXr-package.Rd | 214 ++++++++++----------- man/download_ecotox_data.Rd | 11 - man/figures/logo.svg | 444 ++++++++++++++++++++++---------------------- man/get_ecotox_url.Rd | 8 man/websearch.Rd | 5 man/websearch_comptox.Rd | 5 tests/testthat/test_that.r | 4 14 files changed, 489 insertions(+), 388 deletions(-)
Title: Generate Walk Bouts from GPS and Accelerometry Data
Description: Process GPS and accelerometry data to generate walk bouts. A walk bout is a period of activity with accelerometer movement matching the patterns of walking with corresponding GPS measurements that confirm travel. The inputs of the 'walkboutr' package are individual-level accelerometry and GPS data. The outputs of the model are walk bouts with corresponding times, duration, and summary statistics on the sample population, which collapse all personally identifying information. These bouts can be used to measure walking both as an outcome of a change to the built environment or as a predictor of health outcomes such as a cardioprotective behavior. Kang B, Moudon AV, Hurvitz PM, Saelens BE (2017) <doi:10.1016/j.trd.2017.09.026>.
Author: Lauren Blair Wilner [aut, cre, cph]
,
Stephen J Mooney [aut]
Maintainer: Lauren Blair Wilner <wilnerl@uw.edu>
Diff between walkboutr versions 0.2.0 dated 2023-09-22 and 0.3.0 dated 2023-10-09
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 2 + README.md | 46 ++++++++++++++++----------------- inst/doc/changing_default_parameters.R | 2 - inst/doc/generate_data.R | 2 - inst/doc/process_bouts.R | 4 +- 7 files changed, 38 insertions(+), 36 deletions(-)
Title: Predictive (Classification and Regression) Models Homologator
Description: Methods to unify the different ways of creating predictive models and their different predictive formats for classification and regression. It includes
methods such as K-Nearest Neighbors Schliep, K. P. (2004) <doi:10.5282/ubm/epub.1769>, Decision Trees Leo Breiman, Jerome H. Friedman, Richard A. Olshen, Charles J. Stone (2017) <doi:10.1201/9781315139470>,
ADA Boosting Esteban Alfaro, Matias Gamez, Noelia García (2013) <doi:10.18637/jss.v054.i02>, Extreme Gradient Boosting Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>,
Random Forest Breiman (2001) <doi:10.1023/A:1010933404324>, Neural Networks Venables, W. N., & Ripley, B. D. (2002) <ISBN:0-387-95457-0>,
Support Vector Machines Bennett, K. P. & Campbell, C. (2000) <doi:10.1145/380995.380999>, Bayesian Methods Gelman, A., Carlin, J. B., Stern, H. S., & Rubin, D. B. (1995) <doi:10.1201/9780429258411>,
Linear Discriminant Analysis Venables, W. N., & Ripley, B. D. ( [...truncated...]
Author: Oldemar Rodriguez R. [aut, cre],
Andres Navarro D. [aut],
Ariel Arroyo S. [aut],
Diego Jimenez A. [aut]
Maintainer: Oldemar Rodriguez R. <oldemar.rodriguez@ucr.ac.cr>
Diff between traineR versions 2.0.4 dated 2022-08-22 and 2.1.0 dated 2023-10-09
traineR-2.0.4/traineR/man/boosting.importance.plot.Rd |only traineR-2.0.4/traineR/man/dummy.Rd |only traineR-2.1.0/traineR/DESCRIPTION | 15 +-- traineR-2.1.0/traineR/MD5 | 23 ++--- traineR-2.1.0/traineR/NAMESPACE | 4 traineR-2.1.0/traineR/R/Utilities.R | 79 ++---------------- traineR-2.1.0/traineR/R/predict.R | 6 - traineR-2.1.0/traineR/R/train.R | 10 +- traineR-2.1.0/traineR/R/traineR.R | 6 - traineR-2.1.0/traineR/R/variables.R | 42 ++++++--- traineR-2.1.0/traineR/man/dummy.data.frame.Rd | 11 -- traineR-2.1.0/traineR/man/importance.plot.Rd |only traineR-2.1.0/traineR/man/train.xgboost.Rd | 7 - traineR-2.1.0/traineR/man/traineR.Rd | 4 14 files changed, 80 insertions(+), 127 deletions(-)
Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting sparse generalized linear models. In this version of the package, the user can fit models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family. Furthermore, several link functions can be used to model the relationship between the conditional expected value of the response variable and the linear predictor. The solution curve can be computed using an efficient predictor-corrector or a cyclic coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro [aut, cre],
Angelo Mineo [aut],
Ernst Wit [aut],
Hassan Pazira [aut],
Michael Wichura [ctb, cph],
John Burkardt [ctb, cph]
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between dglars versions 2.1.6 dated 2020-02-26 and 2.1.7 dated 2023-10-09
ChangeLog | 4 +++ DESCRIPTION | 10 +++---- MD5 | 22 ++++++++--------- R/grcv.R | 2 - R/phihat.R | 2 - inst/CITATION | 25 +++++++++---------- man/cvdglars.Rd | 2 - man/dglars-package.Rd | 6 ++-- man/dglars.Rd | 2 - man/gdf.Rd | 2 - man/phihat.Rd | 2 - src/tools.f90 | 64 +++++++++++++++++++++++++------------------------- 12 files changed, 73 insertions(+), 70 deletions(-)
Title: Bayesian Inference for A|B and Bandit Marketing Tests
Description: Uses simple Bayesian conjugate prior update rules to calculate
the win probability of each option, value remaining in the test, and
percent lift over the baseline for various marketing objectives.
References:
Fink, Daniel (1997) "A Compendium of Conjugate Priors" <https://www.johndcook.com/CompendiumOfConjugatePriors.pdf>.
Stucchio, Chris (2015) "Bayesian A/B Testing at VWO" <https://vwo.com/downloads/VWO_SmartStats_technical_whitepaper.pdf>.
Author: Ryan Angi
Maintainer: Ryan Angi <angi.ryan@gmail.com>
Diff between grizbayr versions 1.3.3 dated 2022-12-23 and 1.3.5 dated 2023-10-09
grizbayr-1.3.3/grizbayr/R/grizbayr.R |only grizbayr-1.3.3/grizbayr/man/distribution_column_mapping.Rd |only grizbayr-1.3.3/grizbayr/man/grizbayr.Rd |only grizbayr-1.3.5/grizbayr/DESCRIPTION | 10 grizbayr-1.3.5/grizbayr/MD5 | 29 grizbayr-1.3.5/grizbayr/NEWS.md | 6 grizbayr-1.3.5/grizbayr/R/estimate_lift.R | 4 grizbayr-1.3.5/grizbayr/R/estimate_loss.R | 4 grizbayr-1.3.5/grizbayr/R/grizbayr-package.R |only grizbayr-1.3.5/grizbayr/R/sample_from_posterior.R | 4 grizbayr-1.3.5/grizbayr/R/sample_multi_rev_per_session.R | 20 grizbayr-1.3.5/grizbayr/R/sample_total_cm.R | 8 grizbayr-1.3.5/grizbayr/R/sysdata.R | 2 grizbayr-1.3.5/grizbayr/R/sysdata.rda |binary grizbayr-1.3.5/grizbayr/R/validate_input_df.R | 2 grizbayr-1.3.5/grizbayr/build/vignette.rds |binary grizbayr-1.3.5/grizbayr/inst/doc/intro.html | 1003 ++++++------- grizbayr-1.3.5/grizbayr/man/grizbayr-package.Rd |only 18 files changed, 548 insertions(+), 544 deletions(-)
Title: Regularized and Sparse Generalized Canonical Correlation
Analysis for Multiblock Data
Description: Multi-block data analysis concerns the analysis of several
sets of variables (blocks) observed on the same group of individuals.
The main aims of the RGCCA package are: to study the relationships
between blocks and to identify subsets of variables of each block
which are active in their relationships with the other blocks. This
package allows to (i) run R/SGCCA and related methods,
(ii) help the user to find out the optimal parameters for R/SGCCA such
as regularization parameters (tau or sparsity), (iii) evaluate the
stability of the RGCCA results and their significance, (iv) build predictive
models from the R/SGCCA. (v) Generic print()
and plot() functions apply to all these functionalities.
