Title: Extra 'Recipes' for Text Processing
Description: Converting text to numerical features requires specifically
created procedures, which are implemented as steps according to the
'recipes' package. These steps allows for tokenization, filtering,
counting (tf and tfidf) and feature hashing.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between textrecipes versions 0.5.0 dated 2022-03-20 and 0.5.1 dated 2022-03-29
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 6 R/tfidf.R | 70 +++++- README.md | 102 ++-------- inst/doc/cookbook---using-more-complex-recipes-involving-text.html | 4 man/step_tfidf.Rd | 3 tests/testthat/_snaps/tfidf.md | 18 + tests/testthat/test-tfidf.R | 64 +++++- 9 files changed, 184 insertions(+), 105 deletions(-)
Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine.
Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate
models (counterfactual patient-level quantities, such as the conditional average treatment effect),
(3) subgroup identification models (find subsets of patients with similar treatment effects),
and (4) treatment effect estimation and inference (for the overall population and discovered
subgroups). These tools can be customized and are directly used in PRISM
(patient response identifiers for stratified medicine; Jemielita and Mehrotra 2019
<arXiv:1912.03337>. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>
Diff between StratifiedMedicine versions 1.0.4 dated 2021-09-02 and 1.0.5 dated 2022-03-29
StratifiedMedicine-1.0.4/StratifiedMedicine/R/PRISM_resamp.R |only StratifiedMedicine-1.0.4/StratifiedMedicine/R/plot_ggparty.R |only StratifiedMedicine-1.0.4/StratifiedMedicine/R/resampler_boot.R |only StratifiedMedicine-1.0.5/StratifiedMedicine/DESCRIPTION | 6 StratifiedMedicine-1.0.5/StratifiedMedicine/MD5 | 89 - StratifiedMedicine-1.0.5/StratifiedMedicine/NAMESPACE | 2 StratifiedMedicine-1.0.5/StratifiedMedicine/NEWS.md | 6 StratifiedMedicine-1.0.5/StratifiedMedicine/R/PRISM.R | 224 +- StratifiedMedicine-1.0.5/StratifiedMedicine/R/PRISM_train.R | 71 StratifiedMedicine-1.0.5/StratifiedMedicine/R/filter_train.R | 2 StratifiedMedicine-1.0.5/StratifiedMedicine/R/learners.R | 2 StratifiedMedicine-1.0.5/StratifiedMedicine/R/meta_learners.R | 42 StratifiedMedicine-1.0.5/StratifiedMedicine/R/param_est.R | 2 StratifiedMedicine-1.0.5/StratifiedMedicine/R/ple_train.R | 4 StratifiedMedicine-1.0.5/StratifiedMedicine/R/plot.R | 68 StratifiedMedicine-1.0.5/StratifiedMedicine/R/plot_dependence.R | 8 StratifiedMedicine-1.0.5/StratifiedMedicine/R/plot_importance.R | 4 StratifiedMedicine-1.0.5/StratifiedMedicine/R/plot_resample.R | 6 StratifiedMedicine-1.0.5/StratifiedMedicine/R/plot_tree.R |only StratifiedMedicine-1.0.5/StratifiedMedicine/R/pooler.R | 2 StratifiedMedicine-1.0.5/StratifiedMedicine/R/resampler_general.R |only StratifiedMedicine-1.0.5/StratifiedMedicine/R/subgrp_stability.R |only StratifiedMedicine-1.0.5/StratifiedMedicine/R/submod_train.R | 329 ++- StratifiedMedicine-1.0.5/StratifiedMedicine/R/utils.R | 254 ++ StratifiedMedicine-1.0.5/StratifiedMedicine/README.md | 79 StratifiedMedicine-1.0.5/StratifiedMedicine/build/partial.rdb |binary StratifiedMedicine-1.0.5/StratifiedMedicine/inst/doc/SM_PRISM.R | 22 StratifiedMedicine-1.0.5/StratifiedMedicine/inst/doc/SM_PRISM.Rmd | 62 StratifiedMedicine-1.0.5/StratifiedMedicine/inst/doc/SM_PRISM.html | 880 ++++------ StratifiedMedicine-1.0.5/StratifiedMedicine/inst/doc/SM_User_Models.R | 23 StratifiedMedicine-1.0.5/StratifiedMedicine/inst/doc/SM_User_Models.Rmd | 25 StratifiedMedicine-1.0.5/StratifiedMedicine/inst/doc/SM_User_Models.html | 529 +----- StratifiedMedicine-1.0.5/StratifiedMedicine/man/PRISM.Rd | 36 StratifiedMedicine-1.0.5/StratifiedMedicine/man/figures/README-example-3.png |binary StratifiedMedicine-1.0.5/StratifiedMedicine/man/figures/README-example-4.png |binary StratifiedMedicine-1.0.5/StratifiedMedicine/man/figures/README-example-5.png |binary StratifiedMedicine-1.0.5/StratifiedMedicine/man/figures/README-example-6.png |binary StratifiedMedicine-1.0.5/StratifiedMedicine/man/figures/README-example-7.png |binary StratifiedMedicine-1.0.5/StratifiedMedicine/man/figures/README-example-8.png |binary StratifiedMedicine-1.0.5/StratifiedMedicine/man/plot.PRISM.Rd | 14 StratifiedMedicine-1.0.5/StratifiedMedicine/man/plot_tree.Rd |only StratifiedMedicine-1.0.5/StratifiedMedicine/man/submod_train.Rd | 31 StratifiedMedicine-1.0.5/StratifiedMedicine/man/summary.PRISM.Rd | 12 StratifiedMedicine-1.0.5/StratifiedMedicine/man/summary.submod_train.Rd |only StratifiedMedicine-1.0.5/StratifiedMedicine/tests/testthat/test-plot_ggparty.R | 24 StratifiedMedicine-1.0.5/StratifiedMedicine/tests/testthat/test-resampling.R | 10 StratifiedMedicine-1.0.5/StratifiedMedicine/tests/testthat/test-submod_train.R | 3 StratifiedMedicine-1.0.5/StratifiedMedicine/tests/testthat/test-submod_train_summary.R |only StratifiedMedicine-1.0.5/StratifiedMedicine/vignettes/SM_PRISM.Rmd | 62 StratifiedMedicine-1.0.5/StratifiedMedicine/vignettes/SM_User_Models.Rmd | 25 50 files changed, 1417 insertions(+), 1541 deletions(-)
More information about StratifiedMedicine at CRAN
Permanent link
Title: An Open-Source Loader for Bruker's timsTOF Data Files
Description: A free, open-source package designed for
handling .tdf data files produced by Bruker's 'timsTOF' mass
spectrometers.
Fast, free, crossplatform, with no reading through
EULAs or messing with binary .dll files involved.
Author: Michał Piotr Startek [aut, cre, cph]
,
Mateusz Krzysztof Łącki [aut, cph]
Maintainer: Michał Piotr Startek <michal.startek@mimuw.edu.pl>
Diff between opentimsr versions 1.0.12 dated 2022-03-08 and 1.0.13 dated 2022-03-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/opentimsr.R | 12 ++++++------ man/download_bruker_proprietary_code.Rd | 4 ++-- man/opentims_set_threads.Rd | 2 +- 5 files changed, 17 insertions(+), 17 deletions(-)
Title: Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
Description: Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Nicolas Sauwen <nicolas.sauwen@openanalytics.eu>
Diff between NMF versions 0.23.0 dated 2020-08-01 and 0.24.0 dated 2022-03-29
DESCRIPTION | 12 ++-- MD5 | 44 ++++++++-------- NEWS | 2 R/NMFplots.R | 2 R/algorithms-base.R | 2 R/algorithms-snmf.R | 2 R/data.R | 2 build/vignette.rds |binary inst/CITATION | 4 - inst/doc/NMF-vignette.R | 122 ++++++++++++++++++++++----------------------- inst/doc/NMF-vignette.Rnw | 4 - inst/doc/NMF-vignette.pdf |binary inst/doc/consensus.pdf |binary inst/doc/heatmaps.R | 40 +++++++------- inst/doc/heatmaps.Rnw | 2 inst/doc/heatmaps.pdf |binary man/KL-nmf.Rd | 2 man/esGolub.Rd | 2 man/fcnnls.Rd | 3 - man/profplot.Rd | 2 src/utils.cpp | 2 vignettes/NMF-vignette.Rnw | 4 - vignettes/heatmaps.Rnw | 2 23 files changed, 127 insertions(+), 128 deletions(-)
Title: Vis-NIR Spectral Analysis Wrapper
Description: Originally designed application in the context of
resource-limited plant research and breeding programs, 'waves'
provides an open-source solution to spectral data processing and model
development by bringing useful packages together into a streamlined
pipeline. This package is wrapper for functions related to the
analysis of point visible and near-infrared reflectance measurements.
It includes visualization, filtering, aggregation, preprocessing,
cross-validation set formation, model training, and prediction
functions to enable open-source association of spectral and reference
data. This package is documented in a peer-reviewed manuscript in the
Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized
cross-validation schemes are described in detail in Jarquín et al.
(2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from
Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Author: Jenna Hershberger [aut, cre] ,
Michael Gore [ths],
NSF BREAD IOS-1543958 [fnd]
Maintainer: Jenna Hershberger <jmh579@cornell.edu>
Diff between waves versions 0.2.3 dated 2022-03-07 and 0.2.4 dated 2022-03-29
DESCRIPTION | 6 ++-- MD5 | 26 +++++++++--------- NEWS.md | 8 +++++ R/format_cv.R | 67 ++++++++++++++++++++++++++---------------------- R/plot_spectra.R | 18 +++++++------ R/rename.R | 4 +- R/test_spectra.R | 3 +- R/train_spectra.R | 22 +++++++++------ inst/doc/waves.R | 2 - inst/doc/waves.Rmd | 2 - inst/doc/waves.html | 72 +++++++++++++++++++++++++++------------------------- man/format_cv.Rd | 15 +++------- man/rename.Rd | 2 - vignettes/waves.Rmd | 2 - 14 files changed, 134 insertions(+), 115 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for
density clustering. For that, this package provides an R interface for the
efficient algorithms of the C++ libraries 'GUDHI' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2014) <doi:10.1145/2582112.2582128> for analyzing the statistical significance of persistent homology features.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria,
David L. Millman, Vincent Rouvreau.
