Title: Classification Trees for Ordinal Responses
Description: Recursive partitioning methods to build
classification trees for ordinal responses within the CART
framework. Trees are grown using the Generalized Gini
impurity function, where the misclassification costs are given
by the absolute or squared differences in scores assigned to
the categories of the response. Pruning is based on the total
misclassification rate or on the total misclassification cost.
Author: Giuliano Galimberti, Gabriele Soffritti, Matteo Di Maso
Maintainer: Giuliano Galimberti <giuliano.galimberti@unibo.it>
Diff between rpartScore versions 1.0-1 dated 2012-12-08 and 1.0-2 dated 2022-05-25
DESCRIPTION | 18 +++++++-------- MD5 | 21 +++++++++-------- NAMESPACE | 2 - build |only inst/CITATION | 17 ++++++++------ man/evalMedian.Rd | 9 +++---- man/evalMode.Rd | 8 +++--- man/initScore.Rd | 10 ++++---- man/rpartScore-package.Rd | 55 ++++++++++++++++++---------------------------- man/rpartScore.Rd | 51 ++++++++++++++++-------------------------- man/splitAbs.Rd | 8 +++--- man/splitQuad.Rd | 8 +++--- 12 files changed, 94 insertions(+), 113 deletions(-)
Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (2020). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai, Scott Bartell, Robin Bliss, and Veronica Vieira
Maintainer: Scott Bartell <sbartell@uci.edu>
Diff between MapGAM versions 1.2-5 dated 2019-07-27 and 1.2-6 dated 2022-05-25
ChangeLog | 246 +++++++++++++----------- DESCRIPTION | 10 - MD5 | 26 +- R/MapGAM.version.R | 53 ++--- R/colormap.R | 12 - R/modgam.R | 495 +++++++++++++++++++++++++------------------------- R/predgrid.R | 4 R/sampcont.R | 116 ++++++----- R/summary.gamcox.R | 90 ++++----- R/summary.modgam.R | 11 - R/trimdata.R | 6 man/MapGAM-package.Rd | 16 - man/modgam.Rd | 10 - man/sampcont.Rd | 13 + 14 files changed, 579 insertions(+), 529 deletions(-)
Title: Decision Curve Analysis for Model Evaluation
Description: Diagnostic and prognostic models are typically evaluated with
measures of accuracy that do not address clinical consequences.
Decision-analytic techniques allow assessment of clinical outcomes,
but often require collection of additional information may be
cumbersome to apply to models that yield a continuous result. Decision
curve analysis is a method for evaluating and comparing prediction
models that incorporates clinical consequences, requires only the data
set on which the models are tested, and can be applied to models that
have either continuous or dichotomous results. See the following references
for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>,
Vickers (2008) <doi:10.1186/1472-6947-8-53>,
and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.
Author: Daniel D. Sjoberg [aut, cre, cph],
Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between dcurves versions 0.2.0 dated 2021-07-20 and 0.3.0 dated 2022-05-25
DESCRIPTION | 23 MD5 | 47 - NAMESPACE | 1 NEWS.md | 44 + R/dca.r | 256 +-------- R/plot.R | 2 R/print.R | 1 R/standardize_net_benefit.R | 5 R/test_consequences.R |only README.md | 5 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/dca.R | 2 inst/doc/dca.Rmd | 6 inst/doc/dca.html | 839 +++++++++++++++++++++++++------- man/dca.Rd | 2 man/dcurves-package.Rd | 20 man/df_binary.Rd | 52 - man/df_case_control.Rd | 50 - man/df_surv.Rd | 54 +- man/figures/two-by-two-table.png |only man/print.dca.Rd | 1 man/test_consequences.Rd |only tests/testthat/test-dca.R | 15 tests/testthat/test-test_consequences.R |only vignettes/dca.Rmd | 6 27 files changed, 915 insertions(+), 517 deletions(-)
Title: Simulate IRT-Based Computerized Adaptive Tests
Description: Functions designed to simulate data that conform to basic
unidimensional IRT models (for now 3-parameter binary response models
and graded response models) along with Post-Hoc CAT simulations of
those models given various item selection methods, ability estimation
methods, and termination criteria. See
Wainer (2000) <doi:10.4324/9781410605931>,
van der Linden & Pashley (2010) <doi:10.1007/978-0-387-85461-8_1>,
and Eggen (1999) <doi:10.1177/01466219922031365> for more details.
Author: Steven Nydick [cre, aut]
Maintainer: Steven Nydick <swnydick@gmail.com>
Diff between catIrt versions 0.5-0 dated 2014-10-05 and 0.5.1 dated 2022-05-25
catIrt-0.5-0/catIrt/inst/NEWS.Rd |only catIrt-0.5.1/catIrt/DESCRIPTION | 29 ++++++++---- catIrt-0.5.1/catIrt/MD5 | 47 ++++++++++++++------ catIrt-0.5.1/catIrt/NAMESPACE | 15 +++++- catIrt-0.5.1/catIrt/NEWS.md |only catIrt-0.5.1/catIrt/R/bmeEst.R | 57 +++++++++++------------- catIrt-0.5.1/catIrt/R/eapEst.R | 69 +++++++++++++++--------------- catIrt-0.5.1/catIrt/R/mleEst.R | 47 +++++++++----------- catIrt-0.5.1/catIrt/R/wleEst.R | 56 +++++++++++------------- catIrt-0.5.1/catIrt/README.md |only catIrt-0.5.1/catIrt/inst/ARRT_Updates |only catIrt-0.5.1/catIrt/inst/TODO.rtf |only catIrt-0.5.1/catIrt/man/FI.Rd | 4 - catIrt-0.5.1/catIrt/man/KL.Rd | 2 catIrt-0.5.1/catIrt/man/catIrt-package.Rd | 4 - catIrt-0.5.1/catIrt/man/catIrt.Rd | 4 - catIrt-0.5.1/catIrt/man/itChoose.Rd | 2 catIrt-0.5.1/catIrt/man/mleEst.Rd | 7 +-- catIrt-0.5.1/catIrt/man/simIrt.Rd | 2 catIrt-0.5.1/catIrt/src/catIrt_init.c |only 20 files changed, 189 insertions(+), 156 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are
otherwise performed manually. This includes setting up unit testing,
test coverage, continuous integration, Git, 'GitHub', licenses,
'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Malcolm Barrett [aut] ,
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between usethis versions 2.1.5 dated 2021-12-09 and 2.1.6 dated 2022-05-25
usethis-2.1.5/usethis/tests/testthat/teardown.R |only usethis-2.1.6/usethis/DESCRIPTION | 14 usethis-2.1.6/usethis/MD5 | 153 +++++----- usethis-2.1.6/usethis/NAMESPACE | 1 usethis-2.1.6/usethis/NEWS.md | 28 + usethis-2.1.6/usethis/R/badge.R | 28 + usethis-2.1.6/usethis/R/code-of-conduct.R | 34 +- usethis-2.1.6/usethis/R/course.R | 5 usethis-2.1.6/usethis/R/create.R | 17 - usethis-2.1.6/usethis/R/data-table.R | 18 - usethis-2.1.6/usethis/R/data.R | 6 usethis-2.1.6/usethis/R/description.R | 2 usethis-2.1.6/usethis/R/git-default-branch.R | 2 usethis-2.1.6/usethis/R/github-actions.R | 145 ++++++--- usethis-2.1.6/usethis/R/github-labels.R | 9 usethis-2.1.6/usethis/R/github-pages.R | 17 - usethis-2.1.6/usethis/R/issue.R | 6 usethis-2.1.6/usethis/R/package.R | 25 + usethis-2.1.6/usethis/R/pkgdown.R | 11 usethis-2.1.6/usethis/R/pr.R | 6 usethis-2.1.6/usethis/R/r.R | 35 ++ usethis-2.1.6/usethis/R/readme.R | 11 usethis-2.1.6/usethis/R/release.R | 104 +++++- usethis-2.1.6/usethis/R/roxygen.R | 62 ++-- usethis-2.1.6/usethis/R/tidy-upkeep.R | 40 ++ usethis-2.1.6/usethis/R/tidyverse.R | 8 usethis-2.1.6/usethis/R/use_github_file.R | 6 usethis-2.1.6/usethis/R/usethis-package.R | 6 usethis-2.1.6/usethis/R/utils-github.R | 51 ++- usethis-2.1.6/usethis/R/version.R | 34 +- usethis-2.1.6/usethis/R/vignette.R | 1 usethis-2.1.6/usethis/R/vscode.R |only usethis-2.1.6/usethis/README.md | 56 +-- usethis-2.1.6/usethis/inst/templates/CODE_OF_CONDUCT.md | 41 +- usethis-2.1.6/usethis/inst/templates/testthat.R | 8 usethis-2.1.6/usethis/inst/templates/vscode-c_cpp_properties.json |only usethis-2.1.6/usethis/inst/templates/vscode-debug.R |only usethis-2.1.6/usethis/inst/templates/vscode-launch.json |only usethis-2.1.6/usethis/man/badges.Rd | 9 usethis-2.1.6/usethis/man/create_from_github.Rd | 20 - usethis-2.1.6/usethis/man/git_protocol.Rd | 6 usethis-2.1.6/usethis/man/github_actions.Rd | 25 + usethis-2.1.6/usethis/man/tidyverse.Rd | 8 usethis-2.1.6/usethis/man/use_code_of_conduct.Rd | 4 usethis-2.1.6/usethis/man/use_course_details.Rd | 42 +- usethis-2.1.6/usethis/man/use_data.Rd | 9 usethis-2.1.6/usethis/man/use_data_table.Rd | 14 usethis-2.1.6/usethis/man/use_description.Rd | 6 usethis-2.1.6/usethis/man/use_github_file.Rd | 6 usethis-2.1.6/usethis/man/use_github_pages.Rd | 8 usethis-2.1.6/usethis/man/use_pkgdown.Rd | 2 usethis-2.1.6/usethis/man/use_r.Rd | 36 ++ usethis-2.1.6/usethis/man/use_readme_rmd.Rd | 11 usethis-2.1.6/usethis/man/use_roxygen_md.Rd | 12 usethis-2.1.6/usethis/man/use_version.Rd | 23 - usethis-2.1.6/usethis/man/usethis-package.Rd | 2 usethis-2.1.6/usethis/man/zip-utils.Rd | 6 usethis-2.1.6/usethis/tests/testthat/_snaps/badge.md | 12 usethis-2.1.6/usethis/tests/testthat/_snaps/course.md | 13 usethis-2.1.6/usethis/tests/testthat/_snaps/git-default-branch.md | 2 usethis-2.1.6/usethis/tests/testthat/_snaps/github-actions.md | 22 - usethis-2.1.6/usethis/tests/testthat/_snaps/lifecycle.md | 2 usethis-2.1.6/usethis/tests/testthat/_snaps/package.md | 25 + usethis-2.1.6/usethis/tests/testthat/_snaps/release.md | 21 + usethis-2.1.6/usethis/tests/testthat/_snaps/tibble.md | 2 usethis-2.1.6/usethis/tests/testthat/_snaps/tidy-upkeep.md | 24 + usethis-2.1.6/usethis/tests/testthat/_snaps/tidyverse.md | 2 usethis-2.1.6/usethis/tests/testthat/_snaps/ui.md | 15 usethis-2.1.6/usethis/tests/testthat/_snaps/use_import_from.md | 15 usethis-2.1.6/usethis/tests/testthat/_snaps/utils-github.md | 16 - usethis-2.1.6/usethis/tests/testthat/_snaps/vignette.md | 10 usethis-2.1.6/usethis/tests/testthat/setup.R | 4 usethis-2.1.6/usethis/tests/testthat/test-badge.R | 9 usethis-2.1.6/usethis/tests/testthat/test-data.R | 12 usethis-2.1.6/usethis/tests/testthat/test-github-actions.R | 20 + usethis-2.1.6/usethis/tests/testthat/test-package.R | 8 usethis-2.1.6/usethis/tests/testthat/test-release.R | 8 usethis-2.1.6/usethis/tests/testthat/test-roxygen.R | 18 + usethis-2.1.6/usethis/tests/testthat/test-tidy-upkeep.R | 4 usethis-2.1.6/usethis/tests/testthat/test-utils-github.R | 4 80 files changed, 1053 insertions(+), 454 deletions(-)
Title: Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
Description: The following R functions are used for inference of trait
associations with haplotypes and other covariates in
generalized linear models. The functions are developed
primarily for data collected in cohort or cross-sectional
studies. They can accommodate uncertain haplotype phase and
handle missing genotypes at some SNPs.
Author: K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J.
Graham <jgraham@stat.sfu.ca>, with code for case-control data
contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>
Maintainer: K. Burkett <kburkett@uottawa.ca>
Diff between hapassoc versions 1.2-8 dated 2015-05-10 and 1.2-9 dated 2022-05-25
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NAMESPACE | 5 +++++ build/vignette.rds |binary inst/CITATION | 4 ++-- inst/ChangeLog | 4 ++++ inst/doc/hapassoc.pdf |binary src/hapassoc_init.c |only 8 files changed, 22 insertions(+), 12 deletions(-)
Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to
version, share, deploy, and monitor a trained model. Functions handle
both recording and checking the model's input data prototype, and
predicting from a remote API endpoint. The 'vetiver' package is
extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] ,
RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between vetiver versions 0.1.4 dated 2022-04-28 and 0.1.5 dated 2022-05-25
vetiver-0.1.4/vetiver/inst/rmarkdown/templates/vetiver_dashboard |only vetiver-0.1.5/vetiver/DESCRIPTION | 31 ++++--- vetiver-0.1.5/vetiver/MD5 | 40 +++++----- vetiver-0.1.5/vetiver/NAMESPACE | 22 +++-- vetiver-0.1.5/vetiver/NEWS.md | 6 + vetiver-0.1.5/vetiver/R/endpoint.R | 18 +++- vetiver-0.1.5/vetiver/R/monitor.R |only vetiver-0.1.5/vetiver/R/vetiver-package.R | 15 +-- vetiver-0.1.5/vetiver/R/write-docker.R | 1 vetiver-0.1.5/vetiver/README.md | 14 ++- vetiver-0.1.5/vetiver/inst/doc/model-card.html | 2 vetiver-0.1.5/vetiver/inst/doc/vetiver.R | 3 vetiver-0.1.5/vetiver/inst/doc/vetiver.Rmd | 3 vetiver-0.1.5/vetiver/inst/doc/vetiver.html | 10 +- vetiver-0.1.5/vetiver/man/vetiver-package.Rd | 7 + vetiver-0.1.5/vetiver/man/vetiver_compute_metrics.Rd |only vetiver-0.1.5/vetiver/man/vetiver_endpoint.Rd | 4 - vetiver-0.1.5/vetiver/tests/testthat/_snaps/caret.md | 2 vetiver-0.1.5/vetiver/tests/testthat/_snaps/monitor |only vetiver-0.1.5/vetiver/tests/testthat/_snaps/monitor.md |only vetiver-0.1.5/vetiver/tests/testthat/test-caret.R | 6 - vetiver-0.1.5/vetiver/tests/testthat/test-monitor.R |only vetiver-0.1.5/vetiver/tests/testthat/test-predict.R | 1 vetiver-0.1.5/vetiver/vignettes/vetiver.Rmd | 3 24 files changed, 110 insertions(+), 78 deletions(-)
Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in
'Tidy Eval' code that calculates the predictions. It works with
several databases back-ends because it leverages 'dplyr' and 'dbplyr'
for the final 'SQL' translation of the algorithm. It currently
supports lm(), glm(), randomForest(), ranger(), earth(),
xgb.Booster.complete(), cubist(), and ctree() models.
Author: Max Kuhn [aut, cre],
Edgar Ruiz [aut]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between tidypredict versions 0.4.8 dated 2020-10-28 and 0.4.9 dated 2022-05-25
DESCRIPTION | 47 +-- LICENSE |only MD5 | 130 ++++---- NEWS.md | 10 R/model-cubist.R | 26 - R/model-lm.R | 6 R/model-rf.R | 55 ++- R/model-xgboost.R | 2 R/predict-column.R | 2 R/to_sql.R | 4 README.md | 44 +- build/vignette.rds |binary inst/doc/cubist.Rmd | 2 inst/doc/cubist.html | 277 +++++++----------- inst/doc/glm.Rmd | 2 inst/doc/glm.html | 252 +++++++--------- inst/doc/lm.Rmd | 2 inst/doc/lm.html | 351 ++++++++++------------- inst/doc/mars.Rmd | 2 inst/doc/mars.html | 347 +++++++++-------------- inst/doc/non-r.Rmd | 2 inst/doc/non-r.html | 300 ++++++++----------- inst/doc/ranger.Rmd | 2 inst/doc/ranger.html | 231 +++++---------- inst/doc/regression.Rmd | 2 inst/doc/regression.html | 42 -- inst/doc/rf.R | 7 inst/doc/rf.Rmd | 10 inst/doc/rf.html | 233 +++++---------- inst/doc/save.Rmd | 2 inst/doc/save.html | 265 +++++++---------- inst/doc/sql.R | 7 inst/doc/sql.Rmd | 13 inst/doc/sql.html | 369 +++++++++++------------- inst/doc/tree.Rmd | 2 inst/doc/tree.html | 44 +- inst/doc/xgboost.Rmd | 2 inst/doc/xgboost.html | 587 +++++++++++++++++---------------------- man/tidypredict-package.Rd | 9 tests/testthat/_snaps |only tests/testthat/test-acceptable.R | 7 tests/testthat/test-cubist.R | 11 tests/testthat/test-earth.R | 9 tests/testthat/test-list.R | 8 tests/testthat/test-party.R | 5 tests/testthat/test-ranger.R | 9 tests/testthat/test-rf.R | 14 tests/testthat/test-sql.R | 6 tests/testthat/test-tester.R | 4 tests/testthat/test_glm.R | 9 tests/testthat/test_lm.R | 9 tests/testthat/test_xgboost.R | 17 - vignettes/cubist.Rmd | 2 vignettes/glm.Rmd | 2 vignettes/lm.Rmd | 2 vignettes/mars.Rmd | 2 vignettes/non-r.Rmd | 2 vignettes/ranger.Rmd | 2 vignettes/regression.Rmd | 2 vignettes/rf.Rmd | 10 vignettes/save.Rmd | 2 vignettes/sql.Rmd | 13 vignettes/tree.Rmd | 2 vignettes/xgboost.Rmd | 2 64 files changed, 1689 insertions(+), 2152 deletions(-)
Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of stepped wedge cluster randomized trials (SW CRT) based on a repeated cross-sectional sampling scheme (Hussey MA and Hughes JP (2007) Contemporary Clinical Trials 28:182-191. <doi:10.1016/j.cct.2006.05.007>).
Author: Jim Hughes, Navneet R. Hakhu, Emily Voldal, and Fan Xia
Maintainer: Jim Hughes <jphughes@uw.edu>
Diff between swCRTdesign versions 3.1 dated 2019-10-25 and 3.2 dated 2022-05-25
DESCRIPTION | 12 ++++++------ MD5 | 10 ++++++---- NAMESPACE | 2 +- R/swGlmPwr.R |only man/swCRTdesign-package.Rd | 10 ++++++---- man/swGlmPwr.Rd |only man/swPwr.Rd | 6 +++--- 7 files changed, 22 insertions(+), 18 deletions(-)
Title: A Collection of Physical and Chemical Adsorption Isotherm Models
Description: The PUPAIM R package can generally fit any adsorption experimental data to any of the 55 available adsorption isotherm models - 32 nonlinear models and 23 linear models. This package provides parameter estimation, model accuracy analysis, model error analysis, and adsorption plot created using the package 'ggplot2'. This package will help the users for a much easier way of adsorption model data fitting.
Author: Keith T. Ostan [aut] ,
Paul Angelo C. Manlapaz [aut] ,
Jemimah Christine L. Mesias [aut]
,
Chester C. Deocaris [aut, ths, cre]
Maintainer: Chester C. Deocaris <ccdeocaris@pup.edu.ph>
Diff between PUPAIM versions 0.3.0 dated 2022-05-12 and 0.3.1 dated 2022-05-25
PUPAIM-0.3.0/PUPAIM/R/PUPAIM.R |only PUPAIM-0.3.0/PUPAIM/R/henryLM.r |only PUPAIM-0.3.0/PUPAIM/R/volmeranalysis.R |only PUPAIM-0.3.0/PUPAIM/man/PUPAIM.Rd |only PUPAIM-0.3.0/PUPAIM/man/henry.LM.Rd |only PUPAIM-0.3.1/PUPAIM/DESCRIPTION | 12 - PUPAIM-0.3.1/PUPAIM/MD5 | 198 ++++++++--------- PUPAIM-0.3.1/PUPAIM/NAMESPACE | 6 PUPAIM-0.3.1/PUPAIM/R/BETLM.r | 2 PUPAIM-0.3.1/PUPAIM/R/BETanalysis.R | 5 PUPAIM-0.3.1/PUPAIM/R/FS3analysis.R | 11 PUPAIM-0.3.1/PUPAIM/R/FS4analysis.R | 7 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir1analysis.R | 13 - PUPAIM-0.3.1/PUPAIM/R/SSLangmuir2analysis.R | 13 - PUPAIM-0.3.1/PUPAIM/R/SSLangmuir3.R | 2 PUPAIM-0.3.1/PUPAIM/R/SSLangmuir3analysis.R | 13 - PUPAIM-0.3.1/PUPAIM/R/SSLangmuir4analysis.R | 13 - PUPAIM-0.3.1/PUPAIM/R/aranovichanalysis.R | 6 PUPAIM-0.3.1/PUPAIM/R/bauduanalysis.R | 8 PUPAIM-0.3.1/PUPAIM/R/dubininradushkevichLM.R | 4 PUPAIM-0.3.1/PUPAIM/R/dubininradushkevichanalysis.R | 9 PUPAIM-0.3.1/PUPAIM/R/elovichLM.r | 6 PUPAIM-0.3.1/PUPAIM/R/elovichanalysis.r | 16 - PUPAIM-0.3.1/PUPAIM/R/floryhugginsLM.R | 8 PUPAIM-0.3.1/PUPAIM/R/floryhugginsanalysis.R | 21 + PUPAIM-0.3.1/PUPAIM/R/fowlerguggenheimLM.R | 12 - PUPAIM-0.3.1/PUPAIM/R/fowlerguggenheimanalysis.R | 15 - PUPAIM-0.3.1/PUPAIM/R/freundlichLM.R | 6 PUPAIM-0.3.1/PUPAIM/R/freundlichanalysis.R | 7 PUPAIM-0.3.1/PUPAIM/R/halseyLM.R | 4 PUPAIM-0.3.1/PUPAIM/R/halseyanalysis.R | 9 PUPAIM-0.3.1/PUPAIM/R/harkinsjuraLM.R | 4 PUPAIM-0.3.1/PUPAIM/R/harkinsjuraanalysis.R | 8 PUPAIM-0.3.1/PUPAIM/R/henryanalysis.r |only PUPAIM-0.3.1/PUPAIM/R/hillLM.R | 2 PUPAIM-0.3.1/PUPAIM/R/hillanalysis.R | 14 - PUPAIM-0.3.1/PUPAIM/R/hilldeboerLM.R | 8 PUPAIM-0.3.1/PUPAIM/R/hilldeboeranalysis.R | 13 - PUPAIM-0.3.1/PUPAIM/R/jossensLM.r | 4 PUPAIM-0.3.1/PUPAIM/R/jossensanalysis.r | 15 - PUPAIM-0.3.1/PUPAIM/R/jovanovicLM.R | 6 PUPAIM-0.3.1/PUPAIM/R/jovanovicanalysis.R | 5 PUPAIM-0.3.1/PUPAIM/R/kahnanalysis.R | 8 PUPAIM-0.3.1/PUPAIM/R/kiselevLM.R | 7 PUPAIM-0.3.1/PUPAIM/R/kiselevanalysis.R | 11 PUPAIM-0.3.1/PUPAIM/R/koblecarrigananalysis.R | 5 PUPAIM-0.3.1/PUPAIM/R/koblecorriganLM.R | 4 PUPAIM-0.3.1/PUPAIM/R/langmuir1LM.R |only PUPAIM-0.3.1/PUPAIM/R/langmuir2LM.R |only PUPAIM-0.3.1/PUPAIM/R/langmuir3LM.R |only PUPAIM-0.3.1/PUPAIM/R/langmuir4LM.R |only PUPAIM-0.3.1/PUPAIM/R/langmuiranalysis.R | 15 - PUPAIM-0.3.1/PUPAIM/R/marckzewskijaroniecanalysis.r | 8 PUPAIM-0.3.1/PUPAIM/R/radkeprausnitzanalysis.R | 9 PUPAIM-0.3.1/PUPAIM/R/radkepraustnitzLM.R | 2 PUPAIM-0.3.1/PUPAIM/R/redlichpetersonLM.R | 2 PUPAIM-0.3.1/PUPAIM/R/redlichpetersonanalysis.R | 5 PUPAIM-0.3.1/PUPAIM/R/sipsLM.R | 2 PUPAIM-0.3.1/PUPAIM/R/sipsanalysis.R | 13 - PUPAIM-0.3.1/PUPAIM/R/temkinLM.R | 12 - PUPAIM-0.3.1/PUPAIM/R/temkinanalysis.r | 5 PUPAIM-0.3.1/PUPAIM/R/tothanalysis.R | 10 PUPAIM-0.3.1/PUPAIM/R/volmeranalysis.r |only PUPAIM-0.3.1/PUPAIM/R/webervanvlietanalysis.r | 7 PUPAIM-0.3.1/PUPAIM/inst/doc/PUPAIM.R | 2 PUPAIM-0.3.1/PUPAIM/inst/doc/PUPAIM.Rmd | 9 PUPAIM-0.3.1/PUPAIM/inst/doc/PUPAIM.html | 89 ++++++- PUPAIM-0.3.1/PUPAIM/man/FS3analysis.Rd | 6 PUPAIM-0.3.1/PUPAIM/man/FS4analysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/SSLangmuir3.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/bauduanalysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/dubininradushkevichanalysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/dubininraduskevich.LM.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/elovich.LM.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/elovichanalysis.Rd | 12 - PUPAIM-0.3.1/PUPAIM/man/floryhuggins.LM.Rd | 10 PUPAIM-0.3.1/PUPAIM/man/floryhugginsanalysis.Rd | 10 PUPAIM-0.3.1/PUPAIM/man/fowlerguggenheim.LM.Rd | 12 - PUPAIM-0.3.1/PUPAIM/man/fowlerguggenheimanalysis.Rd | 10 PUPAIM-0.3.1/PUPAIM/man/freundlich.LM.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/freundlichanalysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/halsey.LM.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/halseyanalysis.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/harkinsjura.LM.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/harkinsjuraanalysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/henryanalysis.Rd |only PUPAIM-0.3.1/PUPAIM/man/hillanalysis.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/hilldeboer.LM.Rd | 10 PUPAIM-0.3.1/PUPAIM/man/hilldeboeranalysis.Rd | 10 PUPAIM-0.3.1/PUPAIM/man/jossens.LM.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/jossensanalysis.Rd | 14 - PUPAIM-0.3.1/PUPAIM/man/jovanovic.LM.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/kahnanalysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/kiselev.LM.Rd | 8 PUPAIM-0.3.1/PUPAIM/man/kiselevanalysis.Rd | 8 PUPAIM-0.3.1/PUPAIM/man/koblecarrigan.LM.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/langmuir1.LM.Rd |only PUPAIM-0.3.1/PUPAIM/man/langmuir2.LM.Rd |only PUPAIM-0.3.1/PUPAIM/man/langmuir3.LM.Rd |only PUPAIM-0.3.1/PUPAIM/man/langmuir4.LM.Rd |only PUPAIM-0.3.1/PUPAIM/man/langmuiranalysis.Rd |only PUPAIM-0.3.1/PUPAIM/man/marckzewskijaroniecanalysis.Rd | 2 PUPAIM-0.3.1/PUPAIM/man/radkeprausnitzanalysis.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/temkin.LM.Rd | 4 PUPAIM-0.3.1/PUPAIM/man/temkinanalysis.Rd | 48 ---- PUPAIM-0.3.1/PUPAIM/man/tothanalysis.Rd |only PUPAIM-0.3.1/PUPAIM/man/volmeranalysis.Rd | 10 PUPAIM-0.3.1/PUPAIM/man/webervanvlietanalysis.Rd | 8 PUPAIM-0.3.1/PUPAIM/vignettes/PUPAIM.Rmd | 9 109 files changed, 537 insertions(+), 432 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between StereoMorph versions 1.6.5 dated 2022-05-12 and 1.6.7 dated 2022-05-25
DESCRIPTION | 8 - MD5 | 16 +-- R/XML4R2listLines.R | 9 + R/digitizeImages.R | 2 R/list2XML4R.R | 81 ++++++++-------- R/readShapes.R | 6 - R/readXMLLines.R | 9 + inst/extdata/apps/digitizeImages/session_parameters.txt | 2 man/StereoMorph-package.Rd | 4 9 files changed, 81 insertions(+), 56 deletions(-)
Title: Bayesian Variable Selection for a Poisson-Logistic Model
Description: Bayesian variable selection for regression models of under-reported
count data as well as for (overdispersed) Poisson, negative binomal and
binomial logit regression models using spike and slab priors.
Author: Michaela Dvorzak [aut, cre],
Helga Wagner [aut]
Maintainer: Michaela Dvorzak <m.dvorzak@gmx.at>
Diff between pogit versions 1.2.0 dated 2019-01-17 and 1.3.0 dated 2022-05-25
DESCRIPTION | 11 ++++++----- MD5 | 45 +++++++++++++++++++++++---------------------- R/logitBvs.R | 13 ++++++++----- R/negbinBvs.R | 11 +++++++---- R/pogitBvs.R | 16 ++++++++++------ R/poissonBvs.R | 15 +++++++++------ R/simul1.R | 2 +- R/simul2.R | 2 +- build |only inst/CITATION | 2 +- inst/NEWS.Rd | 6 ++++++ man/cervical.Rd | 6 ++++-- man/cervical_validation.Rd | 6 ++++-- man/logitBvs.Rd | 32 ++++++++++++++++++++++---------- man/negbinBvs.Rd | 27 +++++++++++++++++++-------- man/plot.pogit.Rd | 12 ++++++++++-- man/pogit-package.Rd | 4 ++-- man/pogitBvs.Rd | 38 ++++++++++++++++++++++++++------------ man/poissonBvs.Rd | 29 ++++++++++++++++++++--------- man/simul1.Rd | 8 +++++--- man/simul2.Rd | 8 +++++--- man/simul_binomial.Rd | 6 ++++-- man/simul_pois1.Rd | 6 ++++-- man/simul_pois2.Rd | 6 ++++-- 24 files changed, 201 insertions(+), 110 deletions(-)
Title: Detecting Spatial Clustering Based on Connection Cost Between
Grids
Description: Based on landscape connectivity, spatial boundaries were
identified using community detection algorithm at grid level. Methods
using raster as input and the value of each cell of the raster is the
"smoothness" to indicate how easy the cell connecting with neighbor cells.
Details about the 'habCluster' package methods can be found in Zhang et al.
<bioRxiv:2022.05.06.490926>.
Author: Qiang Dai
Maintainer: Qiang Dai <daiqiang@cib.ac.cn>
Diff between habCluster versions 1.0.3 dated 2022-05-18 and 1.0.5 dated 2022-05-25
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NEWS.md | 8 ++++++++ R/cluster.R | 6 +++--- R/raster2Graph.R | 13 ++++++++++++- inst/WORDLIST |only inst/doc/introduction-to-habCluster.html | 6 +++--- man/cluster.Rd | 4 +++- man/figures/README-Greedy_plot-1.png |binary man/figures/README-cluster-1.png |binary man/figures/README-discard-1.png |binary man/raster2Graph.Rd | 4 +++- src/getEdge.cpp | 2 +- tests/spelling.R |only 14 files changed, 50 insertions(+), 25 deletions(-)
Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [ctb, ctr],
Tim Schreier [ctb, ctr],
Luis Winckelman [ctb, ctr],
Quirin Stier [ctb, ctr],
Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between GeneralizedUmatrix versions 1.2.2 dated 2021-01-12 and 1.2.4 dated 2022-05-25
GeneralizedUmatrix-1.2.2/GeneralizedUmatrix/src/packagename_init.c |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/DESCRIPTION | 20 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/MD5 | 45 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/NAMESPACE | 29 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/DefaultColorSequence.R |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/GeneralizedUmatrix.R | 695 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/LowLand.R |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/RcppExports.R | 4 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/ReduceToLowLand.R |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/TopviewTopographicMap.R | 264 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/Uheights4Data.R |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/UniqueBestMatchingUnits.R |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/plotTopographicMap.R | 2 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/R/sESOM4BMUs.R | 202 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/build/partial.rdb |binary GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/build/vignette.rds |binary GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/inst/doc/GeneralizedUmatrix.html |12817 ++++++---- GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/GeneralizedUmatrix.Rd | 19 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/LowLand.Rd |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/ReduceToLowLand.Rd |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/TopviewTopographicMap.Rd | 26 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/Uheights4Data.Rd |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/UniqueBestMatchingUnits.Rd |only GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/man/sESOM4BMUs.Rd | 11 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/Makevars | 22 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/Makevars.win | 27 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/RcppExports.cpp | 37 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/trainstepC.cpp | 15 GeneralizedUmatrix-1.2.4/GeneralizedUmatrix/src/trainstepC2.cpp |only 29 files changed, 9070 insertions(+), 5165 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: Fitting Bayesian Poisson Regression
Description: Posterior sampling and inference for Bayesian Poisson regression models. The model specification makes use of Gaussian (or conditionally Gaussian) prior distributions on the regression coefficients. Details on the algorithm are found in D'Angelo and Canale (2021) <arXiv:2109.09520>.
Author: Laura D'Angelo
Maintainer: Laura D'Angelo <laura.dangelo@live.com>
Diff between bpr versions 1.0.4 dated 2021-09-22 and 1.0.5 dated 2022-05-25
DESCRIPTION | 10 +++--- MD5 | 8 ++--- build/partial.rdb |binary src/is_polya_adaptive.cpp | 23 +++++--------- src/is_polya_horseshoe_adaptive.cpp | 56 +++++++++++++----------------------- 5 files changed, 39 insertions(+), 58 deletions(-)
Title: Prediction Intervals with Random Forests and Boosted Forests
Description: Implements various prediction interval methods with random forests and boosted forests.
The package has two main functions: pibf() produces prediction intervals with boosted forests
(PIBF) as described in Alakus et al. (2021) <arXiv:2106.08217> and rfpi() builds 15 distinct
variations of prediction intervals with random forests (RFPI) proposed by Roy and Larocque (2020)
<doi:10.1177/0962280219829885>.
Author: Cansu Alakus [aut, cre],
Denis Larocque [aut],
Aurelie Labbe [aut],
Hemant Ishwaran [ctb] ,
Udaya B. Kogalur [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>
Diff between RFpredInterval versions 1.0.5 dated 2022-01-20 and 1.0.6 dated 2022-05-25
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 3 +++ R/RFpredInterval-package.R | 30 +++++++++++++++--------------- R/formpi.functions.R | 2 +- R/piall.R | 29 +++++++++++++++++++++++++---- R/pibf.R | 29 +++++++++++++++++++++++++---- R/rfpi.R | 29 +++++++++++++++++++++++++---- R/utilities.R | 20 ++++++++++---------- README.md | 2 -- configure | 18 +++++++++--------- configure.ac | 2 +- man/RFpredInterval-package.Rd | 29 +++++++++++++++-------------- 13 files changed, 145 insertions(+), 80 deletions(-)
More information about RFpredInterval at CRAN
Permanent link
Title: Graphical Extension with Accuracy in Parameter Estimation
(GAIPE)
Description: Implements graphical extension with accuracy in parameter estimation (AIPE) on RMSEA for sample size planning in structural equation modeling based on Lin, T.-Z. & Weng, L.-J. (2014) <doi: 10.1080/10705511.2014.915380>. And, it can also implement AIPE on RMSEA and power analysis on RMSEA.
Author: Tzu-Yao Lin
Maintainer: Yao Lin <zaiyaolin@gmail.com>
Diff between GAIPE versions 1.0 dated 2013-04-17 and 1.1 dated 2022-05-25
DESCRIPTION | 20 +--- MD5 | 23 ++-- NAMESPACE | 6 + NEWS |only R/AIPE.RMSEA.R | 38 +++++-- R/CI.RMSEA.R | 201 ++++++++++++++++++++++++++++++++-------- R/GAIPE.RMSEA.R | 253 ++++++++++++++++++++++++++++++++------------------- R/PA.RMSEA.R | 91 ++++++++++++------ man/AIPE.RMSEA.Rd | 4 man/CI.RMSEA.Rd | 2 man/GAIPE-package.Rd | 50 +++++----- man/GAIPE.RMSEA.Rd | 128 ++++++++++++------------- man/PA.RMSEA.Rd | 104 ++++++++++++-------- 13 files changed, 585 insertions(+), 335 deletions(-)
Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and
Debian-derived Linux systems with a powerful system to resolve package
dependencies. This package offers access directly from R. This can
only work on a system with a suitable 'libapt-pkg-dev' installation
so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAPT versions 0.0.8 dated 2021-12-04 and 0.0.9 dated 2022-05-25
ChangeLog | 26 + DESCRIPTION | 8 MD5 | 28 - build/vignette.rds |binary cleanup | 2 inst/NEWS.Rd | 7 inst/doc/binnmuAfterR340.html | 863 +++++++++++++++++++++--------------------- inst/doc/binnmuAfterR340.md | 2 inst/scripts/configure.bash | 4 src/Makevars.in | 2 src/buildDepends.cpp | 23 - src/getPackages.cpp | 6 src/hasPackage.cpp | 10 src/reverseDepends.cpp | 7 vignettes/binnmuAfterR340.md | 2 15 files changed, 509 insertions(+), 481 deletions(-)
Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm
for simple linear ordered monotone regression, including two spin-off functions
for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre],
Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>
Diff between monotone versions 0.1.1 dated 2022-05-25 and 0.1.2 dated 2022-05-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/legacy.R | 2 +- R/monotone.R | 2 +- man/legacy.Rd | 2 +- man/monotone.Rd | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
Author: Quentin Grimonprez [aut, cre],
Samuel Blanck [ctb],
Alain Celisse [ths],
Guillemette Marot [ths],
Yi Yang [ctb],
Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between MLGL versions 0.6.5 dated 2020-11-28 and 0.6.7 dated 2022-05-25
DESCRIPTION | 10 +++---- MD5 | 64 +++++++++++++++++++++++------------------------ NAMESPACE | 6 ++-- NEWS | 9 ++++++ R/HMT.R | 12 +++++--- R/MLGL-package.R | 12 +++++--- R/MLGL.R | 48 ++++++++++++++++++++++------------- R/cv.MLGL.R | 12 +++++--- R/fullProcess.R | 30 ++++++++++++++-------- R/hierarchicalFDR.R | 23 ++++++++++------ R/hierarchicalFWER.R | 15 +++++------ R/overlap.R | 9 ++++-- R/plot.R | 2 - R/predict.R | 25 ++++++++++++++++-- R/print.R | 13 ++++----- R/simuBlockGaussian.R | 3 +- R/stability.R | 15 +++++++---- R/uniqueGroupHclust.R | 2 - R/utilities.R | 6 ++-- man/HMT.Rd | 3 +- man/MLGL-package.Rd | 12 +++++--- man/MLGL.Rd | 32 +++++++++++++++-------- man/cv.MLGL.Rd | 6 ++-- man/fullProcess.Rd | 23 +++++++++++----- man/hierarchicalFDR.Rd | 11 +++++--- man/hierarchicalFWER.Rd | 8 +++-- man/listToMatrix.Rd | 6 ++-- man/overlapgglasso.Rd | 9 ++++-- man/predict.MLGL.Rd | 13 ++++++++- man/predict.cv.MLGL.Rd | 3 +- man/selFDR.Rd | 6 ++-- man/simuBlockGaussian.Rd | 3 +- man/stability.MLGL.Rd | 9 ++++-- 33 files changed, 296 insertions(+), 164 deletions(-)
Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks,
predictions, resample results or benchmark results via the autoplot()
generic of 'ggplot2'. The returned 'ggplot' objects are intended to
provide sensible defaults, yet can easily be customized to create
camera-ready figures. Visualizations include barplots, boxplots,
histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.5.8 dated 2022-04-04 and 0.5.9 dated 2022-05-25
mlr3viz-0.5.8/mlr3viz/R/PredictionSurv.R |only mlr3viz-0.5.8/mlr3viz/R/TaskDens.R |only mlr3viz-0.5.8/mlr3viz/R/TaskSurv.R |only mlr3viz-0.5.8/mlr3viz/man/autoplot.PredictionSurv.Rd |only mlr3viz-0.5.8/mlr3viz/man/autoplot.TaskDens.Rd |only mlr3viz-0.5.8/mlr3viz/man/autoplot.TaskSurv.Rd |only mlr3viz-0.5.8/mlr3viz/tests/testthat/_snaps/PredictionSurv |only mlr3viz-0.5.8/mlr3viz/tests/testthat/_snaps/TaskDens |only mlr3viz-0.5.8/mlr3viz/tests/testthat/test_PredictionSurv.R |only mlr3viz-0.5.8/mlr3viz/tests/testthat/test_TaskDens.R |only mlr3viz-0.5.8/mlr3viz/tests/testthat/test_TaskSurv.R |only mlr3viz-0.5.9/mlr3viz/DESCRIPTION | 25 ++++------ mlr3viz-0.5.9/mlr3viz/MD5 | 32 +++---------- mlr3viz-0.5.9/mlr3viz/NAMESPACE | 5 -- mlr3viz-0.5.9/mlr3viz/NEWS.md | 8 +++ mlr3viz-0.5.9/mlr3viz/R/bibentries.R | 11 ---- mlr3viz-0.5.9/mlr3viz/README.md | 10 ++-- mlr3viz-0.5.9/mlr3viz/build/partial.rdb |binary mlr3viz-0.5.9/mlr3viz/man/figures/README-demo-1.png |binary mlr3viz-0.5.9/mlr3viz/man/figures/README-demo-2.png |binary 20 files changed, 33 insertions(+), 58 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3'
with interfaces to essential machine learning packages on
CRAN. This includes, but is not limited to: (penalized) linear and
logistic regression, linear and quadratic discriminant analysis,
k-nearest neighbors, naive Bayes, support vector machines, and
gradient boosting.
Author: Michel Lang [cre, aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3learners versions 0.5.2 dated 2022-01-22 and 0.5.3 dated 2022-05-25
mlr3learners-0.5.2/mlr3learners/R/LearnerSurvCVGlmnet.R |only mlr3learners-0.5.2/mlr3learners/R/LearnerSurvGlmnet.R |only mlr3learners-0.5.2/mlr3learners/R/LearnerSurvRanger.R |only mlr3learners-0.5.2/mlr3learners/R/LearnerSurvXgboost.R |only mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.cv_glmnet.R |only mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.glmnet.R |only mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.ranger.R |only mlr3learners-0.5.2/mlr3learners/inst/paramtest/test_paramtest_surv.xgboost.R |only mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.cv_glmnet.Rd |only mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.glmnet.Rd |only mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.ranger.Rd |only mlr3learners-0.5.2/mlr3learners/man/mlr_learners_surv.xgboost.Rd |only mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_cv_glmnet.R |only mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_glmnet.R |only mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_ranger.R |only mlr3learners-0.5.2/mlr3learners/tests/testthat/test_surv_xgboost.R |only mlr3learners-0.5.3/mlr3learners/DESCRIPTION | 16 - mlr3learners-0.5.3/mlr3learners/MD5 | 96 ++---- mlr3learners-0.5.3/mlr3learners/NAMESPACE | 4 mlr3learners-0.5.3/mlr3learners/NEWS.md | 6 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifGlmnet.R | 4 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifKKNN.R | 22 + mlr3learners-0.5.3/mlr3learners/R/LearnerClassifMultinom.R | 5 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifNnet.R | 7 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifRanger.R | 6 mlr3learners-0.5.3/mlr3learners/R/LearnerClassifXgboost.R | 2 mlr3learners-0.5.3/mlr3learners/R/LearnerRegrKKNN.R | 22 + mlr3learners-0.5.3/mlr3learners/R/LearnerRegrRanger.R | 4 mlr3learners-0.5.3/mlr3learners/R/LearnerRegrXgboost.R | 2 mlr3learners-0.5.3/mlr3learners/R/zzz.R | 6 mlr3learners-0.5.3/mlr3learners/README.md | 11 mlr3learners-0.5.3/mlr3learners/build/partial.rdb |binary mlr3learners-0.5.3/mlr3learners/inst/paramtest/test_paramtest_classif.kknn.R | 3 mlr3learners-0.5.3/mlr3learners/inst/paramtest/test_paramtest_regr.kknn.R | 3 mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.cv_glmnet.Rd | 116 ++------ mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.glmnet.Rd | 114 ++------ mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.kknn.Rd | 80 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.lda.Rd | 71 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.log_reg.Rd | 86 ++---- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.multinom.Rd | 92 ++---- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.naive_bayes.Rd | 67 ++-- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.nnet.Rd | 80 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.qda.Rd | 69 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.ranger.Rd | 109 ++----- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.svm.Rd | 80 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_classif.xgboost.Rd | 138 ++-------- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.cv_glmnet.Rd | 117 ++------ mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.glmnet.Rd | 119 ++------ mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.kknn.Rd | 80 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.km.Rd | 92 ++---- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.lm.Rd | 85 ++---- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.ranger.Rd | 109 ++----- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.svm.Rd | 78 ++--- mlr3learners-0.5.3/mlr3learners/man/mlr_learners_regr.xgboost.Rd | 138 ++-------- mlr3learners-0.5.3/mlr3learners/tests/testthat/helper.R | 4 mlr3learners-0.5.3/mlr3learners/tests/testthat/test_classif_kknn.R | 6 mlr3learners-0.5.3/mlr3learners/tests/testthat/test_regr_kknn.R | 6 57 files changed, 760 insertions(+), 1395 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] ,
Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.2.0 dated 2021-10-18 and 1.2.1-1 dated 2022-05-25
seqHMM-1.2.0/seqHMM/NEWS |only seqHMM-1.2.1-1/seqHMM/DESCRIPTION | 10 seqHMM-1.2.1-1/seqHMM/MD5 | 171 seqHMM-1.2.1-1/seqHMM/NEWS.md |only seqHMM-1.2.1-1/seqHMM/R/build_mm.R | 71 seqHMM-1.2.1-1/seqHMM/R/build_mmm.R | 500 seqHMM-1.2.1-1/seqHMM/R/check_deprecated_args.R | 6 seqHMM-1.2.1-1/seqHMM/R/colorpalette.R | 58 seqHMM-1.2.1-1/seqHMM/R/estimate_coef.R | 126 seqHMM-1.2.1-1/seqHMM/R/fit_model.R | 4 seqHMM-1.2.1-1/seqHMM/R/gridplot.R | 1352 - seqHMM-1.2.1-1/seqHMM/R/hidden_paths.R | 21 seqHMM-1.2.1-1/seqHMM/R/mssplot.R | 789 seqHMM-1.2.1-1/seqHMM/R/plot.hmm.R | 1294 - seqHMM-1.2.1-1/seqHMM/R/plot.mhmm.R | 406 seqHMM-1.2.1-1/seqHMM/R/posterior_probs.R | 62 seqHMM-1.2.1-1/seqHMM/R/seqHMM-package.R | 76 seqHMM-1.2.1-1/seqHMM/R/simulate_hmm.R | 306 seqHMM-1.2.1-1/seqHMM/R/ssp.R | 1422 - seqHMM-1.2.1-1/seqHMM/R/ssplot.R | 499 seqHMM-1.2.1-1/seqHMM/R/zzz.R | 12 seqHMM-1.2.1-1/seqHMM/README.md |only seqHMM-1.2.1-1/seqHMM/build/vignette.rds |binary seqHMM-1.2.1-1/seqHMM/inst/CITATION | 56 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM.R | 84 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM.Rnw | 34 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM.pdf | 4033 ++-- seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_algorithms.Rnw | 446 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_algorithms.pdf |binary seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_estimation.Rnw | 356 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_estimation.pdf |binary seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_visualization.Rnw | 808 seqHMM-1.2.1-1/seqHMM/inst/doc/seqHMM_visualization.pdf | 9038 +++++------ seqHMM-1.2.1-1/seqHMM/man/TraMineR_imports.Rd | 24 seqHMM-1.2.1-1/seqHMM/man/biofam3c.Rd | 176 seqHMM-1.2.1-1/seqHMM/man/build_hmm.Rd | 366 seqHMM-1.2.1-1/seqHMM/man/build_lcm.Rd | 332 seqHMM-1.2.1-1/seqHMM/man/build_mhmm.Rd | 502 seqHMM-1.2.1-1/seqHMM/man/build_mm.Rd | 123 seqHMM-1.2.1-1/seqHMM/man/build_mmm.Rd | 240 seqHMM-1.2.1-1/seqHMM/man/colorpalette.Rd | 66 seqHMM-1.2.1-1/seqHMM/man/estimate_coef.Rd | 36 seqHMM-1.2.1-1/seqHMM/man/forward_backward.Rd | 88 seqHMM-1.2.1-1/seqHMM/man/gridplot.Rd | 300 seqHMM-1.2.1-1/seqHMM/man/hidden_paths.Rd | 92 seqHMM-1.2.1-1/seqHMM/man/hmm_biofam.Rd | 182 seqHMM-1.2.1-1/seqHMM/man/hmm_mvad.Rd | 134 seqHMM-1.2.1-1/seqHMM/man/logLik.hmm.Rd | 66 seqHMM-1.2.1-1/seqHMM/man/logLik.mhmm.Rd | 66 seqHMM-1.2.1-1/seqHMM/man/mc_to_sc.Rd | 102 seqHMM-1.2.1-1/seqHMM/man/mc_to_sc_data.Rd | 148 seqHMM-1.2.1-1/seqHMM/man/mhmm_biofam.Rd | 332 seqHMM-1.2.1-1/seqHMM/man/mhmm_mvad.Rd | 182 seqHMM-1.2.1-1/seqHMM/man/mssplot.Rd | 439 seqHMM-1.2.1-1/seqHMM/man/plot.hmm.Rd | 576 seqHMM-1.2.1-1/seqHMM/man/plot.mhmm.Rd | 474 seqHMM-1.2.1-1/seqHMM/man/plot.ssp.Rd | 92 seqHMM-1.2.1-1/seqHMM/man/plot_colors.Rd | 64 seqHMM-1.2.1-1/seqHMM/man/posterior_probs.Rd | 62 seqHMM-1.2.1-1/seqHMM/man/print.Rd | 58 seqHMM-1.2.1-1/seqHMM/man/separate_mhmm.Rd | 72 seqHMM-1.2.1-1/seqHMM/man/seqHMM-deprecated.Rd | 300 seqHMM-1.2.1-1/seqHMM/man/seqHMM.Rd | 50 seqHMM-1.2.1-1/seqHMM/man/simulate_hmm.Rd | 112 seqHMM-1.2.1-1/seqHMM/man/simulate_mhmm.Rd | 230 seqHMM-1.2.1-1/seqHMM/man/simulate_pars.Rd | 82 seqHMM-1.2.1-1/seqHMM/man/ssp.Rd | 551 seqHMM-1.2.1-1/seqHMM/man/ssplot.Rd | 529 seqHMM-1.2.1-1/seqHMM/man/summary.mhmm.Rd | 136 seqHMM-1.2.1-1/seqHMM/man/trim_model.Rd | 96 seqHMM-1.2.1-1/seqHMM/man/vcov.mhmm.Rd | 78 seqHMM-1.2.1-1/seqHMM/src/EM.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/EMx.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/logSumExp.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/log_EM.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/log_EMx.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/log_objectivex.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/log_optCoef.cpp | 4 seqHMM-1.2.1-1/seqHMM/src/objectivex.cpp | 2 seqHMM-1.2.1-1/seqHMM/src/optCoef.cpp | 4 seqHMM-1.2.1-1/seqHMM/src/sa_opt_coef.cpp | 2 seqHMM-1.2.1-1/seqHMM/vignettes/mhmm.rds |only seqHMM-1.2.1-1/seqHMM/vignettes/references.bib | 1172 - seqHMM-1.2.1-1/seqHMM/vignettes/references_for_vignettes.bib | 5842 +++---- seqHMM-1.2.1-1/seqHMM/vignettes/sc_fit.rds |only seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM.Rnw | 34 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM_algorithms.Rnw | 446 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM_estimation.Rnw | 356 seqHMM-1.2.1-1/seqHMM/vignettes/seqHMM_visualization.Rnw | 808 89 files changed, 19476 insertions(+), 18804 deletions(-)
Title: Format R Output to Look Like SPSS
Description: Create plots and LaTeX tables that look like SPSS output for use in teaching materials. Rather than copying-and-pasting SPSS output into documents, R code that mocks up SPSS output can be integrated directly into dynamic LaTeX documents with tools such as knitr. Functionality includes statistical techniques that are typically covered in introductory statistics classes: descriptive statistics, common hypothesis tests, ANOVA, and linear regression, as well as box plots, histograms, scatter plots, and line plots (including profile plots).
