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(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-13 0.0.1
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(-)
More information about nimbleNoBounds at CRAN
Permanent link
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(-)
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2017-07-30 1.3
2017-07-17 1.2.5
2017-02-20 1.2.3
2016-07-07 1.2.1
2016-06-13 1.2
2016-05-12 1.1.12
2015-10-01 1.1.10
2015-07-10 1.1.9
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2015-01-03 1.1.5
2014-05-01 1.1
2014-02-25 1.0.6
2014-02-21 1.0.5
2013-11-02 1.0
2013-07-21 0.9.8.6
2013-06-10 0.9.8.5
2013-05-06 0.9.8
2013-03-07 0.9.7
2012-12-03 0.9.6
2012-11-06 0.9.5
2012-05-16 0.9.3
2012-04-09 0.9.2
2012-03-07 0.9.1
2012-03-05 0.9
2012-02-25 0.1.1
2012-01-02 0.1
2011-12-30 0.0.7
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2020-05-03 0.8.4.1
2020-03-12 0.8.4
2020-03-07 0.8.3
2020-01-10 0.8.2
2019-12-16 0.8.1
2019-09-14 0.8.0
2019-08-26 0.7.0
2019-07-22 0.6.9.16
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2018-08-23 0.6.9.12
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2017-05-19 0.6.9.3
2017-04-05 0.6.9
2017-03-17 0.6.8.1
2017-01-23 0.6.6
2016-09-08 0.6.5.1
2016-08-29 0.6.5
2016-08-11 0.6
2016-07-07 0.5
2016-07-03 0.4.9.9
2016-05-12 0.4.4
2016-03-05 0.4.3.1
2015-11-26 0.4.3
2015-08-24 0.4.2
2015-08-03 0.4
2015-07-07 0.3.1
2015-06-19 0.3.0.1
2015-06-14 0.3
2015-05-12 0.2.1
2015-04-29 0.2
2015-02-21 0.1.1
2015-01-04 0.1.0
2014-06-20 0.0.9.5
2014-04-19 0.0.9
2014-02-10 0.0.8
2014-01-11 0.0.7
2013-12-31 0.0.5
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2014-02-08 1.0.1
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2011-09-14 0.8.8
2011-07-23 0.8.7
2011-04-24 0.8.6
2009-10-13 0.8-3
2008-10-17 0.8-2
2006-10-04 0.8-1
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2021-07-26 0.4.0
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2013-01-16 0.4.7
2013-01-14 0.4.6
2012-08-01 0.4.5
2012-07-16 0.4.3
2012-05-23 0.4.1
2011-06-20 0.3.8
2011-06-17 0.3.7
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2019-07-26 1.0
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2019-08-22 0.1.0
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2022-04-19 1.7.6
2021-12-14 1.7.5
2021-12-08 1.7.4
2021-09-22 1.7.3
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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 - gtfstools-1.1.0/gtfstools/R/remove_duplicates.R | 2 gtfstools-1.1.0/gtfstools/R/set_trip_speed.R | 95 +-- gtfstools-1.1.0/gtfstools/R/standards.R | 4 gtfstools-1.1.0/gtfstools/R/utils.R | 13 gtfstools-1.1.0/gtfstools/R/validate_gtfs.R | 2 gtfstools-1.1.0/gtfstools/R/write_gtfs.R | 40 - gtfstools-1.1.0/gtfstools/README.md | 22 gtfstools-1.1.0/gtfstools/build/vignette.rds |binary gtfstools-1.1.0/gtfstools/inst/CITATION | 14 gtfstools-1.1.0/gtfstools/inst/doc/filtering.R | 80 +++ gtfstools-1.1.0/gtfstools/inst/doc/filtering.Rmd | 135 ++++- gtfstools-1.1.0/gtfstools/inst/doc/filtering.html | 239 ++++++++-- gtfstools-1.1.0/gtfstools/inst/doc/gtfstools.R | 8 gtfstools-1.1.0/gtfstools/inst/doc/gtfstools.Rmd | 14 gtfstools-1.1.0/gtfstools/inst/doc/gtfstools.html | 35 - gtfstools-1.1.0/gtfstools/man/convert_from_standard.Rd | 2 gtfstools-1.1.0/gtfstools/man/convert_shapes_to_sf.Rd | 2 gtfstools-1.1.0/gtfstools/man/convert_stops_to_sf.Rd | 2 gtfstools-1.1.0/gtfstools/man/convert_time_to_seconds.Rd |only gtfstools-1.1.0/gtfstools/man/convert_to_standard.Rd | 2 gtfstools-1.1.0/gtfstools/man/copy_gtfs_diff_field_class.Rd | 2 gtfstools-1.1.0/gtfstools/man/copy_gtfs_without_field.Rd | 2 gtfstools-1.1.0/gtfstools/man/copy_gtfs_without_file.Rd | 2 gtfstools-1.1.0/gtfstools/man/figures/gtfstools_hex_black.png |only gtfstools-1.1.0/gtfstools/man/figures/logo.png |only gtfstools-1.1.0/gtfstools/man/filter_by_agency_id.Rd |only gtfstools-1.1.0/gtfstools/man/filter_by_route_id.Rd | 8 gtfstools-1.1.0/gtfstools/man/filter_by_route_type.Rd | 8 