Title: An Interface to the 'AutoDesk' 'API' Platform
Description: An interface to the 'AutoDesk' 'API' Platform including the Authentication
'API' for obtaining authentication to the 'AutoDesk' Forge Platform, Data Management
'API' for managing data across the platform's cloud services, Design Automation 'API'
for performing automated tasks on design files in the cloud, Model
Derivative 'API' for translating design files into different formats, sending
them to the viewer app, and extracting design data, and Viewer for rendering
2D and 3D models (see <https://developer.autodesk.com> for more information).
Author: Paul Govan [aut, cre]
Maintainer: Paul Govan <pgovan1@aggienetwork.com>
Diff between AutoDeskR versions 0.1.2 dated 2017-02-18 and 0.1.3 dated 2017-07-09
DESCRIPTION | 8 ++++---- MD5 | 42 ++++++++++++++++++++++-------------------- NEWS.md | 7 +++---- R/viewer.R | 8 ++++++-- inst/doc/AutoDeskR.html | 8 ++++---- inst/samples/airplane.dxf |only inst/viewer3D/vr.html |only man/checkBucket.Rd | 1 - man/checkFile.Rd | 1 - man/checkPdf.Rd | 1 - man/downloadFile.Rd | 1 - man/getData.Rd | 1 - man/getMetadata.Rd | 1 - man/getObjectTree.Rd | 1 - man/getOutputUrn.Rd | 1 - man/getToken.Rd | 1 - man/makeBucket.Rd | 1 - man/makePdf.Rd | 1 - man/translateObj.Rd | 1 - man/translateSvf.Rd | 1 - man/uploadFile.Rd | 1 - man/viewer3D.Rd | 5 ++--- man/viewerUI.Rd | 1 - 23 files changed, 41 insertions(+), 52 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav
Yalamanchi [aut], Mildenberger Thoralf [ctb], Deepak Yadav [ctb], Nacho Cordón
Castillo [ctb], Vandit Jain [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.6.9.3 dated 2017-05-19 and 0.6.9.6 dated 2017-07-09
ChangeLog | 3 DESCRIPTION | 12 MD5 | 80 +++-- NAMESPACE | 11 NEWS | 5 R/0_classesAndMethods.R | 34 +- R/0_ctmcClassesAndMethodsSAI.R | 149 +++++++++ R/1_ctmcProbabilisticSAI.R | 284 +++++++++++++++++++ R/1_functions4Fitting.R | 55 +++ R/1_supplementaryPlot.R | 24 + R/2_probabilistic.R | 186 +++++++++++- R/5_statisticalTests.R | 2 R/RcppExports.R | 78 +++-- R/data.R | 22 + build/vignette.rds |binary data/tm_abs.rda |only demo/00Index | 4 demo/computationTime.R |only demo/quasiBayesian.R | 39 +- demo/reliability.R |only inst/doc/GSoC-2017_additions.R |only inst/doc/GSoC-2017_additions.Rmd |only inst/doc/GSoC-2017_additions.html |only inst/doc/an_introduction_to_markovchain_package.R | 133 ++++++-- inst/doc/an_introduction_to_markovchain_package.Rnw | 91 ++++++ inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/complicateSteadyStates.pdf |binary inst/doc/higher_order_markov_chains.pdf |binary inst/doc/markovchainCrashIntro.pdf |binary man/ExpectedTime.Rd |only man/committorAB.Rd |only man/ctmc-class.Rd | 3 man/firstPassageMultiple.Rd |only man/freq2Generator.Rd |only man/ictmc-class.Rd |only man/impreciseProbabilityatT.Rd |only man/multinomialConfidenceIntervals.Rd | 41 +- man/noofVisitsDist.Rd |only man/probabilityatT.Rd |only man/tm_abs.Rd |only src/1_ctmcProbabilistic.cpp |only src/1_functions4Fitting.cpp | 27 + src/2_probabilistic.cpp | 27 + src/RcppExports.cpp | 65 ++++ src/init.c | 10 tests/testthat/testPlot.R | 20 + tests/testthat/testctmc.R |only vignettes/GSoC-2017_additions.Rmd |only vignettes/an_introduction_to_markovchain_package.Rnw | 91 ++++++ vignettes/markovchainBiblio.bib | 37 ++ 50 files changed, 1363 insertions(+), 170 deletions(-)
Title: Inference of Fuzzy Cognitive Maps (FCMs)
Description: Provides a selection of 3 different inference rules (including additionally the clamped types of the referred inference rules) and 4 threshold functions in order to obtain the inference of the FCM (Fuzzy Cognitive Map). Moreover, the 'fcm' package returns a data frame of the concepts' values of each state after the inference procedure. Fuzzy cognitive maps were introduced by Kosko (1986) <doi:10.1002/int.4550010405> providing ideal causal cognition tools for modeling and simulating dynamic systems.
Author: Zoumpoulia Dikopoulou <dikopoulia@gmail.com> <zoumpolia.dikopoulou@uhasselt.be>, Elpiniki Papageorgiou <epapageorgiou@teiste.gr>, <e.i.papageorgiou75@gmail.com>
Maintainer: Zoumpoulia Dikopoulou <dikopoulia@gmail.com>
Diff between fcm versions 0.1.2 dated 2017-07-04 and 0.1.3 dated 2017-07-09
DESCRIPTION | 10 +-- MD5 | 16 ++--- R/fcm.R | 2 R/fcm.infer.R | 12 ++-- inst/doc/vignettes.Rmd | 79 ++++++++++++++++++--------- inst/doc/vignettes.html | 136 +++++++++++++++++++++++++++++++++--------------- man/fcm.Rd | 2 man/fcm.infer.Rd | 8 +- vignettes/vignettes.Rmd | 14 ++-- 9 files changed, 177 insertions(+), 102 deletions(-)
Title: R Package Installation from Remote Repositories, Including
'GitHub'
Description: Download and install R packages stored in 'GitHub',
'BitBucket', or plain 'subversion' or 'git' repositories. This package
is a lightweight replacement of the 'install_*' functions in 'devtools'.
Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
RStudio [cph],
Martin Morgan [aut],
Dan Tenenbaum [aut],
Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between remotes versions 1.0.0 dated 2016-09-09 and 1.1.0 dated 2017-07-09
DESCRIPTION | 19 ++++--- MD5 | 59 ++++++++++++----------- NAMESPACE | 3 - NEWS.md | 19 +++++++ R/bioc.R | 7 ++ R/circular.R |only R/decompress.R | 2 R/deps.R | 28 +++++++---- R/download.R | 23 ++++++--- R/install-github.R | 6 +- R/install-local.R | 2 R/install.R | 7 ++ R/package.R | 11 ++++ R/utils.R | 24 +++++++++ inst/README.md | 87 +++++++++++++++++++++++++---------- man/bioc_install_repos.Rd | 1 man/download_version.Rd | 5 -- man/github_refs.Rd | 1 man/install_bitbucket.Rd | 1 man/install_deps.Rd | 3 - man/install_git.Rd | 1 man/install_github.Rd | 1 man/install_local.Rd | 1 man/install_svn.Rd | 1 man/install_url.Rd | 1 man/install_version.Rd | 5 -- man/package_deps.Rd | 7 +- man/parse_github_repo_spec.Rd | 1 man/update_packages.Rd | 1 tests/testthat/test-download.R | 18 +++++-- tests/testthat/test-install-github.R | 7 ++ 31 files changed, 234 insertions(+), 118 deletions(-)
Title: Genetic Algorithm for Wind Farm Layout Optimization
Description: The genetic algorithm is designed to optimize small wind farms consisting
of up to 50 turbines. The algorithm works with a fixed amount of turbines, a fixed
rotor radius and a mean wind speed value for every incoming wind direction.
If required, it can include a terrain effect model which downloads an
'SRTM' elevation model automatically and loads a Corine Land Cover raster,
which has to be downloaded previously.
Further information can be found in the description of the function 'windfarmGA'.
To start an optimization run, either the function 'windfarmGA' or 'genAlgo' can
be used. The function 'windfarmGA' checks the user inputs interactively and then
runs the function 'genAlgo'. If the input parameters are already known, an
optimization can be run directly via the function 'genAlgo'.