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between r2spss versions 0.3.1 dated 2022-03-23 and 0.3.2 dated 2022-05-25
DESCRIPTION | 10 +- MD5 | 29 ++++--- NEWS | 5 + R/Eredivisie.R |only R/Exams.R |only R/r2spss-package.R |only build/partial.rdb |binary build/vignette.rds |binary data/Eredivisie.RData |binary data/Exams.RData |binary inst/doc/r2spss-intro.Rnw | 2 inst/doc/r2spss-intro.pdf |binary man/Eredivisie.Rd | 94 ++++++++++++----------- man/Exams.Rd | 63 ++++++++------- man/r2spss-package.Rd | 43 +++++----- vignettes/r2spss-intro.Rnw | 2 vignettes/r2spss.bib | 178 ++++++++++++++++++++++----------------------- 17 files changed, 219 insertions(+), 207 deletions(-)
Title: Statistical Methods for the Item Count Technique and List
Experiment
Description: Allows researchers to conduct multivariate
statistical analyses of survey data with list experiments. This
survey methodology is also known as the item count technique or
the unmatched count technique and is an alternative to the commonly
used randomized response method. The package implements the methods
developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>,
Blair and Imai (2012) <doi:10.1093/pan/mpr048>,
Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>,
Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>,
Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>,
Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and
Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>.
This includes a Bayesian MCMC implementation of regression for the
standard and multiple sensitive item list experiment designs and a
random effects setup, a Bayesian MCMC hierarchical regression model
with up to three hierarchical groups, the combined list experiment
and endorsement experiment regression model, a joint model of the
list experiment that enables the analysis of the list experiment as
a predictor in outcome regression models, a method for combining
list experiments with direct questions, and methods for diagnosing and
adjusting for response error. In addition, the package implements the
statistical test that is designed to detect certain failures of list
experiments, and a placebo test for the list experiment using data from
direct questions.
Author: Graeme Blair [aut, cre],
Winston Chou [aut],
Kosuke Imai [aut],
Bethany Park [ctb],
Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between list versions 9.2.1 dated 2022-05-10 and 9.2.2 dated 2022-05-25
ChangeLog | 3 + DESCRIPTION | 8 ++-- MD5 | 66 +++++++++++++++++----------------- R/ictreg.R | 8 +++- build/vignette.rds |binary inst/doc/combined-list.html | 5 +- man/affirm.Rd | 6 ++- man/combinedListDirect.Rd | 8 +++- man/combinedListExps.Rd | 6 ++- man/comp.listEndorse.Rd | 11 ++++- man/ict.hausman.test.Rd | 2 - man/ict.test.Rd | 11 ++++- man/ictreg.Rd | 36 ++++++++++++++---- man/ictreg.joint.Rd | 13 +++++- man/ictregBayes.Rd | 43 ++++++++++++++++++---- man/ictregBayesHier.Rd | 57 ++++++++++++++++++++++------- man/mexico.Rd | 6 ++- man/mis.Rd | 6 ++- man/multi.Rd | 6 ++- man/plot.predict.ictreg.Rd | 17 ++++++-- man/predict.ictreg.Rd | 19 ++++++++- man/predict.ictreg.joint.Rd | 19 +++++++-- man/predict.ictregBayes.Rd | 14 +++++-- man/predict.ictregBayesHier.Rd | 12 ++++-- man/race.Rd | 6 ++- man/summary.ictreg.Rd | 3 - src/combine.c | 2 - src/init.c | 4 +- tests/testthat/test-combined.R | 1 tests/testthat/test-ict.test.R | 1 tests/testthat/test-ictreg.R | 21 +++++----- tests/testthat/test-ictreg.joint.R | 1 tests/testthat/test-ictregBayes.R | 3 - tests/testthat/test-ictregBayesHier.R | 4 -- 34 files changed, 294 insertions(+), 134 deletions(-)
Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct
social-ecological models that simulate the management of populations and
stakeholder actions. These models build off of a previously developed
management strategy evaluation (MSE) framework to simulate all aspects of
management: population dynamics, manager observation of populations, manager
decision making, and stakeholder responses to management decisions. The
newly developed generalised management strategy evaluation (GMSE)
framework uses genetic algorithms to mimic the decision-making process of
managers and stakeholders under conditions of change, uncertainty, and
conflict. Simulations can be run using gmse(), gmse_apply(), and
gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] ,
Adrian Bach [aut],
Nils Bunnefeld [aut, fnd] ,
Jeremy Cusack [ctb] ,
Isabel Jones [ctb] ,
Jeroen Minderman [aut] ,
Erlend Nilsen [ctb] ,
Ochoa Gabriela [aut] ,
Rocio Pozo [ctb] ,
Sarobidy Rakotonarivo [ctb] ,
Bram Van M [...truncated...]
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>
Diff between GMSE versions 0.7.0.0 dated 2021-08-02 and 1.0.0.1 dated 2022-05-25
DESCRIPTION | 15 + MD5 | 44 ++--- NEWS.md | 13 + R/gmse.R | 29 ++- R/gmse_apply.R | 92 ++++++++-- R/gmse_apply_summary.R | 5 README.md | 2 build/vignette.rds |binary inst/doc/SI9.pdf |only inst/doc/SI9.pdf.asis |only man/gmse.Rd | 14 + src/game.c | 267 ++++++++++++++++++++++++++----- src/game.h | 19 +- src/landscape.c | 10 - src/manager.c | 56 +++--- src/observation.c | 40 ++-- src/resource.c | 20 +- src/user.c | 74 ++++---- src/utilities.c | 2 tests/testthat/test-gmse_sim_annealing.R |only tests/testthat/test-manager.R | 4 tests/testthat/test-observation.R | 8 tests/testthat/test-resource.R | 8 tests/testthat/test-user.R | 6 vignettes/SI9.pdf.asis |only 25 files changed, 529 insertions(+), 199 deletions(-)
Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests.
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>
Diff between eurlex versions 0.4.1 dated 2022-03-31 and 0.4.2 dated 2022-05-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 10 ++++++++++ R/elx_make_query.R | 31 +++++++++++++++++++++++++++---- README.md | 5 +++++ inst/doc/eurlexpkg.html | 22 +++++++++++----------- man/elx_make_query.Rd | 3 +++ 7 files changed, 65 insertions(+), 24 deletions(-)
Title: Identification and Estimation using Group Testing
Description: Methods for the group testing identification problem: 1) Operating
characteristics (e.g., expected number of tests) for commonly used
hierarchical and array-based algorithms, and 2) Optimal testing
configurations for these same algorithms. Methods for the group testing
estimation problem: 1) Estimation and inference procedures for an overall
prevalence, and 2) Regression modeling for commonly used hierarchical and
array-based algorithms.
Author: Brianna Hitt [aut, cre] ,
Christopher Bilder [aut] ,
Frank Schaarschmidt [aut] ,
Brad Biggerstaff [aut] ,
Christopher McMahan [aut] ,
Joshua Tebbs [aut] ,
Boan Zhang [ctb],
Michael Black [ctb],
Peijie Hou [ctb],
Peng Chen [ctb]
Maintainer: Brianna Hitt <brianna.hitt@afacademy.af.edu>
Diff between binGroup2 versions 1.2.3 dated 2022-05-16 and 1.2.4 dated 2022-05-25
DESCRIPTION | 12 ++++++------ MD5 | 38 +++++++++++++++++++------------------- R/OTC1.R | 22 +++++++++++----------- R/OTC2.R | 18 +++++++++--------- R/OTCMethodFunctions.R | 40 ++++++++++++++++++++-------------------- R/SupportingOTCFunctions.R | 28 ++++++++++++++-------------- R/binGroup2-package.R | 12 ++++++------ R/designFunctions.R | 4 ++-- R/gtReg.R | 4 +--- R/opCharMethodFunctions.R | 2 +- R/operatingCharacteristics2.R | 2 +- build/partial.rdb |binary man/OTC1.Rd | 22 +++++++++++----------- man/OTC2.Rd | 16 ++++++++-------- man/binGroup2.Rd | 10 +++++----- man/designPower.Rd | 4 ++-- man/gtReg.Rd | 4 +--- man/plot.OTC.Rd | 18 +++++++++--------- man/summary.OTC.Rd | 22 +++++++++++----------- man/summary.opChar.Rd | 2 +- 20 files changed, 138 insertions(+), 142 deletions(-)
Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm
for simple linear ordered monotone regression, including two spin-off functions
for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre],
Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>
Diff between monotone versions 0.1.0 dated 2021-03-10 and 0.1.1 dated 2022-05-25
DESCRIPTION | 13 ++++++------- MD5 | 19 ++++++++++--------- R/bimonotone.R | 5 +++-- R/legacy.R | 12 +++++++----- R/monotone.R | 6 ++++-- R/unimonotone.R | 5 +++-- inst |only man/bimonotone.Rd | 5 +++-- man/legacy.Rd | 10 +++++----- man/monotone.Rd | 6 ++++-- man/unimonotone.Rd | 5 +++-- 11 files changed, 48 insertions(+), 38 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.46 dated 2022-03-31 and 2.0.48 dated 2022-05-25
DESCRIPTION | 8 - MD5 | 22 ++-- NEWS | 18 +++ R/epi.kappa.R | 8 - R/epi.prev.R | 143 +++++++++++++++++++---------- inst/doc/epiR_descriptive.html | 32 +++--- inst/doc/epiR_measures_of_association.html | 52 +++++----- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.Rmd | 20 ++-- inst/doc/epiR_surveillance.html | 84 ++++++++--------- man/epi.prev.Rd | 18 ++- vignettes/epiR_surveillance.Rmd | 20 ++-- 12 files changed, 253 insertions(+), 176 deletions(-)
Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7].
Main references:
[1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>,
[2] Mualem (1976) <doi:10.1029/WR012i003p00513>,
[3] Peters (2013) <doi:10.1002/wrcr.20548>,
[4] Iden and Durner (2013) <doi:10.1002/2014WR015937>,
[5] Peters (2014) <doi:10.1002/2014WR015937>,
[6] Wind G. P. (1966),
[7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and
[8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre],
Felix Andrews [ctb] which is not on r-cran
. The SCEoptim function is
adapted, and substantially revised from Brecht Donckels MATLAB code
which is in turn adopted from Qingyun Duans MATLAB code),
Brecht Donckels [ctb] ,
[...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>
Diff between SoilHyP versions 0.1.5 dated 2021-01-08 and 0.1.6 dated 2022-05-25
DESCRIPTION | 10 +++++----- MD5 | 52 ++++++++++++++++++++++++++-------------------------- R/DK_to_SWC.R | 11 ++++++----- R/Kcap.R | 2 +- R/Kfilm.R | 2 +- R/Ku.R | 4 ++-- R/SEM.R | 7 +++---- R/SWC.R | 5 +++-- R/Sad.R | 2 +- R/Sat.R | 2 +- R/Sat_old.R | 2 +- R/Scap.R | 2 +- R/dataSEM.R | 9 +++++---- R/dataSHP.R | 8 ++++---- R/dataTestthat.R | 18 +++++++++--------- man/Kcap.Rd | 2 +- man/Kfilm.Rd | 2 +- man/Ku.Rd | 4 ++-- man/SEM.Rd | 7 +++---- man/SWC.Rd | 4 ++-- man/Sad.Rd | 2 +- man/Sat.Rd | 2 +- man/Sat_old.Rd | 2 +- man/Scap.Rd | 2 +- man/dataSEM.Rd | 9 +++++---- man/dataSHP.Rd | 8 ++++---- man/dataTestthat.Rd | 18 +++++++++--------- 27 files changed, 100 insertions(+), 98 deletions(-)
Title: The Second Dimension of Spatial Association
Description: Most of the current methods explore spatial association using
observations at sample locations, which are defined as the first
dimension of spatial association (FDA). The proposed concept of
the second dimension of spatial association (SDA) aims to extract
in-depth information about the geographical environment from
locations outside sample locations for exploring spatial
association.
Author: Yongze Song [aut, cre]
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>
Diff between SecDim versions 1.3 dated 2022-05-02 and 2.2 dated 2022-05-25
DESCRIPTION | 22 ++++++++++++---------- MD5 | 20 ++++++++++++++------ NAMESPACE | 1 + R/data.R | 13 +++++++++++++ R/selectvarlm.R | 5 ++++- R/selectvarsda.R | 2 +- build |only data/sample_vars_fda.rda |only inst |only man/sample_vars_fda.Rd |only man/selectvarsda.Rd | 2 +- vignettes |only 12 files changed, 46 insertions(+), 19 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.4.3 dated 2021-12-21 and 1.4.4 dated 2022-05-25
DESCRIPTION | 10 ++-- MD5 | 40 ++++++++-------- NEWS.md | 4 + R/crtree.R | 6 +- R/evalbin.R | 113 +++++++++++++++++++++++------------------------ R/gbt.R | 2 R/nn.R | 100 +++++++++++++++++++---------------------- README.md | 8 +-- man/auc.Rd | 1 man/confusion.Rd | 1 man/evalbin.Rd | 1 man/nn.Rd | 1 man/plot.confusion.Rd | 1 man/plot.evalbin.Rd | 1 man/plot.nn.Rd | 1 man/predict.nn.Rd | 1 man/profit.Rd | 1 man/rig.Rd | 1 man/summary.confusion.Rd | 1 man/summary.evalbin.Rd | 1 man/summary.nn.Rd | 1 21 files changed, 142 insertions(+), 154 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.4.1 dated 2021-11-12 and 1.4.2 dated 2022-05-25
DESCRIPTION | 16 ++--- MD5 | 26 ++++---- NAMESPACE | 1 NEWS.md | 5 + R/aaa.R | 2 R/radiant.R | 124 +++++++++++++++++++++------------------- R/visualize.R | 18 +---- README.md | 14 ++-- inst/app/global.R | 2 inst/app/radiant.R | 4 - inst/app/tools/app/about.md | 8 +- inst/app/tools/app/tutorials.md | 11 --- man/sshh.Rd | 2 man/sshhr.Rd | 2 14 files changed, 116 insertions(+), 119 deletions(-)
Title: The Online Regularized K-Means Clustering Algorithm
Description: Algorithm of online regularized k-means to deal with online multi(single) view data.
The philosophy of the package is described in Guo G. (2020)
<doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] ,
Miao Yu [aut],
Haoyue Song [aut],
Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between ORKM versions 0.0.2.1 dated 2022-04-25 and 0.1.1.1 dated 2022-05-25
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++++++------------- R/DMC.R | 33 ++++++++++++++------------------- R/KMeans.R | 26 +++++++++++++++----------- R/OGD.R | 4 ++-- R/OMU.R | 5 ++--- R/ORKMeans.R | 23 +++++++++++------------ R/PKMeans.R | 4 ++-- R/RKMeans.R | 17 +++++++++-------- data/QCM.rda |only data/movie1.rda |only data/movie2.rda |only data/turelabel.rda |only man/DMC.Rd | 10 +++++----- man/KMeans.Rd | 10 +++++----- man/ORKMeans.Rd | 2 +- man/PKMeans.Rd | 2 +- man/QCM.Rd |only man/RKMeans.Rd | 10 +++++----- man/movie1.Rd |only man/movie2.Rd |only man/turelabel.Rd |only 22 files changed, 97 insertions(+), 91 deletions(-)
Title: Meteorological Tools
Description: Meteorological Tools following the FAO56 irrigation paper of Allen et al. (1998) [1].
Functions for calculating:
reference evapotranspiration (ETref),
extraterrestrial radiation (Ra),
net radiation (Rn),
saturation vapor pressure (satVP),
global radiation (Rs),
soil heat flux (G),
daylight hours,
and more.
[1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop evapotranspiration-Guidelines for computing crop water requirements-FAO Irrigation and drainage paper 56. FAO, Rome, 300(9).
Author: Ullrich Dettmann [aut, cre],
R. Grima [aut]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>
Diff between MeTo versions 0.1.0 dated 2019-01-11 and 0.1.1 dated 2022-05-25
DESCRIPTION | 13 ++++++------- MD5 | 48 ++++++++++++++++++++++++------------------------ R/ETref.R | 1 + R/Ra.R | 4 ++-- R/Rn.R | 10 +++++----- R/Rns.R | 4 ++-- R/Rso.R | 8 ++++---- R/estG.R | 14 ++++++++------ R/estP.r | 12 ++++++------ R/estRs.R | 6 +++--- R/w.R | 4 ++-- man/ETref.Rd | 25 +++++++++++++++++++++---- man/Ra.Rd | 7 +++---- man/Rn.Rd | 32 +++++++++++++++++++++++--------- man/Rnl.Rd | 20 +++++++++++++++++--- man/Rns.Rd | 4 ++-- man/Rso.Rd | 19 +++++++++++++------ man/VP.Rd | 16 +++++++++++++--- man/constDefaults.Rd | 6 ++++-- man/controlDefaults.Rd | 6 ++++-- man/estG.Rd | 29 ++++++++++++++++++++--------- man/estP.Rd | 12 ++++++------ man/estRs.Rd | 16 +++++++++++----- man/satVP.Rd | 9 +++++++-- man/w.Rd | 4 ++-- 25 files changed, 209 insertions(+), 120 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.1-2 dated 2022-01-14 and 1.1-3 dated 2022-05-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Bernstein.R | 7 ++++++- inst/NEWS.Rd | 7 +++++++ tests/bases-Ex.R | 55 ++++++++++++++++++++++++++++++++++++------------------- 5 files changed, 57 insertions(+), 28 deletions(-)
Title: Selenium Plugin to Manage Multi Level Shadow Elements on Web
Page
Description: Shadow Document Object Model is a web standard that offers component style and markup encapsulation.
It is a critically important piece of the Web Components story as it ensures that a component will work in any environment even if other CSS or JavaScript is at play on the page.
Custom HTML tags can't be directly identified with selenium tools, because Selenium doesn't provide any way to deal with shadow elements.
Using this plugin you can handle any custom HTML tags.
Author: Ricardo Landolt [cre, aut],
Sushil Gupta [ctb]
Maintainer: Ricardo Landolt <ricardo.landolt1@gmail.com>
Diff between shadowr versions 0.0.1 dated 2022-04-22 and 0.0.2 dated 2022-05-25
DESCRIPTION | 6 MD5 | 27 +- NAMESPACE | 60 +++--- NEWS.md | 2 README.md | 11 - inst/figures |only inst/resources/test/button.html | 34 +-- inst/resources/test/index.html | 24 +- inst/resources/test/script.js | 28 +- inst/resources/test/style.css | 6 man/convert_js_to_text.Rd | 24 +- man/shadow-class.Rd | 352 ++++++++++++++++++------------------- man/shadow.Rd | 42 ++-- tests/testthat.R | 8 tests/testthat/test-check-output.R | 155 +++++----------- 15 files changed, 366 insertions(+), 413 deletions(-)
Title: The Truncated Elliptical Family of Distributions
Description: It offers random numbers generation from members of the truncated multivariate elliptical family of distribution such as the truncated versions of the Normal, Student-t, Pearson VII, Slash, Logistic, among others. Particular distributions can be provided by specifying the density generating function. It also computes the first two moments (covariance matrix as well) for some particular distributions.
References used for this package: Galarza, C. E., Matos, L. A., Castro, L. M., & Lachos, V. H. (2022). Moments of the doubly truncated selection elliptical distributions with emphasis on the unified multivariate skew-t distribution. Journal of Multivariate Analysis, 189, 104944 <doi:10.1016/j.jmva.2021.104944>; Ho, H. J., Lin, T. I., Chen, H. Y., & Wang, W. L. (2012). Some results on the truncated multivariate t distribution. Journal of Statistical Planning and Inference, 142(1), 25-40 <doi:10.1016/j.jspi.2011.06.006>; Valeriano, K. A., Galarza, C. E., & Matos, L. A. (2021). Moments and random number generation for the truncated elliptical family of distributions. arXiv preprint <arXiv:2112.09319>.
Author: Katherine A. L. Valeriano [aut, cre]
,
Larissa Avila Matos [ctb] ,
Christian Galarza Morales [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>
Diff between relliptical versions 1.1.0 dated 2022-01-07 and 1.2.0 dated 2022-05-25
DESCRIPTION | 14 +-- MD5 | 21 ++-- NAMESPACE | 1 NEWS.md |only R/Compute_Moments.R | 21 ++-- R/Random_Numbers.R | 26 +++--- README.md | 39 +++++---- build/partial.rdb |binary inst/REFERENCES.bib | 36 +++++--- man/mvtelliptical.Rd | 20 ++-- man/rtelliptical.Rd | 16 ++- src/Functions.cpp | 215 ++++++++++++--------------------------------------- 12 files changed, 169 insertions(+), 240 deletions(-)
Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business
analytics in R, based on the shiny package. The application combines the
functionality of 'radiant.data', 'radiant.design', 'radiant.basics',
'radiant.model', and 'radiant.multivariate'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant versions 1.4.1 dated 2021-11-22 and 1.4.2 dated 2022-05-25
DESCRIPTION | 10 - MD5 | 26 +-- NEWS.md | 5 R/radiant.R | 57 ++++++-- README.md | 8 - build/vignette.rds |binary inst/doc/programming.R | 4 inst/doc/programming.Rmd | 4 inst/doc/programming.html | 321 ++++++++++++++++++++++++++++++++++++++++------ man/launcher.Rd | 8 + man/lin_launcher.Rd | 10 + man/mac_launcher.Rd | 10 + man/win_launcher.Rd | 10 + vignettes/programming.Rmd | 4 14 files changed, 390 insertions(+), 87 deletions(-)
Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG,
Meteoclimatic...).
Author: Victor Granda [aut, cre] ,
Miquel de Caceres [ctb] ,
Aitor Ameztegui [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between meteospain versions 0.0.3 dated 2021-11-05 and 0.0.4 dated 2022-05-25
DESCRIPTION | 10 MD5 | 100 ++++---- NEWS.md | 12 R/aemet_helpers.R | 11 R/get_data.R | 17 + R/meteocat_helpers.R | 8 R/meteoclimatic_helpers.R | 33 +- R/meteogalicia_helpers.R | 14 - R/ria_helpers.R | 13 - R/services_options.R | 4 R/utils.R | 95 +++++++ README.md | 63 ++--- build/vignette.rds |binary inst/doc/aemet.R | 3 inst/doc/aemet.Rmd | 4 inst/doc/aemet.html | 245 ++++++++++++++++++- inst/doc/api_limits.R | 3 inst/doc/api_limits.Rmd | 3 inst/doc/api_limits.html | 254 +++++++++++++++++++- inst/doc/compatibility.R | 3 inst/doc/compatibility.Rmd | 3 inst/doc/compatibility.html | 228 +++++++++++++++++- inst/doc/meteocat.R | 3 inst/doc/meteocat.Rmd | 4 inst/doc/meteocat.html | 252 ++++++++++++++++++-- inst/doc/meteoclimatic.R | 3 inst/doc/meteoclimatic.Rmd | 4 inst/doc/meteoclimatic.html | 216 ++++++++++++++++- inst/doc/meteogalicia.R | 3 inst/doc/meteogalicia.Rmd | 24 + inst/doc/meteogalicia.html | 261 ++++++++++++++++++--- inst/doc/ria.R | 3 inst/doc/ria.Rmd | 24 + inst/doc/ria.html | 261 +++++++++++++++++++-- man/figures/README-plot_stations-1.png |binary man/figures/README-plot_stations-2.png |binary man/get_meteo_from.Rd | 1 man/get_stations_info_from.Rd | 1 tests/testthat/test-aemet.R | 22 + tests/testthat/test-concordance_between_services.R | 3 tests/testthat/test-meteocat.R | 77 ++++-- tests/testthat/test-meteoclimatic.R | 4 tests/testthat/test-meteogalicia.R | 37 ++ tests/testthat/test-riaa.R | 13 - vignettes/aemet.Rmd | 4 vignettes/api_limits.Rmd | 3 vignettes/compatibility.Rmd | 3 vignettes/meteocat.Rmd | 4 vignettes/meteoclimatic.Rmd | 4 vignettes/meteogalicia.Rmd | 24 + vignettes/ria.Rmd | 24 + 51 files changed, 2099 insertions(+), 309 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Pavel N. Krivitsky [aut, cre] ,
Mark S. Handcock [ctb],
David R. Hunter [ctb],
Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm.count versions 4.0.2 dated 2021-06-18 and 4.1.1 dated 2022-05-25
ergm.count-4.0.2/ergm.count/build/partial.rdb |only ergm.count-4.0.2/ergm.count/man/ergm-references.Rd |only ergm.count-4.0.2/ergm.count/man/ergm-terms.Rd |only ergm.count-4.0.2/ergm.count/src/wtMHproposals.h |only ergm.count-4.0.2/ergm.count/tests/testnet3d.RData |only ergm.count-4.0.2/ergm.count/tests/valued_fit.R |only ergm.count-4.0.2/ergm.count/tests/valued_sim.R |only ergm.count-4.1.1/ergm.count/DESCRIPTION | 22 ergm.count-4.1.1/ergm.count/LICENSE | 2 ergm.count-4.1.1/ergm.count/MD5 | 66 +- ergm.count-4.1.1/ergm.count/R/InitErgmReference.R | 99 +++ ergm.count-4.1.1/ergm.count/R/InitWtErgmProposal.R | 113 ++-- ergm.count-4.1.1/ergm.count/R/InitWtErgmTerm.R | 49 + ergm.count-4.1.1/ergm.count/R/data.R | 6 ergm.count-4.1.1/ergm.count/R/ergm.count-package.R | 36 + ergm.count-4.1.1/ergm.count/R/zzz.R | 13 ergm.count-4.1.1/ergm.count/build/ergm.count.pdf |only ergm.count-4.1.1/ergm.count/build/vignette.rds |binary ergm.count-4.1.1/ergm.count/inst/CITATION | 17 ergm.count-4.1.1/ergm.count/inst/NEWS.Rd | 51 + ergm.count-4.1.1/ergm.count/inst/doc/valued.R | 7 ergm.count-4.1.1/ergm.count/inst/doc/valued.Rmd | 10 ergm.count-4.1.1/ergm.count/inst/doc/valued.html | 350 ++++++------ ergm.count-4.1.1/ergm.count/man/Binomial-ergmReference.Rd |only ergm.count-4.1.1/ergm.count/man/CMB-ergmTerm.Rd |only ergm.count-4.1.1/ergm.count/man/CMP-ergmTerm.Rd |only ergm.count-4.1.1/ergm.count/man/Disc-ergmProposal.Rd |only ergm.count-4.1.1/ergm.count/man/DiscTNT-ergmProposal.Rd |only ergm.count-4.1.1/ergm.count/man/Geometric-ergmReference.Rd |only ergm.count-4.1.1/ergm.count/man/Poisson-ergmReference.Rd |only ergm.count-4.1.1/ergm.count/man/ZIPoisson-ergmProposal.Rd |only ergm.count-4.1.1/ergm.count/man/ergm.count-package.Rd | 39 + ergm.count-4.1.1/ergm.count/man/zach.Rd | 4 ergm.count-4.1.1/ergm.count/src/include_stubs.c | 2 ergm.count-4.1.1/ergm.count/src/init.c | 2 ergm.count-4.1.1/ergm.count/src/wtMHproposals.c | 366 ++++--------- ergm.count-4.1.1/ergm.count/src/wtchangestats.c | 2 ergm.count-4.1.1/ergm.count/src/wtchangestats.h | 2 ergm.count-4.1.1/ergm.count/tests/testthat |only ergm.count-4.1.1/ergm.count/tests/testthat.R |only ergm.count-4.1.1/ergm.count/vignettes/timings.csv |only ergm.count-4.1.1/ergm.count/vignettes/valued.Rmd | 10 ergm.count-4.1.1/ergm.count/vignettes/valued.bib | 183 ++---- 43 files changed, 797 insertions(+), 654 deletions(-)
Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant
and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] ,
Christopher McBride [ctb],
Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>
Diff between dycdtools versions 0.4.1 dated 2022-05-08 and 0.4.2 dated 2022-05-25
dycdtools-0.4.1/dycdtools/R/dycdtools.R |only dycdtools-0.4.2/dycdtools/DESCRIPTION | 7 dycdtools-0.4.2/dycdtools/MD5 | 69 +- dycdtools-0.4.2/dycdtools/NAMESPACE | 1 dycdtools-0.4.2/dycdtools/NEWS.md | 5 dycdtools-0.4.2/dycdtools/R/Fun_Calib-assist.R | 261 ++++++---- dycdtools-0.4.2/dycdtools/R/Fun_Change-input-file.R | 8 dycdtools-0.4.2/dycdtools/R/Fun_Contour-plot_sim.R | 107 ++-- dycdtools-0.4.2/dycdtools/R/Fun_Contour-plot_sim_obs.R | 171 +++--- dycdtools-0.4.2/dycdtools/R/Fun_Extract-simulation.R | 64 +- dycdtools-0.4.2/dycdtools/R/Fun_Interpol.R | 48 + dycdtools-0.4.2/dycdtools/R/Fun_Objective-func.R | 44 + dycdtools-0.4.2/dycdtools/R/Fun_Profile-plot.R | 58 +- dycdtools-0.4.2/dycdtools/R/Fun_Run-iteration.R | 29 - dycdtools-0.4.2/dycdtools/R/Fun_Scatter-plot.R | 52 + dycdtools-0.4.2/dycdtools/R/Fun_TS-plot.R | 142 +++-- dycdtools-0.4.2/dycdtools/R/obs_temp.R | 6 dycdtools-0.4.2/dycdtools/R/output_name.R | 5 dycdtools-0.4.2/dycdtools/README.md | 154 +++++ dycdtools-0.4.2/dycdtools/man/calib_assist.Rd | 119 +++- dycdtools-0.4.2/dycdtools/man/change_input_file.Rd | 10 dycdtools-0.4.2/dycdtools/man/ext_output.Rd | 24 dycdtools-0.4.2/dycdtools/man/interpol.Rd | 30 - dycdtools-0.4.2/dycdtools/man/objective_fun.Rd | 33 - dycdtools-0.4.2/dycdtools/man/obs_temp.Rd | 6 dycdtools-0.4.2/dycdtools/man/output_name.Rd | 5 dycdtools-0.4.2/dycdtools/man/plot_cont.Rd | 49 - dycdtools-0.4.2/dycdtools/man/plot_cont_comp.Rd | 76 +- dycdtools-0.4.2/dycdtools/man/plot_prof.Rd | 40 - dycdtools-0.4.2/dycdtools/man/plot_scatter.Rd | 37 - dycdtools-0.4.2/dycdtools/man/plot_ts.Rd | 56 +- dycdtools-0.4.2/dycdtools/man/run_iteration.Rd | 9 dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_cont_comp.R |only dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_prof.R |only dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_scatter.R |only dycdtools-0.4.2/dycdtools/tests/testthat/test-FUN-plot_ts.R |only dycdtools-0.4.2/dycdtools/tests/testthat/test-Fun_Delete-space.R | 2 dycdtools-0.4.2/dycdtools/tests/testthat/test-Fun_Height2Depth.R | 2 38 files changed, 1136 insertions(+), 593 deletions(-)
Title: Algorithmic Experimental Design
Description: Algorithmic experimental designs. Calculates exact and
approximate theory experimental designs for D,A, and I
criteria. Very large designs may be created. Experimental
designs may be blocked or blocked designs created from a
candidate list, using several criteria. The blocking can be
done when whole and within plot factors interact.
Author: Bob Wheeler <bwheelerg@gmail.com>
Maintainer: Jerome Braun <jvbraun.statistics@gmail.com>
Diff between AlgDesign versions 1.2.0 dated 2019-11-29 and 1.2.1 dated 2022-05-25
AlgDesign-1.2.0/AlgDesign/INDEX |only AlgDesign-1.2.1/AlgDesign/DESCRIPTION | 6 +++--- AlgDesign-1.2.1/AlgDesign/MD5 | 15 +++++++-------- AlgDesign-1.2.1/AlgDesign/NEWS | 5 +++++ AlgDesign-1.2.1/AlgDesign/build/vignette.rds |binary AlgDesign-1.2.1/AlgDesign/inst/doc/AlgDesign.Rnw | 4 ++-- AlgDesign-1.2.1/AlgDesign/inst/doc/AlgDesign.pdf |binary AlgDesign-1.2.1/AlgDesign/src/FederovOpt.c | 2 +- AlgDesign-1.2.1/AlgDesign/vignettes/AlgDesign.Rnw | 4 ++-- 9 files changed, 20 insertions(+), 16 deletions(-)
Title: Individual-Level, Summary-Level and Single-Step Bayesian
Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including:
(1) fixed effects and coefficients of covariates,
(2) environmental random effects, and its corresponding variance,
(3) genetic variance,
(4) residual variance,
(5) heritability,
(6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals,
(7) SNP effect size,
(8) phenotype/genetic variance explained (PVE) for single or multiple SNPs,
(9) posterior probability of association of the genomic window (WPPA),
(10) posterior inclusive probability (PIP).
The functions are not limited, we will keep on going in enriching it with more features.
References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
Author: Lilin Yin [aut, cre, cph],
Haohao Zhang [aut, cph],
Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>
Diff between hibayes versions 1.0.1 dated 2022-01-13 and 1.1.0 dated 2022-05-25
DESCRIPTION | 10 - MD5 | 24 +-- R/bayes.r | 42 ++++-- R/ldm.r | 3 R/sbayes.r | 23 ++- R/ssbayes.r | 58 +++++--- man/bayes.Rd | 26 ++- man/sbayes.Rd | 19 +- man/ssbayes.Rd | 30 +++- src/Bayes.cpp | 372 ++++++++++++++++++++++++++++++-------------------------- src/SBayesD.cpp | 176 +++++++++++++++----------- src/SBayesS.cpp | 174 +++++++++++++++----------- src/solver.cpp | 2 13 files changed, 555 insertions(+), 404 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureStor versions 3.6.1 dated 2022-02-03 and 3.7.0 dated 2022-05-25
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++---------- NAMESPACE | 15 +++++++ NEWS.md | 9 ++++ R/AzureStor.R | 2 - R/adls_client_funcs.R | 2 - R/az_storage.R | 4 +- R/blob_client_funcs.R | 24 +++++++++--- R/blob_snapshot.R |only R/blob_transfer_internal.R | 14 +++++-- R/blob_version.R |only R/client_generics.R | 67 ++++++++++++++++++++++++++++++++-- R/file_client_funcs.R | 2 - R/storage_metadata.R | 12 +++++- R/storage_properties.R | 13 +++++- man/adls.Rd | 5 +- man/blob.Rd | 15 ++++--- man/file.Rd | 5 +- man/generics.Rd | 39 ++++++++++++++++++- man/metadata.Rd | 4 +- man/properties.Rd | 6 ++- man/snapshot.Rd |only man/version.Rd |only tests/testthat/test02f_blobsnapshot.R |only tests/testthat/test02g_blobversion.R |only tests/testthat/test10a_service_sas.R | 15 +++++++ 26 files changed, 245 insertions(+), 58 deletions(-)
Title: Infer Constant and Stochastic, Time-Dependent Model Parameters
Description: Infer constant and stochastic, time-dependent parameters to consider intrinsic stochasticity of a dynamic model and/or to analyze model structure modifications that could reduce model deficits.
The concept is based on inferring time-dependent parameters as stochastic processes in the form of Ornstein-Uhlenbeck processes jointly with inferring constant model parameters and parameters of the Ornstein-Uhlenbeck processes.
The package also contains functions to sample from and calculate densities of Ornstein-Uhlenbeck processes.
References:
Tomassini, L., Reichert, P., Kuensch, H.-R. Buser, C., Knutti, R. and Borsuk, M.E. (2009), A smoothing algorithm for estimating stochastic, continuous-time model parameters and its application to a simple climate model, Journal of the Royal Statistical Society: Series C (Applied Statistics) 58, 679-704, <doi:10.1111/j.1467-9876.2009.00678.x>
Reichert, P., and Mieleitner, J. (2009), Analyzing input and structural uncertainty of nonlinear dynamic models with stochastic, time-dependent parameters. Water Resources Research, 45, W10402, <doi:10.1029/2009WR007814>
Reichert, P., Ammann, L. and Fenicia, F. (2021), Potential and challenges of investigating intrinsic uncertainty of hydrological models with time-dependent, stochastic parameters. Water Resources Research 57(8), e2020WR028311, <doi:10.1029/2020WR028311>
Reichert, P. (2022), timedeppar: An R package for inferring stochastic, time-dependent model parameters, in preparation.