Maintainer: Jisu Kim <jisu.kim@inria.fr>
Diff between TDA versions 1.8.6 dated 2022-03-10 and 1.8.7 dated 2022-03-29
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS | 3 +++ inst/doc/article.pdf |binary man/TDA-package.Rd | 4 ++-- src/CGAL/Uncertain.h | 24 ++++++++++++++---------- src/geometry/Arbitdistance.h | 8 ++++++-- src/geometry/l2distance.h | 8 ++++++-- src/geometry/simulator.h | 11 +++++++---- src/geometry/weighted-cechdistance.h | 7 +++++-- src/geometry/weighted-l2distance.h | 7 +++++-- src/tdautils/dionysusUtils.h | 7 +++++-- src/topology/dynamic-persistence.hpp | 7 +++++-- src/topology/lsvineyard.h | 20 ++++++++++++++++---- src/topology/lsvineyard.hpp | 14 ++++++++++---- src/topology/order.h | 9 ++++++--- src/topology/rips.h | 26 +++++++++++++++++++------- 17 files changed, 129 insertions(+), 66 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.2.1 dated 2022-01-07 and 0.3.0 dated 2022-03-29
spOccupancy-0.2.1/spOccupancy/src/PGOccREBoth.cpp |only spOccupancy-0.2.1/spOccupancy/src/PGOccREDet.cpp |only spOccupancy-0.2.1/spOccupancy/src/PGOccREOcc.cpp |only spOccupancy-0.2.1/spOccupancy/src/msPGOccREBoth.cpp |only spOccupancy-0.2.1/spOccupancy/src/msPGOccREDet.cpp |only spOccupancy-0.2.1/spOccupancy/src/msPGOccREOcc.cpp |only spOccupancy-0.2.1/spOccupancy/src/spMsPGOccNNGPRE.cpp |only spOccupancy-0.2.1/spOccupancy/src/spMsPGOccRE.cpp |only spOccupancy-0.2.1/spOccupancy/src/spPGOccNNGPRE.cpp |only spOccupancy-0.2.1/spOccupancy/src/spPGOccRE.cpp |only spOccupancy-0.3.0/spOccupancy/DESCRIPTION | 10 spOccupancy-0.3.0/spOccupancy/MD5 | 159 spOccupancy-0.3.0/spOccupancy/NAMESPACE | 25 spOccupancy-0.3.0/spOccupancy/NEWS.md | 17 spOccupancy-0.3.0/spOccupancy/R/PGOcc.R | 1326 ++---- spOccupancy-0.3.0/spOccupancy/R/generics.R | 2509 +++++++++-- spOccupancy-0.3.0/spOccupancy/R/intPGOcc.R | 61 spOccupancy-0.3.0/spOccupancy/R/lfJSDM.R |only spOccupancy-0.3.0/spOccupancy/R/lfMsPGOcc.R |only spOccupancy-0.3.0/spOccupancy/R/msPGOcc.R | 1793 ++------ spOccupancy-0.3.0/spOccupancy/R/ppcOcc.R | 110 spOccupancy-0.3.0/spOccupancy/R/sfJSDM.R |only spOccupancy-0.3.0/spOccupancy/R/sfMsPGOcc.R |only spOccupancy-0.3.0/spOccupancy/R/simMsOcc.R | 93 spOccupancy-0.3.0/spOccupancy/R/simOcc.R | 5 spOccupancy-0.3.0/spOccupancy/R/spIntPGOcc.R | 88 spOccupancy-0.3.0/spOccupancy/R/spMsPGOcc.R | 2749 +++++-------- spOccupancy-0.3.0/spOccupancy/R/spPGOcc.R | 2176 ++++------ spOccupancy-0.3.0/spOccupancy/R/waicOcc.R | 128 spOccupancy-0.3.0/spOccupancy/README.md | 88 spOccupancy-0.3.0/spOccupancy/build/partial.rdb |binary spOccupancy-0.3.0/spOccupancy/man/PGOcc.Rd | 48 spOccupancy-0.3.0/spOccupancy/man/fitted.PGOcc.Rd | 10 spOccupancy-0.3.0/spOccupancy/man/fitted.intPGOcc.Rd | 10 spOccupancy-0.3.0/spOccupancy/man/fitted.lfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/fitted.lfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/fitted.msPGOcc.Rd | 9 spOccupancy-0.3.0/spOccupancy/man/fitted.sfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/fitted.sfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/fitted.spIntPGOcc.Rd | 9 spOccupancy-0.3.0/spOccupancy/man/fitted.spMsPGOcc.Rd | 9 spOccupancy-0.3.0/spOccupancy/man/fitted.spPGOcc.Rd | 9 spOccupancy-0.3.0/spOccupancy/man/hbef2015.rda.Rd | 7 spOccupancy-0.3.0/spOccupancy/man/intPGOcc.Rd | 58 spOccupancy-0.3.0/spOccupancy/man/lfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/lfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/msPGOcc.Rd | 85 spOccupancy-0.3.0/spOccupancy/man/neon2015.rda.Rd | 7 spOccupancy-0.3.0/spOccupancy/man/ppcOcc.Rd | 33 spOccupancy-0.3.0/spOccupancy/man/predict.PGOcc.Rd | 59 spOccupancy-0.3.0/spOccupancy/man/predict.intPGOcc.Rd | 40 spOccupancy-0.3.0/spOccupancy/man/predict.lfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/predict.lfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/predict.msPGOcc.Rd | 65 spOccupancy-0.3.0/spOccupancy/man/predict.sfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/predict.sfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/predict.spIntPGOcc.Rd | 81 spOccupancy-0.3.0/spOccupancy/man/predict.spMsPGOcc.Rd | 30 spOccupancy-0.3.0/spOccupancy/man/predict.spPGOcc.Rd | 90 spOccupancy-0.3.0/spOccupancy/man/sfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/sfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/simIntOcc.Rd | 6 spOccupancy-0.3.0/spOccupancy/man/simMsOcc.Rd | 27 spOccupancy-0.3.0/spOccupancy/man/simOcc.Rd | 10 spOccupancy-0.3.0/spOccupancy/man/spIntPGOcc.Rd | 93 spOccupancy-0.3.0/spOccupancy/man/spMsPGOcc.Rd | 56 spOccupancy-0.3.0/spOccupancy/man/spPGOcc.Rd | 102 spOccupancy-0.3.0/spOccupancy/man/summary.PGOcc.Rd | 2 spOccupancy-0.3.0/spOccupancy/man/summary.intPGOcc.Rd | 2 spOccupancy-0.3.0/spOccupancy/man/summary.lfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/summary.lfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/summary.msPGOcc.Rd | 4 spOccupancy-0.3.0/spOccupancy/man/summary.ppcOcc.Rd | 2 spOccupancy-0.3.0/spOccupancy/man/summary.sfJSDM.Rd |only spOccupancy-0.3.0/spOccupancy/man/summary.sfMsPGOcc.Rd |only spOccupancy-0.3.0/spOccupancy/man/summary.spIntPGOcc.Rd | 4 spOccupancy-0.3.0/spOccupancy/man/summary.spMsPGOcc.Rd | 4 spOccupancy-0.3.0/spOccupancy/man/waicOcc.Rd | 42 spOccupancy-0.3.0/spOccupancy/src/PGOcc.cpp | 336 + spOccupancy-0.3.0/spOccupancy/src/init.cpp | 35 spOccupancy-0.3.0/spOccupancy/src/intPGOcc.cpp | 19 spOccupancy-0.3.0/spOccupancy/src/lfJSDM.cpp |only spOccupancy-0.3.0/spOccupancy/src/lfMsPGOcc.cpp |only spOccupancy-0.3.0/spOccupancy/src/msPGOcc.cpp | 352 + spOccupancy-0.3.0/spOccupancy/src/sfJSDMNNGP.cpp |only spOccupancy-0.3.0/spOccupancy/src/sfMsPGOccNNGP.cpp |only spOccupancy-0.3.0/spOccupancy/src/sfMsPGOccNNGPPredict.cpp |only spOccupancy-0.3.0/spOccupancy/src/spIntPGOcc.cpp | 35 spOccupancy-0.3.0/spOccupancy/src/spIntPGOccNNGP.cpp | 23 spOccupancy-0.3.0/spOccupancy/src/spMsPGOcc.cpp | 370 + spOccupancy-0.3.0/spOccupancy/src/spMsPGOccNNGP.cpp | 368 + spOccupancy-0.3.0/spOccupancy/src/spMsPGOccNNGPPredict.cpp | 35 spOccupancy-0.3.0/spOccupancy/src/spMsPGOccPredict.cpp | 6 spOccupancy-0.3.0/spOccupancy/src/spOccupancy.h | 372 - spOccupancy-0.3.0/spOccupancy/src/spPGOcc.cpp | 346 + spOccupancy-0.3.0/spOccupancy/src/spPGOccNNGP.cpp | 332 + spOccupancy-0.3.0/spOccupancy/src/spPGOccNNGPPredict.cpp | 34 spOccupancy-0.3.0/spOccupancy/src/spPGOccPredict.cpp | 6 98 files changed, 8306 insertions(+), 6713 deletions(-)
Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a
statistical method that allows to predict survival from
high-dimensional longitudinal predictors. PRC is described in
Signorelli et al. (2021, <doi:10.1002/sim.9178>)).
Author: Mirko Signorelli [aut, cre, cph]
,
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 1.0.2 dated 2022-02-14 and 1.1.0 dated 2022-03-29
pencal-1.0.2/pencal/vignettes/pencal-vignette_files |only pencal-1.1.0/pencal/DESCRIPTION | 35 pencal-1.1.0/pencal/MD5 | 23 pencal-1.1.0/pencal/R/survpred_prclmm.R | 542 +++--- pencal-1.1.0/pencal/R/survpred_prcmlpmm.R | 219 +- pencal-1.1.0/pencal/build/vignette.rds |binary pencal-1.1.0/pencal/data/fitted_prclmm.RData |binary pencal-1.1.0/pencal/data/fitted_prcmlpmm.RData |binary pencal-1.1.0/pencal/inst/NEWS.md | 286 +-- pencal-1.1.0/pencal/inst/doc/pencal-vignette.R |only pencal-1.1.0/pencal/inst/doc/pencal-vignette.html | 1659 +++++++++++--------- pencal-1.1.0/pencal/man/survpred_prclmm.Rd | 10 pencal-1.1.0/pencal/man/survpred_prcmlpmm.Rd | 3 13 files changed, 1498 insertions(+), 1279 deletions(-)
Title: Identification, Tuning, Visualisation and Analysis of Labour
Market Areas
Description: Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.
Author: Daniela Ichim, Luisa Franconi, Michele D'Alo', Guido van den Heuvel
Maintainer: Luisa Franconi <franconi@istat.it>
Diff between LabourMarketAreas versions 3.2.5 dated 2020-09-07 and 3.3 dated 2022-03-29
DESCRIPTION | 12 ++-- MD5 | 9 ++- R/LabourMarketAreas.R | 96 +++++++++++++++++++++++++++++++++++++++ data/SardiniaGrid.rda |only man/LabourMarketAreas-package.Rd | 4 - man/LmaSpatialComparison.Rd |only man/SardiniaGrid.Rd |only 7 files changed, 110 insertions(+), 11 deletions(-)
More information about LabourMarketAreas at CRAN
Permanent link
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 1.5.0 dated 2022-01-03 and 1.6.0 dated 2022-03-29
gert-1.5.0/gert/src/Makevars.ucrt |only gert-1.6.0/gert/DESCRIPTION | 24 +++++++++++------------- gert-1.6.0/gert/MD5 | 27 +++++++++++++++------------ gert-1.6.0/gert/NEWS | 6 ++++++ gert-1.6.0/gert/R/commit.R | 7 +++++-- gert-1.6.0/gert/R/gert-package.R |only gert-1.6.0/gert/build/vignette.rds |binary gert-1.6.0/gert/configure | 6 +++--- gert-1.6.0/gert/inst/doc/gert.html | 13 +++++++------ gert-1.6.0/gert/man/figures |only gert-1.6.0/gert/man/gert-package.Rd |only gert-1.6.0/gert/man/git_commit.Rd | 4 +++- gert-1.6.0/gert/src/Makevars.win | 13 ++++++++----- gert-1.6.0/gert/src/commit.c | 27 +++++++++++++++++---------- gert-1.6.0/gert/src/init.c | 4 ++-- gert-1.6.0/gert/tests/testthat/ssh.key |only gert-1.6.0/gert/tests/testthat/test-auth.R | 18 +++++++++--------- 17 files changed, 86 insertions(+), 63 deletions(-)
More information about BigDataStatMeth at CRAN
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Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models' literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi et al. (2021) <doi:10.1080/01621459.2021.1996377>, and Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.
