Title: Response Probability Functions
Description: The purpose of this package is to factor out logic
and math common to Item Factor Analysis fitting, diagnostics, and
analysis. It is envisioned as core support code suitable for more
specialized IRT packages to build upon. Complete access to optimized C
functions are made available with R_RegisterCCallable().
This software is described in Pritikin & Falk (2020) <doi:10.1177/0146621620929431>.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 1.0.8 dated 2021-08-11 and 1.0.9 dated 2021-09-28
DESCRIPTION | 8 - MD5 | 18 +-- README.md | 2 build/partial.rdb |binary build/rpf.pdf |binary build/vignette.rds |binary inst/doc/diagnostics.html | 44 ++++---- src/Makevars | 2 src/libifa-rpf.cpp | 252 ++++++++++++++++++++++------------------------ tools/rox | 2 10 files changed, 161 insertions(+), 167 deletions(-)
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
Author: Jeff Hallman <jeffhallman@gmail.com>
Maintainer: Brian Salzer <brian.m.salzer@frb.gov>
Diff between tis versions 1.38 dated 2020-02-10 and 1.39 dated 2021-09-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 9 +++++++++ R/holidays.R | 14 ++++++++++++++ R/nber.R | 3 ++- 5 files changed, 32 insertions(+), 8 deletions(-)
Title: Easily Install and Load Interactive Data Visualization Tools
Description: A suite of 'loon' related packages providing data analytic tools for
Direct Interactive Visual Exploration in R ('diveR').
These tools work with and complement those of the 'tidyverse' suite,
extending the grammar of 'ggplot2' to become a grammar of interactive
graphics.
The suite provides many visual tools designed for moderately (100s of variables)
high dimensional data analysis, through 'zenplots' and novel tools in 'loon', and
extends the 'ggplot2' grammar to provide parallel coordinates, Andrews plots, and arbitrary
glyphs through 'ggmulti'.
The 'diveR' package gathers together and installs all these related packages
in a single step.
Author: R. Wayne Oldford [aut, cre]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between diveR versions 0.1.1 dated 2021-05-10 and 0.1.2 dated 2021-09-28
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 7 +++++++ R/attach.R | 15 +++++++++++---- 4 files changed, 27 insertions(+), 13 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.98 dated 2021-09-06 and 1.99 dated 2021-09-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/simFA.R | 9 ++++++--- inst/CITATION | 4 ++-- 4 files changed, 16 insertions(+), 13 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 1.9 dated 2021-07-06 and 2.0 dated 2021-09-28
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- R/ICA.BinCont.R | 4 ++-- R/ICA.ContCont.MultS.MPC.R |only man/ICA.ContCont.MultS.MPC.Rd |only 5 files changed, 10 insertions(+), 8 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
Expectation Maximization, and some other tools. The nimbleFunction system makes
it easy to do things like implement new MCMC samplers from R, customize the
assignment of samplers to different parts of a model from R, and compile the
new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
distributions and functions can be added, including as calls to external
compiled code. Although most people think of MCMC as the main goal of the
'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
arbitrary other kinds of model-generic algorithms as well. A full User Manual is
available at <https://r-nimble.org>.
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system),
Abel Rodrìguez [aut] (Bayesian nonparametrics system),
Duncan Temple Lang [aut] (packaging configuration),
Sally Paganin [aut] (reversible jump MCMC),
Joshua Hug [aut] (WAIC),
Jagadish Babu [ctb] (code for the compilation system for an early
version of NIMBLE),
Lauren Ponisio [ctb] (contributions to the cross-validation code),
Peter Sujan [ctb] (multivariate t distribution code)
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.11.1 dated 2021-05-23 and 0.12.0 dated 2021-09-28
DESCRIPTION | 22 - INSTALL | 8 MD5 | 428 ++++++++++++----------- NAMESPACE | 273 ++++++++++++++ R/BNP_distributions.R | 10 R/BNP_samplers.R | 34 + R/BUGS_BUGSdecl.R | 46 +- R/BUGS_model.R | 134 +------ R/BUGS_modelDef.R | 127 +++--- R/BUGS_readBUGS.R | 9 R/BUGS_testBUGS.R | 2 R/BUGS_utils.R | 18 R/CAR.R | 14 R/MCMC_WAIC.R |only R/MCMC_build.R | 164 +++----- R/MCMC_configuration.R | 47 +- R/MCMC_conjugacy.R | 18 R/MCMC_run.R | 69 ++- R/MCMC_samplers.R | 406 ++++++++++++++++++++++ R/MCMC_utils.R | 4 R/RCfunction_compile.R | 6 R/RCfunction_core.R | 21 - R/all_utils.R | 18 R/config.R | 2 R/cppDefs_cppProject.R | 1 R/cppDefs_nimbleList.R | 38 +- R/cppInterfaces_modelValues.R | 5 R/crossValidation.R | 20 - R/distributions_implementations.R | 45 ++ R/distributions_inputList.R | 4 R/distributions_processInputList.R | 8 R/genCpp_eigenization.R | 16 R/genCpp_operatorLists.R | 2 R/genCpp_processSpecificCalls.R | 3 R/genCpp_sizeProcessing.R | 41 +- R/genCpp_toEigenize.R | 2 R/nimble-package.r | 16 R/nimbleFunction_core.R | 2 R/nimbleFunction_keywordProcessing.R | 1 R/nimbleFunction_nodeFunction.R | 16 R/nimbleFunction_util.R | 14 R/nimbleList_core.R | 66 +++ R/nimbleProject.R | 10 R/options.R | 1 R/types_util.R | 16 R/zzz.R | 2 configure | 1 configure.ac | 6 inst/CppCode/RcppNimbleUtils.cpp | 4 inst/CppCode/RcppUtils.cpp | 7 inst/CppCode/dists.cpp | 145 +++++++ inst/CppCode/nimDists.cpp | 39 ++ inst/CppCode/predefinedNimbleLists.cpp | 375 +++++++++++++++++++- inst/NEWS | 99 +++++ inst/include/nimble/dists.h | 15 inst/include/nimble/nimDists.h | 3 inst/include/nimble/predefinedNimbleLists.h | 52 ++ inst/make/Makevars |only inst/make/Makevars_lib |only man/ADNimbleList.Rd | 6 man/BUGSdeclClass-class.Rd | 2 man/CAR-Normal.Rd | 32 + man/CAR-Proper.Rd | 36 + man/CAR_calcNumIslands.Rd | 7 man/Categorical.Rd | 7 man/ChineseRestaurantProcess.Rd | 7 man/CmodelBaseClass-class.Rd | 2 man/CnimbleFunctionBase-class.Rd | 2 man/Constraint.Rd | 7 man/Dirichlet.Rd | 9 man/Double-Exponential.Rd | 31 + man/Exponential.Rd | 15 man/Interval.Rd | 7 man/Inverse-Gamma.Rd | 31 + man/Inverse-Wishart.Rd | 9 man/LKJ.Rd |only man/MCMCconf-class.Rd | 93 +++-- man/MCMCsuite.Rd | 1 man/Multinomial.Rd | 9 man/Multivariate-t.Rd | 11 man/MultivariateNormal.Rd | 7 man/Rmatrix2mvOneVar.Rd | 1 man/RmodelBaseClass-class.Rd | 2 man/StickBreakingFunction.Rd | 9 man/Wishart.Rd | 9 man/any_na.Rd | 1 man/as.carAdjacency.Rd | 7 man/as.carCM.Rd | 7 man/asRow.Rd | 3 man/autoBlock.Rd | 18 man/buildAuxiliaryFilter.Rd | 1 man/buildBootstrapFilter.Rd | 1 man/buildEnsembleKF.Rd | 1 man/buildIteratedFilter2.Rd | 1 man/buildLiuWestFilter.Rd | 1 man/buildMCEM.Rd | 27 + man/buildMCMC.Rd | 53 -- man/calculateWAIC.Rd |only man/carBounds.Rd | 7 man/carMaxBound.Rd | 7 man/carMinBound.Rd | 7 man/checkInterrupt.Rd | 1 man/codeBlockClass-class.Rd | 2 man/compareMCMCs.Rd | 1 man/compileNimble.Rd | 13 man/configureMCMC.Rd | 31 + man/configureRJ.Rd | 16 man/decide.Rd | 1 man/decideAndJump.Rd | 1 man/declare.Rd | 1 man/deregisterDistributions.Rd | 1 man/distributionInfo.Rd | 15 man/eigenNimbleList.Rd | 11 man/extractControlElement.Rd | 1 man/flat.Rd | 11 man/getBUGSexampleDir.Rd | 7 man/getBound.Rd | 1 man/getConditionallyIndependentSets.Rd | 20 - man/getDefinition.Rd | 1 man/getNimbleOption.Rd | 1 man/getParam.Rd | 1 man/getSamplesDPmeasure.Rd | 15 man/getsize.Rd | 1 man/identityMatrix.Rd | 1 man/initializeModel.Rd | 1 man/is.nf.Rd | 5 man/is.nl.Rd | 1 man/makeBoundInfo.Rd | 1 man/makeParamInfo.Rd | 1 man/modelBaseClass-class.Rd | 153 +++++--- man/modelDefClass-class.Rd | 2 man/modelInitialization.Rd | 1 man/modelValues.Rd | 1 man/modelValuesBaseClass-class.Rd | 16 man/modelValuesConf.Rd | 12 man/model_macro_builder.Rd | 1 man/nfMethod.Rd | 1 man/nfVar.Rd | 3 man/nimCat.Rd | 3 man/nimCopy.Rd | 15 man/nimDerivs.Rd | 1 man/nimDim.Rd | 3 man/nimEigen.Rd | 9 man/nimMatrix.Rd | 37 +- man/nimNumeric.Rd | 44 +- man/nimOptim.Rd | 14 man/nimOptimDefaultControl.Rd | 1 man/nimPrint.Rd | 1 man/nimStop.Rd | 1 man/nimSvd.Rd | 7 man/nimble-R-functions.Rd | 19 - man/nimble-internal.Rd | 67 +++ man/nimble.Rd | 18 man/nimbleCode.Rd | 1 man/nimbleExternalCall.Rd | 17 man/nimbleFunction.Rd | 14 man/nimbleFunctionBase-class.Rd | 2 man/nimbleFunctionList-class.Rd | 4 man/nimbleFunctionVirtual.Rd | 15 man/nimbleList.Rd | 9 man/nimbleMCMC.Rd | 36 + man/nimbleModel.Rd | 25 - man/nimbleOptions.Rd | 1 man/nimbleRcall.Rd | 15 man/nimbleType-class.Rd | 4 man/nodeFunctions.Rd | 3 man/optimControlNimbleList.Rd | 5 man/optimDefaultControl.Rd | 1 man/optimResultNimbleList.Rd | 6 man/printErrors.Rd | 1 man/rankSample.Rd | 1 man/readBUGSmodel.Rd | 21 - man/registerDistributions.Rd | 16 man/resize.Rd | 1 man/run.time.Rd | 1 man/runCrossValidate.Rd | 16 man/runMCMC.Rd | 33 + man/samplers.Rd | 126 ++++-- man/setAndCalculate.Rd | 1 man/setAndCalculateOne.Rd | 1 man/setSize.Rd | 1 man/setupOutputs.Rd | 1 man/simNodes.Rd | 3 man/simNodesMV.Rd | 4 man/singleVarAccessClass-class.Rd | 2 man/svdNimbleList.Rd | 11 man/t.Rd | 17 man/testBUGSmodel.Rd | 15 man/valueInCompiledNimbleFunction.Rd | 1 man/values.Rd | 1 man/waic.Rd |only man/waicDetailsList.Rd |only man/waicList.Rd |only man/withNimbleOptions.Rd | 1 src/nimble.cpp | 2 tests/testthat/distributionsTestLog.Rout |only tests/testthat/dynamicIndexingTestLists.R | 4 tests/testthat/dynamicIndexingTestLog.Rout |only tests/testthat/mathTestLists.R | 5 tests/testthat/mcemTestLog.Rout |only tests/testthat/mcmcTestLog.Rout |only tests/testthat/mcmcTestLog_Correct.Rout | 2 tests/testthat/test-bnp.R | 48 +- tests/testthat/test-car.R | 22 - tests/testthat/test-checkDSL.R | 44 +- tests/testthat/test-crossVal.R | 2 tests/testthat/test-distributions.R | 238 +++++++++---- tests/testthat/test-dynamicIndexing.R | 6 tests/testthat/test-getDependencies.R | 21 - tests/testthat/test-initializeModel.R | 8 tests/testthat/test-mcem.R | 8 tests/testthat/test-mcmc.R | 211 ++++++++++- tests/testthat/test-mcmcrj.R | 10 tests/testthat/test-models.R | 118 +++++- tests/testthat/test-nimbleList_RCfun.R | 4 tests/testthat/test-numericTypes.R | 76 +++- tests/testthat/test-setData.R | 23 + tests/testthat/test-testTools.R | 4 tests/testthat/test-waic.R | 512 +++++++++++++++++++++++++--- tests/testthat/test_utils.R | 10 tests/testthat/truncTestLog_Correct.Rout | 6 221 files changed, 4298 insertions(+), 1561 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Abhraneel Sarma [ctb],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Bulat Yapparov [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hall [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Ellis Hughes [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>),
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.34 dated 2021-09-09 and 1.35 dated 2021-09-28
DESCRIPTION | 8 +- MD5 | 28 ++++---- R/defaults.R | 7 +- R/hooks-md.R | 17 +++-- R/parser.R | 143 +++++++++++++++++++++++++++++++++++++++---- R/utils-vignettes.R | 9 -- R/utils.R | 21 ++++-- inst/doc/knit_expand.html | 4 - inst/doc/knit_print.html | 12 +-- inst/doc/knitr-intro.html | 10 +-- inst/doc/knitr-markdown.html | 2 inst/doc/knitr-refcard.pdf |binary man/combine_words.Rd | 7 +- tests/testit/test-hooks-md.R | 5 + tests/testit/test-utils.R | 22 +++++- 15 files changed, 219 insertions(+), 76 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr2 versions 0.1.0 dated 2021-09-22 and 0.1.1 dated 2021-09-28
DESCRIPTION | 6 +- MD5 | 25 +++++----- NAMESPACE | 1 NEWS.md |only R/curl.R | 4 - R/httr2-package.R | 1 R/multi-req.R | 2 README.md | 6 -- inst/doc/httr2.html | 22 ++++---- inst/doc/wrapping-apis.Rmd | 8 +-- inst/doc/wrapping-apis.html | 94 +++++++++++++++++++------------------- man/curl_translate.Rd | 4 - tests/testthat/test-req-perform.R | 1 vignettes/wrapping-apis.Rmd | 8 +-- 14 files changed, 92 insertions(+), 90 deletions(-)
Title: Creation of Arrays by Mixed Integer Programming
Description: 'CRAN' packages 'DoE.base' and 'Rmosek' and non-'CRAN' package 'gurobi' are enhanced with functionality for the creation of optimized arrays for experimentation, where optimization is in terms of generalized minimum aberration. It is also possible to optimally extend existing arrays to larger run size. The package writes 'MPS' (Mathematical Programming System) files for use with any mixed integer optimization software that can process such files. If at least one of the commercial products 'Gurobi' or 'Mosek' (free academic licenses available for both) is available, the package also creates arrays by optimization. For installing 'Gurobi' and its R package 'gurobi', follow instructions at <https://www.gurobi.com/products/gurobi-optimizer/> and <https://www.gurobi.com/documentation/7.5/refman/r_api_overview.html> (or higher version). For installing 'Mosek' and its R package 'Rmosek', follow instructions at <https://www.mosek.com/downloads/> and <https://docs.mosek.com/8.1/rmosek/install-interface.html>, or use the functionality in the stump CRAN R package 'Rmosek'.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Diff between DoE.MIParray versions 0.13 dated 2019-07-13 and 1.0 dated 2021-09-28
DESCRIPTION | 14 - MD5 | 48 +++--- NAMESPACE | 9 - R/create_ILPlist.R |only R/create_MIQP.R |only R/gurobi_MIParray.R | 71 +++++++- R/gurobi_MIPcontinue.R | 31 ++- R/gurobi_MIPsearch.R | 61 +++---- R/mosek_MIParray.R | 88 ++++++++--- R/mosek_MIPcontinue.R | 38 +++- R/mosek_MIPsearch.R | 68 ++++---- R/util_functions.R | 135 ++++++++++++++++- R/write_MPSILP.R |only R/write_MPSILPlist.R |only R/write_MPSMIQP.R |only inst/NEWS | 51 +++++- inst/testsWithGurobiAndMosek/testMPS.R |only inst/testsWithGurobiAndMosek/testMPS.Rout.save |only inst/testsWithGurobiAndMosek/testcombis.R | 4 inst/testsWithGurobiAndMosek/testcombis.Rout.save | 131 +++++++++++----- inst/testsWithGurobiAndMosek/testfindonly.R |only inst/testsWithGurobiAndMosek/testfindonly.Rout.save |only inst/testsWithGurobiAndMosek/teststartforced.R | 3 inst/testsWithGurobiAndMosek/teststartforced.Rout.save | 84 ++++------ man/DoE.MIParray-package.Rd | 56 +++---- man/create_MIQP.Rd |only man/dToCount.Rd |only man/functionsFromDoEbase.Rd | 3 man/mosek_MIParray.Rd | 33 ++-- man/mosek_MIPsearch.Rd | 13 - man/write_MPSILPlist.Rd |only 31 files changed, 642 insertions(+), 299 deletions(-)
Title: Sensitivity Analysis Tools for LSD Simulations
Description: Tools for sensitivity analysis of LSD simulation models. Reads object-oriented data produced by LSD simulation models and performs screening and global sensitivity analysis (Sobol decomposition method, Saltelli et al. (2008) ISBN:9780470725177). A Kriging or polynomial meta-model (Kleijnen (2009) <doi:10.1016/j.ejor.2007.10.013>) is estimated using the simulation data to provide the data required by the Sobol decomposition. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente (documentation and downloads available at <https://www.labsimdev.org/>).