Author: Peter Reichert <peter.reichert@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>
Diff between timedeppar versions 1.0.1 dated 2020-10-01 and 1.0.2 dated 2022-05-24
DESCRIPTION | 18 ++--- MD5 | 19 +++-- R/calc.acceptfreq.timedeppar.R | 2 R/get.param.timedeppar.R | 2 R/get.parsamp.timedeppar.R | 2 R/infer.timedeppar.R | 131 ++++++++++++++++++++++++++--------------- R/plot.timedeppar.R | 4 - R/readres.timedeppar.R | 2 build |only inst/NEWS.md | 9 ++ man/infer.timedeppar.Rd | 107 ++++++++++++++++++++++----------- 11 files changed, 190 insertions(+), 106 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.0.1 dated 2022-02-01 and 1.0.2 dated 2022-05-24
DESCRIPTION | 14 MD5 | 23 - R/RcppExports.R | 238 ++++++------ R/cv_observed_data_loglik.R | 221 +++++------ R/data.R |only R/logistic2ph.R | 706 +++++++++++--------------------------- R/observed_data_loglik.R | 91 +--- R/profile_out.R | 200 +++------- build |only data |only inst |only man/logistic2ph.Rd | 83 +--- man/mock.vccc.Rd |only tests/testthat/test_logistic2ph.R | 657 +++++++++++++++++------------------ vignettes |only 15 files changed, 895 insertions(+), 1338 deletions(-)
Title: A Metabolomics Analysis Tool for Intuitive Figures and
Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>
Diff between omu versions 1.0.4 dated 2020-05-18 and 1.0.5 dated 2022-05-24
DESCRIPTION | 15 MD5 | 100 +- NAMESPACE | 175 ++-- R/Internal_Functions.R | 242 +++-- R/KEGG_gather.R | 231 ++--- R/PCA_plot.R | 123 ++ R/Pie_Chart.R | 90 +- R/assign_hierarchy.R | 220 ++--- R/check_zeros.R |only R/count_fold_changes.R | 129 +-- R/data.R | 32 R/get_seqs.R |only R/omu_anova.R | 593 +++++++++----- R/omu_summary.R | 483 +++++++---- R/plate_omelette.R | 261 ++++-- R/plot_bar.R | 112 +- R/plot_boxplot.R | 214 +++-- R/plot_heatmap.R | 260 +++--- R/plot_volcano.R | 243 +++-- R/ra_table.R | 102 +- R/random_forest.R |only R/read_metabo.R | 34 R/rf_plot_functions.R |only R/transform_functions.R |only build/vignette.rds |binary inst/CITATION | 18 inst/doc/Omu_vignette.R | 40 inst/doc/Omu_vignette.Rmd | 121 -- inst/doc/Omu_vignette.html | 1581 ++------------------------------------ inst/extdata/read_metabo_test.csv | 6 man/KEGG_gather.Rd | 62 - man/PCA_plot.Rd | 69 + man/assign_hierarchy.Rd | 50 - man/c57_nos2KO_mouse_countDF.Rd | 34 man/c57_nos2KO_mouse_metadata.Rd | 32 man/check_zeros.Rd |only man/count_fold_changes.Rd | 70 - man/get_seqs.Rd |only man/make_omelette.Rd | 36 man/omu_anova.Rd | 102 +- man/omu_summary.Rd | 106 +- man/pie_chart.Rd | 72 - man/plate_omelette.Rd | 47 - man/plate_omelette_rxnko.Rd | 34 man/plot_bar.Rd | 72 - man/plot_boxplot.Rd | 88 +- man/plot_heatmap.Rd | 92 +- man/plot_rf_PCA.Rd |only man/plot_variable_importance.Rd |only man/plot_volcano.Rd | 127 +-- man/ra_table.Rd | 58 - man/random_forest.Rd |only man/read_metabo.Rd | 38 man/transform_metabolites.Rd |only man/transform_samples.Rd |only vignettes/Omu_vignette.Rmd | 121 -- vignettes/vignettes | 130 +-- 57 files changed, 3139 insertions(+), 3726 deletions(-)
Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre],
Gautier Stoll [ctb],
Guido Kroemer [ldr],
Jean-Pierre Marolleau [ldr],
Loïc Garcon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>
Diff between IFC versions 0.1.2 dated 2021-10-13 and 0.1.5 dated 2022-05-24
IFC-0.1.2/IFC/R/gatingML.R |only IFC-0.1.2/IFC/man/convert_to_baseplot.Rd |only IFC-0.1.5/IFC/DESCRIPTION | 8 IFC-0.1.5/IFC/MD5 | 204 +++--- IFC-0.1.5/IFC/NAMESPACE | 5 IFC-0.1.5/IFC/R/ExportToDAF.R | 34 - IFC-0.1.5/IFC/R/ExportToReport.R | 343 +++++++--- IFC-0.1.5/IFC/R/ExtractFromDAF.R | 6 IFC-0.1.5/IFC/R/ExtractFromXIF.R | 4 IFC-0.1.5/IFC/R/GatingML.R |only IFC-0.1.5/IFC/R/RcppExports.R | 332 ++++++++++ IFC-0.1.5/IFC/R/applyGatingStrategy.R | 27 IFC-0.1.5/IFC/R/autoplot.R | 5 IFC-0.1.5/IFC/R/buildBatch.R | 6 IFC-0.1.5/IFC/R/buildGraph.R | 47 - IFC-0.1.5/IFC/R/checksumDAF.R | 2 IFC-0.1.5/IFC/R/data_add_features.R | 6 IFC-0.1.5/IFC/R/data_add_pop_sample.R |only IFC-0.1.5/IFC/R/data_add_pops.R | 10 IFC-0.1.5/IFC/R/data_to_DAF.R | 4 IFC-0.1.5/IFC/R/fastAny.R |only IFC-0.1.5/IFC/R/fastCbind.R |only IFC-0.1.5/IFC/R/fcs.R | 841 ++++++++++++++++++-------- IFC-0.1.5/IFC/R/getFullTag.R | 2 IFC-0.1.5/IFC/R/getIFD.R | 2 IFC-0.1.5/IFC/R/getInfo.R | 2 IFC-0.1.5/IFC/R/getOffsets.R | 2 IFC-0.1.5/IFC/R/graphs_utils.R | 888 +++++++++++++++++++++++----- IFC-0.1.5/IFC/R/group.R |only IFC-0.1.5/IFC/R/plotGraph.R | 382 ++---------- IFC-0.1.5/IFC/R/popsRetrieveGraph.R | 3 IFC-0.1.5/IFC/R/popsWithin.R | 6 IFC-0.1.5/IFC/R/rasterplot.R |only IFC-0.1.5/IFC/R/readGatingStrategy.R | 6 IFC-0.1.5/IFC/R/strings_utils.R | 38 + IFC-0.1.5/IFC/R/toXML2_graphs.R | 15 IFC-0.1.5/IFC/R/trans_utils.R | 23 IFC-0.1.5/IFC/R/whoami.R | 332 +++++----- IFC-0.1.5/IFC/R/writeGatingStrategy.R | 4 IFC-0.1.5/IFC/R/writeIFC.R | 140 ++-- IFC-0.1.5/IFC/R/xml_utils.R | 3 IFC-0.1.5/IFC/build |only IFC-0.1.5/IFC/inst/AUTHORS | 4 IFC-0.1.5/IFC/inst/CITATION | 6 IFC-0.1.5/IFC/inst/COPYRIGHTS | 12 IFC-0.1.5/IFC/inst/include/align.hpp | 6 IFC-0.1.5/IFC/inst/include/cbind.hpp |only IFC-0.1.5/IFC/inst/include/decomp.hpp | 3 IFC-0.1.5/IFC/inst/include/extract.hpp | 3 IFC-0.1.5/IFC/inst/include/group.hpp |only IFC-0.1.5/IFC/inst/include/plot.hpp |only IFC-0.1.5/IFC/inst/include/scan.hpp | 6 IFC-0.1.5/IFC/inst/include/tiff.hpp | 61 - IFC-0.1.5/IFC/inst/include/trans.hpp | 34 + IFC-0.1.5/IFC/inst/include/utils.hpp | 187 +++++ IFC-0.1.5/IFC/man/BatchReport.Rd | 30 IFC-0.1.5/IFC/man/CreateGraphReport.Rd | 12 IFC-0.1.5/IFC/man/ExportToFCS.Rd | 6 IFC-0.1.5/IFC/man/ExportToReport.Rd | 12 IFC-0.1.5/IFC/man/ExtractFromFCS.Rd | 5 IFC-0.1.5/IFC/man/FCS_merge_dataset.Rd |only IFC-0.1.5/IFC/man/FCS_merge_sample.Rd |only IFC-0.1.5/IFC/man/FCS_to_data.Rd |only IFC-0.1.5/IFC/man/applyGatingStrategy.Rd | 15 IFC-0.1.5/IFC/man/applyTrans.Rd | 2 IFC-0.1.5/IFC/man/buildGraph.Rd | 23 IFC-0.1.5/IFC/man/convert_spillover.Rd |only IFC-0.1.5/IFC/man/coord_to_px.Rd |only IFC-0.1.5/IFC/man/cpp_align.Rd | 2 IFC-0.1.5/IFC/man/cpp_as_nativeRaster.Rd |only IFC-0.1.5/IFC/man/cpp_checkTIFF.Rd | 2 IFC-0.1.5/IFC/man/cpp_checksum.Rd | 2 IFC-0.1.5/IFC/man/cpp_coord_to_px.Rd |only IFC-0.1.5/IFC/man/cpp_draw.Rd |only IFC-0.1.5/IFC/man/cpp_fastTAGS.Rd | 2 IFC-0.1.5/IFC/man/cpp_fast_cbind_DF_DF.Rd |only IFC-0.1.5/IFC/man/cpp_fast_cbind_DF_L.Rd |only IFC-0.1.5/IFC/man/cpp_fast_cbind_DF_M.Rd |only IFC-0.1.5/IFC/man/cpp_fast_cbind_L_DF.Rd |only IFC-0.1.5/IFC/man/cpp_fast_cbind_M_DF.Rd |only IFC-0.1.5/IFC/man/cpp_fast_cbind_M_M.Rd |only IFC-0.1.5/IFC/man/cpp_fast_factor.Rd |only IFC-0.1.5/IFC/man/cpp_fast_listAny.Rd |only IFC-0.1.5/IFC/man/cpp_fast_range.Rd |only IFC-0.1.5/IFC/man/cpp_fast_rowAny.Rd |only IFC-0.1.5/IFC/man/cpp_fast_sample.Rd |only IFC-0.1.5/IFC/man/cpp_getTAGS.Rd | 2 IFC-0.1.5/IFC/man/cpp_get_bytes_order.Rd |only IFC-0.1.5/IFC/man/cpp_getoffsets_noid.Rd | 2 IFC-0.1.5/IFC/man/cpp_getoffsets_wid.Rd | 2 IFC-0.1.5/IFC/man/cpp_group_df.Rd |only IFC-0.1.5/IFC/man/cpp_raster.Rd |only IFC-0.1.5/IFC/man/cpp_replace_non_finite.Rd |only IFC-0.1.5/IFC/man/cpp_scanFirst.Rd | 2 IFC-0.1.5/IFC/man/cpp_v_int32_to_uint32.Rd |only IFC-0.1.5/IFC/man/cpp_v_int64_to_uint64.Rd |only IFC-0.1.5/IFC/man/data_add_pop_sample.Rd |only IFC-0.1.5/IFC/man/densCols.Rd | 2 IFC-0.1.5/IFC/man/fastAny.Rd |only IFC-0.1.5/IFC/man/fastCbind.Rd |only IFC-0.1.5/IFC/man/fromXML2_gating.Rd | 2 IFC-0.1.5/IFC/man/getFullTag.Rd | 2 IFC-0.1.5/IFC/man/getIFD.Rd | 2 IFC-0.1.5/IFC/man/getOffsets.Rd | 2 IFC-0.1.5/IFC/man/get_coordmap_adjusted.Rd |only IFC-0.1.5/IFC/man/get_coordmap_raw.Rd |only IFC-0.1.5/IFC/man/group.Rd |only IFC-0.1.5/IFC/man/layoutReport.Rd |only IFC-0.1.5/IFC/man/parseFCSname.Rd |only IFC-0.1.5/IFC/man/plotGraph.Rd | 8 IFC-0.1.5/IFC/man/plot_base.Rd |only IFC-0.1.5/IFC/man/plot_lattice.Rd |only IFC-0.1.5/IFC/man/plot_raster.Rd |only IFC-0.1.5/IFC/man/plot_stats.Rd |only IFC-0.1.5/IFC/man/pow2.Rd |only IFC-0.1.5/IFC/man/rasterplot.Rd |only IFC-0.1.5/IFC/man/readFCS.Rd | 17 IFC-0.1.5/IFC/man/readGatingML.Rd | 2 IFC-0.1.5/IFC/man/remove_ext.Rd | 4 IFC-0.1.5/IFC/man/rev_string.Rd |only IFC-0.1.5/IFC/man/toXML2_boolpop_gs.Rd | 2 IFC-0.1.5/IFC/man/toXML2_graphpop_gs.Rd | 2 IFC-0.1.5/IFC/man/toXML2_graphs_gs.Rd | 2 IFC-0.1.5/IFC/man/toXML2_spillover_gs.Rd | 2 IFC-0.1.5/IFC/man/trunc_string.Rd | 2 IFC-0.1.5/IFC/man/writeGatingStrategy.Rd | 2 IFC-0.1.5/IFC/man/writeIFC.Rd | 5 IFC-0.1.5/IFC/src/RcppExports.cpp | 277 ++++++++ IFC-0.1.5/IFC/src/ifc.cpp | 376 +++++++++++ 129 files changed, 3545 insertions(+), 1341 deletions(-)
Title: General Transit Feed Specification (GTFS) Editing and Analysing
Tools
Description: Utility functions to read, manipulate, analyse and write
transit feeds in the General Transit Feed Specification (GTFS) data
format.
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Pedro R. Andrade [aut] ,
Joao Bazzo [aut] ,
Mark Padgham [ctb],
Marcus Saraiva [ctb] ,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between gtfstools versions 1.0.0 dated 2021-11-16 and 1.1.0 dated 2022-05-24
gtfstools-1.0.0/gtfstools/man/polygon_from_bbox.Rd |only gtfstools-1.1.0/gtfstools/DESCRIPTION | 18 gtfstools-1.1.0/gtfstools/MD5 | 195 ++++---- gtfstools-1.1.0/gtfstools/NAMESPACE | 12 gtfstools-1.1.0/gtfstools/NEWS.md | 29 + gtfstools-1.1.0/gtfstools/R/convert_shapes_to_sf.R | 30 - gtfstools-1.1.0/gtfstools/R/convert_stops_to_sf.R | 6 gtfstools-1.1.0/gtfstools/R/convert_time_to_seconds.R |only gtfstools-1.1.0/gtfstools/R/filter_by_agency_id.R |only gtfstools-1.1.0/gtfstools/R/filter_by_route_id.R | 11 gtfstools-1.1.0/gtfstools/R/filter_by_route_type.R | 7 gtfstools-1.1.0/gtfstools/R/filter_by_service_id.R |only gtfstools-1.1.0/gtfstools/R/filter_by_sf.R | 33 - gtfstools-1.1.0/gtfstools/R/filter_by_shape_id.R | 11 gtfstools-1.1.0/gtfstools/R/filter_by_stop_id.R | 7 gtfstools-1.1.0/gtfstools/R/filter_by_time_of_day.R |only gtfstools-1.1.0/gtfstools/R/filter_by_trip_id.R | 11 gtfstools-1.1.0/gtfstools/R/filter_by_weekday.R |only gtfstools-1.1.0/gtfstools/R/frequencies_to_stop_times.R |only gtfstools-1.1.0/gtfstools/R/get_children_stops.R |only gtfstools-1.1.0/gtfstools/R/get_parent_station.R | 74 +-- gtfstools-1.1.0/gtfstools/R/get_stop_times_patterns.R |only gtfstools-1.1.0/gtfstools/R/get_trip_duration.R | 91 ++- gtfstools-1.1.0/gtfstools/R/get_trip_geometry.R | 85 +-- gtfstools-1.1.0/gtfstools/R/get_trip_length.R |only gtfstools-1.1.0/gtfstools/R/get_trip_segment_duration.R | 116 ++-- gtfstools-1.1.0/gtfstools/R/get_trip_speed.R | 82 +-- gtfstools-1.1.0/gtfstools/R/gtfstools.R | 31 + gtfstools-1.1.0/gtfstools/R/merge_gtfs.R | 164 ++++-- gtfstools-1.1.0/gtfstools/R/read_gtfs.R | 34 - 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Title: User-Friendly Interface for Geographically-Weighted Models
Description: Contains the development of a tool that provides a web-based
graphical user interface (GUI) to perform Techniques from a subset of
spatial statistics known as geographically weighted (GW) models.
Contains methods described by Brunsdon et al., 1996
<doi:10.1111/j.1538-4632.1996.tb00936.x>, Brunsdon et al., 2002
<doi:10.1016/s0198-9715(01)00009-6>, Harris et al., 2011
<doi:10.1080/13658816.2011.554838>, Brunsdon et al., 2007
<doi:10.1111/j.1538-4632.2007.00709.x>.
Author: Javier De La Hoz Maestre [cre, aut]
,
Maria Jose Fernandez Gomez [aut]
,
Susana Mendez [aut]
Maintainer: Javier De La Hoz Maestre <jdelahozmaestre@gmail.com>
Diff between GeoWeightedModel versions 1.0.0 dated 2022-05-11 and 1.0.2 dated 2022-05-24
DESCRIPTION | 6 MD5 | 22 - inst/GeoWeightedModelApp/server.R | 73 ++-- inst/GeoWeightedModelApp/ui.R | 27 - inst/GeoWeightedModelApp/www/Distance_Matrix.html | 261 +++++++++++++- inst/GeoWeightedModelApp/www/Help_Autocorrelation.html | 94 ++--- inst/GeoWeightedModelApp/www/Help_bw.html | 309 +++++++++++++++-- inst/GeoWeightedModelApp/www/Help_gwda.html | 301 ++++++++++++++-- inst/GeoWeightedModelApp/www/Help_gwpca.html | 293 ++++++++++++++-- inst/GeoWeightedModelApp/www/Help_gwss.html | 300 ++++++++++++++-- inst/GeoWeightedModelApp/www/Upload-data.html | 233 ++++++++++++ inst/GeoWeightedModelApp/www/help_gwr.html | 157 +++++--- 12 files changed, 1721 insertions(+), 355 deletions(-)
More information about GeoWeightedModel at CRAN
Permanent link
Title: Compositional, Multivariate and Univariate Time Series Outlier
Ensemble
Description: A compositional, multivariate and univariate time series outlier ensemble.
It uses the four R packages 'forecast', 'tsoutliers', 'otsad' and 'anomalize' to detect time
series outliers (Kandanaarachchi, Menendez 2020) <doi:10.13140/RG.2.2.32217.95845>.
Author: Sevvandi Kandanaarachchi [aut, cre]
,
Patricia Menendez [aut] ,
Ursula Laa [aut] ,
Ruben Loaiza-Maya [aut]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between composits versions 0.1.0 dated 2020-09-30 and 0.1.1 dated 2022-05-24
DESCRIPTION | 16 MD5 | 54 - R/apportion_scores_comp.R | 2 R/apportion_scores_multivariate.R | 2 R/composite_tsout_ensemble.R | 2 R/dimred_methods_tsout_ensemble.R | 2 R/draw_table.R | 8 R/multivariate_tsout_ensemble.R | 3 R/plot_decomposed.R | 13 R/univariate_tsout_ensemble.R | 4 R/utils.R | 1 README.md | 44 - build/vignette.rds |binary inst/doc/composits.R | 44 - inst/doc/composits.Rmd | 12 inst/doc/composits.html | 1548 ++++++++++++++++++++++---------------- man/apportion_scores_comp.Rd | 2 man/apportion_scores_mv.Rd | 2 man/comp_tsout_ens.Rd | 2 man/draw_table.Rd | 6 man/draw_table_html.Rd | 6 man/mv_tsout_ens.Rd | 3 man/plot_biplot.Rd | 3 man/plot_decomposed.Rd | 3 man/plot_decomposed_all.Rd | 3 man/spanish_morte.Rd | 40 man/uv_tsout_ens.Rd | 2 vignettes/composits.Rmd | 12 28 files changed, 1042 insertions(+), 797 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.49-2 dated 2021-01-06 and 0.50-1 dated 2022-05-24
clusterSim-0.49-2/clusterSim/man/plotCategorial3d.rd |only clusterSim-0.50-1/clusterSim/DESCRIPTION | 10 - clusterSim-0.50-1/clusterSim/MD5 | 76 +++++----- clusterSim-0.50-1/clusterSim/NAMESPACE | 1 clusterSim-0.50-1/clusterSim/R/reszta.r | 52 ------ clusterSim-0.50-1/clusterSim/R/shapes.r | 19 -- clusterSim-0.50-1/clusterSim/build/partial.rdb |binary clusterSim-0.50-1/clusterSim/data/data_binary.rda |binary clusterSim-0.50-1/clusterSim/data/data_interval.rda |binary clusterSim-0.50-1/clusterSim/data/data_mixed.rda |binary clusterSim-0.50-1/clusterSim/data/data_nominal.rda |binary clusterSim-0.50-1/clusterSim/data/data_ordinal.rda |binary clusterSim-0.50-1/clusterSim/data/data_ratio.rda |binary clusterSim-0.50-1/clusterSim/inst/pdf/HINoVMod_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/HINoVSymbolic_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/IndexGap_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/clusterGen_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/clusterSim_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/comparingPartitions_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/dataNormalization_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/distBC_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/distGDM_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/distSM_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/distSymbolic_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexC_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexDB_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexG1_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexG2_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexG3_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexH_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexKL_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/indexS_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/ordinalToMetric_details.pdf |only clusterSim-0.50-1/clusterSim/inst/pdf/patternGDM1_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/patternGDM2_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/replicationMod_details.pdf |binary clusterSim-0.50-1/clusterSim/inst/pdf/speccl_details.pdf |binary clusterSim-0.50-1/clusterSim/man/plotCategorial.rd | 2 clusterSim-0.50-1/clusterSim/man/plotInterval.rd | 2 clusterSim-0.50-1/clusterSim/man/shapes.blocks3d.rd | 4 40 files changed, 49 insertions(+), 117 deletions(-)
Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and
'geospatial' data from the British Columbia Data Catalogue
(<https://catalogue.data.gov.bc.ca/>). Search catalogue data records
based on keywords, data licence, sector, data format, and B.C.
government organization. View metadata directly in R, download many
data formats, and query 'geospatial' data available via the B.C.
government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] ,
Sam Albers [aut, ctb] ,
Stephanie Hazlitt [aut, ctb] ,
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>
Diff between bcdata versions 0.3.0 dated 2021-10-28 and 0.3.1 dated 2022-05-24
bcdata-0.3.0/bcdata/man/make_url.Rd |only bcdata-0.3.1/bcdata/DESCRIPTION | 12 bcdata-0.3.1/bcdata/MD5 | 40 +- bcdata-0.3.1/bcdata/NAMESPACE | 5 bcdata-0.3.1/bcdata/NEWS.md | 7 bcdata-0.3.1/bcdata/R/bcdc-get-citation.R |only bcdata-0.3.1/bcdata/R/bcdc-web-services.R | 6 bcdata-0.3.1/bcdata/R/bcdc_browse.R | 1 bcdata-0.3.1/bcdata/R/cql-translator.R | 6 bcdata-0.3.1/bcdata/R/get_data.R | 5 bcdata-0.3.1/bcdata/R/utils-classes.R | 17 - bcdata-0.3.1/bcdata/R/utils.R | 1 bcdata-0.3.1/bcdata/build/vignette.rds |binary bcdata-0.3.1/bcdata/inst/doc/bcdata.html | 97 ++++- bcdata-0.3.1/bcdata/inst/doc/efficiently-query-spatial-data-in-the-bc-data-catalogue.html | 162 ++++++++-- bcdata-0.3.1/bcdata/inst/doc/explore-silviculture-data-using-bcdata.html | 108 +++++- bcdata-0.3.1/bcdata/inst/doc/service_documentation.html | 23 + bcdata-0.3.1/bcdata/man/bcdata-package.Rd | 4 bcdata-0.3.1/bcdata/man/bcdc_get_citation.Rd |only bcdata-0.3.1/bcdata/tests/testthat/test-bcdc-get-citation.R |only bcdata-0.3.1/bcdata/tests/testthat/test-edge-cases.R | 5 bcdata-0.3.1/bcdata/tests/testthat/test-get-data.R | 10 bcdata-0.3.1/bcdata/tests/testthat/test-search.R | 13 23 files changed, 408 insertions(+), 114 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] ,
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut],
Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.1.2 dated 2022-04-11 and 1.2.0 dated 2022-05-24
BayesMallows-1.1.2/BayesMallows/R/lik_db_mix.R |only BayesMallows-1.1.2/BayesMallows/R/misc_likelihood.R |only BayesMallows-1.1.2/BayesMallows/inst/examples/lik_db_mix_example.R |only BayesMallows-1.1.2/BayesMallows/man/lik_db_mix.Rd |only BayesMallows-1.1.2/BayesMallows/man/metropolis_hastings_aug_ranking_pseudo.Rd |only BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_item_rank_alpha_fixed.Rd |only BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_users_complete.Rd |only BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_users_partial.Rd |only BayesMallows-1.1.2/BayesMallows/man/smc_mallows_new_users_partial_alpha_fixed.Rd |only BayesMallows-1.1.2/BayesMallows/src/smc_calculate_backward_probability.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_calculate_forward_probability.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_get_mallows_loglik.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_item_rank_alpha_fixed.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_users_complete.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_users_partial.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_mallows_new_users_partial_alpha_fixed.cpp |only BayesMallows-1.1.2/BayesMallows/src/smc_metropolis_hastings_aug_ranking_pseudo.cpp |only BayesMallows-1.1.2/BayesMallows/tests/testthat/test-lik_db_mix.R |only BayesMallows-1.1.2/BayesMallows/tests/testthat/test-misc_cpp.R |only BayesMallows-1.2.0/BayesMallows/DESCRIPTION | 20 BayesMallows-1.2.0/BayesMallows/MD5 | 284 +++---- BayesMallows-1.2.0/BayesMallows/NAMESPACE | 5 BayesMallows-1.2.0/BayesMallows/NEWS.md | 25 BayesMallows-1.2.0/BayesMallows/R/RcppExports.R | 173 ---- BayesMallows-1.2.0/BayesMallows/R/all_topological_sorts.R | 11 BayesMallows-1.2.0/BayesMallows/R/assess_convergence.R | 61 - 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BayesMallows-1.2.0/BayesMallows/src/distances.h | 3 BayesMallows-1.2.0/BayesMallows/src/importance_sampling.cpp | 42 - BayesMallows-1.2.0/BayesMallows/src/leapandshift.cpp | 60 - BayesMallows-1.2.0/BayesMallows/src/leapandshift.h | 4 BayesMallows-1.2.0/BayesMallows/src/misc.cpp | 154 ---- BayesMallows-1.2.0/BayesMallows/src/misc.h | 13 BayesMallows-1.2.0/BayesMallows/src/missing_data.cpp | 45 - BayesMallows-1.2.0/BayesMallows/src/missing_data.h | 3 BayesMallows-1.2.0/BayesMallows/src/mixtures.cpp | 64 - BayesMallows-1.2.0/BayesMallows/src/mixtures.h | 1 BayesMallows-1.2.0/BayesMallows/src/pairwise_comparisons.cpp | 89 +- BayesMallows-1.2.0/BayesMallows/src/pairwise_comparisons.h | 4 BayesMallows-1.2.0/BayesMallows/src/parameterupdates.cpp | 48 - BayesMallows-1.2.0/BayesMallows/src/parameterupdates.h | 7 BayesMallows-1.2.0/BayesMallows/src/partitionfuns.cpp | 73 - BayesMallows-1.2.0/BayesMallows/src/partitionfuns.h | 4 BayesMallows-1.2.0/BayesMallows/src/rmallows.cpp | 16 BayesMallows-1.2.0/BayesMallows/src/run_mcmc.cpp | 68 - BayesMallows-1.2.0/BayesMallows/src/sample.cpp |only BayesMallows-1.2.0/BayesMallows/src/sample.h |only BayesMallows-1.2.0/BayesMallows/src/setdiff.h |only BayesMallows-1.2.0/BayesMallows/src/smc.h | 8 BayesMallows-1.2.0/BayesMallows/src/smc_calculate_probability.cpp |only BayesMallows-1.2.0/BayesMallows/src/smc_correction_kernel.cpp | 9 BayesMallows-1.2.0/BayesMallows/src/smc_correction_kernel_pseudo.cpp | 43 - BayesMallows-1.2.0/BayesMallows/src/smc_get_exponent_sum.cpp |only BayesMallows-1.2.0/BayesMallows/src/smc_get_sample_probabilities.cpp | 17 BayesMallows-1.2.0/BayesMallows/src/smc_leap_and_shift_probs.cpp | 80 -- BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_item_rank.cpp | 283 +++---- BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_users.cpp |only BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_users.h |only BayesMallows-1.2.0/BayesMallows/src/smc_mallows_new_users_funs.cpp |only BayesMallows-1.2.0/BayesMallows/src/smc_metropolis_hastings_alpha.cpp | 12 BayesMallows-1.2.0/BayesMallows/src/smc_metropolis_hastings_aug_ranking.cpp | 102 +- BayesMallows-1.2.0/BayesMallows/src/smc_metropolis_hastings_rho.cpp | 30 BayesMallows-1.2.0/BayesMallows/src/subset.cpp | 6 BayesMallows-1.2.0/BayesMallows/src/subset.h | 8 BayesMallows-1.2.0/BayesMallows/src/test-leapandshift.cpp |only BayesMallows-1.2.0/BayesMallows/src/test-runner.cpp |only BayesMallows-1.2.0/BayesMallows/tests/testthat/test-assess_convergence.R | 39 - BayesMallows-1.2.0/BayesMallows/tests/testthat/test-assign_cluster.R | 72 - BayesMallows-1.2.0/BayesMallows/tests/testthat/test-classes_compute_consensus_posterior.R | 28 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_consensus.R | 253 ++++-- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_mallows.R | 223 +++-- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_mallows_mixtures.R | 119 +-- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-compute_posterior_intervals.R | 86 +- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-cpp.R |only BayesMallows-1.2.0/BayesMallows/tests/testthat/test-distance_function.R | 55 - BayesMallows-1.2.0/BayesMallows/tests/testthat/test-estimate_partition_function.R | 44 - BayesMallows-1.2.0/BayesMallows/tests/testthat/test-expected_dist.R | 23 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-generate_ranking.R | 63 - BayesMallows-1.2.0/BayesMallows/tests/testthat/test-generate_transitive_closure.R |only BayesMallows-1.2.0/BayesMallows/tests/testthat/test-get_mallows_loglik.R |only BayesMallows-1.2.0/BayesMallows/tests/testthat/test-mcmc_function.R | 23 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-misc_functions.R | 12 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-partition_function.R | 122 +-- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-plot_elbow.R | 12 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-plot_top_k.R | 73 + BayesMallows-1.2.0/BayesMallows/tests/testthat/test-print.R | 18 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-random_number_seed.R | 58 - BayesMallows-1.2.0/BayesMallows/tests/testthat/test-rank_freq_distr.R | 96 +- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-sample_mallows.R | 34 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_compute_rho_consensus.R | 8 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_individual_functions.R | 77 +- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_mallows_complete_rankings.R | 376 +++++----- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_mallows_new_item_rank.R | 71 + BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_mallows_partial_rankings.R | 151 +++- BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_pseudolikelihood.R | 15 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-smc_uniform.R | 18 BayesMallows-1.2.0/BayesMallows/tests/testthat/test-transitive_closure.R | 60 - BayesMallows-1.2.0/BayesMallows/vignettes/SMC-Mallows.Rmd | 72 + 162 files changed, 3190 insertions(+), 3265 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and
batch effect correction operations for 'NanoString nCounter' data,
Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various
metrics are used to determine which samples passed or failed QC. Gene
expression should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.2.0 dated 2021-02-06 and 0.3.0 dated 2022-05-24
DESCRIPTION | 8 LICENSE | 4 MD5 | 63 +- NAMESPACE | 42 - NEWS.md | 100 +-- R/CCplot.R | 218 +++---- R/HKnorm.R | 66 +- R/NanoStringQC.R | 146 ++-- R/check.R | 90 +- R/data.R | 116 +-- R/nanostringr-package.R | 8 R/read_rcc.R | 194 +++--- R/refMethod.R | 54 - R/utils.R | 4 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 38 - inst/doc/Overview.R | 298 ++++----- inst/doc/Overview.Rmd | 688 +++++++++++----------- inst/doc/Overview.html | 1131 ++++++++++++++++++++++--------------- man/CCplot.Rd | 170 ++--- man/cohort.Rd | 136 ++-- man/expQC.Rd | 36 - man/nanostringr-package.Rd | 68 -- man/rcc.Rd | 124 ++-- tests/testthat.R | 8 tests/testthat/test-CCplot.R | 48 - tests/testthat/test-HKnorm.R | 20 tests/testthat/test-NanoStringQC.R | 88 +- tests/testthat/test-order.R | 28 tests/testthat/test-parse.R | 50 - tests/testthat/test-ratioMethod.R | 50 - vignettes/Overview.Rmd | 688 +++++++++++----------- 33 files changed, 2507 insertions(+), 2275 deletions(-)
Title: Tree Branches Evaluated Statistically for Tightness
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun <guolisun87@gmail.com>
Diff between TBEST versions 5.0 dated 2014-12-29 and 5.2 dated 2022-05-24
DESCRIPTION | 10 +-- MD5 | 6 +- NAMESPACE | 10 ++- R/LeafContent.R | 148 ++++++++++++++++++++++++++++---------------------------- 4 files changed, 89 insertions(+), 85 deletions(-)
Title: Analyze High-Dimensional High-Throughput Dataset and Quality
Control Single-Cell RNA-Seq
Description: The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.
Author: Yajing Hao [aut] ,
Shuyang Zhang [ctb] ,
Junhui Li [cre],
Guofeng Zhao [ctb],
Xiang-Dong Fu [cph, fnd]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between ZetaSuite versions 1.0.0 dated 2022-03-31 and 1.0.1 dated 2022-05-24
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NAMESPACE | 1 R/FDRcutoff.R | 14 ++++---- R/QC.R | 2 - inst/doc/ZetaSuite.html | 82 ++++++++++++++---------------------------------- 6 files changed, 43 insertions(+), 76 deletions(-)
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy.ccnr@gmail.com>
Diff between wTO versions 2.0 dated 2022-05-10 and 2.0.1 dated 2022-05-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Cut.off2.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of regular vine copula
models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and
Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Thomas Nagler [aut, cre],
Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthia [...truncated...]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between VineCopula versions 2.4.3 dated 2021-10-07 and 2.4.4 dated 2022-05-24
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NAMESPACE | 1 NEWS.md | 80 +++++++++++++++++++++++++++++++----------------------- R/BiCopLambda.R | 10 +++--- R/BiCopPar2Tau.R | 2 - R/RVineMLE.R | 14 +++++---- R/RVineMatrix.R | 4 -- R/preprocessors.R | 2 - README.md | 2 - build/partial.rdb |binary 11 files changed, 79 insertions(+), 64 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.7.1 dated 2022-03-25 and 1.7.2 dated 2022-05-24
TreeTools-1.7.1/TreeTools/build/TreeTools.pdf |only TreeTools-1.7.2/TreeTools/DESCRIPTION | 13 TreeTools-1.7.2/TreeTools/MD5 | 80 +- TreeTools-1.7.2/TreeTools/NAMESPACE | 7 TreeTools-1.7.2/TreeTools/NEWS.md | 10 TreeTools-1.7.2/TreeTools/R/ClusterTable.R |only TreeTools-1.7.2/TreeTools/R/RcppExports.R | 12 TreeTools-1.7.2/TreeTools/R/tree_display.R | 9 TreeTools-1.7.2/TreeTools/R/tree_numbering.R | 73 +- TreeTools-1.7.2/TreeTools/R/tree_properties.R | 5 TreeTools-1.7.2/TreeTools/R/tree_rearrangement.R | 2 TreeTools-1.7.2/TreeTools/build/partial.rdb |binary TreeTools-1.7.2/TreeTools/build/vignette.rds |binary TreeTools-1.7.2/TreeTools/inst/doc/filesystem-navigation.html | 219 +++++++ TreeTools-1.7.2/TreeTools/inst/doc/load-data.html | 286 +++++++++- TreeTools-1.7.2/TreeTools/inst/doc/load-trees.html | 275 ++++++++- TreeTools-1.7.2/TreeTools/inst/include/TreeTools/ClusterTable.h | 36 - TreeTools-1.7.2/TreeTools/inst/include/TreeTools/SplitList.h | 6 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/keep_tip.h | 2 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/renumber_tree.h | 12 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/root_tree.h | 8 TreeTools-1.7.2/TreeTools/inst/include/TreeTools/types.h | 10 TreeTools-1.7.2/TreeTools/man/ClusterTable-methods.Rd |only TreeTools-1.7.2/TreeTools/man/ClusterTable.Rd |only TreeTools-1.7.2/TreeTools/man/ConstrainedNJ.Rd | 5 TreeTools-1.7.2/TreeTools/man/RenumberTips.Rd | 2 TreeTools-1.7.2/TreeTools/man/Reorder.Rd | 15 TreeTools-1.7.2/TreeTools/man/SortTree.Rd | 3 TreeTools-1.7.2/TreeTools/man/SplitInformation.Rd | 4 TreeTools-1.7.2/TreeTools/man/TreeNumber.Rd | 18 TreeTools-1.7.2/TreeTools/src/ClusterTable.cpp |only TreeTools-1.7.2/TreeTools/src/RcppExports-manual.cpp | 1 TreeTools-1.7.2/TreeTools/src/RcppExports.cpp | 33 + TreeTools-1.7.2/TreeTools/src/TreeTools-init.c | 6 TreeTools-1.7.2/TreeTools/src/as_newick.cpp | 2 TreeTools-1.7.2/TreeTools/src/consensus.cpp | 5 TreeTools-1.7.2/TreeTools/src/int_to_tree.cpp | 12 TreeTools-1.7.2/TreeTools/src/splits.cpp | 16 TreeTools-1.7.2/TreeTools/src/tips_in_splits.cpp | 8 TreeTools-1.7.2/TreeTools/src/tree_shape.cpp | 14 TreeTools-1.7.2/TreeTools/tests/testthat/test-ClusterTable.R |only TreeTools-1.7.2/TreeTools/tests/testthat/test-root_tree.h.R | 6 TreeTools-1.7.2/TreeTools/tests/testthat/test-tree_numbering.R | 60 +- TreeTools-1.7.2/TreeTools/tests/testthat/test-tree_properties.R | 3 44 files changed, 1042 insertions(+), 236 deletions(-)
Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of
the server side file system in shiny apps. In case the app is running
locally this gives the user direct access to the file system without the
need to "download" files to a temporary location. Both file and folder
selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut]
,
Vincent Nijs [aut],
Thomas Schaffner [aut],
Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between shinyFiles versions 0.9.1 dated 2021-11-10 and 0.9.2 dated 2022-05-24
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 6 R/aaa.R | 25 + R/dirchoose.R | 694 +++++++++++++++++++++++----------------------- R/filechoose.R | 16 - R/filesave.R | 66 +--- inst/example/ui.R | 8 inst/www/shinyFiles.js | 3 inst/www/styles.css | 2 man/shinyFiles-buttons.Rd | 16 - 11 files changed, 449 insertions(+), 415 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>
Diff between Rdsdp versions 1.0.5.1 dated 2021-11-02 and 1.0.5.2 dated 2022-05-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/dsdp/src/solver/dsdprescone.c | 2 +- src/dsdp/src/solver/dsdpvec.h | 6 +++--- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: XPtr Add-Ons for 'Rcpp'
Description: Provides the means to compile user-supplied C++ functions with
'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between RcppXPtrUtils versions 0.1.1 dated 2019-01-21 and 0.1.2 dated 2022-05-24
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/check.R | 2 +- README.md | 27 +++++++++++++-------------- man/checkXPtr.Rd | 2 +- man/cppXPtr.Rd | 12 +++++++++--- 8 files changed, 41 insertions(+), 32 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.17.0 dated 2022-03-10 and 0.18.0 dated 2022-05-24
parameters-0.17.0/parameters/R/select_parameters.stanreg.R |only parameters-0.17.0/parameters/man/dot-factor_to_numeric.Rd |only parameters-0.18.0/parameters/DESCRIPTION | 31 parameters-0.18.0/parameters/MD5 | 348 +++++----- parameters-0.18.0/parameters/NAMESPACE | 45 - parameters-0.18.0/parameters/NEWS.md | 202 +---- parameters-0.18.0/parameters/R/1_model_parameters.R | 73 +- parameters-0.18.0/parameters/R/2_ci.R | 23 parameters-0.18.0/parameters/R/3_p_value.R | 31 parameters-0.18.0/parameters/R/4_standard_error.R | 142 ---- parameters-0.18.0/parameters/R/5_simulate_model.R | 48 + parameters-0.18.0/parameters/R/bootstrap_parameters.R | 6 parameters-0.18.0/parameters/R/check_factorstructure.R | 6 parameters-0.18.0/parameters/R/check_heterogeneity.R | 12 parameters-0.18.0/parameters/R/ci_generic.R | 20 parameters-0.18.0/parameters/R/ci_profile_boot.R | 2 parameters-0.18.0/parameters/R/cluster_analysis.R | 22 parameters-0.18.0/parameters/R/cluster_meta.R | 2 parameters-0.18.0/parameters/R/compare_parameters.R | 35 - parameters-0.18.0/parameters/R/convert_efa_to_cfa.R | 2 parameters-0.18.0/parameters/R/display.R | 5 parameters-0.18.0/parameters/R/dof_betwithin.R | 2 parameters-0.18.0/parameters/R/dof_ml1.R | 2 parameters-0.18.0/parameters/R/equivalence_test.R | 6 parameters-0.18.0/parameters/R/extract_parameters.R | 99 +- parameters-0.18.0/parameters/R/extract_parameters_anova.R | 13 parameters-0.18.0/parameters/R/extract_random_variances.R | 189 +++++ parameters-0.18.0/parameters/R/factor_analysis.R | 6 parameters-0.18.0/parameters/R/format.R | 105 --- parameters-0.18.0/parameters/R/format_order.R | 2 parameters-0.18.0/parameters/R/format_p_adjust.R | 10 parameters-0.18.0/parameters/R/format_parameters.R | 2 parameters-0.18.0/parameters/R/methods_BayesFM.R | 6 parameters-0.18.0/parameters/R/methods_BayesFactor.R | 9 parameters-0.18.0/parameters/R/methods_DirichletReg.R | 5 parameters-0.18.0/parameters/R/methods_MCMCglmm.R | 2 parameters-0.18.0/parameters/R/methods_aov.R | 10 parameters-0.18.0/parameters/R/methods_averaging.R | 5 parameters-0.18.0/parameters/R/methods_bamlss.R | 2 parameters-0.18.0/parameters/R/methods_base.R | 56 - parameters-0.18.0/parameters/R/methods_bayesQR.R | 2 parameters-0.18.0/parameters/R/methods_betareg.R | 56 + parameters-0.18.0/parameters/R/methods_bfsl.R | 1 parameters-0.18.0/parameters/R/methods_brglm2.R | 50 + parameters-0.18.0/parameters/R/methods_brms.R | 6 parameters-0.18.0/parameters/R/methods_car.R |only parameters-0.18.0/parameters/R/methods_cgam.R | 8 parameters-0.18.0/parameters/R/methods_cplm.R | 4 parameters-0.18.0/parameters/R/methods_effect_size.R | 6 parameters-0.18.0/parameters/R/methods_emmeans.R | 2 parameters-0.18.0/parameters/R/methods_gam.R | 6 parameters-0.18.0/parameters/R/methods_ggeffects.R | 2 parameters-0.18.0/parameters/R/methods_glm.R | 1 parameters-0.18.0/parameters/R/methods_glmmTMB.R | 71 +- parameters-0.18.0/parameters/R/methods_glmx.R | 2 parameters-0.18.0/parameters/R/methods_htest.R | 36 + parameters-0.18.0/parameters/R/methods_lavaan.R | 4 parameters-0.18.0/parameters/R/methods_lme4.R | 47 - parameters-0.18.0/parameters/R/methods_marginaleffects.R |only parameters-0.18.0/parameters/R/methods_mediate.R | 2 parameters-0.18.0/parameters/R/methods_metafor.R | 4 parameters-0.18.0/parameters/R/methods_metaplus.R | 18 parameters-0.18.0/parameters/R/methods_mfx.R | 12 parameters-0.18.0/parameters/R/methods_mhurdle.R | 2 parameters-0.18.0/parameters/R/methods_mixmod.R | 9 parameters-0.18.0/parameters/R/methods_mixor.R | 3 parameters-0.18.0/parameters/R/methods_mlm.R | 119 ++- parameters-0.18.0/parameters/R/methods_multcomp.R | 4 parameters-0.18.0/parameters/R/methods_mvord.R | 6 parameters-0.18.0/parameters/R/methods_nlme.R | 40 - parameters-0.18.0/parameters/R/methods_ordinal.R | 7 parameters-0.18.0/parameters/R/methods_posterior.R |only parameters-0.18.0/parameters/R/methods_pscl.R | 32 parameters-0.18.0/parameters/R/methods_psych.R | 6 parameters-0.18.0/parameters/R/methods_rstan.R | 2 parameters-0.18.0/parameters/R/methods_rstanarm.R | 15 parameters-0.18.0/parameters/R/methods_selection.R | 2 parameters-0.18.0/parameters/R/methods_survey.R | 2 parameters-0.18.0/parameters/R/methods_survival.R | 2 parameters-0.18.0/parameters/R/methods_varest.R | 2 parameters-0.18.0/parameters/R/methods_wrs2.R | 6 parameters-0.18.0/parameters/R/n_clusters.R | 43 - parameters-0.18.0/parameters/R/n_clusters_easystats.R | 2 parameters-0.18.0/parameters/R/n_factors.R | 2 parameters-0.18.0/parameters/R/p_value_kenward.R | 10 parameters-0.18.0/parameters/R/parameters_type.R | 2 parameters-0.18.0/parameters/R/pool_parameters.R | 16 parameters-0.18.0/parameters/R/principal_components.R | 13 parameters-0.18.0/parameters/R/random_parameters.R | 10 parameters-0.18.0/parameters/R/reduce_parameters.R | 22 parameters-0.18.0/parameters/R/reexports.R | 23 parameters-0.18.0/parameters/R/reshape_loadings.R | 15 parameters-0.18.0/parameters/R/robust_estimation.R | 14 parameters-0.18.0/parameters/R/select_parameters.R | 26 parameters-0.18.0/parameters/R/simulate_parameters.R | 13 parameters-0.18.0/parameters/R/sort_parameters.R |only parameters-0.18.0/parameters/R/standardize_info.R |only parameters-0.18.0/parameters/R/standardize_parameters.R |only parameters-0.18.0/parameters/R/standardize_posteriors.R |only parameters-0.18.0/parameters/R/utils.R | 46 - parameters-0.18.0/parameters/R/utils_cleaners.R | 12 parameters-0.18.0/parameters/R/utils_clustering.R | 46 - parameters-0.18.0/parameters/R/utils_format.R | 53 - parameters-0.18.0/parameters/R/utils_model_parameters.R | 101 +- parameters-0.18.0/parameters/README.md | 64 - parameters-0.18.0/parameters/build/partial.rdb |binary parameters-0.18.0/parameters/build/vignette.rds |binary parameters-0.18.0/parameters/inst/WORDLIST | 5 parameters-0.18.0/parameters/man/bootstrap_parameters.Rd | 9 parameters-0.18.0/parameters/man/check_kmo.Rd | 2 parameters-0.18.0/parameters/man/check_sphericity_bartlett.Rd | 4 parameters-0.18.0/parameters/man/ci.default.Rd | 4 parameters-0.18.0/parameters/man/ci_robust.Rd | 8 parameters-0.18.0/parameters/man/cluster_analysis.Rd | 6 parameters-0.18.0/parameters/man/cluster_meta.Rd | 2 parameters-0.18.0/parameters/man/compare_parameters.Rd | 8 parameters-0.18.0/parameters/man/equivalence_test.lm.Rd | 2 parameters-0.18.0/parameters/man/format_order.Rd | 2 parameters-0.18.0/parameters/man/model_parameters.BFBayesFactor.Rd | 11 parameters-0.18.0/parameters/man/model_parameters.Rd | 30 parameters-0.18.0/parameters/man/model_parameters.averaging.Rd | 12 parameters-0.18.0/parameters/man/model_parameters.befa.Rd | 11 parameters-0.18.0/parameters/man/model_parameters.cgam.Rd | 6 parameters-0.18.0/parameters/man/model_parameters.default.Rd | 31 parameters-0.18.0/parameters/man/model_parameters.glht.Rd | 4 parameters-0.18.0/parameters/man/model_parameters.lavaan.Rd | 2 parameters-0.18.0/parameters/man/model_parameters.merMod.Rd | 50 - parameters-0.18.0/parameters/man/model_parameters.mira.Rd | 2 parameters-0.18.0/parameters/man/model_parameters.mlm.Rd | 35 - parameters-0.18.0/parameters/man/model_parameters.principal.Rd | 6 parameters-0.18.0/parameters/man/model_parameters.rma.Rd | 4 parameters-0.18.0/parameters/man/model_parameters.stanreg.Rd | 103 +- parameters-0.18.0/parameters/man/model_parameters.zcpglm.Rd | 16 parameters-0.18.0/parameters/man/n_clusters.Rd | 4 parameters-0.18.0/parameters/man/n_factors.Rd | 2 parameters-0.18.0/parameters/man/p_value.DirichletRegModel.Rd | 9 parameters-0.18.0/parameters/man/p_value.Rd | 189 +++++ parameters-0.18.0/parameters/man/p_value.poissonmfx.Rd | 2 parameters-0.18.0/parameters/man/p_value.zcpglm.Rd | 15 parameters-0.18.0/parameters/man/p_value_robust.Rd | 23 parameters-0.18.0/parameters/man/pool_parameters.Rd | 6 parameters-0.18.0/parameters/man/principal_components.Rd | 13 parameters-0.18.0/parameters/man/print.parameters_model.Rd | 2 parameters-0.18.0/parameters/man/random_parameters.Rd | 8 parameters-0.18.0/parameters/man/reduce_parameters.Rd | 18 parameters-0.18.0/parameters/man/reexports.Rd | 10 parameters-0.18.0/parameters/man/reshape_loadings.Rd | 13 parameters-0.18.0/parameters/man/select_parameters.Rd | 37 - parameters-0.18.0/parameters/man/simulate_model.Rd | 13 parameters-0.18.0/parameters/man/simulate_parameters.Rd | 18 parameters-0.18.0/parameters/man/sort_parameters.Rd |only parameters-0.18.0/parameters/man/standard_error.Rd | 108 --- parameters-0.18.0/parameters/man/standard_error_robust.Rd | 12 parameters-0.18.0/parameters/man/standardize_info.Rd |only parameters-0.18.0/parameters/man/standardize_parameters.Rd |only parameters-0.18.0/parameters/tests/testthat/test-base.R |only parameters-0.18.0/parameters/tests/testthat/test-betareg.R | 7 parameters-0.18.0/parameters/tests/testthat/test-bracl.R | 6 parameters-0.18.0/parameters/tests/testthat/test-car.R |only parameters-0.18.0/parameters/tests/testthat/test-ci.R | 1 parameters-0.18.0/parameters/tests/testthat/test-cluster_analysis.R |only parameters-0.18.0/parameters/tests/testthat/test-format_parameters.R | 11 parameters-0.18.0/parameters/tests/testthat/test-gamm.R | 3 parameters-0.18.0/parameters/tests/testthat/test-glmer.R | 38 + parameters-0.18.0/parameters/tests/testthat/test-glmmTMB.R | 53 + parameters-0.18.0/parameters/tests/testthat/test-lme.R | 190 +++-- parameters-0.18.0/parameters/tests/testthat/test-marginaleffects.R |only parameters-0.18.0/parameters/tests/testthat/test-mlm.R | 36 + parameters-0.18.0/parameters/tests/testthat/test-model_parameters.anova.R | 26 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.blmerMod.R | 2 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.fixest.R | 39 - parameters-0.18.0/parameters/tests/testthat/test-model_parameters.htest.R | 2 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.metaBMA.R | 9 parameters-0.18.0/parameters/tests/testthat/test-model_parameters.mixed.R | 15 parameters-0.18.0/parameters/tests/testthat/test-model_parameters_random_pars.R |only parameters-0.18.0/parameters/tests/testthat/test-model_parameters_robust.R | 5 parameters-0.18.0/parameters/tests/testthat/test-model_parameters_std_mixed.R | 16 parameters-0.18.0/parameters/tests/testthat/test-p_value.R | 14 parameters-0.18.0/parameters/tests/testthat/test-panelr.R | 7 parameters-0.18.0/parameters/tests/testthat/test-posterior.R |only parameters-0.18.0/parameters/tests/testthat/test-robust.R | 18 parameters-0.18.0/parameters/tests/testthat/test-sort_parameters.R |only parameters-0.18.0/parameters/tests/testthat/test-standardize_info.R |only parameters-0.18.0/parameters/tests/testthat/test-standardize_parameters.R |only parameters-0.18.0/parameters/tests/testthat/test-svytable.R |only parameters-0.18.0/parameters/tests/testthat/test-zeroinfl.R | 3 186 files changed, 2308 insertions(+), 1788 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 2.0.1 dated 2022-05-14 and 2.0.2 dated 2022-05-24
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NEWS | 3 ++ R/cert.R | 4 ++- inst/doc/bignum.html | 32 ++++++++++++++-------------- inst/doc/crypto_hashing.html | 4 +-- inst/doc/keys.html | 48 +++++++++++++++++++++---------------------- inst/doc/secure_rng.html | 18 ++++++++-------- man/certificates.Rd | 2 + tests/testthat/test_google.R | 3 ++ 10 files changed, 74 insertions(+), 64 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.1.5 dated 2022-02-19 and 1.2.1 dated 2022-05-24
DESCRIPTION | 6 MD5 | 42 +- NAMESPACE | 2 NEWS | 11 R/dexter.R | 408 ++++++++++++++++------ R/enorm.R | 2 R/individual_differences.R | 2 R/plots.R | 76 +++- R/predicates.R | 21 - R/reparam.R | 3 R/resp_data.R | 44 -- build/vignette.rds |binary inst/doc/DIF_vignette.html | 262 +++++++++++++- inst/doc/Equating.html | 433 ++++++++++++++++++++--- inst/doc/Plausible_Values.html | 325 ++++++++++++++++- inst/doc/Test_Individual_differences.html | 277 +++++++++++++-- inst/doc/dexter.html | 550 +++++++++++++++++++++++++----- inst/doc/profile-plots.html | 322 +++++++++++++++-- man/add_booklet.Rd | 30 - man/coef.prms.Rd | 2 man/profile_plot.Rd | 3 tests/testthat/test_data_selection.R | 4 22 files changed, 2383 insertions(+), 442 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut, cre],
Martijn Schuemie [aut],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Adam Black <black@ohdsi.org>
Diff between Andromeda versions 0.6.0 dated 2022-01-25 and 0.6.1 dated 2022-05-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/Operations.R | 6 +++--- build/vignette.rds |binary inst/doc/UsingAndromeda.pdf |binary man/Andromeda-package.Rd | 1 - 7 files changed, 19 insertions(+), 14 deletions(-)
Title: Simulate the Extent of Host Switching by Consumers
Description: Using a simulation-based approach, the 'HostSwitch' package provides functions to investigate host switches by consumers.