Author: Reza Mohammadi [aut, cre] ,
Ernst Wit [aut] ,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.64 dated 2021-05-03 and 2.65 dated 2022-03-29
DESCRIPTION | 9 + MD5 | 158 +++++++++++++++++--------------- NAMESPACE | 19 +++ NEWS.md | 17 ++- R/adj2link.R | 2 R/bdgraph.R | 48 ++++++++- R/bdgraph.dw.R |only R/bdgraph.mpl.R | 16 +-- R/bdgraph.npn.R | 6 - R/bdgraph.sim.R | 197 ++++++++++++++++++++++------------------- R/bdw.reg.R |only R/bf.R | 2 R/compare.R | 14 +- R/conf.mat.R | 12 +- R/covariance.R | 6 - R/ddweibull.R | 38 ++++--- R/detect_cores.R | 2 R/get_things.R | 44 ++++----- R/gnorm.R | 10 +- R/graph.sim.R | 84 +++++++++++------ R/hill_climb_algorithm.R | 2 R/hill_climb_binary.R | 4 R/link2adj.R | 10 +- R/pgraph.R | 4 R/plinks.R | 10 +- R/plotcoda.R | 22 ++-- R/plotroc.R | 6 - R/precision.R | 6 - R/rgwish.R | 15 +-- R/rmvnorm.R | 6 - R/roc.R | 17 +-- R/rwish.R | 12 +- R/select.R | 8 - R/sparsity.R | 7 - R/traceplot.R | 91 +++++++++--------- R/transfer.R | 10 +- README.md | 79 +++------------- build/partial.rdb |binary data/churn.RData |binary data/geneExpression.RData |binary data/reinis.RData |binary data/surveyData.RData |binary inst/doc/BDgraph-examples.Rmd |only inst/doc/BDgraph-examples.html |only inst/doc/vignette.pdf |binary man/BDgraph-package.Rd | 56 +++++++---- man/adj2link.Rd | 22 ++-- man/bdgraph.Rd | 105 ++++++++++++--------- man/bdgraph.dw.Rd |only man/bdgraph.mpl.Rd | 72 +++++++------- man/bdgraph.npn.Rd | 9 + man/bdgraph.sim.Rd | 96 +++++++++++-------- man/bdw.reg.Rd |only man/bf.Rd | 23 ++-- man/compare.Rd | 40 ++++---- man/conf.mat.Rd | 12 +- man/conf.mat.plot.Rd | 12 +- man/covariance.Rd | 20 ++-- man/ddweibull.Rd | 27 ++--- man/figures |only man/geneExpression.Rd | 4 man/gnorm.Rd | 18 +-- man/graph.sim.Rd | 36 +++---- man/link2adj.Rd | 20 ++-- man/pgraph.Rd | 24 ++-- man/plinks.Rd | 18 +-- man/plot.bdgraph.Rd | 48 ++++++--- man/plot.graph.Rd | 48 ++++++--- man/plot.sim.Rd | 24 ++-- man/plotcoda.Rd | 22 ++-- man/plotroc.Rd | 33 +++--- man/precision.Rd | 18 +-- man/print.bdgraph.Rd | 18 +-- man/print.sim.Rd | 16 +-- man/rgwish.Rd | 30 +++--- man/roc.Rd | 65 +++++++------ man/rwish.Rd | 20 ++-- man/select.Rd | 20 ++-- man/sparsity.Rd | 13 +- man/summary.bdgraph.Rd | 30 +++--- man/surveyData.Rd | 2 man/traceplot.Rd | 20 ++-- man/trensfer.Rd | 8 - vignettes/BDgraph-examples.Rmd |only 84 files changed, 1095 insertions(+), 947 deletions(-)
Title: Nonparametric Failure Time Bayesian Additive Regression Trees
Description: Nonparametric Failure Time (NFT) Bayesian Additive Regression Trees (BART): Time-to-event Machine Learning with Heteroskedastic Bayesian Additive Regression Trees (HBART) and Low Information Omnibus (LIO) Dirichlet Process Mixtures (DPM). An NFT BART model is of the form Y = mu + f(x) + s(x) E where functions f and s have BART and HBART priors, respectively, while E is a nonparametric error distribution due to a DPM LIO prior hierarchy. See the following for a technical description of the model <https://www.mcw.edu/-/media/MCW/Departments/Biostatistics/tr72.pdf?la=en>.
Author: Rodney Sparapani [aut, cre],
Robert McCulloch [aut],
Matthew Pratola [ctb],
Hugh Chipman [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between nftbart versions 1.2 dated 2022-02-03 and 1.3 dated 2022-03-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ src/DPMLIOneal8.h | 4 +++- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Fast Extraction from Raster Datasets using Polygons
Description: Provides a replacement for the 'extract' function from the 'raster' package
that is suitable for extracting raster values using 'sf' polygons.
Author: Daniel Baston [aut, cre],
ISciences, LLC [cph]
Maintainer: Daniel Baston <dbaston@isciences.com>
Diff between exactextractr versions 0.7.2 dated 2021-12-05 and 0.8.0 dated 2022-03-29
DESCRIPTION | 9 - MD5 | 54 +++--- NEWS.md | 16 +- R/RcppExports.R | 12 - R/coverage_fraction.R | 16 +- R/exact_extract.R | 81 ++++++++-- R/exact_extract_helpers.R | 154 +++++++++++++++++++ R/exact_resample.R | 54 +++++- README.md | 95 ++++++++--- configure | 18 +- inst/doc/vig1_population.html | 167 ++++++++++++-------- inst/doc/vig2_categorical.html | 184 +++++++++++++---------- man/coverage_fraction.Rd | 9 + man/exact_extract.Rd | 34 +++- man/exact_resample.Rd | 9 - src/RcppExports.cpp | 32 ++-- src/coverage_fraction.cpp | 38 +++- src/exact_extract.cpp | 33 ++-- src/exactextract/src/grid.h | 24 +-- src/exactextract/test/test_grid.cpp | 45 ++++- src/resample.cpp | 82 ++++++++-- tests/testthat/helper_functions.R | 14 + tests/testthat/test_coverage_fraction.R | 19 ++ tests/testthat/test_exact_extract_eager_load.R |only tests/testthat/test_exact_extract_include_args.R | 28 +++ tests/testthat/test_exact_extract_terra.R | 19 ++ tests/testthat/test_exact_resample.R | 8 - tests/testthat/test_exact_resample_terra.R | 112 +++++++++++++- tests/testthat/test_helper_blocksize.R |only 29 files changed, 1028 insertions(+), 338 deletions(-)
More information about ClickHouseHTTP at CRAN
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Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a
series of functions related to sample size and power calculations for common analysis in the healthcare
field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and
proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients,
regression coefficients (linear, logistic and Cox), linear mixed model,
Cronbach's alpha, interobserver agreement, intraclass correlation coefficients,
limit of agreement on Bland-Altman plots,
area under the curve, sensitivity and specificity incorporating the prevalence of disease.
You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.
Author: Rogerio Boff Borges [aut, cre]
,
Guilherme Serpa Azambuja [aut]
,
Aline Castello Branco Mancuso [aut]
,
Vanessa Bielefeldt Leotti [aut]
,
Vânia Naomi Hirakata [aut] ,
Suzi Alves Camey [aut] ,
Stela Maris de Jezus Castro [aut]
,
Hospital de Clínicas d [...truncated...]