Author: Fabien Girka [aut],
Etienne Camenen [aut],
Caroline Peltier [aut],
Arnaud Gloaguen [aut],
Vincent Guillemot [aut],
Laurent Le Brusquet [ths],
Arthur Tenenhaus [aut, ths, cre]
Maintainer: Arthur Tenenhaus <arthur.tenenhaus@centralesupelec.fr>
Diff between RGCCA versions 3.0.1 dated 2023-05-08 and 3.0.2 dated 2023-10-09
RGCCA-3.0.1/RGCCA/R/plot.bootstrap.r |only RGCCA-3.0.1/RGCCA/R/plot.cval.R |only RGCCA-3.0.1/RGCCA/R/plot.permutation.R |only RGCCA-3.0.1/RGCCA/R/plot.stability.R |only RGCCA-3.0.1/RGCCA/R/print.bootstrap.r |only RGCCA-3.0.1/RGCCA/R/print.cval.r |only RGCCA-3.0.1/RGCCA/R/print.permutation.R |only RGCCA-3.0.1/RGCCA/R/print.stability.R |only RGCCA-3.0.1/RGCCA/inst/shiny |only RGCCA-3.0.1/RGCCA/man/plot.bootstrap.Rd |only RGCCA-3.0.1/RGCCA/man/plot.cval.Rd |only RGCCA-3.0.1/RGCCA/man/plot.permutation.Rd |only RGCCA-3.0.1/RGCCA/man/plot.rgcca.Rd |only RGCCA-3.0.1/RGCCA/man/plot.stability.Rd |only RGCCA-3.0.1/RGCCA/man/print.bootstrap.Rd |only RGCCA-3.0.1/RGCCA/man/print.cval.Rd |only RGCCA-3.0.1/RGCCA/man/print.permutation.Rd |only RGCCA-3.0.1/RGCCA/man/print.rgcca.Rd |only RGCCA-3.0.1/RGCCA/man/print.stability.Rd |only RGCCA-3.0.1/RGCCA/tests/testthat/Rplots.pdf |only RGCCA-3.0.1/RGCCA/tests/testthat/_snaps |only RGCCA-3.0.1/RGCCA/tests/testthat/test_plot.bootstrap.R |only RGCCA-3.0.1/RGCCA/tests/testthat/test_plot.cval.R |only RGCCA-3.0.1/RGCCA/tests/testthat/test_plot.permutation.r |only RGCCA-3.0.1/RGCCA/tests/testthat/test_plot.stability.R |only RGCCA-3.0.1/RGCCA/tests/testthat/test_print.bootstrap.r |only RGCCA-3.0.1/RGCCA/tests/testthat/test_print.cval.R |only RGCCA-3.0.1/RGCCA/tests/testthat/test_print.permutation.R |only RGCCA-3.0.1/RGCCA/tests/testthat/test_print.rgcca.r |only RGCCA-3.0.1/RGCCA/tests/testthat/test_print.stability.R |only RGCCA-3.0.1/RGCCA/vignettes/RGCCA_cache |only RGCCA-3.0.2/RGCCA/DESCRIPTION | 18 RGCCA-3.0.2/RGCCA/MD5 | 156 - RGCCA-3.0.2/RGCCA/NAMESPACE | 24 RGCCA-3.0.2/RGCCA/NEWS.md | 11 RGCCA-3.0.2/RGCCA/R/as_disjunctive.r | 5 RGCCA-3.0.2/RGCCA/R/get_rgcca_args.R | 4 RGCCA-3.0.2/RGCCA/R/plot.rgcca.R | 157 - RGCCA-3.0.2/RGCCA/R/plot.rgcca_bootstrap.r |only RGCCA-3.0.2/RGCCA/R/plot.rgcca_cv.R |only RGCCA-3.0.2/RGCCA/R/plot.rgcca_permutation.R |only RGCCA-3.0.2/RGCCA/R/plot.rgcca_stability.R |only RGCCA-3.0.2/RGCCA/R/print.rgcca.R | 147 - RGCCA-3.0.2/RGCCA/R/print.rgcca_bootstrap.R |only RGCCA-3.0.2/RGCCA/R/print.rgcca_cv.R |only RGCCA-3.0.2/RGCCA/R/print.rgcca_permutation.R |only RGCCA-3.0.2/RGCCA/R/print.rgcca_stability.R |only RGCCA-3.0.2/RGCCA/R/rgcca.R | 14 RGCCA-3.0.2/RGCCA/R/rgcca_bootstrap.R | 10 RGCCA-3.0.2/RGCCA/R/rgcca_bootstrap_k.R | 7 RGCCA-3.0.2/RGCCA/R/rgcca_cv.r | 13 RGCCA-3.0.2/RGCCA/R/rgcca_permutation.R | 8 RGCCA-3.0.2/RGCCA/R/rgcca_stability.R | 6 RGCCA-3.0.2/RGCCA/R/sgcca_postprocess.R | 6 RGCCA-3.0.2/RGCCA/R/summary.rgcca.R |only RGCCA-3.0.2/RGCCA/R/summary.rgcca_bootstrap.r |only RGCCA-3.0.2/RGCCA/R/summary.rgcca_cv.r |only RGCCA-3.0.2/RGCCA/R/summary.rgcca_permutation.R |only RGCCA-3.0.2/RGCCA/R/summary.rgcca_stability.R |only RGCCA-3.0.2/RGCCA/README.md | 2 RGCCA-3.0.2/RGCCA/inst/doc/RGCCA.R | 99 RGCCA-3.0.2/RGCCA/inst/doc/RGCCA.Rmd | 1468 +++------- RGCCA-3.0.2/RGCCA/inst/doc/RGCCA.pdf |binary RGCCA-3.0.2/RGCCA/man/plot.Rd |only RGCCA-3.0.2/RGCCA/man/print.Rd |only RGCCA-3.0.2/RGCCA/man/rgcca.Rd | 14 RGCCA-3.0.2/RGCCA/man/rgcca_bootstrap.Rd | 6 RGCCA-3.0.2/RGCCA/man/rgcca_cv.Rd | 21 RGCCA-3.0.2/RGCCA/man/rgcca_permutation.Rd | 20 RGCCA-3.0.2/RGCCA/man/rgcca_stability.Rd | 5 RGCCA-3.0.2/RGCCA/man/summary.Rd |only RGCCA-3.0.2/RGCCA/tests/testthat/test_plot.rgcca.r | 22 RGCCA-3.0.2/RGCCA/tests/testthat/test_plot.rgcca_bootstrap.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_plot.rgcca_cv.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_plot.rgcca_permutation.r |only RGCCA-3.0.2/RGCCA/tests/testthat/test_plot.rgcca_stability.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_print.rgcca.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_print.rgcca_bootstrap.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_print.rgcca_cv.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_print.rgcca_permutation.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_print.rgcca_stability.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_rgcca_bootstrap.r | 2 RGCCA-3.0.2/RGCCA/tests/testthat/test_summary.rgcca.r |only RGCCA-3.0.2/RGCCA/tests/testthat/test_summary.rgcca_bootstrap.r |only RGCCA-3.0.2/RGCCA/tests/testthat/test_summary.rgcca_cv.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_summary.rgcca_permutation.R |only RGCCA-3.0.2/RGCCA/tests/testthat/test_summary.rgcca_stability.R |only RGCCA-3.0.2/RGCCA/vignettes/RGCCA.Rmd | 1468 +++------- RGCCA-3.0.2/RGCCA/vignettes/biblio.bib | 144 89 files changed, 1507 insertions(+), 2350 deletions(-)
Title: Applicability Domain Methods of Viral Load and CD4 Lymphocytes
Description: Provides methods for assessing the applicability domain of models that predict viral load and CD4 (Cluster of Differentiation 4) lymphocyte counts. These methods help determine the extent of extrapolation when making predictions.
Author: Juan Pablo Acuna Gonzalez [aut, cre]
Maintainer: Juan Pablo Acuna Gonzalez <22253567@uagro.mx>
Diff between viraldomain versions 0.0.1 dated 2023-09-28 and 0.0.2 dated 2023-10-09
DESCRIPTION | 6 - MD5 | 12 +-- data/viral.rda |binary tests/testthat/_snaps/mars_domain_plot/mars-domain-plot.svg | 40 ++++-------- tests/testthat/_snaps/mars_domain_score.md | 24 +++---- tests/testthat/_snaps/nn_domain_plot/nn-domain-plot.svg | 28 ++++---- tests/testthat/_snaps/nn_domain_score.md | 20 +++--- 7 files changed, 59 insertions(+), 71 deletions(-)
Title: Survival Control Charts Estimation Software
Description: Quality control charts for survival outcomes.
Allows users to construct the Continuous Time Generalized
Rapid Response CUSUM (CGR-CUSUM) <doi:10.1093/biostatistics/kxac041>,
the Biswas & Kalbfleisch (2008) <doi:10.1002/sim.3216> CUSUM,
the Bernoulli CUSUM and the risk-adjusted funnel plot for survival data
<doi:10.1002/sim.1970>.
These procedures can be used to monitor survival processes for a change
in the failure rate.