The individual-based model is based on the concept of ecological fitting.
The mockup model is published by Araujo et al. 2015. Understanding Host-Switching by Ecological Fitting (<doi:10.1371/journal.pone.0139225>).
The package provides an R-friendly and modified version of this model which can be applied to different consumer-resource scenarios.
Author: Valeria Trivellone [aut],
Sabrina B.L. Araujo [aut],
Bernd Panassiti [cre, aut]
Maintainer: Bernd Panassiti <bernd.panassiti@gmail.com>
Diff between HostSwitch versions 0.1.0 dated 2021-09-27 and 0.1.1 dated 2022-05-24
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/HostSwitch.R | 16 ++++++++-------- build/vignette.rds |binary inst/doc/HostSwitch.html | 14 +++++++------- man/simHostSwitch.Rd | 16 ++++++++-------- 7 files changed, 41 insertions(+), 34 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression using the Gaussian elimination secondary suppression algorithm. Primary suppression functions for the minimum frequency rule, the dominance rule and a directly-disclosive rule are included. General primary suppression functions can be supplied as input. Suppressed frequencies can be replaced by synthetic decimal numbers as described in Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oyvind Langsrud [aut, cre],
Daniel Lupp [aut],
Hege Boevelstad [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.2.0 dated 2022-04-05 and 0.3.0 dated 2022-05-24
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/GaussSuppressDec.R | 29 +++++++++++++++++++++++------ R/GaussSuppressionFromData.R | 4 ++++ R/SuppressDec.R | 4 +++- tests/testthat/test-GaussSuppressDec.R |only 6 files changed, 39 insertions(+), 15 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Wrangle Campaign Finance Data
Description: Explore and normalize American campaign finance
data. Created by the Investigative Reporting Workshop to facilitate
work on The Accountability Project, an effort to collect public data
into a central, standard database that is more easily searched:
<https://publicaccountability.org/>.
Author: Kiernan Nicholls [aut, cre, cph],
Investigative Reporting Workshop [cph],
Yanqi Xu [aut],
Schuyler Erle [cph]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between campfin versions 1.0.8 dated 2021-09-02 and 1.0.9 dated 2022-05-24
DESCRIPTION | 8 MD5 | 42 ++- NAMESPACE | 2 NEWS.md | 9 R/col-stats.R | 4 R/file-age.R |only R/guess-delims.R | 4 R/normal-address.R | 29 +- R/normal-state.R | 15 - R/str-normal.R | 12 - R/use-diary.R | 7 README.md | 69 ++---- build/vignette.rds |binary inst/doc/normalize-geography.html | 400 +++++++++++++++++++++++++++++++------ inst/templates/template_diary.Rmd | 221 +++++++++++--------- man/file_age.Rd |only man/guess_delim.Rd | 4 man/normal_address.Rd | 18 + man/str_normal.Rd | 7 man/use_diary.Rd | 5 tests/testthat/test-check-city.R | 2 tests/testthat/test-diary.R | 2 tests/testthat/test-normal-state.R | 6 23 files changed, 592 insertions(+), 274 deletions(-)
Title: Partially Ordered Sets in R
Description: Provides a set of basic tools for generating, analyzing, summarizing and visualizing finite partially ordered sets. In particular, it implements flexible and very efficient algorithms for the extraction of linear extensions and for the computation of mutual ranking probabilities and other user-defined functionals, over them. The package is meant as a computationally efficient "engine", for the implementation of data analysis procedures, on systems of multidimensional ordinal indicators and partially ordered data, in the spirit of Fattore, M. (2016) "Partially ordered sets and the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-015-1059-6>, and Fattore M. and Arcagni, A. (2018) "A reduced posetic approach to the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-016-1501-4>.
Author: Alberto Arcagni [aut, cre],
Alessandro Avellone [aut],
Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>
Diff between POSetR versions 1.0.4 dated 2021-11-24 and 1.1.0 dated 2022-05-24
POSetR-1.0.4/POSetR/R/plot.Rcpp_POSet.R |only POSetR-1.0.4/POSetR/R/print.Rcpp_POSet.R |only POSetR-1.0.4/POSetR/R/summary.Rcpp_POSet.R |only POSetR-1.0.4/POSetR/man/plot.Rcpp_POSet.Rd |only POSetR-1.0.4/POSetR/man/print.Rcpp_POSet.Rd |only POSetR-1.0.4/POSetR/man/summary.Rcpp_POSet.Rd |only POSetR-1.1.0/POSetR/DESCRIPTION | 10 +-- POSetR-1.1.0/POSetR/MD5 | 64 ++++++++++++------------ POSetR-1.1.0/POSetR/NAMESPACE | 14 +++-- POSetR-1.1.0/POSetR/R/LEapply.R | 42 ++++++++------- POSetR-1.1.0/POSetR/R/POSetR-package.R | 1 POSetR-1.1.0/POSetR/R/antiChain.R | 2 POSetR-1.1.0/POSetR/R/chain.R | 2 POSetR-1.1.0/POSetR/R/intersection.R | 8 +-- POSetR-1.1.0/POSetR/R/plot.poset.R |only POSetR-1.1.0/POSetR/R/poset.R | 28 +++++++--- POSetR-1.1.0/POSetR/R/poset_from_igraph.R | 4 - POSetR-1.1.0/POSetR/R/poset_from_incidence.R | 2 POSetR-1.1.0/POSetR/R/print.poset.R |only POSetR-1.1.0/POSetR/R/print.summary_poset.R | 2 POSetR-1.1.0/POSetR/R/productOrder.R | 18 ++++-- POSetR-1.1.0/POSetR/R/summary.poset.R |only POSetR-1.1.0/POSetR/R/utilities.R | 26 +++++---- POSetR-1.1.0/POSetR/build/partial.rdb |binary POSetR-1.1.0/POSetR/man/LEapply.Rd | 8 +-- POSetR-1.1.0/POSetR/man/antiChain.Rd | 2 POSetR-1.1.0/POSetR/man/chain.Rd | 2 POSetR-1.1.0/POSetR/man/coverMatrix.Rd | 6 +- POSetR-1.1.0/POSetR/man/incidenceMatrix.Rd | 6 +- POSetR-1.1.0/POSetR/man/plot.poset.Rd |only POSetR-1.1.0/POSetR/man/poset.Rd | 4 + POSetR-1.1.0/POSetR/man/poset_from_igraph.Rd | 2 POSetR-1.1.0/POSetR/man/poset_from_incidence.Rd | 2 POSetR-1.1.0/POSetR/man/print.poset.Rd |only POSetR-1.1.0/POSetR/man/print.summary_poset.Rd | 2 POSetR-1.1.0/POSetR/man/productOrder.Rd | 6 +- POSetR-1.1.0/POSetR/man/summary.poset.Rd |only POSetR-1.1.0/POSetR/src/RMod.cpp | 3 - POSetR-1.1.0/POSetR/src/RMod.h | 2 39 files changed, 150 insertions(+), 118 deletions(-)
Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling
Japanese iteration marks, Japanese character type conversions,
segmentation by phrase, and text normalization which is based on rules
for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism
dictionary for 'MeCab'). These features are specific to Japanese and
are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut],
Koki Takahashi [cph] ,
Shuhei Iitsuka [cph] ,
Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between audubon versions 0.1.2 dated 2022-04-02 and 0.2.0 dated 2022-05-24
DESCRIPTION | 15 ++++--- LICENSE.note | 4 +- MD5 | 32 ++++++++-------- NAMESPACE | 1 NEWS.md | 33 +++++++++------- R/pack.R | 32 ++++------------ R/strj-fill.R | 2 - R/strj-normalize.R | 5 +- R/strj-rewrite.R | 2 - R/strj-segment.R | 4 -- R/strj-tinyseg.R |only R/strj-tokenize.R | 4 -- inst/WORDLIST | 1 inst/packer/audubon.bundle.js | 2 - man/audubon-package.Rd | 3 + man/ngram_tokenizer.Rd | 6 --- man/strj_tinyseg.Rd |only tests/testthat/test_strj-tokenize-and-segment.R | 47 ++++++++++++++---------- 18 files changed, 97 insertions(+), 96 deletions(-)
Title: Process and Analyse Data from m-Path Sense
Description: Overcomes one of the major challenges in mobile (passive) sensing, namely
being able to pre-process the raw data that comes from a mobile sensing app,
specifically "m-Path Sense" <https://m-path.io>. The main task of 'mpathsenser' is
therefore to read "m-Path Sense" JSON files into a database and provide several
convenience functions to aid in data processing.
Author: Koen Niemeijer [aut, cre]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>
Diff between mpathsenser versions 1.0.1 dated 2022-05-19 and 1.0.2 dated 2022-05-24
mpathsenser-1.0.1/mpathsenser/inst/testdata/broken/backup |only mpathsenser-1.0.2/mpathsenser/DESCRIPTION | 6 mpathsenser-1.0.2/mpathsenser/MD5 | 23 mpathsenser-1.0.2/mpathsenser/R/database.R | 6 mpathsenser-1.0.2/mpathsenser/R/utils.R | 59 mpathsenser-1.0.2/mpathsenser/tests/testthat/test-database.R | 410 +- mpathsenser-1.0.2/mpathsenser/tests/testthat/test-functions.R | 13 mpathsenser-1.0.2/mpathsenser/tests/testthat/test-import-functions.R | 1815 +++++----- mpathsenser-1.0.2/mpathsenser/tests/testthat/test-utils.R | 102 9 files changed, 1252 insertions(+), 1182 deletions(-)
Title: Vegetation Phenological Cycle and Anomaly Detection using Remote
Sensing Data
Description: Calculates phenological cycle and anomalies using a non-parametric
approach applied to time series of vegetation indices derived from remote sensing data
or field measurements. The package implements basic and high-level functions for
manipulating vector data (numerical series) and raster data (satellite derived products).
Processing of very large raster files is supported. For more information, please check
the following paper:
Estay, S., Chávez, R.O. (2018) <doi:10.1101/301143>.
Author: Roberto O. Chavez [cre, aut], Sergio A. Estay [cre, aut], Jose A. Lastra [cre,ctb] & Carlos G. Riquelme [ctb]
Maintainer: Jose A. Lastra <jose.lastra@pucv.cl>
Diff between npphen versions 1.1.1 dated 2021-11-19 and 1.5.0 dated 2022-05-24
npphen-1.1.1/npphen/R/PhenAnoMap.R |only npphen-1.1.1/npphen/R/PhenAnoma.R |only npphen-1.1.1/npphen/inst/extdata |only npphen-1.1.1/npphen/man/PhenAnoMap.Rd |only npphen-1.1.1/npphen/man/PhenAnoma.Rd |only npphen-1.5.0/npphen/DESCRIPTION | 21 npphen-1.5.0/npphen/MD5 | 761 --------------------------- npphen-1.5.0/npphen/NAMESPACE | 35 - npphen-1.5.0/npphen/R/ExtremeAnoMap.R |only npphen-1.5.0/npphen/R/ExtremeAnom.R |only npphen-1.5.0/npphen/R/Phen.R | 155 +++-- npphen-1.5.0/npphen/R/PhenKplot.R | 99 ++- npphen-1.5.0/npphen/R/PhenMap.R | 146 +++-- npphen-1.5.0/npphen/R/data.R |only npphen-1.5.0/npphen/R/npphen-package.R | 9 npphen-1.5.0/npphen/data |only npphen-1.5.0/npphen/inst/CITATION | 33 - npphen-1.5.0/npphen/man/Bdesert_stack.Rd |only npphen-1.5.0/npphen/man/ExtremeAnoMap.Rd |only npphen-1.5.0/npphen/man/ExtremeAnom.Rd |only npphen-1.5.0/npphen/man/MegaDrought_stack.Rd |only npphen-1.5.0/npphen/man/Phen.Rd | 160 ++--- npphen-1.5.0/npphen/man/PhenKplot.Rd | 157 ++--- npphen-1.5.0/npphen/man/PhenMap.Rd | 169 +++-- npphen-1.5.0/npphen/man/modis_dates.Rd |only npphen-1.5.0/npphen/man/npphen.Rd | 48 - npphen-1.5.0/npphen/man/phents.Rd |only 27 files changed, 600 insertions(+), 1193 deletions(-)
Title: Multivariate Analysis for Neuroimaging Data
Description: Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained.
Author: Atsushi Kawaguchi [aut, cre]
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between mand versions 1.0 dated 2021-06-29 and 1.1 dated 2022-05-24
DESCRIPTION | 12 MD5 | 52 +- R/src.r | 15 build/vignette.rds |binary data/atlas.rda |binary data/atlasdatasets.rda |binary data/baseimg.rda |binary data/diffimg.rda |binary data/exbrain.rda |binary data/mask.rda |binary data/sdevimg.rda |binary data/template.rda |binary inst/doc/a_overview.html | 174 +++++--- inst/doc/b_Introduction.html | 95 +++- inst/doc/c_Brain_Imaging_Data.html | 84 ++- inst/doc/d_Common_Statistical_Approach.html | 205 +++++++-- inst/doc/e_Multivariate_Approach_Matrix_Decomposition.R | 35 - inst/doc/e_Multivariate_Approach_Matrix_Decomposition.Rmd | 37 - inst/doc/e_Multivariate_Approach_Matrix_Decomposition.html | 258 +++++++---- inst/doc/f_Multivariate_Approach_Prediction_Model.html | 280 +++++++++---- inst/doc/g_Multi-block_Approach.html | 78 ++- man/basisprod.Rd | 3 man/mand-package.Rd | 2 man/ptest.Rd | 12 man/rec.Rd | 3 man/sizechange.Rd | 3 vignettes/e_Multivariate_Approach_Matrix_Decomposition.Rmd | 37 - 27 files changed, 921 insertions(+), 464 deletions(-)
Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre],
Peter M. Ridland [aut],
David A. Ratkowsky [aut],
Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between IPEC versions 1.0.1 dated 2022-05-17 and 1.0.3 dated 2022-05-24
DESCRIPTION | 8 +++---- MD5 | 24 ++++++++++++----------- R/bootIPEC.R | 22 ++++++++++++++------- R/fitIPEC.R | 34 +++++++++++++++++++++++--------- build/partial.rdb |binary data/crops.rda |only man/IPEC.Rd | 36 ++++++++++++++++++++-------------- man/biasIPEC.Rd | 19 +++++++++++------- man/bootIPEC.Rd | 56 +++++++++++++++++++++++++++++++----------------------- man/crops.Rd |only man/curvIPEC.Rd | 17 ++++++++++------ man/derivIPEC.Rd | 13 ++++++++---- man/fitIPEC.Rd | 45 +++++++++++++++++++++++++------------------ man/skewIPEC.Rd | 17 ++++++++++------ 14 files changed, 179 insertions(+), 112 deletions(-)
Title: Tools for Estimating and Predicting the Cosinor Model
Description: A set of simple functions that transforms longitudinal
data to estimate the cosinor linear model as described in Tong (1976).
Methods are given to summarize the mean, amplitude and acrophase, to
predict the mean annual outcome value, and to test the coefficients.
Author: Michael Sachs <sachsmc@gmail.com>
Maintainer: Michael Sachs <sachsmc@gmail.com>
Diff between cosinor versions 1.1 dated 2014-07-28 and 1.2.2 dated 2022-05-24
DESCRIPTION | 14 - LICENSE | 4 MD5 | 59 ++-- NAMESPACE | 16 + NEWS | 29 +- R/cosinor.lm.R | 368 +++++++++++++-------------- R/cosinor_analyzer.R | 228 ++++++++--------- R/data.R | 21 - R/plot.cosinor.lm.R | 127 ++++----- R/summary.cosinor.lm.R | 252 +++++++++--------- README.md |only build/vignette.rds |binary inst/doc/Intro.R | 58 ++-- inst/doc/Intro.Rmd | 147 +++++------ inst/doc/Intro.html | 534 +++++++++++++++++----------------------- man/cosinor.lm.Rd | 10 man/cosinor.lm.default.Rd | 8 man/cosinor_analyzer.Rd | 7 man/get_varnames.Rd | 4 man/ggplot.cosinor.lm.Rd | 8 man/predict.cosinor.lm.Rd | 6 man/print.cosinor.lm.Rd | 4 man/print.summary.cosinor.lm.Rd | 8 man/print.test.Rd | 4 man/print.test_cosinor.Rd | 4 man/simulate_cosinor.Rd | 4 man/summary.cosinor.lm.Rd | 8 man/test_cosinor.Rd | 8 man/update_covnames.Rd | 4 man/vitamind.Rd | 10 vignettes/Intro.Rmd | 147 +++++------ 31 files changed, 1046 insertions(+), 1055 deletions(-)
Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. 2022. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. International Journal of Epidemiology <doi:10.1093/ije/dyac078>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre],
Piotr Dworzynski [aut],
Leila Arras [ctb],
Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>
Diff between CoOL versions 1.0.3 dated 2021-07-16 and 1.1.2 dated 2022-05-24
DESCRIPTION | 14 - MD5 | 46 +-- NAMESPACE | 1 R/CoOL_functions.R | 215 ++++++++++++++-- man/CoOL_0_binary_encode_exposure_data.Rd | 2 man/CoOL_0_common_simulation.Rd | 2 man/CoOL_0_complex_simulation.Rd | 2 man/CoOL_0_confounding_simulation.Rd | 2 man/CoOL_0_mediation_simulation.Rd | 2 man/CoOL_0_working_example.Rd | 10 man/CoOL_1_initiate_neural_network.Rd | 2 man/CoOL_2_train_neural_network.Rd | 2 man/CoOL_3_plot_neural_network.Rd | 2 man/CoOL_4_AUC.Rd | 2 man/CoOL_4_predict_risks.Rd | 2 man/CoOL_5_layerwise_relevance_propagation.Rd | 2 man/CoOL_6_calibration_plot.Rd |only man/CoOL_6_individual_effects_matrix.Rd | 2 man/CoOL_6_number_of_sub_groups.Rd |only man/CoOL_6_sub_groups.Rd | 2 man/CoOL_6_sum_of_individual_effects.Rd | 2 man/CoOL_7_prevalence_and_mean_risk_plot.Rd | 2 man/CoOL_8_mean_risk_contributions_by_sub_group.Rd | 5 man/CoOL_9_visualised_mean_risk_contributions.Rd |only man/CoOL_9_visualised_mean_risk_contributions_legend.Rd |only man/CoOL_default.Rd | 2 26 files changed, 256 insertions(+), 67 deletions(-)
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Minimally adjust the values of numerical records in a data.frame, such
that each record satisfies a predefined set of equality and/or inequality
constraints. The constraints can be defined using the 'validate' package.
The core algorithms have recently been moved to the 'lintools' package,
refer to 'lintools' for a more basic interface and access to a version
of the algorithm that works with sparse matrices.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.2.5 dated 2019-06-19 and 0.2.6 dated 2022-05-24
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NEWS | 5 ++ R/match_restrictions.R | 12 ++++- R/rspa.R | 7 ++- inst/tinytest/test_match_restrictions.R | 71 ++++++++++++++++---------------- man/adjust.Rd | 18 +++++--- man/adjustRecords.Rd | 10 +++- man/match_restrictions.Rd | 10 +++- man/remove_tag.Rd | 5 +- man/rspa-package.Rd | 10 +--- man/sparseConstraints.Rd | 13 ++++- man/tag_missing.Rd | 5 +- man/tagged_values.Rd | 5 +- 14 files changed, 124 insertions(+), 81 deletions(-)
Title: Robust Small Area Estimation
Description: Empirical best linear unbiased prediction (EBLUP) and
robust prediction of the area-level means under the basic unit-level
model. The model can be fitted by maximum likelihood or a (robust)
M-estimator. Mean square prediction error is computed by a parametric
bootstrap.
Author: Tobias Schoch [aut, cre] ,
Brent Richard [cph]
Maintainer: Tobias Schoch <tobias.schoch@fhnw.ch>
Diff between rsae versions 0.1-5 dated 2014-02-13 and 0.2 dated 2022-05-24
rsae-0.1-5/rsae/R/as.matrix.saemodel.R |only rsae-0.1-5/rsae/R/coef.fitsaemodel.R |only rsae-0.1-5/rsae/R/fitsaemodel.control.R |only rsae-0.1-5/rsae/R/plot.meanssaemodel.R |only rsae-0.1-5/rsae/R/print.fitsaemodel.R |only rsae-0.1-5/rsae/R/print.meanssaemodel.R |only rsae-0.1-5/rsae/R/print.saemodel.R |only rsae-0.1-5/rsae/R/residuals.meanssaemodel.R |only rsae-0.1-5/rsae/R/rsae-internal.R |only rsae-0.1-5/rsae/R/summary.fitsaemodel.R |only rsae-0.1-5/rsae/R/summary.saemodel.R |only rsae-0.1-5/rsae/inst/doc/rsae.R |only rsae-0.1-5/rsae/inst/doc/rsae.Rnw |only rsae-0.1-5/rsae/inst/doc/rsae.pdf |only rsae-0.1-5/rsae/man/rsae-internal.Rd |only rsae-0.1-5/rsae/src/status.c |only rsae-0.1-5/rsae/vignettes/rsae.Rnw |only rsae-0.2/rsae/.Rinstignore |only rsae-0.2/rsae/DESCRIPTION | 38 rsae-0.2/rsae/MD5 | 60 rsae-0.2/rsae/NAMESPACE | 56 rsae-0.2/rsae/NEWS.md |only rsae-0.2/rsae/R/convergence.R | 82 - rsae-0.2/rsae/R/fitsaemodel.R | 55 rsae-0.2/rsae/R/makedata.R | 180 +- rsae-0.2/rsae/R/model_b.R |only rsae-0.2/rsae/R/robpredict.R | 314 +++-- rsae-0.2/rsae/R/saemodel.R | 196 ++- rsae-0.2/rsae/build/partial.rdb |only rsae-0.2/rsae/build/vignette.rds |binary rsae-0.2/rsae/inst/CITATION | 26 rsae-0.2/rsae/inst/doc/rsae.Rmd |only rsae-0.2/rsae/inst/doc/rsae.html |only rsae-0.2/rsae/man/fitsaemodel.Rd | 260 ++-- rsae-0.2/rsae/man/fitsaemodel.control.Rd | 116 + rsae-0.2/rsae/man/landsat.Rd | 148 +- rsae-0.2/rsae/man/makedata.Rd | 201 +-- rsae-0.2/rsae/man/robpredict.Rd | 266 ++-- rsae-0.2/rsae/man/rsae-package.Rd | 152 +- rsae-0.2/rsae/man/saemodel.Rd | 148 +- rsae-0.2/rsae/src/init.c |only rsae-0.2/rsae/src/rsae.f90 | 1734 ++++++++++++++-------------- rsae-0.2/rsae/src/rsaeext.f90 | 312 ++--- rsae-0.2/rsae/vignettes/rsae.Rmd |only 44 files changed, 2372 insertions(+), 1972 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol
for R. The Language Server protocol is used by an editor client to
integrate features like auto completion. See
<https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre],
Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.3.12 dated 2021-10-19 and 0.3.13 dated 2022-05-24
DESCRIPTION | 10 ++--- MD5 | 60 ++++++++++++++++--------------- NEWS.md | 60 ++++++++++++++++++++++++++----- R/completion.R | 14 ++----- R/definition.R | 4 +- R/diagnostics.R | 11 ++++- R/document.R | 18 ++++----- R/formatting.R | 13 +++++- R/handlers-general.R | 3 + R/handlers-protocol.R | 6 +-- R/handlers-textsync.R | 13 +++--- R/handlers-workspace.R | 10 +++-- R/interfaces.R | 4 +- R/languagebase.R | 1 R/link.R | 5 +- R/log.R | 9 ++++ R/namespace.R | 2 - R/settings.R | 1 R/symbol.R | 4 +- R/utils.R | 20 +++++++--- R/workspace.R | 9 ++-- README.md | 18 +++++++-- inst/lua |only man/document_code_action_reply.Rd |only man/languageserver-package.Rd | 5 -- src/reader.c | 8 ++-- src/search.c | 5 ++ tests/testthat/helper-utils.R | 9 +++- tests/testthat/test-completion.R | 71 +++++++++++++++++++++++++++++++++++-- tests/testthat/test-formatting.R | 40 ++++++++++++++++++++ tests/testthat/test-search.R | 4 ++ tests/testthat/test-unicode-path.R | 2 - 32 files changed, 321 insertions(+), 118 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: Weighted Ordered Weighted Average
Description: Introduce weights into Ordered Weighted Averages and extend bivariate means based on n-ary tree construction. Please refer to the following:
G. Beliakov, H. Bustince, and T. Calvo (2016, ISBN: 978-3-319-24753-3),
G. Beliakov(2018) <doi:10.1002/int.21913>,
G. Beliakov, J.J. Dujmovic (2016) <doi:10.1016/j.ins.2015.10.040>,
J.J. Dujmovic and G. Beliakov (2017) <doi:10.1002/int.21828>.
Author: Gleb Beliakov [aut, cre],
Daniela Calderon [aut]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>
Diff between wowa versions 1.0.1 dated 2021-02-05 and 1.0.2 dated 2022-05-24
wowa-1.0.1/wowa/inst/wowa-theory.pdf |only wowa-1.0.1/wowa/man/WOWATree.Rd |only wowa-1.0.2/wowa/DESCRIPTION | 10 +-- wowa-1.0.2/wowa/MD5 | 26 ++++----- wowa-1.0.2/wowa/NAMESPACE | 2 wowa-1.0.2/wowa/R/RcppExports.R | 16 ++--- wowa-1.0.2/wowa/inst/weightedf.Rd |only wowa-1.0.2/wowa/man/ImplicitWOWA.Rd | 20 +++++++ wowa-1.0.2/wowa/man/OWA.Rd | 5 + wowa-1.0.2/wowa/man/WAM.Rd | 5 + wowa-1.0.2/wowa/man/WAn.Rd | 18 ++++++ wowa-1.0.2/wowa/man/weightedOWAQuantifier.Rd | 19 ++++++ wowa-1.0.2/wowa/man/weightedOWAQuantifierBuild.Rd | 19 ++++++ wowa-1.0.2/wowa/man/weightedf.Rd |only wowa-1.0.2/wowa/man/wowa.Rd | 2 wowa-1.0.2/wowa/src/wowa.cpp | 60 +++++++++++++++++++++- 16 files changed, 173 insertions(+), 29 deletions(-)
Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical
Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch [aut,cre] ,
Sebastian Malkusch [aut] ,
Alfred Ultsch [aut]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between opdisDownsampling versions 0.8.1 dated 2021-12-21 and 0.8.2 dated 2022-05-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/CompDistrib.R | 12 +++++++----- R/MakeReducedDataMat.R | 33 +++++++++++++++++++++------------ 4 files changed, 34 insertions(+), 23 deletions(-)
More information about opdisDownsampling at CRAN
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Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2022). An investigation of hypothesis testing procedures for circular and spherical mean vectors. Communications in Statistics-Simulation and Computation (Accepted for publication). <doi:10.1080/03610918.2022.2045499>.
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 5.4 dated 2022-05-15 and 5.5 dated 2022-05-24
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- man/Directional-package.Rd | 4 ++-- man/hcf.aov.Rd | 20 +++++++++++++++----- man/hcf.boot.Rd | 16 ++++++++++++---- man/hcf.circaov.Rd | 19 ++++++++++++++----- man/hcf.perm.Rd | 13 ++++++++++--- man/hcfcirc.boot.Rd | 16 ++++++++++++---- man/hcfcirc.perm.Rd | 13 ++++++++++--- man/spml.regs.Rd | 2 +- 10 files changed, 90 insertions(+), 41 deletions(-)
Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
Author: Diego Mananes [aut, cre] ,
Carlos Torroja [aut] ,
Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>
Diff between digitalDLSorteR versions 0.2.0 dated 2022-03-10 and 0.3.0 dated 2022-05-24
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More information about digitalDLSorteR at CRAN
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Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a
pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4
class system. This package allows the user to read/write a
pharmacometric model from/to files and adapt it further on the fly in
the R environment. For this purpose, this package provides an
intuitive API to add, modify or delete equations, ordinary
differential equations (ODE's), model parameters or compartment
properties (like infusion duration or rate, bioavailability and
initial values). Finally, this package also provides a useful export
of the model for use with simulation packages 'RxODE' and 'mrgsolve'.
This package is designed and intended to be used with package
'campsis', a PK/PD simulation platform built on top of 'RxODE' and
'mrgsolve'.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsismod versions 0.8.0 dated 2022-02-14 and 0.8.1 dated 2022-05-24
campsismod-0.8.0/campsismod/man/variablePattern.Rd |only campsismod-0.8.1/campsismod/DESCRIPTION | 8 campsismod-0.8.1/campsismod/MD5 | 37 - campsismod-0.8.1/campsismod/NEWS.md | 5 campsismod-0.8.1/campsismod/R/code_records.R | 32 + campsismod-0.8.1/campsismod/R/generic_element_position.R | 3 campsismod-0.8.1/campsismod/R/mrgsolve_conversion.R | 11 campsismod-0.8.1/campsismod/build/vignette.rds |binary campsismod-0.8.1/campsismod/inst/doc/campsismod.html | 229 ++++++++ campsismod-0.8.1/campsismod/inst/doc/v01_model_creation.html | 224 ++++++++ campsismod-0.8.1/campsismod/inst/doc/v02_structural_model.html | 257 +++++++++- campsismod-0.8.1/campsismod/inst/doc/v03_model_adaptation.html | 245 ++++++++- campsismod-0.8.1/campsismod/inst/doc/v04_compartment_properties.html | 234 ++++++++- campsismod-0.8.1/campsismod/inst/doc/v05_parameters.html | 232 ++++++++- campsismod-0.8.1/campsismod/inst/doc/v06_append_pd_model.html | 216 ++++++++ campsismod-0.8.1/campsismod/man/Position.Rd | 3 campsismod-0.8.1/campsismod/man/VariablePattern.Rd |only campsismod-0.8.1/campsismod/tests/testthat/testCodeRecords.R | 24 campsismod-0.8.1/campsismod/tests/testthat/testSimulationTimeConversion.R |only campsismod-0.8.1/campsismod/vignettes/path_to_model_folder |only 20 files changed, 1641 insertions(+), 119 deletions(-)
Title: Calculate Correlations and Estimate Causality
Description: This tool performs pairwise correlation analysis and estimate causality.
Particularly, it is useful for detecting the metabolites that would be altered by the gut bacteria.
Author: Tomomi Sugiyama [aut, cre]
Maintainer: Tomomi Sugiyama <sugiyama.t.am@m.titech.ac.jp>
Diff between CausCor versions 0.1.1 dated 2022-05-13 and 0.1.2 dated 2022-05-24
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Title: Tools for Lazy and Non-Standard Evaluation
Description: Functions to capture, inspect, manipulate, and create
lazy values (promises), "..." lists, and active calls.
Author: Peter Meilstrup <peter.meilstrup@gmail.com>
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>
Diff between nseval versions 0.4 dated 2018-08-06 and 0.4.2 dated 2022-05-24
DESCRIPTION | 23 +-- MD5 | 88 +++++++------- NAMESPACE | 25 +++- NEWS.md | 22 +++ R/arg.R | 17 +- R/caller.R | 133 +++++++++++++++++---- R/conversions.R | 13 +- R/dots.R | 47 +++---- R/force.R | 60 +++++---- R/format.R | 40 +++--- R/getpromise.R | 25 ++-- R/missing.R | 2 R/quo.R | 70 +++++++---- R/shortcut.R | 231 ++++++++++++++++++++++++++++++-------- README.md | 51 +++++--- man/arg.Rd | 4 man/caller.Rd | 20 +-- man/compat.Rd | 5 man/do.Rd | 39 ++++-- man/dots.Rd | 52 ++++---- man/dots2env.Rd | 14 +- man/env2dots.Rd | 8 - man/forced.Rd | 31 ----- man/format.Rd | 25 ++-- man/function_.Rd | 4 man/get_call.Rd | 19 ++- man/get_dots.Rd | 6 man/locate.Rd | 46 ++++--- man/missing_value.Rd | 15 -- man/quo.Rd | 66 ++++------ man/set_.Rd |only man/shortcut.Rd | 100 ++++++++++++---- man/unwrap.Rd | 2 src/caller.c | 125 ++++++++++++-------- src/dots.c | 7 + src/getpromise.c | 61 ++++++++-- src/init.c | 6 src/promises.c | 46 +++++-- src/vadr.h | 5 tests/testthat/test-caller.R | 8 + tests/testthat/test-conversions.R | 20 +++ tests/testthat/test-dots.R | 57 +++++++++ tests/testthat/test-format.R | 63 +++++++--- tests/testthat/test-getpromise.R | 95 +++++++++++++++ tests/testthat/test-primitive.R |only tests/testthat/test-with_caller.R | 128 +++++++++++++-------- 46 files changed, 1320 insertions(+), 604 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of
functions. With its progressive approach, we can construct display tables
with a cohesive set of table parts. Table values can be formatted using any
of the included formatting functions. Footnotes and cell styles can be
precisely added through a location targeting system. The way in which 'gt'
handles things for you means that you don't often have to worry about the
fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between gt versions 0.5.0 dated 2022-04-21 and 0.6.0 dated 2022-05-24
gt-0.5.0/gt/man/figures |only gt-0.5.0/gt/tests/testthat/test-fmt_missing.R |only gt-0.5.0/gt/tests/testthat/test-tab_footnote.R |only gt-0.6.0/gt/DESCRIPTION | 20 gt-0.6.0/gt/MD5 | 408 +---- gt-0.6.0/gt/NAMESPACE | 5 gt-0.6.0/gt/NEWS.md | 12 gt-0.6.0/gt/R/data_color.R | 95 - gt-0.6.0/gt/R/datasets.R | 56 gt-0.6.0/gt/R/dt_footnotes.R | 11 gt-0.6.0/gt/R/dt_formats.R | 20 gt-0.6.0/gt/R/dt_heading.R | 16 gt-0.6.0/gt/R/dt_options.R | 14 gt-0.6.0/gt/R/dt_stub_df.R | 2 gt-0.6.0/gt/R/export.R | 287 +-- gt-0.6.0/gt/R/format_data.R | 1145 ++++++++------- gt-0.6.0/gt/R/gt.R | 58 gt-0.6.0/gt/R/gt_preview.R | 30 gt-0.6.0/gt/R/helpers.R | 808 +++++----- gt-0.6.0/gt/R/image.R | 173 +- gt-0.6.0/gt/R/info_tables.R | 130 + gt-0.6.0/gt/R/location_methods.R | 19 gt-0.6.0/gt/R/modify_columns.R | 496 +++--- gt-0.6.0/gt/R/modify_rows.R | 40 gt-0.6.0/gt/R/opts.R | 415 +++-- gt-0.6.0/gt/R/resolver.R | 29 gt-0.6.0/gt/R/shiny.R | 60 gt-0.6.0/gt/R/substitution.R |only gt-0.6.0/gt/R/summary_rows.R | 91 - gt-0.6.0/gt/R/tab_create_modify.R | 866 ++++++----- gt-0.6.0/gt/R/text_transform.R | 99 - gt-0.6.0/gt/R/utils.R | 121 + gt-0.6.0/gt/R/utils_formatters.R | 189 ++ gt-0.6.0/gt/R/utils_render_common.R | 6 gt-0.6.0/gt/R/utils_render_footnotes.R | 157 +- gt-0.6.0/gt/R/utils_render_html.R | 2 gt-0.6.0/gt/R/utils_render_latex.R | 2 gt-0.6.0/gt/R/utils_render_rtf.R | 780 ++++++---- gt-0.6.0/gt/R/zzz.R | 1 gt-0.6.0/gt/man/adjust_luminance.Rd | 44 gt-0.6.0/gt/man/as_latex.Rd | 31 gt-0.6.0/gt/man/as_raw_html.Rd | 30 gt-0.6.0/gt/man/as_rtf.Rd | 25 gt-0.6.0/gt/man/cell_borders.Rd | 110 - gt-0.6.0/gt/man/cell_fill.Rd | 30 gt-0.6.0/gt/man/cell_text.Rd | 30 gt-0.6.0/gt/man/cells_body.Rd | 33 gt-0.6.0/gt/man/cells_column_labels.Rd | 28 gt-0.6.0/gt/man/cells_column_spanners.Rd | 29 gt-0.6.0/gt/man/cells_footnotes.Rd | 32 gt-0.6.0/gt/man/cells_grand_summary.Rd | 35 gt-0.6.0/gt/man/cells_row_groups.Rd | 42 gt-0.6.0/gt/man/cells_source_notes.Rd | 31 gt-0.6.0/gt/man/cells_stub.Rd | 36 gt-0.6.0/gt/man/cells_stub_grand_summary.Rd | 38 gt-0.6.0/gt/man/cells_stub_summary.Rd | 36 gt-0.6.0/gt/man/cells_stubhead.Rd | 30 gt-0.6.0/gt/man/cells_summary.Rd | 41 gt-0.6.0/gt/man/cells_title.Rd | 38 gt-0.6.0/gt/man/cols_align.Rd | 27 gt-0.6.0/gt/man/cols_hide.Rd | 56 gt-0.6.0/gt/man/cols_label.Rd | 44 gt-0.6.0/gt/man/cols_merge.Rd | 34 gt-0.6.0/gt/man/cols_merge_n_pct.Rd | 39 gt-0.6.0/gt/man/cols_merge_range.Rd | 40 gt-0.6.0/gt/man/cols_merge_uncert.Rd | 36 gt-0.6.0/gt/man/cols_move.Rd | 27 gt-0.6.0/gt/man/cols_move_to_end.Rd | 54 gt-0.6.0/gt/man/cols_move_to_start.Rd | 54 gt-0.6.0/gt/man/cols_unhide.Rd | 57 gt-0.6.0/gt/man/cols_width.Rd | 32 gt-0.6.0/gt/man/countrypops.Rd | 24 gt-0.6.0/gt/man/currency.Rd | 31 gt-0.6.0/gt/man/data_color.Rd | 85 - 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Title: Antibody Titer Analysis of Vaccinated Patients
Description: Visualization of antibody titer scores is valuable for examination of vaccination
effects. 'AntibodyTiters' visualizes antibody titers of all or selected patients. This
package also produces empty excel files in a specified format, in which users can fill in
experimental data for visualization. Excel files with toy data can also be produced, so that
users can see how it is visualized before obtaining real data. The data should contain
titer scores at pre-vaccination, after-1st shot, after-2nd shot, and at least one
additional sampling points. Patients with missing values can be included. The first two
sampling points (pre-vaccination and after-1st shot) will be plotted discretely, whereas
those following will be plotted on a continuous time scale that starts from the day of
second shot. Half-life of titer can also be calculated for each pair of sampling points.
Author: Yuuki Mizumoto [aut],
Hiroaki Kato [aut, cre] ,
Takeshi Urano [ctb]
Maintainer: Hiroaki Kato <hkato@med.shimane-u.ac.jp>
Diff between AntibodyTiters versions 0.1.18 dated 2021-10-28 and 0.1.24 dated 2022-05-24
DESCRIPTION | 8 +- MD5 | 22 +++---- NAMESPACE | 1 NEWS.md | 15 +++++ R/halfLifeABT.R | 2 R/idABT.R | 2 R/plotAllABT.R | 93 ++++++++++++++++++++++++-------- R/plotAllABT_discrete.R | 122 +++++++++++++++++++++++++++++++----------- R/plotEachABT.R | 2 R/readABT.R | 30 +++++++++- man/AntibodyTiters-package.Rd | 4 - man/plotAllABT.Rd | 40 +++++++++++++ 12 files changed, 264 insertions(+), 77 deletions(-)
More information about AntibodyTiters at CRAN
Permanent link
Title: Tools for Case 2 Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS2 versions 0.3-1 dated 2021-11-23 and 0.4-0 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/bws2.dataset.marginal.R | 4 ++++ R/bws2.dataset.paired.R | 4 ++++ inst/CITATION | 8 ++++---- 6 files changed, 24 insertions(+), 13 deletions(-)
Title: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events
Description: DNA copy number data evaluation using both their initial form
(copy number as a noisy function of genomic position) and their
approximation by a piecewise-constant function (segmentation),
for the purpose of identifying genomic regions where the copy number
differs from the norm.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>
Diff between CNprep versions 2.0 dated 2014-12-31 and 2.2 dated 2022-05-23
DESCRIPTION | 18 +++++++++++------- MD5 | 4 ++-- NAMESPACE | 5 +++-- 3 files changed, 16 insertions(+), 11 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.25.1 dated 2022-04-20 and 1.26.0 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/python.R | 7 ++++++- R/tracking-server.R | 9 +++++++-- README.md | 4 ++-- man/mlflow_server.Rd | 2 +- tests/testthat/test-keras-model.R | 2 +- 7 files changed, 26 insertions(+), 16 deletions(-)
Title: Cores of Recurrent Events
Description: Given a collection of intervals with integer start and end
positions, find recurrently targeted regions and estimate the significance
of finding. Randomization is implemented by parallel methods, either
using local host machines, or submitting grid engine jobs.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>
Diff between CORE versions 3.0 dated 2014-12-29 and 3.2 dated 2022-05-23
DESCRIPTION | 14 +-- MD5 | 6 - NAMESPACE | 5 - R/CORE.R | 276 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 153 insertions(+), 148 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 4.0.0 dated 2022-01-13 and 4.1.0 dated 2022-05-23
DESCRIPTION | 8 +- MD5 | 6 - R/CMplot.r | 182 ++++++++++++++++++++++++++------------------------ man/CMplot-package.Rd | 23 ++++-- 4 files changed, 118 insertions(+), 101 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. Ordinary R vectors are unsuitable for working with values of
associative maps because elements of an R vector may be accessed by
reference to their location in the vector, but associative maps are
stored in arbitrary order. However, when associating keys with
values one needs both parts to be in 1-1 correspondence, so one
cannot dispense with the order entirely. The 'disordR' package
includes a single S4 class, disord. This class allows one to
perform only those operations appropriate for manipulating values of
associative maps and prevents any other operation (such as accessing
an element at a particular location). A useful heuristic is that
one is only allowed to access or modify a disord object using a
python list comprehension. The idea is to prevent ill-defined
operations on values (or keys) of associative maps, whose order is
undefined or at best implementation-specific, while allowing and
facilitating sensible operations.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.0-9 dated 2021-12-09 and 0.0-9-1 dated 2022-05-23
disordR-0.0-9-1/disordR/DESCRIPTION | 13 disordR-0.0-9-1/disordR/MD5 | 37 - disordR-0.0-9-1/disordR/NAMESPACE | 2 disordR-0.0-9-1/disordR/NEWS.md | 5 disordR-0.0-9-1/disordR/R/disordR.R | 57 +- disordR-0.0-9-1/disordR/README.md | 35 + disordR-0.0-9-1/disordR/build/vignette.rds |binary disordR-0.0-9-1/disordR/inst/doc/disordR.R | 86 +++ disordR-0.0-9-1/disordR/inst/doc/disordR.Rmd | 292 ++++++++----- disordR-0.0-9-1/disordR/inst/doc/disordR.html | 491 +++++++++------------- disordR-0.0-9-1/disordR/man/arith.Rd | 8 disordR-0.0-9-1/disordR/man/disord-class.Rd | 2 disordR-0.0-9-1/disordR/man/disord.Rd | 30 - disordR-0.0-9-1/disordR/man/drop.Rd | 17 disordR-0.0-9-1/disordR/man/extract.Rd | 34 + disordR-0.0-9-1/disordR/man/misc.Rd | 9 disordR-0.0-9-1/disordR/man/rdis.Rd | 21 disordR-0.0-9-1/disordR/tests/testthat/test_aaa.R | 11 disordR-0.0-9-1/disordR/vignettes/disordR.Rmd | 292 ++++++++----- disordR-0.0-9/disordR/man/elements.Rd |only 20 files changed, 855 insertions(+), 587 deletions(-)
Title: Build Machine Learning Models Like Using Python's Scikit-Learn
Library in R
Description: The idea is to provide a standard interface
to users who use both R and Python for building machine learning models.
This package provides a scikit-learn's fit, predict interface to
train machine learning models in R.
Author: Manish Saraswat [aut, cre]
Maintainer: Manish Saraswat <manish06saraswat@gmail.com>
Diff between superml versions 0.5.4 dated 2022-05-12 and 0.5.5 dated 2022-05-23
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 inst/doc/Guide-to-CountVectorizer.html | 18 inst/doc/Guide-to-TfidfVectorizer.html | 32 - inst/doc/introduction.R | 78 +-- inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 767 +++++++-------------------------- vignettes/introduction.Rmd | 8 9 files changed, 259 insertions(+), 678 deletions(-)
Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis
of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous
time sampling (i.e. different time points for different individuals),
inter-individual variability, noisy measurements and large numbers of variables.
Based on a smoothing splines functional model, 'santaR' is able to detect variables
highlighting significantly different temporal trajectories between study groups.
Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology
disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and
parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting
options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] ,
Timothy Ebbels [ctb],
Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>
Diff between santaR versions 1.2.2 dated 2022-05-23 and 1.2.3 dated 2022-05-23
santaR-1.2.2/santaR/vignettes/file3eac108b893.html |only santaR-1.2.2/santaR/vignettes/file3eac2035654c.html |only santaR-1.2.2/santaR/vignettes/file3eac490a1211.html |only santaR-1.2.2/santaR/vignettes/file3eac50e54547.html |only santaR-1.2.2/santaR/vignettes/file3eac6eaa7a38.html |only santaR-1.2.2/santaR/vignettes/file3eac79a54222.html |only santaR-1.2.2/santaR/vignettes/file495459c86ac2.html |only santaR-1.2.2/santaR/vignettes/file49547f98451a.html |only santaR-1.2.2/santaR/vignettes/file54b03fa44385.html |only santaR-1.2.2/santaR/vignettes/file54b0425d69f8.html |only santaR-1.2.3/santaR/DESCRIPTION | 8 +- santaR-1.2.3/santaR/MD5 | 26 ++----- santaR-1.2.3/santaR/inst/doc/advanced-command-line-functions.html | 12 +-- santaR-1.2.3/santaR/inst/doc/plotting-options.html | 36 +++++----- santaR-1.2.3/santaR/inst/doc/theoretical-background.html | 2 santaR-1.2.3/santaR/tests/testthat/test_dfSearch-AIC_smooth_spline.R | 24 +++--- santaR-1.2.3/santaR/tests/testthat/test_dfSearch-AICc_smooth_spline.R | 24 +++--- santaR-1.2.3/santaR/tests/testthat/test_dfSearch-BIC_smooth_spline.R | 24 +++--- santaR-1.2.3/santaR/tests/testthat/test_dfSearch-get_param_evolution.R | 4 - 19 files changed, 75 insertions(+), 85 deletions(-)
Title: Toolbox for Pseudo and Quasi Random Number Generation and Random
Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators,
multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister
algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the
Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some
generator tests - the gap test, the serial test, the poker test.
