Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for some new multivariate frailty models.
This version includes the gamma, inverse Gaussian, weighted Lindley and Birnbaum-Saunders
as the distribution for the frailty terms.
For the basal model, it is considered a parametric approach based on the exponential,
Weibull and the piecewise exponential distributions as well as a semiparametric approach.
For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between extrafrail versions 1.4 dated 2023-03-29 and 1.5 dated 2023-04-05
DESCRIPTION | 14 +++++------ MD5 | 12 ++++----- NEWS.md | 5 ++++ R/baseCH.R | 5 ++++ R/frailty.fit.R | 60 ++++++++++++++++++++++++++++--------------------- R/summary.extrafrail.R | 15 +++++++++++- man/frailty.fit.Rd | 6 ++-- 7 files changed, 75 insertions(+), 42 deletions(-)
Title: RDS Sample Size Estimation and Power Calculation
Description: Provides functionality for carrying out sample size estimation and power calculation in Respondent-Driven Sampling.
Author: Yibo Wang [aut, cre],
Michael R. Elliott [aut],
Sunghee Lee [aut]
Maintainer: Yibo Wang <wangyb@umich.edu>
Diff between RDSsamplesize versions 0.2.0 dated 2022-10-18 and 0.3.0 dated 2023-04-05
DESCRIPTION | 11 MD5 | 18 - R/main.R | 40 +-- build/vignette.rds |binary inst/doc/README.R | 2 inst/doc/README.Rmd | 178 ++++++------- inst/doc/README.html | 117 ++++---- man/calSize.Rd | 6 src/Source.cpp | 665 +++++++++++++++++++++++++-------------------------- vignettes/README.Rmd | 178 ++++++------- 10 files changed, 607 insertions(+), 608 deletions(-)
Title: Helper Tools for Australian Hydrologists
Description: Functions to speed up work flow for hydrological analysis.
Focused on Australian climate data (SILO climate data), hydrological models (eWater Source) and in particular South Australia (<https://water.data.sa.gov.au> hydrological data).
Author: Matt Gibbs [aut, cre]
Maintainer: Matt Gibbs <gibbs.ms@gmail.com>
Diff between SWTools versions 0.2.4 dated 2022-07-04 and 0.2.5 dated 2023-04-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/DEWAquarius.R | 25 +++++++++++++++++++------ R/SILOCorrectSite.R | 15 ++++++++++----- R/SILOMorton.R | 3 ++- man/AQWPDownload.Rd | 6 +++--- 7 files changed, 48 insertions(+), 25 deletions(-)
Title: Make Plots that Glow
Description: Provides a framework for creating plots with glowing points.
Author: Travers Ching [aut, cre, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between glow versions 0.10.1 dated 2020-08-31 and 0.11.0 dated 2023-04-05
glow-0.10.1/glow/README.md |only glow-0.10.1/glow/vignettes/US_coronavirus_8_19_2020.png |only glow-0.10.1/glow/vignettes/volcano.png |only glow-0.11.0/glow/DESCRIPTION | 15 glow-0.11.0/glow/MD5 | 55 ++- glow-0.11.0/glow/NAMESPACE | 8 glow-0.11.0/glow/R/RcppExports.R | 4 glow-0.11.0/glow/R/glow_functions.r | 17 + glow-0.11.0/glow/R/zz_help_files.R | 111 ++++++ glow-0.11.0/glow/build/vignette.rds |binary glow-0.11.0/glow/inst/doc/vignette.R | 112 ++++++ glow-0.11.0/glow/inst/doc/vignette.html | 168 +++++++--- glow-0.11.0/glow/inst/doc/vignette.rmd | 140 ++++++-- glow-0.11.0/glow/inst/examples |only glow-0.11.0/glow/man/circular_palette.Rd |only glow-0.11.0/glow/man/clifford_attractor.Rd |only glow-0.11.0/glow/man/light_heat_colors.Rd |only glow-0.11.0/glow/man/map_colors.Rd |only glow-0.11.0/glow/src/Makevars | 1 glow-0.11.0/glow/src/Makevars.win | 1 glow-0.11.0/glow/src/RcppExports.cpp | 22 + glow-0.11.0/glow/src/glow_functions.cpp | 55 ++- glow-0.11.0/glow/vignettes/GAIA_galaxy_pseudocolor.png |binary glow-0.11.0/glow/vignettes/US_coronavirus_2021.png |only glow-0.11.0/glow/vignettes/airline_mt.png |binary glow-0.11.0/glow/vignettes/clifford_distance_inverse_viridis_50.png |only glow-0.11.0/glow/vignettes/clifford_vignette.png |only glow-0.11.0/glow/vignettes/diamonds.png |binary glow-0.11.0/glow/vignettes/diamonds_vignette_dark.png |only glow-0.11.0/glow/vignettes/diamonds_vignette_light.png |only glow-0.11.0/glow/vignettes/glow_spiral2.png |binary glow-0.11.0/glow/vignettes/gps_trace_8K.png |only glow-0.11.0/glow/vignettes/vignette.rmd | 140 ++++++-- glow-0.11.0/glow/vignettes/volcano_white_bg.png |only 34 files changed, 697 insertions(+), 152 deletions(-)
Title: Classes and Methods for Trajectory Data
Description: Classes and methods for trajectory data, with support for nesting individual Track objects in track sets (Tracks) and track sets for different entities in collections of Tracks. Methods include selection, generalization, aggregation, intersection, simulation, and plotting.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Klus [aut],
Benedikt Graeler [ctb],
Nikolai Gorte [ctb],
Mehdi Moradi [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between trajectories versions 0.2-6 dated 2022-12-22 and 0.2-7 dated 2023-04-05
DESCRIPTION | 12 +- MD5 | 52 ++++----- R/generalize.R | 9 - R/rtracks.R | 6 - build/vignette.rds |binary inst/doc/article.R | 23 ++-- inst/doc/article.Rnw | 7 - inst/doc/article.pdf |binary man/Track-class.Rd | 1 man/Track.idw.Rd | 2 man/as.Track.arrow.Rd | 2 man/as.Track.ppp.Rd | 2 man/auto.arima.Track.Rd | 6 - man/avedistTrack.Rd | 14 +- man/avemove.Rd | 8 - man/chimaps.Rd | 8 - man/density.list.Rd | 8 - man/generalize.Rd | 2 man/pcfinhom.Track.Rd | 10 + man/print.Tracks.Rd | 7 - man/print.TracksCollection.Rd | 7 - man/print.distrack.Rd | 12 +- man/reTrack.Rd | 1 man/tsqTracks.Rd | 1 tests/tracks.R | 2 tests/tracks.Rout.save | 227 ++---------------------------------------- vignettes/article.Rnw | 7 - 27 files changed, 129 insertions(+), 307 deletions(-)
Title: Tools for Biostatistics, Public Policy, and Law
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness, and measures of relative variability, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as robust QQ plot, robust trend tests for variances, etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.
Author: Joseph L. Gastwirth [aut],
Yulia R. Gel [aut, cre],
W. L. Wallace Hui [aut],
Vyacheslav Lyubchich [aut] ,
Weiwen Miao [aut],
Kimihiro Noguchi [aut]
Maintainer: Yulia R. Gel <gel.yulia@gmail.com>
Diff between lawstat versions 3.5 dated 2022-09-07 and 3.6 dated 2023-04-05
DESCRIPTION | 26 +++++++++++++------------- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 15 insertions(+), 15 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.6 dated 2023-03-19 and 1.1.7 dated 2023-04-05
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/utils.R | 10 ++++++++-- build/partial.rdb |binary inst/NEWS.Rd | 10 +++++++++- inst/doc/covstruct.html | 4 ++-- inst/doc/glmmTMB.pdf |binary inst/doc/hacking.html | 4 ++-- inst/doc/mcmc.html | 4 ++-- inst/doc/miscEx.html | 4 ++-- inst/doc/model_evaluation.pdf |binary inst/doc/parallel.html | 4 ++-- inst/doc/sim.html | 4 ++-- inst/doc/troubleshooting.html | 4 ++-- inst/vignette_data/model_evaluation.rda |binary 15 files changed, 48 insertions(+), 34 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.2 dated 2023-01-17 and 4.3 dated 2023-04-05
DESCRIPTION | 11 +-- MD5 | 10 +-- NEWS | 5 + configure | 170 +++++++++++++++++++++++++++++++++--------------------- configure.ac | 118 +++++++++++++++++-------------------- src/fontmetrics.h | 15 +--- 6 files changed, 184 insertions(+), 145 deletions(-)
Title: Variable Importance and Variable Interaction Displays
Description: A suite of plots for displaying variable importance and two-way variable interaction jointly. Can also display partial dependence plots laid out in a pairs plot or 'zenplots' style.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut]
Maintainer: Alan Inglis <alan.n.inglis@gmail.com>
Diff between vivid versions 0.2.5 dated 2023-02-13 and 0.2.6 dated 2023-04-05
vivid-0.2.5/vivid/inst/doc/vivid.R |only vivid-0.2.5/vivid/inst/doc/vivid.Rmd |only vivid-0.2.5/vivid/inst/doc/vivid.html |only vivid-0.2.5/vivid/inst/doc/vividQStart.R |only vivid-0.2.5/vivid/inst/doc/vividQStart.Rmd |only vivid-0.2.5/vivid/inst/doc/vividQStart.html |only vivid-0.2.5/vivid/tests/testthat.R |only vivid-0.2.5/vivid/vignettes/vivid.Rmd |only vivid-0.2.5/vivid/vignettes/vividQStart.Rmd |only vivid-0.2.6/vivid/DESCRIPTION | 14 vivid-0.2.6/vivid/MD5 | 51 +- vivid-0.2.6/vivid/NEWS.md | 12 vivid-0.2.6/vivid/R/pdpPairs.R | 99 ++--- vivid-0.2.6/vivid/R/pdpVars.R | 27 - vivid-0.2.6/vivid/R/pdpZen.R | 42 +- vivid-0.2.6/vivid/R/vip2vivid.R | 11 vivid-0.2.6/vivid/R/vivi.R | 211 +++++++---- vivid-0.2.6/vivid/R/viviHeatmap.R | 35 - vivid-0.2.6/vivid/R/viviNetwork.R | 67 ++- vivid-0.2.6/vivid/R/viviUpdate.R | 16 vivid-0.2.6/vivid/R/zPath.R | 7 vivid-0.2.6/vivid/README.md | 9 vivid-0.2.6/vivid/build/vignette.rds |binary vivid-0.2.6/vivid/inst/doc/vividVignette.R |only vivid-0.2.6/vivid/inst/doc/vividVignette.Rmd |only vivid-0.2.6/vivid/inst/doc/vividVignette.html |only vivid-0.2.6/vivid/man/pdpPairs.Rd | 2 vivid-0.2.6/vivid/man/pdpVars.Rd | 1 vivid-0.2.6/vivid/man/vip2vivid.Rd | 6 vivid-0.2.6/vivid/man/vivi.Rd | 27 + vivid-0.2.6/vivid/tests/testthat/test_plots.R | 460 +++++++++++++------------- vivid-0.2.6/vivid/tests/testthat/test_vivi.R | 61 ++- vivid-0.2.6/vivid/vignettes/vividVignette.Rmd |only 33 files changed, 639 insertions(+), 519 deletions(-)
Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Graeler [ctb],
Tom Gottfried [ctb],
Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between spacetime versions 1.2-8 dated 2022-06-17 and 1.3-0 dated 2023-04-05
DESCRIPTION | 11 MD5 | 52 +-- R/ST-methods.R | 4 R/STFDF-methods.R | 2 build/vignette.rds |binary data/air.rda |binary data/fires.rda |binary inst/CITATION | 6 inst/doc/jss816.R | 149 ++++----- inst/doc/jss816.Rnw | 52 +-- inst/doc/jss816.pdf |binary inst/doc/stgvis.html | 677 ++++++++++++++------------------------------ inst/doc/sto.pdf |binary inst/doc/stpg.pdf |binary inst/doc/stsubs.pdf |binary man/STTDF-class.Rd | 18 - man/air.Rd | 6 man/fires.Rd | 20 - man/stconstruct.Rd | 69 ++-- tests/raster.Rout.save | 8 tests/rw.R | 18 - tests/rw.Rout.save | 37 -- tests/stconstruct.R | 12 tests/stconstruct.Rout.save | 51 +-- tests/wind.R | 92 ----- tests/wind.Rout.save | 102 ------ vignettes/jss816.Rnw | 52 +-- 27 files changed, 475 insertions(+), 963 deletions(-)
Title: Efficient Savitzky-Golay Filtering
Description: Smoothing signals and computing their derivatives is a common
requirement in signal processing workflows. Savitzky-Golay filters are a
established method able to do both (Savitzky and Golay, 1964 <doi:10.1021/ac60214a047>).
This package implements one dimensional Savitzky-Golay filters that can be applied to
vectors and matrices (either row-wise or column-wise).
Vectorization and memory allocations have been profiled to reduce computational
fingerprint. Short filter lengths are implemented in the direct space, while
longer filters are implemented in frequency space, using a Fast Fourier
Transform (FFT).
Author: Sergio Oller Moreno [aut, cre]
,
Robert Gentleman [ctb, cph] ),
Ross Ihaka [ctb, cph] ),
Brian Ripley [ctb, cph] ),
Martin Maechler [ctb, cph] ),
Duncan Murdoch [ctb, cph] ),
Institute for Bioengineering of Catalonia [cph]
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>
Diff between sgolay versions 1.0.2 dated 2022-09-29 and 1.0.3 dated 2023-04-05
DESCRIPTION | 12 ++++++------ MD5 | 8 +++++--- NEWS.md | 7 ++++++- README.md |only man/figures |only src/stats_filter.c | 18 +++++++++++++----- 6 files changed, 30 insertions(+), 15 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Seqinr includes
utilities for sequence data management under the ACNUC system
described in Gouy, M. et al. (1984) Nucleic Acids Res.
12:121-127 <doi:10.1093/nar/12.1Part1.121>.
Author: Delphine Charif [aut],
Olivier Clerc [ctb],
Carolin Frank [ctb],
Jean R. Lobry [aut, cph],
Anamaria Necsulea [ctb],
Leonor Palmeira [ctb],
Simon Penel [cre],
Guy Perriere [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 4.2-23 dated 2022-11-28 and 4.2-30 dated 2023-04-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/CITATION | 6 +++--- man/choosebank.Rd | 4 +++- src/alignment.c | 16 ++++++++++++++++ 5 files changed, 30 insertions(+), 12 deletions(-)
Title: Regression Discontinuity Design Application
Description: Estimation of both single- and multiple-assignment Regression Discontinuity Designs
(RDDs). Provides both parametric (global) and non-parametric (local) estimation choices for
both sharp and fuzzy designs, along with power analysis and assumption checks.
Introductions to the underlying logic and analysis of RDDs are in
Thistlethwaite, D. L., Campbell, D. T. (1960) <doi:10.1037/h0044319> and
Lee, D. S., Lemieux, T. (2010) <doi:10.1257/jel.48.2.281>.