Author: Daniel Gomon [aut, cre] ,
Mirko Signorelli [ctb]
Maintainer: Daniel Gomon <d.gomon@math.leidenuniv.nl>
Diff between success versions 1.0.0 dated 2023-02-17 and 1.0.1 dated 2023-10-09
success-1.0.0/success/R/funnel_survival.R |only success-1.0.1/success/DESCRIPTION | 17 - success-1.0.1/success/MD5 | 93 ++++-- success-1.0.1/success/NAMESPACE | 21 + success-1.0.1/success/NEWS.md | 11 success-1.0.1/success/R/RootLinearInterpolant.R | 6 success-1.0.1/success/R/arrival_rate.R | 11 success-1.0.1/success/R/bernoulli_ARL.R |only success-1.0.1/success/R/bernoulli_control_limit.R | 31 ++ success-1.0.1/success/R/bernoulli_cusum.R | 50 ++- success-1.0.1/success/R/bk_control_limit.R | 24 + success-1.0.1/success/R/bk_cusum.R | 12 success-1.0.1/success/R/cgr_control_limit.R | 23 + success-1.0.1/success/R/cgr_cusum.R | 6 success-1.0.1/success/R/cgr_generic.R | 71 +++- success-1.0.1/success/R/check_data.R | 6 success-1.0.1/success/R/extract_hazard.R | 9 success-1.0.1/success/R/funnel_plot.R | 41 +- success-1.0.1/success/R/interactive_plot.R | 15 - success-1.0.1/success/R/runlength.R | 6 success-1.0.1/success/README.md | 6 success-1.0.1/success/build/partial.rdb |binary success-1.0.1/success/build/vignette.rds |binary success-1.0.1/success/inst/CITATION |only success-1.0.1/success/inst/doc/success_arxiv.pdf |binary success-1.0.1/success/man/bernoulli_ARL.Rd |only success-1.0.1/success/man/bernoulli_ARL_MC.Rd |only success-1.0.1/success/man/bernoulli_ARL_SPRT.Rd |only success-1.0.1/success/man/bernoulli_RL_cdf.Rd |only success-1.0.1/success/man/bernoulli_cdf_MC.Rd |only success-1.0.1/success/man/bernoulli_cusum.Rd | 4 success-1.0.1/success/man/bk_cusum.Rd | 2 success-1.0.1/success/man/calc_MC_trans_matrix.Rd |only success-1.0.1/success/man/calc_Wncdf.Rd |only success-1.0.1/success/man/extract_hazard.Rd | 12 success-1.0.1/success/man/figures |only success-1.0.1/success/man/funnel_plot.Rd | 8 success-1.0.1/success/man/interactive_plot.Rd | 144 +++++----- success-1.0.1/success/man/plot.Rd | 111 ++++--- success-1.0.1/success/tests/testthat/_snaps |only success-1.0.1/success/tests/testthat/test-RootLinearInterpolant.R |only success-1.0.1/success/tests/testthat/test-arrival_rate.R |only success-1.0.1/success/tests/testthat/test-bernoulli_ARL.R |only success-1.0.1/success/tests/testthat/test-bernoulli_control_limit.R |only success-1.0.1/success/tests/testthat/test-bernoulli_cusum.R |only success-1.0.1/success/tests/testthat/test-bk_control_limit.R |only success-1.0.1/success/tests/testthat/test-bk_cusum.R |only success-1.0.1/success/tests/testthat/test-calc_risk.R |only success-1.0.1/success/tests/testthat/test-cgr_control_limit.R | 89 +++++- success-1.0.1/success/tests/testthat/test-cgr_cusum.R | 123 ++++++-- success-1.0.1/success/tests/testthat/test-cgr_generic.R |only success-1.0.1/success/tests/testthat/test-cgr_summary.R |only success-1.0.1/success/tests/testthat/test-check_data.R |only success-1.0.1/success/tests/testthat/test-funnel_plot.R |only success-1.0.1/success/tests/testthat/test-runlength.R |only 55 files changed, 653 insertions(+), 299 deletions(-)
Title: Density Estimation and Visualization of 2D Scatter Plots
Description: The user has the option to utilize the two-dimensional density estimation techniques called smoothed density published by Eilers and Goeman (2004) <doi:10.1093/bioinformatics/btg454>, and pareto density which was evaluated for univariate data by Thrun, Gehlert and Ultsch, 2020 <doi:10.1371/journal.pone.0238835>. Moreover, it provides visualizations of the density estimation in the form of two-dimensional scatter plots in which the points are color-coded based on increasing density. Colors are defined by the one-dimensional clustering technique called 1D distribution cluster algorithm (DDCAL) published by Lux and Rinderle-Ma (2023) <doi:10.1007/s00357-022-09428-6>.
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [aut, rev],
Luca Brinkman [aut],
Quirin Stier [aut]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ScatterDensity versions 0.0.3 dated 2023-07-18 and 0.0.4 dated 2023-10-09
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/DensityScatter.DDCAL.R | 1 + build/partial.rdb |binary man/PointsInPolygon.Rd | 3 +++ man/PolygonGate.Rd | 7 ++++--- man/ScatterDensity-package.Rd | 17 +---------------- src/Makevars | 3 ++- src/Makevars.win | 4 ++-- src/c_inPSphere2D.cpp | 18 +++++++++++++++++- 10 files changed, 43 insertions(+), 36 deletions(-)
More information about ScatterDensity at CRAN
Permanent link
Title: Interface to 'NetCDF' Datasets
Description: An interface to the 'NetCDF' file formats designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
Most capabilities of 'NetCDF' version 4 are supported. Optional conversions
of time units are enabled by 'UDUNITS' version 2, also from Unidata.
Author: Pavel Michna [aut],
Milton Woods [aut, cre]
Maintainer: Milton Woods <miltonjwoods@gmail.com>
Diff between RNetCDF versions 2.6-2 dated 2023-01-16 and 2.7-1 dated 2023-10-09
RNetCDF-2.6-2/RNetCDF/demo/write1_readN.R |only RNetCDF-2.6-2/RNetCDF/demo/writeN_read1.R |only RNetCDF-2.6-2/RNetCDF/src/Makevars.in |only RNetCDF-2.6-2/RNetCDF/src/Makevars.ucrt |only RNetCDF-2.6-2/RNetCDF/src/Makevars.win |only RNetCDF-2.6-2/RNetCDF/tools/winlibs.R |only RNetCDF-2.7-1/RNetCDF/DESCRIPTION | 14 RNetCDF-2.7-1/RNetCDF/INSTALL | 126 - RNetCDF-2.7-1/RNetCDF/MD5 | 83 RNetCDF-2.7-1/RNetCDF/NEWS | 15 RNetCDF-2.7-1/RNetCDF/R/config.R.in |only RNetCDF-2.7-1/RNetCDF/cleanup.win |only RNetCDF-2.7-1/RNetCDF/configure | 2527 +++++++++++++++++++++-- RNetCDF-2.7-1/RNetCDF/configure.ac | 379 +++ RNetCDF-2.7-1/RNetCDF/configure.win | 3 RNetCDF-2.7-1/RNetCDF/demo/00Index | 4 RNetCDF-2.7-1/RNetCDF/demo/Rmpi_writeN_read1.R |only RNetCDF-2.7-1/RNetCDF/demo/pbdMPI_writeN_read1.R |only RNetCDF-2.7-1/RNetCDF/man/att.copy.nc.Rd | 5 RNetCDF-2.7-1/RNetCDF/man/att.delete.nc.Rd | 7 RNetCDF-2.7-1/RNetCDF/man/att.get.nc.Rd | 5 RNetCDF-2.7-1/RNetCDF/man/att.inq.nc.Rd | 5 RNetCDF-2.7-1/RNetCDF/man/att.rename.nc.Rd | 4 RNetCDF-2.7-1/RNetCDF/man/config.nc.Rd |only RNetCDF-2.7-1/RNetCDF/man/create.nc.Rd | 4 RNetCDF-2.7-1/RNetCDF/man/grp.inq.nc.Rd | 55 RNetCDF-2.7-1/RNetCDF/man/open.nc.Rd | 4 RNetCDF-2.7-1/RNetCDF/man/var.get.nc.Rd | 19 RNetCDF-2.7-1/RNetCDF/man/var.put.nc.Rd | 22 RNetCDF-2.7-1/RNetCDF/src/Makefile |only RNetCDF-2.7-1/RNetCDF/src/Makefile.common.in |only RNetCDF-2.7-1/RNetCDF/src/Makefile.win |only RNetCDF-2.7-1/RNetCDF/src/RNetCDF.h | 2 RNetCDF-2.7-1/RNetCDF/src/attribute.c | 12 RNetCDF-2.7-1/RNetCDF/src/common.c | 11 RNetCDF-2.7-1/RNetCDF/src/common.h | 7 RNetCDF-2.7-1/RNetCDF/src/convert.c | 281 +- RNetCDF-2.7-1/RNetCDF/src/convert.h | 2 RNetCDF-2.7-1/RNetCDF/src/dataset.c | 49 RNetCDF-2.7-1/RNetCDF/src/dimension.c | 12 RNetCDF-2.7-1/RNetCDF/src/group.c | 2 RNetCDF-2.7-1/RNetCDF/src/init.c | 2 RNetCDF-2.7-1/RNetCDF/src/type.c | 65 RNetCDF-2.7-1/RNetCDF/src/udunits.c | 2 RNetCDF-2.7-1/RNetCDF/src/variable.c | 141 - RNetCDF-2.7-1/RNetCDF/tests/RNetCDF-test.R | 379 +++ RNetCDF-2.7-1/RNetCDF/tools/convert.m4 | 277 +- RNetCDF-2.7-1/RNetCDF/tools/make-recursive.sh |only RNetCDF-2.7-1/RNetCDF/tools/release.sh | 26 RNetCDF-2.7-1/RNetCDF/tools/update-configure.sh |only RNetCDF-2.7-1/RNetCDF/tools/update-convert-c.sh |only 51 files changed, 3893 insertions(+), 658 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically regular time series and air quality
measurement, meteorological data and dispersion model output can be
analysed. The package is described in Carslaw and Ropkins (2012,
<doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre],
Jack Davison [aut],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.17-0 dated 2023-05-02 and 2.18-0 dated 2023-10-09