Their output is identical.
Author: Sebastian Gatscha
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Diff between windfarmGA versions 1.0 dated 2017-06-24 and 1.1 dated 2017-07-09
windfarmGA-1.0/windfarmGA/R/InitFile.R |only windfarmGA-1.1/windfarmGA/DESCRIPTION | 22 - windfarmGA-1.1/windfarmGA/MD5 | 137 +++++---- windfarmGA-1.1/windfarmGA/NAMESPACE | 25 + windfarmGA-1.1/windfarmGA/R/BaroHoehe.R | 16 - windfarmGA-1.1/windfarmGA/R/GoogleChromePlot.R | 41 -- windfarmGA-1.1/windfarmGA/R/GooglePlot.R | 117 +++++--- windfarmGA-1.1/windfarmGA/R/GridFilter.R | 64 +++- windfarmGA-1.1/windfarmGA/R/HexaTex.R |only windfarmGA-1.1/windfarmGA/R/InfluPoints.R | 10 windfarmGA-1.1/windfarmGA/R/PlotWindfarmGA.R | 116 ++++---- windfarmGA-1.1/windfarmGA/R/PointToLine2.R | 31 -- windfarmGA-1.1/windfarmGA/R/StartGA.R | 20 - windfarmGA-1.1/windfarmGA/R/VekWincelCalc.R | 12 windfarmGA-1.1/windfarmGA/R/WinkelCalc.R | 4 windfarmGA-1.1/windfarmGA/R/calculateEn.R | 164 +++++++++-- windfarmGA-1.1/windfarmGA/R/crossover1.R | 27 - windfarmGA-1.1/windfarmGA/R/eucDist.R | 4 windfarmGA-1.1/windfarmGA/R/fitness.R | 82 ++++- windfarmGA-1.1/windfarmGA/R/genAlgo.R | 234 +++++++++++----- windfarmGA-1.1/windfarmGA/R/getRects.R | 13 windfarmGA-1.1/windfarmGA/R/heatmapGA.R | 64 +--- windfarmGA-1.1/windfarmGA/R/leafPlot.R |only windfarmGA-1.1/windfarmGA/R/mutation.R | 12 windfarmGA-1.1/windfarmGA/R/plotEvolution.R | 45 --- windfarmGA-1.1/windfarmGA/R/plotResults.R | 255 +++++++++++------- windfarmGA-1.1/windfarmGA/R/plotWindrose.R | 14 windfarmGA-1.1/windfarmGA/R/plotbeorwor.R | 32 -- windfarmGA-1.1/windfarmGA/R/plotcloud.R | 37 -- windfarmGA-1.1/windfarmGA/R/plotfitnessevolution.R | 31 -- windfarmGA-1.1/windfarmGA/R/plotparkfitness.R | 175 ++++-------- windfarmGA-1.1/windfarmGA/R/readInteger.R | 4 windfarmGA-1.1/windfarmGA/R/readintegerSel.R | 4 windfarmGA-1.1/windfarmGA/R/selection1.R | 17 - windfarmGA-1.1/windfarmGA/R/splitAt.R | 8 windfarmGA-1.1/windfarmGA/R/tess2SPdf.R |only windfarmGA-1.1/windfarmGA/R/trimton.R | 31 +- windfarmGA-1.1/windfarmGA/R/windfarmGA.R | 179 +++++++++--- windfarmGA-1.1/windfarmGA/inst/extdata/a_weibull.rda |only windfarmGA-1.1/windfarmGA/inst/extdata/k_weibull.rda |only windfarmGA-1.1/windfarmGA/inst/extdata/polygon.rda |only windfarmGA-1.1/windfarmGA/inst/extdata/resulthex.rda |only windfarmGA-1.1/windfarmGA/inst/extdata/resultrect.rda |only windfarmGA-1.1/windfarmGA/inst/extdata/windturdk.png |only windfarmGA-1.1/windfarmGA/man/BaroHoehe.Rd | 3 windfarmGA-1.1/windfarmGA/man/GoogleChromePlot.Rd | 39 -- windfarmGA-1.1/windfarmGA/man/GooglePlot.Rd | 58 ++-- windfarmGA-1.1/windfarmGA/man/GridFilter.Rd | 24 + windfarmGA-1.1/windfarmGA/man/HexaTex.Rd |only windfarmGA-1.1/windfarmGA/man/InfluPoints.Rd | 3 windfarmGA-1.1/windfarmGA/man/PlotWindfarmGA.Rd | 68 ++-- windfarmGA-1.1/windfarmGA/man/PointToLine2.Rd | 15 - windfarmGA-1.1/windfarmGA/man/StartGA.Rd | 9 windfarmGA-1.1/windfarmGA/man/VekWinkelCalc.Rd | 7 windfarmGA-1.1/windfarmGA/man/WinkelCalc.Rd | 2 windfarmGA-1.1/windfarmGA/man/calculateEn.Rd | 89 ++++-- windfarmGA-1.1/windfarmGA/man/crossover1.Rd | 3 windfarmGA-1.1/windfarmGA/man/euc.dist.Rd | 3 windfarmGA-1.1/windfarmGA/man/fitness.Rd | 46 ++- windfarmGA-1.1/windfarmGA/man/genAlgo.Rd | 81 ++++- windfarmGA-1.1/windfarmGA/man/getRects.Rd | 2 windfarmGA-1.1/windfarmGA/man/heatmapGA.Rd | 39 -- windfarmGA-1.1/windfarmGA/man/leafPlot.Rd |only windfarmGA-1.1/windfarmGA/man/mutation.Rd | 9 windfarmGA-1.1/windfarmGA/man/plotCloud.Rd | 32 -- windfarmGA-1.1/windfarmGA/man/plotEvolution.Rd | 37 -- windfarmGA-1.1/windfarmGA/man/plotResult.Rd | 80 +++-- windfarmGA-1.1/windfarmGA/man/plotWindrose.Rd | 3 windfarmGA-1.1/windfarmGA/man/plotbeorwor.Rd | 29 -- windfarmGA-1.1/windfarmGA/man/plotfitnessevolution.Rd | 29 -- windfarmGA-1.1/windfarmGA/man/plotparkfitness.Rd | 34 -- windfarmGA-1.1/windfarmGA/man/selection1.Rd | 10 windfarmGA-1.1/windfarmGA/man/splitAt.Rd | 7 windfarmGA-1.1/windfarmGA/man/tess2SPdf.Rd |only windfarmGA-1.1/windfarmGA/man/trimton.Rd | 2 windfarmGA-1.1/windfarmGA/man/windfarmGA.Rd | 123 ++++++-- 76 files changed, 1693 insertions(+), 1240 deletions(-)
Title: Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods described by Lund, Nettleton, McCarthy, and Smyth (2012) <DOI:10.1515/1544-6115.1826>. Report bias-reduced estimates of log fold changes.
Author: Steve Lund [aut],
Long Qu [aut, cre, ctb],
Klirk Bhasavanich [aut],
Ian Marschner [aut] (The author of glm2::glm.fit2, which was modified
slightly leading to glm.fit3 in this package.),
R Core Team [aut] (The author of stats::glm.fit, which was modified
slightly leading to glm.fit3 in this package.)