Author: Ze Jin [aut],
Wang Liao [aut],
Irena Papst [aut],
Wenyu Zhang [aut],
Kimberly Hochstedler [aut],
Felix Thoemmes [aut, cre]
Maintainer: Felix Thoemmes <fjt36@cornell.edu>
Diff between rddapp versions 1.3.0 dated 2022-02-13 and 1.3.2 dated 2023-04-05
DESCRIPTION | 9 - MD5 | 58 +++---- NAMESPACE | 1 NEWS.md | 13 + R/mfrd_est.R | 20 +- R/mrd_est.R | 15 + R/mrd_impute.R | 85 +++++++++- R/mrd_power.R | 2 R/mrd_sens_bw.R | 4 R/mrd_sens_cutoff.R | 12 - R/plot.mfrd.R | 6 R/plot.rd.R | 2 R/predict.rd.R | 6 R/rd_est.R | 8 R/rd_impute.R | 24 ++ R/rd_power.R | 2 R/rd_sens_bw.R | 4 R/rd_sens_cutoff.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 39 ++-- inst/doc/distance-from-frontier.html | 281 ++++++++++++++++++++++++++++++++--- inst/doc/rddapp.html | 225 ++++++++++++++++++++++++++-- inst/shinyrdd/help/help_page.Rmd | 2 inst/shinyrdd/www/help_page.html | 4 man/mfrd_est.Rd | 2 man/mrd_impute.Rd | 8 man/mrd_sens_cutoff.Rd | 8 man/plot.mfrd.Rd | 4 man/rd_impute.Rd | 8 30 files changed, 710 insertions(+), 144 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
[...truncated...]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.21.1 dated 2023-01-19 and 2.21.8 dated 2023-04-05
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ R/MxAutoStart.R | 5 ++++- R/MxFitFunctionWLS.R | 5 +++-- R/MxModel.R | 2 +- R/MxSummary.R | 4 ++-- R/MxVersion.R | 2 +- build/OpenMx.pdf |binary inst/CITATION | 32 ++++++++------------------------ inst/doc/deriv.html | 16 ++++++++-------- inst/doc/factor_analysis.html | 6 +++--- inst/doc/reg_mimic.html | 18 +++++++++--------- inst/doc/regularization.html | 6 +++--- man/MxModel-class.Rd | 3 --- man/mxAutoStart.Rd | 2 +- man/mxExpectationStateSpace.Rd | 16 +++++++++++----- man/mxParametricBootstrap.Rd | 6 ++++++ src/Makevars.in | 5 +++-- src/Makevars.win | 14 ++++++++------ 19 files changed, 94 insertions(+), 94 deletions(-)
Title: Tools for Processing and Analyzing Files from the Hydrological
Catchment Model HYPE
Description: Work with model files (setup, input, output) from
the hydrological catchment model HYPE: Streamlined file import and export, standard
evaluation plot routines, diverse post-processing and aggregation routines
for hydrological model analysis.
Author: Rene Capell [aut, cre] ,
Conrad Brendel [aut] ,
Jafet Andersson [ctb],
David Gustafsson [ctb],
Jude Musuuza [ctb],
Jude Lubega [ctb]
Maintainer: Rene Capell <hypetools.rene@smhi.se>
Diff between HYPEtools versions 1.2.0 dated 2023-02-10 and 1.3.0 dated 2023-04-05
DESCRIPTION | 25 +-- MD5 | 56 ++++--- NAMESPACE | 5 NEWS.md | 15 +- R/function_CompareFiles.R | 21 ++ R/function_GroupSLCClasses.R | 22 +- R/function_MapRegionalSources.R | 2 R/function_PlotMapOutput.R | 117 ++++++++++----- R/function_PlotMapPoints.R | 284 +++++++++++++++++++++++++------------- R/function_PlotSubbasinRouting.R | 2 R/function_ScalePar.R |only R/function_VariableLookup.R | 1 R/function_VisualizeMapOutput.R |only R/function_VisualizeMapPoints.R |only R/functioncollection_export.R | 15 +- R/functioncollection_import.R | 10 + R/sysdata.rda |binary README.md | 2 inst/doc/basin_network.html | 2 inst/doc/plot_map_statistics.html | 4 inst/visualize_map_output |only inst/visualize_map_points |only man/CompareFiles.Rd | 16 +- man/GroupSLCClasses.Rd | 4 man/MapRegionalSources.Rd | 2 man/PlotMapOutput.Rd | 3 man/PlotMapPoints.Rd | 7 man/ReadMapOutput.Rd | 5 man/ScalePar.Rd |only man/VisualizeMapOutput.Rd |only man/VisualizeMapPoints.Rd |only man/WriteObs.Rd | 13 + 32 files changed, 434 insertions(+), 199 deletions(-)
Title: Aligned Corpus Toolkit
Description: The Aligned Corpus Toolkit (act) is designed for linguists that work with time aligned transcription data. It offers functions to import and export various annotation file formats ('ELAN' .eaf, 'EXMARaLDA .exb and 'Praat' .TextGrid files), create print transcripts in the style of conversation analysis, search transcripts (span searches across multiple annotations, search in normalized annotations, make concordances etc.), export and re-import search results (.csv and 'Excel' .xlsx format), create cuts for the search results (print transcripts, audio/video cuts using 'FFmpeg' and video sub titles in 'Subrib title' .srt format), modify the data in a corpus (search/replace, delete, filter etc.), interact with 'Praat' using 'Praat'-scripts, and exchange data with the 'rPraat' package. The package is itself written in R and may be expanded by other users.
Author: Oliver Ehmer [aut, cre]
Maintainer: Oliver Ehmer <oliver.ehmer@uos.de>
Diff between act versions 1.2.7 dated 2023-03-02 and 1.3.0 dated 2023-04-05
DESCRIPTION | 8 +++--- MD5 | 48 ++++++++++++++++++++-------------------- R/class_corpus.R | 34 ++++++++++++++-------------- R/class_search.R | 14 +++++++---- R/corpus_import.R | 20 ++++++++-------- R/corpus_new.R | 6 ++--- R/helper_no_export.R | 16 +++++++------ R/helper_tiers_sort_table.R | 8 ++++++ R/search_cuts.R | 7 +++-- R/search_cuts_media.R | 38 +++++++++++++++++++------------ R/search_cuts_printtranscript.R | 5 +++- R/search_cuts_srt.R | 4 +++ R/search_new.R | 9 +++++-- R/search_run.R | 2 - R/transcripts_add.R | 12 +++++----- R/transcripts_merge.R | 18 ++++++++++----- R/transcripts_merge2.R | 18 ++++++++++++++- R/zzz.R | 2 - data/examplecorpus.RData |binary inst/doc/install_ffmpeg.html | 4 +-- inst/doc/install_sendpraat.html | 4 +-- man/corpus-class.Rd | 6 ++--- man/search-class.Rd | 4 ++- man/search_cuts_media.Rd | 8 +++++- man/search_new.Rd | 7 ++++- 25 files changed, 185 insertions(+), 117 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.12.0.1.0 dated 2023-02-22 and 0.12.2.0.0 dated 2023-04-05
ChangeLog | 10 DESCRIPTION | 8 MD5 | 74 +- build/partial.rdb |binary build/vignette.rds |binary configure | 18 configure.ac | 2 inst/NEWS.Rd | 13 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 4 inst/include/armadillo_bits/Col_bones.hpp | 6 inst/include/armadillo_bits/Row_bones.hpp | 6 inst/include/armadillo_bits/SpMat_meat.hpp | 164 +---- inst/include/armadillo_bits/SpSubview_meat.hpp | 120 +++ inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/compiler_setup.hpp | 1 inst/include/armadillo_bits/constants.hpp | 25 inst/include/armadillo_bits/debug.hpp | 10 inst/include/armadillo_bits/fft_engine_fftw3.hpp | 2 inst/include/armadillo_bits/fn_spsolve.hpp | 19 inst/include/armadillo_bits/injector_bones.hpp | 55 - inst/include/armadillo_bits/injector_meat.hpp | 487 ++++----------- inst/include/armadillo_bits/memory.hpp | 3 inst/include/armadillo_bits/op_fft_meat.hpp | 14 inst/include/armadillo_bits/running_stat_vec_bones.hpp | 4 inst/include/armadillo_bits/sp_auxlib_bones.hpp | 40 + inst/include/armadillo_bits/sp_auxlib_meat.hpp | 266 +++++--- inst/include/armadillo_bits/spglue_merge_bones.hpp | 8 inst/include/armadillo_bits/spglue_minus_bones.hpp | 6 inst/include/armadillo_bits/spglue_plus_bones.hpp | 6 inst/include/armadillo_bits/spglue_schur_bones.hpp | 6 inst/include/armadillo_bits/spglue_times_bones.hpp | 2 inst/include/armadillo_bits/spop_sum_bones.hpp | 2 inst/include/armadillo_bits/spsolve_factoriser_bones.hpp |only inst/include/armadillo_bits/spsolve_factoriser_meat.hpp |only inst/include/armadillo_bits/translate_fftw3.hpp | 6 src/Makevars.in | 1 src/Makevars.win | 1 39 files changed, 683 insertions(+), 712 deletions(-)
Title: Convert R Models to PMML
Description: R wrapper for the JPMML-R library <https://github.com/jpmml/jpmml-r>,
which converts R models to Predictive Model Markup Language (PMML).
Author: Villu Ruusmann <villu.ruusmann@gmail.com>
Maintainer: Villu Ruusmann <villu.ruusmann@gmail.com>
Diff between r2pmml versions 0.26.0 dated 2021-03-19 and 0.27.1 dated 2023-04-05
r2pmml-0.26.0/r2pmml/inst/java/gson-2.8.6.jar |only r2pmml-0.26.0/r2pmml/inst/java/istack-commons-runtime-3.0.11.jar |only r2pmml-0.26.0/r2pmml/inst/java/jakarta.activation-1.2.2.jar |only r2pmml-0.26.0/r2pmml/inst/java/jakarta.xml.bind-api-2.3.3.jar |only r2pmml-0.26.0/r2pmml/inst/java/jaxb-runtime-2.3.3.jar |only r2pmml-0.26.0/r2pmml/inst/java/jpmml-converter-1.4.6.jar |only r2pmml-0.26.0/r2pmml/inst/java/jpmml-r-1.4.4.jar |only r2pmml-0.26.0/r2pmml/inst/java/jpmml-xgboost-1.5.0.jar |only r2pmml-0.26.0/r2pmml/inst/java/pmml-model-1.5.11.jar |only r2pmml-0.26.0/r2pmml/inst/java/pmml-model-metro-1.5.11.jar |only r2pmml-0.26.0/r2pmml/inst/java/slf4j-api-1.7.30.jar |only r2pmml-0.26.0/r2pmml/inst/java/slf4j-jdk14-1.7.30.jar |only r2pmml-0.26.0/r2pmml/java/jpmml-converter-1.4.6-sources.jar |only r2pmml-0.26.0/r2pmml/java/jpmml-r-1.4.4-sources.jar |only r2pmml-0.26.0/r2pmml/java/jpmml-xgboost-1.5.0-sources.jar |only r2pmml-0.26.0/r2pmml/man/decorate.elmNN.Rd |only r2pmml-0.27.1/r2pmml/DESCRIPTION | 12 - r2pmml-0.27.1/r2pmml/MD5 | 63 +++++----- r2pmml-0.27.1/r2pmml/NAMESPACE | 2 r2pmml-0.27.1/r2pmml/R/decoration.R | 6 r2pmml-0.27.1/r2pmml/R/r2pmml.R | 4 r2pmml-0.27.1/r2pmml/README.md | 11 - r2pmml-0.27.1/r2pmml/inst/java/gson-2.10.jar |only r2pmml-0.27.1/r2pmml/inst/java/guava-21.0-minified.jar |binary r2pmml-0.27.1/r2pmml/inst/java/istack-commons-runtime-4.0.1.jar |only r2pmml-0.27.1/r2pmml/inst/java/jackson-annotations-2.13.3.jar |only r2pmml-0.27.1/r2pmml/inst/java/jakarta.activation-2.0.1.jar |only r2pmml-0.27.1/r2pmml/inst/java/jakarta.xml.bind-api-3.0.1.jar |only r2pmml-0.27.1/r2pmml/inst/java/jaxb-core-3.0.2.jar |only r2pmml-0.27.1/r2pmml/inst/java/jaxb-runtime-3.0.2.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-converter-1.5.4.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-model-1.6.4.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-model-metro-1.6.4.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-rexp-1.5.2.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-rexp-xgboost-1.5.2.jar |only r2pmml-0.27.1/r2pmml/inst/java/pmml-xgboost-1.7.3.jar |only r2pmml-0.27.1/r2pmml/inst/java/r2pmml-1.0-SNAPSHOT.jar |only r2pmml-0.27.1/r2pmml/inst/java/slf4j-api-1.7.36.jar |only r2pmml-0.27.1/r2pmml/inst/java/slf4j-jdk14-1.7.36.jar |only r2pmml-0.27.1/r2pmml/inst/java/ubjson-0.1.8.jar |only r2pmml-0.27.1/r2pmml/inst/java/ubjson-gson-0.1.8.jar |only r2pmml-0.27.1/r2pmml/java/pmml-converter-1.5.4-sources.jar |only r2pmml-0.27.1/r2pmml/java/pmml-rexp-1.5.2-sources.jar |only r2pmml-0.27.1/r2pmml/java/pmml-rexp-xgboost-1.5.2-sources.jar |only r2pmml-0.27.1/r2pmml/java/pmml-xgboost-1.7.3-sources.jar |only r2pmml-0.27.1/r2pmml/man/decorate.default.Rd | 3 r2pmml-0.27.1/r2pmml/man/decorate.elm.Rd |only r2pmml-0.27.1/r2pmml/man/decorate.xgb.Booster.Rd | 13 +- r2pmml-0.27.1/r2pmml/man/r2pmml.Rd | 10 + r2pmml-0.27.1/r2pmml/man/verify.glm.Rd | 3 r2pmml-0.27.1/r2pmml/man/verify.train.Rd | 3 r2pmml-0.27.1/r2pmml/man/verify.xgb.Booster.Rd | 12 + 52 files changed, 82 insertions(+), 60 deletions(-)
Title: Plots for the Quantitative Analysis of Textual Data
Description: Plotting functions for visualising textual data. Extends 'quanteda' and
related packages with plot methods designed specifically for text data, textual statistics,
and models fit to textual data. Plot types include word clouds, lexical dispersion plots,
scaling plots, network visualisations, and word 'keyness' plots.