openair-2.17-0/openair/R/getMeta.R |only openair-2.17-0/openair/R/importAQE.R |only openair-2.17-0/openair/R/importAURN.R |only openair-2.17-0/openair/R/importLocal.R |only openair-2.17-0/openair/R/importNI.R |only openair-2.17-0/openair/R/importSAQN.R |only openair-2.17-0/openair/R/importWAQN.R |only openair-2.17-0/openair/man/importAQE.Rd |only openair-2.17-0/openair/man/importAURN.Rd |only openair-2.17-0/openair/man/importLocal.Rd |only openair-2.17-0/openair/man/importNI.Rd |only openair-2.17-0/openair/man/importSAQN.Rd |only openair-2.17-0/openair/man/importWAQN.Rd |only openair-2.18-0/openair/DESCRIPTION | 11 openair-2.18-0/openair/MD5 | 121 - openair-2.18-0/openair/NAMESPACE | 4 openair-2.18-0/openair/NEWS.md | 60 openair-2.18-0/openair/R/TheilSen.R | 2 openair-2.18-0/openair/R/calcFno2.R | 11 openair-2.18-0/openair/R/calendarPlot.R | 1010 +++++----- openair-2.18-0/openair/R/conditionalEval.R | 147 - openair-2.18-0/openair/R/conditionalQuantile.R | 80 openair-2.18-0/openair/R/importMeta.R |only openair-2.18-0/openair/R/importUKAQ-utils.R |only openair-2.18-0/openair/R/importUKAQ.R | 786 ++++++-- openair-2.18-0/openair/R/openColours.R | 176 + openair-2.18-0/openair/R/percentileRose.R | 12 openair-2.18-0/openair/R/polarAnnulus.R | 7 openair-2.18-0/openair/R/polarCluster.R | 46 openair-2.18-0/openair/R/polarDiff.R | 5 openair-2.18-0/openair/R/polarFreq.R | 21 openair-2.18-0/openair/R/polarPlot.R | 446 ++-- openair-2.18-0/openair/R/quickText.R | 3 openair-2.18-0/openair/R/runRegression.R |only openair-2.18-0/openair/R/scatterPlot.R | 18 openair-2.18-0/openair/R/smoothTrend.R | 2 openair-2.18-0/openair/R/summaryPlot.R | 321 +-- openair-2.18-0/openair/R/timeAverage.R | 3 openair-2.18-0/openair/R/timeVariation.R | 3 openair-2.18-0/openair/R/trajLevel.R | 10 openair-2.18-0/openair/R/trendLevel.R | 1328 +++++++------- openair-2.18-0/openair/R/windRose.R | 5 openair-2.18-0/openair/R/zzz.R | 2 openair-2.18-0/openair/README.md | 99 - openair-2.18-0/openair/man/TheilSen.Rd | 1 openair-2.18-0/openair/man/calendarPlot.Rd | 184 - openair-2.18-0/openair/man/conditionalEval.Rd | 32 openair-2.18-0/openair/man/conditionalQuantile.Rd | 9 openair-2.18-0/openair/man/figures/README-polarCPF-1.png |binary openair-2.18-0/openair/man/figures/README-windrose-1.png |binary openair-2.18-0/openair/man/figures/README-windrose2-1.png |binary openair-2.18-0/openair/man/importADMS.Rd | 6 openair-2.18-0/openair/man/importEurope.Rd | 6 openair-2.18-0/openair/man/importKCL.Rd | 25 openair-2.18-0/openair/man/importMeta.Rd | 68 openair-2.18-0/openair/man/importTraj.Rd | 6 openair-2.18-0/openair/man/importUKAQ-wrapper.Rd |only openair-2.18-0/openair/man/importUKAQ.Rd |only openair-2.18-0/openair/man/openColours.Rd | 110 - openair-2.18-0/openair/man/polarAnnulus.Rd | 4 openair-2.18-0/openair/man/polarCluster.Rd | 15 openair-2.18-0/openair/man/polarDiff.Rd | 4 openair-2.18-0/openair/man/polarFreq.Rd | 4 openair-2.18-0/openair/man/polarPlot.Rd | 8 openair-2.18-0/openair/man/runRegression.Rd |only openair-2.18-0/openair/man/smoothTrend.Rd | 1 openair-2.18-0/openair/man/summaryPlot.Rd | 165 - openair-2.18-0/openair/man/timePlot.Rd | 1 openair-2.18-0/openair/man/timeProp.Rd | 1 openair-2.18-0/openair/man/timeVariation.Rd | 4 openair-2.18-0/openair/man/trendLevel.Rd | 1 71 files changed, 3039 insertions(+), 2355 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and routines for graphical display.
Author: Michael Dewey [aut, cre]
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.8 dated 2022-02-10 and 1.9 dated 2023-10-09
DESCRIPTION | 9 ++++----- MD5 | 29 +++++++++++++++-------------- NEWS | 5 +++++ R/plotp.R | 10 +++++++--- build/metap.pdf |binary build/partial.rdb |binary build/stage23.rdb |only build/vignette.rds |binary inst/CITATION | 17 +---------------- inst/doc/compare.pdf |binary inst/doc/metap.pdf |binary inst/doc/plotmetap.R | 5 ++--- inst/doc/plotmetap.Rnw | 28 ++++++++++++++++------------ inst/doc/plotmetap.pdf |binary man/plotp.Rd | 15 ++++++++++----- vignettes/plotmetap.Rnw | 28 ++++++++++++++++------------ 16 files changed, 76 insertions(+), 70 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting absences under specified criteria, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially described in Barbosa (2015) <doi:10.1111/2041-210X.1237 [...truncated...]
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.9.9 dated 2023-04-14 and 4.10.5 dated 2023-10-09
DESCRIPTION | 14 ++-- MD5 | 34 +++++---- NAMESPACE | 2 NEWS | 142 +++++++++++++++++++++++++++++++++++++++- R/appendData.R |only R/cleanCoords.R | 29 +++++--- R/corSelect.R | 167 +++++++++++++++++++++++++++++++++++------------- R/getPreds.R | 18 ++--- R/gridRecords.R | 5 - R/multGLM.R | 34 +++++++-- data/rotif.env.rda |binary data/rotifers.rda |binary man/Fav.Rd | 13 ++- man/appendData.Rd |only man/cleanCoords.Rd | 30 +++++--- man/corSelect.Rd | 44 +++++++----- man/fuzzyOverlay.Rd | 12 +-- man/fuzzySim-package.Rd | 4 - man/multGLM.Rd | 20 +++-- 19 files changed, 415 insertions(+), 153 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the
'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi'
library. 'textshaping' is a low-level utility package mainly for
graphic devices that expands upon the font tool-set provided by the
'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between textshaping versions 0.3.6 dated 2021-10-13 and 0.3.7 dated 2023-10-09
textshaping-0.3.6/textshaping/src/Makevars.ucrt |only textshaping-0.3.7/textshaping/DESCRIPTION | 38 - textshaping-0.3.7/textshaping/MD5 | 27 textshaping-0.3.7/textshaping/NEWS.md | 4 textshaping-0.3.7/textshaping/build/vignette.rds |binary textshaping-0.3.7/textshaping/configure | 2 textshaping-0.3.7/textshaping/inst/doc/c_interface.html | 410 +++++++++++---- textshaping-0.3.7/textshaping/man/get_font_features.Rd | 5 textshaping-0.3.7/textshaping/man/text_width.Rd | 5 textshaping-0.3.7/textshaping/man/textshaping-package.Rd | 9 textshaping-0.3.7/textshaping/src/Makevars.in | 2 textshaping-0.3.7/textshaping/src/Makevars.win | 17 textshaping-0.3.7/textshaping/src/cpp11.cpp | 8 textshaping-0.3.7/textshaping/src/string_shape.cpp | 6 textshaping-0.3.7/textshaping/tools/winlibs.R | 22 15 files changed, 397 insertions(+), 158 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.0.4 dated 2022-02-11 and 1.0.5 dated 2023-10-09
systemfonts-1.0.4/systemfonts/src/Makevars.ucrt |only systemfonts-1.0.5/systemfonts/DESCRIPTION | 66 - systemfonts-1.0.5/systemfonts/MD5 | 19 systemfonts-1.0.5/systemfonts/NEWS.md | 5 systemfonts-1.0.5/systemfonts/build/vignette.rds |binary systemfonts-1.0.5/systemfonts/inst/doc/c_interface.html | 588 ++++++++---- systemfonts-1.0.5/systemfonts/src/Makevars.in | 2 systemfonts-1.0.5/systemfonts/src/Makevars.win | 14 systemfonts-1.0.5/systemfonts/src/font_matching.h | 2 systemfonts-1.0.5/systemfonts/src/unix/FontManagerLinux.cpp | 4 systemfonts-1.0.5/systemfonts/tools/winlibs.R | 22 11 files changed, 500 insertions(+), 222 deletions(-)
Title: Poisson Network Autoregressive Models
Description: Quasi likelihood-based methods for estimating linear and log-linear Poisson Network Autoregression models with p lags and covariates. Tools for testing the linearity versus several non-linear alternatives. Tools for simulation of multivariate count distributions, from linear and non-linear PNAR models, by using a specific copula construction. References include: Armillotta, M. and K. Fokianos (2022a). Poisson network autoregression. <arXiv:2104.06296>. Armillotta, M. and K. Fokianos (2022b). Testing linearity for network autoregressive models. <arXiv:2202.03852>. Armillotta, M., Tsagris, M. and Fokianos, K. (2022c). The R-package PNAR for modelling count network time series. <arXiv:2211.02582>.