Maintainer: Long Qu <rtistician@gmail.com>
Diff between QuasiSeq versions 1.0-8 dated 2015-05-15 and 1.0-10-1 dated 2017-07-09
QuasiSeq-1.0-10-1/QuasiSeq/DESCRIPTION | 23 QuasiSeq-1.0-10-1/QuasiSeq/MD5 | 58 - QuasiSeq-1.0-10-1/QuasiSeq/NAMESPACE | 46 - QuasiSeq-1.0-10-1/QuasiSeq/R/NBDev.R | 118 +- QuasiSeq-1.0-10-1/QuasiSeq/R/PoisDev.R | 144 ++- QuasiSeq-1.0-10-1/QuasiSeq/R/QL.fit.R | 353 ++++---- QuasiSeq-1.0-10-1/QuasiSeq/R/QL.results.R | 386 ++++----- QuasiSeq-1.0-10-1/QuasiSeq/R/bartlettGlm.R |only QuasiSeq-1.0-10-1/QuasiSeq/R/coefglm.R | 79 + QuasiSeq-1.0-10-1/QuasiSeq/R/fbrNBglm.R | 804 ++++++++++++-------- QuasiSeq-1.0-10-1/QuasiSeq/R/glm.fit3.R | 574 +++++++------- QuasiSeq-1.0-10-1/QuasiSeq/R/glmsolve.R | 268 ++++-- QuasiSeq-1.0-10-1/QuasiSeq/R/mockRNASeqData.R |only QuasiSeq-1.0-10-1/QuasiSeq/R/negbin.R | 248 +++--- QuasiSeq-1.0-10-1/QuasiSeq/R/nlsolve.R | 177 ++-- QuasiSeq-1.0-10-1/QuasiSeq/R/utils.R |only QuasiSeq-1.0-10-1/QuasiSeq/data |only QuasiSeq-1.0-10-1/QuasiSeq/man/NBDev.Rd | 131 ++- QuasiSeq-1.0-10-1/QuasiSeq/man/PoisDev.Rd | 83 +- QuasiSeq-1.0-10-1/QuasiSeq/man/QL.fit.Rd | 266 +++--- QuasiSeq-1.0-10-1/QuasiSeq/man/QL.results.Rd | 173 +--- QuasiSeq-1.0-10-1/QuasiSeq/man/coef.glm.Rd |only QuasiSeq-1.0-10-1/QuasiSeq/man/fbrNBglm.Rd |only QuasiSeq-1.0-10-1/QuasiSeq/man/glmSolve.Rd |only QuasiSeq-1.0-10-1/QuasiSeq/man/mockRNASeqData.Rd |only QuasiSeq-1.0-10-1/QuasiSeq/man/negbin.Rd |only QuasiSeq-1.0-10-1/QuasiSeq/man/nlSolve.Rd |only QuasiSeq-1.0-10-1/QuasiSeq/src/glmBias.c | 5 QuasiSeq-1.0-10-1/QuasiSeq/src/registration.c | 13 QuasiSeq-1.0-10-1/QuasiSeq/tests |only QuasiSeq-1.0-8/QuasiSeq/R/duplicated.matrix.R |only QuasiSeq-1.0-8/QuasiSeq/src/uniqueNumericMatrix.cpp |only 32 files changed, 2200 insertions(+), 1749 deletions(-)
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: The focus of the dnet is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.0.10 dated 2017-01-27 and 1.1.1 dated 2017-07-09
DESCRIPTION | 12 +-- MD5 | 110 +++++++++++++++++----------------- NAMESPACE | 1 R/dGSEA.r | 36 ++++++++--- R/dGSEAview.r | 38 ++++++++--- R/visBoxplotAdv.r | 1 R/visGSEA.r | 40 ++++++++---- R/visNet.r | 6 - R/visNetAnimate.r | 4 - R/visNetCircle.r | 2 data/TCGA_mutations.RData |binary data/ig.HPPA.RData |binary data/org.Hs.egHPPA.RData |binary inst/NEWS | 18 +++++ inst/staticdocs/templates/footer.html | 2 man/dBUMfit.Rd | 1 man/dBUMscore.Rd | 1 man/dCheckParallel.Rd | 1 man/dCommSignif.Rd | 1 man/dContrast.Rd | 1 man/dDAGancestor.Rd | 1 man/dDAGannotate.Rd | 1 man/dDAGgeneSim.Rd | 1 man/dDAGinduce.Rd | 1 man/dDAGlevel.Rd | 1 man/dDAGreverse.Rd | 1 man/dDAGroot.Rd | 1 man/dDAGtermSim.Rd | 1 man/dDAGtip.Rd | 1 man/dEnricher.Rd | 1 man/dEnricherView.Rd | 1 man/dFDRscore.Rd | 1 man/dFunArgs.Rd | 1 man/dGSEA.Rd | 4 - man/dGSEAview.Rd | 9 +- man/dGSEAwrite.Rd | 1 man/dNetConfidence.Rd | 1 man/dNetFind.Rd | 1 man/dNetInduce.Rd | 1 man/dNetPipeline.Rd | 1 man/dNetReorder.Rd | 1 man/dPvalAggregate.Rd | 1 man/dRDataLoader.Rd | 1 man/dRWR.Rd | 1 man/dRWRcontact.Rd | 1 man/dRWRpipeline.Rd | 1 man/dSVDsignif.Rd | 1 man/visBoxplotAdv.Rd | 1 man/visDAG.Rd | 1 man/visGSEA.Rd | 10 --- man/visNet.Rd | 6 + man/visNetAnimate.Rd | 9 +- man/visNetArc.Rd | 1 man/visNetCircle.Rd | 3 man/visNetMul.Rd | 1 man/visNetReorder.Rd | 1 56 files changed, 185 insertions(+), 161 deletions(-)
Title: Methods for Analyzing Binned Income Data
Description: Methods for model selection, model averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation, etc, on binned income data where the topmost bin is right-censored. We provide both a non-parametric method, termed the bounded midpoint estimator (BME), which assigns cases to their bin midpoints; except for the censored bins, where cases are assigned to an income estimated by fitting a Pareto distribution. Because the usual Pareto estimate can be inaccurate or undefined, especially in small samples, we implement a bounded Pareto estimate that yields much better results. We also provide a parametric approach, which fits distributions from the generalized beta (GB) family. Because some GB distributions can have poor fit or undefined estimates, we fit 10 GB-family distributions and use multimodel inference to obtain definite estimates from the best-fitting distributions. We also provide binned income data from all United States of America school districts, counties, and states.
Author: Samuel V. Scarpino, Paul von Hippel, and Igor Holas
Maintainer: Samuel V. Scarpino <scarpino@utexas.edu>
Diff between binequality versions 1.0.1 dated 2016-12-16 and 1.0.2 dated 2017-07-09
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/fitFunc.R | 30 ++++++++++++++++++++++++------ R/run_GB_family.R | 2 +- data/county_bins.rda |binary data/school_district_bins.rda |binary data/state_bins.rda |binary man/binequality-package.Rd | 4 ++-- man/fitFunc.Rd | 8 ++++---- man/run_GB_family.Rd | 2 +- 10 files changed, 45 insertions(+), 27 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods specifically handling sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2017), the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation for 'mice'.