Author: Marcelo C. Pereira [aut, cre] (<https://orcid.org/0000-0002-8069-2734>)
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>
Diff between LSDsensitivity versions 1.1.1 dated 2021-09-26 and 1.1.2 dated 2021-09-28
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/LSDsensitivity.R | 86 ++++++++++++++++++++++++++++++---------------------- build/partial.rdb |binary man/read.doe.lsd.Rd | 2 - 5 files changed, 59 insertions(+), 45 deletions(-)
More information about LSDsensitivity at CRAN
Permanent link
Title: Bayesian Quantile Regression for Ordinal Models
Description: Provides functions for estimating Bayesian quantile regression
for ordinal models, calculating covariate effects, and computing measures for
model comparision. Specifically, the package offers two estimation functions -
one for an ordinal model with more than three outcomes. For each ordinal model,
the package provides functions to calculate the covariate effect using the MCMC
outputs. The package also computes marginal likelihood (recommended) and the
Deviance Information Criterion (DIC) for comparing alternative quantile regression
models. Besides, the package also contains functions for making trace plots of MCMC draws
and other functions that aids the estimation or inference of quantile ordinal models.
Rahman, M. A. (2016).“Bayesian Quantile Regression for Ordinal Models.” Bayesian
Analysis, II(I): 1-24 <doi:10.1214/15-BA939>.
Yu, K., and Moyeed, R. A. (2001). “Bayesian Quantile Regression.” Statistics and
Probability Letters, 54(4): 437–447 <doi:10.1016/S0167-7152(01)00124-9>.
Koenker, R., and Bassett, G. (1978).“Regression Quantiles.” Econometrica,
46(1): 33-50 <doi:10.2307/1913643>.
Chib, S. (1995). “Marginal likelihood from the Gibbs output.” Journal of
the American Statistical Association, 90(432):1313–1321, 1995. <doi: 10.1080/01621459.1995.10476635>.
Chib, S., and Jeliazkov, I. (2001). “Marginal likelihood from the
Metropolis-Hastings output.” Journal of the American Statistical Association, 96(453):270–281, 2001. <doi: 10.1198/016214501750332848>.
Author: Mohammad Arshad Rahman Developer [aut],
Prajual Maheshwari [cre]
Maintainer: Prajual Maheshwari <prajual1391@gmail.com>
Diff between bqror versions 1.1.0 dated 2021-09-12 and 1.2.0 dated 2021-09-28
bqror-1.1.0/bqror/R/Covariate_effect.R |only bqror-1.1.0/bqror/R/ODRI.R |only bqror-1.1.0/bqror/R/ODRII.R |only bqror-1.1.0/bqror/man/logmargLikelihood_or1.Rd |only bqror-1.1.0/bqror/man/logmargLikelihood_or2.Rd |only bqror-1.1.0/bqror/man/negLoglikelihood.Rd |only bqror-1.1.0/bqror/man/qrnegloglikensum.Rd |only bqror-1.2.0/bqror/DESCRIPTION | 37 ++- bqror-1.2.0/bqror/MD5 | 84 ++++---- bqror-1.2.0/bqror/NAMESPACE | 9 bqror-1.2.0/bqror/R/ORI.R |only bqror-1.2.0/bqror/R/ORII.R |only bqror-1.2.0/bqror/R/bqror.R | 51 ++--- bqror-1.2.0/bqror/R/data.R | 239 +++++++++++++----------- bqror-1.2.0/bqror/data/data25j3.RData |binary bqror-1.2.0/bqror/man/Educational_Attainment.Rd | 49 ++-- bqror-1.2.0/bqror/man/Policy_Opinion.Rd | 45 ++-- bqror-1.2.0/bqror/man/alcdf.Rd | 21 -- bqror-1.2.0/bqror/man/alcdfstd.Rd | 19 - bqror-1.2.0/bqror/man/bqror.Rd | 50 ++--- bqror-1.2.0/bqror/man/covariateEffect_or1.Rd | 55 +++-- bqror-1.2.0/bqror/man/covariateEffect_or2.Rd |only bqror-1.2.0/bqror/man/data25j3.Rd | 28 +- bqror-1.2.0/bqror/man/data25j4.Rd | 30 +-- bqror-1.2.0/bqror/man/data50j3.Rd | 30 +-- bqror-1.2.0/bqror/man/data50j4.Rd | 30 +-- bqror-1.2.0/bqror/man/data75j3.Rd | 30 +-- bqror-1.2.0/bqror/man/data75j4.Rd | 30 +-- bqror-1.2.0/bqror/man/deviance_or1.Rd | 38 +-- bqror-1.2.0/bqror/man/deviance_or2.Rd | 40 +--- bqror-1.2.0/bqror/man/drawbeta_or1.Rd | 27 +- bqror-1.2.0/bqror/man/drawbeta_or2.Rd | 27 +- bqror-1.2.0/bqror/man/drawdelta_or1.Rd | 30 +-- bqror-1.2.0/bqror/man/drawlatent_or1.Rd | 24 +- bqror-1.2.0/bqror/man/drawlatent_or2.Rd | 22 +- bqror-1.2.0/bqror/man/drawnu_or2.Rd | 14 - bqror-1.2.0/bqror/man/drawsigma_or2.Rd | 21 +- bqror-1.2.0/bqror/man/draww_or1.Rd | 25 +- bqror-1.2.0/bqror/man/infactor_or1.Rd | 28 +- bqror-1.2.0/bqror/man/infactor_or2.Rd | 26 +- bqror-1.2.0/bqror/man/logMargLikelihood_or1.Rd |only bqror-1.2.0/bqror/man/logMargLikelihood_or2.Rd |only bqror-1.2.0/bqror/man/qrminfundtheorem.Rd | 39 +-- bqror-1.2.0/bqror/man/qrnegLogLike_or2.Rd |only bqror-1.2.0/bqror/man/qrnegLogLikensum_or1.Rd |only bqror-1.2.0/bqror/man/quantreg_or1.Rd | 76 +++---- bqror-1.2.0/bqror/man/quantreg_or2.Rd | 58 +++-- bqror-1.2.0/bqror/man/rndald.Rd | 16 - bqror-1.2.0/bqror/man/traceplot_or1.Rd | 12 - bqror-1.2.0/bqror/man/traceplot_or2.Rd | 12 - 50 files changed, 704 insertions(+), 668 deletions(-)
Title: Projected Polya Tree for Circular Data
Description: Provides functionality for the prior and posterior projected Polya tree for the analysis of circular data (Nieto-Barajas and Nunez-Antonio (2019) <arXiv:1902.06020>).