Author: Kenneth Benoit [cre, aut, cph]
,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
Ian Fellows [cph] ),
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textplots versions 0.94.2 dated 2022-09-01 and 0.94.3 dated 2023-04-05
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/textplot_network.R | 2 +- R/textplot_scale1d.R | 13 +++++++------ README.md | 26 +++++++++++++------------- man/textplot_scale1d.Rd | 13 +++++++------ src/Makevars | 1 - src/Makevars.win | 1 - tests/testthat.R | 2 +- tests/testthat/test-textplot_scale1d.R | 5 +++-- 10 files changed, 45 insertions(+), 44 deletions(-)
More information about quanteda.textplots at CRAN
Permanent link
Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the 'IDSL.IPA' peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [aut] ,
Dinesh Barupal [cre, aut]
Maintainer: Dinesh Barupal <dinesh.barupal@mssm.edu>
Diff between IDSL.UFAx versions 1.9 dated 2023-04-02 and 1.9.1 dated 2023-04-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/UFAx_workflow.R | 20 ++++++++++---------- man/UFAx_workflow.Rd | 1 - 4 files changed, 17 insertions(+), 18 deletions(-)
Title: Shiny App. Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <https:onlinelibrary.wiley.com/doi/abs/10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 2.0.9 dated 2022-09-16 and 2.0.10 dated 2023-04-05
DESCRIPTION | 10 MD5 | 222 NAMESPACE | 1 NEWS.md | 793 R/addAttributesDfChrSize.R | 553 R/addNotes.R | 327 R/armRatioCI.R | 141 R/arrowPlotMark.R | 99 R/asymmetry.R | 119 R/cMPlotMark.R | 108 R/checkArmHolocenError.R | 15 R/checkNameChrDfMarks.R | 138 R/chrbasicdataHolo.R | 2 R/citrusSize.R | 417 R/customCeiling.R | 7 R/dfToListColumn.R | 14 R/filterExtraOTU.R | 33 R/fixChrNameDupDF.R | 30 R/genBankReadIF.R | 332 R/insertInList.R | 20 R/make.uniqueIF.R | 28 R/makeNumCols.R | 29 R/makeVectorNames.R | 12 R/makedfMarkColor.R | 98 R/makedfMarkColorMycolors.R | 58 R/mapGGChr.R | 196 R/mapXY.R | 1129 R/mapXYCenMimic.R | 291 R/markDistCenGISHfix.R | 60 R/markdataholo.R | 4 R/markposDFs.R | 16 R/mimicCenPlotMark.R | 435 R/namesToColumns.R | 531 R/newOrderColumn.R | 25 R/onAttach.R | 3 R/orientation.R | 1673 - R/perMark.R | 188 R/plotDotMarks.R | 167 R/plotIdiograms.R |13839 +++++------ R/plotlabelsright.R | 222 R/posCalc.R | 1363 - R/removeNAFromList.R | 23 R/robert.R | 167 R/rulerPlot.R | 75 R/rulerTitle.R | 44 R/runBoard.R | 168 R/sqPlotMarkCP.R | 679 R/textLabel.R | 262 R/textLabelDots.R | 53 README.md | 904 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 28 inst/doc/AVignette.R | 8 inst/doc/AVignette.Rmd | 10 inst/doc/AVignette.html | 19 inst/doc/index.R | 572 inst/doc/index.Rmd | 558 inst/doc/index.html | 464 inst/shinyApps/iBoard/obser/obserColumnMod.R | 266 inst/shinyApps/iBoard/obser/obserDataframes.R | 686 inst/shinyApps/iBoard/obser/obserIndices.R | 24 inst/shinyApps/iBoard/obser/obserNuccore.R | 510 inst/shinyApps/iBoard/obser/obserPlot.R | 1324 - inst/shinyApps/iBoard/obser/obserPosButtons.R | 43 inst/shinyApps/iBoard/obser/obserPresets.R | 502 inst/shinyApps/iBoard/obser/obserSwap.R | 54 inst/shinyApps/iBoard/output/outputDataframes.R | 442 inst/shinyApps/iBoard/output/outputLogCode.R | 44 inst/shinyApps/iBoard/output/outputMenu.R | 28 inst/shinyApps/iBoard/output/outputNuccore.R | 457 inst/shinyApps/iBoard/output/outputPanels.R | 4866 +-- inst/shinyApps/iBoard/output/outputPlot.R | 858 inst/shinyApps/iBoard/output/outputTabs.R | 182 inst/shinyApps/iBoard/output/outputTabsetpanels.R | 89 inst/shinyApps/iBoard/presetVals.R | 314 inst/shinyApps/iBoard/reactiveV.R | 58 inst/shinyApps/iBoard/rsconnect |only inst/shinyApps/iBoard/server.R | 62 inst/shinyApps/iBoard/ui.R | 65 inst/shinyApps/iBoard/www/DESCRIPTION | 7 inst/shinyApps/iBoard/www/man/figures/cranmanualbookdown.svg | 2 inst/shinyApps/iBoard/www/man/figures/cranversion.svg | 6 inst/shinyApps/iBoard/www/paramValues.rds |binary man/armRatioCI.Rd | 2 man/arrowPlotMark.Rd | 3 man/asymmetry.Rd | 2 man/cMPlotMark.Rd | 5 man/citrusSize.Rd | 92 man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/circular.png |binary man/figures/cranmanualbookdown.svg | 2 man/figures/cranversion.svg | 6 man/figures/develmanualvignette.svg | 2 man/figures/gitbadge.svg | 2 man/figures/manual.svg | 2 man/figures/pkgdownver.svg | 2 man/make.uniqueIF.Rd | 2 man/namesToColumns.Rd | 3 man/perMark.Rd | 8 man/plotDotMarks.Rd | 3 man/plotIdiograms.Rd | 195 man/plotSqMarks.Rd | 3 man/posCalc.Rd | 15 man/robert.Rd | 2 vignettes/AVignette.Rmd | 10 vignettes/bigdfChrSizeHolo.png |only vignettes/bigdfChrSizeHolo2.png |only vignettes/climon.svg |only vignettes/dfOfChrSizeVector.png |only vignettes/firstplot.png |only vignettes/index.Rmd | 558 vignettes/monoholoCS.png |only vignettes/mydfChrSize2.png |only vignettes/secondplot.png |only vignettes/thirdplot.png |only 117 files changed, 20236 insertions(+), 19354 deletions(-)
Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal
Predictions
Description: Set of generalised tools for the flexible computation of climate
related indicators defined by the user. Each method represents a specific
mathematical approach which is combined with the possibility to select an
arbitrary time period to define the indicator. This enables a wide range of
possibilities to tailor the most suitable indicator for each particular climate
service application (agriculture, food security, energy, water management…).
This package is intended for sub-seasonal, seasonal and decadal climate
predictions, but its methods are also applicable to other time-scales,
provided the dimensional structure of the input is maintained. Additionally,
the outputs of the functions in this package are compatible with 'CSTools'.
This package was developed in the context of H2020 MED-GOLD (776467) and
S2S4E (776787) projects. Lledó et al. (2019) <doi:10.1016/j.renene.2019.04.135>.
Author: Eva Rifa [cre],
Nuria Perez-Zanon [aut] ,
Chou Chihchung [aut],
Llorenc Lledo [aut],
Gonzalez-Reviriego Nube [ctb],
Marcos Rauel [ctb],
Palma Lluis [ctb],
An-Chi Ho [ctb],
BSC-CNS [cph]
Maintainer: Eva Rifa <eva.rifarovira@bsc.es>
Diff between CSIndicators versions 0.0.2 dated 2022-10-22 and 1.0.0 dated 2023-04-05
CSIndicators-0.0.2/CSIndicators/vignettes/figures |only CSIndicators-1.0.0/CSIndicators/DESCRIPTION | 8 CSIndicators-1.0.0/CSIndicators/MD5 | 108 +- CSIndicators-1.0.0/CSIndicators/NEWS.md | 11 CSIndicators-1.0.0/CSIndicators/R/AbsToProbs.R | 121 +- CSIndicators-1.0.0/CSIndicators/R/AccumulationExceedingThreshold.R | 442 +++++++--- CSIndicators-1.0.0/CSIndicators/R/MergeRefToExp.R | 166 ++- CSIndicators-1.0.0/CSIndicators/R/PeriodAccumulation.R | 55 - CSIndicators-1.0.0/CSIndicators/R/PeriodMean.R | 40 CSIndicators-1.0.0/CSIndicators/R/QThreshold.R | 52 - CSIndicators-1.0.0/CSIndicators/R/SelectPeriodOnData.R | 89 +- CSIndicators-1.0.0/CSIndicators/R/SelectPeriodOnDates.R | 8 CSIndicators-1.0.0/CSIndicators/R/Threshold.R | 50 - CSIndicators-1.0.0/CSIndicators/R/TotalSpellTimeExceedingThreshold.R | 367 ++++++-- CSIndicators-1.0.0/CSIndicators/R/TotalTimeExceedingThreshold.R | 412 ++++++--- CSIndicators-1.0.0/CSIndicators/R/WindCapacityFactor.R | 88 + CSIndicators-1.0.0/CSIndicators/R/WindPowerDensity.R | 63 - CSIndicators-1.0.0/CSIndicators/R/zzz.R | 11 CSIndicators-1.0.0/CSIndicators/README.md | 76 + CSIndicators-1.0.0/CSIndicators/inst/doc/AgriculturalIndicators.Rmd | 51 - CSIndicators-1.0.0/CSIndicators/inst/doc/AgriculturalIndicators.html | 45 - CSIndicators-1.0.0/CSIndicators/inst/doc/EnergyIndicators.R | 4 CSIndicators-1.0.0/CSIndicators/inst/doc/EnergyIndicators.Rmd | 4 CSIndicators-1.0.0/CSIndicators/inst/doc/EnergyIndicators.html | 4 CSIndicators-1.0.0/CSIndicators/man/AbsToProbs.Rd | 21 CSIndicators-1.0.0/CSIndicators/man/AccumulationExceedingThreshold.Rd | 66 - CSIndicators-1.0.0/CSIndicators/man/CST_AbsToProbs.Rd | 16 CSIndicators-1.0.0/CSIndicators/man/CST_AccumulationExceedingThreshold.Rd | 57 - CSIndicators-1.0.0/CSIndicators/man/CST_MergeRefToExp.Rd | 4 CSIndicators-1.0.0/CSIndicators/man/CST_PeriodAccumulation.Rd | 16 CSIndicators-1.0.0/CSIndicators/man/CST_PeriodMean.Rd | 8 CSIndicators-1.0.0/CSIndicators/man/CST_QThreshold.Rd | 12 CSIndicators-1.0.0/CSIndicators/man/CST_SelectPeriodOnData.Rd | 14 CSIndicators-1.0.0/CSIndicators/man/CST_Threshold.Rd | 12 CSIndicators-1.0.0/CSIndicators/man/CST_TotalSpellTimeExceedingThreshold.Rd | 42 CSIndicators-1.0.0/CSIndicators/man/CST_TotalTimeExceedingThreshold.Rd | 61 - CSIndicators-1.0.0/CSIndicators/man/CST_WindCapacityFactor.Rd | 20 CSIndicators-1.0.0/CSIndicators/man/CST_WindPowerDensity.Rd | 17 CSIndicators-1.0.0/CSIndicators/man/MergeRefToExp.Rd | 10 CSIndicators-1.0.0/CSIndicators/man/SelectPeriodOnData.Rd | 33 CSIndicators-1.0.0/CSIndicators/man/SelectPeriodOnDates.Rd | 4 CSIndicators-1.0.0/CSIndicators/man/TotalSpellTimeExceedingThreshold.Rd | 35 CSIndicators-1.0.0/CSIndicators/man/TotalTimeExceedingThreshold.Rd | 56 - CSIndicators-1.0.0/CSIndicators/man/WindCapacityFactor.Rd | 5 CSIndicators-1.0.0/CSIndicators/vignettes/AgriculturalIndicators.Rmd | 51 - CSIndicators-1.0.0/CSIndicators/vignettes/EnergyIndicators.Rmd | 4 CSIndicators-1.0.0/CSIndicators/vignettes/Figures |only 47 files changed, 1782 insertions(+), 1057 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear
models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>)
with or without multilevel or additive terms (Catalina, Bürkner, and
Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for
some ordinal and nominal regression models (Weber and Vehtari, 2023,
<arXiv:2301.01660>), and for many other regression models (using the latent
projection by Catalina, Bürkner, and Vehtari, 2021, <arXiv:2109.04702>,
which can also be applied to most of the former models). The package is
compatible with the 'rstanarm' and 'brms' packages, but other reference
models can also be used. See the vignettes and the documentation for more
information and examples.
Author: Juho Piironen [aut],
Markus Paasiniemi [aut],
Alejandro Catalina [aut],
Frank Weber [cre, aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Marco Colombo [ctb],
Paul-Christian Buerkner [ctb],
Hamada S. Badr [ctb],
Brian Sullivan [ctb],
Soelvi Roegnvaldsson [c [...truncated...]
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between projpred versions 2.4.0 dated 2023-02-12 and 2.5.0 dated 2023-04-05
projpred-2.4.0/projpred/man/reexports.Rd |only projpred-2.5.0/projpred/DESCRIPTION | 22 projpred-2.5.0/projpred/MD5 | 117 +- projpred-2.5.0/projpred/NAMESPACE | 3 projpred-2.5.0/projpred/NEWS.md | 44 projpred-2.5.0/projpred/R/augdat.R | 24 projpred-2.5.0/projpred/R/cv_varsel.R | 501 ++++---- projpred-2.5.0/projpred/R/divergence_minimizers.R | 58 - projpred-2.5.0/projpred/R/extend_family.R | 44 projpred-2.5.0/projpred/R/formula.R | 103 - projpred-2.5.0/projpred/R/glmfun.R | 8 projpred-2.5.0/projpred/R/latent.R | 5 projpred-2.5.0/projpred/R/methods.R | 384 +++--- projpred-2.5.0/projpred/R/misc.R | 145 +- projpred-2.5.0/projpred/R/project.R | 65 - projpred-2.5.0/projpred/R/projfun.R | 95 - projpred-2.5.0/projpred/R/projpred-package.R | 12 projpred-2.5.0/projpred/R/refmodel.R | 193 +-- projpred-2.5.0/projpred/R/search.R | 110 + projpred-2.5.0/projpred/R/summary_funs.R | 168 +- projpred-2.5.0/projpred/R/varsel.R | 158 +- projpred-2.5.0/projpred/build/partial.rdb |binary projpred-2.5.0/projpred/build/vignette.rds |binary projpred-2.5.0/projpred/inst/doc/latent.R | 16 projpred-2.5.0/projpred/inst/doc/latent.Rmd | 29 projpred-2.5.0/projpred/inst/doc/latent.html | 403 +++---- projpred-2.5.0/projpred/inst/doc/projpred.R | 25 projpred-2.5.0/projpred/inst/doc/projpred.Rmd | 90 + projpred-2.5.0/projpred/inst/doc/projpred.html | 482 ++++---- projpred-2.5.0/projpred/man/extend_family.Rd | 2 projpred-2.5.0/projpred/man/plot.vsel.Rd | 20 projpred-2.5.0/projpred/man/pred-projection.Rd | 62 - projpred-2.5.0/projpred/man/predict.refmodel.Rd | 14 projpred-2.5.0/projpred/man/print.vsel.Rd | 4 projpred-2.5.0/projpred/man/print.vselsummary.Rd | 6 projpred-2.5.0/projpred/man/project.Rd | 20 projpred-2.5.0/projpred/man/projpred-package.Rd | 12 projpred-2.5.0/projpred/man/refmodel-init-get.Rd | 31 projpred-2.5.0/projpred/man/suggest_size.Rd | 37 projpred-2.5.0/projpred/man/summary.vsel.Rd | 22 projpred-2.5.0/projpred/tests/testthat/helpers/getters.R | 11 projpred-2.5.0/projpred/tests/testthat/helpers/testers.R | 629 +++++------ projpred-2.5.0/projpred/tests/testthat/helpers/unlist_cust.R | 2 projpred-2.5.0/projpred/tests/testthat/setup.R | 50 projpred-2.5.0/projpred/tests/testthat/test_as_matrix.R | 5 projpred-2.5.0/projpred/tests/testthat/test_augdat.R | 16 projpred-2.5.0/projpred/tests/testthat/test_datafit.R | 21 projpred-2.5.0/projpred/tests/testthat/test_div_minimizer.R | 34 projpred-2.5.0/projpred/tests/testthat/test_formula.R | 14 projpred-2.5.0/projpred/tests/testthat/test_glm_ridge.R | 9 projpred-2.5.0/projpred/tests/testthat/test_latent.R | 14 projpred-2.5.0/projpred/tests/testthat/test_methods_vsel.R | 6 projpred-2.5.0/projpred/tests/testthat/test_misc.R | 16 projpred-2.5.0/projpred/tests/testthat/test_proj_pred.R | 8 projpred-2.5.0/projpred/tests/testthat/test_project.R | 110 + projpred-2.5.0/projpred/tests/testthat/test_refmodel.R | 81 + projpred-2.5.0/projpred/tests/testthat/test_varsel.R | 137 +- projpred-2.5.0/projpred/vignettes/latent.Rmd | 29 projpred-2.5.0/projpred/vignettes/projpred.Rmd | 90 + projpred-2.5.0/projpred/vignettes/references.bib | 19 60 files changed, 2745 insertions(+), 2090 deletions(-)
Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with
spatial-temporal data together with corresponding functions and
methods (conversions, basic calculations and basic data manipulation).
