Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component is currently supported only for balanced univariate Newton Raphson.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 2.1 dated 2016-08-31 and 2.2 dated 2016-10-01
CHANGELOG | 12 ++ DESCRIPTION | 8 - MD5 | 74 ++++++++--------- NAMESPACE | 4 R/AI.R | 6 - R/EM.R | 4 R/LD.decay.R |only R/MAI.R | 6 - R/MAI2.R | 14 +-- R/MMERM.R | 20 +++- R/MNR.R | 23 +++-- R/NR.R | 2 R/NRR.R | 2 R/ai2help.R | 2 R/atcg1234.R | 18 +++- R/manhattan.R | 9 +- R/mmer.R | 38 ++++++-- R/mmer2.R | 5 - R/mmerSNOW.R | 43 +++++++--- R/score.calcMV.R | 13 ++- inst/doc/sommer.R | 3 inst/doc/sommer.Rmd | 9 +- inst/doc/sommer.pdf |binary man/A.mat.Rd | 7 + man/CPdata.Rd | 3 man/FDdata.Rd | 23 +++++ man/LD.decay.Rd |only man/PolyData.Rd | 3 man/RICE.Rd | 3 man/TP.prep.Rd | 3 man/Technow_data.Rd | 3 man/cornHybrid.Rd | 25 +++++ man/manhattan.Rd | 3 man/mmer.Rd | 214 ++++++++++++++++---------------------------------- man/mmer2.Rd | 185 ++++++++++++++++--------------------------- man/sommer-package.Rd | 69 ++++++++++++---- man/wheatLines.Rd | 3 vignettes/sommer.Rmd | 9 +- vignettes/sommer.html | 97 +++++++++++----------- 39 files changed, 528 insertions(+), 437 deletions(-)
Title: R Bindings for Selenium WebDriver
Description: The RSelenium package provides a set of R bindings for the
Selenium 2.0 WebDriver using the JsonWireProtocol. Selenium automates web
browsers (commonly referred to as browsers). Using RSelenium you can
automate browsers locally or remotely.
Author: John Harrison <johndharrison0@gmail.com>
Maintainer: John Harrison <johndharrison0@gmail.com>
Diff between RSelenium versions 1.4.0 dated 2016-07-30 and 1.4.5 dated 2016-10-01
RSelenium-1.4.0/RSelenium/inst/tests |only RSelenium-1.4.0/RSelenium/tests/test-all.R |only RSelenium-1.4.0/RSelenium/tests/testthat/test-open.r |only RSelenium-1.4.5/RSelenium/DESCRIPTION | 14 - RSelenium-1.4.5/RSelenium/MD5 | 67 +++-- RSelenium-1.4.5/RSelenium/NAMESPACE | 2 RSelenium-1.4.5/RSelenium/NEWS | 30 +- RSelenium-1.4.5/RSelenium/R/errorHandler.R | 20 + RSelenium-1.4.5/RSelenium/R/remoteDriver.R | 8 RSelenium-1.4.5/RSelenium/R/util.R | 134 ++++++---- RSelenium-1.4.5/RSelenium/R/webElement.R | 2 RSelenium-1.4.5/RSelenium/README.md | 23 + RSelenium-1.4.5/RSelenium/build/vignette.rds |binary RSelenium-1.4.5/RSelenium/inst/doc/RSelenium-docker.Rmd |only RSelenium-1.4.5/RSelenium/inst/doc/RSelenium-docker.html |only RSelenium-1.4.5/RSelenium/inst/examples |only RSelenium-1.4.5/RSelenium/inst/sauceTests |only RSelenium-1.4.5/RSelenium/man/RSelenium-package.Rd | 2 RSelenium-1.4.5/RSelenium/man/checkForServer.Rd | 6 RSelenium-1.4.5/RSelenium/man/errorHandler-class.Rd | 2 RSelenium-1.4.5/RSelenium/man/makeFirefoxProfile.Rd | 2 RSelenium-1.4.5/RSelenium/man/remoteDriver-class.Rd | 3 RSelenium-1.4.5/RSelenium/man/startServer.Rd | 4 RSelenium-1.4.5/RSelenium/tests/README.md |only RSelenium-1.4.5/RSelenium/tests/testthat.R |only RSelenium-1.4.5/RSelenium/tests/testthat/helper.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-api_example_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-cookie_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-misc_remoteDriver_methods_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-page_loading_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-takes_screenshots_tests.R |only RSelenium-1.4.5/RSelenium/tests/testthat/test-util_function_tests.R |only RSelenium-1.4.5/RSelenium/vignettes/RSelenium-docker.Rmd |only RSelenium-1.4.5/RSelenium/vignettes/SeleniumDockerHub.png |only RSelenium-1.4.5/RSelenium/vignettes/SeleniumRunUbuntu.png |only RSelenium-1.4.5/RSelenium/vignettes/SeleniumRunWin10.png |only RSelenium-1.4.5/RSelenium/vignettes/TightVNC.png |only RSelenium-1.4.5/RSelenium/vignettes/VinagreVNC.png |only RSelenium-1.4.5/RSelenium/vignettes/Win10PullFirefox.png |only RSelenium-1.4.5/RSelenium/vignettes/node-firefox.png |only RSelenium-1.4.5/RSelenium/vignettes/ubuntuHelloWorld.png |only RSelenium-1.4.5/RSelenium/vignettes/windowsToolbox.png |only 42 files changed, 219 insertions(+), 100 deletions(-)
Title: Color Science Methods and Data
Description: Methods and data for color science - color conversions by observer,
illuminant and gamma. Color matching functions and chromaticity diagrams.