Author: Karla Mayra Perez [aut, cre], Luis E. Nieto-Barajas [aut]
Maintainer: Karla Mayra Perez <karla.mayra25@gmail.com>
Diff between PPTcirc versions 0.2.0 dated 2021-05-14 and 0.2.1 dated 2021-09-28
DESCRIPTION | 10 ++++++---- MD5 | 9 +++++++-- NEWS.md | 4 ++++ build |only inst |only vignettes |only 6 files changed, 17 insertions(+), 6 deletions(-)
Title: Enhanced RTF Wrapper for Use with Existing Table Packages
Description: Enhanced RTF wrapper written in R for use with existing R tables
packages such as 'Huxtable' or 'GT'. This package fills a gap where tables in
certain packages can be written out to RTF, but cannot add certain metadata
or features to the document that are required/expected in a report for a
regulatory submission, such as multiple levels of titles and footnotes,
making the document landscape, and controlling properties such as margins.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Ashley Tarasiewicz [aut],
Michael Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Atorus Research LLC [cph]
Maintainer: Michael Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between pharmaRTF versions 0.1.3 dated 2021-05-27 and 0.1.4 dated 2021-09-28
DESCRIPTION | 6 +++--- MD5 | 20 +++++++++++--------- NEWS.md | 4 ++++ R/read_hf.R | 5 ++++- README.md | 3 ++- build/vignette.rds |binary inst/doc/advanced_usage.html | 5 +++-- inst/doc/huxtable_tips.html | 5 +++-- inst/doc/pharmaRTF.html | 5 +++-- inst/doc/tf_from_file.html | 23 ++++++++++++----------- tests/testthat/data |only tests/testthat/test_read_df_from_file.R |only 12 files changed, 45 insertions(+), 31 deletions(-)
Title: A Grammar of Interactive Graphics
Description: Provides a bridge between the 'loon' and 'ggplot2' packages. Extends the grammar of ggplot to add clauses to create interactive 'loon' plots. Existing ggplot(s) can be turned into interactive 'loon' plots and 'loon' plots into static ggplot(s); the function 'loon.ggplot()' is the bridge from one plot structure to the other.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>
Diff between loon.ggplot versions 1.2.1 dated 2021-06-10 and 1.3.0 dated 2021-09-28
loon.ggplot-1.2.1/loon.ggplot/R/g_getLocations.R |only loon.ggplot-1.2.1/loon.ggplot/R/g_getPlots.R |only loon.ggplot-1.2.1/loon.ggplot/R/ggplot2loon_ggmatrix.R |only loon.ggplot-1.2.1/loon.ggplot/R/ggplot2loon_ggplot.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_compound.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_layer_graph.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_layer_histogram.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_layer_scatterplot.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_pairs.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_serialaxes.R |only loon.ggplot-1.2.1/loon.ggplot/R/loon2ggplot_l_ts.R |only loon.ggplot-1.2.1/loon.ggplot/R/loonGrob_l_ggplot.R |only loon.ggplot-1.2.1/loon.ggplot/R/pch_to_glyph.R |only loon.ggplot-1.2.1/loon.ggplot/inst/doc/ggplots2loon.R |only loon.ggplot-1.2.1/loon.ggplot/inst/doc/ggplots2loon.Rmd |only loon.ggplot-1.2.1/loon.ggplot/inst/doc/ggplots2loon.html |only loon.ggplot-1.2.1/loon.ggplot/inst/doc/loon2ggplots.R |only loon.ggplot-1.2.1/loon.ggplot/inst/doc/loon2ggplots.Rmd |only loon.ggplot-1.2.1/loon.ggplot/inst/doc/loon2ggplots.html |only loon.ggplot-1.2.1/loon.ggplot/vignettes/ggplots2loon.Rmd |only loon.ggplot-1.2.1/loon.ggplot/vignettes/loon2ggplots.Rmd |only loon.ggplot-1.3.0/loon.ggplot/DESCRIPTION | 23 loon.ggplot-1.3.0/loon.ggplot/MD5 | 147 +-- loon.ggplot-1.3.0/loon.ggplot/NAMESPACE | 10 loon.ggplot-1.3.0/loon.ggplot/R/add_glyph.R | 36 loon.ggplot-1.3.0/loon.ggplot/R/as_loon.R | 13 loon.ggplot-1.3.0/loon.ggplot/R/basic_loon_layers.R | 5 loon.ggplot-1.3.0/loon.ggplot/R/deprecated_functions.R | 31 loon.ggplot-1.3.0/loon.ggplot/R/g_getLocations-deprecated.R |only loon.ggplot-1.3.0/loon.ggplot/R/g_getPlots-deprecated.R |only loon.ggplot-1.3.0/loon.ggplot/R/ggCompound.R |only loon.ggplot-1.3.0/loon.ggplot/R/ggplot2loon-ggmatrix.R |only loon.ggplot-1.3.0/loon.ggplot/R/ggplot2loon-ggplot.R |only loon.ggplot-1.3.0/loon.ggplot/R/interactive-ggproto.R | 93 +- loon.ggplot-1.3.0/loon.ggplot/R/l_scatterplot.R | 3 loon.ggplot-1.3.0/loon.ggplot/R/l_serialaxesplot.R | 11 loon.ggplot-1.3.0/loon.ggplot/R/layout_matrix2tlbr.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_compound.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_facet_grid.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_facet_wrap.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_layer_graph.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_layer_histogram.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_layer_scatterplot.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_pairs.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_serialaxes.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-l_ts.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot-zenLoon.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon2ggplot.R | 184 ++-- loon.ggplot-1.3.0/loon.ggplot/R/loonGrob-l_ggplot.R |only loon.ggplot-1.3.0/loon.ggplot/R/loon_ggplot.R | 6 loon.ggplot-1.3.0/loon.ggplot/R/onAttach.R | 25 loon.ggplot-1.3.0/loon.ggplot/R/scatterplotAsAes.R | 430 ++++------ loon.ggplot-1.3.0/loon.ggplot/R/shape.R |only loon.ggplot-1.3.0/loon.ggplot/R/size.R |only loon.ggplot-1.3.0/loon.ggplot/R/themeNULL.R |only loon.ggplot-1.3.0/loon.ggplot/R/unexportedFunctions.R | 48 - loon.ggplot-1.3.0/loon.ggplot/R/utils.R | 50 - loon.ggplot-1.3.0/loon.ggplot/build/vignette.rds |binary loon.ggplot-1.3.0/loon.ggplot/inst/doc/ggplot2loon.R |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/ggplot2loon.Rmd |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/ggplot2loon.html |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/grammarOfInteractiveGraphics.R |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/grammarOfInteractiveGraphics.Rmd |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/grammarOfInteractiveGraphics.html |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/linking.R |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/linking.Rmd |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/linking.html |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/loon2ggplot.R |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/loon2ggplot.Rmd |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/loon2ggplot.html |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/pipes.Rmd | 4 loon.ggplot-1.3.0/loon.ggplot/inst/doc/pipes.html | 8 loon.ggplot-1.3.0/loon.ggplot/inst/doc/thereAndBackAgain.R |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/thereAndBackAgain.Rmd |only loon.ggplot-1.3.0/loon.ggplot/inst/doc/thereAndBackAgain.html |only loon.ggplot-1.3.0/loon.ggplot/man/active.Rd | 92 +- loon.ggplot-1.3.0/loon.ggplot/man/g_getLocations.Rd | 2 loon.ggplot-1.3.0/loon.ggplot/man/g_getPlots.Rd | 29 loon.ggplot-1.3.0/loon.ggplot/man/geom_imageGlyph-deprecated.Rd | 6 loon.ggplot-1.3.0/loon.ggplot/man/ggplot2loon.Rd | 4 loon.ggplot-1.3.0/loon.ggplot/man/hover.Rd | 84 + loon.ggplot-1.3.0/loon.ggplot/man/interactivity.Rd | 212 ++-- loon.ggplot-1.3.0/loon.ggplot/man/itemLabel-deprecated.Rd | 38 loon.ggplot-1.3.0/loon.ggplot/man/l_getSubtitles.Rd | 2 loon.ggplot-1.3.0/loon.ggplot/man/linking.Rd | 112 +- loon.ggplot-1.3.0/loon.ggplot/man/loon.ggplot-package.Rd | 4 loon.ggplot-1.3.0/loon.ggplot/man/loon.ggplot.Rd | 3 loon.ggplot-1.3.0/loon.ggplot/man/loon2ggplot.Rd | 176 +++- loon.ggplot-1.3.0/loon.ggplot/man/selecting-deprecated.Rd | 47 - loon.ggplot-1.3.0/loon.ggplot/man/selection.Rd | 101 +- loon.ggplot-1.3.0/loon.ggplot/man/zoom.Rd | 135 +-- loon.ggplot-1.3.0/loon.ggplot/tests/testthat/test_ggplot2loon_facets.R | 1 loon.ggplot-1.3.0/loon.ggplot/tests/testthat/test_ggplot2loon_geometricObjects.R | 28 loon.ggplot-1.3.0/loon.ggplot/tests/testthat/test_ggplot2loon_polarCoord.R | 1 loon.ggplot-1.3.0/loon.ggplot/tests/testthat/test_ggplot2loon_serialAxesCoord.R | 1 loon.ggplot-1.3.0/loon.ggplot/tests/testthat/test_ggplot2loon_themes.R | 1 loon.ggplot-1.3.0/loon.ggplot/tests/testthat/test_loon2ggplot.R | 9 loon.ggplot-1.3.0/loon.ggplot/vignettes/ggplot2loon.Rmd |only loon.ggplot-1.3.0/loon.ggplot/vignettes/grammarOfInteractiveGraphics.Rmd |only loon.ggplot-1.3.0/loon.ggplot/vignettes/images/loon2ggplots/loon_l_pairs.png |binary loon.ggplot-1.3.0/loon.ggplot/vignettes/images/loon2ggplots/loon_l_pairs_modification.png |binary loon.ggplot-1.3.0/loon.ggplot/vignettes/linking.Rmd |only loon.ggplot-1.3.0/loon.ggplot/vignettes/loon2ggplot.Rmd |only loon.ggplot-1.3.0/loon.ggplot/vignettes/pipes.Rmd | 4 loon.ggplot-1.3.0/loon.ggplot/vignettes/thereAndBackAgain.Rmd |only 105 files changed, 1230 insertions(+), 989 deletions(-)
Title: The Scalable Highly Adaptive Lasso
Description: A scalable implementation of the highly adaptive lasso algorithm,
including routines for constructing sparse matrices of basis functions of the
observed data, as well as a custom implementation of Lasso regression tailored
to enhance efficiency when the matrix of predictors is composed exclusively of
indicator functions. For ease of use and increased flexibility, the Lasso
fitting routines invoke code from the 'glmnet' package by default. The highly
adaptive lasso was first formulated and described by MJ van der Laan (2017)
<doi:10.1515/ijb-2015-0097>, with practical demonstrations of its performance
given by Benkeser and van der Laan (2016) <doi:10.1109/DSAA.2016.93>. This
implementation of the highly adaptive lasso algorithm was described by Hejazi,
Coyle, and van der Laan (2020) <doi:10.21105/joss.02526>.
Author: Jeremy Coyle [aut, cre] (<https://orcid.org/0000-0002-9874-6649>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
Rachael Phillips [aut] (<https://orcid.org/0000-0002-8474-591X>),
Lars van der Laan [aut],
David Benkeser [ctb] (<https://orcid.org/0000-0002-1019-8343>),
Oleg Sofrygin [ctb],
Weixin Cai [ctb] (<https://orcid.org/0000-0003-2680-3066>),
Mark van der Laan [aut, cph, ths]
(<https://orcid.org/0000-0003-1432-5511>)
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>
Diff between hal9001 versions 0.2.7 dated 2021-01-22 and 0.4.1 dated 2021-09-28
hal9001-0.2.7/hal9001/src/irls_lassi.cpp |only hal9001-0.2.7/hal9001/src/lassi.cpp |only hal9001-0.2.7/hal9001/tests/testthat/test-hal_big.R |only hal9001-0.2.7/hal9001/tests/testthat/test-sl.R |only hal9001-0.4.1/hal9001/DESCRIPTION | 26 hal9001-0.4.1/hal9001/MD5 | 116 - hal9001-0.4.1/hal9001/NAMESPACE | 17 hal9001-0.4.1/hal9001/NEWS.md | 71 hal9001-0.4.1/hal9001/R/RcppExports.R | 52 hal9001-0.4.1/hal9001/R/cv_lasso.R | 2 hal9001-0.4.1/hal9001/R/cv_lasso_early_stopping.R | 5 hal9001-0.4.1/hal9001/R/formula_hal9001.R |only hal9001-0.4.1/hal9001/R/hal.R | 550 ++++-- hal9001-0.4.1/hal9001/R/make_basis.R | 252 ++ hal9001-0.4.1/hal9001/R/predict.R | 91 - hal9001-0.4.1/hal9001/R/reduce_basis_filter.R | 2 hal9001-0.4.1/hal9001/R/sl_hal9001.R | 119 - hal9001-0.4.1/hal9001/R/squash_hal.R | 18 hal9001-0.4.1/hal9001/R/summary.R | 265 +-- hal9001-0.4.1/hal9001/R/zzz.R | 3 hal9001-0.4.1/hal9001/README.md | 39 hal9001-0.4.1/hal9001/build/vignette.rds |binary hal9001-0.4.1/hal9001/inst/CITATION | 2 hal9001-0.4.1/hal9001/inst/REFERENCES.bib | 34 hal9001-0.4.1/hal9001/inst/doc/intro_hal9001.R | 254 ++ hal9001-0.4.1/hal9001/inst/doc/intro_hal9001.Rmd | 443 ++++- hal9001-0.4.1/hal9001/inst/doc/intro_hal9001.html | 878 +++++----- hal9001-0.4.1/hal9001/man/SL.hal9001.Rd | 76 hal9001-0.4.1/hal9001/man/apply_copy_map.Rd | 4 hal9001-0.4.1/hal9001/man/basis_list_cols.Rd | 29 hal9001-0.4.1/hal9001/man/basis_of_degree.Rd | 29 hal9001-0.4.1/hal9001/man/calc_pnz.Rd |only hal9001-0.4.1/hal9001/man/calc_xscale.Rd |only hal9001-0.4.1/hal9001/man/enumerate_basis.Rd | 42 hal9001-0.4.1/hal9001/man/enumerate_edge_basis.Rd |only hal9001-0.4.1/hal9001/man/fit_hal.Rd | 273 ++- hal9001-0.4.1/hal9001/man/formula_hal.Rd |only hal9001-0.4.1/hal9001/man/formula_helpers.Rd |only hal9001-0.4.1/hal9001/man/h.Rd |only hal9001-0.4.1/hal9001/man/lassi_predict.Rd |only hal9001-0.4.1/hal9001/man/make_basis_list.Rd | 4 hal9001-0.4.1/hal9001/man/make_copy_map.Rd | 2 hal9001-0.4.1/hal9001/man/make_design_matrix.Rd | 7 hal9001-0.4.1/hal9001/man/make_reduced_basis_map.Rd | 4 hal9001-0.4.1/hal9001/man/meets_basis.Rd | 6 hal9001-0.4.1/hal9001/man/num_knots_generator.Rd |only hal9001-0.4.1/hal9001/man/plus-.formula_hal9001.Rd |only hal9001-0.4.1/hal9001/man/predict.SL.hal9001.Rd | 4 hal9001-0.4.1/hal9001/man/predict.hal9001.Rd | 55 hal9001-0.4.1/hal9001/man/print.formula_hal9001.Rd |only hal9001-0.4.1/hal9001/man/print.summary.hal9001.Rd |only hal9001-0.4.1/hal9001/man/quantizer.Rd |only hal9001-0.4.1/hal9001/man/squash_hal_fit.Rd | 5 hal9001-0.4.1/hal9001/man/summary.hal9001.Rd | 57 hal9001-0.4.1/hal9001/src/RcppExports.cpp | 82 hal9001-0.4.1/hal9001/src/lassi_fit.cpp | 10 hal9001-0.4.1/hal9001/src/make_hal_basis.cpp | 58 hal9001-0.4.1/hal9001/src/utils.cpp | 47 hal9001-0.4.1/hal9001/tests/testthat/test-formula.R |only hal9001-0.4.1/hal9001/tests/testthat/test-general_families.R |only hal9001-0.4.1/hal9001/tests/testthat/test-hal_hazards.R | 15 hal9001-0.4.1/hal9001/tests/testthat/test-hal_nocv.R |only hal9001-0.4.1/hal9001/tests/testthat/test-higher_order_smoothness.R |only hal9001-0.4.1/hal9001/tests/testthat/test-make_basis_additional_args.R |only hal9001-0.4.1/hal9001/tests/testthat/test-reduce_basis_filter.R | 26 hal9001-0.4.1/hal9001/tests/testthat/test-single_lambda.R | 21 hal9001-0.4.1/hal9001/tests/testthat/test-sl_ecpolley.R |only hal9001-0.4.1/hal9001/tests/testthat/test-summary.R | 74 hal9001-0.4.1/hal9001/tests/testthat/test-varselect_hal.R |only hal9001-0.4.1/hal9001/tests/testthat/test-x_unpenalized.R | 32 hal9001-0.4.1/hal9001/vignettes/intro_hal9001.Rmd | 443 ++++- 71 files changed, 3218 insertions(+), 1426 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn [aut, cre],
Jed Wing [ctb],
Steve Weston [ctb],
Andre Williams [ctb],
Chris Keefer [ctb],
Allan Engelhardt [ctb],
Tony Cooper [ctb],
Zachary Mayer [ctb],
Brenton Kenkel [ctb],
R Core Team [ctb],
Michael Benesty [ctb],
Reynald Lescarbeau [ctb],
Andrew Ziem [ctb],
Luca Scrucca [ctb],
Yuan Tang [ctb],
Can Candan [ctb],
Tyler Hunt [ctb]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-88 dated 2021-05-15 and 6.0-89 dated 2021-09-28
DESCRIPTION | 100 ++++++++++++++++++++++------------ MD5 | 34 +++++------ R/common_code.R | 30 +++++----- R/confusionMatrix.R | 1 R/misc.R | 2 R/modelLookup.R | 13 +++- R/safs.R | 8 ++ R/trainControl.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 11 +++ inst/doc/caret.html | 2 man/createDataPartition.Rd | 4 - man/recall.Rd | 4 - man/safs.Rd | 2 man/sensitivity.Rd | 2 man/trainControl.Rd | 8 +- tests/testthat/test_recipe_upsample.R | 4 - tests/testthat/test_safs.R | 29 +++++++++ 18 files changed, 171 insertions(+), 85 deletions(-)
Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic
factor analysis is a dimension reduction tool for multivariate time series.