Author: Vincent Audigier [aut, cre] (INSERM ECSTRA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@univ-paris-diderot.fr>
Diff between micemd versions 1.0.0 dated 2017-05-12 and 1.1.0 dated 2017-07-09
DESCRIPTION | 10 - MD5 | 18 +-- R/mice.impute.2l.glm.bin.R | 29 +++-- R/mice.impute.2l.glm.norm.R | 25 +++- R/mice.impute.2l.glm.pois.R | 25 +++- R/mice.impute.2l.jomo.R | 35 +++++- R/micemd-internal.R | 250 ++++++++++++++++++++++---------------------- data/CHEM97Na.rda |binary data/IPDNa.rda |binary man/micemd-package.Rd | 4 10 files changed, 233 insertions(+), 163 deletions(-)
Title: Exploratory Data Analysis and Data Preparation Tool-Box Book
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book Data Science Live Book (<http://livebook.datascienceheroes.com/>) are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas
Maintainer: Pablo Casas <pcasas.biz@gmail.com>
Diff between funModeling versions 1.6.4 dated 2017-06-17 and 1.6.5 dated 2017-07-09
DESCRIPTION | 8 +- MD5 | 27 ++++---- NAMESPACE | 4 + R/attach.R | 2 R/cross_plot.R | 2 R/models_lib.R | 12 +++ R/numbers.R | 160 ++++---------------------------------------------- R/outliers.R |only man/auto_grouping.Rd | 2 man/df_status.Rd | 4 - man/freq.Rd | 4 - man/hampel_outlier.Rd |only man/plot_num.Rd | 4 - man/prep_outliers.Rd | 42 +++++++++---- man/profiling_num.Rd | 2 man/tukey_outlier.Rd |only 16 files changed, 88 insertions(+), 185 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.12.1 dated 2017-06-16 and 2.12.2 dated 2017-07-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ man/prediction.Rd | 4 ++-- src/Makevars | 2 +- src/predictionfam.f90 | 4 ++-- 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Manipulation Testing Based on Density Discontinuity
Description: Density discontinuity test (a.k.a. manipulation test) is commonly employed in regression discontinuity designs and other treatment effect settings to detect whether there is evidence suggesting perfect self-selection (manipulation) around a cutoff where a treatment/policy assignment changes. This package provides tools for conducting the aforementioned statistical test: rddensity() to construct local polynomial based density discontinuity test given a prespecified cutoff, rdbwdensity() to perform bandwidth selection, and rdplotdensity() to construct density plot near the cutoff.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <xinweima@umich.edu>
Diff between rddensity versions 0.2 dated 2017-06-04 and 0.2.1 dated 2017-07-09
DESCRIPTION | 6 ++--- MD5 | 19 ++++++++------- R/rdbwdensity.R | 14 ++++++----- R/rddensity-package.R |only R/rddensity.R | 56 +++++------------------------------------------ R/rddensity_senate.R | 10 +------- R/rdplotdensity.R | 13 +++++----- man/rdbwdensity.Rd | 15 ++++++------ man/rddensity-package.Rd | 13 ++++++---- man/rddensity.Rd | 14 +++++------ man/rdplotdensity.Rd | 12 +++++----- 11 files changed, 66 insertions(+), 106 deletions(-)
Title: Local Polynomial Density Estimation and Inference
Description: Without imposing stringent distributional assumptions or shape restrictions, nonparametric density estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density estimator based on local polynomial regression, documented in Cattaneo, Jansson and Ma (2017a): lpdensity() to construct local polynomial based density (and derivatives) estimator; lpbwdensity() to perform data-driven bandwidth selection; and lpdensity.plot() for density plot with robust confidence interval.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <xinweima@umich.edu>
Diff between lpdensity versions 0.2.1 dated 2017-06-03 and 0.2.2 dated 2017-07-09
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/lpbwdensity.R | 8 ++++---- R/lpdensity-package.R | 6 +++--- R/lpdensity.R | 6 +++--- R/lpdensity.plot.R | 6 +++--- man/lpbwdensity.Rd | 8 ++++---- man/lpdensity-package.Rd | 6 +++--- man/lpdensity.Rd | 6 +++--- man/lpdensity.plot.Rd | 6 +++--- 10 files changed, 38 insertions(+), 38 deletions(-)
Title: Multinomial Logit Models with Random Parameters
Description: An implementation of maximum simulated likelihood method for the
estimation of multinomial logit models with random coefficients.
Specifically, it allows estimating models with continuous heterogeneity
such as the mixed multinomial logit and the generalized multinomial logit.
It also allows estimating models with discrete heterogeneity such as the
latent class and the mixed-mixed multinomial logit model.
Author: Mauricio Sarrias [aut, cre],
Ricardo Daziano [aut],
Yves Croissant [ctb]
Maintainer: Mauricio Sarrias <msarrias86@gmail.com>
Diff between gmnl versions 1.1-1 dated 2015-11-07 and 1.1-3 dated 2017-07-09
DESCRIPTION | 8 +- MD5 | 13 ++-- R/gmnl.R | 46 +++++++++----- R/gmnl.logliks.R | 173 +++++++++++++++++++++++++++---------------------------- R/gmnl.methods.R | 20 +++--- R/gmnl.tools.R | 3 inst/CITATION |only inst/NEWS.Rd | 20 ++++++ 8 files changed, 160 insertions(+), 123 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging and a distance based on global alignment kernels
are also provided. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 4.0.1 dated 2017-06-08 and 4.0.2 dated 2017-07-09
dtwclust-4.0.1/dtwclust/tests/testthat/regression/centroids.R |only dtwclust-4.0.1/dtwclust/tests/testthat/regression/methods.R |only dtwclust-4.0.2/dtwclust/DESCRIPTION | 30 dtwclust-4.0.2/dtwclust/MD5 | 222 - dtwclust-4.0.2/dtwclust/NAMESPACE | 5 dtwclust-4.0.2/dtwclust/R/DBA.R | 297 - dtwclust-4.0.2/dtwclust/R/Distmat.R | 187 - dtwclust-4.0.2/dtwclust/R/GAK.R | 258 - dtwclust-4.0.2/dtwclust/R/NCCc.R | 52 dtwclust-4.0.2/dtwclust/R/SBD.R | 148 dtwclust-4.0.2/dtwclust/R/SparseDistmat.R | 93 dtwclust-4.0.2/dtwclust/R/TADPole.R | 291 - dtwclust-4.0.2/dtwclust/R/all-cent.R | 554 +-- dtwclust-4.0.2/dtwclust/R/all-cent2.R | 392 +- dtwclust-4.0.2/dtwclust/R/as-methods.R | 2 dtwclust-4.0.2/dtwclust/R/compare-clusterings.R | 11 dtwclust-4.0.2/dtwclust/R/compute-envelope.R | 116 dtwclust-4.0.2/dtwclust/R/create-dtwclust.R | 266 - dtwclust-4.0.2/dtwclust/R/cvi.R | 9 dtwclust-4.0.2/dtwclust/R/ddist.R | 344 +- dtwclust-4.0.2/dtwclust/R/ddist2.R | 371 +- dtwclust-4.0.2/dtwclust/R/dtw-basic.R | 174 - dtwclust-4.0.2/dtwclust/R/dtw-lb.R | 535 +-- dtwclust-4.0.2/dtwclust/R/dtw2.R | 106 dtwclust-4.0.2/dtwclust/R/dtwclust-classes.R | 398 +- dtwclust-4.0.2/dtwclust/R/dtwclust-methods.R | 1706 +++++----- dtwclust-4.0.2/dtwclust/R/dtwclust.R | 8 dtwclust-4.0.2/dtwclust/R/fuzzy.R | 34 dtwclust-4.0.2/dtwclust/R/globals-internal.R | 3 dtwclust-4.0.2/dtwclust/R/lb-improved.R | 439 +- dtwclust-4.0.2/dtwclust/R/lb-keogh.R | 385 +- dtwclust-4.0.2/dtwclust/R/partitional.R | 506 +- dtwclust-4.0.2/dtwclust/R/pkg.R | 58 dtwclust-4.0.2/dtwclust/R/reinterpolate.R | 100 dtwclust-4.0.2/dtwclust/R/tsclust-classes.R | 9 dtwclust-4.0.2/dtwclust/R/tsclust-controls.R | 392 +- dtwclust-4.0.2/dtwclust/R/tsclust-family.R | 64 dtwclust-4.0.2/dtwclust/R/tsclust-methods.R | 83 