Color indices, color differences and spectral data conversion/analysis.
Author: Jose Gama [aut, cre]
Maintainer: Jose Gama <rxprtgama@gmail.com>
Diff between colorscience versions 1.0.2 dated 2016-02-28 and 1.0.4 dated 2016-10-01
DESCRIPTION | 10 MD5 | 144 ++++---- NAMESPACE | 5 R/colorscience.R | 176 +++++----- data/CentralsISCCNBS.rda |binary data/ChromaticAdaptation.rda |binary data/DeMarcoPokornySmith2degConeFundamentals1992.rda |binary data/ISObrightnessReflectometerRSD.rda |binary data/MaterialReferenceData.rda |binary data/MaxChromaFromExtrapRenotationData.rda |binary data/MaxChromasForStandardMunsellHuesAndValues.rda |binary data/Munsell100hues55.rda |binary data/Munsell100hues55FM100.rda |binary data/MunsellHues.rda |binary data/MunsellNeutrals2sRGB.rda |binary data/MunsellSpectral.rda |binary data/SmithPokorny2degConeFundamentals1975.rda |binary data/StockmanMacLeodJohnson10degConeFundamentals1993.rda |binary data/StockmanMacLeodJohnson2degCIEadjConeFundamentals1993.rda |binary data/StockmanMacLeodJohnson2degStilesBurchConeFundamentals1993.rda |binary data/StockmanSharpe10degCMFS2000.rda |binary data/StockmanSharpe2degCMFadj2000.rda |binary data/SystemISCCNBS.rda |binary data/TCSdata.rda |binary data/VosEstevezWalraven2degConeFundamentals1990.rda |binary data/VosWalraven2degConeFundamentals1971.rda |binary data/XYZperfectreflectingdiffuser.rda |binary data/cccie31.rda |binary data/cccie64.rda |binary data/ciexyz31.rda |binary data/ciexyz64.rda |binary data/conversionIlluminance.rda |binary data/conversionLuminance.rda |binary data/daylightcomponents.rda |binary data/huedegreemunsell.rda |binary data/illuminantA.rda |binary data/illuminantD65.rda |binary data/illuminants.rda |binary data/tristimulusMunsell.rda |binary data/whitepointsRGB.rda |binary data/whitepointsilluminants.rda |binary man/Berger59.Whiteness.Rd | 2 man/CIE.Whiteness.Rd | 2 man/CIE1960UCS2CIE1964.Rd | 2 man/CIE1976uvSaturation.Rd | 5 man/CheckColorLookup.Rd | 7 man/ColorBlockFromMunsell.Rd | 6 man/DIN6167.YellownessIndex.Rd | 2 man/DominantWavelength.Rd | 2 man/HunterLab2XYZ.Rd | 2 man/Lab2XYZ.Rd | 2 man/Luv2XYZ.Rd | 2 man/Luv2Yuv.Rd | 2 man/Maxwell.triangle.Rd | 2 man/MunsellSpecToHVC.Rd | 2 man/RGB2XYZ.Rd | 10 man/RxRyRz2XYZ.Rd | 2 man/SystemISCCNBS.Rd | 11 man/Taube60.Whiteness.Rd | 2 man/XYZ2HunterLab.Rd | 2 man/XYZ2Lab.Rd | 2 man/XYZ2Luv.Rd | 2 man/XYZ2RGB.Rd | 10 man/XYZ2RxRyRz.Rd | 2 man/XYZ2xyY.Rd | 2 man/Yuv2Luv.Rd | 2 man/chromaticity.diagram.Rd | 2 man/chromaticity.diagram.color.Rd | 2 man/createIsoTempLinesTable.Rd | 4 man/makeChromaticAdaptationMatrix.Rd | 4 man/spectra2CCT.Rd | 3 man/spectra2CRIGAIFSCI.Rd | 3 man/spectra2ISObrightness.Rd | 2 73 files changed, 236 insertions(+), 206 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.7 dated 2015-11-15 and 0.0.8 dated 2016-10-01
ChangeLog | 32 +++++++++++++ DESCRIPTION | 8 +-- MD5 | 13 ++--- README.md | 6 +- inst/NEWS.Rd |only inst/include/annoylib.h | 35 +++++++++----- inst/tests/runit.index.R | 7 ++ src/annoy.cpp | 115 ++++++++++++++++++++++++++++++++++++++++++----- 8 files changed, 181 insertions(+), 35 deletions(-)
Title: 3D Lever and Linkage Mechanism Modeling
Description: Creates kinematic and static force models of 3D levers and linkage mechanisms, with particular application to the fields of engineering and biomechanics.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between linkR versions 1.0.1 dated 2015-06-19 and 1.1.1 dated 2016-10-01