Author: Michail Tsagris [aut, cre],
Mirko Armillotta [aut, cph],
Konstantinos Fokianos [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between PNAR versions 1.5 dated 2023-09-15 and 1.6 dated 2023-10-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/lin_ic_plot.R | 23 ++++++++++++++++++----- R/log_lin_ic_plot.R | 24 ++++++++++++++++++------ man/PNAR-package.Rd | 4 ++-- man/lin_ic_plot.Rd | 11 +++++++---- man/log_lin_ic_plot.Rd | 13 ++++++++----- 7 files changed, 63 insertions(+), 32 deletions(-)
Title: Parallel Partitioning-Around-Medoids (PAM) for Big Sets of Data
Description: Application of the Partitioning-Around-Medoids (PAM) clustering algorithm described in Schubert, E. and Rousseeuw, P.J.:
"Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms." Information Systems,
vol. 101, p. 101804, (2021). <doi:10.1016/j.is.2021.101804>.
It uses a binary format for storing and retrieval of matrices developed for the 'jmatrix' package but the functionality of 'jmatrix'
is included here, so you do not need to install it. Also, it is used by package 'scellpam', so if you have installed it, you do not need
to install this package.
PAM can be applied to sets of data whose dissimilarity matrix can be very big. It has been tested with up to 100.000 points.
It does this with the help of the code developed for other package, 'jmatrix', which allows the matrix not to be loaded in 'R' memory (which
would force it to be of double type) but it gets from disk, which allows using float (or even smaller data types). Moreover [...truncated...]
Author: Juan Domingo [aut, cre] ,
Guillermo Ayala [ctb] ,
Spanish Ministry of Science and Innovation, MCIN/AEI
<doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <Juan.Domingo@uv.es>
Diff between parallelpam versions 1.3 dated 2023-06-23 and 1.4 dated 2023-10-09
DESCRIPTION | 6 MD5 | 47 - NAMESPACE | 3 NEWS | 5 R/RcppExports.R | 117 ++++ build/vignette.rds |binary inst/doc/jmatrixpp.R | 43 + inst/doc/jmatrixpp.Rmd | 84 ++- inst/doc/jmatrixpp.html | 909 +++++++++++++++++++++++---------- inst/doc/parallelpam.html | 799 +++++++++++++++++++++-------- inst/include/jmatrix.h | 1 inst/include/symmetricmatrix.h | 18 man/CalcAndWriteDissimilarityMatrix.Rd | 6 man/CsvToJMat.Rd |only man/FilterJMatByName.Rd |only man/JMatToCsv.Rd |only src/RcppExports.cpp | 46 + src/csvtojmat.cpp |only src/dissimmat_full.cpp | 5 src/dissimmat_sparse.cpp | 5 src/filternames.cpp |only src/fullmatrix.cpp | 11 src/jmatrix.cpp | 53 + src/sparsematrix.cpp | 8 src/symmetricmatrix.cpp | 122 +++- vignettes/jmatrixpp.Rmd | 84 ++- vignettes/parallelpam.bib | 12 27 files changed, 1842 insertions(+), 542 deletions(-)
Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
Transcriptomics
Description: An open, multi-algorithmic pipeline for easy, fast and efficient
analysis of cellular sub-populations and the molecular signatures that
characterize them. The pipeline consists of four successive steps: data
pre-processing, cellular clustering with pseudo-temporal ordering, defining
differential expressed genes and biomarker identification. More details on
Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
extensions of the work published by Ghannoum et. al. (2019)
<doi:10.1101/700989>.
Author: Salim Ghannoum [aut, cph],
Alvaro Koehn-Luque [aut, ths],
Waldir Leoncio [cre, aut],
Damiano Fantini [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between DIscBIO versions 1.2.0 dated 2021-04-28 and 1.2.1 dated 2023-10-09
DESCRIPTION | 79 MD5 | 111 NAMESPACE | 4 NEWS.md | 46 R/DIscBIO-classes.R | 181 - R/DIscBIO-generic-ClassVectoringDT.R | 150 - R/DIscBIO-generic-ClustDiffGenes.R | 441 +-- R/DIscBIO-generic-Clustexp.R | 202 - R/DIscBIO-generic-DEGanalysis.R | 813 +++--- R/DIscBIO-generic-DEGanalysis2clust.R | 580 ++-- R/DIscBIO-generic-Exprmclust.R | 210 - R/DIscBIO-generic-FinalPreprocessing.R | 107 R/DIscBIO-generic-FindOutliers.R | 533 ++-- R/DIscBIO-generic-NoiseFiltering.R | 451 +-- R/DIscBIO-generic-Normalizedata.R | 116 R/DIscBIO-generic-PCAplotSymbols.R | 82 R/DIscBIO-generic-PlotmclustMB.R | 431 +-- R/DIscBIO-generic-clusteringOrder.R | 73 R/DIscBIO-generic-clustheatmap.R | 302 +- R/DIscBIO-generic-comptSNE.R | 95 R/DIscBIO-generic-plotExptSNE.R | 169 - R/DIscBIO-generic-plotGap.R | 35 R/DIscBIO-generic-plotLabelstSNE.R | 101 R/DIscBIO-generic-plotOrderTsne.R | 161 - R/DIscBIO-generic-plotSilhouette.R | 71 R/DIscBIO-generic-plotSymbolstSNE.R | 79 R/DIscBIO-generic-plottSNE.R | 93 R/DIscBIO-generic-pseudoTimeOrdering.R | 95 R/J48DT.R | 40 R/J48DTeval.R | 107 R/Jaccard.R | 73 R/NetAnalysis.R | 69 R/Networking.R | 84 R/PPI.R | 16 R/PlotMBpca.R | 171 - R/RpartDT.R | 24 R/RpartEVAL.R | 107 R/VolcanoPlot.R | 116 R/bootstrap.R |only R/calc_pcareduceres.R |only R/cross.val.R |only R/customConverters.R | 152 - R/datasets.R | 2 R/internal-functions-samr-adapted.R | 4018 ++++++++++++++++----------------- R/internal-functions.R | 691 ++--- man/ClustDiffGenes.Rd | 4 man/Clustexp.Rd | 2 man/DISCBIO.Rd | 2 man/DISCBIO2SingleCellExperiment.Rd | 1 man/FinalPreprocessing.Rd | 6 man/FindOutliers.Rd | 7 man/Jaccard.Rd | 4 man/NoiseFiltering.Rd | 2 man/Normalizedata.Rd | 5 man/PlotMBpca.Rd | 9 man/clustheatmap.Rd | 3 man/comptSNE.Rd | 4 man/sammy.Rd | 67 58 files changed, 5829 insertions(+), 5768 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjaerde [trl],
Brad J. Biggerstaff [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 2.1.1 dated 2023-08-21 and 2.2.0 dated 2023-10-09
DESCRIPTION | 9 - MD5 | 29 ++-- NEWS.md | 53 ++++--- R/Exact_cond_midP_linear_rank_tests_2xc.R | 4 R/Exact_cond_midP_unspecific_ordering_rx2.R | 27 ++- R/Fisher_midP_test_2x2.R | 8 - R/McNemar_exact_unconditional_test_paired_2x2.R | 8 - R/contingencytables-package.R | 1 R/generics.R | 142 ++++----------------- R/the_paired_2x2_table_tests.R | 11 - R/validateArguments.R | 8 + man/McNemar_exact_unconditional_test_paired_2x2.Rd | 10 + man/contingencytables.Rd | 1 man/the_paired_2x2_table_tests.Rd | 8 - tests/testthat/test-issue51.R |only tests/testthat/test-validation.R | 4 16 files changed, 134 insertions(+), 189 deletions(-)
More information about contingencytables at CRAN
Permanent link
Title: Composite Indicator Construction and Analysis
Description: A comprehensive high-level package, for composite indicator construction and analysis. It is a "development environment"
for composite indicators and scoreboards, which includes utilities for construction (indicator selection, denomination, imputation,
data treatment, normalisation, weighting and aggregation) and analysis (multivariate analysis, correlation plotting, short cuts for
principal component analysis, global sensitivity analysis, and more). A composite indicator is completely encapsulated inside a single
hierarchical list called a "coin". This allows a fast and efficient work flow, as well as making quick copies, testing methodological variations and making comparisons.