dtwclust-4.0.2/dtwclust/R/tsclust.R | 240 - dtwclust-4.0.2/dtwclust/R/tslist.R |only dtwclust-4.0.2/dtwclust/R/uciCT.R | 64 dtwclust-4.0.2/dtwclust/R/utils.R | 186 + dtwclust-4.0.2/dtwclust/R/zscore.R | 12 dtwclust-4.0.2/dtwclust/build/vignette.rds |binary dtwclust-4.0.2/dtwclust/inst/COPYRIGHT.txt | 36 dtwclust-4.0.2/dtwclust/inst/NEWS.Rd | 57 dtwclust-4.0.2/dtwclust/inst/doc/dtwclust.Rnw | 21 dtwclust-4.0.2/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-4.0.2/dtwclust/inst/include/dtwclust.h | 101 dtwclust-4.0.2/dtwclust/inst/include/dtwclust.hpp | 116 dtwclust-4.0.2/dtwclust/man/DBA.Rd | 21 dtwclust-4.0.2/dtwclust/man/Distmat-class.Rd | 2 dtwclust-4.0.2/dtwclust/man/GAK.Rd | 27 dtwclust-4.0.2/dtwclust/man/SBD.Rd | 21 dtwclust-4.0.2/dtwclust/man/SparseDistmat-class.Rd | 3 dtwclust-4.0.2/dtwclust/man/TADPole.Rd | 53 dtwclust-4.0.2/dtwclust/man/as.matrix.Rd | 2 dtwclust-4.0.2/dtwclust/man/compare_clusterings.Rd | 11 dtwclust-4.0.2/dtwclust/man/cvi.Rd | 5 dtwclust-4.0.2/dtwclust/man/dtw_basic.Rd | 20 dtwclust-4.0.2/dtwclust/man/dtw_lb.Rd | 42 dtwclust-4.0.2/dtwclust/man/dtwclust-deprecated.Rd | 16 dtwclust-4.0.2/dtwclust/man/dtwclust-package.Rd | 22 dtwclust-4.0.2/dtwclust/man/dtwclust.Rd | 4 dtwclust-4.0.2/dtwclust/man/lb_improved.Rd | 15 dtwclust-4.0.2/dtwclust/man/lb_keogh.Rd | 15 dtwclust-4.0.2/dtwclust/man/tsclust-controls.Rd | 4 dtwclust-4.0.2/dtwclust/man/tsclust.Rd | 64 dtwclust-4.0.2/dtwclust/man/tsclustFamily-class.Rd | 61 dtwclust-4.0.2/dtwclust/man/tsclusters-methods.Rd | 7 dtwclust-4.0.2/dtwclust/man/tslist.Rd |only dtwclust-4.0.2/dtwclust/src/Makevars |only dtwclust-4.0.2/dtwclust/src/SparseDistmatIndices.cpp |only dtwclust-4.0.2/dtwclust/src/dba.cpp | 55 dtwclust-4.0.2/dtwclust/src/dtw-basic.c | 20 dtwclust-4.0.2/dtwclust/src/dtw-lb.cpp | 104 dtwclust-4.0.2/dtwclust/src/dtwb-loop.cpp |only dtwclust-4.0.2/dtwclust/src/dtwclustpp.h | 115 dtwclust-4.0.2/dtwclust/src/envelope.cpp | 8 dtwclust-4.0.2/dtwclust/src/gak-loop.cpp |only dtwclust-4.0.2/dtwclust/src/init.cpp | 13 dtwclust-4.0.2/dtwclust/src/lbi-loop.cpp |only dtwclust-4.0.2/dtwclust/src/lbk-loop.cpp |only dtwclust-4.0.2/dtwclust/src/lbs.cpp | 81 dtwclust-4.0.2/dtwclust/src/logGAK.c | 5 dtwclust-4.0.2/dtwclust/src/pairs.c | 2 dtwclust-4.0.2/dtwclust/src/sbd-loop.cpp |only dtwclust-4.0.2/dtwclust/src/tadpole.cpp |only dtwclust-4.0.2/dtwclust/src/utils.cpp |only dtwclust-4.0.2/dtwclust/tests/testthat.R | 28 dtwclust-4.0.2/dtwclust/tests/testthat/acceptance/dtwb.R | 160 dtwclust-4.0.2/dtwclust/tests/testthat/acceptance/gak.R | 16 dtwclust-4.0.2/dtwclust/tests/testthat/acceptance/lbs.R | 57 dtwclust-4.0.2/dtwclust/tests/testthat/acceptance/symmetric-proxy.R |only dtwclust-4.0.2/dtwclust/tests/testthat/helper-all.R | 92 dtwclust-4.0.2/dtwclust/tests/testthat/integration/custom-dist.R | 52 dtwclust-4.0.2/dtwclust/tests/testthat/integration/families.R | 20 dtwclust-4.0.2/dtwclust/tests/testthat/integration/proxy.R | 20 dtwclust-4.0.2/dtwclust/tests/testthat/regression/clusterings.R | 150 dtwclust-4.0.2/dtwclust/tests/testthat/regression/cvis.R | 58 dtwclust-4.0.2/dtwclust/tests/testthat/regression/family-centroids.R | 1 dtwclust-4.0.2/dtwclust/tests/testthat/regression/proxy.R | 97 dtwclust-4.0.2/dtwclust/tests/testthat/system/data-formats.R | 142 dtwclust-4.0.2/dtwclust/tests/testthat/system/fuzzy.R | 228 - dtwclust-4.0.2/dtwclust/tests/testthat/system/hierarchical.R | 252 - dtwclust-4.0.2/dtwclust/tests/testthat/system/partitional.R | 658 +-- dtwclust-4.0.2/dtwclust/tests/testthat/system/preproc.R | 174 - dtwclust-4.0.2/dtwclust/tests/testthat/test-01-unit.R | 2 dtwclust-4.0.2/dtwclust/tests/testthat/test-03-acceptance.R | 11 dtwclust-4.0.2/dtwclust/tests/testthat/test-04-system.R | 18 dtwclust-4.0.2/dtwclust/tests/testthat/test-05-regression.R | 2 dtwclust-4.0.2/dtwclust/tests/testthat/test-06-parallel.R | 2 dtwclust-4.0.2/dtwclust/tests/testthat/unit/centroids.R | 250 - dtwclust-4.0.2/dtwclust/tests/testthat/unit/configs.R | 291 - dtwclust-4.0.2/dtwclust/tests/testthat/unit/cvis.R | 14 dtwclust-4.0.2/dtwclust/tests/testthat/unit/distances.R | 79 dtwclust-4.0.2/dtwclust/tests/testthat/unit/methods.R | 274 + dtwclust-4.0.2/dtwclust/vignettes/REFERENCES.bib | 768 ++-- dtwclust-4.0.2/dtwclust/vignettes/dtwclust.Rnw | 21 119 files changed, 7241 insertions(+), 6995 deletions(-)
More information about datastructures at CRAN
Permanent link
Title: Variance Component Models
Description: Variance component models: REML estimation, testing fixed effect contrasts through Satterthwaite or Kenward-Roger methods, testing the nullity of variance components through (linear or quadratic) score tests or likelihood ratio tests.
Author: Long Qu
Maintainer: Long Qu <rtistician@gmail.com>
Diff between varComp versions 0.1-360 dated 2015-02-06 and 0.2-0 dated 2017-07-09
DESCRIPTION | 14 INDEX | 6 MD5 | 120 +-- NAMESPACE | 155 ++-- R/KR.varComp.R | 174 ++-- R/anova.varComp.R | 180 ++-- R/coef.varComp.R | 80 +- R/fixef.varComp.R | 200 ++--- R/formulas.R | 64 - R/kernels.R | 84 +- R/logLik.varComp.R | 30 R/minque.R | 70 - R/model.matrix.varComp.R | 34 R/p.value.R | 78 +- R/pchibarsq.R | 154 ++-- R/print.varComp.R | 48 - R/print.varComp.test.R | 12 R/satterth.R | 132 +-- R/varComp-const.R | 22 R/varComp-defunct.R | 256 +++--- R/varComp-internal.R | 374 ++++----- R/varComp-notImplemented.R | 52 - R/varComp-utilities.R | 58 - R/varComp.LinScore.Normal.R | 68 - R/varComp.LinScore.SSAS155.R | 106 +- R/varComp.LinScore.Satterthwaite.R | 70 - R/varComp.LinScore.test.R | 202 ++--- R/varComp.R | 1406 ++++++++++++++++++------------------- R/varComp.RLRT.test.R | 108 +- R/varComp.SS95.test.R | 110 +- R/varComp.VM03.test.R | 248 +++--- R/varComp.test.R | 830 ++++++++++----------- R/varComp.test.control.R | 224 ++--- R/vcov.varComp.R | 120 +-- man/Wald.varComp.Rd | 172 ++-- man/anova.varComp.Rd | 216 ++--- man/chibarsq.Rd | 146 +-- man/cholRoot.Rd | 78 +- man/coef.varComp.Rd | 124 +-- man/formulas.Rd | 100 +- man/get.seed.Rd | 60 - man/is.formula.Rd | 62 - man/kernels.Rd | 216 ++--- man/logLik.varComp.Rd | 90 +- man/minque.Rd | 114 +-- man/model.matrix.varComp.Rd | 116 +-- man/normalizeTrace.Rd | 72 - man/p.value.varComp.test.Rd | 106 +- man/print.varComp.Rd | 76 +- man/print.varComp.test.Rd | 54 - man/safeseq.Rd | 78 +- man/symbols.Rd | 54 - man/varComp-defunct.Rd | 38 - man/varComp-internal.Rd | 270 +++---- man/varComp-notImplemented.Rd | 56 - man/varComp-package.Rd | 140 +-- man/varComp.Rd | 416 +++++----- man/varComp.control.Rd | 194 ++--- man/varComp.test.Rd | 222 ++--- man/varComp.test.control.Rd | 202 ++--- man/vcov.varComp.Rd | 102 +- 61 files changed, 4733 insertions(+), 4730 deletions(-)
Title: Doubly Robust Inverse Probability Weighted Augmented GEE
Estimator
Description: Implements a semi-parametric GEE estimator accounting for missing data with Inverse-probability weighting (IPW) and for imbalance in covariates with augmentation (AUG). The estimator IPW-AUG-GEE is Doubly robust (DR).
