Title: Parallel Versions of the Gradient-Based optim() Methods
Description: Provides parallel versions of the gradient-based optim() methods. The main function of the package is optimParallel(), which has the same usage and output as optim(). Using optimParallel() can significantly reduce the optimization time.
Author: Florian Gerber
Maintainer: Florian Gerber <florian.gerber@math.uzh.ch>
Diff between optimParallel versions 0.7-3 dated 2018-07-28 and 0.7-4 dated 2018-10-15
DESCRIPTION | 8 ++--- MD5 | 17 ++++++------ NEWS | 10 ++++++- R/evalParallel.R | 36 +++++++++++++------------ R/optimParallel.R | 10 ++++--- build/vignette.rds |binary man/optimParallel.Rd | 3 +- tests/testthat/test-issues.R | 51 +++++++++++++++++++----------------- tests/testthat/test-optimParallel.R | 20 ++++++++++++++ tests/testthat/test-spam.R |only 10 files changed, 97 insertions(+), 58 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis
of spectral data including nuclear magnetic resonance (NMR), infrared (IR),
Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy.
Includes functions for plotting and inspecting spectra, peak alignment,
hierarchical cluster analysis (HCA), principal components analysis (PCA) and
model-based clustering. Robust methods appropriate for this type of high-dimensional
data are available. ChemoSpec is designed for structured experiments, such as
metabolomics investigations, where the samples fall into treatment and
control groups. Graphical output is formatted consistently for publication quality
plots. ChemoSpec is intended to be very user friendly and to help you get usable
results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson [aut, cre] (ORCID 0000-0003-3536-8246),
Mike Bostock [cph, ctb] (author of the d3.js library used by
plotSpectraJS, http://d3js.org)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.4.97 dated 2017-12-12 and 5.0.88 dated 2018-10-15
ChemoSpec-4.4.97/ChemoSpec/R/chkSpectra.R |only ChemoSpec-4.4.97/ChemoSpec/R/groupNcolor.R |only ChemoSpec-4.4.97/ChemoSpec/R/labelExtremes.R |only ChemoSpec-4.4.97/ChemoSpec/R/plotScoresCor.R |only ChemoSpec-4.4.97/ChemoSpec/R/plotScoresDecoration.R |only ChemoSpec-4.4.97/ChemoSpec/R/removeFreq.R |only ChemoSpec-4.4.97/ChemoSpec/R/removeGroup.R |only ChemoSpec-4.4.97/ChemoSpec/R/removeSample.R |only ChemoSpec-4.4.97/ChemoSpec/R/sumGroups.R |only ChemoSpec-4.4.97/ChemoSpec/R/sumSpectra.R |only ChemoSpec-4.4.97/ChemoSpec/inst/doc/ChemoSpec.Rnw |only ChemoSpec-4.4.97/ChemoSpec/man/avgFacLvls.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/binData.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/colLeaf.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/coordProjCS.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/groupNcolor.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/isWholeNo.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/labelExtremes.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/labelExtremes3d.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/makeEllipsoid.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/normVec.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/plotScoresCor.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/plotScoresDecoration.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/q2rPCA.