Maintainer: Rogerio Boff Borges <roborges@hcpa.edu.br>
Diff between PSS.Health versions 0.3.1 dated 2021-10-07 and 0.4.0 dated 2022-03-29
PSS.Health-0.3.1/PSS.Health/inst/PSS.Health/www/Favicon.gif |only PSS.Health-0.4.0/PSS.Health/DESCRIPTION | 12 PSS.Health-0.4.0/PSS.Health/MD5 | 19 PSS.Health-0.4.0/PSS.Health/build |only PSS.Health-0.4.0/PSS.Health/inst/CITATION |only PSS.Health-0.4.0/PSS.Health/inst/PSS.Health/R/modulo_medidas_repetidas.R | 2 PSS.Health-0.4.0/PSS.Health/inst/PSS.Health/global.R | 39 PSS.Health-0.4.0/PSS.Health/inst/PSS.Health/server.R | 1076 +++++----- PSS.Health-0.4.0/PSS.Health/inst/PSS.Health/ui.R | 449 ++-- PSS.Health-0.4.0/PSS.Health/inst/PSS.Health/www/Effect_size_f.md | 8 PSS.Health-0.4.0/PSS.Health/inst/doc |only PSS.Health-0.4.0/PSS.Health/vignettes |only 12 files changed, 985 insertions(+), 620 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obspy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut],
Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISSeismic versions 1.6.3 dated 2021-10-07 and 1.6.4 dated 2022-03-29
DESCRIPTION | 6 +- MD5 | 93 ++++++++++++++++++----------------- R/Class-IrisClient.R | 102 +++++++++++++++++++------------------- R/Class-Stream.R | 6 +- R/Utils.R | 3 - R/spectralUtils.R | 13 ++-- inst/doc/IRISSeismic-intro.html | 5 + man/IRISSeismic-package.Rd | 7 ++ man/IrisClient-class.Rd | 4 - man/STALTA.Rd | 3 - man/getAvailability.Rd | 4 - man/getChannel.Rd | 4 - man/getDataAvailability.Rd | 6 +- man/getDataselect.Rd | 4 - man/getDistaz.Rd | 2 man/getEvalresp.Rd | 4 - man/getEvent.Rd | 2 man/getNetwork.Rd | 4 - man/getRotation.Rd | 4 - man/getSNCL.Rd | 2 man/getStation.Rd | 4 - man/getTimeseries.Rd | 4 - man/getTraveltime.Rd | 2 man/getUnavailability.Rd | 4 - man/rotate2D.Rd | 4 - man/triggerOnset.Rd | 2 src/libmseed/ChangeLog | 13 ++++ src/libmseed/doc/ms_gswap.3 | 12 +--- src/libmseed/doc/ms_gswap2.3 | 12 +--- src/libmseed/doc/ms_gswap2a.3 | 12 +--- src/libmseed/doc/ms_gswap3.3 | 12 +--- src/libmseed/doc/ms_gswap4.3 | 12 +--- src/libmseed/doc/ms_gswap4a.3 | 12 +--- src/libmseed/doc/ms_gswap8.3 | 12 +--- src/libmseed/doc/ms_gswap8a.3 | 12 +--- src/libmseed/doc/ms_intro.3 | 3 - src/libmseed/gswap.c | 106 +++++++++++----------------------------- src/libmseed/libmseed.h | 52 +++++++++++++------ src/libmseed/libmseed.map |only src/libmseed/mseed.pc.in |only src/libmseed/msrutils.c | 4 - src/libmseed/pack.c | 4 - src/libmseed/packdata.c | 28 +++++----- src/libmseed/parseutils.c | 16 +++--- src/libmseed/temp.sh |only src/libmseed/tracelist.c | 15 +---- src/libmseed/traceutils.c | 93 +++++++++++++++-------------------- src/libmseed/unpack.c | 12 ++-- src/libmseed/unpackdata.c | 40 +++++++-------- 49 files changed, 376 insertions(+), 404 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 3.1.2 dated 2022-01-20 and 3.1.3 dated 2022-03-29
DESCRIPTION | 12 - MD5 | 62 ++++---- NEWS.md | 28 +++ R/edition.R | 7 R/expectation.R | 9 - R/local.R | 4 R/snapshot.R | 9 - inst/doc/custom-expectation.html | 199 --------------------------- inst/doc/parallel.html | 197 --------------------------- inst/doc/skipping.html | 197 --------------------------- inst/doc/snapshotting.html | 203 ---------------------------- inst/doc/test-fixtures.html | 202 --------------------------- inst/doc/third-edition.html | 201 --------------------------- tests/testthat/_snaps/edition.md | 3 tests/testthat/_snaps/quasi-label.md | 5 tests/testthat/_snaps/reporter-check.md | 26 +-- tests/testthat/_snaps/reporter-junit.md | 9 - tests/testthat/_snaps/reporter-progress.md | 126 +++++++++++------ tests/testthat/_snaps/reporter-stop.md | 6 tests/testthat/_snaps/reporter-summary.md | 36 +++- tests/testthat/_snaps/reporter-tap.md | 18 +- tests/testthat/_snaps/reporter-teamcity.md | 4 tests/testthat/_snaps/rlang-1.0/snapshot.md | 22 +-- tests/testthat/_snaps/skip.md | 5 tests/testthat/_snaps/snapshot-cleanup.md | 2 tests/testthat/_snaps/snapshot-manage.md | 14 - tests/testthat/_snaps/snapshot.md | 64 ++++---- tests/testthat/helper-testthat.R | 4 tests/testthat/reporters/backtraces.R | 2 tests/testthat/test-parallel-crash.R | 4 tests/testthat/test-reporter-progress.R | 8 + tests/testthat/test-verify-output.R | 2 32 files changed, 338 insertions(+), 1352 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph]
,
Marco A. Aquino Lopez [aut],
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.5.7 dated 2021-08-12 and 2.5.8 dated 2022-03-29
DESCRIPTION | 60 ++++++++++++++++++++++++++++++------------- MD5 | 54 +++++++++++++++++++------------------- NEWS.md | 5 ++- R/Bacon.R | 9 +++++- R/agedepth.R | 2 - R/internal_plots.R | 6 ++-- README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/FAQ.Rmd | 16 +++++------ inst/doc/FAQ.html | 7 ++--- inst/doc/contents.Rmd | 4 +- inst/doc/contents.html | 1 inst/doc/foldersfiles.Rmd | 12 ++++---- inst/doc/foldersfiles.html | 7 ++--- inst/doc/intro.Rmd | 4 +- inst/doc/intro.html | 1 inst/doc/postrun.Rmd | 4 +- inst/doc/postrun.html | 19 +++++++------ inst/doc/priorssettings.Rmd | 6 ++-- inst/doc/priorssettings.html | 1 src/input.cpp | 3 +- vignettes/FAQ.Rmd | 16 +++++------ vignettes/contents.Rmd | 4 +- vignettes/foldersfiles.Rmd | 12 ++++---- vignettes/intro.Rmd | 4 +- vignettes/postrun.Rmd | 4 +- vignettes/priorssettings.Rmd | 6 ++-- 28 files changed, 155 insertions(+), 114 deletions(-)
Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges [aut, cre, cph] ,
Sebastian Krey [aut, cph],
Olaf Mersmann [aut, cph],
Sarah Schnackenberg [aut, cph],
Guillaume Guenard [aut, cph] ,
Daniel P. W. Ellis [aut, cph] ,
Underbit Technologies [aut, cph] ,
Andrea Preusser [ctb],
Anita Thieler [ [...truncated...]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between tuneR versions 1.3.3.1 dated 2021-08-04 and 1.4.0 dated 2022-03-29
tuneR-1.3.3.1/tuneR/R/MFCC.R |only tuneR-1.3.3.1/tuneR/man/MFCC.Rd |only tuneR-1.4.0/tuneR/DESCRIPTION | 44 ++++++++++++++++++++++++--------- tuneR-1.4.0/tuneR/MD5 | 40 ++++++++++++++---------------- tuneR-1.4.0/tuneR/NAMESPACE | 2 - tuneR-1.4.0/tuneR/R/bark2hz.R | 3 -- tuneR-1.4.0/tuneR/R/hz2bark.R | 1 tuneR-1.4.0/tuneR/R/mel2hz.R | 1 tuneR-1.4.0/tuneR/R/readWave.R | 20 +++++++-------- tuneR-1.4.0/tuneR/man/audspec.Rd | 2 - tuneR-1.4.0/tuneR/man/deltas.Rd | 2 - tuneR-1.4.0/tuneR/man/dolpc.Rd | 2 - tuneR-1.4.0/tuneR/man/fftfreqconvmx.Rd | 2 - tuneR-1.4.0/tuneR/man/freqconv.Rd | 2 - tuneR-1.4.0/tuneR/man/lifter.Rd | 2 - tuneR-1.4.0/tuneR/man/lpc2cep.Rd | 2 - tuneR-1.4.0/tuneR/man/melfcc.Rd | 4 +-- tuneR-1.4.0/tuneR/man/postaud.Rd | 2 - tuneR-1.4.0/tuneR/man/powspec.Rd | 2 - tuneR-1.4.0/tuneR/man/spec2cep.Rd | 2 - tuneR-1.4.0/tuneR/src/frame.c | 6 ++-- tuneR-1.4.0/tuneR/src/synth.c | 36 +++++++++++++-------------- 22 files changed, 96 insertions(+), 81 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values. Methods available in this package include SKAT described in Micheal Wu, Seunggeun Lee et al. (2011) <doi:10.1016/j.ajhg.2011.05.029>, SKAT-O in Seunggeun Lee et al. (2012) <doi:10.1093/biostatistics/kxs014>, combined test of rare and common variants in Iuliana Ionita-Laza and Seunggeun Lee et al. (2013) <doi:10.1016/j.ajhg.2013.04.015>, efficient resampling for binary traits in Seunggeun Lee et al. (2016) <doi:10.1093/biostatistics/kxv033>, and robust test for binary traits in Zhangchen Zhao et al. (2020) <doi:10.1016/j.ajhg.2019.11.012>.
Author: Seunggeun Lee [aut, cre, cph],
Zhangchen Zhao [aut],
Larisa Miropolsky [aut],
Michael Wu [aut]
Maintainer: Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>
Diff between SKAT versions 2.0.1 dated 2020-10-20 and 2.2.4 dated 2022-03-29
DESCRIPTION | 22 MD5 | 76 - NAMESPACE | 75 - R/Binary_MAIN.R | 867 +++++++++---------- R/Binary_MAIN_ExactBin.R | 1081 ++++++++++++------------ R/Binary_MAIN_Robust.R | 987 ++++++++++------------ R/Binary_Result_Calibration.R | 6 R/Function.R | 254 ++++- R/Joint_CommonRare.R | 1606 +++++++++++++++++------------------- R/Joint_CommonRare_Robust.R | 606 ++++++------- R/MAIN.R | 40 R/Main_SSD.R | 619 ++++++------- R/SKAT_EMMAX.R | 95 -- R/SKAT_Meta_Optimal.R | 19 R/SSD.R | 936 ++++++++++---------- R/X_Chrom.R | 530 +++++++---- build/vignette.rds |binary data/SKAT.example.ChrX.rda |binary data/SKAT.example.rda |binary data/SKAT.fam.example.rda |binary data/SKAT.haplotypes.rda |binary data/SKATBinary.example.rda |binary inst/doc/SKAT.R | 107 +- inst/doc/SKAT.Rnw | 1265 ++++++++++++++-------------- inst/doc/SKAT.pdf |binary man/Get_Genotypes_SSD.rd | 44 man/Get_Logistic_Weights.rd | 122 +- man/SKAT.SSD.All.rd | 82 + man/SKAT.rd | 410 ++++----- man/SKATBinary.rd | 331 +++---- man/SKATBinary_Robust.rd | 191 ++-- man/SKATBinary_Single.rd | 202 ++-- man/SKAT_ChrX.rd | 29 man/SKAT_CommonRare.rd | 270 ++---- man/SKAT_CommonRare_Robust.rd | 205 ++-- man/SKAT_NULL_emmaX.rd | 106 +- man/SKAT_Null_Model.rd | 202 ++-- man/SKAT_Null_Model_MomentAdjust.rd | 129 +- vignettes/SKAT.Rnw | 1265 ++++++++++++++-------------- 39 files changed, 6534 insertions(+), 6245 deletions(-)
Title: 'Rcpp' Bindings for the Boost Date_Time Library
Description: Access to Boost Date_Time functionality for dates,
durations (both for days and date time objects), time zones, and
posix time ('ptime') is provided by using 'Rcpp modules'. The
posix time implementation can support high-resolution of up to
nano-second precision by using 96 bits (instead of R's 64)
to present a 'ptime' object (but this needs recompilation with
a #define set).
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppBDT versions 0.2.4 dated 2021-08-15 and 0.2.5 dated 2022-03-29
ChangeLog | 21 ++++++++++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- README.md | 1 - inst/NEWS.Rd | 11 ++++++++++- src/Makevars | 3 --- src/Makevars.win | 6 +----- src/init.c | 2 +- src/toPOSIXct.cpp | 5 +---- 9 files changed, 45 insertions(+), 28 deletions(-)
Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and
'purrr' that formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrrlyr versions 0.0.7 dated 2020-12-16 and 0.0.8 dated 2022-03-29
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ README.md | 6 +++--- src/rows-formatter.cpp | 5 ++--- src/rows-formatter.h | 5 +++-- src/utils.h | 4 ++-- 7 files changed, 28 insertions(+), 21 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 3.0.10 dated 2019-11-26 and 3.0.11 dated 2022-03-29
DESCRIPTION | 6 +- MD5 | 35 ++++++++--------- NAMESPACE | 4 - NEWS | 9 +++- R/RcppExports.R | 4 + R/object.distances.R | 91 +++++++++++++++++++++++++++++++++++++++++++-- R/plot.kohonen.R | 31 ++++----------- R/som.R | 4 + R/supersom.R | 2 build/partial.rdb |binary inst/Distances/wcc.cpp | 2 man/layer.distances.Rd |only man/map.kohonen.Rd | 6 +- man/plot.kohonen.Rd | 4 + man/predict.kohonen.Rd | 4 + man/supersom.Rd | 10 +++- src/RcppExports.cpp | 18 ++++++++ src/distance-functions.cpp | 84 ++++++++++++++++++++++++++++++++--------- src/distance-functions.h | 17 ++++++-- 19 files changed, 255 insertions(+), 76 deletions(-)
Title: Pearson Distribution System
Description: Implementation of the Pearson distribution system, including full
support for the (d,p,q,r)-family of functions for probability distributions
and fitting via method of moments and maximum likelihood method.