linkR-1.0.1/linkR/R/avectors.R |only linkR-1.0.1/linkR/R/findOptimalPointAlignment.R |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH488595.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH490463.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH492487.txt |only linkR-1.0.1/linkR/inst/extdata/bubo_virginianus_FMNH493661.txt |only linkR-1.0.1/linkR/inst/extdata/owl_landmarks.txt |only linkR-1.0.1/linkR/inst/extdata/owl_link_associations.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_1.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_2.txt |only linkR-1.0.1/linkR/inst/extdata/salmo_salar_3.txt |only linkR-1.0.1/linkR/inst/extdata/salmon_landmarks.txt |only linkR-1.0.1/linkR/inst/extdata/salmon_link_associations.txt |only linkR-1.1.1/linkR/DESCRIPTION | 14 linkR-1.1.1/linkR/MD5 | 100 ++- linkR-1.1.1/linkR/NAMESPACE | 6 linkR-1.1.1/linkR/R/CSToEA.R | 3 linkR-1.1.1/linkR/R/angleOnCircleFromPoint.R | 2 linkR-1.1.1/linkR/R/animateLinkage.R | 132 +++- linkR-1.1.1/linkR/R/applySolveChain.R | 21 linkR-1.1.1/linkR/R/applyTransformationsChain.R | 56 +- linkR-1.1.1/linkR/R/avec.R |only linkR-1.1.1/linkR/R/centroidSize.R |only linkR-1.1.1/linkR/R/combineLinkages.R | 10 linkR-1.1.1/linkR/R/copyTransformation.R | 41 + linkR-1.1.1/linkR/R/defineLinkage.R | 57 +- linkR-1.1.1/linkR/R/drawLinkage.R | 269 ++++++++-- linkR-1.1.1/linkR/R/intersectCircles.R | 2 linkR-1.1.1/linkR/R/linkR_data.R |only linkR-1.1.1/linkR/R/linkR_examples.R | 132 +--- linkR-1.1.1/linkR/R/linkageKinematics.R | 56 +- linkR-1.1.1/linkR/R/minAngle.R |only linkR-1.1.1/linkR/R/proj3DTo2D.R | 9 linkR-1.1.1/linkR/R/solveKinematicChain.R | 21 linkR-1.1.1/linkR/R/sourcePartial_linkR.R |only linkR-1.1.1/linkR/R/tMatrixEP.R | 17 linkR-1.1.1/linkR/R/vectorsToEP.R | 2 linkR-1.1.1/linkR/R/writeLinkageLayers.R |only linkR-1.1.1/linkR/inst/CITATION |only linkR-1.1.1/linkR/inst/extdata/specimens |only linkR-1.1.1/linkR/inst/extdata/test_configs |only linkR-1.1.1/linkR/man/animateLinkage.Rd | 54 -- linkR-1.1.1/linkR/man/cprod.Rd |only linkR-1.1.1/linkR/man/defineLinkage.Rd | 75 -- linkR-1.1.1/linkR/man/drawLinkage.Rd |only linkR-1.1.1/linkR/man/linkR-package.Rd | 20 linkR-1.1.1/linkR/man/rotationMatrixZYX.Rd |only 47 files changed, 680 insertions(+), 419 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.6 dated 2016-07-18 and 1.7 dated 2016-10-01
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NEWS | 13 +++++++++++-- R/HelpersMG-package.R | 4 ++-- R/MHalgoGen.R | 30 +++++++++++++++++++++++++++++- R/asc.R | 2 +- R/chr.R | 3 ++- R/radioButtons_withHTML.R |only man/HelpersMG-package.Rd | 4 ++-- man/MHalgoGen.Rd | 30 +++++++++++++++++++++++++++++- man/chr.Rd | 2 +- 11 files changed, 92 insertions(+), 25 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 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-76 dated 2016-09-24 and 0.1-77 dated 2016-10-01
DESCRIPTION | 8 MD5 | 8 NEWS | 4 R/CausalDiagramBinBin.R | 657 +++++++++++++++++++++++---------------------- man/CausalDiagramBinBin.Rd | 126 ++++---- 5 files changed, 415 insertions(+), 388 deletions(-)
Title: Supervised Classification Learning and Prediction using Patient
Rule Induction Method (PRIM)
Description: The Patient Rule Induction Method (PRIM) is typically
used for "bump hunting" data mining to identify regions with abnormally
high concentrations of data with large or small values. This package
extends this methodology so that it can be applied to binary classification
problems and used for prediction.