'bayesdfa' extends conventional dynamic factor models in several ways.
First, extreme events may be estimated in the latent trend by modeling
process error with a student-t distribution. Second, alternative constraints
(including proportions are allowed). Third, the estimated
dynamic factors can be analyzed with hidden Markov models to evaluate
support for latent regimes.
Author: Eric J. Ward [aut, cre],
Sean C. Anderson [aut],
Luis A. Damiano [aut],
Michael J. Malick [aut],
Mary E. Hunsicker, [ctb],
Mike A. Litzow [ctb],
Mark D. Scheuerell [ctb],
Elizabeth E. Holmes [ctb],
Nick Tolimieri [ctb],
Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Diff between bayesdfa versions 1.1.0 dated 2021-05-28 and 1.2.0 dated 2021-09-28
DESCRIPTION | 12 MD5 | 45 - NAMESPACE | 5 NEWS.md | 6 R/fit_dfa.R | 119 ++- R/plot_fitted.R | 10 R/sim.R | 2 build/vignette.rds |binary inst/doc/bayesdfa.html | 22 inst/doc/bigdata.R |only inst/doc/bigdata.Rmd |only inst/doc/bigdata.html |only inst/doc/combining_data.html | 10 inst/doc/compositional.html | 8 inst/doc/covariates.html | 8 inst/doc/estimate_process_sigma.html | 6 inst/doc/smooth.R |only inst/doc/smooth.Rmd |only inst/doc/smooth.html |only inst/stan/dfa.stan | 13 man/fit_dfa.Rd | 31 - man/plot_fitted.Rd | 10 src/RcppExports.cpp | 5 src/stanExports_dfa-ec272765.o.tmp |only src/stanExports_dfa.h | 1076 +++++++++++++++++------------------ tests/testthat/test-fit.R | 4 vignettes/bigdata.Rmd |only vignettes/smooth.Rmd |only 28 files changed, 745 insertions(+), 647 deletions(-)
Title: Manual Tours, Manual Control of Dynamic Projections of Numeric
Multivariate Data
Description: Data visualization tours animates linear projection
of multivariate data as its basis (ie. orientation) changes. The 'spinifex'
packages generates paths for manual tours by manipulating the contribution of
a single variable at a time Cook & Buja (1997)
<doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand
(random walk) and guided (optimizing some objective function) are available
in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>.
'spinifex' builds on 'tourr' and can render tours with 'gganimate' and
'plotly' graphics, and allows for exporting as an .html widget and as an .gif,
respectively. This work is fully discussed in Spyrison & Cook (2020)
<doi:10.32614/RJ-2020-027>.
Author: Nicholas Spyrison [aut, cre],
Dianne Cook [aut, ths]
Maintainer: Nicholas Spyrison <spyrison@gmail.com>
Diff between spinifex versions 0.2.8 dated 2021-04-18 and 0.3.1 dated 2021-09-28
spinifex-0.2.8/spinifex/inst/doc/spinifex.R |only spinifex-0.2.8/spinifex/inst/doc/spinifex.Rmd |only spinifex-0.2.8/spinifex/inst/doc/spinifex.html |only spinifex-0.2.8/spinifex/inst/shiny_apps/intro |only spinifex-0.2.8/spinifex/man/pan_zoom.Rd |only spinifex-0.2.8/spinifex/man/scale_axes.Rd |only spinifex-0.2.8/spinifex/vignettes/spinifex.Rmd |only spinifex-0.3.1/spinifex/DESCRIPTION | 30 spinifex-0.3.1/spinifex/MD5 | 156 ++- spinifex-0.3.1/spinifex/NAMESPACE | 23 spinifex-0.3.1/spinifex/NEWS.md | 43 spinifex-0.3.1/spinifex/R/0_util.r | 471 +++++----- spinifex-0.3.1/spinifex/R/1_manual_tour.r | 279 ++++- spinifex-0.3.1/spinifex/R/2_ggproto_visualize.r |only spinifex-0.3.1/spinifex/R/2_render.r | 156 +-- spinifex-0.3.1/spinifex/R/3_visualize.r | 105 +- spinifex-0.3.1/spinifex/R/8_run_app.r | 58 - spinifex-0.3.1/spinifex/R/9_data.r | 259 +++-- spinifex-0.3.1/spinifex/R/9_spinifex-depricated.r | 91 - spinifex-0.3.1/spinifex/R/spinifex-package.r | 96 +- spinifex-0.3.1/spinifex/README.md | 5 spinifex-0.3.1/spinifex/build/partial.rdb |only spinifex-0.3.1/spinifex/build/vignette.rds |binary spinifex-0.3.1/spinifex/data/BreastCancer.rda |binary spinifex-0.3.1/spinifex/data/PimaIndiansDiabetes_long.rda |binary spinifex-0.3.1/spinifex/data/PimaIndiansDiabetes_wide.rda |binary spinifex-0.3.1/spinifex/data/penguins.rda |only spinifex-0.3.1/spinifex/data/weather.rda |binary spinifex-0.3.1/spinifex/data/wine.rda |binary spinifex-0.3.1/spinifex/inst/WORDLIST |only spinifex-0.3.1/spinifex/inst/doc/getting_started_with_spinifex.R |only spinifex-0.3.1/spinifex/inst/doc/getting_started_with_spinifex.Rmd |only spinifex-0.3.1/spinifex/inst/doc/getting_started_with_spinifex.html |only spinifex-0.3.1/spinifex/inst/doc/ggproto_api.R |only spinifex-0.3.1/spinifex/inst/doc/ggproto_api.Rmd |only spinifex-0.3.1/spinifex/inst/doc/ggproto_api.html |only spinifex-0.3.1/spinifex/inst/shiny_apps/radial_tour |only spinifex-0.3.1/spinifex/man/BreastCancer.Rd | 81 - spinifex-0.3.1/spinifex/man/PimaIndiansDiabetes_long.Rd | 55 - spinifex-0.3.1/spinifex/man/PimaIndiansDiabetes_wide.Rd | 54 - spinifex-0.3.1/spinifex/man/animate_gganimate.Rd |only spinifex-0.3.1/spinifex/man/animate_plotly.Rd |only spinifex-0.3.1/spinifex/man/array2df.Rd | 53 - spinifex-0.3.1/spinifex/man/as_history_array.Rd | 12 spinifex-0.3.1/spinifex/man/basis_guided.Rd | 6 spinifex-0.3.1/spinifex/man/basis_half_circle.Rd | 2 spinifex-0.3.1/spinifex/man/basis_odp.Rd | 106 +- spinifex-0.3.1/spinifex/man/basis_olda.Rd | 4 spinifex-0.3.1/spinifex/man/basis_onpp.Rd | 104 +- spinifex-0.3.1/spinifex/man/basis_pca.Rd | 11 spinifex-0.3.1/spinifex/man/create_manip_space.Rd | 17 spinifex-0.3.1/spinifex/man/dot-bind_elements2df.Rd |only spinifex-0.3.1/spinifex/man/dot-init4proto.Rd |only spinifex-0.3.1/spinifex/man/dot-lapply_rep_len.Rd |only spinifex-0.3.1/spinifex/man/figures/lifecycle-archived.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-defunct.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-deprecated.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-experimental.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-maturing.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-questioning.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-stable.svg |only spinifex-0.3.1/spinifex/man/figures/lifecycle-superseded.svg |only spinifex-0.3.1/spinifex/man/filmstrip.Rd |only spinifex-0.3.1/spinifex/man/ggtour.Rd |only spinifex-0.3.1/spinifex/man/interpolate_manual_tour.Rd |only spinifex-0.3.1/spinifex/man/is_orthonormal.Rd | 10 spinifex-0.3.1/spinifex/man/last_ggtour.Rd |only spinifex-0.3.1/spinifex/man/manip_var_of.Rd | 12 spinifex-0.3.1/spinifex/man/manual_tour.Rd | 32 spinifex-0.3.1/spinifex/man/map_absolute.Rd |only spinifex-0.3.1/spinifex/man/map_relative.Rd |only spinifex-0.3.1/spinifex/man/penguins.Rd |only spinifex-0.3.1/spinifex/man/play_manual_tour.Rd | 6 spinifex-0.3.1/spinifex/man/play_tour_path.Rd | 11 spinifex-0.3.1/spinifex/man/proto_basis.Rd |only spinifex-0.3.1/spinifex/man/proto_default.Rd |only spinifex-0.3.1/spinifex/man/proto_density.Rd |only spinifex-0.3.1/spinifex/man/proto_hex.Rd |only spinifex-0.3.1/spinifex/man/proto_highlight.Rd |only spinifex-0.3.1/spinifex/man/proto_origin.Rd |only spinifex-0.3.1/spinifex/man/proto_point.Rd |only spinifex-0.3.1/spinifex/man/proto_text.Rd |only spinifex-0.3.1/spinifex/man/render_.Rd | 23 spinifex-0.3.1/spinifex/man/render_gganimate.Rd | 32 spinifex-0.3.1/spinifex/man/render_plotly.Rd | 40 spinifex-0.3.1/spinifex/man/rotate_manip_space.Rd | 9 spinifex-0.3.1/spinifex/man/run_app.Rd | 9 spinifex-0.3.1/spinifex/man/save_history.Rd |only spinifex-0.3.1/spinifex/man/scale_sd.Rd | 6 spinifex-0.3.1/spinifex/man/spinifex-deprecated.Rd | 25 spinifex-0.3.1/spinifex/man/spinifex.Rd | 27 spinifex-0.3.1/spinifex/man/theme_spinifex.Rd | 8 spinifex-0.3.1/spinifex/man/view_frame.Rd | 27 spinifex-0.3.1/spinifex/man/view_manip_space.Rd | 15 spinifex-0.3.1/spinifex/man/weather.Rd | 95 -- spinifex-0.3.1/spinifex/man/wine.Rd | 56 - spinifex-0.3.1/spinifex/tests/testthat/test-0_util.R | 153 ++- spinifex-0.3.1/spinifex/tests/testthat/test-1_manual_tour.R | 35 spinifex-0.3.1/spinifex/tests/testthat/test-2_ggproto_visualize.r |only spinifex-0.3.1/spinifex/tests/testthat/test-2_render.R | 47 spinifex-0.3.1/spinifex/tests/testthat/test-3_visualize.r | 98 +- spinifex-0.3.1/spinifex/vignettes/getting_started_with_spinifex.Rmd |only spinifex-0.3.1/spinifex/vignettes/ggproto_api.Rmd |only 103 files changed, 1706 insertions(+), 1347 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] (<https://orcid.org/0000-0003-4152-5308>),
Rudolf Debelak [aut] (<https://orcid.org/0000-0001-8900-2106>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.6-1 dated 2021-05-21 and 0.7-0 dated 2021-09-28
DESCRIPTION | 8 - MD5 | 22 ++-- NEWS | 20 ++++ R/anchor.R | 74 ++++++++++----- R/mptmodel.R | 14 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 10 +- inst/doc/toolbox-simulation.pdf |binary man/anchor.Rd | 149 +++++++++++++++++++------------- man/anchortest.Rd | 36 +++---- tests/Examples/psychotools-Ex.Rout.save | 58 ++++++------ 12 files changed, 239 insertions(+), 152 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre],
Sebastian Krantz [ctb],
Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>)
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between fixest versions 0.9.0 dated 2021-06-19 and 0.10.0 dated 2021-09-28
fixest-0.10.0/fixest/DESCRIPTION | 8 fixest-0.10.0/fixest/MD5 | 151 fixest-0.10.0/fixest/NAMESPACE | 24 fixest-0.10.0/fixest/NEWS.md | 154 fixest-0.10.0/fixest/R/ESTIMATION_FUNS.R | 289 + fixest-0.10.0/fixest/R/Methods.R | 9 fixest-0.10.0/fixest/R/MiscFuns.R | 2079 ++++++++---- fixest-0.10.0/fixest/R/RcppExports.R | 16 fixest-0.10.0/fixest/R/VCOV.R | 2666 ++++++++++++---- fixest-0.10.0/fixest/R/VCOV_aliases.R |only fixest-0.10.0/fixest/R/alias_generator.R |only fixest-0.10.0/fixest/R/coefplot.R | 199 - fixest-0.10.0/fixest/R/did.R | 111 fixest-0.10.0/fixest/R/etable.R | 1983 ++++++++--- fixest-0.10.0/fixest/R/etable_aliases.R | 8 fixest-0.10.0/fixest/R/fitstats.R | 277 + fixest-0.10.0/fixest/R/fixest_env.R | 416 +- fixest-0.10.0/fixest/R/fixest_multi.R | 8 fixest-0.10.0/fixest/R/index.R | 2 fixest-0.10.0/fixest/R/iplot.R | 4 fixest-0.10.0/fixest/R/onLoad.R | 48 fixest-0.10.0/fixest/R/test_fun.R | 74 fixest-0.10.0/fixest/R/xaxis.R | 4 fixest-0.10.0/fixest/build/vignette.rds |binary fixest-0.10.0/fixest/inst/doc/exporting_tables.R | 34 fixest-0.10.0/fixest/inst/doc/exporting_tables.Rmd | 48 fixest-0.10.0/fixest/inst/doc/exporting_tables.html | 100 fixest-0.10.0/fixest/inst/doc/fixest_walkthrough.R | 123 fixest-0.10.0/fixest/inst/doc/fixest_walkthrough.Rmd | 251 + fixest-0.10.0/fixest/inst/doc/fixest_walkthrough.html | 1542 +++++---- fixest-0.10.0/fixest/inst/doc/multiple_estimations.Rmd | 2 fixest-0.10.0/fixest/inst/doc/multiple_estimations.html | 78 fixest-0.10.0/fixest/inst/doc/standard_errors.R | 202 - fixest-0.10.0/fixest/inst/doc/standard_errors.Rmd | 265 - fixest-0.10.0/fixest/inst/doc/standard_errors.html | 445 +- fixest-0.10.0/fixest/man/bin.Rd |only fixest-0.10.0/fixest/man/coefplot.Rd | 21 fixest-0.10.0/fixest/man/coeftable.Rd | 23 fixest-0.10.0/fixest/man/confint.fixest.Rd | 10 