The class distinguishes between spatial, temporal and other dimensions
to facilitate the development and interoperability of tools build for
it. Additional features are name-based addressing of data and internal
consistency checks (e.g. checking for the right data order in
calculations).
Author: Jan Philipp Dietrich [aut, cre],
Benjamin Leon Bodirsky [aut],
Markus Bonsch [aut],
Florian Humpenoeder [aut],
Stephen Bi [aut],
Kristine Karstens [aut],
Debbora Leip [aut],
Lavinia Baumstark [ctb],
Christoph Bertram [ctb],
Anastasis Giannousakis [ct [...truncated...]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between magclass versions 6.8.2 dated 2023-04-03 and 6.8.3 dated 2023-04-05
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- README.md | 6 +++--- inst/doc/magclass-concept.html | 4 ++-- inst/doc/magclass-expansion.html | 4 ++-- inst/doc/magclass.html | 4 ++-- inst/doc/magclass6.html | 4 ++-- tests/testthat/test-readwritemagpie.R | 2 +- 8 files changed, 24 insertions(+), 24 deletions(-)
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.20-45 dated 2021-09-22 and 0.21-8 dated 2023-04-05
lattice-0.20-45/lattice/NEWS |only lattice-0.21-8/lattice/ChangeLog | 173 ----- lattice-0.21-8/lattice/DESCRIPTION | 29 lattice-0.21-8/lattice/MD5 | 148 ++-- lattice-0.21-8/lattice/NAMESPACE | 14 lattice-0.21-8/lattice/NEWS.md |only lattice-0.21-8/lattice/R/axis.R | 330 +++++----- lattice-0.21-8/lattice/R/bwplot.R | 233 ++++--- lattice-0.21-8/lattice/R/cloud.R | 61 - lattice-0.21-8/lattice/R/densityplot.R | 42 - lattice-0.21-8/lattice/R/histogram.R | 41 - lattice-0.21-8/lattice/R/imports.R |only lattice-0.21-8/lattice/R/interaction.R | 4 lattice-0.21-8/lattice/R/layout.R | 25 lattice-0.21-8/lattice/R/legend.R | 61 + lattice-0.21-8/lattice/R/levelplot.R | 88 +- lattice-0.21-8/lattice/R/miscellaneous.R | 2 lattice-0.21-8/lattice/R/panel.smoothscatter.R | 11 lattice-0.21-8/lattice/R/panel.superpose.R | 4 lattice-0.21-8/lattice/R/parallel.R | 35 - lattice-0.21-8/lattice/R/qq.R | 6 lattice-0.21-8/lattice/R/qqmath.R | 33 - lattice-0.21-8/lattice/R/rfs.R | 26 lattice-0.21-8/lattice/R/settings.R | 159 ++++ lattice-0.21-8/lattice/R/shingle.R | 2 lattice-0.21-8/lattice/R/splom.R | 49 - lattice-0.21-8/lattice/R/tmd.R | 21 lattice-0.21-8/lattice/R/update.trellis.R | 57 + lattice-0.21-8/lattice/R/xyplot.R | 85 +- lattice-0.21-8/lattice/R/xyplot.ts.R | 24 lattice-0.21-8/lattice/build |only lattice-0.21-8/lattice/data/barley.rda |binary lattice-0.21-8/lattice/data/environmental.rda |binary lattice-0.21-8/lattice/data/ethanol.rda |binary lattice-0.21-8/lattice/data/melanoma.rda |binary lattice-0.21-8/lattice/data/singer.rda |binary lattice-0.21-8/lattice/inst/CITATION | 20 lattice-0.21-8/lattice/inst/doc |only lattice-0.21-8/lattice/inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary lattice-0.21-8/lattice/man/USMortality.Rd | 4 lattice-0.21-8/lattice/man/cloud.Rd | 2 lattice-0.21-8/lattice/man/ethanol.Rd | 4 lattice-0.21-8/lattice/man/foo |only lattice-0.21-8/lattice/man/histogram.Rd | 4 lattice-0.21-8/lattice/man/lattice.options.Rd | 24 lattice-0.21-8/lattice/man/latticeParseFormula.Rd | 5 lattice-0.21-8/lattice/man/level.colors.Rd | 2 lattice-0.21-8/lattice/man/levelplot.Rd | 4 lattice-0.21-8/lattice/man/panel.cloud.Rd | 50 + lattice-0.21-8/lattice/man/panel.densityplot.Rd | 43 - lattice-0.21-8/lattice/man/panel.dotplot.Rd | 16 lattice-0.21-8/lattice/man/panel.functions.Rd | 9 lattice-0.21-8/lattice/man/panel.levelplot.Rd | 29 lattice-0.21-8/lattice/man/panel.pairs.Rd | 4 lattice-0.21-8/lattice/man/panel.smoothScatter.Rd | 17 lattice-0.21-8/lattice/man/panel.stripplot.Rd | 14 lattice-0.21-8/lattice/man/panel.superpose.Rd | 3 lattice-0.21-8/lattice/man/panel.xyplot.Rd | 122 ++- lattice-0.21-8/lattice/man/qqmath.Rd | 2 lattice-0.21-8/lattice/man/singer.Rd | 12 lattice-0.21-8/lattice/man/splom.Rd | 4 lattice-0.21-8/lattice/man/standard.theme.Rd |only lattice-0.21-8/lattice/man/trellis.device.Rd | 73 -- lattice-0.21-8/lattice/man/trellis.par.get.Rd | 2 lattice-0.21-8/lattice/man/xyplot.Rd | 51 - lattice-0.21-8/lattice/po/R-de.po | 109 ++- lattice-0.21-8/lattice/po/R-fr.po | 150 +++- lattice-0.21-8/lattice/po/R-it.po | 31 lattice-0.21-8/lattice/po/R-ko.po | 141 +++- lattice-0.21-8/lattice/po/R-lattice.pot | 31 lattice-0.21-8/lattice/po/R-pl.po | 115 ++- lattice-0.21-8/lattice/tests/MASSch04.R | 2 lattice-0.21-8/lattice/tests/auto-key.R |only lattice-0.21-8/lattice/tests/barchart-width.R |only lattice-0.21-8/lattice/tests/call.R |only lattice-0.21-8/lattice/tests/fontsize.R | 14 lattice-0.21-8/lattice/tests/levelplot.R | 46 + lattice-0.21-8/lattice/tests/shade-wireframe.R |only lattice-0.21-8/lattice/tests/wireframe.R | 6 lattice-0.21-8/lattice/vignettes |only 80 files changed, 1714 insertions(+), 1214 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-16 1.5.2
2019-03-15 1.5.1
2018-05-07 1.5.0
2018-01-04 1.4.0
2017-09-07 1.3.0
2017-06-15 1.2.1
2017-06-13 1.2.0
2017-03-29 1.1.0
2017-02-17 1.0.0
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] ,
Albrecht Gebhardt [trl] ,
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-58.3 dated 2023-03-07 and 7.3-58.4 dated 2023-04-05
MASS-7.3-58.3/MASS/MD5 |only MASS-7.3-58.4/MASS/ChangeLog | 4 + MASS-7.3-58.4/MASS/DESCRIPTION | 8 +- MASS-7.3-58.4/MASS/build/partial.rdb |binary MASS-7.3-58.4/MASS/tests/Examples/MASS-Ex.Rout.save | 74 ++++---------------- 5 files changed, 25 insertions(+), 61 deletions(-)
Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut],
Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between TOSTER versions 0.6.0 dated 2022-12-13 and 0.7.1 dated 2023-04-05
TOSTER-0.6.0/TOSTER/tests/testthat/Rplots.pdf |only TOSTER-0.7.1/TOSTER/DESCRIPTION | 8 TOSTER-0.7.1/TOSTER/MD5 | 333 - TOSTER-0.7.1/TOSTER/NAMESPACE | 218 TOSTER-0.7.1/TOSTER/NEWS.md | 241 TOSTER-0.7.1/TOSTER/R/00jmv.R | 36 TOSTER-0.7.1/TOSTER/R/TOSTmeta.R | 230 TOSTER-0.7.1/TOSTER/R/TOSTone.R | 230 TOSTER-0.7.1/TOSTER/R/TOSTone.raw.R | 222 TOSTER-0.7.1/TOSTER/R/TOSTpaired.R | 258 TOSTER-0.7.1/TOSTER/R/TOSTpaired.raw.R | 232 TOSTER-0.7.1/TOSTER/R/TOSTr.R | 222 TOSTER-0.7.1/TOSTER/R/TOSTtwo.R | 314 - TOSTER-0.7.1/TOSTER/R/TOSTtwo.prop.R | 290 - TOSTER-0.7.1/TOSTER/R/TOSTtwo.raw.R | 300 - TOSTER-0.7.1/TOSTER/R/anova_summary.R | 470 - TOSTER-0.7.1/TOSTER/R/boot_compare_cor.R |only TOSTER-0.7.1/TOSTER/R/boot_compare_smd.R | 522 - TOSTER-0.7.1/TOSTER/R/boot_cor_test.R |only TOSTER-0.7.1/TOSTER/R/boot_log_TOST.R | 884 +-- TOSTER-0.7.1/TOSTER/R/boot_t_TOST.R | 978 +-- TOSTER-0.7.1/TOSTER/R/boot_t_test.R |only TOSTER-0.7.1/TOSTER/R/cohend_calcs.R | 1487 ++--- TOSTER-0.7.1/TOSTER/R/compare_cor.R | 232 TOSTER-0.7.1/TOSTER/R/compare_smd.R | 309 - TOSTER-0.7.1/TOSTER/R/compare_smd_functions.R | 76 TOSTER-0.7.1/TOSTER/R/cor_test.R |only TOSTER-0.7.1/TOSTER/R/corr_calcs.R | 352 - TOSTER-0.7.1/TOSTER/R/corsum_test.R |only TOSTER-0.7.1/TOSTER/R/data.R | 14 TOSTER-0.7.1/TOSTER/R/datatostone.b.R | 374 - TOSTER-0.7.1/TOSTER/R/datatostone.h.R | 992 +-- TOSTER-0.7.1/TOSTER/R/datatostpaired.b.R | 808 +- TOSTER-0.7.1/TOSTER/R/datatostpaired.h.R | 972 +-- TOSTER-0.7.1/TOSTER/R/datatostr.b.R | 382 - TOSTER-0.7.1/TOSTER/R/datatostr.h.R | 656 +- TOSTER-0.7.1/TOSTER/R/datatosttwo.b.R | 616 +- TOSTER-0.7.1/TOSTER/R/datatosttwo.h.R | 1152 ++-- TOSTER-0.7.1/TOSTER/R/datatosttwoprop.b.R | 248 TOSTER-0.7.1/TOSTER/R/datatosttwoprop.h.R | 714 +- TOSTER-0.7.1/TOSTER/R/equ_anova.R | 174 TOSTER-0.7.1/TOSTER/R/equ_ftest.R | 200 TOSTER-0.7.1/TOSTER/R/extract_r_paired.R | 73 TOSTER-0.7.1/TOSTER/R/gg_curv_t.R | 390 - TOSTER-0.7.1/TOSTER/R/globals.R | 10 TOSTER-0.7.1/TOSTER/R/htest.R | 263 TOSTER-0.7.1/TOSTER/R/htest_helpers.R |only TOSTER-0.7.1/TOSTER/R/jamovi_functions.R | 928 +-- TOSTER-0.7.1/TOSTER/R/log_TOST.R | 778 +- TOSTER-0.7.1/TOSTER/R/log_pair.R | 462 - TOSTER-0.7.1/TOSTER/R/methods.TOSTnp.R | 158 TOSTER-0.7.1/TOSTER/R/methods.TOSTt.R | 1439 +++-- TOSTER-0.7.1/TOSTER/R/others.R | 104 TOSTER-0.7.1/TOSTER/R/pes_calc.R | 440 - TOSTER-0.7.1/TOSTER/R/plot.R | 28 TOSTER-0.7.1/TOSTER/R/plot_corr.R | 75 TOSTER-0.7.1/TOSTER/R/plot_pes.R | 86 TOSTER-0.7.1/TOSTER/R/plot_scripts.R | 214 TOSTER-0.7.1/TOSTER/R/plot_smd.R | 126 TOSTER-0.7.1/TOSTER/R/powerTOSTanova.R | 112 TOSTER-0.7.1/TOSTER/R/powerTOSTone.R | 106 TOSTER-0.7.1/TOSTER/R/powerTOSTone.raw.R | 108 TOSTER-0.7.1/TOSTER/R/powerTOSTpaired.R | 102 TOSTER-0.7.1/TOSTER/R/powerTOSTpaired.raw.R | 120 TOSTER-0.7.1/TOSTER/R/powerTOSTr.R | 116 TOSTER-0.7.1/TOSTER/R/powerTOSTtwo.R | 102 TOSTER-0.7.1/TOSTER/R/powerTOSTtwo.prop.R | 142 TOSTER-0.7.1/TOSTER/R/powerTOSTtwo.raw.R | 120 TOSTER-0.7.1/TOSTER/R/power_TOST_functions.R | 596 +- TOSTER-0.7.1/TOSTER/R/power_t_TOST.R | 222 TOSTER-0.7.1/TOSTER/R/rbs.R | 376 - TOSTER-0.7.1/TOSTER/R/rbs_calcs.R | 230 TOSTER-0.7.1/TOSTER/R/ses_calc.R | 270 TOSTER-0.7.1/TOSTER/R/simple_htest.R |only TOSTER-0.7.1/TOSTER/R/smd_calc.R | 462 - TOSTER-0.7.1/TOSTER/R/t_TOST.R | 919 +-- TOSTER-0.7.1/TOSTER/R/tsum_TOST.R | 720 +- TOSTER-0.7.1/TOSTER/R/tsum_funcs.R | 240 TOSTER-0.7.1/TOSTER/R/wilcox_TOST.R | 653 +- TOSTER-0.7.1/TOSTER/README.md | 98 TOSTER-0.7.1/TOSTER/build/vignette.rds |binary TOSTER-0.7.1/TOSTER/inst/CITATION | 33 TOSTER-0.7.1/TOSTER/inst/doc/IntroTOSTt.R | 489 - TOSTER-0.7.1/TOSTER/inst/doc/IntroTOSTt.Rmd | 692 +- TOSTER-0.7.1/TOSTER/inst/doc/IntroTOSTt.html | 1639 +++--- TOSTER-0.7.1/TOSTER/inst/doc/IntroductionToTOSTER.R | 72 TOSTER-0.7.1/TOSTER/inst/doc/IntroductionToTOSTER.Rmd | 345 - TOSTER-0.7.1/TOSTER/inst/doc/IntroductionToTOSTER.html | 1833 +++--- TOSTER-0.7.1/TOSTER/inst/doc/SMD_calcs.R | 136 TOSTER-0.7.1/TOSTER/inst/doc/SMD_calcs.Rmd | 1377 ++--- TOSTER-0.7.1/TOSTER/inst/doc/SMD_calcs.html | 2323 ++++---- TOSTER-0.7.1/TOSTER/inst/doc/correlations.R |only TOSTER-0.7.1/TOSTER/inst/doc/correlations.Rmd |only TOSTER-0.7.1/TOSTER/inst/doc/correlations.html |only TOSTER-0.7.1/TOSTER/inst/doc/robustTOST.R | 140 TOSTER-0.7.1/TOSTER/inst/doc/robustTOST.Rmd | 529 - 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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 0.20.2 dated 2023-01-27 and 0.20.3 dated 2023-04-05