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/seXy.Rd |only ChemoSpec-4.4.97/ChemoSpec/man/shrinkLeaf.Rd |only ChemoSpec-4.4.97/ChemoSpec/vignettes/ChemoSpec.Rnw |only ChemoSpec-5.0.88/ChemoSpec/DESCRIPTION | 52 +- ChemoSpec-5.0.88/ChemoSpec/MD5 | 194 ++++------ ChemoSpec-5.0.88/ChemoSpec/NAMESPACE | 58 +-- ChemoSpec-5.0.88/ChemoSpec/NEWS | 52 ++ ChemoSpec-5.0.88/ChemoSpec/R/ChemoSpec-package.R | 15 ChemoSpec-5.0.88/ChemoSpec/R/Spectra.R | 2 ChemoSpec-5.0.88/ChemoSpec/R/aov_pcaSpectra.R | 29 - ChemoSpec-5.0.88/ChemoSpec/R/avgFacLvls.R | 7 ChemoSpec-5.0.88/ChemoSpec/R/baselineSpectra.R | 5 ChemoSpec-5.0.88/ChemoSpec/R/binData.R | 13 ChemoSpec-5.0.88/ChemoSpec/R/binSpectra.R | 10 ChemoSpec-5.0.88/ChemoSpec/R/c_pcaSpectra.R | 3 ChemoSpec-5.0.88/ChemoSpec/R/chkSpectraStub.R |only ChemoSpec-5.0.88/ChemoSpec/R/clupaSpectra.R | 9 ChemoSpec-5.0.88/ChemoSpec/R/colLeaf.R | 5 ChemoSpec-5.0.88/ChemoSpec/R/coordProjCS.R | 6 ChemoSpec-5.0.88/ChemoSpec/R/files2SpectraObject.R | 10 ChemoSpec-5.0.88/ChemoSpec/R/hcaScores.R | 3 ChemoSpec-5.0.88/ChemoSpec/R/isWholeNo.R | 9 ChemoSpec-5.0.88/ChemoSpec/R/labelExtremes3d.R | 13 ChemoSpec-5.0.88/ChemoSpec/R/loopThruSpectra.R | 10 ChemoSpec-5.0.88/ChemoSpec/R/makeEllipsoid.R | 13 ChemoSpec-5.0.88/ChemoSpec/R/matrix2SpectraObject.R | 2 ChemoSpec-5.0.88/ChemoSpec/R/mclust3D.R | 2 ChemoSpec-5.0.88/ChemoSpec/R/mclustSpectra.R | 6 ChemoSpec-5.0.88/ChemoSpec/R/normSpectra.R | 31 + ChemoSpec-5.0.88/ChemoSpec/R/normVec.R | 9 ChemoSpec-5.0.88/ChemoSpec/R/pcaDiag.R | 14 ChemoSpec-5.0.88/ChemoSpec/R/plot2Loadings.R | 2 ChemoSpec-5.0.88/ChemoSpec/R/plotHCA.R | 17 ChemoSpec-5.0.88/ChemoSpec/R/plotScores.R | 185 ---------- ChemoSpec-5.0.88/ChemoSpec/R/plotScores3D.R | 15 ChemoSpec-5.0.88/ChemoSpec/R/plotScoresRGL.R | 7 ChemoSpec-5.0.88/ChemoSpec/R/plotScree.R | 3 ChemoSpec-5.0.88/ChemoSpec/R/plotScree2.R | 5 ChemoSpec-5.0.88/ChemoSpec/R/plotSpectra.R | 17 ChemoSpec-5.0.88/ChemoSpec/R/q2rPCA.R | 7 ChemoSpec-5.0.88/ChemoSpec/R/r2qPCA.R | 3 ChemoSpec-5.0.88/ChemoSpec/R/r_pcaSpectra.R | 7 ChemoSpec-5.0.88/ChemoSpec/R/removeFreqStub.R |only ChemoSpec-5.0.88/ChemoSpec/R/removeGroupStub.R |only ChemoSpec-5.0.88/ChemoSpec/R/removeSampleStub.R |only ChemoSpec-5.0.88/ChemoSpec/R/rowDist.R | 2 ChemoSpec-5.0.88/ChemoSpec/R/sPlotSpectra.R | 2 ChemoSpec-5.0.88/ChemoSpec/R/seXy.R | 46 +- ChemoSpec-5.0.88/ChemoSpec/R/shrinkLeaf.R | 6 ChemoSpec-5.0.88/ChemoSpec/R/sumGroupsStub.R |only ChemoSpec-5.0.88/ChemoSpec/R/sumSpectraStub.R |only ChemoSpec-5.0.88/ChemoSpec/R/surveySpectra.R | 20 - ChemoSpec-5.0.88/ChemoSpec/R/surveySpectra2.R | 8 ChemoSpec-5.0.88/ChemoSpec/build/vignette.rds |binary ChemoSpec-5.0.88/ChemoSpec/data/SrE.IR.RData |binary ChemoSpec-5.0.88/ChemoSpec/data/SrE.NMR.RData |binary ChemoSpec-5.0.88/ChemoSpec/data/alignMUD.RData |binary ChemoSpec-5.0.88/ChemoSpec/data/metMUD1.RData |binary ChemoSpec-5.0.88/ChemoSpec/data/metMUD2.RData |binary ChemoSpec-5.0.88/ChemoSpec/inst/doc/ChemoSpec.R | 305 ++++++++++------- ChemoSpec-5.0.88/ChemoSpec/inst/doc/ChemoSpec.Rmd |only ChemoSpec-5.0.88/ChemoSpec/inst/doc/ChemoSpec.pdf |binary ChemoSpec-5.0.88/ChemoSpec/man/Spectra.Rd | 2 ChemoSpec-5.0.88/ChemoSpec/man/aovPCAscores.Rd | 3 ChemoSpec-5.0.88/ChemoSpec/man/aov_pcaSpectra.