Author: David Shaub [aut, cre]
Maintainer: David Shaub <davidshaub@gmx.com>
Diff between supervisedPRIM versions 1.0.1 dated 2016-08-22 and 2.0.0 dated 2016-10-01
DESCRIPTION | 12 +- MD5 | 16 +-- R/supervisedPRIM-package.R | 3 R/supervisedPRIM.R | 166 ++++++++++++++++++++--------------- README.md | 29 ++++++ inst/NEWS.md | 3 man/predict.supervisedPRIM.Rd | 5 - man/supervisedPRIM.Rd | 7 + tests/testthat/test-supervisedPRIM.R | 40 ++++++-- 9 files changed, 183 insertions(+), 98 deletions(-)
More information about supervisedPRIM at CRAN
Permanent link
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers. Among available
features there are: pattern searching (e.g., with ICU Java-like regular
expressions or the Unicode Collation Algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 1.1.1 dated 2016-05-27 and 1.1.2 dated 2016-10-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 +++++++- configure | 23 ++++++++++++++++++----- src/icu55/common/putil.cpp | 9 ++++++++- src/stri_sub.cpp | 8 ++++---- src/stri_time_calendar.cpp | 3 ++- 7 files changed, 49 insertions(+), 22 deletions(-)
Title: Statistical Modeling of Animal Movements
Description: Animal movement models including moving-resting process
with embedded Brownian motion, Brownian motion with measurement error.
Author: Jun Yan <jun.yan@uconn.edu> and
Vladimir Pozdnyakov <vladimir.pozdnyakov@uconn.edu>
Maintainer: Jun Yan <jun.yan@uconn.edu>
Diff between smam versions 0.2-2 dated 2013-11-04 and 0.3-0 dated 2016-10-01
ChangeLog | 6 + DESCRIPTION | 19 ++- MD5 | 24 ++-- NAMESPACE | 30 +++-- R/RcppExports.R |only R/bmme.R | 83 +++++++++++++++- R/movres.R | 256 ++++++++++++++++++++++++++++++++++++++++++++------ man/dtm.Rd | 80 +++++++-------- man/fitBmme.Rd | 76 ++++++-------- man/fitMovRes.Rd | 106 ++++++++++---------- man/integr.control.Rd |only man/rMovRes.Rd | 72 ++++++-------- man/rbmme.Rd | 51 ++++----- src/RcppExports.cpp |only src/movres-llk.cpp |only 15 files changed, 533 insertions(+), 270 deletions(-)
Title: Simultaneous Confidence Bands for the Mean of Functional Data
Description: Statistical methods for estimating and inferring the mean of functional data. The methods include simultaneous confidence bands, local polynomial fitting, bandwidth selection by plug-in and cross-validation, goodness-of-fit tests for parametric models, equality tests for two-sample problems, and plotting functions.
Author: David Degras
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between SCBmeanfd versions 1.2 dated 2016-09-24 and 1.2.1 dated 2016-10-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.SCBand.R | 14 +++++++------- R/scb.model.R | 27 +++++++++++++-------------- man/SCBmeanfd-package.Rd | 11 +++++------ 5 files changed, 33 insertions(+), 35 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between phenology versions 5.2 dated 2016-07-18 and 5.3 dated 2016-10-01
DESCRIPTION | 8 MD5 | 29 +-- NEWS | 17 + R/add_phenology.R | 2 R/phenology-package.R | 4 R/phenology.R | 3 R/plot.phenology.R | 17 + inst/shiny/babel.Rdata |only inst/shiny/server.R | 394 +++++++++++++++++++++++++++++++++-------- inst/shiny/ui.R | 172 +++++++++++++---- inst/shiny/www/fr.png |only inst/shiny/www/gb.png |only inst/shiny/www/logoRASTOMA.png |only inst/shiny/www/logoSWOT.png |only inst/shiny/www/pt.png |only inst/shiny/www/sp.png |only man/phenology-package.Rd | 4 man/phenology.Rd | 3 man/plot.phenology.Rd | 4 19 files changed, 507 insertions(+), 150 deletions(-)
More information about expandFunctions at CRAN
Permanent link