Permanent link
Title: Interface to the 'Spectator Earth' API
Description: Provides interface to the 'Spectator Earth' API <https://api.spectator.earth/>,
mainly for obtaining the acquisition plans and satellite overpasses for Sentinel-1,
Sentinel-2, Landsat-8 and Landsat-9 satellites. Current position and trajectory can
also be obtained for a much larger set of satellites. It is also possible to search
the archive for available images over the area of interest for a given (past) period,
get the URL links to download the whole image tiles, or alternatively to download the
image for just the area of interest based on selected spectral bands.
Author: Zivan Karaman [aut, cre, cph]
Maintainer: Zivan Karaman <zivan.karaman@gmail.com>
Diff between spectator versions 0.1.0 dated 2021-12-03 and 0.1.1 dated 2022-03-29
DESCRIPTION | 19 MD5 | 51 NEWS |only R/GetAcquisitionPlan.R | 10 R/GetAllSatellites.R | 1 R/GetHighResolutionImage.R | 18 R/GetImageryFilesList.R | 9 R/GetOverpasses.R | 55 R/GetSatellite.R | 1 R/GetTrajectory.R | 1 R/SearchImages.R | 14 R/data.R | 2 R/internals.R | 16 R/spectator-package.R | 4 build/vignette.rds |binary data/satellites_db.rda |binary demo/imagery.R | 2 inst/doc/UsingSpectator.Rmd | 16 inst/doc/UsingSpectator.html | 2765 ++++++++++++++++++++++++++++++++++++++++++- inst/examples/imagery.R | 2 inst/extdata/README.txt | 12 man/GetAcquisitionPlan.Rd | 6 man/GetImageryFilesList.Rd | 11 man/GetOverpasses.Rd | 2 man/SearchImages.Rd | 2 man/satellites_db.Rd | 2 man/spectator-package.Rd | 4 27 files changed, 2808 insertions(+), 217 deletions(-)
Title: Simulation of Legal Exemption System for European Cartel Law
Description: Monte Carlo simulations of a game-theoretic model for the
legal exemption system of the European cartel law are implemented
in order to estimate the (mean) deterrent effect of this system.
The input and output parameters of the simulated cartel
opportunities can be visualized by three-dimensional projections.
A description of the model is given in Moritz et al. (2018)
<doi:10.1515/bejeap-2017-0235>.
Author: Martin Becker [aut, cre]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between SimEUCartelLaw versions 1.0.1 dated 2018-05-30 and 1.0.2 dated 2022-03-29
DESCRIPTION | 10 ++++++---- MD5 | 4 ++-- src/SimEUCartelLaw.c | 2 +- 3 files changed, 9 insertions(+), 7 deletions(-)
More information about SimEUCartelLaw at CRAN
Permanent link
Title: Provide the Stepwise Procedure for Beta Regression Models
Description: Starting from a Beta Regression Model, it provides a stepwise
procedure to select the linear predictor.
Author: Sergio Garofalo
Maintainer: Sergio Garofalo <sergio.garofalo96@gmail.com>
Diff between StepBeta versions 0.1.0 dated 2022-02-01 and 0.1.1 dated 2022-03-29
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 1 + R/Check_formual_terms.R |only R/Step_Aic_beta_regression.R | 25 ++++++++++++++++--------- man/check_formula_terms.Rd |only 6 files changed, 25 insertions(+), 15 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The
functions are pipe-friendly and provide a consistent syntax to work
with tidy data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.3.0 dated 2022-01-14 and 1.3.1 dated 2022-03-29
DESCRIPTION | 16 LICENSE | 4 MD5 | 105 - NAMESPACE | 88 - NEWS.md | 818 ++++----- R/centrality_description.R | 12 R/contingency_table.R | 14 R/corr_test.R | 14 R/helpers_easystats.R | 1 R/meta_analysis.R | 17 R/one_sample_test.R | 25 R/oneway_anova.R | 13 R/statsExpressions-package.R | 25 R/two_sample_test.R | 14 README.md | 1442 ++++++++--------- build/vignette.rds |binary inst/CITATION | 28 inst/WORDLIST | 158 - inst/doc/statsExpressions.R | 126 - inst/doc/statsExpressions.Rmd | 410 ++-- inst/doc/statsExpressions.html | 1517 +++++++++--------- inst/doc/stats_details.R | 22 inst/doc/stats_details.Rmd | 386 +--- inst/doc/stats_details.html | 2413 +++++++++++++++-------------- man/bugs_long.Rd | 86 - man/centrality_description.Rd | 137 - man/contingency_table.Rd | 336 ++-- man/corr_test.Rd | 220 +- man/figures/README-anova_parametric2-1.png |binary man/iris_long.Rd | 82 man/long_to_wide_converter.Rd | 172 +- man/meta_analysis.Rd | 234 +- man/movies_long.Rd | 92 - man/movies_wide.Rd | 96 - man/one_sample_test.Rd | 308 +-- man/oneway_anova.Rd | 453 +++-- man/reexports.Rd | 70 man/rmd-fragments |only man/statsExpressions-package.Rd | 99 - man/stats_type_switch.Rd | 58 man/tidy_model_expressions.Rd | 90 - man/tidy_model_parameters.Rd | 50 man/two_sample_test.Rd | 464 +++-- tests/testthat/test-oneway_anova_bayes.R | 58 vignettes/apa.csl | 886 +++++----- vignettes/paper.bib | 364 ++-- vignettes/statsExpressions.Rmd | 410 ++-- vignettes/stats_details.Rmd | 386 +--- vignettes/web_only/dataframe_outputs.Rmd | 1090 ++++++------- 49 files changed, 7039 insertions(+), 6870 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Slow Feature Analysis
Description: Slow Feature Analysis (SFA), ported to R based on
'matlab' implementations of SFA: 'SFA toolkit' 1.0 by Pietro Berkes and 'SFA toolkit'
2.8 by Wolfgang Konen.
Author: Wolfgang Konen <wolfgang.konen@fh-koeln.de>, Martin Zaefferer,
Patrick Koch; Bug hunting and testing by Ayodele Fasika, Ashwin
Kumar, Prawyn Jebakumar
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>
Diff between rSFA versions 1.04 dated 2014-12-17 and 1.5 dated 2022-03-29
DESCRIPTION | 20 ++++---- MD5 | 96 +++++++++++++++++++-------------------- NAMESPACE | 10 +++- NEWS | 12 +++- R/gauss.R | 2 R/sfa.R | 13 ++--- R/sfaClassify.R | 3 + R/sfaHelperFunctions.R | 2 R/sfaStep.R | 4 - man/addNoisyCopies.Rd | 64 +++++++++++++------------- man/customRep.Rd | 40 ++++++++-------- man/customRepmat.Rd | 44 +++++++++--------- man/customSize.Rd | 40 ++++++++-------- man/etaval.Rd | 38 +++++++-------- man/gaussClassifier.Rd | 84 +++++++++++++++++----------------- man/gaussCreate.Rd | 44 +++++++++--------- man/gaussLoad.Rd | 42 ++++++++--------- man/gaussSave.Rd | 40 ++++++++-------- man/lcovCreate.Rd | 42 ++++++++--------- man/lcovFix.Rd | 46 +++++++++---------- man/lcovPca.Rd | 68 ++++++++++++++-------------- man/lcovPca2.Rd | 74 +++++++++++++++--------------- man/lcovTransform.Rd | 56 +++++++++++------------ man/lcovUpdate.Rd | 48 +++++++++---------- man/nlDim.Rd | 42 ++++++++--------- man/nlExpand.Rd | 46 +++++++++---------- man/rSFA-package.Rd | 69 +++++++++++++--------------- man/sfa1.Rd | 50 ++++++++++---------- man/sfa1Create.Rd | 52 ++++++++++----------- man/sfa1Step.Rd | 72 ++++++++++++++--------------- man/sfa2.Rd | 113 ++++++++++++++++++++++++----------------------- man/sfa2Create.Rd | 90 ++++++++++++++++++++----------------- man/sfa2Step.Rd | 82 +++++++++++++++++----------------- man/sfaBSh.Rd | 40 ++++++++-------- man/sfaCheckCondition.Rd | 34 +++++++------- man/sfaClassPredict.Rd | 70 ++++++++++++++--------------- man/sfaClassify.Rd | 82 +++++++++++++++++----------------- man/sfaExecute.Rd | 66 +++++++++++++-------------- man/sfaExpand.Rd | 46 +++++++++---------- man/sfaGetHf.Rd | 92 +++++++++++++++++++------------------- man/sfaGetIntRange.Rd | 36 +++++++------- man/sfaLoad.Rd | 42 ++++++++--------- man/sfaNlRegress.Rd | 56 +++++++++++------------ man/sfaPBootstrap.Rd | 62 ++++++++++++------------- man/sfaPreproc.Rd | 50 ++++++++++---------- man/sfaSave.Rd | 40 ++++++++-------- man/sfaStep.Rd | 99 ++++++++++++++++++++--------------------- man/sfaTimediff.Rd | 46 +++++++++---------- man/xpDim.Rd | 42 ++++++++--------- 49 files changed, 1239 insertions(+), 1212 deletions(-)
Title: Diversity Indices for Numerical Matrices
Description: Providing functions to calculate indices of diversity on numerical matrices based on information theory. The rationale behind the package is described in Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039> and Rocchini, Marcantonio,..., Ricotta (2021) <doi:10.1101/2021.01.23.427872>.
Author: Matteo Marcantonio [aut, cre],
Martina Iannacito [aut, ctb],
Elisa Marchetto [ctb],
Elisa Thouverai [aut, ctb],
Michele Torresani [aut, ctb],
Daniele Da Re [aut],
Clara Tattoni [aut],
Giovanni Bacaro [aut],
Saverio Vicario [aut, ctb],
Carlo Ricotta [ [...truncated...]