It also includes many plotting options, both statistical (scatter plots, distribution plots) as well as for presenting results.
Author: William Becker [aut, cre, cph]
Maintainer: William Becker <william.becker@bluefoxdata.eu>
Diff between COINr versions 1.1.2 dated 2023-02-10 and 1.1.7 dated 2023-10-09
DESCRIPTION | 6 MD5 | 100 +++--- NAMESPACE | 2 NEWS.md | 22 + R/aggregate.R | 3 R/check_and_get.R | 3 R/correlations.R | 15 - R/impute.R | 1 R/new_coin.R | 43 ++ R/normalise.R | 2 R/plot_bar.R | 26 + R/plot_corr.R | 29 + R/plot_dist.R | 2 R/plot_scatter.R | 4 R/results.R | 37 ++ R/sensitivity.R | 9 R/stats.R | 73 ++-- R/treat.R | 36 ++ R/utils.R | 55 +++ R/weights.R | 2 README.md | 96 ++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/adjustments.html | 608 ++++++++++++++++++++--------------------- inst/doc/aggregate.html | 254 ++++++++--------- inst/doc/analysis.html | 284 +++++++++---------- inst/doc/coins.html | 562 ++++++++++++++++++------------------- inst/doc/data_selection.html | 272 +++++++++--------- inst/doc/denomination.html | 160 +++++----- inst/doc/imputation.html | 324 ++++++++++----------- inst/doc/normalise.html | 460 +++++++++++++++---------------- inst/doc/other_functions.html | 156 +++++----- inst/doc/overview.html | 160 +++++----- inst/doc/results.html | 198 ++++++------- inst/doc/screening.html | 182 ++++++------ inst/doc/sensitivity.html | 176 +++++------ inst/doc/treat.R | 40 +- inst/doc/treat.html | 557 ++++++++++++++++++------------------- inst/doc/v1.html | 6 inst/doc/visualisation.html | 56 +-- inst/doc/weights.html | 224 +++++++-------- man/Aggregate.coin.Rd | 3 man/Treat.coin.Rd | 4 man/get_results.Rd | 5 man/get_sensitivity.Rd | 6 man/get_stats.coin.Rd | 38 +- man/get_stats.data.frame.Rd | 41 +- man/get_str_weak.Rd | 5 man/icodes_to_inames.Rd |only man/plot_bar.Rd | 5 man/ucodes_to_unames.Rd |only tests/testthat/test-new_coin.R | 5 52 files changed, 2797 insertions(+), 2560 deletions(-)
Title: Generate Code Lists for the OMOP Common Data Model
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 1.7.0 dated 2023-08-16 and 2.0.0 dated 2023-10-09
DESCRIPTION | 8 MD5 | 79 NAMESPACE | 1 NEWS.md | 52 R/codesFromConceptSet.R | 769 +- R/drugCodes.R | 591 +- R/getCandidateCodes.R | 117 R/getICD10StandardCodes.R | 67 R/getMappings.R | 286 - R/inputValidation.R | 71 R/mockVocabRef.R | 707 +- R/runSearch.R | 338 - R/summariseCodeUse.R | 308 - README.md | 143 inst/doc/a01_Introduction_to_CodelistGenerator.R | 42 inst/doc/a01_Introduction_to_CodelistGenerator.html | 20 inst/doc/a02_Candidate_codes_OA.R | 125 inst/doc/a02_Candidate_codes_OA.Rmd | 99 inst/doc/a02_Candidate_codes_OA.html | 234 inst/doc/a03_Options_for_CodelistGenerator.R | 40 inst/doc/a03_Options_for_CodelistGenerator.Rmd | 32 inst/doc/a03_Options_for_CodelistGenerator.html | 504 - inst/doc/a04_codelists_for_medications.R | 80 inst/doc/a04_codelists_for_medications.Rmd | 85 inst/doc/a04_codelists_for_medications.html | 300 - inst/not_all_concept_sets/cohort_def.json | 5706 ++++++++++---------- man/codesFromConceptSet.Rd | 46 man/getCandidateCodes.Rd | 39 man/getDoseForm.Rd | 44 man/summariseCodeUse.Rd | 6 man/summariseCohortCodeUse.Rd |only tests/testthat/test-codesFrom.R | 272 tests/testthat/test-drugCodes.R | 11 tests/testthat/test-getCandidateCodes.R | 766 +- tests/testthat/test-getICD10StandardCodes.R | 15 tests/testthat/test-summariseCodeUse.R | 994 ++- tests/testthat/test-synthea_sql_server.R | 118 tests/testthat/test-vocabUtilities.R | 10 vignettes/a02_Candidate_codes_OA.Rmd | 99 vignettes/a03_Options_for_CodelistGenerator.Rmd | 32 vignettes/a04_codelists_for_medications.Rmd | 85 41 files changed, 6165 insertions(+), 7176 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
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 1.0.0 dated 2023-09-15 and 1.0.1 dated 2023-10-09
DESCRIPTION | 24 MD5 | 68 - NAMESPACE | 3 NEWS.md | 16 R/additionalData_readRs.R | 320 +++++++ R/beesChecklist.R | 63 + R/beesTaxonomy.R | 63 + R/chordDiagramR.R | 102 ++ R/countryOutliers.R | 64 + R/harmoniseR.R | 5 R/interactiveMapR.R | 3 R/jbd_Ctrans_chunker.R | 5 R/jbd_coordCountryInconsistent.R | 54 + R/plotFlagSummary.R | 2 README.md | 86 +- inst/BeeBDC_basicWorkflow.R | 5 inst/BeeBDC_fullWorkflow.R | 114 +- inst/CITATION | 10 inst/doc/BeeBDC_main.R | 41 - inst/doc/BeeBDC_main.Rmd | 74 + inst/doc/BeeBDC_main.html | 1376 +++++++++++++++++----------------- inst/doc/basic_workflow.R | 25 inst/doc/basic_workflow.Rmd | 23 inst/doc/basic_workflow.html | 350 ++++---- man/beesTaxonomy.Rd | 2 man/chordDiagramR.Rd | 8 man/countryOutlieRs.Rd | 3 man/readr_BeeBDC.Rd | 13 tests/testthat/test-BeeBDCQuery.R | 25 tests/testthat/test-beesChecklist.R | 2 tests/testthat/test-beesTaxonomy.R | 19 tests/testthat/test-countryOutlieRs.R | 4 tests/testthat/test-readr_BeeBDC.R | 57 + vignettes/BeeBDC_main.Rmd | 74 + vignettes/basic_workflow.Rmd | 23 35 files changed, 1940 insertions(+), 1186 deletions(-)
Title: Area-to-Area Kriging
Description: Point-scale variogram deconvolution from irregular/regular spatial support according to Goovaerts, P., (2008) <doi: 10.1007/s11004-007-9129-1>; ordinary area-to-area (co)Kriging and area-to-point (co)Kriging.