parameters-0.20.2/parameters/R/parameters-package.r |only parameters-0.20.2/parameters/tests/testthat/helper.R |only parameters-0.20.2/parameters/tests/testthat/test-printing-stan.r |only parameters-0.20.2/parameters/tests/testthat/test-printing.r |only parameters-0.20.2/parameters/tests/testthat/test-printing2.r |only parameters-0.20.3/parameters/DESCRIPTION | 42 parameters-0.20.3/parameters/MD5 | 452 ++-- parameters-0.20.3/parameters/NAMESPACE | 23 parameters-0.20.3/parameters/NEWS.md | 37 parameters-0.20.3/parameters/R/1_model_parameters.R | 26 parameters-0.20.3/parameters/R/2_ci.R | 2 parameters-0.20.3/parameters/R/3_p_value.R | 38 parameters-0.20.3/parameters/R/4_standard_error.R | 38 parameters-0.20.3/parameters/R/bootstrap_model.R | 67 parameters-0.20.3/parameters/R/ci_generic.R | 2 parameters-0.20.3/parameters/R/ci_profile_boot.R | 34 parameters-0.20.3/parameters/R/cluster_analysis.R | 32 parameters-0.20.3/parameters/R/cluster_centers.R | 8 parameters-0.20.3/parameters/R/cluster_meta.R | 2 parameters-0.20.3/parameters/R/compare_parameters.R | 20 parameters-0.20.3/parameters/R/dof.R | 28 parameters-0.20.3/parameters/R/dof_betwithin.R | 2 parameters-0.20.3/parameters/R/dof_ml1.R | 2 parameters-0.20.3/parameters/R/equivalence_test.R | 171 + parameters-0.20.3/parameters/R/extract_parameters.R | 34 parameters-0.20.3/parameters/R/extract_parameters_anova.R | 2 parameters-0.20.3/parameters/R/extract_random_variances.R | 25 parameters-0.20.3/parameters/R/factor_analysis.R | 2 parameters-0.20.3/parameters/R/format.R | 14 parameters-0.20.3/parameters/R/format_p_adjust.R | 6 parameters-0.20.3/parameters/R/format_parameters.R | 15 parameters-0.20.3/parameters/R/methods_BayesFM.R | 6 parameters-0.20.3/parameters/R/methods_BayesFactor.R | 28 parameters-0.20.3/parameters/R/methods_DirichletReg.R | 6 parameters-0.20.3/parameters/R/methods_aod.R | 6 parameters-0.20.3/parameters/R/methods_aov.R | 9 parameters-0.20.3/parameters/R/methods_averaging.R | 6 parameters-0.20.3/parameters/R/methods_base.R | 8 parameters-0.20.3/parameters/R/methods_betareg.R | 6 parameters-0.20.3/parameters/R/methods_bfsl.R | 6 parameters-0.20.3/parameters/R/methods_brglm2.R | 15 parameters-0.20.3/parameters/R/methods_car.R | 6 parameters-0.20.3/parameters/R/methods_cplm.R | 8 parameters-0.20.3/parameters/R/methods_emmeans.R | 6 parameters-0.20.3/parameters/R/methods_fixest.R | 158 + parameters-0.20.3/parameters/R/methods_ggeffects.R | 21 parameters-0.20.3/parameters/R/methods_gjrm.R | 8 parameters-0.20.3/parameters/R/methods_glmm.R | 4 parameters-0.20.3/parameters/R/methods_glmmTMB.R | 16 parameters-0.20.3/parameters/R/methods_glmx.R | 4 parameters-0.20.3/parameters/R/methods_hglm.R |only parameters-0.20.3/parameters/R/methods_htest.R | 2 parameters-0.20.3/parameters/R/methods_ivfixed.R | 4 parameters-0.20.3/parameters/R/methods_kmeans.R | 5 parameters-0.20.3/parameters/R/methods_lme4.R | 4 parameters-0.20.3/parameters/R/methods_lmodel2.R | 8 parameters-0.20.3/parameters/R/methods_marginaleffects.R | 26 parameters-0.20.3/parameters/R/methods_mclogit.R |only parameters-0.20.3/parameters/R/methods_merTools.R | 4 parameters-0.20.3/parameters/R/methods_metafor.R | 10 parameters-0.20.3/parameters/R/methods_metaplus.R | 22 parameters-0.20.3/parameters/R/methods_mfx.R | 10 parameters-0.20.3/parameters/R/methods_mhurdle.R | 4 parameters-0.20.3/parameters/R/methods_mice.R | 8 parameters-0.20.3/parameters/R/methods_mixor.R | 12 parameters-0.20.3/parameters/R/methods_mlm.R | 14 parameters-0.20.3/parameters/R/methods_multcomp.R | 4 parameters-0.20.3/parameters/R/methods_mvord.R | 14 parameters-0.20.3/parameters/R/methods_ordinal.R | 6 parameters-0.20.3/parameters/R/methods_panelr.R | 8 parameters-0.20.3/parameters/R/methods_phylolm.R |only parameters-0.20.3/parameters/R/methods_pscl.R | 4 parameters-0.20.3/parameters/R/methods_psych.R | 10 parameters-0.20.3/parameters/R/methods_quantreg.R | 7 parameters-0.20.3/parameters/R/methods_rstanarm.R | 4 parameters-0.20.3/parameters/R/methods_selection.R | 6 parameters-0.20.3/parameters/R/methods_sem.R | 2 parameters-0.20.3/parameters/R/methods_survey.R | 11 parameters-0.20.3/parameters/R/methods_systemfit.R | 4 parameters-0.20.3/parameters/R/n_clusters_easystats.R | 4 parameters-0.20.3/parameters/R/n_factors.R | 2 parameters-0.20.3/parameters/R/p_function.r | 15 parameters-0.20.3/parameters/R/p_value_kenward.R | 2 parameters-0.20.3/parameters/R/parameters-package.R |only parameters-0.20.3/parameters/R/parameters_type.R | 6 parameters-0.20.3/parameters/R/pool_parameters.R | 8 parameters-0.20.3/parameters/R/principal_components.R | 16 parameters-0.20.3/parameters/R/random_parameters.R | 10 parameters-0.20.3/parameters/R/reduce_parameters.R | 2 parameters-0.20.3/parameters/R/select_parameters.R | 4 parameters-0.20.3/parameters/R/standardize_info.R | 64 parameters-0.20.3/parameters/R/standardize_parameters.R | 85 parameters-0.20.3/parameters/R/standardize_posteriors.R | 4 parameters-0.20.3/parameters/R/utils.R | 10 parameters-0.20.3/parameters/R/utils_format.R | 35 parameters-0.20.3/parameters/R/utils_model_parameters.R | 52 parameters-0.20.3/parameters/R/utils_pca_efa.R | 10 parameters-0.20.3/parameters/build/partial.rdb |binary parameters-0.20.3/parameters/build/vignette.rds |binary parameters-0.20.3/parameters/inst/WORDLIST | 9 parameters-0.20.3/parameters/inst/doc/overview_of_vignettes.html | 14 parameters-0.20.3/parameters/man/cluster_analysis.Rd | 6 parameters-0.20.3/parameters/man/cluster_centers.Rd | 4 parameters-0.20.3/parameters/man/equivalence_test.lm.Rd | 48 parameters-0.20.3/parameters/man/model_parameters.Rd | 19 parameters-0.20.3/parameters/man/model_parameters.aov.Rd | 4 parameters-0.20.3/parameters/man/model_parameters.averaging.Rd | 138 + parameters-0.20.3/parameters/man/model_parameters.befa.Rd | 4 parameters-0.20.3/parameters/man/model_parameters.default.Rd | 22 parameters-0.20.3/parameters/man/model_parameters.htest.Rd | 36 parameters-0.20.3/parameters/man/model_parameters.merMod.Rd | 60 parameters-0.20.3/parameters/man/model_parameters.mira.Rd | 2 parameters-0.20.3/parameters/man/model_parameters.mlm.Rd | 47 parameters-0.20.3/parameters/man/model_parameters.principal.Rd | 10 parameters-0.20.3/parameters/man/model_parameters.rma.Rd | 29 parameters-0.20.3/parameters/man/model_parameters.stanreg.Rd | 4 parameters-0.20.3/parameters/man/model_parameters.zcpglm.Rd | 2 parameters-0.20.3/parameters/man/p_function.Rd | 31 parameters-0.20.3/parameters/man/principal_components.Rd | 12 parameters-0.20.3/parameters/man/standardize_info.Rd | 10 parameters-0.20.3/parameters/man/standardize_parameters.Rd | 25 parameters-0.20.3/parameters/tests/testthat.R | 43 parameters-0.20.3/parameters/tests/testthat/_snaps/compare_parameters.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/emmGrid-df_colname.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/equivalence_test.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/gam.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/glmer.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/glmmTMB-profile_CI.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/glmmTMB.md | 269 ++ parameters-0.20.3/parameters/tests/testthat/_snaps/ivreg.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/model_parameters.anova.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/model_parameters.fixest_multi.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/model_parameters.glm.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/model_parameters.mclogit.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/model_parameters.mixed.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/model_parameters_ordinal.md |only parameters-0.20.3/parameters/tests/testthat/_snaps/printing-stan.md | 26 parameters-0.20.3/parameters/tests/testthat/_snaps/printing.md | 25 parameters-0.20.3/parameters/tests/testthat/test-GLMMadaptive.R | 326 +-- parameters-0.20.3/parameters/tests/testthat/test-Hmisc.R | 20 parameters-0.20.3/parameters/tests/testthat/test-MCMCglmm.R | 103 - parameters-0.20.3/parameters/tests/testthat/test-PMCMRplus.R | 17 parameters-0.20.3/parameters/tests/testthat/test-backticks.R | 218 +- parameters-0.20.3/parameters/tests/testthat/test-betareg.R | 143 - parameters-0.20.3/parameters/tests/testthat/test-bootstrap_emmeans.R | 171 - parameters-0.20.3/parameters/tests/testthat/test-bracl.R | 82 parameters-0.20.3/parameters/tests/testthat/test-car.R | 69 parameters-0.20.3/parameters/tests/testthat/test-ci.R | 30 parameters-0.20.3/parameters/tests/testthat/test-cluster_analysis.R | 6 parameters-0.20.3/parameters/tests/testthat/test-compare_parameters.R | 65 parameters-0.20.3/parameters/tests/testthat/test-coxph.R | 97 - parameters-0.20.3/parameters/tests/testthat/test-dominance_analysis.R | 158 - parameters-0.20.3/parameters/tests/testthat/test-efa.R |only parameters-0.20.3/parameters/tests/testthat/test-emmGrid-df_colname.R | 92 parameters-0.20.3/parameters/tests/testthat/test-equivalence_test.R | 5 parameters-0.20.3/parameters/tests/testthat/test-estimatr.R | 8 parameters-0.20.3/parameters/tests/testthat/test-format.R | 8 parameters-0.20.3/parameters/tests/testthat/test-format_model_parameters.R | 349 +-- parameters-0.20.3/parameters/tests/testthat/test-format_model_parameters2.R |only parameters-0.20.3/parameters/tests/testthat/test-format_p_adjust.R | 4 parameters-0.20.3/parameters/tests/testthat/test-format_parameters.R | 726 +++---- parameters-0.20.3/parameters/tests/testthat/test-gam.R | 110 - parameters-0.20.3/parameters/tests/testthat/test-gamm.R | 127 - parameters-0.20.3/parameters/tests/testthat/test-gee.R | 69 parameters-0.20.3/parameters/tests/testthat/test-geeglm.R | 77 parameters-0.20.3/parameters/tests/testthat/test-get_scores.R | 21 parameters-0.20.3/parameters/tests/testthat/test-glmer.R | 186 - parameters-0.20.3/parameters/tests/testthat/test-glmmTMB-2.R | 111 - parameters-0.20.3/parameters/tests/testthat/test-glmmTMB-profile_CI.R |only parameters-0.20.3/parameters/tests/testthat/test-glmmTMB.R | 964 +++++----- parameters-0.20.3/parameters/tests/testthat/test-gls.R | 69 parameters-0.20.3/parameters/tests/testthat/test-ivreg.R | 104 - parameters-0.20.3/parameters/tests/testthat/test-lavaan.R | 92 parameters-0.20.3/parameters/tests/testthat/test-lme.R | 71 parameters-0.20.3/parameters/tests/testthat/test-lmerTest.R | 39 parameters-0.20.3/parameters/tests/testthat/test-marginaleffects.R | 57 parameters-0.20.3/parameters/tests/testthat/test-mira.R | 31 parameters-0.20.3/parameters/tests/testthat/test-mlm.R | 18 parameters-0.20.3/parameters/tests/testthat/test-mmrm.R | 161 - parameters-0.20.3/parameters/tests/testthat/test-model_parameters.BFBayesFactor.R | 286 +- parameters-0.20.3/parameters/tests/testthat/test-model_parameters.MASS.R | 27 parameters-0.20.3/parameters/tests/testthat/test-model_parameters.afex_aov.R | 43 parameters-0.20.3/parameters/tests/testthat/test-model_parameters.anova.R | 440 ++-- parameters-0.20.3/parameters/tests/testthat/test-model_parameters.aov.R | 175 - parameters-0.20.3/parameters/tests/testthat/test-model_parameters.aov_es_ci.R | 778 ++++---- parameters-0.20.3/parameters/tests/testthat/test-model_parameters.blmerMod.R | 54 parameters-0.20.3/parameters/tests/testthat/test-model_parameters.cgam.R | 313 +-- parameters-0.20.3/parameters/tests/testthat/test-model_parameters.cpglmm.R | 29 parameters-0.20.3/parameters/tests/testthat/test-model_parameters.efa_cfa.R | 131 - parameters-0.20.3/parameters/tests/testthat/test-model_parameters.fixest.R | 52 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parameters-0.20.3/parameters/tests/testthat/test-model_parameters.mfx.R | 119 - parameters-0.20.3/parameters/tests/testthat/test-model_parameters.mixed.R | 288 +- parameters-0.20.3/parameters/tests/testthat/test-model_parameters.mle2.R | 23 parameters-0.20.3/parameters/tests/testthat/test-model_parameters.truncreg.R | 25 parameters-0.20.3/parameters/tests/testthat/test-model_parameters.vgam.R | 81 parameters-0.20.3/parameters/tests/testthat/test-model_parameters_df.R | 661 +++--- parameters-0.20.3/parameters/tests/testthat/test-model_parameters_df_method.R | 381 +++ parameters-0.20.3/parameters/tests/testthat/test-model_parameters_labels.R | 233 +- parameters-0.20.3/parameters/tests/testthat/test-model_parameters_mixed_coeforder.R | 14 parameters-0.20.3/parameters/tests/testthat/test-model_parameters_ordinal.R | 154 - parameters-0.20.3/parameters/tests/testthat/test-model_parameters_random_pars.R | 262 +- parameters-0.20.3/parameters/tests/testthat/test-model_parameters_robust.R | 196 +- parameters-0.20.3/parameters/tests/testthat/test-model_parameters_std.R | 69 parameters-0.20.3/parameters/tests/testthat/test-model_parameters_std_mixed.R | 284 ++ parameters-0.20.3/parameters/tests/testthat/test-n_factors.R | 21 parameters-0.20.3/parameters/tests/testthat/test-p_adjust.R | 113 - parameters-0.20.3/parameters/tests/testthat/test-p_value.R | 143 - parameters-0.20.3/parameters/tests/testthat/test-panelr.R | 136 - parameters-0.20.3/parameters/tests/testthat/test-parameters_table.R | 52 parameters-0.20.3/parameters/tests/testthat/test-pca.R | 150 - parameters-0.20.3/parameters/tests/testthat/test-plm.R | 181 - parameters-0.20.3/parameters/tests/testthat/test-pool_parameters.R | 18 parameters-0.20.3/parameters/tests/testthat/test-posterior.R | 99 - parameters-0.20.3/parameters/tests/testthat/test-printing-stan.R |only parameters-0.20.3/parameters/tests/testthat/test-printing.R |only parameters-0.20.3/parameters/tests/testthat/test-printing2.R |only parameters-0.20.3/parameters/tests/testthat/test-quantreg.R | 122 - parameters-0.20.3/parameters/tests/testthat/test-random_effects_ci-glmmTMB.R | 515 ++--- parameters-0.20.3/parameters/tests/testthat/test-random_effects_ci.R | 664 +++--- parameters-0.20.3/parameters/tests/testthat/test-rank_deficienty.R | 4 parameters-0.20.3/parameters/tests/testthat/test-robust.R | 759 +++---- parameters-0.20.3/parameters/tests/testthat/test-rstanarm.R | 72 parameters-0.20.3/parameters/tests/testthat/test-simulate_model.R | 133 - parameters-0.20.3/parameters/tests/testthat/test-simulate_parameters.R | 98 - parameters-0.20.3/parameters/tests/testthat/test-standardize_info.R | 22 parameters-0.20.3/parameters/tests/testthat/test-standardize_parameters.R | 54 parameters-0.20.3/parameters/tests/testthat/test-svytable.R | 18 parameters-0.20.3/parameters/tests/testthat/test-tobit.R | 69 parameters-0.20.3/parameters/tests/testthat/test-wrs2.R | 89 parameters-0.20.3/parameters/tests/testthat/test-zeroinfl.R | 185 - 242 files changed, 9493 insertions(+), 8288 deletions(-)
Title: Eigenvalue CAR Models
Description: Fits Leroux model in spectral domain to estimate causal spatial effect as detailed in
Guan, Y; Page, G.L.; Reich, B.J.; Ventrucci, M.; Yang, S; (2020) <arXiv:2012.11767>.
Both the parametric and semi-parametric models are available. The semi-parametric model
relies on 'INLA'. The 'INLA' package can be obtained from <https://www.r-inla.org/>.
Author: Garritt L. Page [aut, cre],
Massimo Ventrucci [aut],
S. McKay Curtis [cph],
Radford M. Neal [cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between eCAR versions 0.1.1 dated 2021-05-14 and 0.1.2 dated 2023-04-05
DESCRIPTION | 6 MD5 | 16 +- R/par_eCAR.R | 47 ++++--- R/plot_eCAR.R | 2 R/semi_eCAR.R | 253 ++++++++++++++++++++++++++++++++++++++- man/par.eCAR.Leroux.Rd | 14 +- man/semipar.eCAR.Leroux.Rd | 2 src/init.c | 5 src/mcmcloop.eCAR.Leroux.Gauss.c | 34 ++--- 9 files changed, 327 insertions(+), 52 deletions(-)
Title: Bayesian State-Space Modeling of Mouse-Tracking Experiments via
Stan
Description: Estimates previously compiled state-space modeling for mouse-tracking experiments using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.
Author: Antonio Calcagnì, Massimiliano Pastore
Maintainer: Antonio Calcagnì <ant.calcagni@gmail.com>
Diff between ssMousetrack versions 1.1.5 dated 2019-01-16 and 1.1.6 dated 2023-04-05
ssMousetrack-1.1.5/ssMousetrack/cleanup |only ssMousetrack-1.1.5/ssMousetrack/cleanup.win |only ssMousetrack-1.1.5/ssMousetrack/inst/include/meta_header.hpp |only ssMousetrack-1.1.5/ssMousetrack/src/init.cpp |only ssMousetrack-1.1.5/ssMousetrack/src/stan_files |only ssMousetrack-1.1.5/ssMousetrack/tools |only ssMousetrack-1.1.6/ssMousetrack/DESCRIPTION | 16 - ssMousetrack-1.1.6/ssMousetrack/MD5 | 61 +++--- ssMousetrack-1.1.6/ssMousetrack/NAMESPACE | 1 ssMousetrack-1.1.6/ssMousetrack/NEWS | 21 +- ssMousetrack-1.1.6/ssMousetrack/R/ssMousetrack-package.R | 101 +++++----- ssMousetrack-1.1.6/ssMousetrack/R/stanmodels.R | 61 ++---- ssMousetrack-1.1.6/ssMousetrack/R/zzz.R | 11 - ssMousetrack-1.1.6/ssMousetrack/configure |only ssMousetrack-1.1.6/ssMousetrack/configure.win |only ssMousetrack-1.1.6/ssMousetrack/inst/include/stan_meta_header.hpp |only ssMousetrack-1.1.6/ssMousetrack/inst/stan |only ssMousetrack-1.1.6/ssMousetrack/man/congruency.Rd | 6 ssMousetrack-1.1.6/ssMousetrack/man/generate_data.Rd | 23 +- ssMousetrack-1.1.6/ssMousetrack/man/language.Rd | 6 ssMousetrack-1.1.6/ssMousetrack/man/prepare_data.Rd | 11 - ssMousetrack-1.1.6/ssMousetrack/man/run_ssm.Rd | 26 ++ ssMousetrack-1.1.6/ssMousetrack/man/ssMousetrack-package.Rd | 28 +- ssMousetrack-1.1.6/ssMousetrack/src/Makevars | 22 -- ssMousetrack-1.1.6/ssMousetrack/src/Makevars.win | 23 -- ssMousetrack-1.1.6/ssMousetrack/src/RcppExports.cpp |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_fit_model.cc |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_fit_model.h |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_fit_model_gomp.cc |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_fit_model_gomp.h |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_fit_model_log.cc |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_fit_model_log.h |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_simulate_data.cc |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_simulate_data.h |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_simulate_data_gomp.cc |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_simulate_data_gomp.h |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_simulate_data_log.cc |only ssMousetrack-1.1.6/ssMousetrack/src/stanExports_simulate_data_log.h |only 38 files changed, 224 insertions(+), 193 deletions(-)
Title: Secure in-Browser Storage for 'Shiny' Inputs, Outputs and
Variables
Description: Store persistent and synchronized data from 'Shiny' inputs within the browser in a secure format. Refresh 'Shiny' applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using 'Dexie.js' <https://dexie.org>, a minimal wrapper for 'IndexedDB'. Transfer browser link parameters to 'Shiny' input or output values.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between shinyStorePlus versions 0.9 dated 2023-02-15 and 1.1 dated 2023-04-05
DESCRIPTION | 13 +- MD5 | 25 ++--- NEWS.md | 11 +- R/includes.R | 2 R/seeex.R | 4 R/setup.R | 9 + README.md | 2 inst/doc/introduction_to_shinystoreplus.html | 128 ++++++++++++++------------- inst/doc/shinystoreplus_v08.html | 128 ++++++++++++++------------- inst/doc/using_shinystoreplus.html | 128 ++++++++++++++------------- inst/example/shinyWidgetsExamples |only inst/scripts/shinystoreplus.js | 2 man/seeexample.Rd | 6 - man/shinyStorePlus-package.Rd | 2 14 files changed, 246 insertions(+), 214 deletions(-)
More information about shinyStorePlus at CRAN
Permanent link
Title: Design Experiments for Batches
Description: Distributes samples in batches while making batches
homogeneous according to their description. Allows for an arbitrary
number of variables, both numeric and categorical. For quality control
it provides functions to subset a representative sample.
Author: Lluis Revilla Sancho [aut, cre]
,
Juanjo Lozano [ths] ,
Azucena Salas Martinez [ths]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between experDesign versions 0.1.0 dated 2021-04-22 and 0.2.0 dated 2023-04-05
DESCRIPTION | 41 LICENSE | 4 MD5 | 150 +- NAMESPACE | 64 - NEWS.md | 16 R/QC.R | 47 R/designer.R | 77 - R/entropy.R | 122 +- R/evaluate.R | 240 ++-- R/evaluate_category.R | 110 + R/evaluate_num.R | 6 R/experDesign-package.R | 30 R/follow_up.R |only R/indexing.R | 260 ++-- R/optimum.R | 8 R/reporting.R | 145 +- R/spatial.R | 34 R/utils.R | 71 + README.md | 157 +- build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 7 inst/doc/experdesign.R | 58 - inst/doc/experdesign.Rmd | 110 + inst/doc/experdesign.html | 1871 +++++++++++++++++++++++++++++---- man/batch_names.Rd | 52 man/check_data.Rd |only man/check_index.Rd | 66 - man/compare_index.Rd |only man/create_subset.Rd | 62 - man/design.Rd | 74 - man/distribution.Rd | 61 - man/entropy.Rd | 56 man/evaluate_entropy.Rd | 90 - man/evaluate_independence.Rd | 86 - man/evaluate_index.Rd | 80 - man/evaluate_mad.Rd | 88 - man/evaluate_mean.Rd | 86 - man/evaluate_na.Rd | 96 - man/evaluate_orig.Rd | 68 - man/evaluate_sd.Rd | 88 - man/experDesign-package.Rd | 42 man/extreme_cases.Rd | 68 - man/follow_up.Rd |only man/follow_up2.Rd |only man/inspect.Rd | 62 - man/optimum.Rd | 92 - man/qcSubset.Rd | 50 man/replicates.Rd | 76 - man/spatial.Rd | 92 - man/use_index.Rd | 44 man/valid_followup.Rd |only tests/README.md | 202 +-- tests/spelling.R | 4 tests/testthat.R | 8 tests/testthat/test-batch_names.R | 18 tests/testthat/test-check_data.R |only tests/testthat/test-compare_index.R |only tests/testthat/test-create_subset.R | 36 tests/testthat/test-design.R | 48 tests/testthat/test-distribution.R | 21 tests/testthat/test-entropy.R | 24 tests/testthat/test-evaluate_entropy.R | 19 tests/testthat/test-evaluate_helper.R | 30 tests/testthat/test-evaluate_index.R | 26 tests/testthat/test-evaluate_mad.R | 18 tests/testthat/test-evaluate_mean.R | 18 tests/testthat/test-evaluate_na.R | 20 tests/testthat/test-evaluate_orig.R | 32 tests/testthat/test-evaluate_sd.R | 18 tests/testthat/test-extreme_cases.R | 40 tests/testthat/test-follow_up.R |only tests/testthat/test-indexing.R | 16 tests/testthat/test-insert.R | 26 tests/testthat/test-inspect.R | 58 - tests/testthat/test-optimum.R | 3 tests/testthat/test-qc.R | 26 tests/testthat/test-replicates.R | 16 tests/testthat/test-simplify2matrix.R | 11 tests/testthat/test-spatial.R | 52 vignettes/experdesign.Rmd | 110 + 81 files changed, 4062 insertions(+), 2045 deletions(-)
Title: Synthesizing Causal Evidence in a Distributed Research Network
Description: Routines for combining causal effect estimates and study diagnostics across multiple data sites in a distributed study, without sharing patient-level data.
Allows for normal and non-normal approximations of the data-site likelihood of the effect parameter.