Maintainer: Matteo Marcantonio <marcantoniomatteo@gmail.com>
Diff between rasterdiv versions 0.2-5 dated 2022-02-24 and 0.2-5.2 dated 2022-03-29
DESCRIPTION | 8 ++-- MD5 | 30 ++++++++--------- NAMESPACE | 2 - NEWS.md | 11 +++++- R/paRao.R | 10 +++-- R/paRaoAreaS.R | 39 ++++++++++++++++------- R/paRaoS.R | 6 +-- TODO | 3 + build/vignette.rds |binary inst/doc/rasterdiv_advanced_multimensionRao.html | 4 +- inst/doc/rasterdiv_basics.R | 10 +++-- inst/doc/rasterdiv_basics.Rmd | 11 ++++-- inst/doc/rasterdiv_basics.html | 19 ++++------- man/paRaoAreaS.Rd | 3 + tests/testthat/test_paRao.R | 13 +++++++ vignettes/rasterdiv_basics.Rmd | 11 ++++-- 16 files changed, 115 insertions(+), 65 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-39 dated 2022-02-24 and 1.8-40 dated 2022-03-29
mgcv-1.8-39/mgcv/inst/po/it |only mgcv-1.8-39/mgcv/po/R-it.po |only mgcv-1.8-39/mgcv/po/it.po |only mgcv-1.8-40/mgcv/ChangeLog | 14 +++++++++++++- mgcv-1.8-40/mgcv/DESCRIPTION | 6 +++--- mgcv-1.8-40/mgcv/MD5 | 20 ++++++++------------ mgcv-1.8-40/mgcv/R/gam.fit3.r | 5 +++-- mgcv-1.8-40/mgcv/R/gam.fit4.r | 28 ++++++++++++++++++---------- mgcv-1.8-40/mgcv/R/smooth.r | 2 +- mgcv-1.8-40/mgcv/build/partial.rdb |binary mgcv-1.8-40/mgcv/src/mat.c | 1 + mgcv-1.8-40/mgcv/src/tprs.c | 4 +++- 12 files changed, 50 insertions(+), 30 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann, Victor Moreno
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 2.0 dated 2021-07-17 and 2.3.4 dated 2022-03-29
jmv-2.0/jmv/build |only jmv-2.0/jmv/inst/doc |only jmv-2.0/jmv/man/linRegClass.Rd |only jmv-2.0/jmv/man/logRegBinClass.Rd |only jmv-2.0/jmv/vignettes |only jmv-2.3.4/jmv/DESCRIPTION | 16 - jmv-2.3.4/jmv/MD5 | 123 +++++++----- jmv-2.3.4/jmv/NAMESPACE | 2 jmv-2.3.4/jmv/R/00meta.R | 27 ++ jmv-2.3.4/jmv/R/ancova.b.R | 132 ++++++++----- jmv-2.3.4/jmv/R/anova.b.R | 12 - jmv-2.3.4/jmv/R/anovaonew.b.R | 52 +++-- jmv-2.3.4/jmv/R/anovarm.b.R | 145 ++++++++++---- jmv-2.3.4/jmv/R/anovarmnp.b.R | 2 jmv-2.3.4/jmv/R/cfa.b.R | 39 ++-- jmv-2.3.4/jmv/R/constants.R | 2 jmv-2.3.4/jmv/R/conttables.b.R | 140 ++++++++------ jmv-2.3.4/jmv/R/conttablespaired.b.R | 29 +- jmv-2.3.4/jmv/R/corrmatrix.b.R | 27 +- jmv-2.3.4/jmv/R/corrpart.b.R | 29 +- jmv-2.3.4/jmv/R/data.R | 9 jmv-2.3.4/jmv/R/descriptives.b.R | 253 +++++++++++++++----------- jmv-2.3.4/jmv/R/descriptives.h.R | 12 + jmv-2.3.4/jmv/R/efa.b.R | 15 - jmv-2.3.4/jmv/R/efa.h.R | 43 +++- jmv-2.3.4/jmv/R/errors.R | 28 +- jmv-2.3.4/jmv/R/linreg.b.R | 158 +++++++++++----- jmv-2.3.4/jmv/R/linreg.h.R | 62 ++++-- jmv-2.3.4/jmv/R/loglinear.b.R | 49 ++--- jmv-2.3.4/jmv/R/logregbin.b.R | 148 ++++++++++----- jmv-2.3.4/jmv/R/logregmulti.b.R | 67 +++--- jmv-2.3.4/jmv/R/logregord.b.R | 38 ++- jmv-2.3.4/jmv/R/mancova.b.R | 31 +-- jmv-2.3.4/jmv/R/pca.b.R | 122 +++++++++--- jmv-2.3.4/jmv/R/pca.h.R | 3 jmv-2.3.4/jmv/R/proptest2.b.R | 36 ++- jmv-2.3.4/jmv/R/reliability.b.R | 41 ++-- jmv-2.3.4/jmv/R/ttestis.b.R | 88 +++++---- jmv-2.3.4/jmv/R/ttestones.b.R | 37 +-- jmv-2.3.4/jmv/R/ttestps.b.R | 61 +++--- jmv-2.3.4/jmv/R/utils.R | 23 -- jmv-2.3.4/jmv/data/Big5.csv.gz |only jmv-2.3.4/jmv/data/ToothGrowth.csv.gz |only jmv-2.3.4/jmv/data/bugs.csv.gz |binary jmv-2.3.4/jmv/data/iris.csv.gz |only jmv-2.3.4/jmv/inst/i18n |only jmv-2.3.4/jmv/man/Big5.Rd |only jmv-2.3.4/jmv/man/ToothGrowth.Rd |only jmv-2.3.4/jmv/man/bugs.Rd | 11 - jmv-2.3.4/jmv/man/descriptives.Rd | 17 + jmv-2.3.4/jmv/man/efa.Rd | 12 - jmv-2.3.4/jmv/man/iris.Rd |only jmv-2.3.4/jmv/man/linReg.Rd | 21 +- jmv-2.3.4/jmv/tests/testthat/Rplots.pdf |only jmv-2.3.4/jmv/tests/testthat/testanovaonew.R | 16 + jmv-2.3.4/jmv/tests/testthat/testanovarmnp.R | 30 ++- jmv-2.3.4/jmv/tests/testthat/testconttables.R | 34 ++- jmv-2.3.4/jmv/tests/testthat/testlinreg.R | 105 ++++++++++ jmv-2.3.4/jmv/tests/testthat/testlogregbin.R | 34 +++ 59 files changed, 1555 insertions(+), 826 deletions(-)
Title: Risk Measure Calculation in Financial TS
Description: Enables the user to calculate Value at Risk (VaR) and Expected
Shortfall (ES) by means of various parametric and semiparametric
GARCH-type models. For the latter the estimation of the nonparametric scale
function is carried out by means of a data-driven smoothing approach. Model
quality, in terms of forecasting VaR and ES, can be assessed by means of
various backtesting methods such as the traffic light test for VaR and a
newly developed traffic light test for ES. The approaches implemented in
this package are described in e.g. Feng Y., Beran J., Letmathe S. and
Ghosh S. (2020) <https://ideas.repec.org/p/pdn/ciepap/137.html> as well as
Letmathe S., Feng Y. and Uhde A. (2021)
<https://ideas.repec.org/p/pdn/ciepap/141.html>.
Author: Yuanhua Feng [aut] ,
Xuehai Zhang [aut] ,
Christian Peitz [aut] ,
Dominik Schulz [aut] ,
Shujie Li [aut] ,
Sebastian Letmathe [aut, cre]
Maintainer: Sebastian Letmathe <sebastian.letmathe@uni-paderborn.de>
Diff between ufRisk versions 1.0.3 dated 2022-03-06 and 1.0.4 dated 2022-03-29
ufRisk-1.0.3/ufRisk/R/arfilt.R |only ufRisk-1.0.4/ufRisk/DESCRIPTION | 6 ufRisk-1.0.4/ufRisk/MD5 | 13 - ufRisk-1.0.4/ufRisk/NEWS.md | 7 ufRisk-1.0.4/ufRisk/R/sysdata.rda |binary ufRisk-1.0.4/ufRisk/R/trafftest.R | 13 + ufRisk-1.0.4/ufRisk/R/varcast.R | 286 +++++++++++++++---------------------- ufRisk-1.0.4/ufRisk/man/varcast.Rd | 8 - 8 files changed, 153 insertions(+), 180 deletions(-)
Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut] ,
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-34 dated 2020-08-26 and 0.6-35 dated 2022-03-29
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ build/vignette.rds |binary data/gSRouter.rda |binary data/georgia.rda |binary inst/doc/GWR.pdf |binary src/gwe.c | 6 +++--- 7 files changed, 14 insertions(+), 13 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>,
'saddlepoint' approximations ('Tiefelsdorf' 2002)
<doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests
for global and local 'Moran's I' ('Bivand et al.' 2009)
<doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators
of spatial heteroscedasticity ('Ord' and 'Getis')
<doi:10.1007/s00168-011-0492-y>. The implementation of most of
the measures is described in 'Bivand' and 'Wong' (2018)
<doi:10.1007/s11749-018-0599-x>, with further extensions in 'Bivand' (2022)
<doi:10.1111/gean.12319>.
From 'spdep' and 'spatialreg' versions >= 1.2-1, the model fitting functions
previously present in this package are defunct in 'spdep' and may be found
in 'spatialreg'.