fixest-0.10.0/fixest/man/degrees_freedom.Rd | 11 fixest-0.10.0/fixest/man/estfun.fixest.Rd | 1 fixest-0.10.0/fixest/man/etable.Rd | 256 + fixest-0.10.0/fixest/man/feNmlm.Rd | 51 fixest-0.10.0/fixest/man/feglm.Rd | 57 fixest-0.10.0/fixest/man/femlm.Rd | 54 fixest-0.10.0/fixest/man/feols.Rd | 79 fixest-0.10.0/fixest/man/fitstat_register.Rd | 126 fixest-0.10.0/fixest/man/fixest.Rd | 2 fixest-0.10.0/fixest/man/fixest_startup_msg.Rd | 38 fixest-0.10.0/fixest/man/i.Rd | 27 fixest-0.10.0/fixest/man/obs.Rd | 72 fixest-0.10.0/fixest/man/predict.fixest.Rd | 72 fixest-0.10.0/fixest/man/setFixest_coefplot.Rd | 2 fixest-0.10.0/fixest/man/setFixest_estimation.Rd | 9 fixest-0.10.0/fixest/man/setFixest_fml.Rd | 49 fixest-0.10.0/fixest/man/setFixest_vcov.Rd |only fixest-0.10.0/fixest/man/ssc.Rd |only fixest-0.10.0/fixest/man/stepwise.Rd | 92 fixest-0.10.0/fixest/man/style.df.Rd | 13 fixest-0.10.0/fixest/man/style.tex.Rd | 10 fixest-0.10.0/fixest/man/summary.fixest.Rd | 113 fixest-0.10.0/fixest/man/summary.fixest_multi.Rd | 13 fixest-0.10.0/fixest/man/sunab.Rd | 63 fixest-0.10.0/fixest/man/to_integer.Rd | 8 fixest-0.10.0/fixest/man/update.fixest.Rd | 10 fixest-0.10.0/fixest/man/vcov.fixest.Rd | 188 - fixest-0.10.0/fixest/man/vcov_cluster.Rd |only fixest-0.10.0/fixest/man/vcov_conley.Rd |only fixest-0.10.0/fixest/man/vcov_hac.Rd |only fixest-0.10.0/fixest/man/wald.Rd | 140 fixest-0.10.0/fixest/man/xpd.Rd | 77 fixest-0.10.0/fixest/src/RcppExports.cpp | 70 fixest-0.10.0/fixest/src/lm_related.cpp | 15 fixest-0.10.0/fixest/src/quf.cpp | 6 fixest-0.10.0/fixest/src/vcov_related.cpp |only fixest-0.10.0/fixest/tests/fixest_tests.R | 422 ++ fixest-0.10.0/fixest/vignettes/exporting_tables.Rmd | 48 fixest-0.10.0/fixest/vignettes/fixest_walkthrough.Rmd | 251 + fixest-0.10.0/fixest/vignettes/multiple_estimations.Rmd | 2 fixest-0.10.0/fixest/vignettes/standard_errors.Rmd | 265 - fixest-0.9.0/fixest/man/dof.Rd |only fixest-0.9.0/fixest/man/setFixest_se.Rd |only 82 files changed, 10111 insertions(+), 4275 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' 'GLMMadaptive' and 'spaMM', generalized additive models
('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and
'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>),
Lukas Lohse [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.4.3 dated 2021-07-07 and 0.4.4 dated 2021-09-28
DESCRIPTION | 19 - MD5 | 74 +++--- NAMESPACE | 1 NEWS | 32 ++ R/DHARMa.R | 6 R/compatibility.R | 9 R/helper.R | 24 +- R/runBenchmarks.R | 39 ++- R/simulateResiduals.R | 18 - R/startup.R | 2 R/tests.R | 56 +++- inst/doc/DHARMa.R | 73 +++--- inst/doc/DHARMa.Rmd | 23 + inst/doc/DHARMa.html | 277 ++++++++++++++---------- inst/doc/DHARMaForBayesians.html | 4 inst/examples/runBenchmarksHelp.R | 1 inst/examples/testQuantilesHelp.R | 5 inst/examples/testTemporalAutocorrelationHelp.R | 36 +++ man/createDHARMa.Rd | 4 man/getQuantile.Rd | 10 man/getSimulations.Rd | 8 man/hurricanes.Rd | 30 +- man/outliers.Rd | 2 man/plot.DHARMa.Rd | 2 man/plot.DHARMaBenchmark.Rd | 2 man/plotResiduals.Rd | 2 man/recalculateResiduals.Rd | 5 man/runBenchmarks.Rd | 1 man/simulateResiduals.Rd | 16 - man/testCategorical.Rd | 4 man/testDispersion.Rd | 12 - man/testQuantiles.Rd | 5 man/testSpatialAutocorrelation.Rd | 20 + man/testTemporalAutocorrelation.Rd | 53 ++++ man/testZeroInflation.Rd | 8 tests/manualTests/DHARMa-rhub.R |only tests/testthat/Rplots.pdf |only tests/testthat/testModelTypes.R |only tests/testthat/testSimulateResiduals.R |only vignettes/DHARMa.Rmd | 23 + 40 files changed, 576 insertions(+), 330 deletions(-)
More information about wordpiece.data at CRAN
Permanent link
Title: Sparse Principal Component Regression
Description: The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano <skawano@ai.lab.uec.ac.jp>
Diff between spcr versions 2.0 dated 2016-10-03 and 2.1 dated 2021-09-28
DESCRIPTION | 10 +-- MD5 | 12 +-- man/cv.spcr.Rd | 168 +++++++++++++++++++++++++++--------------------------- man/cv.spcrglm.Rd | 138 ++++++++++++++++++++++---------------------- man/spcr.Rd | 154 ++++++++++++++++++++++++------------------------- man/spcrglm.Rd | 145 +++++++++++++++++++++++----------------------- src/SPCR.c | 5 + 7 files changed, 318 insertions(+), 314 deletions(-)
Title: Longitudinal Concordance Correlation
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Author: Thiago de Paula Oliveira [aut, cre]
(<https://orcid.org/0000-0002-4555-2584>),
Rafael de Andrade Moral [aut] (<https://orcid.org/0000-0002-0875-3563>),
Silvio Sandoval Zocchi [ctb] (<https://orcid.org/0000-0003-2535-908X>),
Clarice Garcia Borges Demetrio [ctb]
(<https://orcid.org/0000-0002-3609-178X>),
John Hinde [aut] (<https://orcid.org/0000-0001-6507-5204>)
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@alumni.usp.br>
Diff between lcc versions 1.1.2 dated 2021-02-26 and 1.1.3 dated 2021-09-28
DESCRIPTION | 10 ++-- MD5 | 106 +++++++++++++++++++++++------------------------ R/ciCompute.R | 42 +++++++++--------- R/lccModel.R | 2 R/lcc_intervals.R | 14 +++--- R/plotmethod_lcc.R | 2 man/AIC.lcc.Rd | 2 man/CCC.Rd | 2 man/CCC_lin.Rd | 2 man/Pearson.Rd | 2 man/anova.lcc.Rd | 2 man/bootstrapSamples.Rd | 2 man/ciBuilder.Rd | 2 man/ciCompute.Rd | 2 man/coef.lcc.Rd | 2 man/dataBootstrap.Rd | 2 man/dataBuilder.Rd | 2 man/fitted.lcc.Rd | 2 man/fittedBuilder.Rd | 2 man/getDelta.Rd | 2 man/getVarCov.lcc.Rd | 2 man/init.Rd | 2 man/is.lcc.Rd | 2 man/laBootstrap.Rd | 2 man/laBuilder.Rd | 2 man/laWrapper.Rd | 2 man/lcc.Rd | 7 ++- man/lccBootstrap.Rd | 2 man/lccBuilder.Rd | 2 man/lccInternal.Rd | 2 man/lccModel.Rd | 2 man/lccPlot.Rd | 2 man/lccSummary.Rd | 2 man/lccWrapper.Rd | 2 man/lcc_intervals.Rd | 2 man/logLik.lcc.Rd | 2 man/lpcBootstrap.Rd | 2 man/lpcBuilder.Rd | 2 man/lpcWrapper.Rd | 2 man/plot.lcc.Rd | 2 man/plotBuilder_la.Rd | 2 man/plotBuilder_lcc.Rd | 2 man/plotBuilder_lpc.Rd | 2 man/plotControl.Rd | 2 man/plot_la.Rd | 2 man/plot_lcc.Rd | 2 man/plot_lpc.Rd | 2 man/print.anova.lcc.Rd | 2 man/print.lcc.Rd | 2 man/print.summary.lcc.Rd | 2 man/ranef.lcc.Rd | 2 man/residuals.lcc.Rd | 2 man/summary.lcc.Rd | 2 man/vcov.lcc.Rd | 2 54 files changed, 141 insertions(+), 136 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.1-5 dated 2021-05-28 and 1.1-6 dated 2021-09-28
DESCRIPTION | 10 MD5 | 53 NAMESPACE | 3 R/CIcdfplot.R | 160 +- R/Surv2fitdistcens.R |only R/cdfcomp.R | 6 R/fitdist.R | 1 build/vignette.rds |binary data/endosulfan.rda |binary data/fremale.rda |only inst/CITATION | 4 inst/NEWS | 15 inst/doc/FAQ.R | 19 inst/doc/FAQ.Rmd | 50 inst/doc/FAQ.html | 1678 ++++++++++--------------- inst/doc/Optimalgo.html | 639 ++++++--- inst/doc/paper2JSS.Rnw | 2938 ++++++++++++++++++++++----------------------- inst/doc/paper2JSS.pdf |binary man/CIcdfplot.Rd | 59 man/Surv2fitdistcens.Rd |only man/endosulfan.Rd | 208 +-- man/fitdistrplus.Rd | 2 man/fremale.Rd |only man/graphcomp.Rd | 17 tests/t-CIcdfplot.R | 51 tests/t-Surv2fitdistcens.R |only tests/t-cdfcomp.R | 16 tests/t-gofstat.R | 12 vignettes/FAQ.Rmd | 50 vignettes/paper2JSS.Rnw | 2938 ++++++++++++++++++++++----------------------- 30 files changed, 4508 insertions(+), 4421 deletions(-)
Title: Partition/Decomposition of Breeding Values by Paths of
Information
Description: A software that implements a method for partitioning genetic trends to
quantify the sources of genetic gain in breeding programmes.
The partitioning method is described in Garcia-Cortes et al.
(2008) <doi:10.1017/S175173110800205X>. The package includes the
main function AlphaPart for partitioning breeding values and auxiliary
functions for manipulating data and summarizing, visualizing, and saving
results.
Author: Gregor Gorjanc [aut, cre] (<https://orcid.org/0000-0001-8008-2787>),
Jana Obsteter [aut] (<https://orcid.org/0000-0003-1511-3916>),
Thiago de Paula Oliveira [aut]
(<https://orcid.org/0000-0002-4555-2584>)
Maintainer: Gregor Gorjanc <gregor.gorjanc@roslin.ed.ac.uk>
Diff between AlphaPart versions 0.8.2 dated 2021-09-21 and 0.8.3 dated 2021-09-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/AlphaPart.R | 5 +++-- build/partial.rdb |binary inst/doc/alphapart-vignette.html | 4 ++-- tests/testthat/test-printPlotSummaryAlphaPart.R | 3 +-- 6 files changed, 15 insertions(+), 15 deletions(-)
More information about statsearchanalyticsr at CRAN
Permanent link
Title: Visualization of Patient Profiles
Description: Creation of patient profile visualizations for
exploration, diagnostic or monitoring purposes during a clinical trial.
These static visualizations display a patient-specific overview
of the evolution during the trial time frame of
parameters of interest (as laboratory, ECG, vital signs),
presence of adverse events, exposure to a treatment;
associated with metadata patient information,
as demography, concomitant medication.
The visualizations can be tailored for specific domain(s) or endpoint(s) of interest.
Visualizations are exported into patient profile report(s)
or can be embedded in custom report(s).
Author: Laure Cougnaud [aut, cre],
Margaux Faes [rev] (tests),
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between patientProfilesVis versions 2.0.1 dated 2021-07-13 and 2.0.2 dated 2021-09-28
DESCRIPTION | 21 ++-- MD5 | 48 ++++----- NAMESPACE | 1 R/miscellaneous.R | 12 +- R/palettes.R | 14 +- R/report_subjectProfileCombine.R | 10 -- R/subjectProfileIntervalPlot.R | 15 +-- build/vignette.rds |binary inst/NEWS | 8 + inst/doc/patientProfiles-template-SDTM.html | 23 ++-- inst/doc/patientProfilesVis-introduction.html | 31 ++---- inst/template/subjectProfile.Rnw | 13 ++ man/subjectProfileIntervalPlot.Rd | 3 tests/testthat/test_addReferenceLinesProfilePlot.R | 26 ++--- tests/testthat/test_createSubjectProfileReport.R | 42 ++++---- tests/testthat/test_filterData.R | 65 +++++-------- tests/testthat/test_miscellaneous.R | 30 +++--- tests/testthat/test_palettes.R | 102 +++++++++++---------- tests/testthat/test_subjectProfileCombine.R | 41 +++----- tests/testthat/test_subjectProfileEventPlot.R | 50 +++++----- tests/testthat/test_subjectProfileIntervalPlot.R | 102 ++++++++++++++------- tests/testthat/test_subjectProfileLinePlot.R | 56 +++++------ tests/testthat/test_subjectProfileTextPlot.R | 40 ++++---- tests/testthat/test_timeAlignment.R | 52 ++-------- tests/testthat/test_timeTransformations.R | 10 +- 25 files changed, 422 insertions(+), 393 deletions(-)
More information about patientProfilesVis at CRAN
Permanent link
Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman
filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in
BLAS and LAPACK. Due to the speed of the filter, the fitting of
high-dimensional linear state space models to large datasets
becomes possible. This package also contains a plot function
for the visualization of the state vector and graphical
diagnostics of the residuals.