See e.g. Gentle (2003) <doi:10.1007/b97336>. The package can be provided
without the rngWELL dependency on demand.
Take a look at the Distribution task view of types and tests of random number generators.
Package in Memoriam of Diethelm and Barbara Wuertz.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with some underlying C codes of the SFMT algorithm from M. Matsumoto and M. Saito, the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between randtoolbox versions 1.31.1 dated 2021-10-30 and 2.0.0 dated 2022-05-23
randtoolbox-1.31.1/randtoolbox/R/qmc.R |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy-sobol.c |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy-sobol.h |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy.f |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy.s |only randtoolbox-1.31.1/randtoolbox/tests/test-sobol-Ccode.R |only randtoolbox-1.31.1/randtoolbox/tests/testHalton.R |only randtoolbox-1.31.1/randtoolbox/tests/testSobol.R |only randtoolbox-1.31.1/randtoolbox/tests/testStirling.R |only randtoolbox-1.31.1/randtoolbox/tests/testTorus.R |only randtoolbox-1.31.1/randtoolbox/tests/testWELL.R |only randtoolbox-1.31.1/randtoolbox/tests/testenvir.R |only randtoolbox-2.0.0/randtoolbox/DESCRIPTION | 10 randtoolbox-2.0.0/randtoolbox/MD5 | 77 - randtoolbox-2.0.0/randtoolbox/NAMESPACE | 5 randtoolbox-2.0.0/randtoolbox/R/binary-operator.R |only randtoolbox-2.0.0/randtoolbox/R/quasiRNG.R | 264 ---- randtoolbox-2.0.0/randtoolbox/R/randtoolboxEnv.R | 4 randtoolbox-2.0.0/randtoolbox/R/sobol-basic.R | 341 ++++-- randtoolbox-2.0.0/randtoolbox/build/vignette.rds |binary randtoolbox-2.0.0/randtoolbox/configure | 18 randtoolbox-2.0.0/randtoolbox/configure.ac | 2 randtoolbox-2.0.0/randtoolbox/inst/NEWS | 10 randtoolbox-2.0.0/randtoolbox/inst/doc/fullpres.R | 34 randtoolbox-2.0.0/randtoolbox/inst/doc/fullpres.Rnw | 113 +- randtoolbox-2.0.0/randtoolbox/inst/doc/fullpres.pdf |binary randtoolbox-2.0.0/randtoolbox/inst/doc/shortintro.pdf |binary randtoolbox-2.0.0/randtoolbox/man/quasiRNG.Rd | 37 randtoolbox-2.0.0/randtoolbox/man/sobol-test-func.Rd | 32 randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-halton.c | 93 - randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-halton.h | 88 - randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-sobol-orig1111.c |only randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-sobol-orig1111.h |only randtoolbox-2.0.0/randtoolbox/src/SFMT.h | 34 randtoolbox-2.0.0/randtoolbox/src/config.h | 4 randtoolbox-2.0.0/randtoolbox/src/init.c | 16 randtoolbox-2.0.0/randtoolbox/src/randtoolbox.c | 78 + randtoolbox-2.0.0/randtoolbox/src/randtoolbox.h | 6 randtoolbox-2.0.0/randtoolbox/src/version.c | 2 randtoolbox-2.0.0/randtoolbox/tests/test-Halton.R |only randtoolbox-2.0.0/randtoolbox/tests/test-Sobol.R |only randtoolbox-2.0.0/randtoolbox/tests/test-Stirling.R |only randtoolbox-2.0.0/randtoolbox/tests/test-Torus.R |only randtoolbox-2.0.0/randtoolbox/tests/test-WELL.R |only randtoolbox-2.0.0/randtoolbox/tests/test-binary-op.R |only randtoolbox-2.0.0/randtoolbox/tests/test-envir.R |only randtoolbox-2.0.0/randtoolbox/tests/test-mjrec.R |only randtoolbox-2.0.0/randtoolbox/tests/test-sobol-basic.R | 40 randtoolbox-2.0.0/randtoolbox/tests/test-sobol.V.R |only randtoolbox-2.0.0/randtoolbox/tests/test-sobol.directions.R |only randtoolbox-2.0.0/randtoolbox/vignettes/fullpres.Rnw | 113 +- randtoolbox-2.0.0/randtoolbox/vignettes/randtoolbox.bib | 553 +++++----- 52 files changed, 993 insertions(+), 981 deletions(-)
Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the
L0-Pseudonorm
Description: Optimal Subset Cardinality Regression (OSCAR) models offer
regularized linear regression using the L0-pseudonorm, conventionally
known as the number of non-zero coefficients. The package estimates an
optimal subset of features using the L0-penalization via
cross-validation, bootstrapping and visual diagnostics. Effective
Fortran implementations are offered along the package for finding
optima for the DC-decomposition, which is used for transforming the
discrete L0-regularized optimization problem into a continuous
non-convex optimization task. These optimization modules include DBDC
('Double Bundle method for nonsmooth DC optimization' as described in
Joki et al. (2018) <doi:10.1137/16M1115733>) and LMBM ('Limited
Memory Bundle Method for large-scale nonsmooth optimization' as
in Haarala et al. (2004) <doi:10.1080/10556780410001689225>).
Multiple regression model families are supported: Cox, logistic,
and Gaussian.
Author: Teemu Daniel Laajala [aut, cre]
,
Kaisa Joki [aut],
Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between oscar versions 1.0.3 dated 2022-05-20 and 1.0.4 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/example.html | 6 +++--- src/Makevars | 1 - src/dbdc.f90 | 30 +++++++++++++++++++++--------- 5 files changed, 32 insertions(+), 21 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut],
Julian Zhou [aut],
Nima Nouri [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut, cre],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between shazam versions 1.1.0 dated 2021-07-08 and 1.1.1 dated 2022-05-23
shazam-1.1.0/shazam/vignettes/Shmulate-Vignette.html |only shazam-1.1.1/shazam/DESCRIPTION | 25 - shazam-1.1.1/shazam/MD5 | 52 +- shazam-1.1.1/shazam/NAMESPACE | 6 shazam-1.1.1/shazam/NEWS.md | 27 + shazam-1.1.1/shazam/R/ConvertNumbering.R |only shazam-1.1.1/shazam/R/DistToNearest.R | 2 shazam-1.1.1/shazam/R/MutationDefinitions.R | 2 shazam-1.1.1/shazam/R/MutationProfiling.R | 308 +++++++++++---- shazam-1.1.1/shazam/R/RegionsExtend.R | 4 shazam-1.1.1/shazam/R/Shazam.R | 11 shazam-1.1.1/shazam/R/TargetingModels.R | 6 shazam-1.1.1/shazam/R/kedd.R |only shazam-1.1.1/shazam/R/sysdata.rda |binary shazam-1.1.1/shazam/build/vignette.rds |binary shazam-1.1.1/shazam/inst/doc/Baseline-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/DistToNearest-Vignette.R | 2 shazam-1.1.1/shazam/inst/doc/DistToNearest-Vignette.Rmd | 2 shazam-1.1.1/shazam/inst/doc/DistToNearest-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/Mutation-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/Shmulate-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/Targeting-Vignette.pdf |binary shazam-1.1.1/shazam/man/MUTATION_SCHEMES.Rd | 2 shazam-1.1.1/shazam/man/convertNumbering.Rd |only shazam-1.1.1/shazam/man/slideWindowDb.Rd | 11 shazam-1.1.1/shazam/man/slideWindowSeq.Rd | 2 shazam-1.1.1/shazam/man/slideWindowTune.Rd | 11 shazam-1.1.1/shazam/man/slideWindowTunePlot.Rd | 30 + shazam-1.1.1/shazam/vignettes/DistToNearest-Vignette.Rmd | 2 29 files changed, 371 insertions(+), 134 deletions(-)
Title: Parameter Estimation in Conditional GEE for Recurrent Event Gap
Times
Description: Solves for the mean parameters, the variance parameter, and their asymptotic variance in a conditional GEE for recurrent event gap times, as described by Clement and Strawderman (2009) in the journal Biostatistics. Makes a parametric assumption for the length of the censored gap time.
Author: David Clement
Maintainer: David Clement <dyc24@cornell.edu>
Diff between condGEE versions 0.1-4 dated 2013-08-17 and 0.2.0 dated 2022-05-23
condGEE-0.1-4/condGEE/data/asthma.txt.gz |only condGEE-0.1-4/condGEE/demo |only condGEE-0.1-4/condGEE/man/condMoments.Rd |only condGEE-0.2.0/condGEE/DESCRIPTION | 17 - condGEE-0.2.0/condGEE/MD5 | 32 ++- condGEE-0.2.0/condGEE/NAMESPACE | 16 - condGEE-0.2.0/condGEE/NEWS.md |only condGEE-0.2.0/condGEE/R/condGEE.R | 320 +++++++++++++++++-------------- condGEE-0.2.0/condGEE/R/condMoments.R | 99 +++++++-- condGEE-0.2.0/condGEE/README.md |only condGEE-0.2.0/condGEE/build |only condGEE-0.2.0/condGEE/data/asthma.txt |only condGEE-0.2.0/condGEE/inst |only condGEE-0.2.0/condGEE/man/K1.exp.Rd |only condGEE-0.2.0/condGEE/man/K1.norm.Rd |only condGEE-0.2.0/condGEE/man/K1.t3.Rd |only condGEE-0.2.0/condGEE/man/K2.exp.Rd |only condGEE-0.2.0/condGEE/man/K2.norm.Rd |only condGEE-0.2.0/condGEE/man/K2.t3.Rd |only condGEE-0.2.0/condGEE/man/asthma.Rd | 23 +- condGEE-0.2.0/condGEE/man/condGEE.Rd | 163 +++++++++------ condGEE-0.2.0/condGEE/tests |only condGEE-0.2.0/condGEE/vignettes |only 23 files changed, 397 insertions(+), 273 deletions(-)
Title: Revealed Preference and Attention Analysis in Random Limited
Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and Cattaneo, Cheung, Ma, and Masatlioglu (2022) <arXiv:2110.10650>, which utilizes standard choice data to partially identify and estimate a decision maker's preference and attention. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Paul Cheung, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between ramchoice versions 2.0 dated 2021-10-22 and 2.1 dated 2022-05-23
DESCRIPTION | 8 +++---- MD5 | 34 +++++++++++++++++--------------- NAMESPACE | 3 ++ R/auxiliaryFunctions.R | 24 +++++++++++----------- R/ramchoice-package.R | 8 +++---- R/revealAtte.R | 6 ++--- R/revealPref.R | 30 ++++++++++++++-------------- R/revealPrefModel.R |only build/partial.rdb |binary man/genMat.Rd | 4 +-- man/logitAtte.Rd | 8 +++---- man/logitSimu.Rd | 8 +++---- man/print.ramchoiceRevealPrefModel.Rd |only man/rAtte.Rd | 12 +++++------ man/ramchoice-package.Rd | 8 +++---- man/revealAtte.Rd | 6 ++--- man/revealPref.Rd | 12 +++++------ man/revealPrefModel.Rd |only man/sumData.Rd | 4 +-- man/summary.ramchoiceRevealPrefModel.Rd |only 20 files changed, 91 insertions(+), 84 deletions(-)
Title: Combined miRNA- And mRNA-Testing
Description: Package for combined miRNA- and mRNA-testing.
Author: Stephan Artmann, Klaus Jung, Tim Beissbarth
Maintainer: Stephan Artmann <stephanartmann@gmx.net>
Diff between miRtest versions 1.8 dated 2014-11-26 and 2.0 dated 2022-05-23
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- R/miRtest.R | 31 +++++-------------------------- build/vignette.rds |binary inst/doc/miRtest.Rnw | 3 +-- inst/doc/miRtest.pdf |binary man/miRtest.Rd | 3 --- vignettes/miRtest.Rnw | 3 +-- 9 files changed, 25 insertions(+), 50 deletions(-)
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via a (fast and robust) bootstrap test.
Author: Andreas Alfons [aut, cre] ,
Nufer Y. Ates [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 0.10.1 dated 2022-03-17 and 0.11.0 dated 2022-05-23
robmed-0.10.1/robmed/vignettes/static-figures |only robmed-0.11.0/robmed/DESCRIPTION | 10 robmed-0.11.0/robmed/MD5 | 127 - robmed-0.11.0/robmed/NAMESPACE | 8 robmed-0.11.0/robmed/NEWS | 17 robmed-0.11.0/robmed/R/BSG2014.R |only robmed-0.11.0/robmed/R/boot.R | 506 ++--- robmed-0.11.0/robmed/R/ci_plot.R | 451 ++-- robmed-0.11.0/robmed/R/coef.R | 232 +- robmed-0.11.0/robmed/R/confint.R | 544 ++--- robmed-0.11.0/robmed/R/control.R | 8 robmed-0.11.0/robmed/R/density_plot.R | 363 +-- robmed-0.11.0/robmed/R/ellipse_plot.R | 431 ++-- robmed-0.11.0/robmed/R/fit_mediation.R | 136 + robmed-0.11.0/robmed/R/formula.R | 299 +-- robmed-0.11.0/robmed/R/p_value.R | 588 +++--- robmed-0.11.0/robmed/R/plot.R | 10 robmed-0.11.0/robmed/R/retest.R | 374 +-- robmed-0.11.0/robmed/R/robmed-package.R |only robmed-0.11.0/robmed/R/setup_ci_plot.R | 506 ++--- robmed-0.11.0/robmed/R/setup_density_plot.R | 450 ++-- robmed-0.11.0/robmed/R/setup_ellipse_plot.R | 1248 ++++++------- robmed-0.11.0/robmed/R/setup_weight_plot.R | 4 robmed-0.11.0/robmed/R/sim_mediation.R |only robmed-0.11.0/robmed/R/skew_elliptical.R | 777 ++++---- robmed-0.11.0/robmed/R/summary.R | 64 robmed-0.11.0/robmed/R/test_mediation.R | 53 robmed-0.11.0/robmed/R/utils.R | 418 ++-- robmed-0.11.0/robmed/R/weight_plot.R | 6 robmed-0.11.0/robmed/build/partial.rdb |binary robmed-0.11.0/robmed/build/vignette.rds |binary robmed-0.11.0/robmed/data/BSG2014.RData |binary robmed-0.11.0/robmed/inst/doc/robmed-intro.R | 35 robmed-0.11.0/robmed/inst/doc/robmed-intro.Rnw | 831 ++++---- robmed-0.11.0/robmed/inst/doc/robmed-intro.pdf |binary robmed-0.11.0/robmed/man/BSG2014.Rd | 278 +- robmed-0.11.0/robmed/man/boot_samples.Rd | 12 robmed-0.11.0/robmed/man/ci_plot.Rd | 23 robmed-0.11.0/robmed/man/coef.test_mediation.Rd | 6 robmed-0.11.0/robmed/man/confint.test_mediation.Rd | 14 robmed-0.11.0/robmed/man/cov_control.Rd | 4 robmed-0.11.0/robmed/man/density_plot.Rd | 23 robmed-0.11.0/robmed/man/ellipse_plot.Rd | 21 robmed-0.11.0/robmed/man/fit_mediation.Rd | 137 + robmed-0.11.0/robmed/man/m.Rd | 4 robmed-0.11.0/robmed/man/p_value.Rd | 12 robmed-0.11.0/robmed/man/plot-methods.Rd | 10 robmed-0.11.0/robmed/man/reg_control.Rd | 4 robmed-0.11.0/robmed/man/retest.Rd | 6 robmed-0.11.0/robmed/man/robmed-package.Rd | 9 robmed-0.11.0/robmed/man/setup_ci_plot.Rd | 4 robmed-0.11.0/robmed/man/setup_density_plot.Rd | 4 robmed-0.11.0/robmed/man/setup_ellipse_plot.Rd | 4 robmed-0.11.0/robmed/man/setup_weight_plot.Rd | 4 robmed-0.11.0/robmed/man/sim_mediation.Rd |only robmed-0.11.0/robmed/man/summary.test_mediation.Rd | 60 robmed-0.11.0/robmed/man/test_mediation.Rd | 131 + robmed-0.11.0/robmed/man/weight_plot.Rd | 6 robmed-0.11.0/robmed/tests/testthat/test_boot_covariance.R | 924 ++++----- robmed-0.11.0/robmed/tests/testthat/test_simulate.R |only robmed-0.11.0/robmed/vignettes/figures |only robmed-0.11.0/robmed/vignettes/robmed-intro.Rnw | 831 ++++---- robmed-0.11.0/robmed/vignettes/robmed.bib | 157 + 63 files changed, 6039 insertions(+), 5145 deletions(-)
Title: Fast Extrapolation of Time Features using K-Nearest Neighbors
Description: Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between jenga versions 1.1.0 dated 2022-04-16 and 1.2.0 dated 2022-05-23
jenga-1.1.0/jenga/R/engine.R |only jenga-1.1.0/jenga/R/hood.R |only jenga-1.1.0/jenga/man/engine.Rd |only jenga-1.1.0/jenga/man/hood.Rd |only jenga-1.2.0/jenga/DESCRIPTION | 14 - jenga-1.2.0/jenga/MD5 | 14 - jenga-1.2.0/jenga/NAMESPACE | 14 + jenga-1.2.0/jenga/NEWS.md | 6 jenga-1.2.0/jenga/R/main.R | 487 ++++++++++++++++++++++++++++++++++------ jenga-1.2.0/jenga/man/jenga.Rd | 12 10 files changed, 456 insertions(+), 91 deletions(-)
Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with
with various kinds of text matrices. Focusing on
the text matrix as the primary object - represented
either as a base R dense matrix or a 'Matrix' package sparse
matrix - allows for a consistent and intuitive interface
that stays close to the underlying mathematical foundation
of computational text analysis. In particular, the package
includes functions for working with word embeddings,
text networks, and document-term matrices. Methods developed in
Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>,
Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>,
Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and
Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] ,
Marshall Taylor [aut]
Maintainer: Dustin Stoltz <maintainers@textmapping.com>
Diff between text2map versions 0.1.4 dated 2022-04-12 and 0.1.5 dated 2022-05-23
DESCRIPTION | 14 +- MD5 | 49 ++++----- NAMESPACE | 28 ++++- NEWS.md | 18 +++ R/data.R | 28 +++++ R/utils-dtm.R | 147 +++++++++++++++++++++++++-- R/utils-embedding.R | 37 ++---- R/utils-methods.R | 26 ++++ README.md | 4 build/partial.rdb |binary build/vignette.rds |binary data/meta_shakespeare.rda |only inst/REFERENCES.bib |only inst/doc/CMDist-concept-movers-distance.R | 20 +++ inst/doc/CMDist-concept-movers-distance.Rmd | 101 +++++++++--------- inst/doc/CMDist-concept-movers-distance.html | 101 +++++++++--------- inst/doc/concept-class-analysis.html | 4 man/Matrix.Rd | 2 man/dtm_builder.Rd | 5 man/dtm_stats.Rd | 9 + man/dtm_stopper.Rd | 6 + man/get_regions.Rd | 26 ---- man/meta_shakespeare.Rd |only man/seq_builder.Rd |only tests/testthat/test-utils-dtm.R | 134 ------------------------ tests/testthat/test-utils-embeddings.R | 2 tests/testthat/test-utils-stopper.R |only vignettes/CMDist-concept-movers-distance.Rmd | 101 +++++++++--------- 28 files changed, 484 insertions(+), 378 deletions(-)
Title: Subtests Using Algorithmic Rummaging Techniques
Description: Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling.
Schultze (2017) <doi:10.17169/refubium-622>.
Author: Martin Schultze [aut, cre],
Johanna Schueller [ctb]
Maintainer: Martin Schultze <schultze@psych.uni-frankfurt.de>
Diff between stuart versions 0.9.1 dated 2020-08-26 and 0.10.0 dated 2022-05-23
DESCRIPTION | 14 +++--- MD5 | 85 +++++++++++++++++++++++++---------------- NAMESPACE | 11 +++++ R/bf.cycle.R | 6 +- R/bruteforce.R | 6 +- R/combinations.R | 2 R/crossvalidate.Mplus.R | 44 ++++++++++++--------- R/crossvalidate.R | 6 +- R/crossvalidate.lavaan.R | 41 +++++++++++++------ R/data.documentation.R | 29 +++++++++++++ R/data.prep.R | 12 ++--- R/empiricalobjective.R |only R/extractobjective.R |only R/fitness.R | 16 +++---- R/fixedobjective.R |only R/gene.R | 8 ++- R/helpers.R |only R/heuristics.R | 2 R/holdout.R | 50 ++++++++++++++++++++++-- R/kfold.R |only R/manualobjective.R |only R/mmas.R | 36 ++--------------- R/objectivematrices.R |only R/print.objectives.R |only R/print.stuartKfold.R |only R/print.summary.stuartKfold.R |only R/print.summary.stuartOutput.R | 5 +- R/randomsamples.R | 6 +- R/run.Mplus.R | 2 R/run.lavaan.R | 14 +++--- R/sanitycheck.R | 24 ++++++----- R/stuart.R | 6 +- R/stuart.bruteforce.R | 42 ++++++++++++++++---- R/stuart.gene.R | 60 ++++++++++++++++++++++++++-- R/stuart.mmas.R | 65 +++++++++++++++++++++++++++---- R/stuart.randomsamples.R | 45 ++++++++++++++++++--- R/summary.stuartKfold.R |only R/summary.stuartOutput.R | 3 - data/sia.rda |only man/as.stuartFixedObjective.Rd |only man/bruteforce.Rd | 1 man/crossvalidate.Rd | 10 ++++ man/empiricalobjective.Rd |only man/extractobjective.Rd |only man/fixedobjective.Rd |only man/gene.Rd | 4 + man/holdout.Rd | 4 + man/kfold.Rd |only man/mmas.Rd | 32 +-------------- man/objectivematrices.Rd |only man/randomsamples.Rd | 1 man/sia.Rd |only man/stuart-package.Rd | 6 +- 53 files changed, 484 insertions(+), 214 deletions(-)
Title: Orthogonal B-Spline Basis Functions
Description: Represents the basis functions for B-splines in a simple matrix
formulation that facilitates, taking integrals, derivatives, and
making orthogonal the basis functions.
Author: Andrew Redd
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between orthogonalsplinebasis versions 0.1.6 dated 2015-03-31 and 0.1.7 dated 2022-05-23
DESCRIPTION | 10 ++- MD5 | 32 +++++----- NAMESPACE | 55 +++++++++--------- NEWS | 14 +++- inst |only man/Hankel.Rd | 1 man/MatrixPower.Rd | 7 +- man/OrthogonalizeBasis.Rd | 5 - man/OuterProdSecondDerivative.Rd | 7 +- man/SplineBasis-class.Rd | 115 +++++++++++++++++++-------------------- man/SplineBasis.Rd | 86 ++++++++++++++--------------- man/evaluate-methods.Rd | 2 man/expand.knots.Rd | 64 ++++++++++----------- man/fitLS.Rd | 7 +- man/integrate-methods.Rd | 2 man/orthogonalize-methods.Rd | 2 man/orthogonalsplinebasis.Rd | 28 ++++----- tests |only 18 files changed, 221 insertions(+), 216 deletions(-)
More information about orthogonalsplinebasis at CRAN
Permanent link
Title: Analysis of MHC Data in Non-Model Species
Description: Twelve tools for bioinformatical processing and analysis of major
histocompatibility complex (MHC) data. The functions are tailored for amplicon data
sets that have been filtered using the 'dada2' method (for more information on
'dada2', visit <https://benjjneb.github.io/dada2/> ), but even other types of data
sets can be analyzed.
The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise
comparisons of all sequences in a data set, and mean distances of all pairwise
comparisons within each sample in a data set. The function additionally outputs five
tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for
each amino acid position in all sequences in the data set. These tables may be useful
for further downstream analyses, such as estimation of MHC supertypes.
The BootKmeans() function is a wrapper for the kmeans() function of the 'stats'
package, which allows for bootstrapping. Bootstrapping k-estimates may be
desirable in data sets, where e.g. BIC- vs. k-values do not produce clear
inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and
estimates optimal k-values based on a user-defined threshold of BIC reduction. The
method is an automated and bootstrapped version of visually inspecting elbow plots
of BIC- vs. k-values.
The ClusterMatch() function is a tool for evaluating whether different k-means()
clustering models identify similar clusters, and summarize bootstrap model stats as
means for different estimated values of k. It is designed to take files produced by
the BootKmeans() function as input, but other data can be analysed if the
descriptions of the required data formats are observed carefully.
The HpltFind() function infers putative haplotypes from families in the data
set.
The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of
the haplotype inference.
The PapaDiv() function compares parent pairs in the data set and calculate their
joint MHC diversity, taking into account sequence variants that occur in both
parents.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates individual fasta files for each sample in
the data set.
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.4.1 dated 2021-10-11 and 1.4.2 dated 2022-05-23
DESCRIPTION | 6 ++-- MD5 | 54 ++++++++++++++++++------------------- NEWS.md | 10 ++++++ R/BootKmeans_func_20210910.R | 13 ++++---- R/ClusterMatch_func_20210910.R | 13 ++++---- R/CreateFas_func_20170924.R | 13 ++++---- R/CreateSamplesFas_func_20170924.R | 13 ++++---- R/DistCalc_func_20200902.R | 13 ++++---- R/GetHpltStats_func_20200915.R | 13 ++++---- R/GetHpltTable_func_20200915.R | 13 ++++---- R/GetReplStats_func_20200914.R | 13 ++++---- R/GetReplTable_func_20200914.R | 13 ++++---- R/HpltFind_func_20200915.R | 13 ++++---- R/PapaDiv_func_20200915.R | 13 ++++---- R/ReplMatch_func_20200914.R | 13 ++++---- README.md | 6 ++++ man/BootKmeans.Rd | 13 ++++---- man/ClusterMatch.Rd | 13 ++++---- man/CreateFas.Rd | 13 ++++---- man/CreateSamplesFas.Rd | 13 ++++---- man/DistCalc.Rd | 13 ++++---- man/GetHpltStats.Rd | 13 ++++---- man/GetHpltTable.Rd | 13 ++++---- man/GetReplStats.Rd | 13 ++++---- man/GetReplTable.Rd | 13 ++++---- man/HpltFind.Rd | 13 ++++---- man/PapaDiv.Rd | 13 ++++---- man/ReplMatch.Rd | 13 ++++---- 28 files changed, 214 insertions(+), 174 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>); model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre]
,
Pascal Obstetar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 3.1.2 dated 2021-12-09 and 4.0.1 dated 2022-05-23
lidaRtRee-3.1.2/lidaRtRee/man/pointList2SPDF.Rd |only lidaRtRee-3.1.2/lidaRtRee/tests |only lidaRtRee-4.0.1/lidaRtRee/DESCRIPTION | 19 lidaRtRee-4.0.1/lidaRtRee/MD5 | 135 ++-- lidaRtRee-4.0.1/lidaRtRee/NAMESPACE | 4 lidaRtRee-4.0.1/lidaRtRee/R/aba.R | 193 +++--- lidaRtRee-4.0.1/lidaRtRee/R/chm_chablais3-data.R | 6 lidaRtRee-4.0.1/lidaRtRee/R/common.R | 365 ++++++------ lidaRtRee-4.0.1/lidaRtRee/R/coregistration.R | 286 ++++----- lidaRtRee-4.0.1/lidaRtRee/R/extdata.R | 8 lidaRtRee-4.0.1/lidaRtRee/R/gap_detection.R | 44 - lidaRtRee-4.0.1/lidaRtRee/R/metrics.R | 44 - lidaRtRee-4.0.1/lidaRtRee/R/optical_metrics.R | 4 lidaRtRee-4.0.1/lidaRtRee/R/quatre_montagnes-data.R | 4 lidaRtRee-4.0.1/lidaRtRee/R/raster_metrics.R | 46 - lidaRtRee-4.0.1/lidaRtRee/R/tree_detection.R | 324 +++++----- lidaRtRee-4.0.1/lidaRtRee/R/tree_inventory_chablais3-data.R | 6 lidaRtRee-4.0.1/lidaRtRee/R/tree_match.R | 52 - lidaRtRee-4.0.1/lidaRtRee/build/partial.rdb |binary lidaRtRee-4.0.1/lidaRtRee/data/chm_chablais3.rda |binary lidaRtRee-4.0.1/lidaRtRee/data/quatre_montagnes.rda |binary lidaRtRee-4.0.1/lidaRtRee/man/aa_las_chablais3.Rd |only lidaRtRee-4.0.1/lidaRtRee/man/aba_combine_strata.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/aba_metrics.Rd | 5 lidaRtRee-4.0.1/lidaRtRee/man/aba_plot.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/aba_predict.Rd | 23 lidaRtRee-4.0.1/lidaRtRee/man/add_vegetation_indices.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/boxcox_itr.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/boxcox_itr_bias_cor.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/boxcox_tr.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/chm_chablais3.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/cimg2Raster.Rd | 23 lidaRtRee-4.0.1/lidaRtRee/man/circle2Raster.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/clean_raster.Rd | 23 lidaRtRee-4.0.1/lidaRtRee/man/clouds_metrics.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/clouds_tree_metrics.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/convert_raster.Rd |only lidaRtRee-4.0.1/lidaRtRee/man/coregistration.Rd | 22 lidaRtRee-4.0.1/lidaRtRee/man/dem_filtering.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/edge_detection.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/ellipses4Crown.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/gap_detection.Rd | 15 lidaRtRee-4.0.1/lidaRtRee/man/las_chablais3.Rd | 5 lidaRtRee-4.0.1/lidaRtRee/man/maxima_detection.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/maxima_selection.Rd | 21 lidaRtRee-4.0.1/lidaRtRee/man/plot_matched.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/plot_tree_inventory.Rd | 3 lidaRtRee-4.0.1/lidaRtRee/man/pointList2poly.Rd |only lidaRtRee-4.0.1/lidaRtRee/man/points2DSM.Rd | 10 lidaRtRee-4.0.1/lidaRtRee/man/points2DTM.Rd | 11 lidaRtRee-4.0.1/lidaRtRee/man/quatre_montagnes.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/raster2Cimg.Rd | 15 lidaRtRee-4.0.1/lidaRtRee/man/raster_chull_mask.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/raster_local_max.Rd | 17 lidaRtRee-4.0.1/lidaRtRee/man/raster_metrics.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/raster_xy_mask.Rd | 8 lidaRtRee-4.0.1/lidaRtRee/man/raster_zonal_stats.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/rasters2Cor.Rd | 31 - lidaRtRee-4.0.1/lidaRtRee/man/rasters_moving_cor.Rd | 29 lidaRtRee-4.0.1/lidaRtRee/man/seg_adjust.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/segmentation.Rd | 15 lidaRtRee-4.0.1/lidaRtRee/man/std_tree_metrics.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/terrain_points_metrics.Rd | 10 lidaRtRee-4.0.1/lidaRtRee/man/tree_extraction.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/tree_inventory_chablais3.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/tree_segmentation.Rd | 15 66 files changed, 1045 insertions(+), 978 deletions(-)
Title: Download Data from Kobotoolbox to R
Description: Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
Author: Asitav Sen [aut, cre, cph]
Maintainer: Asitav Sen <hello@asitavsen.com>
Diff between KoboconnectR versions 1.1.0 dated 2022-05-16 and 1.1.1 dated 2022-05-23
DESCRIPTION | 6 - MD5 | 18 ++-- NAMESPACE | 2 NEWS.md | 5 + R/Koboconnect.R | 68 +++++++++++------- R/other.R | 112 +++++++++++++++++++------------ man/kobo_export_create.Rd | 5 + tests/testthat/test-kobo_df_download.R | 9 +- tests/testthat/test-kobo_export_create.R | 52 ++++++++++---- tests/testthat/test-kobotools_kpi_data.R | 7 - 10 files changed, 183 insertions(+), 101 deletions(-)
Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages
and R modules. The syntax allows for importing multiple objects with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports.
Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut],
Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>
Diff between import versions 1.2.0 dated 2020-09-24 and 1.3.0 dated 2022-05-23
DESCRIPTION | 10 MD5 | 54 +- NEWS.md | 36 + R/S3.R |only R/badge.R |only R/from.R | 106 ++-- R/here.R | 2 R/into.R | 2 R/make_import_call.R | 4 build/vignette.rds |binary inst/WORDLIST |only inst/doc/import.R | 35 + inst/doc/import.Rmd | 119 +++- inst/doc/import.html | 714 ++++++++++++++++++--------- man/figures |only man/importfunctions.Rd | 25 tests/test_import/cleanup_environment.R | 4 tests/test_import/module_S3.R |only tests/test_import/module_hidden_objects.R |only tests/test_import/packageToTest |only tests/test_import/packageToTest_0.1.0.tar.gz |only tests/test_import/test_S3.R |only tests/test_import/test_from.R | 87 +++ tests/test_import/test_hidden_objects.R |only tests/test_import/test_into_and_here.R | 9 tests/test_import/test_into_param.R |only vignettes/import.Rmd | 119 +++- vignettes/lifecycle-experimental.svg |only 28 files changed, 965 insertions(+), 361 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.6 dated 2022-04-15 and 2.6.2 dated 2022-05-23
DESCRIPTION | 8 MD5 | 16 R/gjamHfunctions.R | 974 +++++++++++++++++++++------------------ inst/doc/gjamVignette.R | 8 inst/doc/gjamVignette.Rmd | 10 inst/doc/gjamVignette.html | 86 +-- man/gjam-package.Rd | 4 man/gjamConditionalParameters.Rd | 2 vignettes/gjamVignette.Rmd | 10 9 files changed, 603 insertions(+), 515 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut],
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Joe Heywood [ctb],
Evgeny Mirkes [ctb],
Joan Capdevila Pujol [ctb],
Dan Jackson [ctb],
Lena Kushleyeva [ctb] [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 2.6-0 dated 2022-02-02 and 2.7-0 dated 2022-05-23
DESCRIPTION | 36 MD5 | 196 - NAMESPACE | 11 R/GGIR.R |only R/check_params.R | 31 R/cosinorAnalyses.R |only R/createConfigFile.R | 30 R/create_test_sleeplog_csv.R | 11 R/datadir2fnames.R | 10 R/extract_params.R | 20 R/g.IVIS.R | 113 - R/g.analyse.R | 28 R/g.analyse.avday.R | 104 R/g.analyse.perday.R | 6 R/g.analyse.perfile.R | 255 +- R/g.binread.R | 846 +++---- R/g.calibrate.R | 18 R/g.conv.actlog.R | 2 R/g.convert.part2.long.R | 18 R/g.cwaread.R | 12 R/g.dotorcomma.R | 5 R/g.extractheadervars.R | 17 R/g.getidfromheaderobject.R | 2 R/g.getmeta.R | 8 R/g.getstarttime.R | 2 R/g.imputeTimegaps.R | 44 R/g.inspectfile.R | 137 - R/g.loadlog.R | 74 R/g.part1.R | 28 R/g.part2.R | 62 R/g.part3.R | 21 R/g.part4.R | 78 R/g.part4_extractid.R | 65 R/g.part5.R | 19 R/g.part5.addfirstwake.R | 1 R/g.readaccfile.R | 20 R/g.readtemp_movisens.R | 8 R/g.report.part2.R | 113 - R/g.report.part4.R | 28 R/g.report.part5.R | 22 R/g.shell.GGIR.R | 287 -- R/g.sib.det.R | 3 R/get_nw_clip_block_params.R | 8 R/load_params.R | 32 R/read.myacc.csv.R | 17 R/tidyup_df.R |only build/vignette.rds |binary inst/NEWS.Rd | 77 inst/doc/ExternalFunction.R | 6 inst/doc/ExternalFunction.Rmd | 14 inst/doc/ExternalFunction.pdf |binary inst/doc/GGIR.R | 10 inst/doc/GGIR.Rmd | 137 - inst/doc/GGIR.html | 3484 ++++++++++++++++++++++++++----- inst/doc/TutorialDaySegmentAnalyses.R | 4 inst/doc/TutorialDaySegmentAnalyses.Rmd | 14 inst/doc/TutorialDaySegmentAnalyses.html | 1467 ++++++++++++- inst/doc/readmyacccsv.R |only inst/doc/readmyacccsv.Rmd |only inst/doc/readmyacccsv.html |only man/GGIR-package.Rd | 6 man/GGIR.Rd |only man/applyExtFunction.Rd | 4 man/cosinorAnalyses.Rd |only man/createConfigFile.Rd | 12 man/extract_params.Rd | 9 man/g.IVIS.Rd | 38 man/g.analyse.Rd | 5 man/g.analyse.avday.Rd | 9 man/g.analyse.perday.Rd | 4 man/g.analyse.perfile.Rd | 9 man/g.calibrate.Rd | 4 man/g.cwaread.Rd | 2 man/g.getmeta.Rd | 5 man/g.imputeTimegaps.Rd | 11 man/g.loadlog.Rd | 2 man/g.part1.Rd | 285 -- man/g.part2.Rd | 198 - man/g.part3.Rd | 92 man/g.part4.Rd | 29 man/g.part4_extradctid.Rd | 17 man/g.part5.Rd | 35 man/g.plot5.Rd | 16 man/g.readtemp_movisens.Rd | 2 man/g.report.part2.Rd | 27 man/g.report.part4.Rd | 14 man/g.report.part5.Rd | 14 man/g.shell.GGIR.Rd | 196 - man/get_nw_clip_block_params.Rd | 2 man/read.myacc.csv.Rd | 28 man/tidyup_df.Rd |only tests/testthat/test_chainof5parts.R | 20 tests/testthat/test_cosinor.R |only tests/testthat/test_g.IVIS.R | 33 tests/testthat/test_gbinread.R | 21 tests/testthat/test_gloadlog.R | 50 tests/testthat/test_greadaccfile.R | 40 tests/testthat/test_imputeTimegaps.R | 17 tests/testthat/test_load_check_params.R | 4 tests/testthat/test_part3_1_night.R | 4 tests/testthat/test_tidyup_df.R |only vignettes/ExternalFunction.Rmd | 14 vignettes/GGIR.Rmd | 137 - vignettes/TutorialDaySegmentAnalyses.Rmd | 14 vignettes/readmyacccsv.Rmd |only 105 files changed, 6587 insertions(+), 2903 deletions(-)
Title: Number Names
Description: Converts numeric vectors to character vectors of English
number names. Provides conversion to cardinals, ordinals, numerators,
and denominators. Supports negative and non-integer numbers.
Author: Alexander Rossell Hayes [aut, cre, cph]
,
Eli Pousson [ctb]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between nombre versions 0.4.0 dated 2021-10-25 and 0.4.1 dated 2022-05-23
DESCRIPTION | 14 ++++---- MD5 | 37 ++++++++++----------- NEWS.md | 7 ++++ R/adverbial.R | 26 ++++++++++---- R/cardinal.R | 66 ++++++++++++++++++++++---------------- R/collective.R | 8 +++- R/convert_fraction.R | 12 +++++- R/denominator.R | 33 ++++++++++++------- R/numerator.R | 2 - R/ordinal.R | 55 ++++++++++++------------------- R/ratio.R | 7 ++-- R/uncardinal.R | 12 +++--- R/utils.R |only man/nombre-package.Rd | 4 +- tests/testthat/test-adverbial.R | 8 ++++ tests/testthat/test-cardinal.R | 8 ++++ tests/testthat/test-collective.R | 8 ++++ tests/testthat/test-denominator.R | 8 ++++ tests/testthat/test-ordinal.R | 8 ++++ tests/testthat/test-ratio.R | 10 +++++ 20 files changed, 212 insertions(+), 121 deletions(-)
Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information
returned online by Google Trends is provided. Trends (number of
hits) over the time as well as geographic representation of the
results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.5.0 dated 2021-10-24 and 1.5.1 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/countries.R | 2 +- R/related_queries.R | 1 + R/related_topics.R | 5 +++-- R/zzz.R | 3 +++ man/countries.Rd | 2 +- 8 files changed, 24 insertions(+), 15 deletions(-)
Title: Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares
implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
against convergence issues.
Author: Jared Huling [aut, cre],
Douglas Bates [cph],
Dirk Eddelbuettel [cph],
Romain Francois [cph],
Yixuan Qiu [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between fastglm versions 0.0.2 dated 2022-04-24 and 0.0.3 dated 2022-05-23
fastglm-0.0.2/fastglm/src/bigmemory.h |only fastglm-0.0.2/fastglm/src/glm.h |only fastglm-0.0.2/fastglm/src/glm_base.h |only fastglm-0.0.2/fastglm/src/glm_big.h |only fastglm-0.0.3/fastglm/DESCRIPTION | 6 +-- fastglm-0.0.3/fastglm/MD5 | 16 +++++----- fastglm-0.0.3/fastglm/inst/doc/quick-usage-guide-to-the-fastglm-package.html | 12 +++---- fastglm-0.0.3/fastglm/inst/include |only fastglm-0.0.3/fastglm/src/bigmemory.cpp | 2 - fastglm-0.0.3/fastglm/src/fit_glm_dense.cpp | 2 - 10 files changed, 19 insertions(+), 19 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>
Diff between keras versions 2.8.0 dated 2022-02-09 and 2.9.0 dated 2022-05-23
keras-2.8.0/keras/R/generics.R |only keras-2.9.0/keras/DESCRIPTION | 14 keras-2.9.0/keras/MD5 | 246 +- keras-2.9.0/keras/NAMESPACE | 69 keras-2.9.0/keras/NEWS.md | 104 + keras-2.9.0/keras/R/Layer.R | 27 keras-2.9.0/keras/R/backend.R | 56 keras-2.9.0/keras/R/freeze.R | 124 + keras-2.9.0/keras/R/history.R | 4 keras-2.9.0/keras/R/initializers.R | 4 keras-2.9.0/keras/R/install.R | 17 keras-2.9.0/keras/R/layer-custom.R | 44 keras-2.9.0/keras/R/layer-methods.R | 22 keras-2.9.0/keras/R/layers-convolutional.R | 6 keras-2.9.0/keras/R/layers-core.R | 16 keras-2.9.0/keras/R/layers-noise.R | 30 keras-2.9.0/keras/R/layers-normalization.R | 39 keras-2.9.0/keras/R/layers-preprocessing.R | 48 keras-2.9.0/keras/R/layers-recurrent-cells.R | 2 keras-2.9.0/keras/R/layers-recurrent.R | 2 keras-2.9.0/keras/R/learning_rate_schedules.R |only keras-2.9.0/keras/R/metrics.R | 32 keras-2.9.0/keras/R/model.R | 100 - keras-2.9.0/keras/R/new-py-types.R |only keras-2.9.0/keras/R/package.R | 11 keras-2.9.0/keras/R/preprocessing.R | 205 +- keras-2.9.0/keras/R/py-classes.R | 164 + keras-2.9.0/keras/R/reexports.R | 4 keras-2.9.0/keras/R/regularizers.R | 37 keras-2.9.0/keras/R/utils.R | 241 ++ keras-2.9.0/keras/build/vignette.rds |binary keras-2.9.0/keras/inst/doc/applications.html | 252 +-- keras-2.9.0/keras/inst/doc/custom_layers.html | 569 +++--- keras-2.9.0/keras/inst/doc/custom_models.html | 175 -- keras-2.9.0/keras/inst/doc/faq.html | 823 +++------- keras-2.9.0/keras/inst/doc/functional_api.html | 648 +++---- keras-2.9.0/keras/inst/doc/guide_keras.html | 661 +++----- keras-2.9.0/keras/inst/doc/index.html | 247 --- keras-2.9.0/keras/inst/doc/saving_serializing.html | 483 ++--- keras-2.9.0/keras/inst/doc/sequential_model.html | 759 ++++----- keras-2.9.0/keras/inst/doc/training_callbacks.html | 246 +- keras-2.9.0/keras/inst/doc/training_visualization.html | 284 +-- keras-2.9.0/keras/man/Layer.Rd | 11 keras-2.9.0/keras/man/Metric.Rd | 47 keras-2.9.0/keras/man/adapt.Rd | 8 keras-2.9.0/keras/man/backend.Rd | 2 keras-2.9.0/keras/man/constraints.Rd | 4 keras-2.9.0/keras/man/create_layer_wrapper.Rd | 8 keras-2.9.0/keras/man/evaluate.keras.engine.training.Model.Rd | 2 keras-2.9.0/keras/man/fit.keras.engine.training.Model.Rd | 2 keras-2.9.0/keras/man/fit_generator.Rd | 6 keras-2.9.0/keras/man/freeze_weights.Rd | 49 keras-2.9.0/keras/man/get_config.Rd | 6 keras-2.9.0/keras/man/get_layer.Rd | 3 keras-2.9.0/keras/man/get_weights.Rd | 9 keras-2.9.0/keras/man/grapes-py_class-grapes.Rd | 36 keras-2.9.0/keras/man/grapes-set-active-grapes.Rd | 1 keras-2.9.0/keras/man/image_dataset_from_directory.Rd | 94 - keras-2.9.0/keras/man/initializer_glorot_normal.Rd | 2 keras-2.9.0/keras/man/initializer_glorot_uniform.Rd | 2 keras-2.9.0/keras/man/install_keras.Rd | 8 keras-2.9.0/keras/man/k_clip.Rd | 2 keras-2.9.0/keras/man/k_squeeze.Rd | 2 keras-2.9.0/keras/man/k_unstack.Rd |only keras-2.9.0/keras/man/keras_model_sequential.Rd | 2 keras-2.9.0/keras/man/layer_alpha_dropout.Rd | 38 keras-2.9.0/keras/man/layer_category_encoding.Rd | 1 keras-2.9.0/keras/man/layer_center_crop.Rd | 1 keras-2.9.0/keras/man/layer_conv_1d_transpose.Rd | 6 keras-2.9.0/keras/man/layer_conv_lstm_1d.Rd | 2 keras-2.9.0/keras/man/layer_conv_lstm_2d.Rd | 2 keras-2.9.0/keras/man/layer_conv_lstm_3d.Rd | 2 keras-2.9.0/keras/man/layer_cudnn_lstm.Rd | 2 keras-2.9.0/keras/man/layer_discretization.Rd | 1 keras-2.9.0/keras/man/layer_gru_cell.Rd | 4 keras-2.9.0/keras/man/layer_hashing.Rd | 17 keras-2.9.0/keras/man/layer_integer_lookup.Rd | 1 keras-2.9.0/keras/man/layer_lstm.Rd | 2 keras-2.9.0/keras/man/layer_lstm_cell.Rd | 6 keras-2.9.0/keras/man/layer_normalization.Rd | 1 keras-2.9.0/keras/man/layer_random_brightness.Rd |only keras-2.9.0/keras/man/layer_random_contrast.Rd | 2 keras-2.9.0/keras/man/layer_random_crop.Rd | 2 keras-2.9.0/keras/man/layer_random_flip.Rd | 2 keras-2.9.0/keras/man/layer_random_height.Rd | 2 keras-2.9.0/keras/man/layer_random_rotation.Rd | 2 keras-2.9.0/keras/man/layer_random_translation.Rd | 2 keras-2.9.0/keras/man/layer_random_width.Rd | 2 keras-2.9.0/keras/man/layer_random_zoom.Rd | 2 keras-2.9.0/keras/man/layer_rescaling.Rd | 1 keras-2.9.0/keras/man/layer_resizing.Rd | 1 keras-2.9.0/keras/man/layer_string_lookup.Rd | 1 keras-2.9.0/keras/man/layer_text_vectorization.Rd | 1 keras-2.9.0/keras/man/layer_unit_normalization.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_cosine_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_cosine_decay_restarts.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_exponential_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_inverse_time_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_piecewise_constant_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_polynomial_decay.Rd |only keras-2.9.0/keras/man/loss-functions.Rd | 6 keras-2.9.0/keras/man/metric_categorical_crossentropy.Rd | 6 keras-2.9.0/keras/man/metric_cosine_similarity.Rd | 4 keras-2.9.0/keras/man/metric_hinge.Rd | 4 keras-2.9.0/keras/man/metric_kullback_leibler_divergence.Rd | 4 keras-2.9.0/keras/man/metric_mean.Rd | 12 keras-2.9.0/keras/man/metric_mean_iou.Rd | 6 keras-2.9.0/keras/man/metric_mean_relative_error.Rd | 12 keras-2.9.0/keras/man/metric_mean_wrapper.Rd | 4 keras-2.9.0/keras/man/multi_gpu_model.Rd | 4 keras-2.9.0/keras/man/new-classes.Rd |only keras-2.9.0/keras/man/new_learning_rate_schedule_class.Rd |only keras-2.9.0/keras/man/plot.keras.engine.training.Model.Rd |only keras-2.9.0/keras/man/predict.keras.engine.training.Model.Rd | 6 keras-2.9.0/keras/man/predict_proba.Rd | 12 keras-2.9.0/keras/man/reexports.Rd | 3 keras-2.9.0/keras/man/regularizer_orthogonal.Rd |only keras-2.9.0/keras/man/summary.keras.engine.training.Model.Rd | 13 keras-2.9.0/keras/man/text_dataset_from_directory.Rd | 6 keras-2.9.0/keras/man/time_distributed.Rd | 4 keras-2.9.0/keras/man/timeseries_dataset_from_array.Rd | 63 keras-2.9.0/keras/man/zip_lists.Rd |only keras-2.9.0/keras/tests/testthat/test-Layer.R | 22 keras-2.9.0/keras/tests/testthat/test-freeze.R | 44 keras-2.9.0/keras/tests/testthat/test-layers-normalization.R | 12 keras-2.9.0/keras/tests/testthat/test-layers-preprocessing.R | 7 keras-2.9.0/keras/tests/testthat/test-metrics.R | 3 keras-2.9.0/keras/tests/testthat/test-model-persistence.R | 58 keras-2.9.0/keras/tests/testthat/test-preprocessing.R | 10 keras-2.9.0/keras/tests/testthat/test-py-class.R | 55 keras-2.9.0/keras/tests/testthat/test-utils.R | 52 keras-2.9.0/keras/tools/make-layer-wrapper.R | 4 keras-2.9.0/keras/tools/make-wrapper.R |only 133 files changed, 4071 insertions(+), 3592 deletions(-)
Title: Harmonizing CN8 and PC8 Product Codes
Description: Several functions are provided to harmonize CN8 (Combined Nomenclature
8 digits) and PC8 (Production Communautaire 8 digits) product codes over
time and the classification systems HS6 and BEC. Harmonization of CN8
codes are possible by default from 1995 to 2022 and of PC8 from 2001 to
2021, respectively.