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stephane Dray [ctb],
Virg [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.2-2 dated 2022-01-28 and 1.2-3 dated 2022-03-29
DESCRIPTION | 11 ++++++----- MD5 | 30 +++++++++++++++--------------- NEWS.md | 12 +++++++++++- R/LOSH.mc.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 10 ++++++++++ inst/doc/CO69.html | 10 +++++++--- inst/doc/nb.html | 6 +++++- inst/doc/nb_sf.html | 40 ++++++++++++++++++++-------------------- inst/doc/sids.html | 6 +++++- man/LOSH.mc.Rd | 2 ++ man/dnearneigh.Rd | 8 ++++---- man/localmoran.Rd | 6 +++++- src/dnn.c | 4 ++-- src/knn.c | 7 ++----- 16 files changed, 95 insertions(+), 59 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Sebastian Meyer [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 2.3-2 dated 2022-02-12 and 2.4-0 dated 2022-03-29
DESCRIPTION | 8 +-- MD5 | 73 ++++++++++++++--------------- NAMESPACE | 2 NEWS | 115 ++++++++++++++++++++++++++++++++++++++++++++++ R/as.im.R | 15 ++++-- R/close3Dpairs.R | 46 ++++++++++++------ R/closepairs.R | 76 ++++++++++++++++++++---------- R/convexdist.R | 21 ++++---- R/covering.R | 4 - R/deldir.R | 6 +- R/distbdry.R | 30 ++++++++++-- R/distmap.R | 56 +++++++++++++++------- R/exactPdt.R | 26 ++++++---- R/exactdt.R | 19 +++++-- R/images.R | 6 +- R/metricPdt.R | 20 ++++---- R/nncross.R | 15 +++--- R/tess.R | 36 ++++++++------ R/unnormdensity.R | 61 ++++++++++++++---------- R/weightedStats.R | 35 ++++++++------ R/window.R | 11 ++-- inst/doc/packagesizes.txt | 1 man/bdist.pixels.Rd | 39 +++++++++------ man/distfun.Rd | 6 ++ man/distmap.ppp.Rd | 26 ++++++---- man/distmap.psp.Rd | 21 ++++---- man/framedist.pixels.Rd |only man/intersect.tess.Rd | 13 +++-- man/macros/defns.Rd | 1 man/unnormdensity.Rd | 34 ++++++++----- man/weighted.median.Rd | 6 +- src/exactdist.c | 48 ++++++++++++------- src/metricPdist.h | 5 +- src/raster.c | 5 -- src/raster.h | 55 +++++++++++----------- src/uniquemap.h | 4 - tests/testsAtoC.R | 39 +++++++++++++++ tests/testsGtoJ.R | 2 38 files changed, 669 insertions(+), 317 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
[...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 2.1-2 dated 2021-12-16 and 2.1-4 dated 2022-03-29
DESCRIPTION | 11 +-- MD5 | 170 ++++++++++++++++++++++++------------------------ NEWS | 14 +++ R/copyExampleFiles.R | 2 data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/btb.rda |binary data/cells.rda |binary data/cetaceans.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/concrete.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwood3.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary man/amacrine.Rd | 6 + man/bei.Rd | 2 man/bramblecanes.Rd | 7 + man/chicago.Rd | 2 man/concrete.Rd | 2 man/copper.Rd | 1 man/demopat.Rd | 3 man/dendrite.Rd | 2 man/flu.Rd | 3 man/hamster.Rd | 8 ++ man/heather.Rd | 3 man/humberside.Rd | 6 + man/japanesepines.Rd | 9 ++ man/lansing.Rd | 2 man/longleaf.Rd | 4 - man/macros/defns.Rd | 5 - man/mucosa.Rd | 6 + man/murchison.Rd | 2 man/nbfires.Rd | 2 man/ponderosa.Rd | 1 man/redwood.Rd | 1 man/spiders.Rd | 2 man/swedishpines.Rd | 10 ++ man/urkiola.Rd | 4 - 86 files changed, 186 insertions(+), 104 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.5.1 dated 2022-03-06 and 0.5.2 dated 2022-03-29
RcppCWB-0.5.1/RcppCWB/man/corpus_data_dir.Rd |only RcppCWB-0.5.2/RcppCWB/DESCRIPTION | 8 RcppCWB-0.5.2/RcppCWB/MD5 | 31 - RcppCWB-0.5.2/RcppCWB/NAMESPACE | 2 RcppCWB-0.5.2/RcppCWB/NEWS.md | 12 RcppCWB-0.5.2/RcppCWB/R/RcppExports.R | 32 + RcppCWB-0.5.2/RcppCWB/R/cl.R | 114 +++- RcppCWB-0.5.2/RcppCWB/R/region_matrix.R | 22 RcppCWB-0.5.2/RcppCWB/inst/extdata/cwb/indexed_corpora/reuters/info.md | 5 RcppCWB-0.5.2/RcppCWB/inst/extdata/cwb/registry/reuters | 2 RcppCWB-0.5.2/RcppCWB/inst/include/RcppCWB_RcppExports.h | 147 +++++ RcppCWB-0.5.2/RcppCWB/man/region_matrix_ops.Rd | 10 RcppCWB-0.5.2/RcppCWB/man/registry_info.Rd |only RcppCWB-0.5.2/RcppCWB/src/RcppExports.cpp | 278 ++++++++++ RcppCWB-0.5.2/RcppCWB/src/addons.cpp | 20 RcppCWB-0.5.2/RcppCWB/src/cl.cpp | 176 ++++++ RcppCWB-0.5.2/RcppCWB/tests/testthat/test_region_matrix_to_ids.R | 16 RcppCWB-0.5.2/RcppCWB/tests/testthat/test_registry_info.R |only 18 files changed, 847 insertions(+), 28 deletions(-)
Title: Mean Length-Based Estimators of Mortality using TMB
Description: Estimation functions and diagnostic tools for mean length-based total mortality estimators based on Gedamke and Hoenig (2006) <doi:10.1577/T05-153.1>.
Author: Quang Huynh [aut, cre],
Todd Gedamke [ctb],
Amy Then [ctb]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between MLZ versions 0.1.3 dated 2019-09-20 and 0.1.4 dated 2022-03-29
MLZ-0.1.3/MLZ/inst/include/ML.h |only MLZ-0.1.3/MLZ/inst/include/MLCR.h |only MLZ-0.1.3/MLZ/inst/include/MLeffort.h |only MLZ-0.1.3/MLZ/inst/include/MSM1S.h |only MLZ-0.1.3/MLZ/inst/include/MSM23.h |only MLZ-0.1.3/MLZ/inst/include/functions.h |only MLZ-0.1.4/MLZ/DESCRIPTION | 15 - MLZ-0.1.4/MLZ/MD5 | 31 +-- MLZ-0.1.4/MLZ/R/estimation.R | 4 MLZ-0.1.4/MLZ/R/zzz.R |only MLZ-0.1.4/MLZ/README.md | 2 MLZ-0.1.4/MLZ/build/vignette.rds |binary MLZ-0.1.4/MLZ/inst/doc/MLZ.R | 58 ++--- MLZ-0.1.4/MLZ/inst/doc/MLZ.Rmd | 16 + MLZ-0.1.4/MLZ/inst/doc/MLZ.html | 320 +++++++++++++++++++++---------- MLZ-0.1.4/MLZ/inst/include/ML.hpp |only MLZ-0.1.4/MLZ/inst/include/MLCR.hpp |only MLZ-0.1.4/MLZ/inst/include/MLeffort.hpp |only MLZ-0.1.4/MLZ/inst/include/MSM1S.hpp |only MLZ-0.1.4/MLZ/inst/include/MSM23.hpp |only MLZ-0.1.4/MLZ/inst/include/functions.hpp |only MLZ-0.1.4/MLZ/src/MLZ.cpp | 30 +- MLZ-0.1.4/MLZ/vignettes/MLZ.Rmd | 16 + 23 files changed, 321 insertions(+), 171 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-20 dated 2021-10-08 and 0.9-22 dated 2022-03-29
DESCRIPTION | 10 MD5 | 139 ++++---- NAMESPACE | 2 R/A_class.R | 15 R/bart.R | 16 - R/dbarts.R | 6 R/generics.R | 83 ++++- R/model.R | 76 ++++ R/plotTree.R | 23 - R/utility.R | 5 R/xbart.R | 4 build/vignette.rds |binary cleanup | 4 configure | 22 - configure.ac | 6 inst/NEWS.Rd | 31 + inst/doc/gibbs_sampler_mixture_model.pdf |binary inst/doc/working_with_saved_trees.R |only inst/doc/working_with_saved_trees.Rmd |only inst/doc/working_with_saved_trees.pdf |only inst/include/dbarts/R_C_interface.hpp | 20 - inst/include/dbarts/bartFit.hpp | 6 inst/include/dbarts/model.hpp | 4 inst/include/dbarts/results.hpp | 7 man/bart.Rd | 438 ++++++++++------------------ man/dbarts.Rd | 93 +++-- man/dbartsControl.Rd | 115 +++---- man/dbartsData.Rd | 8 man/dbartsSampler-class.Rd | 128 ++++---- man/guessNumCores.Rd | 11 man/makeind.Rd | 55 +-- man/pdbart.Rd | 212 ++++--------- man/rbart.Rd | 155 ++++----- man/xbart.Rd | 117 ++----- src/R_C_interface.cpp | 39 +- src/R_interface.cpp | 66 +++- src/R_interface_common.cpp | 62 +++ src/R_interface_common.hpp | 2 src/R_interface_crossvalidate.cpp | 8 src/R_interface_rbart.cpp |only src/R_interface_rbart.hpp |only src/R_interface_sampler.cpp | 15 src/config.hpp.win | 4 src/crossvalidate.cpp | 294 +++++++++++++++++- src/dbarts/Makefile | 6 src/dbarts/bartFit.cpp | 34 +- src/dbarts/birthDeathRule.cpp | 7 src/dbarts/changeRule.cpp | 1 src/dbarts/config.hpp.win | 4 src/dbarts/treePrior.cpp | 41 ++ src/external/Makefile | 6 src/external/config.h.win | 4 src/external/random.c | 20 - src/external/randomBase.c | 51 ++- src/guessNumCores.cpp | 8 src/include/external/R.h | 2 src/include/external/io.h | 9 src/include/misc/intrinsic.h | 4 src/misc/Makefile | 8 src/misc/adaptiveRadixTree.c | 13 src/misc/binaryIO.c | 5 src/misc/blockingThreadManager.c | 11 src/misc/config.h.win | 9 src/misc/hierarchicalThreadManager.c | 4 src/misc/partition_body.c | 42 +- src/misc/thread.c | 7 src/rc/Makefile | 6 src/rc/bounds.c | 1 tests/testthat/test-08-xbart.R | 37 ++ tests/testthat/test-14-rbart.R | 1 tests/testthat/test-18-extractedTrees.R |only tests/testthat/test-19-splitProbabilities.R |only tools/m4/ax_compiler_ext.m4 | 2 vignettes/references.bib |only vignettes/working_with_saved_trees.Rmd |only 75 files changed, 1572 insertions(+), 1072 deletions(-)
Title: Missing Person Identification Tools
Description: Open-source software for computing Likelihood ratios thresholds and error rates in DNA kinship testing. Marsico FL. et al (2021) <doi:10.1016/j.fsigen.2021.102519>.