Author: David Luethi [aut],
Philipp Erb [aut],
Simon Otziger [aut],
Daniel McDonald [aut],
Paul Smith [aut, cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between FKF versions 0.1.7 dated 2020-06-14 and 0.2.1 dated 2021-09-28
FKF-0.1.7/FKF/inst/unitTests |only FKF-0.1.7/FKF/tests/doRUnit.R |only FKF-0.2.1/FKF/DESCRIPTION | 23 + FKF-0.2.1/FKF/MD5 | 40 +-- FKF-0.2.1/FKF/NAMESPACE | 2 FKF-0.2.1/FKF/NEWS.md | 11 FKF-0.2.1/FKF/R/fkf.R | 185 ++++---------- FKF-0.2.1/FKF/R/fks.R |only FKF-0.2.1/FKF/R/plot.fkf.R | 2 FKF-0.2.1/FKF/R/plot.fks.R |only FKF-0.2.1/FKF/README.md | 6 FKF-0.2.1/FKF/build/vignette.rds |binary FKF-0.2.1/FKF/inst/doc/FKF.R | 104 +------- FKF-0.2.1/FKF/inst/doc/FKF.Rmd | 167 ++++--------- FKF-0.2.1/FKF/inst/doc/FKF.html | 339 +++++++++++--------------- FKF-0.2.1/FKF/man/fkf.Rd | 164 +++--------- FKF-0.2.1/FKF/man/fks.Rd |only FKF-0.2.1/FKF/man/plot.fkf.Rd | 2 FKF-0.2.1/FKF/man/plot.fks.Rd |only FKF-0.2.1/FKF/src/fkflib.c | 497 ++++++++++++++++++++++++++++++++++----- FKF-0.2.1/FKF/src/init.c | 5 FKF-0.2.1/FKF/tests/testthat |only FKF-0.2.1/FKF/tests/testthat.R |only FKF-0.2.1/FKF/vignettes/FKF.Rmd | 167 ++++--------- 24 files changed, 892 insertions(+), 822 deletions(-)
Title: Classification and Clustering of Preference Rankings
Description: Tree-based classification and soft-clustering method for preference rankings, with tools for external validation of fuzzy clustering.
It contains the recursive partitioning algorithm for preference rankings, non-parametric tree-based method for a matrix of preference rankings as a response variable. It contains also the distribution-free soft clustering method for preference rankings, namely the K-median cluster component analysis (CCA).
The package depends on the 'ConsRank' R package.
Options for validate the tree-based method are both test-set procedure and V-fold cross validation.
The package contains the routines to compute the adjusted concordance index (a fuzzy version of the adjusted rand index) and the normalized degree of concordance (the corresponding fuzzy version of the rand index).
Essential references:
D'Ambrosio, A., Amodio, S., Iorio, C., Pandolfo, G., and Siciliano, R. (2021) <doi:10.1007/s00357-020-09367-0>
D'Ambrosio, A., and Heiser, W.J. (2019) <doi:10.1007/s41237-018-0069-5>;
D'Ambrosio, A., and Heiser W.J. (2016) <doi:10.1007/s11336-016-9505-1>;
Hullermeier, E., Rifqi, M., Henzgen, S., and Senge, R. (2012) <doi:10.1109/TFUZZ.2011.2179303>.
Author: Antonio D'Ambrosio [aut, cre]
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRankClass versions 1.0.0 dated 2021-05-18 and 1.0.1 dated 2021-09-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cca.R | 2 +- R/ranktree.R | 16 +++++++++++++++- 4 files changed, 23 insertions(+), 9 deletions(-)
Title: Compute the Median Ranking(s) According to the Kemeny's
Axiomatic Approach
Description: Compute the median ranking according to the Kemeny's axiomatic approach.
Rankings can or cannot contain ties, rankings can be both complete or incomplete.
The package contains both branch-and-bound algorithms and heuristic solutions recently proposed.
The searching space of the solution can either be restricted to the universe of the permutations or unrestricted to all possible ties.
The package also provide some useful utilities for deal with preference rankings.
This release declare as deprecated some functions that are still in the package for compatibility. Next release will not contains these functions.
Please type '?ConsRank-deprecated'
Essential references:
Emond, E.J., and Mason, D.W. (2002) <doi:10.1002/mcda.313>;
D'Ambrosio, A., Amodio, S., and Iorio, C. (2015) <doi:10.1285/i20705948v8n2p198>;
Amodio, S., D'Ambrosio, A., and Siciliano R. (2016) <doi:10.1016/j.ejor.2015.08.048>;
D'Ambrosio, A., Mazzeo, G., Iorio, C., and Siciliano, R. (2017) <doi:10.1016/j.cor.2017.01.017>.
Author: Antonio D'Ambrosio [aut, cre],
Sonia Amodio [ctb],
Giulio Mazzeo [ctb]
Maintainer: Antonio D'Ambrosio <antdambr@unina.it>
Diff between ConsRank versions 2.1.1 dated 2021-03-10 and 2.1.2 dated 2021-09-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/order2rank.R | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
More information about bistablehistory at CRAN
Permanent link
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.7.21 dated 2021-09-06 and 1.7.22 dated 2021-09-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 10 ++++++++++ R/zzz.R | 4 ++++ inst/include/tmbutils/array.hpp | 10 ++++++++++ src/solve_subset.c | 26 +++++++++++++++++++------- 6 files changed, 52 insertions(+), 16 deletions(-)
Title: A Framework for Comparing the Performance of MCMC Samplers
Description: A framework for running sets of MCMC samplers on sets of distributions with a variety of tuning parameters, along with plotting functions to visualize the results of those simulations.
Author: Madeleine Thompson, except dchud.f and dchdd.f, which were written by G. W. Stewart.
Maintainer: Madeleine Thompson <madeleineth@gmail.com>
Diff between SamplerCompare versions 1.3.0 dated 2018-09-10 and 1.3.1 dated 2021-09-28
DESCRIPTION | 12 +- MD5 | 62 +++++++-------- R/00dist-util.R | 4 R/act.R | 6 - R/basic-slice.R | 130 ++++++++++++------------------- R/c-samplers.R | 12 +- R/compare-samplers.R | 8 - R/comparison-plot.R | 37 ++++---- R/cov-match.R | 73 +++++++++-------- R/distributions.R | 173 ++++++++++++++++++++---------------------- R/metropolis.R | 84 +++++++++----------- R/oblique-hyperrect.R | 54 +++++-------- R/univar-eigen.R | 73 +++++++---------- R/util.R | 2 build/vignette.rds |binary inst/CITATION | 38 ++++----- inst/doc/glue.pdf |binary inst/doc/indep-mh-sampler.c | 32 +++---- inst/doc/sc-intro.pdf |binary inst/include/SamplerCompare.h | 2 man/ar.act.Rd | 2 src/arms.c | 6 + src/distributions.c | 30 +++---- src/sampler-glue.c | 135 +++++++++++++++++--------------- src/slice.c | 71 ++++++++++------- tests/test-chud.R | 20 +--- tests/test-gradients.R | 2 tests/test-indep-mh.R | 14 --- tests/test-lint.R | 10 -- tests/test-misc.R | 17 ++-- tests/test-samplers.R | 4 vignettes/jss668.bib | 4 32 files changed, 538 insertions(+), 579 deletions(-)
More information about SamplerCompare at CRAN
Permanent link
Title: Spherical Geometry Operators Using the S2 Geometry Library
Description: Provides R bindings for Google's s2 library for geometric calculations on
the sphere. High-performance constructors and exporters provide high compatibility
with existing spatial packages, transformers construct new geometries from existing
geometries, predicates provide a means to select geometries based on spatial
relationships, and accessors extract information about geometries.
Author: Dewey Dunnington [aut] (<https://orcid.org/0000-0002-9415-4582>),
Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Ege Rubak [aut],
Jeroen Ooms [ctb] (configure script),
Google, Inc. [cph] (Original s2geometry.io source code)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between s2 versions 1.0.6 dated 2021-06-17 and 1.0.7 dated 2021-09-28
s2-1.0.6/s2/inst/include |only s2-1.0.6/s2/src/s2/third_party |only s2-1.0.7/s2/DESCRIPTION | 11 s2-1.0.7/s2/MD5 | 728 ++++++---- s2-1.0.7/s2/NEWS.md | 5 s2-1.0.7/s2/README.md | 54 s2-1.0.7/s2/build/partial.rdb |binary s2-1.0.7/s2/inst/extdata |only s2-1.0.7/s2/src/Makevars.in | 99 + s2-1.0.7/s2/src/Makevars.win | 100 + s2-1.0.7/s2/src/RcppExports.cpp | 5 s2-1.0.7/s2/src/absl |only s2-1.0.7/s2/src/cpp-compat.h |only s2-1.0.7/s2/src/s2/_fp_contract_off.h |only s2-1.0.7/s2/src/s2/base/casts.h |only s2-1.0.7/s2/src/s2/base/commandlineflags.h |only s2-1.0.7/s2/src/s2/base/integral_types.h |only s2-1.0.7/s2/src/s2/base/log_severity.h |only s2-1.0.7/s2/src/s2/base/logging.h |only s2-1.0.7/s2/src/s2/base/mutex.h |only s2-1.0.7/s2/src/s2/base/port.h |only s2-1.0.7/s2/src/s2/base/spinlock.h |only s2-1.0.7/s2/src/s2/base/stringprintf.cc | 10 s2-1.0.7/s2/src/s2/base/stringprintf.h |only s2-1.0.7/s2/src/s2/base/strtoint.h |only s2-1.0.7/s2/src/s2/base/timer.h |only s2-1.0.7/s2/src/s2/encoded_s2cell_id_vector.h |only s2-1.0.7/s2/src/s2/encoded_s2point_vector.cc | 2 s2-1.0.7/s2/src/s2/encoded_s2point_vector.h |only s2-1.0.7/s2/src/s2/encoded_s2shape_index.cc | 2 s2-1.0.7/s2/src/s2/encoded_s2shape_index.h |only s2-1.0.7/s2/src/s2/encoded_string_vector.cc | 2 s2-1.0.7/s2/src/s2/encoded_string_vector.h |only s2-1.0.7/s2/src/s2/encoded_uint_vector.h |only s2-1.0.7/s2/src/s2/id_set_lexicon.h |only s2-1.0.7/s2/src/s2/mutable_s2shape_index.h |only s2-1.0.7/s2/src/s2/r1interval.h |only s2-1.0.7/s2/src/s2/r2.h |only s2-1.0.7/s2/src/s2/r2rect.h |only s2-1.0.7/s2/src/s2/s1angle.h |only s2-1.0.7/s2/src/s2/s1chord_angle.h |only s2-1.0.7/s2/src/s2/s1interval.h |only s2-1.0.7/s2/src/s2/s2boolean_operation.cc | 6 s2-1.0.7/s2/src/s2/s2boolean_operation.h |only s2-1.0.7/s2/src/s2/s2builder.cc | 2 s2-1.0.7/s2/src/s2/s2builder.h |only s2-1.0.7/s2/src/s2/s2builder_graph.cc | 4 s2-1.0.7/s2/src/s2/s2builder_graph.h |only s2-1.0.7/s2/src/s2/s2builder_layer.h |only s2-1.0.7/s2/src/s2/s2builderutil_closed_set_normalizer.cc | 2 s2-1.0.7/s2/src/s2/s2builderutil_closed_set_normalizer.h |only s2-1.0.7/s2/src/s2/s2builderutil_find_polygon_degeneracies.cc | 2 s2-1.0.7/s2/src/s2/s2builderutil_find_polygon_degeneracies.h |only s2-1.0.7/s2/src/s2/s2builderutil_graph_shape.h |only s2-1.0.7/s2/src/s2/s2builderutil_lax_polygon_layer.cc | 2 s2-1.0.7/s2/src/s2/s2builderutil_lax_polygon_layer.h |only s2-1.0.7/s2/src/s2/s2builderutil_s2point_vector_layer.h |only s2-1.0.7/s2/src/s2/s2builderutil_s2polygon_layer.cc | 2 s2-1.0.7/s2/src/s2/s2builderutil_s2polygon_layer.h |only s2-1.0.7/s2/src/s2/s2builderutil_s2polyline_layer.h |only s2-1.0.7/s2/src/s2/s2builderutil_s2polyline_vector_layer.h |only s2-1.0.7/s2/src/s2/s2builderutil_snap_functions.cc | 2 s2-1.0.7/s2/src/s2/s2builderutil_snap_functions.h |only s2-1.0.7/s2/src/s2/s2builderutil_testing.h |only s2-1.0.7/s2/src/s2/s2cap.h |only s2-1.0.7/s2/src/s2/s2cell.h |only s2-1.0.7/s2/src/s2/s2cell_id.cc | 16 s2-1.0.7/s2/src/s2/s2cell_id.h |only s2-1.0.7/s2/src/s2/s2cell_index.h |only s2-1.0.7/s2/src/s2/s2cell_union.h |only s2-1.0.7/s2/src/s2/s2centroids.h |only s2-1.0.7/s2/src/s2/s2closest_cell_query.cc | 2 s2-1.0.7/s2/src/s2/s2closest_cell_query.h |only s2-1.0.7/s2/src/s2/s2closest_cell_query_base.h |only s2-1.0.7/s2/src/s2/s2closest_edge_query.cc | 2 s2-1.0.7/s2/src/s2/s2closest_edge_query.h |only s2-1.0.7/s2/src/s2/s2closest_edge_query_base.h |only s2-1.0.7/s2/src/s2/s2closest_edge_query_testing.h |only s2-1.0.7/s2/src/s2/s2closest_point_query.h |only s2-1.0.7/s2/src/s2/s2closest_point_query_base.h |only s2-1.0.7/s2/src/s2/s2contains_point_query.h |only s2-1.0.7/s2/src/s2/s2contains_vertex_query.h |only s2-1.0.7/s2/src/s2/s2convex_hull_query.cc | 2 s2-1.0.7/s2/src/s2/s2convex_hull_query.h |only s2-1.0.7/s2/src/s2/s2coords.h |only s2-1.0.7/s2/src/s2/s2coords_internal.h |only s2-1.0.7/s2/src/s2/s2crossing_edge_query.h |only s2-1.0.7/s2/src/s2/s2debug.h |only s2-1.0.7/s2/src/s2/s2distance_target.h |only s2-1.0.7/s2/src/s2/s2earth.h |only s2-1.0.7/s2/src/s2/s2edge_clipping.h |only s2-1.0.7/s2/src/s2/s2edge_crosser.h |only s2-1.0.7/s2/src/s2/s2edge_crossings.h |only s2-1.0.7/s2/src/s2/s2edge_crossings_internal.h |only s2-1.0.7/s2/src/s2/s2edge_distances.h |only s2-1.0.7/s2/src/s2/s2edge_tessellator.h |only s2-1.0.7/s2/src/s2/s2edge_vector_shape.h |only s2-1.0.7/s2/src/s2/s2error.h |only s2-1.0.7/s2/src/s2/s2furthest_edge_query.h |only s2-1.0.7/s2/src/s2/s2latlng.cc | 4 s2-1.0.7/s2/src/s2/s2latlng.h |only s2-1.0.7/s2/src/s2/s2latlng_rect.h |only s2-1.0.7/s2/src/s2/s2latlng_rect_bounder.h |only s2-1.0.7/s2/src/s2/s2lax_loop_shape.h |only s2-1.0.7/s2/src/s2/s2lax_polygon_shape.h |only s2-1.0.7/s2/src/s2/s2lax_polyline_shape.h |only s2-1.0.7/s2/src/s2/s2loop.cc | 4 s2-1.0.7/s2/src/s2/s2loop.h |only s2-1.0.7/s2/src/s2/s2loop_measures.cc | 2 s2-1.0.7/s2/src/s2/s2loop_measures.h |only s2-1.0.7/s2/src/s2/s2max_distance_targets.cc | 2 s2-1.0.7/s2/src/s2/s2max_distance_targets.h |only