Author: Maogui Hu [aut, cre],
Yanwei Huang [ctb],
Roger Bivand [ctb]
Maintainer: Maogui Hu <humg@lreis.ac.cn>
Diff between atakrig versions 0.9.8 dated 2021-04-30 and 0.9.8.1 dated 2023-10-09
DESCRIPTION | 10 +-- MD5 | 32 +++++----- NAMESPACE | 3 R/prediction.r | 14 ++-- R/preparation.r | 153 +++++++++++------------------------------------- R/variogramdeconv.r | 12 ++- demo/00Index | 4 - demo/aod.r | 25 ++++--- demo/runoff.r | 8 +- man/ataCoKriging.Rd | 34 +++++----- man/ataKriging.Rd | 6 - man/deconvPointVgm.Rd | 9 +- man/discretizeRaster.Rd | 2 src/Makevars | 6 - src/Makevars.win | 6 - src/RcppExports.cpp | 5 + src/areaVgm.cpp | 6 + 17 files changed, 134 insertions(+), 201 deletions(-)
Title: Support Technical Processes Following 'Maelstrom Research'
Standards
Description: Functions to support rigorous processes in data cleaning,
evaluation, and documentation across datasets from different studies based
on Maelstrom Research guidelines. The package includes the core functions
to evaluate and format the main inputs that define the process, diagnose
errors, and summarize and evaluate datasets and their associated
data dictionaries. The main outputs are clean datasets and associated
metadata, and tabular and visual summary reports. As described in
Maelstrom Research guidelines for rigorous retrospective data
harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Author: Guillaume Fabre [aut, cre] ,
Maelstrom-research group [cph, fnd],
Alexandre Trottier [ctb],
Tina Wey [ctb],
Samuel El Bouzaidi Tiali [ctb]
Maintainer: Guillaume Fabre <guijoseph.fabre@gmail.com>
Diff between madshapR versions 1.0.0 dated 2023-06-20 and 1.0.2 dated 2023-10-09
madshapR-1.0.0/madshapR/R/00-utils.R |only madshapR-1.0.0/madshapR/R/01-dictionaries_functions.R |only madshapR-1.0.0/madshapR/R/02-dataset_functions.R |only madshapR-1.0.0/madshapR/R/03-catalogue_functions.R |only madshapR-1.0.0/madshapR/man/open_visual_report.Rd |only madshapR-1.0.2/madshapR/DESCRIPTION | 26 madshapR-1.0.2/madshapR/MD5 | 152 +-- madshapR-1.0.2/madshapR/NAMESPACE | 11 madshapR-1.0.2/madshapR/NEWS.md | 172 ++++ madshapR-1.0.2/madshapR/R/00-import-from-fabR.R |only madshapR-1.0.2/madshapR/R/01-utils.R |only madshapR-1.0.2/madshapR/R/02-dictionaries_functions.R |only madshapR-1.0.2/madshapR/R/03-dataset_functions.R |only madshapR-1.0.2/madshapR/R/04-catalogue_functions.R |only madshapR-1.0.2/madshapR/R/05-unit_checks.R | 167 ++-- madshapR-1.0.2/madshapR/R/06-data_evaluate.R | 285 ++++-- madshapR-1.0.2/madshapR/R/07-data_summarise.R | 298 +++++-- madshapR-1.0.2/madshapR/R/08-data_visualize.R | 449 ++++++----- madshapR-1.0.2/madshapR/R/deprecated.R |only madshapR-1.0.2/madshapR/build/partial.rdb |binary madshapR-1.0.2/madshapR/build/vignette.rds |binary madshapR-1.0.2/madshapR/data/DEMO_files.rda |binary madshapR-1.0.2/madshapR/data/valueType_list.rda |binary madshapR-1.0.2/madshapR/inst/WORDLIST | 43 - madshapR-1.0.2/madshapR/inst/doc/madshapR-vignette.R | 4 madshapR-1.0.2/madshapR/inst/doc/madshapR-vignette.html | 18 madshapR-1.0.2/madshapR/man/DEMO_files.Rd | 120 +- madshapR-1.0.2/madshapR/man/as_data_dict.Rd | 90 +- madshapR-1.0.2/madshapR/man/as_data_dict_mlstr.Rd | 106 +- madshapR-1.0.2/madshapR/man/as_data_dict_shape.Rd | 90 +- madshapR-1.0.2/madshapR/man/as_dataset.Rd | 94 +- madshapR-1.0.2/madshapR/man/as_dossier.Rd | 90 +- madshapR-1.0.2/madshapR/man/as_taxonomy.Rd | 92 +- madshapR-1.0.2/madshapR/man/as_valueType.Rd | 2 madshapR-1.0.2/madshapR/man/check_data_dict_categories.Rd | 90 +- madshapR-1.0.2/madshapR/man/check_data_dict_variables.Rd | 84 +- madshapR-1.0.2/madshapR/man/check_dataset_categories.Rd | 112 +- madshapR-1.0.2/madshapR/man/check_dataset_variables.Rd | 108 +- madshapR-1.0.2/madshapR/man/check_name_standards.Rd | 80 - madshapR-1.0.2/madshapR/man/data_dict_apply.Rd | 120 +- madshapR-1.0.2/madshapR/man/data_dict_collapse.Rd | 136 +-- madshapR-1.0.2/madshapR/man/data_dict_evaluate.Rd | 124 +-- madshapR-1.0.2/madshapR/man/data_dict_expand.Rd | 136 +-- madshapR-1.0.2/madshapR/man/data_dict_extract.Rd | 128 +-- madshapR-1.0.2/madshapR/man/data_dict_filter.Rd | 168 ++-- madshapR-1.0.2/madshapR/man/data_dict_group_by.Rd | 116 +- madshapR-1.0.2/madshapR/man/data_dict_group_split.Rd | 126 +-- madshapR-1.0.2/madshapR/man/data_dict_list_nest.Rd | 108 +- madshapR-1.0.2/madshapR/man/data_dict_match_dataset.Rd | 132 +-- madshapR-1.0.2/madshapR/man/data_dict_pivot_longer.Rd | 126 +-- madshapR-1.0.2/madshapR/man/data_dict_pivot_wider.Rd | 126 +-- madshapR-1.0.2/madshapR/man/data_dict_ungroup.Rd | 116 +- madshapR-1.0.2/madshapR/man/data_extract.Rd | 96 +- madshapR-1.0.2/madshapR/man/dataset_cat_as_labels.Rd | 106 +- madshapR-1.0.2/madshapR/man/dataset_evaluate.Rd | 178 ++-- madshapR-1.0.2/madshapR/man/dataset_preprocess.Rd | 130 +-- madshapR-1.0.2/madshapR/man/dataset_visualize.Rd | 265 +++--- madshapR-1.0.2/madshapR/man/dataset_zap_data_dict.Rd | 90 +- madshapR-1.0.2/madshapR/man/deprecated.Rd |only madshapR-1.0.2/madshapR/man/dossier_create.Rd | 100 +- madshapR-1.0.2/madshapR/man/dossier_evaluate.Rd | 124 +-- madshapR-1.0.2/madshapR/man/dossier_summarize.Rd | 14 madshapR-1.0.2/madshapR/man/is_data_dict.Rd | 90 +- madshapR-1.0.2/madshapR/man/is_data_dict_mlstr.Rd | 94 +- madshapR-1.0.2/madshapR/man/is_data_dict_shape.Rd | 92 +- madshapR-1.0.2/madshapR/man/is_dataset.Rd | 88 +- madshapR-1.0.2/madshapR/man/is_dossier.Rd | 76 - madshapR-1.0.2/madshapR/man/is_taxonomy.Rd | 86 +- madshapR-1.0.2/madshapR/man/is_valueType.Rd | 2 madshapR-1.0.2/madshapR/man/madshapR-package.Rd | 8 madshapR-1.0.2/madshapR/man/madshapR_help.Rd | 48 - madshapR-1.0.2/madshapR/man/reexports.Rd |only madshapR-1.0.2/madshapR/man/summary_variables.Rd | 114 +- madshapR-1.0.2/madshapR/man/summary_variables_categorical.Rd | 146 +-- madshapR-1.0.2/madshapR/man/summary_variables_date.Rd | 140 +-- madshapR-1.0.2/madshapR/man/summary_variables_datetime.Rd |only madshapR-1.0.2/madshapR/man/summary_variables_numeric.Rd | 122 +- madshapR-1.0.2/madshapR/man/summary_variables_text.Rd | 126 +-- madshapR-1.0.2/madshapR/man/valueType_adjust.Rd | 4 madshapR-1.0.2/madshapR/man/valueType_guess.Rd | 2 madshapR-1.0.2/madshapR/man/valueType_list.Rd | 6 madshapR-1.0.2/madshapR/man/valueType_of.Rd | 8 madshapR-1.0.2/madshapR/man/valueType_self_adjust.Rd | 6 madshapR-1.0.2/madshapR/man/variable_visualize.Rd | 220 ++--- 84 files changed, 3806 insertions(+), 3220 deletions(-)
Title: Importing 'SVG' Graphics
Description: Functions for importing external vector images and
drawing them as part of 'R' plots. This package is different from the
'grImport' package because, where that package imports 'PostScript'
format images, this package imports 'SVG' format images. Furthermore,
this package imports a specific subset of 'SVG', so external images
must be preprocessed using a package like 'rsvg' to produce 'SVG'
that this package can import. 'SVG' features that are not supported
by 'R' graphics, e.g., gradient fills, can be imported and then
exported via the 'gridSVG' package.