Author: Christoph Baumgartner [cre, aut]
,
Stjepan Srhoj [aut] ,
Janette Walde [aut]
Maintainer: Christoph Baumgartner <Christoph.Baumgartner@uibk.ac.at>
Diff between harmonizer versions 0.2.1 dated 2022-03-07 and 0.3.0 dated 2022-05-23
DESCRIPTION | 22 MD5 | 71 NAMESPACE | 3 NEWS.md | 10 R/cn8_to_bec.R | 56 R/harmonize_cn8.R | 97 R/harmonize_pc8.R | 101 R/history_matrix_cn8.R | 6 R/pc8_to_bec.R | 59 R/utilize_cn8.R | 58 R/utilize_pc8.R | 50 inst/doc/harmonizer.Rmd | 49 inst/doc/harmonizer.html | 671 + inst/extdata/CN8/CN8_2021.rds |only inst/extdata/CN8/CN8_2022.rds |only inst/extdata/CN8/CN8_concordances_1988_2022.csv |only inst/extdata/HS6toBEC/HS1996toBEC.csv |only inst/extdata/HS6toBEC/HS2012toBEC.csv |10411 +++++++++++------------ inst/extdata/HS6toBEC/HS2017toBEC.csv |10775 ++++++++++++------------ inst/extdata/PC8/PC8_2001.rds |only inst/extdata/PC8/PC8_2001_2002.rds |only inst/extdata/PC8/PC8_2002.rds |only inst/extdata/PC8/PC8_2002_2003.rds |only inst/extdata/PC8/PC8_2003.rds |only inst/extdata/PC8/PC8_2003_2004.rds |only inst/extdata/PC8/PC8_2004.rds |only inst/extdata/PC8/PC8_2004_2005.rds |only inst/extdata/PC8/PC8_2005.rds |only inst/extdata/PC8/PC8_2005_2006.rds |only inst/extdata/PC8/PC8_2006.rds |only inst/extdata/PC8/PC8_2006_2007.rds |only inst/extdata/PC8/PC8_2017_2018.rds |only inst/extdata/PC8/PC8_2018.rds |only inst/extdata/PC8/PC8_2018_2019.rds |only inst/extdata/PC8/PC8_2019.rds |only inst/extdata/PC8/PC8_2019_2020.rds |only inst/extdata/PC8/PC8_2020.rds |only inst/extdata/PC8/PC8_2020_2021.rds |only inst/extdata/PC8/PC8_2021.rds |only inst/extdata/PC8/PC8_CN8_2001.rds |only inst/extdata/PC8/PC8_CN8_2002.rds |only inst/extdata/PC8/PC8_CN8_2003.rds |only inst/extdata/PC8/PC8_CN8_2004.rds |only inst/extdata/PC8/PC8_CN8_2005.rds |only inst/extdata/PC8/PC8_CN8_2020.rds |only inst/extdata/PC8/PC8_CN8_2021.rds |only man/harmonize_cn8.Rd | 14 man/harmonize_pc8.Rd | 14 man/history_martix_cn8.Rd | 2 man/utilize_cn8.Rd | 18 man/utilize_pc8.Rd | 18 vignettes/harmonizer.Rmd | 49 52 files changed, 11686 insertions(+), 10868 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 1.1.10 dated 2021-10-22 and 1.1.11 dated 2022-05-23
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NAMESPACE | 4 +++- R/functions.R | 28 +++++++++++++++++++++++++++- R/gsea.R | 2 +- build/vignette.rds |binary inst/doc/corto_vignette.html | 6 +++++- man/barplot2.Rd |only 8 files changed, 49 insertions(+), 16 deletions(-)
Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis provided, as described in for CATA data analysis by Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis. The quality of cluster analysis solutions can be evaluated using various measures. The methods related to b-cluster analysis are described in a manuscript by Castura, Meyners, Varela & Naes (2022) <doi:10.1016/j.foodqual.2022.104564>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>
Diff between cata versions 0.0.10.8 dated 2022-03-05 and 0.0.10.9 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cata.R | 2 +- build/partial.rdb |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.5.0 dated 2021-12-16 and 2.6.2 dated 2022-05-23
rfacebookstat-2.5.0/rfacebookstat/build/vignette.rds |only rfacebookstat-2.5.0/rfacebookstat/inst/doc |only rfacebookstat-2.5.0/rfacebookstat/vignettes |only rfacebookstat-2.6.2/rfacebookstat/DESCRIPTION | 12 rfacebookstat-2.6.2/rfacebookstat/MD5 | 72 +-- rfacebookstat-2.6.2/rfacebookstat/NEWS.md | 20 rfacebookstat-2.6.2/rfacebookstat/R/authorization.R | 18 rfacebookstat-2.6.2/rfacebookstat/R/fbActions.R | 235 +++++----- rfacebookstat-2.6.2/rfacebookstat/R/fbDeleteAdAccountUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountCustomAudiences.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountUsersPermissions.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccounts.R | 6 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountsConversions.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdCreative.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdSets.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdVideos.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAds.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetApps.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetBusinessManagers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetBusinessManagersUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetBusinessUserAdAccounts.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetCampaigns.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetCatalogs.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetLongTimeToken.R |only rfacebookstat-2.6.2/rfacebookstat/R/fbGetMarketingStat.R | 8 rfacebookstat-2.6.2/rfacebookstat/R/fbGetPages.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetUserAdAccounts.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbUpdateAdAccountUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/zzz.R | 2 rfacebookstat-2.6.2/rfacebookstat/README.md | 119 ----- rfacebookstat-2.6.2/rfacebookstat/build/partial.rdb |binary rfacebookstat-2.6.2/rfacebookstat/man/fbGetCostData.Rd | 5 rfacebookstat-2.6.2/rfacebookstat/man/fbGetToken.Rd | 58 +- 34 files changed, 269 insertions(+), 330 deletions(-)
Title: 'Rcmdr' Plug-in GUI for Biclustering
Description: A plug-in for R Commander ('Rcmdr'). The package is a Graphical
User Interface (GUI) in which several biclustering methods can be executed,
followed by diagnostics and plots of the results. Further, the GUI also has
the possibility to connect the methods to more general diagnostic packages for
biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG',
'isa2', 'BiBitR', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and
'BcDiag' are also implemented to be able to further investigate results. The
GUI also provides a couple of extra utilities to export, save, search through
and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific
framework for biclustering in which new methods, diagnostics and plots can be
added. Scripts were prepared so that R-package developers can freely design
their own dialogs in the GUI which can then be added by the maintainer of
'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk'
and 'Rcmdr' and are easy to fill in. (Note: rqubic currently requires manual installation through BiocManager::install('rqubic').)
Author: De Troyer Ewoud, Otava Martin
Maintainer: De Troyer Ewoud <ewoud.detroyer@uhasselt.be>
Diff between RcmdrPlugin.BiclustGUI versions 1.1.3 dated 2020-07-13 and 1.1.3.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/doc/GuideBiclustGUI.pdf |binary 3 files changed, 5 insertions(+), 5 deletions(-)
More information about RcmdrPlugin.BiclustGUI at CRAN
Permanent link
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F,
Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Author: Thibaut Jombart [aut],
Finlay Campbell [aut, cre],
Rich Fitzjohn [aut],
Gerry Tonkin-Hill [ctb],
Kristjan Eldjarn [ctb],
Alexis Robert [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Diff between outbreaker2 versions 1.1.2 dated 2021-02-09 and 1.1.3 dated 2022-05-23
outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_new_move_5726c9b3e30924d986e3e44ffd6e0036.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_new_move_5726c9b3e30924d986e3e44ffd6e0036.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_new_move_5726c9b3e30924d986e3e44ffd6e0036.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_null_model_d112d898e13cade05279d2d90d34e60f.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_null_model_d112d898e13cade05279d2d90d34e60f.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_null_model_d112d898e13cade05279d2d90d34e60f.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_wt_ffbe1bb0ebffddc18bb5d3ae3b1b3a5f.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_wt_ffbe1bb0ebffddc18bb5d3ae3b1b3a5f.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_wt_ffbe1bb0ebffddc18bb5d3ae3b1b3a5f.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/config2_e0d3ea2635745de041b80aae763904c7.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/config2_e0d3ea2635745de041b80aae763904c7.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/config2_e0d3ea2635745de041b80aae763904c7.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/first_run_931e937e4e7a0450deb5a082d5d9b15b.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/first_run_931e937e4e7a0450deb5a082d5d9b15b.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/first_run_931e937e4e7a0450deb5a082d5d9b15b.rdx |only outbreaker2-1.1.3/outbreaker2/DESCRIPTION | 12 outbreaker2-1.1.3/outbreaker2/MD5 | 86 outbreaker2-1.1.3/outbreaker2/NEWS.md | 13 outbreaker2-1.1.3/outbreaker2/R/get_cpp_api.R | 204 - outbreaker2-1.1.3/outbreaker2/R/outbreaker_data.R | 3 outbreaker2-1.1.3/outbreaker2/R/package.R | 82 outbreaker2-1.1.3/outbreaker2/R/palettes.R | 6 outbreaker2-1.1.3/outbreaker2/R/ref_priors.R | 100 outbreaker2-1.1.3/outbreaker2/R/zzz.R | 20 outbreaker2-1.1.3/outbreaker2/build/vignette.rds |binary outbreaker2-1.1.3/outbreaker2/inst/doc/Rcpp_API.html | 18 outbreaker2-1.1.3/outbreaker2/inst/doc/customisation.Rmd | 1370 +++++----- outbreaker2-1.1.3/outbreaker2/inst/doc/customisation.html | 42 outbreaker2-1.1.3/outbreaker2/inst/doc/introduction.html | 592 ++-- outbreaker2-1.1.3/outbreaker2/inst/doc/overview.html | 14 outbreaker2-1.1.3/outbreaker2/man/custom_likelihoods.Rd | 194 - outbreaker2-1.1.3/outbreaker2/man/get_cpp_api.Rd | 184 - outbreaker2-1.1.3/outbreaker2/man/outbreaker_package.Rd | 82 outbreaker2-1.1.3/outbreaker2/man/palettes.Rd | 2 outbreaker2-1.1.3/outbreaker2/src/RcppExports.cpp | 5 outbreaker2-1.1.3/outbreaker2/tests/testthat/test_sim_ctd.R | 56 outbreaker2-1.1.3/outbreaker2/vignettes/customisation.Rmd | 1370 +++++----- outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/__packages | 1 outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/figs-customisation/res_null_priors-1.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-customisation/traces_custom_priors-4.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-customisation/traces_custom_priors-5.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-introduction/many_plots-1.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-introduction/many_plots-2.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/__packages | 1 outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdx |only 59 files changed, 2320 insertions(+), 2137 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 2.0.6 dated 2022-05-12 and 2.0.7 dated 2022-05-23
nlmixr2est-2.0.6/nlmixr2est/R/mu-cov-downgrade.R |only nlmixr2est-2.0.7/nlmixr2est/DESCRIPTION | 10 - nlmixr2est-2.0.7/nlmixr2est/MD5 | 48 +++--- nlmixr2est-2.0.7/nlmixr2est/NAMESPACE | 1 nlmixr2est-2.0.7/nlmixr2est/NEWS.md | 19 ++ nlmixr2est-2.0.7/nlmixr2est/R/augPred.R | 49 ++++-- nlmixr2est-2.0.7/nlmixr2est/R/nlme.R | 6 nlmixr2est-2.0.7/nlmixr2est/R/nlmeRxUiGet.R | 2 nlmixr2est-2.0.7/nlmixr2est/R/nlmixr2Est.R | 57 ++++--- nlmixr2est-2.0.7/nlmixr2est/R/nlmixr2_md5.R |only nlmixr2est-2.0.7/nlmixr2est/R/nmObjHandle.R | 1 nlmixr2est-2.0.7/nlmixr2est/R/preProcessModel.R | 9 - nlmixr2est-2.0.7/nlmixr2est/R/saem.R | 3 nlmixr2est-2.0.7/nlmixr2est/R/saemRxUiGetModel.R | 21 +- nlmixr2est-2.0.7/nlmixr2est/R/sharedControl.R | 2 nlmixr2est-2.0.7/nlmixr2est/R/validate.R | 1 nlmixr2est-2.0.7/nlmixr2est/R/vpc.R | 30 +++- nlmixr2est-2.0.7/nlmixr2est/man/dot-saemDropMuRefFromModel.Rd | 4 nlmixr2est-2.0.7/nlmixr2est/man/vpcSim.Rd | 13 + nlmixr2est-2.0.7/nlmixr2est/src/inner.cpp | 73 +++++----- nlmixr2est-2.0.7/nlmixr2est/tests/testthat.R | 8 - nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-augpred.R | 32 ++++ nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-focei-wang2007.R | 8 - nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-saem-translate.R | 6 nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-update-estimates.R | 62 ++++---- nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-vpcSim.R | 14 - 26 files changed, 300 insertions(+), 179 deletions(-)
Title: Tools for Plotting Skew-T Diagrams and Wind Profiles
Description: A
collection of programs for
plotting SKEW-T,log p diagrams and wind profiles for data
collected by radiosondes (the typical weather balloon-borne
instrument). The format of this plot with companion lines to
assess atmospheric stability are both standard in meteorology
and difficult to create from basic graphics functions. Hence
this package. One novel feature is being able add several
profiles to the same plot for comparison.
Use "help(ExampleSonde)" for an explanation of the variables
needed and how they should be named in a data frame. See
<https://github.com/dnychka/Radiosonde> for the package home page.
Author: Doug Nychka, Eric Gilleland, Liangying Zhang, Tim Hoar, Kate Young
Maintainer: Doug Nychka <nychka@mines.edu>
Diff between RadioSonde versions 1.4 dated 2014-09-17 and 4.2 dated 2022-05-23
RadioSonde-1.4/RadioSonde/R/PWV.R |only RadioSonde-1.4/RadioSonde/R/getsonde.R |only RadioSonde-1.4/RadioSonde/R/plotsonde.R |only RadioSonde-1.4/RadioSonde/R/plotwind.R |only RadioSonde-1.4/RadioSonde/R/skewt.axis.R |only RadioSonde-1.4/RadioSonde/R/skewt.data.R |only RadioSonde-1.4/RadioSonde/R/skewt.points.R |only RadioSonde-1.4/RadioSonde/R/td.to.q.R |only RadioSonde-1.4/RadioSonde/data/ExampleSonde.rda |only RadioSonde-1.4/RadioSonde/data/ExampleSondeText.rda |only RadioSonde-1.4/RadioSonde/man/PWV.Rd |only RadioSonde-1.4/RadioSonde/man/getsonde.Rd |only RadioSonde-1.4/RadioSonde/man/plotsonde.Rd |only RadioSonde-1.4/RadioSonde/man/plotwind.Rd |only RadioSonde-1.4/RadioSonde/man/skewt.axis.Rd |only RadioSonde-1.4/RadioSonde/man/skewt.points.Rd |only RadioSonde-4.2/RadioSonde/DESCRIPTION | 33 ++++-- RadioSonde-4.2/RadioSonde/MD5 | 41 +++----- RadioSonde-4.2/RadioSonde/NAMESPACE | 8 + RadioSonde-4.2/RadioSonde/R/plotWind.R |only RadioSonde-4.2/RadioSonde/R/setupSkewt.R |only RadioSonde-4.2/RadioSonde/R/skewtPlot.R |only RadioSonde-4.2/RadioSonde/R/skewtUtilities.R |only RadioSonde-4.2/RadioSonde/R/skewty.R | 2 RadioSonde-4.2/RadioSonde/R/station.symbol.R | 9 + RadioSonde-4.2/RadioSonde/data/sonde1.RData |only RadioSonde-4.2/RadioSonde/data/sonde2.RData |only RadioSonde-4.2/RadioSonde/inst |only RadioSonde-4.2/RadioSonde/man/Example.Rd | 90 +++++++++++-------- RadioSonde-4.2/RadioSonde/man/RadioSonde-internal.Rd | 38 ++++++-- RadioSonde-4.2/RadioSonde/man/plotWind.Rd |only RadioSonde-4.2/RadioSonde/man/skewt.lines.Rd | 19 ---- RadioSonde-4.2/RadioSonde/man/skewtPlot.Rd |only RadioSonde-4.2/RadioSonde/man/station.symbol.Rd | 18 ++- 34 files changed, 148 insertions(+), 110 deletions(-)
Title: Metabolomics-Based Models for Imputing Risk
Description: Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Author: Daniele Bizzarri [aut, cre] ,
Marcel Reinders [aut, ths] ,
Marian Beekman [aut] ,
Pieternella Eline Slagboom [aut, ths]
,
Erik van den Akker [aut, ths]
Maintainer: Daniele Bizzarri <d.bizzarri@lumc.nl>
Diff between MiMIR versions 1.3 dated 2022-05-18 and 1.4 dated 2022-05-23
DESCRIPTION | 8 - MD5 | 60 +++++++------- R/datasets.R | 24 ++--- R/launchApp.R | 10 +- R/predictors_functions.R | 40 +++------ R/utils.R | 14 +-- inst/shinyApp/tabs/tab_surro_tables/server_surro_tables.R | 30 ++----- man/Ahola_Olli_betas.Rd | 2 man/BBMRI_hist_plot.Rd | 8 - man/BMI_LDL_eGFR.Rd | 6 - man/CVD_score_betas.Rd | 2 man/PARAM_metaboAge.Rd | 2 man/QCprep.Rd | 2 man/apply.fit.Rd | 2 man/apply.scale.Rd | 2 man/comp.CVD_score.Rd | 11 -- man/comp.T2D_Ahola_Olli.Rd | 2 man/comp.mort_score.Rd | 2 man/impute_miss.Rd | 2 man/metabolites_subsets.Rd | 8 - man/mort_betas.Rd | 2 man/plattCalibration.Rd | 2 man/prep_met_for_scores.Rd | 6 - man/report.dim.Rd | 2 man/startApp.Rd | 10 +- man/subset_metabolites_overlap.Rd | 2 man/subset_samples_miss.Rd | 2 man/subset_samples_sd.Rd | 2 man/subset_samples_zero.Rd | 2 man/synthetic_metabolic_dataset.Rd | 4 man/synthetic_phenotypic_dataset.Rd | 4 31 files changed, 125 insertions(+), 150 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria.
Optimization methods are available nonsmooth reformulation, fixed-point formulation,
minimization problem and constrained-equation reformulation.
See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between GNE versions 0.99-3.1 dated 2022-05-23 and 0.99-4 dated 2022-05-23
GNE-0.99-3.1/GNE/inst/TODOlist.txt |only GNE-0.99-3.1/GNE/vignettes/img |only GNE-0.99-4/GNE/DESCRIPTION | 10 +++++----- GNE-0.99-4/GNE/MD5 | 21 +++++++++------------ GNE-0.99-4/GNE/R/solv-eq.R | 2 +- GNE-0.99-4/GNE/R/solv-minpb.R | 4 ++-- GNE-0.99-4/GNE/R/util-minfindingFunc.R | 14 ++++++++------ GNE-0.99-4/GNE/build/vignette.rds |binary GNE-0.99-4/GNE/inst/NEWS | 5 +++++ GNE-0.99-4/GNE/inst/doc/GNE-howto.Rnw | 24 ++++++++++++------------ GNE-0.99-4/GNE/inst/doc/GNE-howto.pdf |binary GNE-0.99-4/GNE/vignettes/GNE-howto.Rnw | 24 ++++++++++++------------ 12 files changed, 54 insertions(+), 50 deletions(-)
Title: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment,
Peak Based Processing, Quantitative Analysis and Visualizations
Description: Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
Author: Charlie Beirnaert, Trung Nghia Vu, Pieter Meysman, Kris Laukens and Dirk Valkenborg
Maintainer: Charlie Beirnaert <charlie_beirnaert@icloud.com>
Diff between speaq versions 2.6.1 dated 2019-12-10 and 2.7.0 dated 2022-05-23
speaq-2.6.1/speaq/data/datalist |only speaq-2.7.0/speaq/DESCRIPTION | 13 - speaq-2.7.0/speaq/MD5 | 21 +- speaq-2.7.0/speaq/NAMESPACE | 1 speaq-2.7.0/speaq/NEWS.md | 6 speaq-2.7.0/speaq/R/SCANT.R | 16 - speaq-2.7.0/speaq/R/Winedata.R | 2 speaq-2.7.0/speaq/build/vignette.rds |binary speaq-2.7.0/speaq/inst/doc/classic_speaq_vignette.html | 150 ++++++++++------- speaq-2.7.0/speaq/inst/doc/speaq2_illustrations.html | 69 ++++--- speaq-2.7.0/speaq/man/SCANT.Rd | 6 speaq-2.7.0/speaq/man/Winedata.Rd | 6 12 files changed, 170 insertions(+), 120 deletions(-)
Title: HTML Exportation for R Objects
Description: Includes HTML function and methods to write in an HTML
file. Thus, making HTML reports is easy. Includes a function
that allows redirection on the fly, which appears to be very
useful for teaching purpose, as the student can keep a copy of
the produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for 'Sweave'
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and
graphs).
Author: Eric Lecoutre [aut],
Milan Bouchet-Valat [cre, ctb],
Thomas Friedrichsmeier [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between R2HTML versions 2.3.2 dated 2016-06-23 and 2.3.3 dated 2022-05-23
DESCRIPTION | 8 MD5 | 86 NAMESPACE | 398 - NEWS | 336 - R/HTMLcore.R | 8198 +++++++++++++------------- R/HTMLlme.R | 458 - R/LaTeX.R | 84 R/grid.R | 594 - demo/00Index | 6 demo/dataframe.R | 10 demo/equations.R | 24 demo/grids.R | 28 inst/CITATION | 2 inst/doc/R2HTML.css | 72 inst/doc/dynamic.html | 6 inst/doc/dynamic_main.html | 44 inst/doc/dynamic_menu.html | 14 inst/doc/page1.html | 4 inst/doc/page2.html | 6 inst/doc/page3.html | 24 inst/doc/page4.html | 12 inst/output/Pastel.css | 164 inst/output/R2HTML.css | 490 - inst/output/SciViews.css | 160 inst/output/gridR2HTML.css | 14 inst/output/gridR2HTML.js | 558 - inst/output/runtime/lib/grid.js | 44 inst/output/runtime/styles/classic/Picasa.ini | 10 inst/output/runtime/styles/classic/grid.css | 44 inst/output/runtime/styles/flat/Picasa.ini | 10 inst/output/runtime/styles/flat/grid.css | 44 inst/output/runtime/styles/xp/Picasa.ini | 10 inst/output/runtime/styles/xp/grid.css | 64 inst/output/tablesort.htc | 412 - inst/samples/Pastel.css | 98 inst/samples/R2HTML.css | 118 inst/samples/example1.html | 82 inst/samples/example1.snw | 78 inst/samples/example2.html | 134 inst/samples/example2.snw | 104 inst/samples/example3.html | 158 inst/samples/example3.snw | 196 inst/samples/index.html | 130 man/HTMLInsertGraph.Rd | 2 44 files changed, 6773 insertions(+), 6765 deletions(-)
Title: Elitist Non-Dominated Sorting Genetic Algorithm
Description: Box-constrained multiobjective optimization using the
elitist non-dominated sorting genetic algorithm - NSGA-II.
Fast non-dominated sorting, crowding distance, tournament
selection, simulated binary crossover, and polynomial
mutation are called in the main program. The methods are
described in Deb et al. (2002) <doi:10.1109/4235.996017>.
Author: Ching-Shih Tsou <cstsou@mail.ntcb.edu.tw>
Maintainer: Ming-Chang (Alan) Lee <alan9956@ydu.edu.tw>
Diff between nsga2R versions 1.0 dated 2013-06-16 and 1.1 dated 2022-05-23
DESCRIPTION | 22 +++++++++++----------- MD5 | 4 ++-- NAMESPACE | 4 +++- 3 files changed, 16 insertions(+), 14 deletions(-)
Title: Implementation of the SVM-Maj Algorithm
Description: Implements the SVM-Maj algorithm to train data with support vector machine
as described in Groenen et al. (2008) <doi:10.1007/s11634-008-0020-9>.
This algorithm uses two efficient updates, one for linear kernel and one
for the nonlinear kernel.
Author: Hoksan Yip, Patrick J.F. Groenen, Georgi Nalbantov
Maintainer: Hok San Yip <hoksan@gmail.com>
Diff between SVMMaj versions 0.2.9 dated 2019-01-26 and 0.2.9.1 dated 2022-05-23
SVMMaj-0.2.9.1/SVMMaj/DESCRIPTION | 6 +++--- SVMMaj-0.2.9.1/SVMMaj/MD5 | 14 +++++++------- SVMMaj-0.2.9.1/SVMMaj/build/vignette.rds |binary SVMMaj-0.2.9.1/SVMMaj/data/AusCredit.rda |only SVMMaj-0.2.9.1/SVMMaj/data/diabetes.rda |only SVMMaj-0.2.9.1/SVMMaj/data/supermarket1996.RData |binary SVMMaj-0.2.9.1/SVMMaj/data/voting.rda |only SVMMaj-0.2.9.1/SVMMaj/inst/doc/paper.pdf |binary SVMMaj-0.2.9/SVMMaj/data/AusCredit.r |only SVMMaj-0.2.9/SVMMaj/data/diabetes.r |only SVMMaj-0.2.9/SVMMaj/data/voting.r |only 11 files changed, 10 insertions(+), 10 deletions(-)
Title: Breiman and Cutler's Random Forests for Classification and
Regression
Description: Classification and regression based on a forest of trees using random inputs, based on Breiman (2001) <DOI:10.1023/A:1010933404324>.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between randomForest versions 4.7-1 dated 2022-02-03 and 4.7-1.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- data/imports85.rda |binary man/combine.Rd | 2 +- man/getTree.Rd | 2 +- man/grow.Rd | 2 +- man/partialPlot.Rd | 2 +- man/predict.randomForest.Rd | 4 ++-- man/randomForest.Rd | 4 ++-- man/treesize.Rd | 2 +- man/varImpPlot.Rd | 2 +- 11 files changed, 23 insertions(+), 23 deletions(-)
Title: Convenient Tool for Solving the Prize-Collecting Steiner Tree
Problem
Description: The Prize-Collecting Steiner Tree problem asks to find a subgraph
connecting a given set of vertices with the most expensive nodes and least
expensive edges. Since it is proven to be NP-hard, exact and efficient algorithm
does not exist. This package provides convenient functionality for obtaining an
approximate solution to this problem using loopy belief propagation algorithm.
Author: Aleksei Krasikov <krasikov.as@phystech.edu>
Maintainer: Aleksei Krasikov <krasikov.as@phystech.edu>
Diff between pcSteiner versions 1.0.0 dated 2020-08-31 and 1.0.0.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/tutorial.pdf |binary 4 files changed, 6 insertions(+), 6 deletions(-)
Title: Variational Autoencoder Models for IRT Parameter Estimation
Description: Based on the work of Curi, Converse, Hajewski, and Oliveira (2019) <doi:10.1109/IJCNN.2019.8852333>. This package provides easy-to-use functions which create a variational autoencoder (VAE) to be used for parameter estimation in Item Response Theory (IRT) - namely the Multidimensional Logistic 2-Parameter (ML2P) model. To use a neural network as such, nontrivial modifications to the architecture must be made, such as restricting the nonzero weights in the decoder according to some binary matrix Q. The functions in this package allow for straight-forward construction, training, and evaluation so that minimal knowledge of 'tensorflow' or 'keras' is required.
Author: Geoffrey Converse [aut, cre, cph],
Suely Oliveira [ctb, ths],
Mariana Curi [ctb]
Maintainer: Geoffrey Converse <converseg@gmail.com>
Diff between ML2Pvae versions 1.0.0 dated 2020-11-16 and 1.0.0.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- build/vignette.rds |binary data/correlation_matrix.rda |binary data/diff_true.rda |binary data/disc_true.rda |binary data/q_matrix.rda |binary data/responses.rda |binary data/theta_true.rda |binary inst/doc/ml2p_vae_vignette.pdf |binary 10 files changed, 12 insertions(+), 12 deletions(-)
Title: Limited-memory BFGS Optimization
Description: A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of minimizing an objective, given its gradient, by iteratively computing approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the optimum of an objective plus the L1-norm of the problem's parameters. The package offers a fast and memory-efficient implementation of these optimization routines, which is particularly suited for high-dimensional problems.
Author: Antonio Coppola [aut, cre, cph],
Brandon Stewart [aut, cph],
Naoaki Okazaki [aut, cph],
David Ardia [ctb, cph],
Dirk Eddelbuettel [ctb, cph],
Katharine Mullen [ctb, cph],
Jorge Nocedal [ctb, cph]
Maintainer: Antonio Coppola <acoppola@college.harvard.edu>
Diff between lbfgs versions 1.2.1 dated 2014-08-31 and 1.2.1.1 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 3 ++- build/vignette.rds |binary data/Leukemia.RData |binary inst/doc/Vignette.pdf |binary 6 files changed, 11 insertions(+), 10 deletions(-)
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binsearch'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- generate significance stars from p-values ('stars.pval'),
- convert characters to/from ASCII codes ('asc', 'chr'),
- convert character vector to ASCII representation ('ASCIIfy'),
- apply title capitalization rules to a character vector ('capwords').
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gtools versions 3.9.2 dated 2021-06-06 and 3.9.2.1 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- data/ELISA.rda |binary data/badDend.rda |binary man/checkRVersion.Rd | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria.
Optimization methods are available nonsmooth reformulation, fixed-point formulation,
minimization problem and constrained-equation reformulation.
See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between GNE versions 0.99-3 dated 2020-01-08 and 0.99-3.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/GNE-howto.R | 1 - inst/doc/GNE-howto.pdf |binary 5 files changed, 7 insertions(+), 8 deletions(-)
Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications
including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford ,
Sunil Arya and David Mount , Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>
Diff between FNN versions 1.1.3 dated 2019-02-15 and 1.1.3.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- man/KL.dist.Rd | 2 +- man/KL.divergence.Rd | 2 +- man/crossentropy.Rd | 2 +- man/entropy.Rd | 2 +- man/get.knn.Rd | 2 +- man/knn.Rd | 2 +- man/knn.cv.Rd | 2 +- man/knn.dist.Rd | 2 +- man/knn.index.Rd | 2 +- man/knn.reg.Rd | 2 +- man/mutual_information.Rd | 2 +- man/ownn.rd | 2 +- man/print.knnRegCV.Rd | 2 +- 15 files changed, 30 insertions(+), 30 deletions(-)
Title: Family of Lasso Regression
Description: Provide the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output. For more information, please refer to <https://www.jmlr.org/papers/volume16/li15a/li15a.pdf>.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan, and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>
Diff between flare versions 1.7.0 dated 2020-11-30 and 1.7.0.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary data/eyedata.rda |binary inst/doc/vignette.pdf |binary 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.8.6 dated 2022-04-13 and 0.8.7 dated 2022-05-23
bruceR-0.8.6/bruceR/R/bruceR_basic.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_01_basic.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_02_scale.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_03_manova.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_04_regress.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_05_advance.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_06_plot.R |only bruceR-0.8.6/bruceR/man/figures/logo.gif |only bruceR-0.8.7/bruceR/DESCRIPTION | 15 - bruceR-0.8.7/bruceR/MD5 | 136 +++++----- bruceR-0.8.7/bruceR/NAMESPACE | 16 + bruceR-0.8.7/bruceR/NEWS.md | 13 bruceR-0.8.7/bruceR/R/bruceR-stats_1_basic.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_2_scale.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_3_manova.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_4_regress.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_5_advance.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_6_plot.R |only bruceR-0.8.7/bruceR/R/bruceR.R | 38 +- bruceR-0.8.7/bruceR/R/bruceR_utils.R |only bruceR-0.8.7/bruceR/README.md | 31 +- bruceR-0.8.7/bruceR/man/Alpha.Rd | 20 - bruceR-0.8.7/bruceR/man/CFA.Rd | 2 bruceR-0.8.7/bruceR/man/Corr.Rd | 20 - bruceR-0.8.7/bruceR/man/Describe.Rd | 20 - bruceR-0.8.7/bruceR/man/EFA.Rd | 2 bruceR-0.8.7/bruceR/man/EMMEANS.Rd | 15 - bruceR-0.8.7/bruceR/man/Freq.Rd | 2 bruceR-0.8.7/bruceR/man/GLM_summary.Rd | 2 bruceR-0.8.7/bruceR/man/HLM_ICC_rWG.Rd | 2 bruceR-0.8.7/bruceR/man/HLM_summary.Rd | 2 bruceR-0.8.7/bruceR/man/LOOKUP.Rd | 2 bruceR-0.8.7/bruceR/man/MANOVA.Rd | 19 + bruceR-0.8.7/bruceR/man/PROCESS.Rd | 2 bruceR-0.8.7/bruceR/man/Print.Rd | 2 bruceR-0.8.7/bruceR/man/RECODE.Rd | 6 bruceR-0.8.7/bruceR/man/RESCALE.Rd | 8 bruceR-0.8.7/bruceR/man/RGB.Rd | 2 bruceR-0.8.7/bruceR/man/Run.Rd | 2 bruceR-0.8.7/bruceR/man/TTEST.Rd | 2 bruceR-0.8.7/bruceR/man/add.Rd |only bruceR-0.8.7/bruceR/man/bruceR-demodata.Rd | 3 bruceR-0.8.7/bruceR/man/bruceR-package.Rd | 14 - bruceR-0.8.7/bruceR/man/cc.Rd | 11 bruceR-0.8.7/bruceR/man/ccf_plot.Rd | 2 bruceR-0.8.7/bruceR/man/cor_diff.Rd | 4 bruceR-0.8.7/bruceR/man/dtime.Rd | 2 bruceR-0.8.7/bruceR/man/export.Rd | 2 bruceR-0.8.7/bruceR/man/formatF.Rd | 2 bruceR-0.8.7/bruceR/man/formatN.Rd | 2 bruceR-0.8.7/bruceR/man/formula_expand.Rd | 2 bruceR-0.8.7/bruceR/man/formula_paste.Rd | 2 bruceR-0.8.7/bruceR/man/grand_mean_center.Rd | 2 bruceR-0.8.7/bruceR/man/granger_causality.Rd | 4 bruceR-0.8.7/bruceR/man/granger_test.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-allin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-anyin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-grapes-COMPUTE-grapes-grapes.Rd | 72 ++++- bruceR-0.8.7/bruceR/man/grapes-nonein-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-notin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-partin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-pow-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/group_mean_center.Rd | 2 bruceR-0.8.7/bruceR/man/import.Rd | 2 bruceR-0.8.7/bruceR/man/lavaan_summary.Rd | 2 bruceR-0.8.7/bruceR/man/med_summary.Rd | 2 bruceR-0.8.7/bruceR/man/model_summary.Rd | 2 bruceR-0.8.7/bruceR/man/p.Rd | 2 bruceR-0.8.7/bruceR/man/pkg_depend.Rd | 4 bruceR-0.8.7/bruceR/man/pkg_install_suggested.Rd | 2 bruceR-0.8.7/bruceR/man/print_table.Rd | 2 bruceR-0.8.7/bruceR/man/regress.Rd | 2 bruceR-0.8.7/bruceR/man/rep_char.Rd | 2 bruceR-0.8.7/bruceR/man/scaler.Rd | 2 bruceR-0.8.7/bruceR/man/set.wd.Rd | 2 bruceR-0.8.7/bruceR/man/show_colors.Rd | 2 bruceR-0.8.7/bruceR/man/theme_bruce.Rd | 8 77 files changed, 332 insertions(+), 225 deletions(-)
Title: Robust Quality Control Chart
Description: Constructs various robust quality control charts based on the median or Hodges-Lehmann estimator (location) and the median absolute deviation (MAD) or Shamos estimator (scale). The estimators used for the robust control charts are all unbiased with a sample of finite size. For more details, see Park, Kim and Wang (2022) <doi:10.1080/03610918.2019.1699114>. In addition, using this R package, the conventional quality control charts such as X-bar, S, R, p, np, u, c, g and h charts are also easily constructed. This work was partially supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (NRF-2017R1A2B4004169).
Author: Chanseok Park [aut, cre] ,
Min Wang [ctb]
Maintainer: Chanseok Park <statpnu@gmail.com>
Diff between rQCC versions 2.22.1 dated 2022-01-25 and 2.22.5 dated 2022-05-23
DESCRIPTION | 8 +- MD5 | 64 ++++++++++--------- NAMESPACE | 10 ++- R/racc.R |only build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 +++--- inst/NEWS.Rd | 10 ++- inst/doc/acc.Rnw | 21 +++--- inst/doc/acc.pdf |binary inst/doc/d3-calculations.pdf |only inst/doc/factors.cc.Rnw | 1 inst/doc/factors.cc.pdf |binary inst/doc/racc.Rnw |only inst/doc/racc.pdf |only inst/doc/rcc.Rnw | 5 - inst/doc/rcc.pdf |binary man/HL.Rd | 3 man/MAD.Rd | 3 man/RE.Rd | 3 man/Shamos.Rd | 3 man/acc.Rd | 21 +++--- man/evar.Rd | 3 man/finite.breakdown.Rd | 3 man/n.times.eBias.Rd | 3 man/n.times.eVar.Rd | 3 man/plot.Rd | 5 + man/pooledEstimator.Rd | 3 man/racc.Rd |only man/rcc.Rd | 3 man/unbiasing.factor.Rd | 3 vignettes/acc.Rnw | 21 +++--- vignettes/factors.cc.Rnw | 1 vignettes/rQCC.bib | 140 +++++++++++++++++++++++++++++-------------- vignettes/racc.Rnw |only vignettes/rcc.Rnw | 5 - 36 files changed, 234 insertions(+), 133 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.3.0 dated 2022-02-21 and 1.3.1 dated 2022-05-23
DESCRIPTION | 8 +- MD5 | 64 ++++++++-------- NEWS.md | 10 ++ R/ichimoku-package.R | 4 - R/iplot.R | 2 R/methods.R | 29 ++++--- R/mltools.R | 41 +++++----- R/oanda.R | 78 +++++++++++--------- R/plot.R | 18 +++- R/sysdata.rda |binary R/utils.R | 22 +++++ README.md | 2 build/vignette.rds |binary inst/doc/reference.R | 3 inst/doc/reference.Rmd | 9 ++ inst/doc/reference.html | 136 +++++++++++++++++++---------------- inst/doc/strategies.Rmd | 2 inst/doc/strategies.html | 103 +++++++++++++-------------- inst/doc/utilities.Rmd | 2 inst/doc/utilities.html | 14 +-- inst/doc/xoanda.Rmd | 4 - inst/doc/xoanda.html | 43 ++++++----- man/autoplot.ichimoku.Rd | 5 - man/figures/README-ichimoku-1.png |binary man/ichimoku-package.Rd | 2 man/oanda_chart.Rd | 5 - man/plot.ichimoku.Rd | 5 - src/shikokuchuo.c | 144 +++++++++++++++++--------------------- tests/testthat/test-plot.R | 5 - vignettes/reference.Rmd | 9 ++ vignettes/strategies.Rmd | 2 vignettes/utilities.Rmd | 2 vignettes/xoanda.Rmd | 4 - 33 files changed, 427 insertions(+), 350 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.3.1 dated 2022-04-13 and 0.3.2 dated 2022-05-23
DESCRIPTION | 9 MD5 | 54 ++--- NAMESPACE | 1 NEWS.md | 8 R/generics.R | 31 +- R/mkSpCov.R |only R/spIntPGOcc.R | 111 ++++++++-- R/spMsPGOcc.R | 161 +++++++++++--- R/spPGOcc.R | 529 +++++++++++++++++++++++++++++++++---------------- R/waicOcc.R | 2 README.md | 47 ++-- build/partial.rdb |binary inst/CITATION | 16 - man/spIntPGOcc.Rd | 8 man/spMsPGOcc.Rd | 8 man/spPGOcc.Rd | 8 src/init.cpp | 12 - src/mkSpCov.cpp |only src/sfJSDMNNGP.cpp | 7 src/sfMsPGOccNNGP.cpp | 7 src/spIntPGOcc.cpp | 79 +++++-- src/spIntPGOccNNGP.cpp | 69 ++++-- src/spMsPGOcc.cpp | 68 ++++-- src/spMsPGOccNNGP.cpp | 67 ++++-- src/spOccupancy.h | 16 - src/spPGOcc.cpp | 80 +++++-- src/spPGOccNNGP.cpp | 328 +++++++++++++++++------------- src/util.cpp | 45 ++++ src/util.h | 2 29 files changed, 1214 insertions(+), 559 deletions(-)
Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis
of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous
time sampling (i.e. different time points for different individuals),
inter-individual variability, noisy measurements and large numbers of variables.
Based on a smoothing splines functional model, 'santaR' is able to detect variables
highlighting significantly different temporal trajectories between study groups.
Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology
disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and
parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting
options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] ,
Timothy Ebbels [ctb],
Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>
Diff between santaR versions 1.2.0 dated 2022-04-09 and 1.2.2 dated 2022-05-23
DESCRIPTION | 12 ++-- MD5 | 55 +++++++++++++++------- NAMESPACE | 2 R/santaR.R | 2 R/santaR_pvalue_dist.R | 4 - R/santaR_pvalue_fit.R | 4 - R/santaR_start_GUI.R | 2 README.md | 2 inst/NEWS | 3 + inst/doc/advanced-command-line-functions.html | 12 ++-- inst/doc/plotting-options.html | 36 +++++++------- inst/doc/theoretical-background.html | 2 inst/shiny-GUI/SANTA-App/data/chooser.R | 4 - inst/shiny-GUI/SANTA-App/server.R | 7 +- inst/shiny-GUI/SANTA-App/server/server_analysis.R | 12 ++-- inst/shiny-GUI/SANTA-App/server/server_dfSearch.R | 2 inst/shiny-GUI/SANTA-App/ui.R | 13 ++--- inst/testdata |only tests |only vignettes/file495459c86ac2.html |only vignettes/file49547f98451a.html |only vignettes/file54b03fa44385.html |only vignettes/file54b0425d69f8.html |only 23 files changed, 102 insertions(+), 72 deletions(-)
Title: Pedigree Models
Description: Provides functions to estimate mixed probit models using, for
instance, pedigree data like in <doi:10.1002/sim.1603>. The models are also
commonly called liability threshold models. The approximation is
based on direct log marginal likelihood approximations like the randomized
Quasi-Monte Carlo suggested by <doi:10.1198/106186002394> with a similar
procedure to approximate the derivatives. The minimax tilting method
suggested by <doi:10.1111/rssb.12162> is also supported. Graph-based methods
are also provided that can be used to simplify pedigrees.
Author: Benjamin Christoffersen [cre, aut]
,
Alan Genz [cph],
Frank Bretz [cph],
Bjoern Bornkamp [cph],
Torsten Hothorn [cph],
Christophe Dutang [cph],
Diethelm Wuertz [cph],
R-core [cph],
Leo Belzile [cph],
Zdravko Botev [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between pedmod versions 0.2.0 dated 2022-04-28 and 0.2.1 dated 2022-05-23
pedmod-0.2.0/pedmod/man/figures |only pedmod-0.2.1/pedmod/DESCRIPTION | 8 pedmod-0.2.1/pedmod/MD5 | 137 - pedmod-0.2.1/pedmod/NAMESPACE | 3 pedmod-0.2.1/pedmod/NEWS.md | 18 pedmod-0.2.1/pedmod/R/RcppExports.R | 4 pedmod-0.2.1/pedmod/R/eval_wrappers.R | 92 + pedmod-0.2.1/pedmod/R/opt.R | 402 ++++ pedmod-0.2.1/pedmod/build/partial.rdb |binary pedmod-0.2.1/pedmod/inst/doc/pedigree_partitioning.html | 100 - pedmod-0.2.1/pedmod/inst/doc/pedmod.html | 794 +++++++-- pedmod-0.2.1/pedmod/man/eval_pedigree.Rd | 54 pedmod-0.2.1/pedmod/man/pedmod_profile.Rd | 6 pedmod-0.2.1/pedmod/man/pedmod_profile_nleq.Rd |only pedmod-0.2.1/pedmod/man/pedmod_profile_prop.Rd | 4 pedmod-0.2.1/pedmod/src/RcppExports.cpp | 25 pedmod-0.2.1/pedmod/src/cdfaprx.cpp | 807 +++++++++- pedmod-0.2.1/pedmod/src/cdfaprx.h | 562 +----- pedmod-0.2.1/pedmod/src/graph-partitioning.cpp | 2 pedmod-0.2.1/pedmod/src/norm-cdf-approx.h | 5 pedmod-0.2.1/pedmod/src/pedigree-ll.cpp | 387 ++++ pedmod-0.2.1/pedmod/src/pedigree-ll.h | 316 --- pedmod-0.2.1/pedmod/src/pnorm.h | 2 pedmod-0.2.1/pedmod/src/r-api.cpp | 151 + pedmod-0.2.1/pedmod/src/test-cdfaprx.cpp | 371 ++++ pedmod-0.2.1/pedmod/tests/testthat/test-eval-x.R | 29 pedmod-0.2.1/pedmod/tests/testthat/test-man-pages.R | 56 pedmod-0.2.1/pedmod/vignettes/figures/partitioning-also_reduce_cost-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-connected_start_pedigree_unconnected-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-find_partition_simulate_small_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-find_partition_simulate_small_graph-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-larger_ex-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-more_clear_only_balanced-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-only_balanced-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-partion_w_cut_simulate_small_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-partion_w_cut_simulate_small_graph-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_example-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_unconnected-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_unconnected-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_unconnected-3.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-show_family_as_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-simulate_small_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-unconnected_larger_ex-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-unconnected_larger_ex-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-unconnected_larger_ex-3.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_edge_weights_too-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_edge_weights_too-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_weights-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_weights-2.png |binary 49 files changed, 3171 insertions(+), 1164 deletions(-)
Title: Fetch Economic and Financial Time Series Data from Public
Sources
Description: Download economic and financial time series from public sources,
including the St Louis Fed's FRED system, Yahoo Finance, the US Bureau of Labor Statistics,
the US Energy Information Administration, the World Bank, Eurostat, the European Central Bank,
the Bank of England, the UK's Office of National Statistics, Deutsche Bundesbank, and INSEE.