s2-1.0.7/s2/src/s2/s2measures.h |only s2-1.0.7/s2/src/s2/s2metrics.h |only s2-1.0.7/s2/src/s2/s2min_distance_targets.cc | 2 s2-1.0.7/s2/src/s2/s2min_distance_targets.h |only s2-1.0.7/s2/src/s2/s2padded_cell.h |only s2-1.0.7/s2/src/s2/s2point.h |only s2-1.0.7/s2/src/s2/s2point_compression.cc | 8 s2-1.0.7/s2/src/s2/s2point_compression.h |only s2-1.0.7/s2/src/s2/s2point_index.h |only s2-1.0.7/s2/src/s2/s2point_region.h |only s2-1.0.7/s2/src/s2/s2point_span.h |only s2-1.0.7/s2/src/s2/s2point_vector_shape.h |only s2-1.0.7/s2/src/s2/s2pointutil.h |only s2-1.0.7/s2/src/s2/s2polygon.cc | 6 s2-1.0.7/s2/src/s2/s2polygon.h |only s2-1.0.7/s2/src/s2/s2polyline.cc | 2 s2-1.0.7/s2/src/s2/s2polyline.h |only s2-1.0.7/s2/src/s2/s2polyline_alignment.cc | 4 s2-1.0.7/s2/src/s2/s2polyline_alignment.h |only s2-1.0.7/s2/src/s2/s2polyline_alignment_internal.h |only s2-1.0.7/s2/src/s2/s2polyline_measures.h |only s2-1.0.7/s2/src/s2/s2polyline_simplifier.h |only s2-1.0.7/s2/src/s2/s2predicates.h |only s2-1.0.7/s2/src/s2/s2predicates_internal.h |only s2-1.0.7/s2/src/s2/s2projections.h |only s2-1.0.7/s2/src/s2/s2r2rect.h |only s2-1.0.7/s2/src/s2/s2region.h |only s2-1.0.7/s2/src/s2/s2region_coverer.cc | 2 s2-1.0.7/s2/src/s2/s2region_coverer.h |only s2-1.0.7/s2/src/s2/s2region_intersection.h |only s2-1.0.7/s2/src/s2/s2region_term_indexer.cc | 26 s2-1.0.7/s2/src/s2/s2region_term_indexer.h |only s2-1.0.7/s2/src/s2/s2region_union.h |only s2-1.0.7/s2/src/s2/s2shape.h |only s2-1.0.7/s2/src/s2/s2shape_index.h |only s2-1.0.7/s2/src/s2/s2shape_index_buffered_region.h |only s2-1.0.7/s2/src/s2/s2shape_index_measures.h |only s2-1.0.7/s2/src/s2/s2shape_index_region.h |only s2-1.0.7/s2/src/s2/s2shape_measures.h |only s2-1.0.7/s2/src/s2/s2shapeutil_build_polygon_boundaries.cc | 6 s2-1.0.7/s2/src/s2/s2shapeutil_build_polygon_boundaries.h |only s2-1.0.7/s2/src/s2/s2shapeutil_coding.cc | 2 s2-1.0.7/s2/src/s2/s2shapeutil_coding.h |only s2-1.0.7/s2/src/s2/s2shapeutil_contains_brute_force.h |only s2-1.0.7/s2/src/s2/s2shapeutil_count_edges.h |only s2-1.0.7/s2/src/s2/s2shapeutil_edge_iterator.cc | 4 s2-1.0.7/s2/src/s2/s2shapeutil_edge_iterator.h |only s2-1.0.7/s2/src/s2/s2shapeutil_get_reference_point.h |only s2-1.0.7/s2/src/s2/s2shapeutil_range_iterator.h |only s2-1.0.7/s2/src/s2/s2shapeutil_shape_edge.h |only s2-1.0.7/s2/src/s2/s2shapeutil_shape_edge_id.h |only s2-1.0.7/s2/src/s2/s2shapeutil_testing.h |only s2-1.0.7/s2/src/s2/s2shapeutil_visit_crossing_edge_pairs.h |only s2-1.0.7/s2/src/s2/s2testing.cc | 4 s2-1.0.7/s2/src/s2/s2testing.h |only s2-1.0.7/s2/src/s2/s2text_format.cc | 72 s2-1.0.7/s2/src/s2/s2text_format.h |only s2-1.0.7/s2/src/s2/s2wedge_relations.h |only s2-1.0.7/s2/src/s2/sequence_lexicon.h |only s2-1.0.7/s2/src/s2/strings/ostringstream.h |only s2-1.0.7/s2/src/s2/strings/serialize.cc | 4 s2-1.0.7/s2/src/s2/strings/serialize.h |only s2-1.0.7/s2/src/s2/util/bits/bit-interleave.h |only s2-1.0.7/s2/src/s2/util/bits/bits.cc | 2 s2-1.0.7/s2/src/s2/util/bits/bits.h |only s2-1.0.7/s2/src/s2/util/coding/coder.h |only s2-1.0.7/s2/src/s2/util/coding/nth-derivative.h |only s2-1.0.7/s2/src/s2/util/coding/transforms.h |only s2-1.0.7/s2/src/s2/util/coding/varint.cc | 4 s2-1.0.7/s2/src/s2/util/coding/varint.h |only s2-1.0.7/s2/src/s2/util/endian |only s2-1.0.7/s2/src/s2/util/gtl |only s2-1.0.7/s2/src/s2/util/hash |only s2-1.0.7/s2/src/s2/util/math/exactfloat/exactfloat.cc | 22 s2-1.0.7/s2/src/s2/util/math/exactfloat/exactfloat.h |only s2-1.0.7/s2/src/s2/util/math/mathutil.h |only s2-1.0.7/s2/src/s2/util/math/matrix3x3.h |only s2-1.0.7/s2/src/s2/util/math/vector.h |only s2-1.0.7/s2/src/s2/util/math/vector3_hash.h |only s2-1.0.7/s2/src/s2/util/units/length-units.h |only s2-1.0.7/s2/src/s2/util/units/physical-units.h |only s2-1.0.7/s2/src/s2/value_lexicon.h |only 194 files changed, 810 insertions(+), 434 deletions(-)
Title: Creation of in-Text Summary Table
Description: Creation of tables of summary statistics or counts for clinical data (for 'TLFs').
These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report
(Word format) or a 'topline' presentation (PowerPoint format),
or as interactive table (with the 'DT' package) to an html document for clinical data review.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Margaux Faes [rev] (tests),
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between inTextSummaryTable versions 3.0.1 dated 2021-07-13 and 3.1.0 dated 2021-09-28
inTextSummaryTable-3.0.1/inTextSummaryTable/tests/testthat/table-base-test.txt |only inTextSummaryTable-3.0.1/inTextSummaryTable/tests/testthat/table-base.txt |only inTextSummaryTable-3.0.1/inTextSummaryTable/tests/testthat/table-test.txt |only inTextSummaryTable-3.0.1/inTextSummaryTable/tests/testthat/table.txt |only inTextSummaryTable-3.1.0/inTextSummaryTable/DESCRIPTION | 24 inTextSummaryTable-3.1.0/inTextSummaryTable/MD5 | 153 - inTextSummaryTable-3.1.0/inTextSummaryTable/NAMESPACE | 5 inTextSummaryTable-3.1.0/inTextSummaryTable/R/computeSummaryStatistics.R | 28 inTextSummaryTable-3.1.0/inTextSummaryTable/R/computeSummaryStatisticsTable.R | 134 - inTextSummaryTable-3.1.0/inTextSummaryTable/R/decimals.R | 8 inTextSummaryTable-3.1.0/inTextSummaryTable/R/exportSummaryStatisticsTable.R | 22 inTextSummaryTable-3.1.0/inTextSummaryTable/R/formatSummaryStatisticsTable.R | 5 inTextSummaryTable-3.1.0/inTextSummaryTable/R/getSummaryStatisticsTable.R | 10 inTextSummaryTable-3.1.0/inTextSummaryTable/R/inTextSummaryTable-common-args-doc.R | 6 inTextSummaryTable-3.1.0/inTextSummaryTable/R/miscellaneous.R | 53 inTextSummaryTable-3.1.0/inTextSummaryTable/R/stats-getStats.R | 4 inTextSummaryTable-3.1.0/inTextSummaryTable/R/subjectProfileSummaryPlot.R | 4 inTextSummaryTable-3.1.0/inTextSummaryTable/R/summaryTable-combine.R |only inTextSummaryTable-3.1.0/inTextSummaryTable/R/summaryTable-doc.R |only inTextSummaryTable-3.1.0/inTextSummaryTable/build/vignette.rds |binary inTextSummaryTable-3.1.0/inTextSummaryTable/inst/NEWS | 8 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-advanced.Rmd | 32 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-advanced.html | 129 + inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-aesthetics.html | 65 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-createTables.Rmd | 2 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-createTables.html | 911 ++++------ inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-exportTables.Rmd | 4 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-exportTables.html | 220 +- inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-introduction.html | 17 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-standardTables.html | 163 - inTextSummaryTable-3.1.0/inTextSummaryTable/inst/doc/inTextSummaryTable-visualization.html | 17 inTextSummaryTable-3.1.0/inTextSummaryTable/inst/examples/summaryTable-combine.R |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/combine.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/combine.summaryTable.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/combineColTotal.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/computeSummaryStatistics.Rd | 7 inTextSummaryTable-3.1.0/inTextSummaryTable/man/computeSummaryStatisticsByRowColVar.Rd | 9 inTextSummaryTable-3.1.0/inTextSummaryTable/man/computeSummaryStatisticsTable.Rd | 70 inTextSummaryTable-3.1.0/inTextSummaryTable/man/computeSummaryStatisticsTableTotal.Rd | 3 inTextSummaryTable-3.1.0/inTextSummaryTable/man/convertSummaryStatisticsTableToFlextable.Rd | 3 inTextSummaryTable-3.1.0/inTextSummaryTable/man/convertVarFlag.Rd | 9 inTextSummaryTable-3.1.0/inTextSummaryTable/man/export.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/exportSummaryStatisticsTable.Rd | 26 inTextSummaryTable-3.1.0/inTextSummaryTable/man/formatSummaryStatisticsTable.Rd | 3 inTextSummaryTable-3.1.0/inTextSummaryTable/man/formatSummaryStatisticsTableFlextable.Rd | 3 inTextSummaryTable-3.1.0/inTextSummaryTable/man/getNDecimals.Rd | 6 inTextSummaryTable-3.1.0/inTextSummaryTable/man/getNDecimalsRule.Rd | 6 inTextSummaryTable-3.1.0/inTextSummaryTable/man/getSummaryStatisticsTable.Rd | 75 inTextSummaryTable-3.1.0/inTextSummaryTable/man/inTextSummaryTable-common-args.Rd | 7 inTextSummaryTable-3.1.0/inTextSummaryTable/man/postProcessVarFlag.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/subjectProfileSummaryPlot.Rd | 2 inTextSummaryTable-3.1.0/inTextSummaryTable/man/summaryTable.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/man/uniqueVarWithOrder.Rd |only inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_combine.R |only inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_combineVariables.R | 265 +- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatistics.R | 470 ++++- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-colVar.R | 157 + inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-general.R | 70 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-rowVar.R | 616 ++++-- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-stats.R | 150 + inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-total.R | 126 + inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_computeSummaryStatisticsTable-var.R | 827 ++++++--- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_createFlextableWithHeader.R | 224 +- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_decimals.R | 88 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_exportSummaryStatisticsTable-DT.R | 549 +++--- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_exportSummaryStatisticsTable-df.R | 40 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_exportSummaryStatisticsTable-flextable.R | 854 ++++----- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_exportSummaryStatisticsTable.R | 4 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_getListing.R | 334 +-- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_getStats.R | 62 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_getStatsData.R | 22 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_getSummaryStatisticsTable.R | 53 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_miscellaneous.R | 252 +- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_stats_utility.R | 34 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-aesthetics.R | 59 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-byVar.R | 47 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-general.R | 142 - inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-labels.R | 109 - inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-table.R | 384 ++-- inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-theme.R | 8 inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-xVar.R | 159 + inTextSummaryTable-3.1.0/inTextSummaryTable/tests/testthat/test_subjectProfileSummaryPlot-yVar.R | 225 +- inTextSummaryTable-3.1.0/inTextSummaryTable/vignettes/inTextSummaryTable-advanced.Rmd | 32 inTextSummaryTable-3.1.0/inTextSummaryTable/vignettes/inTextSummaryTable-createTables.Rmd | 2 inTextSummaryTable-3.1.0/inTextSummaryTable/vignettes/inTextSummaryTable-exportTables.Rmd | 4 85 files changed, 5178 insertions(+), 3443 deletions(-)
More information about inTextSummaryTable at CRAN
Permanent link
Title: Routines for Performing Empirical Calibration of Observational
Study Estimates
Description: Routines for performing empirical calibration of observational
study estimates. By using a set of negative control hypotheses we can
estimate the empirical null distribution of a particular observational
study setup. This empirical null distribution can be used to compute a
calibrated p-value, which reflects the probability of observing an
estimated effect size when the null hypothesis is true taking both random
and systematic error into account. A similar approach can be used to
calibrate confidence intervals, using both negative and positive controls.
For more details, see Schuemie et al. (2013) <doi:10.1002/sim.5925> and
Schuemie et al. (2018) <doi:10.1073/pnas.1708282114>.