Author: Melanie Prague [aut, cre],
Paul Gilbert [ctb] (Author of R package numDeriv, which has been
acknowledged in numDeriv.R),
Ravi Varadhan [ctb] (Author of R package numDeriv, which has been
acknowledged in numDeriv.R),
Ming Wang [ctb] (Author of R package geesmv, which has been
acknowledged in getFay.R),
Lee McDaniel [ctb] (Author of R package geeM, which has been modfied
and references in multiple R files),
Nick Henderson [ctb] (Author of R package geeM, which has been modfied
and references in multiple R files)
Maintainer: Melanie Prague <mprague@hsph.harvard.edu>
Diff between CRTgeeDR versions 1.2 dated 2016-04-07 and 2.0 dated 2017-07-09
DESCRIPTION | 34 ++++-- MD5 | 8 - R/CRTgeeDR-main.R | 270 +++++++++++++++++++++++++++--------------------------- R/print.R | 70 +++++++------- R/updatebeta.R | 2 5 files changed, 195 insertions(+), 189 deletions(-)
Title: Continued Fractions
Description: Various utilities for evaluating continued fractions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between contfrac versions 1.1-10 dated 2016-05-26 and 1.1-11 dated 2017-07-09
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NAMESPACE | 3 ++- R/contfrac.R | 8 ++++---- man/convergents.Rd | 4 ++++ src/contfrac.c | 11 ++++++----- src/contfrac_init.c |only 7 files changed, 25 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-08 1.13
2016-08-30 1.5.5
2016-08-28 1.5.4
2016-05-14 1.4.0
2016-04-09 1.3.4
2016-02-29 1.2.8
2016-02-19 1.2.6
2015-11-10 1.2.1
2015-10-29 1.1.1
2015-06-13 1.1
Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts
<https://fonts.google.com/> into R, in order to
support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between sysfonts versions 0.5 dated 2015-04-27 and 0.6 dated 2017-07-09
sysfonts-0.5/sysfonts/NEWS |only sysfonts-0.6/sysfonts/DESCRIPTION | 20 sysfonts-0.6/sysfonts/MD5 | 58 +- sysfonts-0.6/sysfonts/R/font.R | 266 ++++------ sysfonts-0.6/sysfonts/R/google.R | 208 ++++--- sysfonts-0.6/sysfonts/R/zzz.R | 14 sysfonts-0.6/sysfonts/cleanup |only sysfonts-0.6/sysfonts/inst/AUTHORS | 5 sysfonts-0.6/sysfonts/inst/NEWS.Rd |only sysfonts-0.6/sysfonts/inst/fonts/LiberationMono-Bold.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationMono-BoldItalic.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationMono-Italic.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationMono-Regular.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSans-Bold.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSans-BoldItalic.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSans-Italic.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSans-Regular.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSerif-Bold.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSerif-BoldItalic.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSerif-Italic.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/LiberationSerif-Regular.ttf |binary sysfonts-0.6/sysfonts/inst/fonts/webfonts.bz2 |binary sysfonts-0.6/sysfonts/man/font.add.Rd | 39 - sysfonts-0.6/sysfonts/man/font.add.google.Rd | 57 +- sysfonts-0.6/sysfonts/man/font.families.Rd | 22 sysfonts-0.6/sysfonts/man/font.families.google.Rd | 18 sysfonts-0.6/sysfonts/man/font.files.Rd | 16 sysfonts-0.6/sysfonts/man/font.paths.Rd | 18 sysfonts-0.6/sysfonts/src/register_routines.c |only sysfonts-0.6/sysfonts/src/sysfonts-win.def | 4 sysfonts-0.6/sysfonts/src/sysfonts.c | 26 sysfonts-0.6/sysfonts/src/sysfonts.h | 6 32 files changed, 387 insertions(+), 390 deletions(-)
Title: Generating Various Numerical Representation Schemes for Protein
Sequences
Description: Comprehensive toolkit for generating various numerical
features of protein sequences described in Xiao et al. (2015)
<DOI:10.1093/bioinformatics/btv042>. For full functionality,
the software 'ncbi-blast+' is needed, see
<https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao [aut, cre],
Qing-Song Xu [aut],
Dong-Sheng Cao [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between protr versions 1.4-0 dated 2017-06-06 and 1.4-1 dated 2017-07-09
protr-1.4-0/protr/vignettes/tables |only protr-1.4-1/protr/DESCRIPTION | 6 protr-1.4-1/protr/MD5 | 22 - protr-1.4-1/protr/NEWS.md | 61 +- protr-1.4-1/protr/README.md | 2 protr-1.4-1/protr/build/vignette.rds |binary protr-1.4-1/protr/inst/doc/protr.Rmd | 103 ++++ protr-1.4-1/protr/inst/doc/protr.html | 475 +++++++++++++++++++++-- protr-1.4-1/protr/vignettes/figures/protrweb.png |binary protr-1.4-1/protr/vignettes/protr.Rmd | 103 ++++ 10 files changed, 679 insertions(+), 93 deletions(-)
Title: Parses Web Pages using Postlight Mercury
Description: This is a wrapper for the Mercury Parser API. The Mercury Parser is
a single API endpoint that takes a URL and gives you back the content reliably
and easily.
With just one API request, Mercury takes any web article and returns
only the relevant content — headline, author, body text, relevant images and
more — free from any clutter. It’s reliable, easy-to-use and free.
See the webpage here: <https://mercury.postlight.com/>.
Author: Mikkel Freltoft Krogsholm
Maintainer: Mikkel Freltoft Krogsholm <mikkel@56n.dk>
Diff between postlightmercury versions 1.1 dated 2017-07-08 and 1.2 dated 2017-07-09
DESCRIPTION | 8 +++--- MD5 | 13 +++++---- NAMESPACE | 1 NEWS.md | 2 + R/mercury.R | 55 +++++++++++++++++++++++++++++++++++++++--- man/remove_html.Rd |only man/web_parser.Rd | 5 +-- tests/testthat/test_mercury.R | 11 +++++++- 8 files changed, 78 insertions(+), 17 deletions(-)
More information about postlightmercury at CRAN
Permanent link
Title: Estimating the Proportion of True Null Hypotheses for FDR
Description: Methods for estimating the proportion of true null hypotheses, i.e., the pi0, when a very large number of hypotheses are simultaneously tested, especially for the purpose of (local) false discovery rate control for microarray data. It also contains functions to estimate the distribution of noncentrality parameters from a large number of parametric tests.
Author: Long Qu [aut, cre, ctb],
Kun Liang [ctb],
Yudi Pawitan [aut] (The author(s) of OCplus::tMixture, which was
modified slightly leading to discTMix in this package.),
Alexander Ploner [aut] (The author(s) of OCplus::tMixture, which was
modified slightly leading to discTMix in this package.),
Egil Ferkingstad [aut] (The author(s) of limma::convest, which was
modified slightly leading to convest in this package.),
Mette Langaas [aut] (The author(s) of limma::convest, which was
modified slightly leading to convest in this package.),
Marcus Davy [aut] (The author(s) of limma::convest, which was modified
slightly leading to convest in this package.)