gtfstools-1.1.0/gtfstools/man/filter_by_service_id.Rd |only gtfstools-1.1.0/gtfstools/man/filter_by_sf.Rd | 8 gtfstools-1.1.0/gtfstools/man/filter_by_shape_id.Rd | 8 gtfstools-1.1.0/gtfstools/man/filter_by_stop_id.Rd | 8 gtfstools-1.1.0/gtfstools/man/filter_by_time_of_day.Rd |only gtfstools-1.1.0/gtfstools/man/filter_by_trip_id.Rd | 8 gtfstools-1.1.0/gtfstools/man/filter_by_weekday.Rd |only gtfstools-1.1.0/gtfstools/man/frequencies_to_stop_times.Rd |only gtfstools-1.1.0/gtfstools/man/get_children_stops.Rd |only gtfstools-1.1.0/gtfstools/man/get_parent_station.Rd | 23 gtfstools-1.1.0/gtfstools/man/get_stop_times_patterns.Rd |only gtfstools-1.1.0/gtfstools/man/get_trip_duration.Rd | 14 gtfstools-1.1.0/gtfstools/man/get_trip_geometry.Rd | 2 gtfstools-1.1.0/gtfstools/man/get_trip_length.Rd |only gtfstools-1.1.0/gtfstools/man/get_trip_segment_duration.Rd | 11 gtfstools-1.1.0/gtfstools/man/get_trip_speed.Rd | 35 - gtfstools-1.1.0/gtfstools/man/gtfstools.Rd | 8 gtfstools-1.1.0/gtfstools/man/merge_gtfs.Rd | 48 +- gtfstools-1.1.0/gtfstools/man/read_gtfs.Rd | 9 gtfstools-1.1.0/gtfstools/man/remove_duplicates.Rd | 2 gtfstools-1.1.0/gtfstools/man/roxygen |only gtfstools-1.1.0/gtfstools/man/set_trip_speed.Rd | 59 +- gtfstools-1.1.0/gtfstools/man/validate_gtfs.Rd | 2 gtfstools-1.1.0/gtfstools/man/write_gtfs.Rd | 15 gtfstools-1.1.0/gtfstools/src/convert-time.cpp | 45 + gtfstools-1.1.0/gtfstools/src/convert-time.h | 10 gtfstools-1.1.0/gtfstools/src/cpp11.cpp | 2 gtfstools-1.1.0/gtfstools/tests/testthat/test-convert_shapes_to_sf.R | 16 gtfstools-1.1.0/gtfstools/tests/testthat/test-convert_stops_to_sf.R | 7 gtfstools-1.1.0/gtfstools/tests/testthat/test-convert_time_to_seconds.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_agency_id.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_route_id.R | 35 + gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_route_type.R | 2 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_service_id.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_sf.R | 10 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_shape_id.R | 35 + gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_stop_id.R | 8 gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_time_of_day.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_trip_id.R | 35 + gtfstools-1.1.0/gtfstools/tests/testthat/test-filter_by_weekday.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-frequencies_to_stop_times.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-get_children_stops.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-get_parent_station.R | 85 +-- gtfstools-1.1.0/gtfstools/tests/testthat/test-get_stop_times_patterns.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_duration.R | 134 ++--- gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_geometry.R | 220 +++------ gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_length.R |only gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_segment_duration.R | 124 ++--- gtfstools-1.1.0/gtfstools/tests/testthat/test-get_trip_speed.R | 214 +++++--- gtfstools-1.1.0/gtfstools/tests/testthat/test-merge_gtfs.R | 72 ++- gtfstools-1.1.0/gtfstools/tests/testthat/test-read_gtfs.R | 10 gtfstools-1.1.0/gtfstools/tests/testthat/test-set_trip_speed.R | 41 - gtfstools-1.1.0/gtfstools/tests/testthat/test-utils.R | 3 gtfstools-1.1.0/gtfstools/tests/testthat/test-write_gtfs.R | 19 gtfstools-1.1.0/gtfstools/vignettes/filtering.Rmd | 135 ++++- gtfstools-1.1.0/gtfstools/vignettes/gtfstools.Rmd | 14 114 files changed, 1891 insertions(+), 1425 deletions(-)