Author: Simon Potter [aut],
Paul Murrell [aut, cre]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between grImport2 versions 0.2-0 dated 2019-11-25 and 0.3-0 dated 2023-10-09
DESCRIPTION | 6 - MD5 | 32 ++++----- NAMESPACE | 2 R/classes.R | 23 ++++++ R/grobs.R | 17 ++-- R/import.R | 8 ++ R/parser.R | 10 +- R/utils.R | 111 +++++++++++++++++++++++++++----- inst/NEWS.Rd | 21 ++++++ man/Picture-class.Rd | 7 ++ tests/test-bboxclip-output.svg.save | 2 tests/test-noclip-output.svg.save | 2 tests/test-path-complex-output.svg.save | 2 tests/test-path-simple-output.svg.save | 2 tests/test-raster.R | 9 +- tests/test-rect-output.svg.save | 2 tests/test-symbol-output.svg.save | 2 17 files changed, 199 insertions(+), 59 deletions(-)
Title: Translate English Words into Chinese, or Translate Chinese Words
into English
Description: If translate English words into Chinese, there is a faster
way for R user. 'RYoudaoTranslate' package provides interface to
'Youdao' <http://youdao.com/> translation open API for R user. 'entcn'
package also provides similar features. But it does not support Chinese
words translation into English, I have made some improvements on the basis
of this software. You can pass in an English or Chinese word, ecce package
support both English and Chinese translation. It also support browse
translation results in website. In addition, also support obtain the pinyin
of the Chinese character, so that you can more easily understand the
pronunciation of the Chinese character.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between ecce versions 2.0.5 dated 2023-09-02 and 2.0.6 dated 2023-10-09
DESCRIPTION | 8 ++--- MD5 | 24 +++++++-------- R/pinyin.R | 3 - R/translate.R | 1 R/translate_view.R | 1 README.md | 80 ++++++++++++++++++++++++++------------------------ inst/doc/ecce.R | 12 +++---- inst/doc/ecce.Rmd | 2 - inst/doc/ecce.html | 6 +-- man/pinyin.Rd | 3 - man/translate.Rd | 1 man/translate_view.Rd | 1 vignettes/ecce.Rmd | 2 - 13 files changed, 72 insertions(+), 72 deletions(-)
Title: Logging in 'R' and Post to 'Azure Log Analytics' Workspace
Description: It extends the functionality of 'logger' package. Additional
logging metadata can be configured to be collected. Logging messages are
displayed on console and optionally they are sent to 'Azure Log Analytics'
workspace in real-time.
Author: Vivek Atal [aut, cre]
Maintainer: Vivek Atal <atalvivek@yahoo.co.in>
Diff between azlogr versions 0.0.4 dated 2023-01-14 and 0.0.5 dated 2023-10-09
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 4 R/logger_level.R | 38 ++++---- README.md | 5 - build/vignette.rds |binary inst/doc/how-to-use-azlogr.html | 170 ++++++++++++++++++------------------- tests/testthat/test-logger_level.R | 46 ++++++---- 8 files changed, 152 insertions(+), 131 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 3.0.0 dated 2023-09-06 and 3.0.1 dated 2023-10-09
ChangeLog | 5 DESCRIPTION | 8 MD5 | 44 - R/build_score_cache.R | 4 R/build_score_cache_bayes.R | 8 R/build_score_cache_mle.R | 60 +- R/fitabn.R | 4 R/fitabn_bayes.R | 65 ++ configure | 713 ++++++++++++++-------------- configure.ac | 2 man/buildScoreCache.Rd | 4 man/getMSEfromModes.Rd |only man/modes2coefs.Rd |only src/fit_single_node.c | 76 +- src/irls_poisson_fast.cpp | 31 + src/node_binomial.h | 6 src/node_binomial_rv_inner.h | 16 src/node_gaussian_rv_inner.c | 48 + src/node_poisson_rv_inner.h | 7 src/utility.c | 156 +++--- tests/testthat/test-build_score_cache_mle.R | 30 - tests/testthat/test-fitabn_bayes.R | 2 tests/testthat/test-fitabn_mle.R | 8 tests/testthat/test-simulateabn.R | 102 +++- 24 files changed, 864 insertions(+), 535 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-30 0.3.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-20 1.6.0
2023-05-28 1.5.4
2022-11-24 1.5.0
2022-08-28 1.4.7
2022-03-31 1.4.5
2021-12-20 1.4.3
2021-11-06 1.4.2
2021-11-03 1.4.1
2021-10-24 1.4.0
2021-07-30 0.3.1
2021-06-13 0.2.0
2021-03-31 0.1.3
2021-02-16 0.1.0
Title: Database Interface and MariaDB Driver
Description: Implements a DBI-compliant interface to MariaDB
(<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>)
databases.
Author: Kirill Mueller [aut, cre] ,
Jeroen Ooms [aut] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RMariaDB versions 1.2.2 dated 2022-06-18 and 1.3.0 dated 2023-10-09
RMariaDB-1.2.2/RMariaDB/R/RcppExports.R |only RMariaDB-1.2.2/RMariaDB/src/Makevars.ucrt |only RMariaDB-1.2.2/RMariaDB/src/RcppExports.cpp |only RMariaDB-1.3.0/RMariaDB/DESCRIPTION | 65 ++---- RMariaDB-1.3.0/RMariaDB/MD5 | 90 ++++---- RMariaDB-1.3.0/RMariaDB/NAMESPACE | 2 RMariaDB-1.3.0/RMariaDB/NEWS.md | 26 ++ RMariaDB-1.3.0/RMariaDB/R/MariaDBConnection.R | 31 ++ RMariaDB-1.3.0/RMariaDB/R/RMariaDB-package.R | 1 RMariaDB-1.3.0/RMariaDB/R/cpp11.R |only RMariaDB-1.3.0/RMariaDB/R/dbConnect_MariaDBDriver.R | 58 ++++- RMariaDB-1.3.0/RMariaDB/R/default.R | 35 +++ RMariaDB-1.3.0/RMariaDB/README.md | 4 RMariaDB-1.3.0/RMariaDB/man/MariaDBConnection-class.Rd | 19 + RMariaDB-1.3.0/RMariaDB/man/RMariaDB-package.Rd | 2 RMariaDB-1.3.0/RMariaDB/man/dbConnect-MariaDBDriver-method.Rd | 9 RMariaDB-1.3.0/RMariaDB/src/CMakeLists.txt |only RMariaDB-1.3.0/RMariaDB/src/DbConnection.cpp | 105 ++++------ RMariaDB-1.3.0/RMariaDB/src/DbConnection.h | 16 - RMariaDB-1.3.0/RMariaDB/src/DbResult.cpp | 24 +- RMariaDB-1.3.0/RMariaDB/src/DbResult.h | 8 RMariaDB-1.3.0/RMariaDB/src/Makevars.in | 2 RMariaDB-1.3.0/RMariaDB/src/Makevars.win | 17 - RMariaDB-1.3.0/RMariaDB/src/MariaBinding.cpp | 12 - RMariaDB-1.3.0/RMariaDB/src/MariaBinding.h | 4 RMariaDB-1.3.0/RMariaDB/src/MariaResultImpl.h | 6 RMariaDB-1.3.0/RMariaDB/src/MariaResultPrep.cpp | 23 +- RMariaDB-1.3.0/RMariaDB/src/MariaResultPrep.h | 6 RMariaDB-1.3.0/RMariaDB/src/MariaResultSimple.cpp | 15 - RMariaDB-1.3.0/RMariaDB/src/MariaResultSimple.h | 6 RMariaDB-1.3.0/RMariaDB/src/MariaRow.cpp | 9 RMariaDB-1.3.0/RMariaDB/src/MariaTypes.cpp | 25 +- RMariaDB-1.3.0/RMariaDB/src/MariaTypes.h | 4 RMariaDB-1.3.0/RMariaDB/src/MariaUtils.cpp | 32 +-- RMariaDB-1.3.0/RMariaDB/src/MariaUtils.h | 6 RMariaDB-1.3.0/RMariaDB/src/RMariaDB_types.h | 20 + RMariaDB-1.3.0/RMariaDB/src/connection.cpp | 88 +++----- RMariaDB-1.3.0/RMariaDB/src/cpp11.cpp |only RMariaDB-1.3.0/RMariaDB/src/custom.cmake |only RMariaDB-1.3.0/RMariaDB/src/driver.cpp | 18 - RMariaDB-1.3.0/RMariaDB/src/pch.h | 4 RMariaDB-1.3.0/RMariaDB/src/result.cpp | 48 +--- RMariaDB-1.3.0/RMariaDB/tests/testthat.R | 8 RMariaDB-1.3.0/RMariaDB/tests/testthat/helper-DBItest.R | 8 RMariaDB-1.3.0/RMariaDB/tests/testthat/test-DBItest.R | 1 RMariaDB-1.3.0/RMariaDB/tests/testthat/test-astyle.R | 2 RMariaDB-1.3.0/RMariaDB/tests/testthat/test-dbConnect.R |only RMariaDB-1.3.0/RMariaDB/tests/testthat/test-dbWriteTable.R | 10 RMariaDB-1.3.0/RMariaDB/tests/testthat/test-queries.R | 32 ++- RMariaDB-1.3.0/RMariaDB/tools/winlibs.R | 23 +- 50 files changed, 545 insertions(+), 379 deletions(-)