Author: Franco Marsico [aut, cre]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between mispitools versions 0.2.0 dated 2022-03-26 and 0.2.1 dated 2022-03-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/combLR.R | 4 ++-- R/makePOIprelim.R | 4 ++-- R/simLRprelim.R | 53 +++++++++++++++++++++++++++++++++++++++++++++++++---- man/simLRprelim.Rd | 16 ++++++++++++++-- 6 files changed, 75 insertions(+), 18 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut] ,
Vincent Arel-Bundock [ctb] ,
Alex Hayes [rev]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.16.0 dated 2022-02-16 and 0.17.0 dated 2022-03-29
insight-0.16.0/insight/man/get_predicted_ci.Rd |only insight-0.17.0/insight/DESCRIPTION | 20 insight-0.17.0/insight/MD5 | 292 +++++---- insight-0.17.0/insight/NAMESPACE | 41 + insight-0.17.0/insight/NEWS.md | 75 ++ insight-0.17.0/insight/R/check_if_installed.R | 86 ++ insight-0.17.0/insight/R/clean_names.R | 71 +- insight-0.17.0/insight/R/clean_parameters.R | 8 insight-0.17.0/insight/R/color_if.R | 2 insight-0.17.0/insight/R/compute_variances.R | 46 + insight-0.17.0/insight/R/ellipsis_info.R | 149 ++++ insight-0.17.0/insight/R/export_table.R | 216 +++++-- insight-0.17.0/insight/R/find_algorithm.R | 2 insight-0.17.0/insight/R/find_formula.R | 299 +++++---- insight-0.17.0/insight/R/find_interactions.R | 6 insight-0.17.0/insight/R/find_offset.R | 11 insight-0.17.0/insight/R/find_parameter_zi.R | 6 insight-0.17.0/insight/R/find_parameters.R | 12 insight-0.17.0/insight/R/find_parameters_bayesian.R | 68 +- insight-0.17.0/insight/R/find_parameters_gam.R | 14 insight-0.17.0/insight/R/find_parameters_mfx.R | 6 insight-0.17.0/insight/R/find_parameters_mixed.R | 32 - insight-0.17.0/insight/R/find_parameters_other.R | 13 insight-0.17.0/insight/R/find_predictors.R | 50 + insight-0.17.0/insight/R/find_random.R | 12 insight-0.17.0/insight/R/find_random_slopes.R | 10 insight-0.17.0/insight/R/find_response.R | 48 - insight-0.17.0/insight/R/find_smooth.R | 4 insight-0.17.0/insight/R/find_statistic.R | 8 insight-0.17.0/insight/R/find_terms.R | 24 insight-0.17.0/insight/R/find_weights.R | 28 insight-0.17.0/insight/R/format_ci.R | 2 insight-0.17.0/insight/R/format_message.R | 6 insight-0.17.0/insight/R/format_p.R | 6 insight-0.17.0/insight/R/format_table.R | 97 +-- insight-0.17.0/insight/R/format_value.R | 6 insight-0.17.0/insight/R/get_call.R | 31 - insight-0.17.0/insight/R/get_data.R | 45 + insight-0.17.0/insight/R/get_datagrid.R | 302 +++++++--- insight-0.17.0/insight/R/get_deviance.R | 6 insight-0.17.0/insight/R/get_df.R | 88 ++ insight-0.17.0/insight/R/get_loglikelihood.R | 189 +++++- insight-0.17.0/insight/R/get_modelmatrix.R | 9 insight-0.17.0/insight/R/get_parameters.R | 33 - insight-0.17.0/insight/R/get_parameters_bayesian.R | 4 insight-0.17.0/insight/R/get_parameters_gam.R | 2 insight-0.17.0/insight/R/get_parameters_mixed.R | 34 - insight-0.17.0/insight/R/get_parameters_others.R | 9 insight-0.17.0/insight/R/get_predicted.R | 238 ++++++- insight-0.17.0/insight/R/get_predicted_args.R | 172 ++++- insight-0.17.0/insight/R/get_predicted_bayesian.R | 51 - insight-0.17.0/insight/R/get_predicted_ci.R | 64 -- insight-0.17.0/insight/R/get_predicted_ci_zeroinflated.R | 4 insight-0.17.0/insight/R/get_predicted_methods.R | 3 insight-0.17.0/insight/R/get_predicted_mixed.R | 8 insight-0.17.0/insight/R/get_predicted_ordinal.R | 17 insight-0.17.0/insight/R/get_predicted_se.R | 161 +++-- insight-0.17.0/insight/R/get_predicted_zeroinfl.R | 1 insight-0.17.0/insight/R/get_predictors.R | 4 insight-0.17.0/insight/R/get_priors.R | 20 insight-0.17.0/insight/R/get_random.R | 2 insight-0.17.0/insight/R/get_residuals.R | 127 ++++ insight-0.17.0/insight/R/get_sigma.R | 14 insight-0.17.0/insight/R/get_statistic.R | 21 insight-0.17.0/insight/R/helper_functions.R | 94 --- insight-0.17.0/insight/R/is_gam_model.R | 2 insight-0.17.0/insight/R/is_model.R | 7 insight-0.17.0/insight/R/is_model_supported.R | 18 insight-0.17.0/insight/R/link_function.R | 12 insight-0.17.0/insight/R/link_inverse.R | 14 insight-0.17.0/insight/R/model_info.R | 37 - insight-0.17.0/insight/R/n_obs.R | 14 insight-0.17.0/insight/R/null_model.R | 2 insight-0.17.0/insight/R/print_parameters.R | 20 insight-0.17.0/insight/R/standardize_names.R | 9 insight-0.17.0/insight/R/text_remove_backticks.R | 12 insight-0.17.0/insight/R/utilities.R |only insight-0.17.0/insight/R/utils_compact.R |only insight-0.17.0/insight/R/utils_get_data.R | 249 ++++++-- insight-0.17.0/insight/R/utils_model_info.R | 126 ++-- insight-0.17.0/insight/R/utils_object.R |only insight-0.17.0/insight/README.md | 29 insight-0.17.0/insight/build/partial.rdb |binary insight-0.17.0/insight/build/vignette.rds |binary insight-0.17.0/insight/inst/WORDLIST | 5 insight-0.17.0/insight/inst/doc/display.R | 11 insight-0.17.0/insight/inst/doc/display.Rmd | 11 insight-0.17.0/insight/inst/doc/display.html | 185 +++--- insight-0.17.0/insight/inst/doc/export.R | 18 insight-0.17.0/insight/inst/doc/export.Rmd | 18 insight-0.17.0/insight/inst/doc/export.html | 89 +- insight-0.17.0/insight/inst/doc/insight.R | 2 insight-0.17.0/insight/inst/doc/insight.Rmd | 2 insight-0.17.0/insight/inst/doc/insight.html | 3 insight-0.17.0/insight/man/check_if_installed.Rd | 10 insight-0.17.0/insight/man/compact_character.Rd |only insight-0.17.0/insight/man/compact_list.Rd |only insight-0.17.0/insight/man/ellipsis_info.Rd | 6 insight-0.17.0/insight/man/export_table.Rd | 4 insight-0.17.0/insight/man/find_offset.Rd | 72 +- insight-0.17.0/insight/man/find_smooth.Rd | 54 - insight-0.17.0/insight/man/find_transformation.Rd | 74 +- insight-0.17.0/insight/man/fish.Rd | 20 insight-0.17.0/insight/man/format_pd.Rd | 56 - insight-0.17.0/insight/man/get_datagrid.Rd | 158 +++-- insight-0.17.0/insight/man/get_deviance.Rd | 6 insight-0.17.0/insight/man/get_loglikelihood.Rd | 17 insight-0.17.0/insight/man/get_predicted.Rd | 186 +++++- insight-0.17.0/insight/man/has_intercept.Rd | 68 +- insight-0.17.0/insight/man/is_empty_object.Rd |only insight-0.17.0/insight/man/is_gam_model.Rd | 68 +- insight-0.17.0/insight/man/is_mixed_model.Rd | 58 - insight-0.17.0/insight/man/is_model_supported.Rd | 14 insight-0.17.0/insight/man/model_info.Rd | 3 insight-0.17.0/insight/man/object_has_names.Rd |only insight-0.17.0/insight/man/text_remove_backticks.Rd | 6 insight-0.17.0/insight/man/trim_ws.Rd |only insight-0.17.0/insight/tests/testthat/helper-requiet.R | 1 insight-0.17.0/insight/tests/testthat/test-LORgee.R | 2 insight-0.17.0/insight/tests/testthat/test-MCMCglmm.R | 2 insight-0.17.0/insight/tests/testthat/test-backticks.R | 6 insight-0.17.0/insight/tests/testthat/test-betabin.R | 2 insight-0.17.0/insight/tests/testthat/test-clmm.R | 4 insight-0.17.0/insight/tests/testthat/test-compact-character.R |only insight-0.17.0/insight/tests/testthat/test-compact-list.R |only insight-0.17.0/insight/tests/testthat/test-coxph.R | 242 ++++---- insight-0.17.0/insight/tests/testthat/test-ellipses_info.R | 76 ++ insight-0.17.0/insight/tests/testthat/test-find_predictors-strata.R |only insight-0.17.0/insight/tests/testthat/test-fixest.R | 15 insight-0.17.0/insight/tests/testthat/test-format_table_ci.R | 64 ++ insight-0.17.0/insight/tests/testthat/test-gee.R | 2 insight-0.17.0/insight/tests/testthat/test-geeglm.R | 2 insight-0.17.0/insight/tests/testthat/test-get_data.R | 88 ++ insight-0.17.0/insight/tests/testthat/test-get_datagrid.R |only insight-0.17.0/insight/tests/testthat/test-get_loglikelihood.R | 54 + insight-0.17.0/insight/tests/testthat/test-get_predicted.R | 50 + insight-0.17.0/insight/tests/testthat/test-get_variance.R | 115 +++ insight-0.17.0/insight/tests/testthat/test-glmmTMB.R | 19 insight-0.17.0/insight/tests/testthat/test-gls.R | 13 insight-0.17.0/insight/tests/testthat/test-is-empty-object.R |only insight-0.17.0/insight/tests/testthat/test-ivreg_AER.R | 2 insight-0.17.0/insight/tests/testthat/test-lme.R | 15 insight-0.17.0/insight/tests/testthat/test-lmer.R | 35 - insight-0.17.0/insight/tests/testthat/test-marginaleffects.R |only insight-0.17.0/insight/tests/testthat/test-model_info.R | 13 insight-0.17.0/insight/tests/testthat/test-negbin.R | 2 insight-0.17.0/insight/tests/testthat/test-object_has_helpers.R |only insight-0.17.0/insight/tests/testthat/test-plm.R | 6 insight-0.17.0/insight/tests/testthat/test-polr.R | 5 insight-0.17.0/insight/tests/testthat/test-rlmer.R | 22 insight-0.17.0/insight/tests/testthat/test-rstanarm.R | 12 insight-0.17.0/insight/tests/testthat/test-standardize_names.R | 111 +-- insight-0.17.0/insight/vignettes/display.Rmd | 11 insight-0.17.0/insight/vignettes/export.Rmd | 18 insight-0.17.0/insight/vignettes/insight.Rmd | 2 155 files changed, 4234 insertions(+), 2081 deletions(-)
Title: Evaluating Individualized Treatment Rules
Description: Provides various statistical methods for evaluating Individualized Treatment Rules under randomized data. The provided metrics include Population Average Value (PAV), Population Average Prescription Effect (PAPE), Area Under Prescription Effect Curve (AUPEC). It also provides the tools to analyze Individualized Treatment Rules under budget constraints. Detailed reference in Imai and Li (2019) <arXiv:1905.05389>.
Author: Michael Lingzhi Li [aut, cre],
Kosuke Imai [aut]
Maintainer: Michael Lingzhi Li <mlli@mit.edu>
Diff between evalITR versions 0.2.2 dated 2021-10-16 and 0.3.0 dated 2022-03-29
DESCRIPTION | 14 ++++++++------ MD5 | 22 +++++++++++++++++----- NAMESPACE | 13 +++++++++++++ NEWS.md | 5 +++++ R/GATE.R |only R/GATEcv.R |only R/PAPEcv.R | 6 +++++- R/consist.test.R |only R/consistcv.test.R |only R/het.test.R |only R/hetcv.test.R |only man/GATE.Rd |only man/GATEcv.Rd |only man/consist.test.Rd |only man/consistcv.test.Rd |only man/het.test.Rd |only man/hetcv.test.Rd |only tests/testthat/test_functionality.R | 8 ++++++++ 18 files changed, 56 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-25 0.5.1
2022-03-21 0.5.0
2022-02-08 0.4.10
2022-01-16 0.4.9
2022-01-05 0.4.8
2021-11-25 0.4.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-31 1.1.0
2020-10-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-02 3.0.1
2021-04-01 3.0.0
2020-03-29 2.0.2
2019-06-14 2.0.1
2019-05-30 2.0.0
2019-05-23 1.0.1
2019-04-09 1.0.0