Author: Martijn Schuemie [aut, cre] (<https://orcid.org/0000-0002-0817-5361>),
Marc Suchard [aut] (<https://orcid.org/0000-0001-9818-479X>)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EmpiricalCalibration versions 2.1.0 dated 2021-03-04 and 3.0.0 dated 2021-09-28
EmpiricalCalibration-2.1.0/EmpiricalCalibration/R/EmpiricalCalibrationUsingPLikelihood.R |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/DESCRIPTION | 17 - EmpiricalCalibration-3.0.0/EmpiricalCalibration/MD5 | 61 +++- EmpiricalCalibration-3.0.0/EmpiricalCalibration/NAMESPACE | 7 EmpiricalCalibration-3.0.0/EmpiricalCalibration/NEWS.md | 19 + EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/EmpiricalCalibration.R | 2 EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/EmpiricalCalibrationUsingAsymptotics.R | 143 ++++++++-- EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/EmpiricalCalibrationUsingMcmc.R | 32 +- EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/Likelihoods.R | 91 ++++-- EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/LlrCalibration.R |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/MaxSprtCriticalValues.R |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/RcppExports.R |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/R/Simulation.R | 94 ++++++ EmpiricalCalibration-3.0.0/EmpiricalCalibration/README.md | 8 EmpiricalCalibration-3.0.0/EmpiricalCalibration/build/vignette.rds |binary EmpiricalCalibration-3.0.0/EmpiricalCalibration/inst/doc/EmpiricalCiCalibrationVignette.pdf |binary EmpiricalCalibration-3.0.0/EmpiricalCalibration/inst/doc/EmpiricalMaxSprtCalibrationVignette.R |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/inst/doc/EmpiricalMaxSprtCalibrationVignette.Rmd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/inst/doc/EmpiricalMaxSprtCalibrationVignette.pdf |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/inst/doc/EmpiricalPCalibrationVignette.pdf |binary EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/calibrateLlr.Rd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/calibrateP.Rd | 130 ++++----- EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/computeCvBinomial.Rd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/computeCvPoisson.Rd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/computeTraditionalP.Rd | 60 ++-- EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/convertNullToErrorModel.Rd | 86 +++--- EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/fitMcmcNull.Rd | 80 ++--- EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/fitNullNonNormalLl.Rd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/man/simulateMaxSprtData.Rd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/src |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/tests |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/vignettes/EmpiricalMaxSprtCalibrationVignette.Rmd |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/vignettes/allLlrs.rds |only EmpiricalCalibration-3.0.0/EmpiricalCalibration/vignettes/cvs.rds |only 34 files changed, 579 insertions(+), 251 deletions(-)
More information about EmpiricalCalibration at CRAN
Permanent link
Title: Create, Manipulate and Query Parameter Terms
Description: Creates, manipulates, queries and repairs vectors of
parameter terms. Parameter terms are the labels used to reference
values in vectors, matrices and arrays. They represent the names in
coefficient tables and the column names in 'mcmc' and 'mcmc.list'
objects.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between term versions 0.3.2 dated 2021-09-06 and 0.3.3 dated 2021-09-28
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md | 10 ++++++++++ README.md | 6 +++--- build/term.pdf |binary man/figures/logo.png |only tests/testthat/test-npars.R | 4 ++-- 7 files changed, 25 insertions(+), 14 deletions(-)
Title: Generalized Framework for Cross-Validation
Description: A general framework for the application of cross-validation schemes
to particular functions. By allowing arbitrary lists of results, origami
accommodates a range of cross-validation applications. This implementation
was first described by Coyle and Hejazi (2018) <doi:10.21105/joss.00512>.
Author: Jeremy Coyle [aut, cre, cph] (<https://orcid.org/0000-0002-9874-6649>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
Ivana Malenica [aut] (<https://orcid.org/0000-0002-7404-8088>),
Rachael Phillips [aut] (<https://orcid.org/0000-0002-8474-591X>)
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>
Diff between origami versions 1.0.3 dated 2020-01-16 and 1.0.5 dated 2021-09-28
origami-1.0.3/origami/R/Fold.R |only origami-1.0.3/origami/man/Combiners.Rd |only origami-1.0.5/origami/DESCRIPTION | 24 origami-1.0.5/origami/MD5 | 39 - origami-1.0.5/origami/R/combine_results.R | 18 origami-1.0.5/origami/R/cross_validate.R | 4 origami-1.0.5/origami/R/fold.R |only origami-1.0.5/origami/R/fold_funs.R | 383 ++++++---- origami-1.0.5/origami/build/vignette.rds |binary origami-1.0.5/origami/inst/doc/generalizedCV.html | 292 +++---- origami-1.0.5/origami/inst/examples/cv_parallel_example.R | 22 origami-1.0.5/origami/inst/examples/cv_simple_example.R | 12 origami-1.0.5/origami/inst/rebuild.R | 11 origami-1.0.5/origami/inst/test/recursivesltest.R | 96 +- origami-1.0.5/origami/inst/test/testsplitfuns.R | 18 origami-1.0.5/origami/man/check_id_and_time.Rd |only origami-1.0.5/origami/man/combine_results.Rd | 4 origami-1.0.5/origami/man/combiners.Rd |only origami-1.0.5/origami/man/cross_validate.Rd | 34 origami-1.0.5/origami/man/fold_funs.Rd | 60 - origami-1.0.5/origami/man/fold_helpers.Rd | 2 origami-1.0.5/origami/man/make_fold.Rd | 2 origami-1.0.5/origami/tests/testthat/test-overall_timeseries.R | 107 ++ 23 files changed, 680 insertions(+), 448 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.7.1 dated 2021-07-21 and 0.8.0 dated 2021-09-28
hereR-0.7.1/hereR/man/set_rate_limit.Rd |only hereR-0.7.1/hereR/tests/testthat/test-rate_limit.R |only hereR-0.8.0/hereR/DESCRIPTION | 8 hereR-0.8.0/hereR/MD5 | 67 +- hereR-0.8.0/hereR/NAMESPACE | 3 hereR-0.8.0/hereR/NEWS.md | 6 hereR-0.8.0/hereR/R/checks.R | 522 ++++++++++---------- hereR-0.8.0/hereR/R/deprecated.R | 29 + hereR-0.8.0/hereR/R/geocode.R | 374 +++++++------- hereR-0.8.0/hereR/R/isoline.R | 546 ++++++++++----------- hereR-0.8.0/hereR/R/options.R | 13 hereR-0.8.0/hereR/R/route_matrix.R | 466 +++++++++-------- hereR-0.8.0/hereR/R/sysdata.rda |binary hereR-0.8.0/hereR/R/utils.R | 6 hereR-0.8.0/hereR/README.md | 286 +++++------ hereR-0.8.0/hereR/build/vignette.rds |binary hereR-0.8.0/hereR/inst/doc/authentication.Rmd | 2 hereR-0.8.0/hereR/inst/doc/authentication.html | 2 hereR-0.8.0/hereR/inst/doc/geocoder.R | 43 + hereR-0.8.0/hereR/inst/doc/geocoder.Rmd | 284 +++++----- hereR-0.8.0/hereR/inst/doc/geocoder.html | 68 +- hereR-0.8.0/hereR/inst/doc/intermodal.html | 32 - hereR-0.8.0/hereR/inst/doc/routing.Rmd | 258 ++++----- hereR-0.8.0/hereR/inst/doc/routing.html | 96 +-- hereR-0.8.0/hereR/inst/doc/transit.html | 86 +-- hereR-0.8.0/hereR/inst/doc/weather.html | 177 +++--- hereR-0.8.0/hereR/man/geocode.Rd | 2 hereR-0.8.0/hereR/man/hereR-deprecated.Rd | 9 hereR-0.8.0/hereR/man/isoline.Rd | 2 hereR-0.8.0/hereR/man/route_matrix.Rd | 2 hereR-0.8.0/hereR/man/set_freemium.Rd |only hereR-0.8.0/hereR/man/set_rate_limit-deprecated.Rd |only hereR-0.8.0/hereR/tests/testthat/test-freemium.R |only hereR-0.8.0/hereR/tests/testthat/test-geocode.R | 111 ++-- hereR-0.8.0/hereR/vignettes/authentication.Rmd | 2 hereR-0.8.0/hereR/vignettes/geocoder.Rmd | 284 +++++----- hereR-0.8.0/hereR/vignettes/routing.Rmd | 258 ++++----- 37 files changed, 2124 insertions(+), 1920 deletions(-)
Title: Manipulate DESCRIPTION Files
Description: Tools to read, write, create, and manipulate DESCRIPTION files.
It is intended for packages that create or manipulate other packages.
Author: Gábor Csárdi [aut, cre],
Kirill Müller [aut],
Jim Hester [aut],
Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>)
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between desc versions 1.3.0 dated 2021-03-05 and 1.4.0 dated 2021-09-28
desc-1.3.0/desc/tests/spelling.R |only desc-1.4.0/desc/DESCRIPTION | 10 +- desc-1.4.0/desc/MD5 | 81 ++++++++++---------- desc-1.4.0/desc/NAMESPACE | 2 desc-1.4.0/desc/NEWS.md | 37 +++++++++ desc-1.4.0/desc/R/authors-at-r.R | 71 ++++++++++++++++- desc-1.4.0/desc/R/classes.R | 7 + desc-1.4.0/desc/R/description.R | 46 ++++++++--- desc-1.4.0/desc/R/non-oo-api.R | 23 +++++ desc-1.4.0/desc/R/read.R | 6 + desc-1.4.0/desc/R/utils.R | 3 desc-1.4.0/desc/inst/WORDLIST | 4 - desc-1.4.0/desc/man/desc_get_field.Rd | 19 ++++ desc-1.4.0/desc/man/desc_set.Rd | 13 +++ desc-1.4.0/desc/man/description.Rd | 6 + desc-1.4.0/desc/tests/testthat/D12 |only desc-1.4.0/desc/tests/testthat/_snaps |only desc-1.4.0/desc/tests/testthat/output/to_latex.tex | 1 desc-1.4.0/desc/tests/testthat/test-archives.R | 2 desc-1.4.0/desc/tests/testthat/test-assertions.R | 2 desc-1.4.0/desc/tests/testthat/test-authors.R | 84 +++++++++++++-------- desc-1.4.0/desc/tests/testthat/test-built.R | 2 desc-1.4.0/desc/tests/testthat/test-checks.R | 3 desc-1.4.0/desc/tests/testthat/test-collate.R | 2 desc-1.4.0/desc/tests/testthat/test-create.R | 4 - desc-1.4.0/desc/tests/testthat/test-deps.R | 2 desc-1.4.0/desc/tests/testthat/test-desc.R | 2 desc-1.4.0/desc/tests/testthat/test-encoding.R | 20 ++++- desc-1.4.0/desc/tests/testthat/test-idempotent.R | 2 desc-1.4.0/desc/tests/testthat/test-non-oo.R | 26 +++--- desc-1.4.0/desc/tests/testthat/test-queries.R | 30 +++++++ desc-1.4.0/desc/tests/testthat/test-read.R | 9 +- desc-1.4.0/desc/tests/testthat/test-remotes.R | 2 desc-1.4.0/desc/tests/testthat/test-repair.R | 5 - desc-1.4.0/desc/tests/testthat/test-spelling.R |only desc-1.4.0/desc/tests/testthat/test-str.R | 22 ----- desc-1.4.0/desc/tests/testthat/test-to_latex.R | 1 desc-1.4.0/desc/tests/testthat/test-trailing-ws.R | 6 - desc-1.4.0/desc/tests/testthat/test-urls.R | 2 desc-1.4.0/desc/tests/testthat/test-utils.R | 2 desc-1.4.0/desc/tests/testthat/test-validation.R | 2 desc-1.4.0/desc/tests/testthat/test-versions.R | 2 desc-1.4.0/desc/tests/testthat/test-write.R | 2 43 files changed, 384 insertions(+), 181 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between ztable versions 0.2.2 dated 2020-10-08 and 0.2.3 dated 2021-09-28
DESCRIPTION | 6 MD5 | 22 - NEWS | 7 R/ztable2flextable.R | 22 - R/zzz.R | 2 build/vignette.rds |binary inst/doc/heatmapTable.html | 377 +++------------------- inst/doc/ztable.R | 2 inst/doc/ztable.Rmd | 2 inst/doc/ztable.html | 690 ++++++++++++---------------------------- inst/doc/ztable_update.html | 742 +++++++++++++++++++------------------------- vignettes/ztable.Rmd | 2 12 files changed, 645 insertions(+), 1229 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, PBC [cph],
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>),
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.33 dated 2021-08-05 and 0.34 dated 2021-09-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/install.R | 1 + R/tlmgr.R | 2 +- tests/test-travis/test-tlmgr.R | 6 ++++++ 5 files changed, 15 insertions(+), 8 deletions(-)
Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data
derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jeffrey Horner [ctb],
Beilei Bian [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between mime versions 0.11 dated 2021-06-23 and 0.12 dated 2021-09-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/parse.R | 2 +- src/rawmatch.c | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer and in
Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009).
Functional Data Analysis with R and Matlab (Springer).
The package includes data sets and script files working many examples
including all but one of the 76 figures in this latter book. Matlab versions
are available by ftp from
<https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre],
Spencer Graves <spencer.graves@effectivedefense.org> [ctb],
Giles Hooker <gjh27@cornell.edu> [ctb]
Maintainer: J. O. Ramsay <ramsay@psych.mcgill.ca>
Diff between fda versions 5.1.9 dated 2020-12-16 and 5.4.0 dated 2021-09-28
DESCRIPTION | 14 ++++---- MD5 | 55 +++++++++++++++++++++++++++++----- NAMESPACE | 23 ++++++++++---- R/eval.surp.R |only R/fdPar.R | 8 +++-- R/lnsrch.R |only R/smooth.monotone.R | 18 +++++++++-- R/smooth.surp.R |only R/surp.fit.R |only R/varmx.pca.fd.R | 2 - R/zerofind.R |only demo/gait.R | 78 +++++-------------------------------------------- inst |only man/eval.surp.Rd |only man/fdParcheck.Rd |only man/lnsrch.Rd |only man/smooth.monotone.Rd | 30 +++++++++--------- man/smooth.pos.Rd | 9 ++--- man/smooth.surp.Rd |only man/stepchk.Rd |only man/stepit.Rd |only man/surp.fit.Rd |only man/ycheck.Rd |only man/zerobasis.Rd |only 24 files changed, 120 insertions(+), 117 deletions(-)