Author: Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EvidenceSynthesis versions 0.4.0 dated 2023-01-11 and 0.4.1 dated 2023-04-05
EvidenceSynthesis-0.4.0/EvidenceSynthesis/tests/testthat/Rplots.pdf |only EvidenceSynthesis-0.4.1/EvidenceSynthesis/DESCRIPTION | 8 +++--- EvidenceSynthesis-0.4.1/EvidenceSynthesis/MD5 | 13 ++++++---- EvidenceSynthesis-0.4.1/EvidenceSynthesis/NEWS.md | 8 ++++++ EvidenceSynthesis-0.4.1/EvidenceSynthesis/build/vignette.rds |binary EvidenceSynthesis-0.4.1/EvidenceSynthesis/inst/doc/NonNormalEffectSynthesis.pdf |binary EvidenceSynthesis-0.4.1/EvidenceSynthesis/inst/doc/VideoVignette.R |only EvidenceSynthesis-0.4.1/EvidenceSynthesis/inst/doc/VideoVignette.Rmd |only EvidenceSynthesis-0.4.1/EvidenceSynthesis/inst/doc/VideoVignette.pdf |only EvidenceSynthesis-0.4.1/EvidenceSynthesis/vignettes/VideoVignette.Rmd |only 10 files changed, 20 insertions(+), 9 deletions(-)
More information about EvidenceSynthesis at CRAN
Permanent link
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Jianxiao Yang [aut],
Eric Kawaguchi [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] ,
Ru [...truncated...]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 3.2.1 dated 2022-08-10 and 3.3.0 dated 2023-04-05
Cyclops-3.2.1/Cyclops/src/Makevars |only Cyclops-3.2.1/Cyclops/src/Makevars.win |only Cyclops-3.3.0/Cyclops/DESCRIPTION | 7 + Cyclops-3.3.0/Cyclops/MD5 | 38 +++++----- Cyclops-3.3.0/Cyclops/NEWS.md | 9 +- Cyclops-3.3.0/Cyclops/R/Survfit.R | 6 + Cyclops-3.3.0/Cyclops/README.md | 4 - Cyclops-3.3.0/Cyclops/cleanup |only Cyclops-3.3.0/Cyclops/configure |only Cyclops-3.3.0/Cyclops/configure.win |only Cyclops-3.3.0/Cyclops/inst/CITATION | 10 +- Cyclops-3.3.0/Cyclops/man/survfit.cyclopsFit.Rd | 6 + Cyclops-3.3.0/Cyclops/src/Makevars.in |only Cyclops-3.3.0/Cyclops/src/Makevars.win.in |only Cyclops-3.3.0/Cyclops/src/RcppCyclopsInterface.cpp | 6 - Cyclops-3.3.0/Cyclops/src/RcppModelData.cpp | 2 Cyclops-3.3.0/Cyclops/src/cyclops/CyclicCoordinateDescent.h | 2 Cyclops-3.3.0/Cyclops/src/cyclops/Types.h | 18 ++-- Cyclops-3.3.0/Cyclops/src/cyclops/drivers/HierarchyGridSearchCrossValidationDriver.cpp | 6 - Cyclops-3.3.0/Cyclops/tests/testthat/test-dataConversionStratified.R | 3 Cyclops-3.3.0/Cyclops/tests/testthat/test-dataConversionUnstratified.R | 3 Cyclops-3.3.0/Cyclops/tests/testthat/test-predict.R | 4 - Cyclops-3.3.0/Cyclops/tests/testthat/test-smallFineGray.R | 2 Cyclops-3.3.0/Cyclops/tools |only 24 files changed, 63 insertions(+), 63 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 2.0.59 dated 2023-03-28 and 2.0.60 dated 2023-04-05
DESCRIPTION | 14 ++-- MD5 | 20 ++--- NEWS | 11 ++- inst/doc/epiR_descriptive.R | 51 +++++++------- inst/doc/epiR_descriptive.Rmd | 53 +++++++-------- inst/doc/epiR_descriptive.html | 99 ++++++++++++++--------------- inst/doc/epiR_measures_of_association.html | 44 ++++++------ inst/doc/epiR_sample_size.html | 4 - inst/doc/epiR_surveillance.html | 54 +++++++-------- man/epi.realrisk.Rd | 2 vignettes/epiR_descriptive.Rmd | 53 +++++++-------- 11 files changed, 204 insertions(+), 201 deletions(-)
Title: Utilities for Dates and Times
Description: Utilities for handling dates and times, such
as selecting particular days of the week or month,
formatting timestamps as required by RSS feeds, or
converting timestamp representations of other software
(such as 'MATLAB' and 'Excel') to R. The package is
lightweight (no dependencies, pure R implementations) and
relies only on R's standard classes to represent dates
and times ('Date' and 'POSIXt'); it aims to provide
efficient implementations, through vectorisation and the
use of R's native numeric representations of timestamps
where possible.
Author: Enrico Schumann [aut, cre] ,
Unicode, Inc. [dtc, cph]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between datetimeutils versions 0.6-0 dated 2023-04-01 and 0.6-1 dated 2023-04-05
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 5 +++++ README.md | 22 ++++++++++++++++------ build/partial.rdb |binary inst/doc/datetimeutils_examples.pdf |binary inst/tinytest/test.R | 14 +++++++++----- man/convertTZ.Rd | 4 ++-- man/datetimeutils-package.Rd | 2 +- man/end_of_period.Rd | 8 ++++---- man/lastWeekday.Rd | 10 +++++----- man/nth_day.Rd | 12 ++++++------ man/roundPOSIXt.Rd | 8 ++++---- man/timegrid.Rd | 6 +++--- tests/tinytest.R | 4 +++- 15 files changed, 76 insertions(+), 55 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.9.6 dated 2023-03-06 and 0.9.7 dated 2023-04-05
sasLM-0.9.6/sasLM/inst/doc/Report-Different-Simplest2302091426.pdf |only sasLM-0.9.6/sasLM/inst/doc/Report-NOT-OKs2302091426.pdf |only sasLM-0.9.6/sasLM/inst/doc/Validation-Report-GLM-2302091427.pdf |only sasLM-0.9.7/sasLM/DESCRIPTION | 6 sasLM-0.9.7/sasLM/MD5 | 71 +- sasLM-0.9.7/sasLM/R/Kurtosis.R | 2 sasLM-0.9.7/sasLM/R/LIbin.R |only sasLM-0.9.7/sasLM/R/LInorm.R |only sasLM-0.9.7/sasLM/R/LIpois.R |only sasLM-0.9.7/sasLM/R/ORmn.R | 46 - sasLM-0.9.7/sasLM/R/ORmn1.R | 52 +- sasLM-0.9.7/sasLM/R/RD.R | 1 sasLM-0.9.7/sasLM/R/RDLI.R |only sasLM-0.9.7/sasLM/R/RDinv.R | 7 sasLM-0.9.7/sasLM/R/RDmn.R | 55 +- sasLM-0.9.7/sasLM/R/RDmn1.R | 33 - sasLM-0.9.7/sasLM/R/RR.R | 1 sasLM-0.9.7/sasLM/R/RRinv.R | 2 sasLM-0.9.7/sasLM/R/RRmn.R | 32 - sasLM-0.9.7/sasLM/R/RRmn1.R | 64 ++ sasLM-0.9.7/sasLM/R/ScoreCI.R | 2 sasLM-0.9.7/sasLM/R/sysdata.rda |binary sasLM-0.9.7/sasLM/inst/NEWS.Rd | 10 sasLM-0.9.7/sasLM/inst/doc/Report-Different-Simplest2303161228.pdf |only sasLM-0.9.7/sasLM/inst/doc/Report-NOT-OKs2303161229.pdf |only sasLM-0.9.7/sasLM/inst/doc/Validation-Report-GLM-2303161229.pdf |only sasLM-0.9.7/sasLM/inst/doc/sasLM-manual.pdf |binary sasLM-0.9.7/sasLM/man/LIbin.Rd |only sasLM-0.9.7/sasLM/man/LInorm.Rd |only sasLM-0.9.7/sasLM/man/LIpois.Rd |only sasLM-0.9.7/sasLM/man/ORcmh.Rd | 2 sasLM-0.9.7/sasLM/man/ORinv.Rd | 6 sasLM-0.9.7/sasLM/man/ORmn.Rd | 2 sasLM-0.9.7/sasLM/man/ORmn1.Rd | 4 sasLM-0.9.7/sasLM/man/RDLI.Rd |only sasLM-0.9.7/sasLM/man/RDinv.Rd | 5 sasLM-0.9.7/sasLM/man/RDmn.Rd | 6 sasLM-0.9.7/sasLM/man/RDmn1.Rd | 8 sasLM-0.9.7/sasLM/man/RRinv.Rd | 5 sasLM-0.9.7/sasLM/man/RRmn.Rd | 2 sasLM-0.9.7/sasLM/man/RRmn1.Rd | 6 sasLM-0.9.7/sasLM/man/ScoreCI.Rd | 10 sasLM-0.9.7/sasLM/man/aspirinCHD.Rd |only sasLM-0.9.7/sasLM/tests/Test.R | 238 ++++++++++ 44 files changed, 490 insertions(+), 188 deletions(-)
Title: Robust Statistics: Theory and Methods
Description: Companion package for the book: "Robust Statistics: Theory and Methods, second edition", <http://www.wiley.com/go/maronna/robust>. This package contains code that implements the robust estimators discussed in the recent second edition of the book above, as well as the scripts reproducing all the examples in the book.
Author: Matias Salibian-Barrera [cre],
Victor Yohai [aut],
Ricardo Maronna [aut],
Doug Martin [aut],
Gregory Brownson [aut] ,
Kjell Konis [aut],
Kjell Konis [cph] ,
Christophe Croux [ctb] ,
Gentiane Haesbroeck [ctb] ,
Martin Maechler [cph] ,
Manuel Koller [c [...truncated...]
Maintainer: Matias Salibian-Barrera <matias@stat.ubc.ca>
Diff between RobStatTM versions 1.0.5 dated 2022-04-18 and 1.0.7 dated 2023-04-05
DESCRIPTION | 12 MD5 | 42 +-- NAMESPACE | 2 NEWS.md | 9 R/DCML.R | 8 R/MLocDis.R | 30 +- R/RFPE.R | 8 R/lmrob.MM.R | 203 ++++++++++------ R/lmrobdet.R | 111 ++++++-- R/psiFunUtils.R | 163 ++++++++++++ R/psiFuns.R | 86 ++++++ R/utils.R | 4 build/vignette.rds |binary inst/doc/OptimalBiasRobustRegressionPsiandRho.pdf |only inst/doc/OptimalBiasRobustRegressionPsiandRho.pdf.asis |only inst/doc/PolynomialOptandmOptRhoFunctions.pdf |only inst/doc/PolynomialOptandmOptRhoFunctions.pdf.asis |only man/lmrobdet.control.Rd | 40 ++- man/lmrobdetMM.RFPE.Rd | 2 man/lmrobdetMM.Rd | 29 ++ man/moptv0.Rd |only man/optv0.Rd |only man/refine.sm.Rd | 7 src/lmrob.c | 156 +++++++++--- vignettes/OptimalBiasRobustRegressionPsiandRho.pdf.asis |only vignettes/PolynomialOptandmOptRhoFunctions.pdf.asis |only 26 files changed, 712 insertions(+), 200 deletions(-)
Title: Score Optimal Probabilistic Forecast Reconciliation
Description: Training of reconciliation weights for probabilistic forecasts to optimise total energy (or variogram) score using Stochastic Gradient Descent with automatically differentiated gradients. See Panagiotelis, Gamakumara, Athanasopoulos and Hyndman, (2020) <https://www.monash.edu/business/ebs/research/publications/ebs/wp26-2020.pdf> for a description of the methods.
Author: Anastasios Panagiotelis [aut, cre]
Maintainer: Anastasios Panagiotelis <anastasios.panagiotelis@sydney.edu.au>
Diff between ProbReco versions 0.1.0.1 dated 2020-09-24 and 0.1.2 dated 2023-04-05
DESCRIPTION | 16 - MD5 | 32 +-- NAMESPACE | 4 R/RcppExports.R | 2 R/scoreopt_functions.R | 176 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ProbReco-with-fable.html | 358 +++++++++++++++++++------------------- inst/doc/ProbReco.html | 225 +++++++++++++---------- man/ProbReco-package.Rd | 2 man/inscoreopt.Rd | 11 - man/scoreopt.Rd | 5 man/scoreopt.control.Rd | 4 man/total_score.Rd | 4 src/Makevars | 14 + src/Makevars.win | 14 + src/RcppExports.cpp | 5 17 files changed, 482 insertions(+), 390 deletions(-)
Title: A Bayesian Tool for Fast and Flexible Estimation of the
Reproduction Number
Description: Estimation of the instantaneous reproduction number with
Laplacian-P-splines following the methodology of Gressani et al. (2022)
<doi:10.1371/journal.pcbi.1010618>. The negative binomial
distribution is used to model the time series of incidence data. Two methods are
available for inference : (1) a sampling-free approach based on a maximum a
posteriori calibration of the hyperparameter vector and (2) a fully stochastic
approach with a Metropolis-adjusted Langevin algorithm for
efficient sampling of the posterior distribution.