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 - BayesMallows-1.2.0/BayesMallows/R/assign_cluster.R | 57 - BayesMallows-1.2.0/BayesMallows/R/catch-routine-registration.R |only BayesMallows-1.2.0/BayesMallows/R/compute_consensus.R | 278 ++----- BayesMallows-1.2.0/BayesMallows/R/compute_mallows.R | 84 +- BayesMallows-1.2.0/BayesMallows/R/compute_mallows_mixtures.R | 1 BayesMallows-1.2.0/BayesMallows/R/compute_posterior_intervals.R | 191 +---- BayesMallows-1.2.0/BayesMallows/R/estimate_partition_function.R | 32 BayesMallows-1.2.0/BayesMallows/R/expected_dist.R | 18 BayesMallows-1.2.0/BayesMallows/R/generate_constraints.R | 21 BayesMallows-1.2.0/BayesMallows/R/generate_initial_ranking.R | 54 - BayesMallows-1.2.0/BayesMallows/R/generate_transitive_closure.R | 20 BayesMallows-1.2.0/BayesMallows/R/get_mallows_loglik.R |only BayesMallows-1.2.0/BayesMallows/R/misc.R | 47 - BayesMallows-1.2.0/BayesMallows/R/misc_expected_dist.R | 76 +- BayesMallows-1.2.0/BayesMallows/R/plot.BayesMallows.R | 30 BayesMallows-1.2.0/BayesMallows/R/plot_elbow.R | 9 BayesMallows-1.2.0/BayesMallows/R/plot_top_k.R | 23 BayesMallows-1.2.0/BayesMallows/R/predict_top_k.R | 47 - BayesMallows-1.2.0/BayesMallows/R/print.BayesMallowsMixtures.R | 6 BayesMallows-1.2.0/BayesMallows/R/rank_conversion.R | 1 BayesMallows-1.2.0/BayesMallows/R/rank_distance.R | 8 BayesMallows-1.2.0/BayesMallows/R/rank_freq_distr.R | 2 BayesMallows-1.2.0/BayesMallows/R/sample_mallows.R | 48 - BayesMallows-1.2.0/BayesMallows/R/smc_mallows_deprecated.R |only BayesMallows-1.2.0/BayesMallows/R/smc_post_processing_functions.R | 26 BayesMallows-1.2.0/BayesMallows/R/sysdata.rda |binary BayesMallows-1.2.0/BayesMallows/R/tidy_mcmc.R | 53 - BayesMallows-1.2.0/BayesMallows/build/partial.rdb |binary BayesMallows-1.2.0/BayesMallows/build/vignette.rds |binary BayesMallows-1.2.0/BayesMallows/data/beach_preferences.rda |binary BayesMallows-1.2.0/BayesMallows/inst/REFERENCES.bib | 48 - BayesMallows-1.2.0/BayesMallows/inst/doc/SMC-Mallows.R | 14 BayesMallows-1.2.0/BayesMallows/inst/doc/SMC-Mallows.Rmd | 72 + BayesMallows-1.2.0/BayesMallows/inst/doc/SMC-Mallows.html | 274 +++---- BayesMallows-1.2.0/BayesMallows/inst/examples/compute_consensus_example.R | 10 BayesMallows-1.2.0/BayesMallows/inst/examples/compute_mallows_example.R | 4 BayesMallows-1.2.0/BayesMallows/inst/examples/compute_mallows_mixtures_example.R | 17 BayesMallows-1.2.0/BayesMallows/inst/examples/estimate_partition_function_example.R | 25 BayesMallows-1.2.0/BayesMallows/inst/examples/generate_transitive_closure_example.R | 29 BayesMallows-1.2.0/BayesMallows/inst/examples/get_mallows_loglik_example.R |only BayesMallows-1.2.0/BayesMallows/inst/examples/label_switching_example.R | 15 BayesMallows-1.2.0/BayesMallows/inst/examples/obs_freq_example.R | 22 BayesMallows-1.2.0/BayesMallows/inst/examples/plot_top_k_example.R | 4 BayesMallows-1.2.0/BayesMallows/inst/examples/smc_mallows_new_users_complete_example.R | 44 - 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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 - 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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(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-13 1.01
2012-02-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-11 1.1
2015-03-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-07 0.2.0
2019-01-24 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-21 2.0.0
2013-03-11 1.01
2011-03-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-12 0.1.2
2020-06-03 0.1.1
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(-)
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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
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-03 1.2.1
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
CausCor-0.1.1/CausCor/man/excel.Rd |only CausCor-0.1.2/CausCor/DESCRIPTION | 6 +++--- CausCor-0.1.2/CausCor/MD5 | 18 +++++++++--------- CausCor-0.1.2/CausCor/NAMESPACE | 4 +++- CausCor-0.1.2/CausCor/NEWS.md | 4 ++++ CausCor-0.1.2/CausCor/R/CausCor.R | 18 +++++++++++++----- CausCor-0.1.2/CausCor/README.md | 25 ++++++++++++++++--------- CausCor-0.1.2/CausCor/man/filter_40.Rd | 3 --- CausCor-0.1.2/CausCor/man/filter_n.Rd | 3 --- CausCor-0.1.2/CausCor/man/plot_16.Rd | 3 --- CausCor-0.1.2/CausCor/man/save_text.Rd |only 11 files changed, 48 insertions(+), 36 deletions(-)
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(-)