Maintainer: Long Qu <rtistician@gmail.com>
Diff between pi0 versions 1.4-0 dated 2015-07-06 and 1.4-1 dated 2017-07-09
DESCRIPTION | 18 MD5 | 253 +++---- NAMESPACE | 372 +++++------ R/CBUM.R | 172 ++--- R/NBsplines.R | 40 - R/ToDoList.R | 20 R/agjack.pi0.R | 88 +- R/clean.cdf.R | 58 - R/combn2R.R | 168 ++--- R/combn2RRepl.R | 112 +-- R/combnBt2RAllDifc.R | 142 ++-- R/combnBt2Rc.R | 168 ++--- R/combnBtRc.R | 122 +-- R/combnRRepl.R | 90 +- R/cond.cdf.R | 296 ++++----- R/convest.R | 164 ++--- R/dFsnc.mix.R | 112 +-- R/discTMix.R | 348 +++++----- R/dncp.R | 126 +-- R/dtn.mix.R | 36 - R/extrp.pi0.known.gam2.R | 232 +++---- R/extrp.pi0.master.R | 150 ++-- R/extrp.pi0.unknown.gam2.R | 366 +++++------ R/fdr.R | 24 R/geomean.R | 8 R/gjack.R | 6 R/harmean.R | 8 R/histf1.R | 170 ++--- R/hypergeometric1F1.R | 36 - R/int.nct.R | 222 +++--- R/laplace.nct.R | 44 - R/lastbin.R | 10 R/lfdr.R | 124 +-- R/lfdr2p.R | 148 ++-- R/matrix.t.test.R | 64 - R/mdt.R | 98 +-- R/momeff.R | 122 +-- R/momeff.nonzeromean.R | 322 +++++----- R/momeff.zeromean.R | 172 ++--- R/ncpest.R | 698 ++++++++++----------- R/ncpest.helpers.R | 12 R/ncpest.iter.R | 86 +- R/nparncp.R | 1328 ++++++++++++++++++++--------------------- R/nparncpF.R | 1370 +++++++++++++++++++++--------------------- R/parncp.R | 452 +++++++------- R/parncp2.R | 992 +++++++++++++++--------------- R/parncpF.R | 504 +++++++-------- R/pavaf1.R | 100 +-- R/pdf.dist.R | 28 R/plot.extrpi0.R | 56 - R/plot.subex.R | 66 +- R/plot.subt.R | 38 - R/print.extrpi0.R | 36 - R/print.subex.R | 22 R/print.subt.R | 28 R/reflection.R | 18 R/saddlepoint.nct.R | 330 +++++----- R/sim.dat.R | 34 - R/sparncp.R | 1446 ++++++++++++++++++++++----------------------- R/sparncpF.R | 1390 +++++++++++++++++++++---------------------- R/subex.R | 50 - R/subt.R | 156 ++-- R/summary.extrpi0.R | 6 R/summary.subex.R | 6 R/summary.subt.R | 6 R/varB.R | 8 R/znormix.R | 142 ++-- man/CBUM.Rd | 94 +- man/agjack.Rd | 114 +-- man/clean.cdf.Rd | 118 +-- man/coef.ncpest.Rd | 128 +-- man/combn2R.Rd | 252 +++---- man/cond.cdf.Rd | 128 +-- man/convest.Rd | 92 +- man/discTMix.Rd | 180 ++--- man/dncp.Rd | 120 +-- man/dt.int2.Rd | 126 +-- man/dt.lap.Rd | 134 ++-- man/dtn.mix.Rd | 136 ++-- man/extrp.pi0.master.Rd | 244 +++---- man/fdr.Rd | 100 +-- man/fitted.discTMix.Rd | 106 +-- man/fitted.nparncp.Rd | 134 ++-- man/geomean.Rd | 114 +-- man/gjack.Rd | 118 +-- man/grid.search.Rd | 164 ++--- man/histf1.Rd | 138 ++-- man/lastbin.Rd | 76 +- man/lfdr.Rd | 164 ++--- man/logLik.ncpest.Rd | 106 +-- man/mTruncNorm.Rd | 162 ++--- man/matrix.t.test.Rd | 108 +-- man/mdt.Rd | 94 +- man/ncpest.Rd | 178 ++--- man/ncpest.iter.Rd | 130 ++-- man/nparncp.Rd | 244 +++---- man/parncp.Rd | 210 +++--- man/pavaf1.Rd | 124 +-- man/pdf.dist.Rd | 86 +- man/pi0-internal.Rd | 102 +-- man/pi0-package.Rd | 168 ++--- man/plot.extrpi0.Rd | 104 +-- man/plot.nparncp.Rd | 120 +-- man/plot.parncp.Rd | 122 +-- man/plot.sparncp.Rd | 116 +-- man/plot.subex.Rd | 114 +-- man/plot.subt.Rd | 102 +-- man/print.extrpi0.Rd | 88 +- man/print.subex.Rd | 90 +- man/print.subt.Rd | 84 +- man/pt.sad.Rd | 134 ++-- man/reflection.Rd | 98 +-- man/sim.dat.Rd | 116 +-- man/simulatedDat.Rd | 56 - man/simulatedExtrpi0.Rd | 64 - man/simulatedSubex.Rd | 64 - man/simulatedSubt.Rd | 62 - man/simulatedtstat.Rd | 70 +- man/sparncp.Rd | 138 ++-- man/subex.Rd | 152 ++-- man/subt.Rd | 184 ++--- man/summary.nparncp.Rd | 112 +-- man/summary.parncp.Rd | 118 +-- man/summary.sparncp.Rd | 98 +-- man/varB.Rd | 104 +-- man/vcov.ncpest.Rd | 104 +-- man/znormix.Rd | 108 +-- src/init.c |only 128 files changed, 11027 insertions(+), 11026 deletions(-)
Title: Hierarchical Semiparametric Regression of Test Statistics
Description: Methods for hierarchical semiparametric regression models for test statistics are implemented in this package. Specifically, test statistics given the null/alternative hypotheses are modeled parametrically, whereas the unobservable status of null/alternative hypotheses are modeled using nonparametric additive logistic regression over covariates.