Author: Oswaldo Gressani [aut, cre]
Maintainer: Oswaldo Gressani <oswaldo_gressani@hotmail.fr>
Diff between EpiLPS versions 1.0.7 dated 2023-01-18 and 1.1.0 dated 2023-04-05
EpiLPS-1.0.7/EpiLPS/R/S3_epilps_plot.R |only EpiLPS-1.0.7/EpiLPS/R/perfcheck.R |only EpiLPS-1.0.7/EpiLPS/man/epilps.Rd |only EpiLPS-1.0.7/EpiLPS/man/perfcheck.Rd |only EpiLPS-1.0.7/EpiLPS/man/plot.epilps.Rd |only EpiLPS-1.0.7/EpiLPS/src/Laplace.cpp |only EpiLPS-1.0.7/EpiLPS/src/cubicBspline.cpp |only EpiLPS-1.1.0/EpiLPS/DESCRIPTION | 18 EpiLPS-1.1.0/EpiLPS/MD5 | 87 ++- EpiLPS-1.1.0/EpiLPS/NAMESPACE | 11 EpiLPS-1.1.0/EpiLPS/NEWS.md | 13 EpiLPS-1.1.0/EpiLPS/R/Idist.R |only EpiLPS-1.1.0/EpiLPS/R/KerCori.R |only EpiLPS-1.1.0/EpiLPS/R/KerDateTicker.R |only EpiLPS-1.1.0/EpiLPS/R/KerIncidCheck.R |only EpiLPS-1.1.0/EpiLPS/R/KerLikelihood.R |only EpiLPS-1.1.0/EpiLPS/R/KerMCMC.R |only EpiLPS-1.1.0/EpiLPS/R/KerPtheta.R |only EpiLPS-1.1.0/EpiLPS/R/KerWT.R |only EpiLPS-1.1.0/EpiLPS/R/RcppExports.R | 24 EpiLPS-1.1.0/EpiLPS/R/Rmodelpriors.R |only EpiLPS-1.1.0/EpiLPS/R/S3_Idist_plot.R |only EpiLPS-1.1.0/EpiLPS/R/S3_Rt_plot.R |only EpiLPS-1.1.0/EpiLPS/R/S3_Rt_summary.R |only EpiLPS-1.1.0/EpiLPS/R/epicurve.R | 165 ++---- EpiLPS-1.1.0/EpiLPS/R/epilps.R | 38 - EpiLPS-1.1.0/EpiLPS/R/episim.R | 43 - EpiLPS-1.1.0/EpiLPS/R/estimR.R |only EpiLPS-1.1.0/EpiLPS/R/estimRmcmc.R |only EpiLPS-1.1.0/EpiLPS/R/influenza2009.R |only EpiLPS-1.1.0/EpiLPS/R/perfRestim.R |only EpiLPS-1.1.0/EpiLPS/R/sars2003.R |only EpiLPS-1.1.0/EpiLPS/R/zika2015.R |only EpiLPS-1.1.0/EpiLPS/README.md | 372 +------------- EpiLPS-1.1.0/EpiLPS/build/vignette.rds |binary EpiLPS-1.1.0/EpiLPS/data |only EpiLPS-1.1.0/EpiLPS/inst/CITATION | 15 EpiLPS-1.1.0/EpiLPS/inst/COPYRIGHTS | 6 EpiLPS-1.1.0/EpiLPS/inst/doc/EpiLPS-vignette.R | 148 +++++ EpiLPS-1.1.0/EpiLPS/inst/doc/EpiLPS-vignette.Rmd | 281 ++++++++++ EpiLPS-1.1.0/EpiLPS/inst/doc/EpiLPS-vignette.html | 566 +++++++++++++++++++++- EpiLPS-1.1.0/EpiLPS/man/Idist.Rd |only EpiLPS-1.1.0/EpiLPS/man/Rmodelpriors.Rd |only EpiLPS-1.1.0/EpiLPS/man/epicurve.Rd | 42 - EpiLPS-1.1.0/EpiLPS/man/episim.Rd | 21 EpiLPS-1.1.0/EpiLPS/man/estimR.Rd |only EpiLPS-1.1.0/EpiLPS/man/estimRmcmc.Rd |only EpiLPS-1.1.0/EpiLPS/man/influenza2009.Rd |only EpiLPS-1.1.0/EpiLPS/man/perfRestim.Rd |only EpiLPS-1.1.0/EpiLPS/man/plot.Idist.Rd |only EpiLPS-1.1.0/EpiLPS/man/plot.Rt.Rd |only EpiLPS-1.1.0/EpiLPS/man/sars2003.Rd |only EpiLPS-1.1.0/EpiLPS/man/summary.Rt.Rd |only EpiLPS-1.1.0/EpiLPS/man/zika2015.Rd |only EpiLPS-1.1.0/EpiLPS/src/KerLaplace.cpp |only EpiLPS-1.1.0/EpiLPS/src/KerMVN.cpp |only EpiLPS-1.1.0/EpiLPS/src/KerRpostmap.cpp |only EpiLPS-1.1.0/EpiLPS/src/KerRpostmcmc.cpp |only EpiLPS-1.1.0/EpiLPS/src/KercubicBspline.cpp |only EpiLPS-1.1.0/EpiLPS/src/Kerhyperoptim.cpp |only EpiLPS-1.1.0/EpiLPS/src/Makevars | 1 EpiLPS-1.1.0/EpiLPS/src/Makevars.win | 1 EpiLPS-1.1.0/EpiLPS/src/RcppExports.cpp | 80 ++- EpiLPS-1.1.0/EpiLPS/vignettes/EpiLPS-Arch.png |only EpiLPS-1.1.0/EpiLPS/vignettes/EpiLPS-Chart.jpg |only EpiLPS-1.1.0/EpiLPS/vignettes/EpiLPS-vignette.Rmd | 281 ++++++++++ 66 files changed, 1627 insertions(+), 586 deletions(-)
Title: Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
Description: Contains various routines for drawing
ellipses and ellipse-like confidence regions, implementing the plots
described in Murdoch and Chow (1996, <doi:10.2307/2684435>). There are
also routines implementing the profile plots described in Bates and
Watts (1988, <doi:10.1002/9780470316757>).
Author: Duncan Murdoch and E. D. Chow
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between ellipse versions 0.4.4 dated 2023-03-29 and 0.4.5 dated 2023-04-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 34 +++++++++++++++++++--------------- R/ellipse.default.R | 6 +++--- 4 files changed, 28 insertions(+), 24 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Estimation of survival functions via copula-graphic (CG) estimators is also implemented, which is useful for
sensitivity analyses under dependent censoring (Yeh et al 2023) <DOI:10.3390/biomedicines11030797>.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.27 dated 2023-02-13 and 3.28 dated 2023-04-05
DESCRIPTION | 12 +++++++----- MD5 | 14 +++++++------- R/CG.Gumbel.R | 2 ++ man/CG.Clayton.Rd | 27 +++++++++++++++------------ man/CG.Frank.Rd | 25 ++++++++++++++----------- man/CG.Gumbel.Rd | 7 +++++-- man/CG.test.Rd | 7 +++++-- man/compound.Cox-package.Rd | 9 +++++++-- 8 files changed, 62 insertions(+), 41 deletions(-)
Title: Statistical Methods for Life Data Analysis
Description: Provides statistical methods and visualizations that are often
used in reliability engineering. Comprises a compact and easily
accessible set of methods and visualization tools that make the
examination and adjustment as well as the analysis and interpretation
of field data (and bench tests) as simple as possible.
Non-parametric estimators like Median Ranks,
Kaplan-Meier (Abernethy, 2006, <ISBN:978-0-9653062-3-2>),
Johnson (Johnson, 1964, <ISBN:978-0444403223>), and Nelson-Aalen
for failure probability estimation within samples that contain
failures as well as censored data are included.
The package supports methods like Maximum Likelihood and Rank Regression,
(Genschel and Meeker, 2010, <DOI:10.1080/08982112.2010.503447>)
for the estimation of multiple parametric lifetime distributions,
as well as the computation of confidence intervals of quantiles and
probabilities using the delta method related to Fisher's confidence
intervals (Meeker and Escobar, 1998, <ISBN:9 [...truncated...]
Author: Tim-Gunnar Hensel [aut, cre],
David Barkemeyer [aut]
Maintainer: Tim-Gunnar Hensel <tim-gunnar.hensel@tu-berlin.de>
Diff between weibulltools versions 2.0.0 dated 2021-01-12 and 2.1.0 dated 2023-04-05
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weibulltools-2.1.0/weibulltools/R/plot_functions_plotly.R | 299 +- weibulltools-2.1.0/weibulltools/R/plot_helpers.R | 306 +- weibulltools-2.1.0/weibulltools/R/predict.R | 168 - weibulltools-2.1.0/weibulltools/R/probability_estimators.R | 327 +- weibulltools-2.1.0/weibulltools/R/r_squared_function.R |only weibulltools-2.1.0/weibulltools/R/rank_regression.R | 696 +----- weibulltools-2.1.0/weibulltools/R/rank_regression_helpers.R |only weibulltools-2.1.0/weibulltools/R/reliability_data.R | 75 weibulltools-2.1.0/weibulltools/R/utils.R |only weibulltools-2.1.0/weibulltools/R/utils_parametric_models.R |only weibulltools-2.1.0/weibulltools/R/weibulltools-package.R | 1 weibulltools-2.1.0/weibulltools/README.md | 32 weibulltools-2.1.0/weibulltools/build/vignette.rds |binary weibulltools-2.1.0/weibulltools/data/field_data.rda |only weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_I.R | 4 weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_I.Rmd | 142 - weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_I.html | 481 ++-- weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_II.R | 2 weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_II.Rmd | 85 weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_II.html | 509 ++-- weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_III.R | 180 - weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_III.Rmd | 390 ++- weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_III.html | 689 ++++- weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_IV.R |only weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_IV.Rmd |only weibulltools-2.1.0/weibulltools/inst/doc/Life_Data_Analysis_Part_IV.html |only weibulltools-2.1.0/weibulltools/man/confint_betabinom.Rd | 77 weibulltools-2.1.0/weibulltools/man/confint_betabinom.default.Rd | 88 weibulltools-2.1.0/weibulltools/man/confint_fisher.Rd | 73 weibulltools-2.1.0/weibulltools/man/confint_fisher.default.Rd | 92 weibulltools-2.1.0/weibulltools/man/delta_method.Rd | 52 weibulltools-2.1.0/weibulltools/man/dist_delay.Rd | 123 - weibulltools-2.1.0/weibulltools/man/dist_delay.default.Rd |only weibulltools-2.1.0/weibulltools/man/dist_delay_register.Rd | 8 weibulltools-2.1.0/weibulltools/man/dist_delay_report.Rd | 8 weibulltools-2.1.0/weibulltools/man/dist_mileage.Rd | 86 weibulltools-2.1.0/weibulltools/man/dist_mileage.default.Rd |only weibulltools-2.1.0/weibulltools/man/estimate_cdf.Rd | 109 weibulltools-2.1.0/weibulltools/man/estimate_cdf.default.Rd | 99 weibulltools-2.1.0/weibulltools/man/field_data.Rd |only weibulltools-2.1.0/weibulltools/man/figures/README-model_visualization-1.png |binary weibulltools-2.1.0/weibulltools/man/figures/README-probability_visualization-1.png |binary weibulltools-2.1.0/weibulltools/man/figures/logo.ico |only weibulltools-2.1.0/weibulltools/man/johnson_method.Rd | 31 weibulltools-2.1.0/weibulltools/man/kaplan_method.Rd | 22 weibulltools-2.1.0/weibulltools/man/loglik_function.Rd | 93 weibulltools-2.1.0/weibulltools/man/loglik_function.default.Rd |only weibulltools-2.1.0/weibulltools/man/loglik_profiling.Rd | 51 weibulltools-2.1.0/weibulltools/man/loglik_profiling.default.Rd |only weibulltools-2.1.0/weibulltools/man/mcs_delay.Rd | 257 -- weibulltools-2.1.0/weibulltools/man/mcs_delay.default.Rd |only weibulltools-2.1.0/weibulltools/man/mcs_delay_data.Rd |only weibulltools-2.1.0/weibulltools/man/mcs_delay_register.Rd | 29 weibulltools-2.1.0/weibulltools/man/mcs_delay_report.Rd | 29 weibulltools-2.1.0/weibulltools/man/mcs_delays.Rd | 43 weibulltools-2.1.0/weibulltools/man/mcs_mileage.Rd | 153 - 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weibulltools-2.1.0/weibulltools/man/rank_regression.default.Rd | 113 weibulltools-2.1.0/weibulltools/man/reliability_data.Rd | 21 weibulltools-2.1.0/weibulltools/src/Makevars | 6 weibulltools-2.1.0/weibulltools/src/Makevars.win | 6 weibulltools-2.1.0/weibulltools/src/RcppExports.cpp | 5 weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/confidence_intervals.md | 706 +++++- weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/delay_distributions.md | 226 - weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/delta_method.md |only weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/likelihood_functions.md |only weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/mileage_distribution.md | 94 weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/mixture_identification.md | 60 weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/ml_estimation.md | 282 +- weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/plot_helpers.md | 339 +- weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/predict.md |only weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/probability_estimators.md | 338 +- weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/r_squared_function.md |only weibulltools-2.1.0/weibulltools/tests/testthat/_snaps/rank_regression.md | 604 ++++- weibulltools-2.1.0/weibulltools/tests/testthat/setup_models.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-confidence_intervals.R | 209 - weibulltools-2.1.0/weibulltools/tests/testthat/test-delay_distributions.R | 28 weibulltools-2.1.0/weibulltools/tests/testthat/test-delta_method.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-likelihood_functions.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-mcs_data.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-mileage_distribution.R | 30 weibulltools-2.1.0/weibulltools/tests/testthat/test-ml_estimation.R | 81 weibulltools-2.1.0/weibulltools/tests/testthat/test-plot_functions.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-plot_helpers.R | 17 weibulltools-2.1.0/weibulltools/tests/testthat/test-predict.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-probability_estimators.R | 18 weibulltools-2.1.0/weibulltools/tests/testthat/test-r_squared_function.R |only weibulltools-2.1.0/weibulltools/tests/testthat/test-rank_regression.R | 70 weibulltools-2.1.0/weibulltools/tests/testthat/test-reliability_data.R | 9 weibulltools-2.1.0/weibulltools/vignettes/Life_Data_Analysis_Part_I.Rmd | 142 - weibulltools-2.1.0/weibulltools/vignettes/Life_Data_Analysis_Part_II.Rmd | 85 weibulltools-2.1.0/weibulltools/vignettes/Life_Data_Analysis_Part_III.Rmd | 390 ++- weibulltools-2.1.0/weibulltools/vignettes/Life_Data_Analysis_Part_IV.Rmd |only 139 files changed, 8157 insertions(+), 7508 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-01 0.11.1
2020-04-28 0.10.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-28 1.5-6
2013-04-01 1.5-5
2012-06-22 1.5-3
2010-02-03 1.5-1
2009-05-11 1.4-4
2009-02-16 1.4-3
2008-05-02 1.4-2
2007-02-28 1.4-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-09 0.2.1
2020-03-24 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-03 0.9.9.2
2018-06-24 0.9.9.1
2017-10-24 0.9.9
2016-04-01 0.9.7
2016-02-01 0.9.6
2016-01-29 0.9.5
2015-11-06 0.9.4
2014-12-12 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-30 0.11.2
2022-05-03 0.11.1
2021-10-18 0.11.0
2021-09-17 0.10-9
2021-07-15 0.10-8
2020-10-03 0.10-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-17 0.1.1
2019-01-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-26 1.0-10
2022-08-11 1.0-9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-12 1.0-2
2019-02-04 1.0-1
2018-12-04 1.0-0
2018-10-23 0.3-6
2018-02-23 0.3-5
2018-01-11 0.3-4
2017-03-26 0.3-3
2016-08-27 0.3-2
2016-08-21 0.3-1
2016-01-30 0.2-1
2015-10-11 0.1-7
2015-10-06 0.1-6
2015-07-08 0.1-5
2015-05-18 0.1-4
2015-04-02 0.1-3
2014-11-23 0.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-22 0.1.14
2023-03-21 0.1.13
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-02 1.1.2
2021-04-13 1.1.1
2021-03-25 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-13 1.3.7
2019-04-19 1.3.6
2018-08-28 1.3.5
2018-06-15 1.3.4
2018-06-05 1.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-20 0.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-18 1.4
2020-06-02 1.3
2019-02-13 1.2
2018-05-08 1.1
2018-04-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-07 0.2.1.0
2020-02-02 0.1.7.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-07 2.3.4
2019-02-25 2.3.2
2016-06-17 2.3.1
2015-07-02 2.3
2015-01-29 2.2
2013-11-06 2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-16 1.3.2
2020-09-23 1.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-08 2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-03 1.2.0
2022-04-13 1.1.1
2022-03-31 1.1.0
2022-01-27 1.0.2
2021-11-18 1.0.1
2021-05-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-25 0.1-4
2016-01-20 0.1-3
2015-12-03 0.1-2
2015-11-20 0.1-1