Author: Abiel Reinhart <abielr@gmail.com>
Maintainer: Abiel Reinhart <abielr@gmail.com>
Diff between pdfetch versions 0.2.6 dated 2022-02-25 and 0.2.7 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/pdfetch.R | 24 +++++++++++------------- 4 files changed, 22 insertions(+), 20 deletions(-)
Title: Structural Handling of Finnish Personal Identity Codes
Description: Structural handling of Finnish identity codes (natural persons and
organizations); extract information, check ID validity and diagnostics.
Author: Pyry Kantanen [aut, cre] ,
Mans Magnusson [aut],
Jussi Paananen [aut],
Juho Kopra [ctb],
Oskari Luomala [ctb],
Tuomo Nieminen [ctb],
Leo Lahti [aut]
Maintainer: Pyry Kantanen <pyry.kantanen@gmail.com>
Diff between hetu versions 1.0.1 dated 2020-10-24 and 1.0.7 dated 2022-05-23
DESCRIPTION | 66 +- MD5 | 67 +- NAMESPACE | 14 NEWS.md | 38 + R/hetu-deprecated.R | 2 R/hetu.R | 272 +++++---- R/hetu_control_char.R |only R/hetu_diagnostic.R | 58 - R/pin_age.R | 54 + R/pin_ctrl.R | 109 ++- R/pin_date.R | 8 R/pin_sex.R | 22 R/pin_to_date.R | 4 R/quickdf.R |only R/rpin.R | 242 ++++---- README.md | 138 +++- build/vignette.rds |binary inst/CITATION | 41 - inst/doc/hetu.R | 4 inst/doc/hetu.Rmd | 18 inst/doc/hetu.html | 1323 +++++++++++++++++++++++++++------------------ man/bid_ctrl.Rd | 6 man/figures |only man/hetu.Rd | 59 +- man/hetu_control_char.Rd |only man/hetu_diagnostic.Rd | 36 - man/pin_age.Rd | 19 man/pin_ctrl.Rd | 21 man/pin_date.Rd | 12 man/pin_sex.Rd | 17 man/quickdf.Rd |only man/rbid.Rd | 5 man/rpin.Rd | 55 + man/satu_control_char.Rd |only man/satu_ctrl.Rd |only tests/testthat.R | 1 tests/testthat/test_hetu.R | 80 +- vignettes/hetu.Rmd | 18 38 files changed, 1688 insertions(+), 1121 deletions(-)
Title: Automated Cleaning of Fossil Occurrence Data
Description: Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Author: Joe Flannery-Sutherland [aut, cre]
,
Nussaïbah Raja-Schoob [aut, ctb],
Ádam Kocsis [aut, ctb],
Wolfgang Kiessling [aut]
Maintainer: Joe Flannery-Sutherland <jf15558@bristol.ac.uk>
Diff between fossilbrush versions 1.0.1 dated 2022-05-19 and 1.0.2 dated 2022-05-23
fossilbrush-1.0.1/fossilbrush/R/GTS2020_scale.R |only fossilbrush-1.0.1/fossilbrush/man/GTS2020_scale.Rd |only fossilbrush-1.0.2/fossilbrush/DESCRIPTION | 6 fossilbrush-1.0.2/fossilbrush/MD5 | 24 fossilbrush-1.0.2/fossilbrush/NAMESPACE | 3 fossilbrush-1.0.2/fossilbrush/R/chrono_scale.R |only fossilbrush-1.0.2/fossilbrush/R/flag_ranges.R | 572 ++-- fossilbrush-1.0.2/fossilbrush/R/get_pbdb.R | 1159 ++++------ fossilbrush-1.0.2/fossilbrush/inst/doc/fossilbrush_vignette.R | 7 fossilbrush-1.0.2/fossilbrush/inst/doc/fossilbrush_vignette.Rmd | 373 +-- fossilbrush-1.0.2/fossilbrush/inst/doc/fossilbrush_vignette.pdf |binary fossilbrush-1.0.2/fossilbrush/man/chrono_scale.Rd |only fossilbrush-1.0.2/fossilbrush/man/flag_ranges.Rd | 6 fossilbrush-1.0.2/fossilbrush/man/get_pbdb.Rd | 2 fossilbrush-1.0.2/fossilbrush/vignettes/fossilbrush_vignette.Rmd | 373 +-- 15 files changed, 1260 insertions(+), 1265 deletions(-)
Title: Robust and Sparse Methods for High Dimensional Linear and Binary
and Multinomial Regression
Description: Fully robust versions of the elastic net estimator are introduced for linear and binary and multinomial regression, in particular high dimensional data. The algorithm searches for outlier free subsets on which the classical elastic net estimators can be applied. A reweighting step is added to improve the statistical efficiency of the proposed estimators. Selecting appropriate tuning parameters for elastic net penalties are done via cross-validation.
Author: Fatma Sevinc Kurnaz and Irene Hoffmann and Peter Filzmoser
Maintainer: Fatma Sevinc Kurnaz <fatmasevinckurnaz@gmail.com>
Diff between enetLTS versions 0.1.0 dated 2018-01-22 and 1.1.0 dated 2022-05-23
enetLTS-0.1.0/enetLTS/R/InitialSubsets.R |only enetLTS-0.1.0/enetLTS/R/enetLTS-internal.R |only enetLTS-0.1.0/enetLTS/R/enetLTS.R |only enetLTS-1.1.0/enetLTS/DESCRIPTION | 20 enetLTS-1.1.0/enetLTS/MD5 | 76 +-- enetLTS-1.1.0/enetLTS/NAMESPACE | 25 - enetLTS-1.1.0/enetLTS/R/Csteps.R | 212 +++++---- enetLTS-1.1.0/enetLTS/R/coef.enetLTS.R | 31 - enetLTS-1.1.0/enetLTS/R/cv.binomial.enetLTS.R |only enetLTS-1.1.0/enetLTS/R/cv.enetLTS.R | 220 ++------- enetLTS-1.1.0/enetLTS/R/cv.gaussian.enetLTS.R |only enetLTS-1.1.0/enetLTS/R/cv.multinomial.enetLTS.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.binom.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.gaus.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.main.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.multinom.R |only enetLTS-1.1.0/enetLTS/R/fitted.enetLTS.R | 164 ++++--- enetLTS-1.1.0/enetLTS/R/initialSubsets.R |only enetLTS-1.1.0/enetLTS/R/lambda00.R | 3 enetLTS-1.1.0/enetLTS/R/nonzeroCoef.enetLTS.R | 38 + enetLTS-1.1.0/enetLTS/R/objectiveFunc.R | 54 +- enetLTS-1.1.0/enetLTS/R/plotCoef.enetLTS.R | 154 ++++-- enetLTS-1.1.0/enetLTS/R/plotDiagnostic.enetLTS.R | 222 ++++++---- enetLTS-1.1.0/enetLTS/R/plotResid.enetLTS.R | 441 +++++++++++--------- enetLTS-1.1.0/enetLTS/R/predict.enetLTS.R | 320 ++++++-------- enetLTS-1.1.0/enetLTS/R/print.enetLTS.R | 17 enetLTS-1.1.0/enetLTS/R/residuals.enetLTS.R | 92 ++-- enetLTS-1.1.0/enetLTS/R/standardizeXY.R |only enetLTS-1.1.0/enetLTS/R/startCstep500.R |only enetLTS-1.1.0/enetLTS/R/utilities.R | 109 ---- enetLTS-1.1.0/enetLTS/R/warmCsteps.R | 223 ++++++---- enetLTS-1.1.0/enetLTS/R/weights.enetLTS.R | 1 enetLTS-1.1.0/enetLTS/R/weightsFuncs.R |only enetLTS-1.1.0/enetLTS/man/coef.enetLTS.Rd | 56 +- enetLTS-1.1.0/enetLTS/man/cv.enetLTS.Rd | 31 - enetLTS-1.1.0/enetLTS/man/enetLTS-package.Rd | 211 +++++---- enetLTS-1.1.0/enetLTS/man/fitted.enetLTS.Rd | 64 +- enetLTS-1.1.0/enetLTS/man/nonzeroCoef.enetLTS.Rd | 70 ++- enetLTS-1.1.0/enetLTS/man/plot.enetLTS.Rd | 44 + enetLTS-1.1.0/enetLTS/man/plotCoef.enetLTS.Rd | 53 +- enetLTS-1.1.0/enetLTS/man/plotDiagnostic.enetLTS.Rd | 52 +- enetLTS-1.1.0/enetLTS/man/plotResid.enetLTS.Rd | 56 +- enetLTS-1.1.0/enetLTS/man/predict.enetLTS.Rd | 74 +-- enetLTS-1.1.0/enetLTS/man/print.enetLTS.Rd | 55 +- enetLTS-1.1.0/enetLTS/man/residuals.enetLTS.Rd | 52 +- enetLTS-1.1.0/enetLTS/man/weights.enetLTS.Rd | 52 +- 46 files changed, 1837 insertions(+), 1455 deletions(-)
Title: Constrained Regression for Survey Data
Description: Domain mean estimation with monotonicity or block monotone constraints. See Xu X, Meyer MC and Opsomer JD (2021)<doi:10.1016/j.jspi.2021.02.004> for more details.
Author: Xiyue Liao
Maintainer: Xiyue Liao <xiyue.liao@csulb.edu>
Diff between csurvey versions 1.2 dated 2021-08-12 and 1.3 dated 2022-05-23
csurvey-1.2/csurvey/man/csvy.fit.Rd |only csurvey-1.2/csurvey/man/decr.Rd |only csurvey-1.2/csurvey/man/fitted.csvy.Rd |only csurvey-1.2/csurvey/man/incr.Rd |only csurvey-1.2/csurvey/man/plotpersp.Rd |only csurvey-1.2/csurvey/man/plotpersp.csvy.Rd |only csurvey-1.2/csurvey/man/print.csvy.Rd |only csurvey-1.3/csurvey/ChangeLog |only csurvey-1.3/csurvey/DESCRIPTION | 16 csurvey-1.3/csurvey/MD5 | 16 csurvey-1.3/csurvey/NAMESPACE | 26 csurvey-1.3/csurvey/R/csurvey.R | 1399 ++++++++++++++++++++---------- csurvey-1.3/csurvey/man/csvy.Rd | 232 +++- 13 files changed, 1153 insertions(+), 536 deletions(-)
Title: Bayesian Group Sequential Design for Ordinal Data
Description: The proposed group-sequential trial design is based on Bayesian methods for ordinal endpoints,
including three methods, the proportional-odds-model (PO)-based, non-proportional-odds-model (NPO)-based,
and PO/NPO switch-model-based designs, which makes our proposed methods generic to be able to deal with
various scenarios.
Richard J. Barker, William A. Link (2013) <doi:10.1080/00031305.2013.791644>.
Thomas A. Murray, Ying Yuan, Peter F. Thall, Joan H. Elizondo, Wayne L.Hofstetter (2018) <doi:10.1111/biom.12842>.
Chengxue Zhong, Haitao Pan, Hongyu Miao (2021) <arXiv:2108.06568>.
Author: Chengxue Zhong [aut, cre],
Haitao Pan [aut],
Hongyu Miao [aut]
Maintainer: Chengxue Zhong <chengxue.zhong@uth.tmc.edu>
Diff between BayesOrdDesign versions 0.1.0 dated 2021-09-21 and 0.1.1 dated 2022-05-23
DESCRIPTION | 9 +- MD5 | 26 +++---- R/Bayes_Ord_Design_NPO.R | 26 +++---- R/Bayes_Ord_Design_PO.R | 19 ++--- R/Bayes_Ord_Design_Switch.R | 37 ++++++---- R/OC_func_NPO.R | 21 +++-- R/OC_func_PO.R | 19 +++-- R/OC_func_Switch.R | 60 ++++++++-------- R/funcs.R | 157 +++++++++++++++++++++++++++++++++++++++----- R/rjmcmc_internal.R | 8 +- man/get_oc_NPO.Rd | 4 - man/get_oc_Switch.Rd | 20 ++--- man/ss_npo.Rd | 5 - man/ss_switch.Rd | 6 - 14 files changed, 281 insertions(+), 136 deletions(-)
More information about BayesOrdDesign at CRAN
Permanent link
Title: Plot a Model's Residuals, Response, and Partial Dependence Plots
Description: Plot model surfaces for a wide variety of models
using partial dependence plots and other techniques.
Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.6.1 dated 2021-07-17 and 3.6.2 dated 2022-05-21
DESCRIPTION | 6 +- MD5 | 90 ++++++++++++++++---------------- NEWS | 4 + R/c50.R | 2 R/do.par.R | 4 - R/grid.func.R | 2 R/plotmo.R | 6 +- inst/slowtests/make.README.bat | 2 inst/slowtests/make.bat | 2 inst/slowtests/test.c50.bat | 2 inst/slowtests/test.caret.Rout.save | 2 inst/slowtests/test.caret.bat | 2 inst/slowtests/test.center.bat | 2 inst/slowtests/test.degree.bat | 2 inst/slowtests/test.dots.bat | 2 inst/slowtests/test.fac.bat | 2 inst/slowtests/test.gbm.bat | 2 inst/slowtests/test.glmnet.Rout.save | 4 - inst/slowtests/test.glmnet.bat | 2 inst/slowtests/test.glmnetUtils.bat | 2 inst/slowtests/test.linmod.R | 2 inst/slowtests/test.linmod.Rout.save | 4 - inst/slowtests/test.linmod.bat | 2 inst/slowtests/test.mlr.Rout.save | 2 inst/slowtests/test.mlr.bat | 2 inst/slowtests/test.modguide.bat | 2 inst/slowtests/test.non.earth.Rout.save | 26 ++++----- inst/slowtests/test.non.earth.bat | 2 inst/slowtests/test.parsnip.Rout.save | 24 +++----- inst/slowtests/test.parsnip.bat | 6 +- inst/slowtests/test.partdep.Rout.save | 2 inst/slowtests/test.partdep.bat | 2 inst/slowtests/test.partykit.bat | 2 inst/slowtests/test.plotmo.Rout.save | 2 inst/slowtests/test.plotmo.args.bat | 2 inst/slowtests/test.plotmo.bat | 2 inst/slowtests/test.plotmo.dots.bat | 2 inst/slowtests/test.plotmo.x.bat | 2 inst/slowtests/test.plotmo3.Rout.save | 4 - inst/slowtests/test.plotmo3.bat | 2 inst/slowtests/test.plotres.Rout.save | 4 - inst/slowtests/test.plotres.bat | 2 inst/slowtests/test.pre.Rout.save | 6 +- inst/slowtests/test.pre.bat | 2 inst/slowtests/test.printcall.bat | 2 inst/slowtests/test.unusual.vars.bat | 2 46 files changed, 131 insertions(+), 123 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi' (www.jamovi.org)
aims to make statistical analyses easy and intuitive. 'jamovi' produces
syntax that can directly be used in R (in connection with the R-package 'jmv').
Having import / export routines for the data files 'jamovi' produces ('.omv')
permits an easy transfer of analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.3.1 dated 2022-02-28 and 0.3.2 dated 2022-05-21
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 6 R/read_omv.R | 6 README.md | 4 build/vignette.rds |binary inst/doc/jmvReadWrite.html | 293 ++++++++++++++++++++++++--------------------- tests/testthat.R | 10 - 8 files changed, 192 insertions(+), 149 deletions(-)
Title: Basic and Advanced Statistical Power Analysis
Description: This is a collection of tools for conducting both basic and advanced statistical power analysis including correlation, proportion, t-test, one-way ANOVA, two-way ANOVA, linear regression, logistic regression, Poisson regression, mediation analysis, longitudinal data analysis, structural equation modeling and multilevel modeling. It also serves as the engine for conducting power analysis online at <https://webpower.psychstat.org>.
Author: Zhiyong Zhang [aut, cre],
Yujiao Mai [aut],
Miao Yang [ctb]
Maintainer: Zhiyong Zhang <johnnyzhz@gmail.com>
Diff between WebPower versions 0.6 dated 2021-05-18 and 0.7 dated 2022-05-21
WebPower-0.6/WebPower/README.md |only WebPower-0.7/WebPower/DESCRIPTION | 8 WebPower-0.7/WebPower/MD5 | 27 WebPower-0.7/WebPower/NAMESPACE | 6 WebPower-0.7/WebPower/R/webpower.R | 648 +++++++++++---------- WebPower-0.7/WebPower/man/nuniroot.Rd | 3 WebPower-0.7/WebPower/man/plot.webpower.Rd | 2 WebPower-0.7/WebPower/man/print.webpower.Rd | 2 WebPower-0.7/WebPower/man/sem.effect.size.Rd |only WebPower-0.7/WebPower/man/wp.mc.chisq.diff.Rd |only WebPower-0.7/WebPower/man/wp.mc.sem.power.curve.Rd | 2 WebPower-0.7/WebPower/man/wp.mediation.Rd | 2 WebPower-0.7/WebPower/man/wp.poisson.Rd | 6 WebPower-0.7/WebPower/man/wp.regression.Rd | 2 WebPower-0.7/WebPower/man/wp.rmanova.Rd | 3 WebPower-0.7/WebPower/man/wp.sem.chisq.Rd | 3 16 files changed, 374 insertions(+), 340 deletions(-)
Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre],
Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotRgui versions 4.3 dated 2022-03-07 and 4.4 dated 2022-05-21
DESCRIPTION | 10 MD5 | 54 ++--- R/IsoplotR.R | 8 R/server.R | 16 - build/git.md | 199 ++++++++++-------- inst/www/help/evolution.html | 4 inst/www/help/isochron.html | 9 inst/www/home/news.html | 33 +-- inst/www/js/IsoplotR.js | 280 ++++++++++++++------------ inst/www/js/js2R.js | 25 +- inst/www/js/settings.json | 10 inst/www/locales/en/contextual_help.json | 12 - inst/www/locales/en/dictionary_id.json | 44 ++-- inst/www/locales/en/home_id.json | 2 inst/www/locales/es/contextual_help.json | 29 ++ inst/www/locales/es/dictionary_class.json | 11 - inst/www/locales/es/dictionary_id.json | 10 inst/www/locales/es/home_id.json | 8 inst/www/locales/zh_Hans/contextual_help.json | 10 inst/www/locales/zh_Hans/dictionary_id.json | 2 inst/www/options/CAD.html | 6 inst/www/options/KDE.html | 6 inst/www/options/Th-U.html | 40 ++- inst/www/options/ages.html | 5 inst/www/options/average.html | 6 inst/www/options/isochron.html | 33 +-- inst/www/options/radial.html | 6 inst/www/version.txt | 2 28 files changed, 486 insertions(+), 394 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 4.3 dated 2022-03-06 and 4.4 dated 2022-05-21
DESCRIPTION | 8 +- MD5 | 60 ++++++++-------- R/ThU.R | 94 +++++++++++-------------- R/age.R | 33 ++++---- R/cad.R | 41 +++++----- R/classes.R | 9 +- R/constants.R | 18 ++-- R/diseq.R | 12 +-- R/evolution.R | 195 ++++++++++++++++++++++++++-------------------------- R/io.R | 34 +++++---- R/isochron.R | 107 +++++++++++++++++++++------- R/kde.R | 34 ++++----- R/peakfit.R | 46 ++++++------ R/radialplot.R | 61 ++++++++-------- R/regression.R | 2 R/titterington.R | 50 +++++++------ R/toolbox.R | 4 - R/weightedmean.R | 32 +++++--- R/york.R | 2 inst/constants.json | 1 man/age.Rd | 35 +++------ man/cad.Rd | 23 +++--- man/classes.Rd | 9 +- man/evolution.Rd | 41 ++++++---- man/isochron.Rd | 30 ++++++-- man/kde.Rd | 23 +++--- man/peakfit.Rd | 29 ++++--- man/radialplot.Rd | 23 +++--- man/read.data.Rd | 21 +++-- man/settings.Rd | 18 ++-- man/weightedmean.Rd | 35 +++++---- 31 files changed, 628 insertions(+), 502 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.9.1 dated 2022-01-14 and 0.9.2 dated 2022-05-21
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ggstatsplot-0.9.2/ggstatsplot/vignettes/additional.Rmd | 192 ggstatsplot-0.9.2/ggstatsplot/vignettes/apa.csl |only ggstatsplot-0.9.2/ggstatsplot/vignettes/ggstatsplot.Rmd |only ggstatsplot-0.9.2/ggstatsplot/vignettes/paper.bib |only ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/apa.csl | 886 +- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/faq.Rmd | 1230 ++-- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggbarstats.Rmd |only ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 872 +- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 1209 ++-- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 676 +- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd | 432 - ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 454 - ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 834 +- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 430 - ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 830 +- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/pairwise.Rmd | 453 - ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/paper.bib | 184 ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/principles.Rmd | 842 +- ggstatsplot-0.9.2/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 1411 ++-- 222 files changed, 19521 insertions(+), 22100 deletions(-)
Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data published in Thrun, M.C. et al.: "Analyzing the Fine Structure of Distributions" (2020), PLoS ONE, <DOI:10.1371/journal.pone.0238835>. The MD-plot outperforms the box-and-whisker diagram (box plot), violin plot and bean plot and geom_violin plot of ggplot2. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] ,
Felix Pape [aut, rev],
Onno Hansen-Goos [ctr, ctb],
Hamza Tayyab [ctr, ctb],
Dirk Eddelbuettel [ctr],
Craig Varrichio [ctr],
Alfred Ultsch [dtc, ctb, ctr]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between DataVisualizations versions 1.2.2 dated 2021-01-12 and 1.2.3 dated 2022-05-21
DESCRIPTION | 12 MD5 | 92 NAMESPACE | 164 - R/ABCbarplot.R | 5 R/ClassMDplot.R | 2 R/Classplot.R | 41 R/DensityScatter.R | 68 R/DualaxisClassplot.R | 4 R/InspectCorrelation.R | 30 R/InspectDistances.R | 2 R/InspectVariable.R | 454 ++-- R/MAplot.R | 137 - R/MDplot.R | 1029 +++++----- R/PDEplot.R | 31 R/PDEscatter.R | 4 R/ParetoDensityEstimation.R | 140 - R/Pixelmatrix.R | 249 +- R/PlotProductratio.R | 22 R/QQplot.R | 9 R/RcppExports.R | 30 R/checkFeature.R | 17 R/internpiechart.R | 2 R/smooth1D.R | 10 build/partial.rdb |binary build/vignette.rds |binary data/world_country_polygons.rda |binary inst/NEWS | 12 inst/doc/DataVisualizations.R | 262 +- inst/doc/DataVisualizations.Rmd | 6 inst/doc/DataVisualizations.html | 3871 +++++++++++++++++++------------------- man/ABCbarplot.Rd | 2 man/Choroplethmap.Rd | 8 man/Classplot.Rd | 10 man/DataVisualizations-package.Rd | 2 man/DensityScatter.Rd | 8 man/InspectCorrelation.Rd | 8 man/InspectVariable.Rd | 8 man/MAplot.Rd | 50 man/MDplot.Rd | 41 man/PDEplot.Rd | 6 man/ParetoDensityEstimation.Rd | 45 man/Pixelmatrix.Rd | 88 man/Plot3D.Rd | 2 man/PlotProductratio.Rd | 6 man/QQplot.Rd | 2 src/RcppExports.cpp | 5 vignettes/DataVisualizations.Rmd | 6 47 files changed, 3663 insertions(+), 3339 deletions(-)
More information about DataVisualizations at CRAN
Permanent link
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Any unverified black box model is the path to failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore the model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] ,
Szymon Maksymiuk [aut] ,
Hubert Baniecki [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.4.0 dated 2022-02-21 and 2.4.1 dated 2022-05-21
DESCRIPTION | 12 +-- MD5 | 17 ++-- NAMESPACE | 1 R/explain.R | 19 +++- R/misc_loss_functions.R | 73 +++++++++++++++++++ R/misc_yhat.R | 2 R/model_info.R | 3 man/loss_yardstick.Rd |only man/model_info.Rd | 21 ++--- tests/external_tests/external_test_yhat_model_info.R | 51 ++++++++----- 10 files changed, 146 insertions(+), 53 deletions(-)
Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>,
an open source software library for numerical computation using data
flow graphs. Nodes in the graph represent mathematical operations,
while the graph edges represent the multidimensional data arrays
(tensors) communicated between them. The flexible architecture allows
you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop,
server, or mobile device with a single 'API'. 'TensorFlow' was originally
developed by researchers and engineers working on the Google Brain Team
within Google's Machine Intelligence research organization for the
purposes of conducting machine learning and deep neural networks research,
but the system is general enough to be applicable in a wide variety
of other domains as well.
Author: Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Nick Golding [ctb, cph],
Tomasz Kalinowski [ctb, cph, cre],
Google Inc. [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>
Diff between tensorflow versions 2.8.0 dated 2022-02-09 and 2.9.0 dated 2022-05-21
DESCRIPTION | 11 MD5 | 46 +-- NAMESPACE | 29 ++ NEWS.md | 35 ++ R/eager.R | 66 ++++- R/estimator-generics.R | 7 R/extract.R | 40 ++- R/generics.R | 419 +++++++++++++++++++++++++++++--- R/install.R | 42 +-- R/package.R | 3 R/seed.R | 2 R/shape.R | 12 man/as_tensor.Rd | 11 man/export_savedmodel.Rd | 1 man/install_tensorflow.Rd | 16 - man/shape.Rd | 11 man/train.Rd | 3 man/train_and_evaluate.Rd | 2 tests/testthat/helper-utils.R | 3 tests/testthat/test-as_tensor.R | 46 +++ tests/testthat/test-export-savedmodel.R | 6 tests/testthat/test-generic-methods.R | 124 +++++++++ tests/testthat/test-seed.R | 4 tests/testthat/test-shape.R | 11 24 files changed, 812 insertions(+), 138 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.1.0 dated 2021-07-24 and 3.1.1 dated 2022-05-21
DESCRIPTION | 7 +++-- MD5 | 38 +++++++++++++++--------------- NEWS | 6 +++- R/describe.col.R | 2 - inst/slowtests/make.bat | 7 +++-- inst/slowtests/rpart.report.bat | 2 - inst/slowtests/test.describe.col.bat | 2 - inst/slowtests/test.imports.bat | 2 - inst/slowtests/test.na.bat | 2 - inst/slowtests/test.palette.Rout.save | 2 - inst/slowtests/test.palette.bat | 2 - inst/slowtests/test.rpart.plot.Rout.save | 18 +++++++------- inst/slowtests/test.rpart.plot.bat | 2 - inst/slowtests/test.rpart.rules.Rout.save | 2 - inst/slowtests/test.rpart.rules.bat | 2 - inst/slowtests/test.type5.bat | 2 - inst/slowtests/usersplits.bat | 2 - inst/slowtests/vignette.Rout.save | 4 +-- inst/slowtests/vignette.bat | 2 - inst/slowtests/webpage.figs.bat | 2 - 20 files changed, 59 insertions(+), 49 deletions(-)
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb],
Li Wang [ctb],
Pavel N. Krivitsky [ctb] ,
Brendan Knapp [ctb] ,
Michal Bojanowski [ctb],
Chad Klumb [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.17.1 dated 2021-06-14 and 1.17.2 dated 2022-05-21
network-1.17.1/network/README.md |only network-1.17.2/network/ChangeLog | 3 network-1.17.2/network/DESCRIPTION | 8 - network-1.17.2/network/MD5 | 34 ++-- network-1.17.2/network/build/vignette.rds |binary network-1.17.2/network/inst/CITATION | 2 network-1.17.2/network/inst/doc/networkVignette.pdf |binary network-1.17.2/network/src/access.c | 140 +++++++++++--------- network-1.17.2/network/tests/general.tests.R | 3 network-1.17.2/network/tests/general.tests2.R | 4 network-1.17.2/network/tests/list.attribute.tests.R | 4 network-1.17.2/network/tests/network.access.test.R | 6 network-1.17.2/network/tests/network.battery.R | 4 network-1.17.2/network/tests/oldbench |only network-1.17.2/network/tests/pathological.tests.R | 4 network-1.17.2/network/tests/plotflo.R | 4 network-1.17.2/network/tests/speedTests.R | 4 network-1.17.2/network/tests/testthat.R | 4 network-1.17.2/network/tests/vignette.R | 3 19 files changed, 143 insertions(+), 84 deletions(-)
Title: Convert Decimals to Fractions
Description: Provides functions for converting decimals to a
matrix of numerators and denominators or a character vector of
fractions. Supports mixed or improper fractions, finding common
denominators for vectors of fractions, limiting denominators to powers
of ten, and limiting denominators to a maximum value. Also includes
helper functions for finding the least common multiple and greatest
common divisor for a vector of integers. Implemented using C++ for
maximum speed.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between fracture versions 0.2.0 dated 2021-10-25 and 0.2.1 dated 2022-05-21
DESCRIPTION | 8 +-- MD5 | 20 ++++----- NEWS.md | 10 ++++ R/frac_mat.R | 51 ++++++++++++++++++----- R/frac_style.R | 57 +++++++++++++++++++++---- R/fracture.R | 28 +++++++++--- R/sysdata.rda |binary README.md | 90 +++++++++++++++++++++-------------------- man/fracture-package.Rd | 2 tests/testthat/test-frac_mat.R | 23 ++++++++++ tests/testthat/test-fracture.R | 22 ++++++++-- 11 files changed, 223 insertions(+), 88 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple rectangular
data. The 'rtables' package provides a framework for declaring complex multi-level tabulations
and then applying them to data. This framework models both tabulation and the resulting
tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting
or grouping of data in row and column dimensions, cells containing multiple values,
and the concept of contextual summary computations. A convenient pipe-able interface is provided
for declaring table layouts and the corresponding computations, and then applying them to data.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between rtables versions 0.5.0 dated 2022-03-31 and 0.5.1 dated 2022-05-21
DESCRIPTION | 10 MD5 | 95 +-- NAMESPACE | 8 NEWS.md | 9 R/00tabletrees.R | 28 R/argument_conventions.R | 12 R/format_rcell.R | 3 R/tree_accessors.R | 78 ++ R/tt_afun_utils.R | 49 + R/tt_compatibility.R | 10 R/tt_dotabulation.R | 23 R/tt_export.R | 18 R/tt_toString.R | 36 - R/utils.R | 1 build/vignette.rds |binary inst/doc/baseline.html | 4 inst/doc/clinical_trials.html | 922 +++++++++++++++----------------- inst/doc/introduction.html | 6 inst/doc/manual_table_construction.html | 4 inst/doc/sorting_pruning.html | 4 inst/doc/subsetting_tables.html | 4 inst/doc/tabulation_concepts.html | 4 inst/doc/tabulation_dplyr.html | 26 man/CellValue.Rd | 5 man/build_table.Rd | 6 man/export_as_pdf.Rd | 9 man/export_as_txt.Rd | 11 man/format_rcell.Rd | 7 man/gen_args.Rd | 9 man/horizontal_sep.Rd |only man/in_rows.Rd | 5 man/lab_name.Rd | 18 man/lyt_args.Rd | 5 man/make_afun.Rd | 3 man/matrix_form-VTableTree-method.Rd | 4 man/rcell.Rd | 8 man/rtable.Rd | 9 man/tabclasses.Rd | 11 man/table_shell.Rd | 6 man/tostring.Rd | 12 tests/testthat/setup-fakedata.R | 3 tests/testthat/test-accessors.R | 23 tests/testthat/test-formatting.R | 16 tests/testthat/test-header-footer.R | 4 tests/testthat/test-lyt-tabulation.R | 19 tests/testthat/test-make-afun.R | 12 tests/testthat/test-printing.R | 40 - tests/testthat/test-regressions.R | 42 + tests/unit_test_results.xml | 637 +++++++++++++++++----- 49 files changed, 1498 insertions(+), 780 deletions(-)
Title: Database Agnostic Package to Generate and Process 'SQL' Queries
in R
Description: Allows the user to generate and execute select, insert, update and delete 'SQL' queries the underlying database without having to explicitly write 'SQL' code.
Author: Alejandro Baranek [cre, aut],
Leonardo Belen [aut]
Maintainer: Alejandro Baranek <abaranek@dc.uba.ar>
Diff between RSQL versions 0.2.0 dated 2022-04-14 and 0.2.1 dated 2022-05-21
DESCRIPTION | 8 +- MD5 | 95 +++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 6 + R/sql-lib.R | 133 ++++++++++++++++++++++++++++++++++++------ R/util-lib.R |only README.md | 3 build/vignette.rds |binary man/RSQL.class.Rd | 63 +++++++++++++++---- man/add_grep_exact_match.Rd | 3 man/add_quotes.Rd | 3 man/cbind_coerced.Rd | 7 +- man/check_fields_values.Rd | 3 man/createRSQL.Rd | 3 man/dequote.Rd | 3 man/df_verify.Rd | 3 man/genLogger.Rd |only man/getLogger.Rd |only man/getMtcarsdbPath.Rd | 3 man/getPackageDir.Rd | 3 man/grapes-IN-grapes.Rd | 7 +- man/is_quoted.Rd | 3 man/needs_quotes.Rd | 3 man/parse_where_clause.Rd | 3 man/re_quote.Rd | 3 man/re_quote_alt.Rd | 3 man/rename_col.Rd | 3 man/replaceNAwithNULL.Rd | 3 man/rm_quotes.Rd | 3 man/rm_vector_quotes.Rd | 3 man/sql_execute_delete.Rd | 3 man/sql_execute_get_insert.Rd | 3 man/sql_execute_insert.Rd | 3 man/sql_execute_select.Rd | 3 man/sql_execute_update.Rd | 3 man/sql_gen_delete.Rd | 3 man/sql_gen_insert.Rd | 3 man/sql_gen_select.Rd | 3 man/sql_gen_update.Rd | 3 man/sql_gen_where.Rd | 3 man/sql_gen_where_list.Rd | 3 man/sql_gen_where_or.Rd | 3 man/sql_retrieve.Rd | 3 man/sql_retrieve_insert.Rd | 3 man/stuff_df_quoted.Rd | 3 man/stuff_quote.Rd | 3 man/trim.Rd | 3 man/trim_leading.Rd | 3 man/trim_trailing.Rd | 3 tests/testthat/test_sql_lib.R | 1 50 files changed, 345 insertions(+), 88 deletions(-)
Title: Non-Parametric Causal Effects of Feasible Interventions Based on
Modified Treatment Policies
Description: Non-parametric estimators for casual effects based on longitudinal modified treatment
policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment,
and traditional longitudinal effects. Continuous, binary, and categorical treatments are allowed as well are
censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure
irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects
can be calculated and relative risks and odds ratios may be calculated for binary outcomes.
Author: Nicholas Williams [aut, cre, cph]
,
Ivan Diaz [aut, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between lmtp versions 1.0.0 dated 2021-09-29 and 1.3.0 dated 2022-05-21
lmtp-1.0.0/lmtp/R/checks-warnings.R |only lmtp-1.0.0/lmtp/R/cross-fit.R |only lmtp-1.0.0/lmtp/R/m-engine.R |only lmtp-1.0.0/lmtp/R/prepare-estimators.R |only lmtp-1.0.0/lmtp/R/r-engine.R |only lmtp-1.0.0/lmtp/R/zzz.R |only lmtp-1.0.0/lmtp/build/vignette.rds |only lmtp-1.0.0/lmtp/inst/doc |only lmtp-1.0.0/lmtp/vignettes |only lmtp-1.3.0/lmtp/DESCRIPTION | 16 lmtp-1.3.0/lmtp/MD5 | 68 - lmtp-1.3.0/lmtp/NAMESPACE | 3 lmtp-1.3.0/lmtp/NEWS.md | 34 lmtp-1.3.0/lmtp/R/checks.R |only lmtp-1.3.0/lmtp/R/contrasts.R | 35 lmtp-1.3.0/lmtp/R/density_ratios.R |only lmtp-1.3.0/lmtp/R/estimators.R | 593 ++++++----- lmtp-1.3.0/lmtp/R/gcomp.R |only lmtp-1.3.0/lmtp/R/lmtp-package.R | 1 lmtp-1.3.0/lmtp/R/lmtp_Task.R |only lmtp-1.3.0/lmtp/R/sdr.R |only lmtp-1.3.0/lmtp/R/sl.R | 12 lmtp-1.3.0/lmtp/R/theta.R | 9 lmtp-1.3.0/lmtp/R/tidy.R | 2 lmtp-1.3.0/lmtp/R/tmle.R |only lmtp-1.3.0/lmtp/R/utils.R | 82 - lmtp-1.3.0/lmtp/README.md | 33 lmtp-1.3.0/lmtp/build/partial.rdb |only lmtp-1.3.0/lmtp/inst/CITATION | 18 lmtp-1.3.0/lmtp/man/lmtp-package.Rd | 7 lmtp-1.3.0/lmtp/man/lmtp_contrast.Rd | 11 lmtp-1.3.0/lmtp/man/lmtp_ipw.Rd | 67 - lmtp-1.3.0/lmtp/man/lmtp_sdr.Rd | 78 - lmtp-1.3.0/lmtp/man/lmtp_sub.Rd | 60 - lmtp-1.3.0/lmtp/man/lmtp_tmle.Rd | 78 - lmtp-1.3.0/lmtp/tests/testthat/test-censoring.R | 30 lmtp-1.3.0/lmtp/tests/testthat/test-checks.R | 205 ++- lmtp-1.3.0/lmtp/tests/testthat/test-dynamic.R | 31 lmtp-1.3.0/lmtp/tests/testthat/test-node_list.R | 1 lmtp-1.3.0/lmtp/tests/testthat/test-point_treatment.R | 12 lmtp-1.3.0/lmtp/tests/testthat/test-shifted.R |only lmtp-1.3.0/lmtp/tests/testthat/test-time_varying_treatment.R | 19 42 files changed, 877 insertions(+), 628 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between formatters versions 0.2.0 dated 2022-03-29 and 0.3.1 dated 2022-05-20
formatters-0.2.0/formatters/tests/tinytest |only formatters-0.3.1/formatters/DESCRIPTION | 14 ++-- formatters-0.3.1/formatters/MD5 | 29 ++++----- formatters-0.3.1/formatters/NAMESPACE | 2 formatters-0.3.1/formatters/NEWS.md | 15 ++++ formatters-0.3.1/formatters/R/format_value.R | 26 +++++--- formatters-0.3.1/formatters/R/generics.R | 29 +++++---- formatters-0.3.1/formatters/R/matrix_form.R | 25 ++++++-- formatters-0.3.1/formatters/R/tostring.R | 59 ++++++++++++++----- formatters-0.3.1/formatters/README.md | 11 +-- formatters-0.3.1/formatters/build/vignette.rds |binary formatters-0.3.1/formatters/inst/doc/formatters.html | 15 ++-- formatters-0.3.1/formatters/man/default_hsep.Rd |only formatters-0.3.1/formatters/man/matrix_form.Rd | 7 +- formatters-0.3.1/formatters/man/tostring.Rd | 4 - formatters-0.3.1/formatters/tests/run_tests.R | 5 - formatters-0.3.1/formatters/tests/testthat |only 17 files changed, 158 insertions(+), 83 deletions(-)
Title: Ecological Limit Function Model Generation, Analysis, and
Visualization using 'ggplot2' and Statistical Methods
Description: A toolset for generating Ecological Limit Function (ELF) models and evaluating potential species loss resulting from flow change, based on the "elfgen" framework. ELFs describe the relation between aquatic species richness (fish or benthic macroinvertebrates) and stream size characteristics (streamflow or drainage area). Journal publications are available outlining framework methodology (Kleiner et al. (2020) <doi:10.1111/1752-1688.12876>) and application (Rapp et al. (2020) <doi:10.1111/1752-1688.12877>).
Author: Joseph Kleiner [aut, cre]
Maintainer: Joseph Kleiner <joseph.d.kleiner@gmail.com>
Diff between elfgen versions 2.2.8 dated 2022-03-29 and 2.3.0 dated 2022-05-20
DESCRIPTION | 10 ++++---- MD5 | 30 ++++++++++++------------- NAMESPACE | 3 +- R/bkpt-pwit.R | 13 +++++++---- R/bkpt-ymax.R | 2 - R/elfchange.R | 2 - R/elfdata.R | 57 +++++++++++++------------------------------------ R/elfgen.R | 2 - R/richness-change.R | 2 - README.md | 7 ++++-- man/bkpt_pwit.Rd | 9 ++++++- man/bkpt_ymax.Rd | 2 - man/elfchange.Rd | 2 - man/elfdata.Rd | 2 - man/elfgen.Rd | 2 - man/richness_change.Rd | 2 - 16 files changed, 68 insertions(+), 79 deletions(-)
Title: Covariance Based Single-Cell Decomposition of Bulk Expression
Data
Description: Provides accurate cell type proportion estimation by incorporating covariance structure in both single-cell and bulk RNA-seq datasets into the analysis. For more detail, see Karimnezhad, A. (2022) <doi:10.1101/2022.05.13.491858>.
Author: Ali Karimnezhad [aut, cre, ctb]
Maintainer: Ali Karimnezhad <ali.karimnezhad@gmail.com>
Diff between CSCDRNA versions 1.0.1 dated 2022-05-17 and 1.0.2 dated 2022-05-20
CSCDRNA-1.0.1/CSCDRNA/R/sample_data.R |only CSCDRNA-1.0.1/CSCDRNA/data/sample_data.rda |only CSCDRNA-1.0.1/CSCDRNA/man/sample_data.Rd |only CSCDRNA-1.0.2/CSCDRNA/DESCRIPTION | 12 +++++------ CSCDRNA-1.0.2/CSCDRNA/MD5 | 13 ++++++------ CSCDRNA-1.0.2/CSCDRNA/R/CSCD.R | 30 ++++++++++++++++------------ CSCDRNA-1.0.2/CSCDRNA/R/example_data.R |only CSCDRNA-1.0.2/CSCDRNA/README.md |only CSCDRNA-1.0.2/CSCDRNA/data/example_data.rda |only CSCDRNA-1.0.2/CSCDRNA/man/CSCD.Rd | 18 ++++++++++------ CSCDRNA-1.0.2/CSCDRNA/man/example_data.Rd |only 11 files changed, 42 insertions(+), 31 deletions(-)
Title: Predict Information Cascade by Self-Exciting Point Process
Description: An implementation of self-exciting point process model for information cascades, which occurs when many people engage in the same acts after observing the actions of others (e.g. post resharings on Facebook or Twitter). It provides functions to estimate the infectiousness of an information cascade and predict its popularity given the observed history. See <http://snap.stanford.edu/seismic/> for more information and datasets.
Author: Hera He, Murat Erdogdu, Qingyuan Zhao
Maintainer: Qingyuan Zhao <qingyzhao@gmail.com>
Diff between seismic versions 1.0 dated 2015-06-05 and 1.1 dated 2022-05-20
DESCRIPTION | 11 +++--- MD5 | 18 +++++----- NAMESPACE | 3 + R/tweetfunctions.R | 79 +++++++++++++++++++++++----------------------- man/get.infectiousness.Rd | 13 +++++-- man/linear.kernel.Rd | 35 ++++++++++++++------ man/memory.pdf.Rd | 8 ++-- man/pred.cascade.Rd | 13 +++++-- man/seismic.Rd | 4 -- man/tweet.Rd | 8 +--- 10 files changed, 108 insertions(+), 84 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.1.2 dated 2022-05-13 and 0.1.3 dated 2022-05-20
DESCRIPTION | 13 - MD5 | 68 ++++----- NAMESPACE | 16 +- NEWS.md | 11 + R/DanielBiostatistics10th.R | 3 R/Gosset_Welch.R | 16 -- R/chp12.R | 12 - R/chp2.R | 1 R/chp3.R | 117 ++++++++++----- R/chp4.R | 3 R/chp5.6.7.R | 204 +++++++++++++++------------ inst/example/Chapter1.R | 4 inst/example/Chapter10.R | 8 - inst/example/Chapter11.R | 73 ++++----- inst/example/Chapter12.R | 18 +- inst/example/Chapter13.R |only inst/example/Chapter14.R | 22 +- inst/example/Chapter2.R | 36 +--- inst/example/Chapter3.R | 28 ++- inst/example/Chapter4.R | 10 - inst/example/Chapter5.6.7.R | 82 +++++----- inst/example/Chapter7.power.R | 22 +- inst/example/Chapter8.R | 64 ++++---- inst/example/Chapter9.R | 9 - inst/example/Exercises.R |only inst/example/LDS_chp6.R | 10 - inst/example/LDS_chp8.R | 52 +++--- inst/example/LargeData_Chapter2_NCBIRTH800.R | 60 +++---- man/Chapter01.Rd | 4 man/Chapter02.Rd | 36 +--- man/Chapter03.Rd | 59 +++++-- man/Chapter04.Rd | 10 - man/Chapter05to07.Rd | 169 +++++++++++----------- man/Chapter07_power.Rd | 22 +- man/Chapter12.Rd | 26 +-- man/Gosset_Welch.Rd | 15 - 36 files changed, 701 insertions(+), 602 deletions(-)
More information about DanielBiostatistics10th at CRAN
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Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem.