Author: Long Qu
Maintainer: Long Qu <rtistician@gmail.com>
Diff between hisemi versions 1.0-319 dated 2013-08-31 and 1.1-0 dated 2017-07-09
DESCRIPTION | 15 MD5 | 68 +- NAMESPACE | 62 +- R/EM.Newton.R | 1448 ++++++++++++++++++++++++------------------------- R/EM.Newton.support.R | 628 ++++++++++----------- R/EMupdate.R | 276 ++++----- R/NRupdate.R | 364 ++++++------ R/OsplinePen.R | 620 ++++++++++---------- R/logistic.enp.R | 146 ++-- R/n.knots.R | 6 R/rt.R |only R/scaledTMix.R | 594 ++++++++++---------- R/tPoly.newton.R | 1384 +++++++++++++++++++++++----------------------- man/EMupdate.Rd | 90 +-- man/NRupdate.Rd | 94 +-- man/OsplinePen.Rd | 148 ++--- man/coef.hisemit.Rd | 80 +- man/confint.hisemit.Rd | 100 +-- man/directSum.Rd | 80 +- man/fitted.hisemit.Rd | 98 +-- man/hisemi-internal.Rd | 20 man/hisemi-package.Rd | 154 ++--- man/logLik.hisemit.Rd | 64 +- man/logistic.enp.Rd | 84 +- man/logit.Rd | 64 +- man/n.knots.Rd | 92 +-- man/penLik.EMNewton.Rd | 2 man/plot.hisemit.Rd | 100 +-- man/print.hisemit.Rd | 70 +- man/resid.hisemit.Rd | 76 +- man/rt.Rd |only man/scaledTMix.null.Rd | 92 +-- man/scaledTMix.psat.Rd | 86 +- man/scaledTMix.sat.Rd | 78 +- man/tPoly.newton.Rd | 200 +++--- man/vcov.hisemit.Rd | 64 +- 36 files changed, 3775 insertions(+), 3772 deletions(-)
Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the embedded
'ReadStat' C library, <https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between haven versions 1.0.0 dated 2016-09-23 and 1.1.0 dated 2017-07-09
haven-1.0.0/haven/tests/testthat/write-sas.R |only haven-1.1.0/haven/DESCRIPTION | 21 haven-1.1.0/haven/LICENSE | 2 haven-1.1.0/haven/MD5 | 141 +- haven-1.1.0/haven/NAMESPACE | 8 haven-1.1.0/haven/NEWS.md | 35 haven-1.1.0/haven/R/RcppExports.R | 20 haven-1.1.0/haven/R/as_factor.R | 27 haven-1.1.0/haven/R/haven.R | 79 + haven-1.1.0/haven/R/update.R | 2 haven-1.1.0/haven/R/zap_widths.R |only haven-1.1.0/haven/README.md | 75 - haven-1.1.0/haven/build/vignette.rds |binary haven-1.1.0/haven/inst/doc/datetimes.Rmd | 4 haven-1.1.0/haven/inst/doc/datetimes.html | 8 haven-1.1.0/haven/inst/doc/semantics.Rmd | 7 haven-1.1.0/haven/inst/doc/semantics.html | 67 - haven-1.1.0/haven/man/as_factor.Rd | 9 haven-1.1.0/haven/man/figures |only haven-1.1.0/haven/man/labelled.Rd | 3 haven-1.1.0/haven/man/labelled_spss.Rd | 1 haven-1.1.0/haven/man/print_labels.Rd | 1 haven-1.1.0/haven/man/read_dta.Rd | 17 haven-1.1.0/haven/man/read_sas.Rd | 7 haven-1.1.0/haven/man/read_spss.Rd | 24 haven-1.1.0/haven/man/read_xpt.Rd |only haven-1.1.0/haven/man/tagged_na.Rd | 7 haven-1.1.0/haven/man/zap_empty.Rd | 3 haven-1.1.0/haven/man/zap_formats.Rd | 3 haven-1.1.0/haven/man/zap_labels.Rd | 3 haven-1.1.0/haven/man/zap_missing.Rd | 1 haven-1.1.0/haven/man/zap_widths.Rd |only haven-1.1.0/haven/src/DfReader.cpp | 102 + haven-1.1.0/haven/src/DfWriter.cpp | 31 haven-1.1.0/haven/src/RcppExports.cpp | 78 + haven-1.1.0/haven/src/haven_types.h | 6 haven-1.1.0/haven/src/readstat/readstat.h | 30 haven-1.1.0/haven/src/readstat/readstat_error.c | 3 haven-1.1.0/haven/src/readstat/readstat_variable.c | 4 haven-1.1.0/haven/src/readstat/readstat_writer.c | 55 haven-1.1.0/haven/src/readstat/readstat_writer.h | 5 haven-1.1.0/haven/src/readstat/sas/ieee.c |only haven-1.1.0/haven/src/readstat/sas/ieee.h |only haven-1.1.0/haven/src/readstat/sas/readstat_sas.c | 53 haven-1.1.0/haven/src/readstat/sas/readstat_sas.h | 1 haven-1.1.0/haven/src/readstat/sas/readstat_sas7bcat_read.c | 9 haven-1.1.0/haven/src/readstat/sas/readstat_sas7bcat_write.c | 2 haven-1.1.0/haven/src/readstat/sas/readstat_sas7bdat_read.c | 61 - haven-1.1.0/haven/src/readstat/sas/readstat_sas7bdat_write.c | 75 - haven-1.1.0/haven/src/readstat/sas/readstat_xport.c |only haven-1.1.0/haven/src/readstat/sas/readstat_xport.h |only haven-1.1.0/haven/src/readstat/sas/readstat_xport_read.c |only haven-1.1.0/haven/src/readstat/sas/readstat_xport_write.c |only haven-1.1.0/haven/src/readstat/spss/readstat_por.c | 11 haven-1.1.0/haven/src/readstat/spss/readstat_por.h | 2 haven-1.1.0/haven/src/readstat/spss/readstat_por_read.c | 30 haven-1.1.0/haven/src/readstat/spss/readstat_por_write.c | 43 haven-1.1.0/haven/src/readstat/spss/readstat_sav.h | 4 haven-1.1.0/haven/src/readstat/spss/readstat_sav_parse_timestamp.c | 112 +- haven-1.1.0/haven/src/readstat/spss/readstat_sav_read.c | 73 - haven-1.1.0/haven/src/readstat/spss/readstat_sav_write.c | 35 haven-1.1.0/haven/src/readstat/spss/readstat_spss.c | 3 haven-1.1.0/haven/src/readstat/spss/readstat_spss.h | 2 haven-1.1.0/haven/src/readstat/spss/readstat_spss_parse.c | 553 +++++----- haven-1.1.0/haven/src/readstat/stata/readstat_dta.h | 14 haven-1.1.0/haven/src/readstat/stata/readstat_dta_parse_timestamp.c | 142 +- haven-1.1.0/haven/src/readstat/stata/readstat_dta_read.c | 69 - haven-1.1.0/haven/src/readstat/stata/readstat_dta_write.c | 57 - haven-1.1.0/haven/tests/testthat/helper-roundtrip.R | 20 haven-1.1.0/haven/tests/testthat/labelled-str.sav |binary haven-1.1.0/haven/tests/testthat/test-read-sav.R | 26 haven-1.1.0/haven/tests/testthat/test-write-dta.R | 7 haven-1.1.0/haven/tests/testthat/test-write-sas.R |only haven-1.1.0/haven/tests/testthat/test-write-sav.R | 8 haven-1.1.0/haven/tests/testthat/test-write-xpt.R |only haven-1.1.0/haven/vignettes/datetimes.Rmd | 4 haven-1.1.0/haven/vignettes/releases |only haven-1.1.0/haven/vignettes/semantics.Rmd | 7 78 files changed, 1453 insertions(+), 859 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding in Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding in
random-effects meta-analysis per Mathur & VanderWeele (in preparation).
Given output from a random-effects meta-analysis with a relative risk
outcome, computes point estimates and inference for: (1) the proportion
of studies with true causal effect sizes more extreme than a specified threshold
of scientific significance; and (2) the minimum bias factor and confounding
strength required to reduce to less than a specified threshold the proportion
of studies with true effect sizes of scientifically significant size.
Creates plots and tables for visualizing these metrics across a range of bias values.
Provides tools to easily scrape study-level data from a published forest plot or
summary table to obtain the needed estimates when these are not reported.
Author: Maya B. Mathur, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <maya.z.mathur@gmail.com>
Diff between ConfoundedMeta versions 1.1.0 dated 2017-06-12 and 1.2.0 dated 2017-07-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/ConfoundedMeta.R | 15 +++++++++++---- man/scrape_meta.Rd | 2 +- 4 files changed, 18 insertions(+), 11 deletions(-)
More information about ConfoundedMeta at CRAN
Permanent link
Title: Optimal and Fast Univariate Clustering
Description: Fast optimal univariate clustering and segementation
by dynamic programming. Three types of problem including
univariate k-means, k-median, and k-segments are solved with
guaranteed optimality and reproducibility. The core algorithm
minimizes the sum of within-cluster distances using respective
metrics. Its advantage over heuristic clustering algorithms in
efficiency and accuracy is increasingly pronounced as the
number of clusters k increases. Weighted k-means and unweighted
k-segments algorithms can also optimally segment time series
and perform peak calling. An auxiliary function generates
histograms that are adaptive to patterns in data. In contrast to
heuristic methods, this package provides a powerful set of tools
for univariate data analysis with guaranteed optimality.
Author: Joe Song [aut, cre], Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between Ckmeans.1d.dp versions 4.2.0 dated 2017-05-30 and 4.2.1 dated 2017-07-09
DESCRIPTION | 33 +++++++++--------- MD5 | 24 ++++++++----- NEWS | 6 +++ build/vignette.rds |binary inst/doc/Ckmeans.1d.dp.html | 16 ++++----- inst/doc/Weights.Rmd |only inst/doc/Weights.html |only inst/doc/ahist.html | 12 +++--- man/Ckmeans.1d.dp-package.Rd | 6 +-- man/Ckmeans.1d.dp.Rd | 75 +++++-------------------------------------- man/Cksegs.1d.dp.Rd |only man/plot.Ckmeans.1d.dp.Rd | 15 +------- man/plot.Cksegs.1d.dp.Rd |only man/print.Ckmeans.1d.dp.Rd | 16 +++------ man/print.Cksegs.1d.dp.Rd |only vignettes/Weights.Rmd |only 16 files changed, 72 insertions(+), 131 deletions(-)