Author: Dominique Makowski [aut, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.0 dated 2022-02-14 and 0.8.1 dated 2022-05-20
DESCRIPTION | 12 MD5 | 202 +-- NAMESPACE | 153 +- NEWS.md | 344 +++--- R/backports.R | 16 R/cor_lower.R |only R/cor_smooth.R | 306 ++--- R/cor_sort.R | 170 +-- R/cor_test.R | 626 +++++------ R/cor_test_bayes.R | 214 +-- R/cor_test_biserial.R | 150 +- R/cor_test_biweight.R | 82 - R/cor_test_blomqvist.R | 52 R/cor_test_distance.R | 286 ++--- R/cor_test_freq.R | 159 +- R/cor_test_gamma.R | 58 - R/cor_test_gaussian.R | 24 R/cor_test_hoeffding.R | 50 R/cor_test_percentage.R | 101 - R/cor_test_polychoric.R | 94 - R/cor_test_shepherd.R | 36 R/cor_test_somers.R | 46 R/cor_test_tetrachoric.R | 70 - R/cor_text.R | 168 +-- R/cor_to_ci.R | 178 +-- R/cor_to_cov.R | 120 +- R/cor_to_p.R | 97 - R/cor_to_pcor.R | 523 ++++----- R/cor_to_spcor.R | 44 R/correlation.R | 1287 +++++++++++------------ R/display.R | 170 +-- R/mahalanobis.R | 125 +- R/matrix_inverse.R | 108 - R/methods.easycorrelation.R | 423 +++---- R/methods_format.R | 392 +++---- R/methods_plot.R | 24 R/methods_print.R | 359 +++--- R/reexports.R | 38 R/utils.R | 68 - R/utils_clean_data.R | 22 R/utils_create_diagonal.R | 92 - R/utils_find_correlationtype.R | 132 +- R/utils_get_combinations.R | 80 - R/utils_get_matrix.R | 32 R/utils_remove_redundant.R | 130 +- R/visualisation_recipe.cor_test.R | 346 +++--- R/visualisation_recipe.easycormatrix.R | 549 ++++----- R/visualisation_recipe.easycorrelation.R | 92 - R/z_fisher.R | 56 - README.md | 693 ++++++------ build/vignette.rds |binary inst/CITATION | 28 inst/WORDLIST | 188 +-- inst/doc/multilevel.R | 104 - inst/doc/multilevel.Rmd | 268 ++-- inst/doc/multilevel.html | 752 ++++++++----- inst/doc/types.R | 218 +-- inst/doc/types.Rmd | 524 ++++----- inst/doc/types.html | 1017 +++++++++++------- man/cor_lower.Rd |only man/cor_smooth.Rd | 88 - man/cor_sort.Rd | 62 - man/cor_test.Rd | 543 ++++----- man/cor_text.Rd | 56 - man/cor_to_cov.Rd | 60 - man/cor_to_p.Rd | 136 +- man/cor_to_pcor.Rd | 113 +- man/correlation.Rd | 653 +++++------ man/display.easycormatrix.Rd | 158 +- man/distance_mahalanobis.Rd | 90 - man/is.cor.Rd | 34 man/isSquare.Rd | 34 man/matrix_inverse.Rd | 52 man/reexports.Rd | 48 man/visualisation_recipe.easycormatrix.Rd | 247 ++-- man/z_fisher.Rd | 56 - tests/spelling.R | 12 tests/testthat.R | 22 tests/testthat/_snaps/as.list.md | 512 ++++----- tests/testthat/_snaps/correlation.md | 76 - tests/testthat/_snaps/display_print_dataframe.md | 64 - tests/testthat/_snaps/display_print_matrix.md | 96 - tests/testthat/_snaps/methods.md | 102 - tests/testthat/_snaps/renaming.md | 96 - tests/testthat/_snaps/selecting_variables.md | 100 - tests/testthat/test-as.list.R | 46 tests/testthat/test-cor_multilevel.R | 84 - tests/testthat/test-cor_test.R | 388 +++--- tests/testthat/test-cor_test_na_present.R | 260 ++-- tests/testthat/test-cor_to_cov.R | 16 tests/testthat/test-cor_to_p.R | 16 tests/testthat/test-cor_to_pcor.R | 164 +- tests/testthat/test-correlation.R | 372 +++--- tests/testthat/test-display_print_dataframe.R | 82 - tests/testthat/test-display_print_matrix.R | 110 - tests/testthat/test-grouped_data2.R | 36 tests/testthat/test-methods.R | 28 tests/testthat/test-misc.R | 76 - tests/testthat/test-renaming.R | 40 tests/testthat/test-selecting_variables.R | 76 - vignettes/bibliography.bib | 316 ++--- vignettes/multilevel.Rmd | 268 ++-- vignettes/types.Rmd | 524 ++++----- 103 files changed, 9803 insertions(+), 9307 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The
functions are pipe-friendly and provide a consistent syntax to work
with tidy data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.3.1 dated 2022-03-29 and 1.3.2 dated 2022-05-20
statsExpressions-1.3.1/statsExpressions/tests/testthat/_snaps/tidy_model_expressions_F.md |only statsExpressions-1.3.1/statsExpressions/tests/testthat/_snaps/windows |only statsExpressions-1.3.1/statsExpressions/tests/testthat/test-grouped_dataframes.R |only statsExpressions-1.3.1/statsExpressions/tests/testthat/test-tidy_model_expressions_F.R |only statsExpressions-1.3.2/statsExpressions/DESCRIPTION | 17 statsExpressions-1.3.2/statsExpressions/MD5 | 179 +-- statsExpressions-1.3.2/statsExpressions/NAMESPACE | 2 statsExpressions-1.3.2/statsExpressions/NEWS.md | 20 statsExpressions-1.3.2/statsExpressions/R/add_expression_col.R | 33 statsExpressions-1.3.2/statsExpressions/R/centrality_description.R | 20 statsExpressions-1.3.2/statsExpressions/R/contingency_table.R | 438 +++---- statsExpressions-1.3.2/statsExpressions/R/corr_test.R | 14 statsExpressions-1.3.2/statsExpressions/R/global_vars.R | 78 - statsExpressions-1.3.2/statsExpressions/R/helpers_easystats.R | 1 statsExpressions-1.3.2/statsExpressions/R/long_to_wide_converter.R | 44 statsExpressions-1.3.2/statsExpressions/R/meta_analysis.R | 13 statsExpressions-1.3.2/statsExpressions/R/one_sample_test.R | 16 statsExpressions-1.3.2/statsExpressions/R/oneway_anova.R | 25 statsExpressions-1.3.2/statsExpressions/R/pairwise_comparisons.R |only statsExpressions-1.3.2/statsExpressions/R/switch_functions.R | 209 +-- statsExpressions-1.3.2/statsExpressions/R/tidy_model_expressions.R | 161 +- statsExpressions-1.3.2/statsExpressions/R/two_sample_test.R | 13 statsExpressions-1.3.2/statsExpressions/README.md | 182 +-- statsExpressions-1.3.2/statsExpressions/build/vignette.rds |binary statsExpressions-1.3.2/statsExpressions/inst/WORDLIST | 5 statsExpressions-1.3.2/statsExpressions/inst/doc/statsExpressions.html | 52 statsExpressions-1.3.2/statsExpressions/inst/doc/stats_details.Rmd | 8 statsExpressions-1.3.2/statsExpressions/inst/doc/stats_details.html | 69 - statsExpressions-1.3.2/statsExpressions/man/add_expression_col.Rd | 4 statsExpressions-1.3.2/statsExpressions/man/centrality_description.Rd | 16 statsExpressions-1.3.2/statsExpressions/man/contingency_table.Rd | 15 statsExpressions-1.3.2/statsExpressions/man/corr_test.Rd | 11 statsExpressions-1.3.2/statsExpressions/man/figures/README-anova_parametric2-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-anova_rob1-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-centrality-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-corr-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-custom_expr-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-gof-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-metaanalysis-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-t_one-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-t_two-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-t_two_paired1-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/card.png |binary statsExpressions-1.3.2/statsExpressions/man/long_to_wide_converter.Rd | 28 statsExpressions-1.3.2/statsExpressions/man/meta_analysis.Rd | 10 statsExpressions-1.3.2/statsExpressions/man/one_sample_test.Rd | 11 statsExpressions-1.3.2/statsExpressions/man/oneway_anova.Rd | 28 statsExpressions-1.3.2/statsExpressions/man/p_adjust_text.Rd |only statsExpressions-1.3.2/statsExpressions/man/pairwise_comparisons.Rd |only statsExpressions-1.3.2/statsExpressions/man/reexports.Rd | 2 statsExpressions-1.3.2/statsExpressions/man/rmd-fragments/functionality.Rmd | 13 statsExpressions-1.3.2/statsExpressions/man/rmd-fragments/pairwise_comparisons.Rmd |only statsExpressions-1.3.2/statsExpressions/man/rmd-fragments/return.Rmd | 4 statsExpressions-1.3.2/statsExpressions/man/tidy_model_expressions.Rd | 6 statsExpressions-1.3.2/statsExpressions/man/two_sample_test.Rd | 28 statsExpressions-1.3.2/statsExpressions/tests/spelling.R | 12 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/centrality_description.md | 298 +++-- statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/contingency_table.md | 105 + statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/corr_test.md | 168 ++- statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/long_to_wide_converter.md | 192 +-- statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/meta_random_parametric.md | 8 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/meta_random_robust.md | 8 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/one_sample.md | 69 - statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/one_two_sample_dataframes.md | 56 - statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_bayes.md |only statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_nonparametric.md | 36 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_parametric.md | 40 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_robust.md | 26 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/pairwise_comparisons.md |only statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/tidy_model_expressions.md | 147 ++ statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_bayes.md | 20 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_nonparametric.md | 17 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_parametric.md | 34 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_robust.md | 32 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/z_meta_random_bayes.md | 17 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-centrality_description.R | 29 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-contingency_table.R | 554 ++++------ statsExpressions-1.3.2/statsExpressions/tests/testthat/test-corr_test.R | 167 +-- statsExpressions-1.3.2/statsExpressions/tests/testthat/test-long_to_wide_converter.R | 21 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-meta_random_parametric.R | 4 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-meta_random_robust.R | 4 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-one_sample.R | 24 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-one_two_sample_dataframes.R | 10 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_bayes.R | 50 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_nonparametric.R | 91 - statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_parametric.R | 18 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_robust.R | 18 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-pairwise_comparisons.R |only statsExpressions-1.3.2/statsExpressions/tests/testthat/test-tidy_model_expressions.R | 190 ++- statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_bayes.R | 15 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_nonparametric.R | 8 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_parametric.R | 16 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_robust.R | 16 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-z_meta_random_bayes.R | 10 statsExpressions-1.3.2/statsExpressions/vignettes/stats_details.Rmd | 8 statsExpressions-1.3.2/statsExpressions/vignettes/web_only/dataframe_outputs.Rmd | 127 ++ 96 files changed, 2501 insertions(+), 1939 deletions(-)
More information about statsExpressions at CRAN
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Title: Nonparametric Methods for Generating High Quality Comparative
Effectiveness Evidence
Description: Implements novel nonparametric approaches to address
biases and confounding when comparing treatments or exposures in
observational studies of outcomes. While designed and appropriate for use
in studies involving medicine and the life sciences, the package can be
used in other situations involving outcomes with multiple confounders.
The package implements a family of methods for non-parametric bias correction
when comparing treatments in observational studies, including survival
analysis settings, where competing risks and/or censoring may be present.
The approach extends to bias-corrected personalized predictions of treatment
outcome differences, and analysis of heterogeneity of treatment effect-sizes
across patient subgroups. For further details, please see:
Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
An R Package for Comparative Safety and Effectiveness Research.
Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Author: Nicolas R. Lauve [aut] ,
Stuart J. Nelson [aut] ,
S. Stanley Young [aut] ,
Robert L. Obenchain [aut] ,
Melania Pintilie [ctb],
Martin Kutz [ctb],
Christophe G. Lambert [aut, cre]
Maintainer: Christophe G. Lambert <cglambert@unm.edu>
Diff between LocalControl versions 1.1.2.2 dated 2020-11-26 and 1.1.3 dated 2022-05-20
LocalControl-1.1.2.2/LocalControl/inst/doc/LocalControl-jss-2018.R |only LocalControl-1.1.2.2/LocalControl/inst/doc/LocalControl-jss-2018.Rnw |only LocalControl-1.1.2.2/LocalControl/inst/doc/LocalControl-jss-2018.pdf |only LocalControl-1.1.2.2/LocalControl/vignettes/LocalControl-jss-2018.Rnw |only LocalControl-1.1.3/LocalControl/DESCRIPTION | 10 +- LocalControl-1.1.3/LocalControl/MD5 | 22 ++-- LocalControl-1.1.3/LocalControl/NEWS.md | 8 + LocalControl-1.1.3/LocalControl/R/clusteringLC.R | 2 LocalControl-1.1.3/LocalControl/R/localControl.R | 2 LocalControl-1.1.3/LocalControl/build/vignette.rds |binary LocalControl-1.1.3/LocalControl/inst/CITATION | 48 ++++------ LocalControl-1.1.3/LocalControl/inst/doc/LocalControl-jss-2020.R |only LocalControl-1.1.3/LocalControl/inst/doc/LocalControl-jss-2020.Rnw |only LocalControl-1.1.3/LocalControl/inst/doc/LocalControl-jss-2020.pdf |only LocalControl-1.1.3/LocalControl/src/RcppExports.cpp | 5 + LocalControl-1.1.3/LocalControl/vignettes/LocalControl-jss-2020.Rnw |only 16 files changed, 51 insertions(+), 46 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis
of confidence region simulations and (3) calculating confidence intervals and the associated
actual coverage for binomial proportions. Each is given in greater detail next.
(1) Plots the two-dimensional confidence region for probability distribution parameters
(supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif,
weibull) corresponding to a user-given complete or right-censored dataset and level of
significance. The crplot() algorithm plots more points in areas of greater curvature to
ensure a smooth appearance throughout the confidence region boundary. An alternative
heuristic plots a specified number of points at roughly uniform intervals along its boundary.
Both heuristics build upon the radial profile log-likelihood ratio technique for plotting
confidence regions given by Jaeger (2016) <doi:10.1080/00031305.2016.1182946>, and
are detailed in a publication by Weld (2019) <doi:10.1080/00031305.2018.1564696>.
(2) Performs confidence region coverage simulations for a random sample drawn from a user-
specified parametric population distribution, or for a user-specified dataset and point of
interest with coversim(). (3) Calculates confidence interval bounds for a binomial proportion
with binomTest(), calculates the actual coverage with binomTestCoverage(), and plots the
actual coverage with binomTestCoveragePlot(). Calculates confidence interval bounds for the
binomial proportion using an ensemble of constituent confidence intervals with
binomTestEnsemble(). Calculates confidence interval bounds for the binomial proportion using
a complete enumeration of all possible transitions from one actual coverage acceptance curve
to another which minimizes the root mean square error for n <= 15 and follows the transitions
for well-known confidence intervals for n > 15 using binomTestMSE().
Author: Christopher Weld [aut, cre] ,
Hayeon Park [aut],
Kexin Feng [aut],
Heather Sasinowska [aut],
Lawrence Leemis [aut],
Andrew Loh [ctb],
Yuan Chang [ctb],
Brock Crook [ctb],
Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>
Diff between conf versions 1.7.0 dated 2020-08-24 and 1.7.1 dated 2022-05-20
DESCRIPTION | 13 MD5 | 22 NAMESPACE | 15 R/STAR_package_functions.R |only R/coversim.R | 66 - R/crplot.R | 1688 +++++++++++++++++++++--------------------- inst/CITATION | 2 inst/doc/coversim.html | 22 inst/doc/crplot.html | 32 inst/doc/crplot_advanced.html | 28 man/dinvgauss.Rd |only man/dllogis.Rd |only man/gammaMLE.Rd |only man/invgaussMLE.Rd |only man/llogisMLE.Rd |only 15 files changed, 959 insertions(+), 929 deletions(-)
Title: Interactive Model Exploration using 'GGobi'
Description: Exploratory model analysis with <http://ggobi.org>.
Fit and graphical explore ensembles of linear models.
Author: Hadley Wickham <h.wickham@gmail.com>
Maintainer: Hadley Wickham <h.wickham@gmail.com>
Diff between meifly versions 0.3 dated 2014-04-23 and 0.3.1 dated 2022-05-20
meifly-0.3.1/meifly/DESCRIPTION | 22 ++++++------ meifly-0.3.1/meifly/MD5 | 32 +++++++++--------- meifly-0.3.1/meifly/NAMESPACE | 2 - meifly-0.3.1/meifly/NEWS.md |only meifly-0.3.1/meifly/R/generate.r | 30 ++++++++--------- meifly-0.3.1/meifly/R/summarise.r | 33 +++++++++---------- meifly-0.3.1/meifly/man/coef.ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/findmodels.Rd | 4 +- meifly-0.3.1/meifly/man/fitall.Rd | 4 +- meifly-0.3.1/meifly/man/fitbest.Rd | 4 +- meifly-0.3.1/meifly/man/lmboot.Rd | 4 +- meifly-0.3.1/meifly/man/meifly.Rd | 4 +- meifly-0.3.1/meifly/man/new_ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/residuals.ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/summary.ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/summary.resid_ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/summary.variable_ensemble.Rd | 4 +- meifly-0.3/meifly/NEWS |only 18 files changed, 82 insertions(+), 81 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] ,
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.3.0 dated 2021-07-07 and 1.3.1 dated 2022-05-20
DESCRIPTION | 12 MD5 | 68 NAMESPACE | 199 - R/ClusterAccuracy.R | 204 - R/ClusterChallenge.R | 393 +- R/ClusterCount.R | 3 R/ClusterDaviesBouldinIndex.R | 12 R/ClusterDunnIndex.R | 125 R/ClusterEqualWeighting.R | 91 R/ClusterMCC.R |only R/ClusterNoEstimation.R | 662 ++-- R/ClusterNormalize.R |only R/ClusterRedefine.R |only R/ClusterRenameDescendingSize.R | 18 R/ClusterUpsamplingMinority.R |only R/ModelBasedVarSelClustering.R | 176 - R/NetworkClustering.R |only R/SparseClustering.R | 168 - README.md | 17 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FCPS.R | 208 - inst/doc/FCPS.Rmd | 332 +- inst/doc/FCPS.html | 4928 ++++++++++++++++++------------------- man/ClusterAccuracy.Rd | 136 - man/ClusterDaviesBouldinIndex.Rd | 4 man/ClusterDunnIndex.Rd | 143 - man/ClusterEqualWeighting.Rd | 4 man/ClusterMCC.Rd |only man/ClusterNoEstimation.Rd | 303 +- man/ClusterNormalize.Rd |only man/ClusterRedefine.Rd |only man/ClusterRenameDescendingSize.Rd | 27 man/ClusterUpsamplingMinority.Rd |only man/DivisiveAnalysisClustering.Rd | 104 man/FCPS-package.Rd | 1 man/MoGclustering.Rd | 156 - man/NetworkClustering.Rd |only man/SparseClustering.Rd | 147 - vignettes/FCPS.Rmd | 332 +- 40 files changed, 4598 insertions(+), 4375 deletions(-)
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 10.0.0 dated 2021-11-09 and 11.0.0 dated 2022-05-20
DESCRIPTION | 13 +++++++------ MD5 | 32 ++++++++++++++++---------------- R/praznik.R | 2 +- R/transforms.R | 4 ++-- inst/CITATION | 16 ++++++++++++++++ inst/NEWS | 3 +++ man/kInverse.Rd | 2 +- man/kTransform.Rd | 2 +- man/praznik-package.Rd | 2 +- src/trips.h | 2 +- tests/testthat/test-engine.R | 2 -- tests/testthat/test-input.R | 2 -- tests/testthat/test-madelon.R | 2 -- tests/testthat/test-matrix.R | 2 -- tests/testthat/test-native-pure.R | 2 -- tests/testthat/test-tools.R | 2 -- tests/testthat/test-transform.R | 2 -- 17 files changed, 49 insertions(+), 43 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoğlu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.2.2 dated 2022-02-03 and 1.3.0 dated 2022-05-20
DESCRIPTION | 12 MD5 | 84 ++-- NAMESPACE | 2 NEWS.md | 7 R/checks.R | 2 R/compare_models.R |only R/cross_val.R | 1 R/data.R | 10 R/feature_importance.R | 61 ++- R/utils.R | 6 build/partial.rdb |binary build/vignette.rds |binary data/otu_mini_bin.rda |binary data/otu_mini_bin_results_glmnet.rda |binary data/otu_mini_bin_results_rf.rda |binary data/otu_mini_bin_results_rpart2.rda |binary data/otu_mini_bin_results_svmRadial.rda |binary data/otu_mini_bin_results_xgbTree.rda |binary data/otu_mini_cont_results_glmnet.rda |binary data/otu_mini_cont_results_nocv.rda |binary data/otu_mini_cv.rda |binary data/otu_mini_multi.rda |binary data/otu_mini_multi_group.rda |binary data/otu_mini_multi_results_glmnet.rda |binary data/otu_small.rda |binary inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 605 ++++++++++++++++++++++++++----- inst/doc/paper.Rmd | 2 inst/doc/paper.html | 497 ++++++++++++++++++++++--- man/compare_models.Rd |only man/get_feature_importance.Rd | 61 ++- man/otu_mini_bin_results_glmnet.Rd | 4 man/otu_mini_bin_results_rf.Rd | 4 man/otu_mini_bin_results_rpart2.Rd | 4 man/otu_mini_bin_results_svmRadial.Rd | 4 man/otu_mini_bin_results_xgbTree.Rd | 4 man/permute_p_value.Rd |only man/reexports.Rd | 2 tests/testthat/test-compare_models.R |only tests/testthat/test-cross_val.R | 26 - tests/testthat/test-feature_importance.R | 20 - tests/testthat/test-run_ml.R | 5 tests/testthat/test-utils.R | 5 vignettes/introduction.Rmd | 4 vignettes/paper.Rmd | 2 45 files changed, 1161 insertions(+), 277 deletions(-)
Title: Threshold Regression that Fits the (Randomized Drift) Inverse
Gaussian Distribution to Survival Data
Description: Fits the (randomized drift) inverse Gaussian distribution to survival data. The model is described in Aalen OO, Borgan O, Gjessing HK. Survival and Event History Analysis. A Process Point of View. Springer, 2008. It is based on describing time to event as the barrier hitting time of a Wiener process, where drift towards the barrier has been randomized with a Gaussian distribution. The model allows covariates to influence starting values of the Wiener process and/or average drift towards a barrier, with a user-defined choice of link functions.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between invGauss versions 1.1 dated 2014-03-28 and 1.2 dated 2022-05-20
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NAMESPACE | 3 ++- R/predict.invGauss.R | 7 +++++-- man/d.oropha.rec.Rd | 2 +- 5 files changed, 20 insertions(+), 16 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 3.4.0 dated 2022-04-26 and 3.5.0 dated 2022-05-20
DESCRIPTION | 12 +- MD5 | 83 ++++++++++--------- NAMESPACE | 1 NEWS.md | 5 + R/delete_trailing_blank_lines.R |only R/test_helpers.R | 7 - R/view.R | 9 +- inst/NEWS.rd | 7 + inst/files/blanks.txt |only inst/runit_tests/runit-delete_trailing_blank_lines.R |only inst/runit_tests/runit-delete_trailing_whitespace.R |only inst/source/R/delete_trailing_blank_lines.R |only inst/source/R/test_helpers.R | 7 - inst/source/R/view.R | 9 +- inst/source/man/clipboard_path.Rd | 1 inst/source/man/delete_trailing_blank_lines.Rd |only inst/source/man/delete_trailing_whitespace.Rd | 1 inst/source/man/develop_test.Rd | 1 inst/source/man/file_copy.Rd | 1 inst/source/man/file_modified_last.Rd | 1 inst/source/man/file_save.Rd | 1 inst/source/man/find_files.Rd | 1 inst/source/man/get_mtime.Rd | 1 inst/source/man/get_unique_string.Rd | 1 inst/source/man/is_files_current.Rd | 1 inst/source/man/is_path.Rd | 1 inst/source/man/paths.Rd | 1 inst/source/man/search_files.Rd | 1 inst/source/man/split_code_file.Rd | 1 inst/source/man/touch.Rd | 1 man/clipboard_path.Rd | 1 man/delete_trailing_blank_lines.Rd |only man/delete_trailing_whitespace.Rd | 1 man/develop_test.Rd | 1 man/file_copy.Rd | 1 man/file_modified_last.Rd | 1 man/file_save.Rd | 1 man/find_files.Rd | 1 man/get_mtime.Rd | 1 man/get_unique_string.Rd | 1 man/is_files_current.Rd | 1 man/is_path.Rd | 1 man/paths.Rd | 1 man/search_files.Rd | 1 man/split_code_file.Rd | 1 man/touch.Rd | 1 46 files changed, 112 insertions(+), 58 deletions(-)
Title: Unbinned Weighted Histogram Analysis Method (UWHAM)
Description: A method for estimating log-normalizing constants (or free
energies) and expectations from multiple distributions (such as
multiple generalized ensembles).
Author: Zhiqiang Tan and Emilio Gallicchio
Maintainer: Zhiqiang Tan <ztan@stat.rutgers.edu>
Diff between UWHAM versions 1.0 dated 2013-01-26 and 1.1 dated 2022-05-20
DESCRIPTION | 14 ++++++++------ MD5 | 5 +++-- NAMESPACE | 2 ++ NEWS.md |only 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 2.5.1 dated 2022-01-26 and 2.6.0 dated 2022-05-20
DESCRIPTION | 8 - MD5 | 83 ++++++------- NAMESPACE | 1 NEWS.md | 12 + R/Connection.R | 113 ++++++++++------- R/Driver.R | 49 +++++++ R/File_Parser.R | 4 R/Options.R | 20 ++- R/Result.R | 38 ++--- R/View.R | 70 ++++++---- R/athena_low_api.R | 68 ++++++---- R/dplyr_integration.R | 6 R/fetch_utils.R | 10 - R/table.R | 10 - R/utils.R | 185 ++++++++++++++++++----------- R/zzz.R | 4 README.md | 1 build/vignette.rds |binary inst/doc/aws_athena_query_caching.html | 22 +-- inst/doc/aws_athena_unload.Rmd | 9 - inst/doc/aws_athena_unload.html | 13 +- inst/doc/aws_s3_backend.html | 9 - inst/doc/changing_backend_file_parser.Rmd | 2 inst/doc/changing_backend_file_parser.html | 3 inst/doc/convert_and_save_cost.html | 1 inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 25 ++- inst/doc/how_to_retry.Rmd | 2 inst/doc/how_to_retry.html | 7 - man/RAthena_options.Rd | 5 man/dbClearResult.Rd | 3 man/dbConnect-AthenaDriver-method.Rd | 49 +++++++ man/dbGetQuery.Rd | 4 man/db_compute.Rd | 6 man/install_boto.Rd | 4 tests/testthat/test-endpoint-override.R |only tests/testthat/test-keyboard-interrupt.R | 8 - tests/testthat/test-metadata.R | 44 ++++++ tests/testthat/test-view.R | 2 vignettes/aws_athena_unload.Rmd | 9 - vignettes/changing_backend_file_parser.Rmd | 2 vignettes/getting_started.Rmd | 2 vignettes/how_to_retry.Rmd | 2 43 files changed, 592 insertions(+), 325 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:10.1080/10618600.2019.1604374>). Additionally, the porridge-package facilitates the ridge penalized estimation of a mixture of Gaussian graphical models (Aflakparast et al., 2018). On another note, the package also includes functionality for ridge-type estimation of the generalized linear model (as presented in van Wieringen, Binder, 2022, <doi:10.1080/10618600.2022.2035231>).
Author: Wessel N. van Wieringen [aut, cre]
,
Mehran Aflakparast [ctb]
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between porridge versions 0.3.0 dated 2022-01-08 and 0.3.1 dated 2022-05-20
DESCRIPTION | 23 ++++++----- MD5 | 30 +++++++------- R/ridgeGGMmixtureAndCo.R | 18 ++++---- R/ridgePgenAndCo.R | 75 +++++++++++++++++++------------------ R/ridgePmultitTandCo.R | 10 ++-- R/ridgePrepAndCo.R | 34 ++++++++-------- inst/CITATION | 19 +++++++++ inst/NEWS.Rd | 12 +++++ man/genRidgePenaltyMat.Rd | 5 +- man/makeFoldsGLMcv.Rd | 8 +-- man/optPenaltyGLM.kCVauto.Rd | 2 man/optPenaltyGLMmultiT.kCVauto.Rd | 2 man/porridge-package.Rd | 25 +++--------- man/ridgeGLM.Rd | 2 src/RcppExports.cpp | 6 ++ src/ridgeGGMmix.h | 29 ++++++++------ 16 files changed, 169 insertions(+), 131 deletions(-)
Title: Improved Methods for Causal Inference and Missing Data Problems
Description: Improved methods based on inverse probability weighting
and outcome regression for causal inference and missing data
problems.
Author: Zhiqiang Tan and Heng Shu
Maintainer: Zhiqiang Tan <ztan@stat.rutgers.edu>
Diff between iWeigReg versions 1.0 dated 2013-02-25 and 1.1 dated 2022-05-20
DESCRIPTION | 12 ++++++------ MD5 | 9 ++++++--- NAMESPACE | 1 + NEWS.md |only build |only inst/doc/vig.R |only inst/doc/vig.pdf |binary 7 files changed, 13 insertions(+), 9 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [ctb]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.1.1 dated 2022-01-09 and 0.2.0 dated 2022-05-20
DESCRIPTION | 8 MD5 | 34 +- NAMESPACE | 26 - NEWS.md | 18 + R/data.R | 16 - R/frscore.R | 74 +++-- R/frscored_cna.R | 505 ++++++++++++++++++------------------- README.md | 14 - inst/WORDLIST | 54 +-- man/d.error.Rd | 36 +- man/frscore.Rd | 208 +++++++-------- man/frscored_cna.Rd | 15 - man/rean_cna.Rd | 124 ++++----- tests/spelling.R | 6 tests/testthat.R | 10 tests/testthat/_snaps |only tests/testthat/test_frscore.R | 143 +++++----- tests/testthat/test_frscored_cna.R | 41 +-- 18 files changed, 695 insertions(+), 637 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.5.1 dated 2022-02-03 and 0.5.3 dated 2022-05-20
DESCRIPTION | 12 MD5 | 28 - NAMESPACE | 9 R/pillar_utilities.R |only R/print_method.R | 519 +++++++----------------- R/tidyr_methods.R | 8 R/utilities.R | 775 ++++++++++++++++++------------------ README.md | 100 ---- build/tidyseurat.pdf |binary inst/doc/introduction.R | 195 ++++----- inst/doc/introduction.html | 174 ++------ man/figures/pc_plot-1.png |binary man/figures/plot2-1.png |binary man/figures/unnamed-chunk-12-1.png |binary man/fragments/intro.Rmd | 789 ++++++++++++++++++------------------- man/tbl_format_header-methods.Rd |only 16 files changed, 1150 insertions(+), 1459 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 1.0.3 dated 2021-03-05 and 1.0.4 dated 2022-05-20
tidyquant-1.0.3/tidyquant/inst/doc/TQ06-excel-in-r.R |only tidyquant-1.0.3/tidyquant/inst/doc/TQ06-excel-in-r.Rmd |only tidyquant-1.0.3/tidyquant/inst/doc/TQ06-excel-in-r.html |only tidyquant-1.0.3/tidyquant/vignettes/TQ06-excel-in-r.Rmd |only tidyquant-1.0.3/tidyquant/vignettes/r-for-excel-users.jpg |only tidyquant-1.0.4/tidyquant/DESCRIPTION | 13 tidyquant-1.0.4/tidyquant/LICENSE | 4 tidyquant-1.0.4/tidyquant/MD5 | 205 tidyquant-1.0.4/tidyquant/NAMESPACE | 400 - tidyquant-1.0.4/tidyquant/NEWS.md | 530 +- tidyquant-1.0.4/tidyquant/R/api-alphavantager.R | 58 tidyquant-1.0.4/tidyquant/R/api-quandl.R | 124 tidyquant-1.0.4/tidyquant/R/api-tiingo.R | 66 tidyquant-1.0.4/tidyquant/R/data.R | 38 tidyquant-1.0.4/tidyquant/R/deprecated.R | 78 tidyquant-1.0.4/tidyquant/R/excel-date-functions.R | 1216 ++-- tidyquant-1.0.4/tidyquant/R/excel-financial-math-functions.R | 380 - tidyquant-1.0.4/tidyquant/R/excel-if-functions.R | 422 - tidyquant-1.0.4/tidyquant/R/excel-pivot-table.R | 540 +- tidyquant-1.0.4/tidyquant/R/excel-ref-functions.R | 130 tidyquant-1.0.4/tidyquant/R/excel-stat-mutation-functions.R | 382 - 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tidyquant-1.0.4/tidyquant/man/excel_pivot_table.Rd | 170 tidyquant-1.0.4/tidyquant/man/excel_ref_functions.Rd | 124 tidyquant-1.0.4/tidyquant/man/excel_stat_mutation_functions.Rd | 246 tidyquant-1.0.4/tidyquant/man/excel_stat_summary_functions.Rd | 260 - tidyquant-1.0.4/tidyquant/man/geom_bbands.Rd | 418 - tidyquant-1.0.4/tidyquant/man/geom_chart.Rd | 296 - tidyquant-1.0.4/tidyquant/man/geom_ma.Rd | 346 - tidyquant-1.0.4/tidyquant/man/palette_tq.Rd | 46 tidyquant-1.0.4/tidyquant/man/pipe.Rd | 24 tidyquant-1.0.4/tidyquant/man/quandl_api_key.Rd | 58 tidyquant-1.0.4/tidyquant/man/quandl_search.Rd | 70 tidyquant-1.0.4/tidyquant/man/scale_manual.Rd | 124 tidyquant-1.0.4/tidyquant/man/theme_tq.Rd | 100 tidyquant-1.0.4/tidyquant/man/tidyquant.Rd | 62 tidyquant-1.0.4/tidyquant/man/tiingo_api_key.Rd | 60 tidyquant-1.0.4/tidyquant/man/tq_get.Rd | 362 - tidyquant-1.0.4/tidyquant/man/tq_index.Rd | 140 tidyquant-1.0.4/tidyquant/man/tq_mutate.Rd | 347 - tidyquant-1.0.4/tidyquant/man/tq_performance.Rd | 208 tidyquant-1.0.4/tidyquant/man/tq_portfolio.Rd | 302 - 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Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 2.5.1 dated 2022-01-26 and 2.6.0 dated 2022-05-20
DESCRIPTION | 8 +-- MD5 | 55 ++++++++++---------- NAMESPACE | 1 NEWS.md | 6 ++ R/Connection.R | 76 +++++++++++++++++++---------- R/Driver.R | 35 ++++++++++++- R/File_Parser.R | 4 - R/Options.R | 19 +++++-- R/Result.R | 8 +-- R/dplyr_integration.R | 2 R/utils.R | 30 +++++++++++ README.md | 1 build/vignette.rds |binary inst/doc/aws_athena_query_caching.html | 22 ++++---- inst/doc/aws_athena_unload.html | 5 + inst/doc/aws_s3_backend.html | 1 inst/doc/changing_backend_file_parser.Rmd | 2 inst/doc/changing_backend_file_parser.html | 3 - inst/doc/convert_and_save_cost.html | 1 inst/doc/getting_started.html | 21 ++++---- inst/doc/how_to_retry.html | 5 + man/dbClearResult.Rd | 4 + man/dbConnect-AthenaDriver-method.Rd | 35 ++++++++++++- man/dbGetQuery.Rd | 4 + man/db_compute.Rd | 6 -- man/noctua_options.Rd | 5 + tests/testthat/test-endpoint-override.R |only tests/testthat/test-metadata.R | 50 +++++++++++++++++-- vignettes/changing_backend_file_parser.Rmd | 2 29 files changed, 301 insertions(+), 110 deletions(-)
Title: Demand Analysis with the Almost Ideal Demand System (AIDS)
Description: Functions and tools
for analysing consumer demand
with the Almost Ideal Demand System (AIDS)
suggested by Deaton and Muellbauer (1980).
Author: Arne Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between micEconAids versions 0.6-18 dated 2017-03-16 and 0.6-20 dated 2022-05-20
DESCRIPTION | 8 ++--- MD5 | 34 +++++++++++----------- NEWS | 10 +++++- R/aidsCalc.R | 57 ++++++++++++++++++++++++++++++-------- R/aidsElas.R | 44 ++++++++++++++++++++++++----- R/aidsElasJacobian.R | 32 +++++++++++++++++++-- R/aidsEst.R | 9 ++++++ R/aidsPx.R | 8 ++--- R/aidsUtility.R | 2 - R/aidsUtilityDeriv.R | 2 - R/elas.aidsEst.R | 1 R/lrtest.aidsEst.R | 8 ++--- build/vignette.rds |binary inst/doc/micEconAids_vignette.R | 1 inst/doc/micEconAids_vignette.pdf |binary man/aidsCalc.Rd | 4 ++ man/aidsElas.Rd | 29 ++----------------- man/aidsEst.Rd | 1 18 files changed, 167 insertions(+), 83 deletions(-)
Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in `mrgsolve`, typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format.
Author: Felicien Le Louedec [aut, cre]
,
Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <lelouedec.felicien@iuct-oncopole.fr>
Diff between mapbayr versions 0.6.0 dated 2022-02-18 and 0.7.0 dated 2022-05-20
mapbayr-0.6.0/mapbayr/inst/models |only mapbayr-0.6.0/mapbayr/inst/nm001/data_to_fit001.csv |only mapbayr-0.6.0/mapbayr/inst/nm001/mrg_001.cpp |only mapbayr-0.6.0/mapbayr/man/add_covariates.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/man/adm_lines.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/man/derivatives.Rd |only mapbayr-0.6.0/mapbayr/man/get_cov.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_data.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_data.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/man/get_eta.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_param.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_phi.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/mbrlib.Rd |only mapbayr-0.6.0/mapbayr/man/obs_lines.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/tests/testthat/test-derivatives.R |only mapbayr-0.6.0/mapbayr/tests/testthat/test-oneindividual.R |only mapbayr-0.7.0/mapbayr/DESCRIPTION | 13 mapbayr-0.7.0/mapbayr/MD5 | 153 +- mapbayr-0.7.0/mapbayr/NAMESPACE | 5 mapbayr-0.7.0/mapbayr/NEWS.md | 32 mapbayr-0.7.0/mapbayr/R/data.R | 7 mapbayr-0.7.0/mapbayr/R/exmodel.R |only mapbayr-0.7.0/mapbayr/R/get.R | 473 +++--- mapbayr-0.7.0/mapbayr/R/mapbayest.R | 35 mapbayr-0.7.0/mapbayr/R/mapbayest_check_and_preprocess.R | 87 - mapbayr-0.7.0/mapbayr/R/mapbayest_ofv_computation.R | 129 + mapbayr-0.7.0/mapbayr/R/mapbayest_optimization.R | 56 mapbayr-0.7.0/mapbayr/R/mapbayests.R | 720 +++++----- mapbayr-0.7.0/mapbayr/R/mrgmod.R | 43 mapbayr-0.7.0/mapbayr/R/read_mrgsolve_model.R | 195 -- mapbayr-0.7.0/mapbayr/R/use_posterior.R | 23 mapbayr-0.7.0/mapbayr/R/vs_nonmem.R | 196 +- mapbayr-0.7.0/mapbayr/R/zzz_utils.R | 21 mapbayr-0.7.0/mapbayr/README.md | 24 mapbayr-0.7.0/mapbayr/data/est001.rda |binary mapbayr-0.7.0/mapbayr/inst/WORDLIST | 129 - mapbayr-0.7.0/mapbayr/inst/exmodel |only mapbayr-0.7.0/mapbayr/inst/nm001/run001.phi | 13 mapbayr-0.7.0/mapbayr/man/adm_0_cmt.Rd | 43 mapbayr-0.7.0/mapbayr/man/adm_cmt.Rd | 43 mapbayr-0.7.0/mapbayr/man/augment.mapbayests.Rd | 116 - mapbayr-0.7.0/mapbayr/man/check_mapbayr_model.Rd | 4 mapbayr-0.7.0/mapbayr/man/compute_ofv.Rd | 33 mapbayr-0.7.0/mapbayr/man/data_helpers.Rd | 33 mapbayr-0.7.0/mapbayr/man/est001.Rd | 12 mapbayr-0.7.0/mapbayr/man/exmodel_exdata.Rd |only mapbayr-0.7.0/mapbayr/man/get_x.Rd | 50 mapbayr-0.7.0/mapbayr/man/h.Rd |only mapbayr-0.7.0/mapbayr/man/hist.mapbayests.Rd | 5 mapbayr-0.7.0/mapbayr/man/mapbayest.Rd | 5 mapbayr-0.7.0/mapbayr/man/obs_cmt.Rd | 43 mapbayr-0.7.0/mapbayr/man/plot.mapbayests.Rd | 5 mapbayr-0.7.0/mapbayr/man/preprocess.ofv.Rd | 29 mapbayr-0.7.0/mapbayr/man/qparam.Rd |only mapbayr-0.7.0/mapbayr/man/use_posterior.Rd | 9 mapbayr-0.7.0/mapbayr/man/vs_nonmem.Rd | 134 - mapbayr-0.7.0/mapbayr/tests/testthat.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-adm_lines.R | 32 mapbayr-0.7.0/mapbayr/tests/testthat/test-annotated.R | 54 mapbayr-0.7.0/mapbayr/tests/testthat/test-augment.R | 69 mapbayr-0.7.0/mapbayr/tests/testthat/test-compute_ofv.R | 87 - mapbayr-0.7.0/mapbayr/tests/testthat/test-covariance.R | 81 - mapbayr-0.7.0/mapbayr/tests/testthat/test-evid_egal_2.R | 19 mapbayr-0.7.0/mapbayr/tests/testthat/test-exmodels.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-get_data.R | 27 mapbayr-0.7.0/mapbayr/tests/testthat/test-get_eta.R | 91 - mapbayr-0.7.0/mapbayr/tests/testthat/test-get_param.R | 107 - mapbayr-0.7.0/mapbayr/tests/testthat/test-get_phi.R | 30 mapbayr-0.7.0/mapbayr/tests/testthat/test-hist.R | 33 mapbayr-0.7.0/mapbayr/tests/testthat/test-mbrest.R | 11 mapbayr-0.7.0/mapbayr/tests/testthat/test-mdv_egal_0.R | 110 - mapbayr-0.7.0/mapbayr/tests/testthat/test-methods.R | 28 mapbayr-0.7.0/mapbayr/tests/testthat/test-multi-ID.R | 86 - mapbayr-0.7.0/mapbayr/tests/testthat/test-newini2.R | 45 mapbayr-0.7.0/mapbayr/tests/testthat/test-no_data.R | 24 mapbayr-0.7.0/mapbayr/tests/testthat/test-output.R | 137 - mapbayr-0.7.0/mapbayr/tests/testthat/test-plot.R | 13 mapbayr-0.7.0/mapbayr/tests/testthat/test-progress.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-qparam.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-read_mrgsolve_model.R | 129 + mapbayr-0.7.0/mapbayr/tests/testthat/test-rename_as_eta.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-reset-conditions.R | 28 mapbayr-0.7.0/mapbayr/tests/testthat/test-use_posterior.R | 204 -- mapbayr-0.7.0/mapbayr/tests/testthat/test-valid_dataset.R | 40 mapbayr-0.7.0/mapbayr/tests/testthat/test-verbose.R | 24 mapbayr-0.7.0/mapbayr/tests/testthat/test-vs_nonmem.R | 37 86 files changed, 2101 insertions(+), 2363 deletions(-)
Title: Estimation of Time Varying Reproduction Numbers and Restored
Incidence Curves Using Variational Techniques
Description: Estimation, by inverting a renewal equation,
of time-varying reproduction numbers and restored incidence curves with
festive days and weekly biases corrected as described in
Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and
Alvarez et al. (2022) <doi:10.3390/biology11040540>.
Author: Luis Alvarez [aut, cre] ,
Jean-David Morel [ctb] ,
Jean-Michel Morel [ctb]
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>
Diff between EpiInvert versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2022-05-20
EpiInvert-0.1.0/EpiInvert/build |only EpiInvert-0.1.0/EpiInvert/inst |only EpiInvert-0.1.0/EpiInvert/vignettes |only EpiInvert-0.1.1/EpiInvert/DESCRIPTION | 11 +- EpiInvert-0.1.1/EpiInvert/MD5 | 30 ++---- EpiInvert-0.1.1/EpiInvert/NEWS.md | 12 ++ EpiInvert-0.1.1/EpiInvert/R/EpiInvert.R | 49 +++++----- EpiInvert-0.1.1/EpiInvert/R/data.R | 11 +- EpiInvert-0.1.1/EpiInvert/R/plot.R | 8 - EpiInvert-0.1.1/EpiInvert/README.md | 75 +++------------- EpiInvert-0.1.1/EpiInvert/man/EpiInvert.Rd | 57 ++++++------ EpiInvert-0.1.1/EpiInvert/man/EpiInvert_plot.Rd | 8 - EpiInvert-0.1.1/EpiInvert/man/figures/README-fig1-1.png |binary EpiInvert-0.1.1/EpiInvert/man/incidence.Rd | 14 +- 14 files changed, 126 insertions(+), 149 deletions(-)
Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 2.1.1 dated 2021-09-27 and 2.1.2 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/DJac.R | 2 +- R/FunImbalance.R |only R/PADDis.R | 2 ++ build/partial.rdb |binary man/FunImbalance.Rd |only man/betaUniqueness.Rd | 2 +- 8 files changed, 15 insertions(+), 11 deletions(-)
Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre],
Daniel Herszenhut [aut] ,
Mark Padgham [aut],
Tom Buckley [aut],
Danton Noriega-Goodwin [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between tidytransit versions 1.3.0 dated 2022-01-31 and 1.3.1 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/raptor.R | 7 +++---- inst/doc/frequency.html | 5 +++-- inst/doc/introduction.html | 21 +++++++++++---------- inst/doc/servicepatterns.html | 5 +++-- inst/doc/timetable.html | 1 + 7 files changed, 31 insertions(+), 28 deletions(-)
Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled
time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007)
<doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints
where significance of an effect begins and ends, and the results can be plotted in various
types of heatmap for reporting. Mixed-effects models are supported using an implementation of
the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between permutes versions 2.3.2 dated 2021-12-16 and 2.4 dated 2022-05-20
DESCRIPTION | 12 ++--- MD5 | 20 ++++---- NAMESPACE | 2 R/buildmer.R | 107 ++++++++++++++++++++++++++++++++------------- R/discoverability.R | 41 ++++++++++++----- R/lmPerm.R | 2 build/vignette.rds |binary inst/doc/buildmer.pdf |binary inst/doc/permutes.pdf |binary man/clusterperm.glmmTMB.Rd |only man/perm.glmmTMB.Rd |only man/permu.test.Rd | 4 - 12 files changed, 129 insertions(+), 59 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".
Author: Hakon K. Gjessing [aut, cre],
Miriam Gjerdevik [ctb] ,
Julia Romanowska [ctb] ,
Oivind Skare [ctb]
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 7.2.3 dated 2020-09-07 and 7.3.0 dated 2022-05-20
DESCRIPTION | 14 - MD5 | 93 ++++---- R/coef.haptable.hapSlide.R | 20 + R/f.create.snp.names.R | 6 R/f.get.which.gen.el.names.R | 5 R/genDataGetPart.R | 8 R/genDataRead.R | 3 R/getDyads_or_Triads.R | 59 ++++- R/haplinStrat0.R | 2 R/plot.haplinSlide.R | 17 + R/showPheno.R | 4 build/vignette.rds |binary inst/CITATION | 1 inst/doc/A_Haplin_intro_installation.html | 92 +++++--- inst/doc/B_Reading_data.html | 268 ++++++++++++++--------- inst/doc/C_Running_Haplin.html | 343 ++++++++++++++++++------------ inst/doc/D_Running_Haplin_on_cluster.html | 145 ++++++++---- inst/doc/E_hapRelEff.html | 305 +++++++++++++++++++------- inst/extdata/qc_all.map |only inst/extdata/qc_all_ok_gen.RData |only inst/extdata/qc_all_ok_gen.ffData |only man/cbindFiles.Rd | 2 man/convertPed.Rd | 2 man/gxe.Rd | 2 man/hapPower.Rd | 4 man/hapPowerAsymp.Rd | 2 man/hapRelEff.Rd | 2 man/hapRun.Rd | 4 man/hapSim.Rd | 6 man/haplin.Rd | 2 man/haplinSlide.Rd | 2 man/haplinStrat.Rd | 2 man/haptable.Rd | 14 - man/lineByLine.Rd | 2 man/output.Rd | 2 man/pQQ.Rd | 2 man/pedToHaplin.Rd | 2 man/plot.haplin.Rd | 7 man/plot.haptable.Rd | 5 man/print.haplin.Rd | 2 man/print.summary.haplin.Rd | 2 man/rbindFiles.Rd | 2 man/snpPos.Rd | 2 man/snpPower.Rd | 2 man/snpSampleSize.Rd | 2 man/suest.Rd | 2 man/summary.haplin.Rd | 2 man/toDataFrame.Rd | 2 vignettes/Styrke_artikkel_rmd.bib | 2 49 files changed, 953 insertions(+), 516 deletions(-)