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/baselineSpectra.Rd | 5 ChemoSpec-5.0.88/ChemoSpec/man/c_pcaSpectra.Rd | 3 ChemoSpec-5.0.88/ChemoSpec/man/check4Gaps.Rd | 3 ChemoSpec-5.0.88/ChemoSpec/man/chkSpectra.Rd | 59 --- ChemoSpec-5.0.88/ChemoSpec/man/clupaSpectra.Rd | 7 ChemoSpec-5.0.88/ChemoSpec/man/conColScheme.Rd | 3 ChemoSpec-5.0.88/ChemoSpec/man/cv_pcaSpectra.Rd | 6 ChemoSpec-5.0.88/ChemoSpec/man/evalClusters.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/files2SpectraObject.Rd | 5 ChemoSpec-5.0.88/ChemoSpec/man/mclust3dSpectra.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/mclustSpectra.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/normSpectra.Rd | 29 + ChemoSpec-5.0.88/ChemoSpec/man/pcaDiag.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/plotScores.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/plotScoresRGL.Rd | 7 ChemoSpec-5.0.88/ChemoSpec/man/plotScree.Rd | 1 ChemoSpec-5.0.88/ChemoSpec/man/plotSpectra.Rd | 10 ChemoSpec-5.0.88/ChemoSpec/man/plotSpectraDist.Rd | 3 ChemoSpec-5.0.88/ChemoSpec/man/r_pcaSpectra.Rd | 4 ChemoSpec-5.0.88/ChemoSpec/man/removeFreq.Rd | 67 --- ChemoSpec-5.0.88/ChemoSpec/man/removeGroup.Rd | 74 ---- ChemoSpec-5.0.88/ChemoSpec/man/removeSample.Rd |only ChemoSpec-5.0.88/ChemoSpec/man/rowDist.Rd | 2 ChemoSpec-5.0.88/ChemoSpec/man/sumGroups.Rd | 41 -- ChemoSpec-5.0.88/ChemoSpec/man/sumSpectra.Rd | 45 -- ChemoSpec-5.0.88/ChemoSpec/vignettes/ChemoSpec.Rmd |only ChemoSpec-5.0.88/ChemoSpec/vignettes/chemometrics.bib | 191 +++++----- 116 files changed, 766 insertions(+), 1067 deletions(-)
Title: Import Data in the JCAMP-DX Format
Description: Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
Author: Bryan A. Hanson [aut, cre] (ORCID 0000-0003-3536-8246)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between readJDX versions 0.2.3 dated 2016-12-21 and 0.3.250 dated 2018-10-15
readJDX-0.2.3/readJDX/inst/doc/readJDX.Rnw |only readJDX-0.2.3/readJDX/vignettes/readJDX.Rnw |only readJDX-0.3.250/readJDX/DESCRIPTION | 18 +- readJDX-0.3.250/readJDX/MD5 | 38 ++-- readJDX-0.3.250/readJDX/NAMESPACE | 2 readJDX-0.3.250/readJDX/NEWS | 29 +++ readJDX-0.3.250/readJDX/R/deDIF.R | 65 +++----- readJDX-0.3.250/readJDX/R/decompressJDXxyy.R | 210 +++++++++++++++++--------- readJDX-0.3.250/readJDX/R/extractParams.R | 84 ++++++++-- readJDX-0.3.250/readJDX/R/findDataTables.R | 121 +++++++++----- readJDX-0.3.250/readJDX/R/getJDXcompression.R | 15 + readJDX-0.3.250/readJDX/R/insertDUPs.R | 60 +++---- readJDX-0.3.250/readJDX/R/processDataTable.R | 86 +++++++++- readJDX-0.3.250/readJDX/R/readJDX.R | 174 +++++++++++++-------- readJDX-0.3.250/readJDX/R/repDUPs.R | 58 ++++--- readJDX-0.3.250/readJDX/R/unDIF.R | 64 +++++-- readJDX-0.3.250/readJDX/build/vignette.rds |binary readJDX-0.3.250/readJDX/inst/doc/readJDX.R | 19 -- readJDX-0.3.250/readJDX/inst/doc/readJDX.Rmd |only readJDX-0.3.250/readJDX/inst/doc/readJDX.pdf |binary readJDX-0.3.250/readJDX/man/readJDX.Rd | 72 ++++++-- readJDX-0.3.250/readJDX/vignettes/readJDX.Rmd |only 22 files changed, 729 insertions(+), 386 deletions(-)
Title: Projection Pursuit Based on Gaussian Mixtures and Evolutionary
Algorithms
Description: Projection Pursuit (PP) algorithm for dimension reduction based on Gaussian Mixture Models (GMMs) for density estimation using Genetic Algorithms (GAs) to maximise an approximated negentropy index.
Author: Alessio Serafini [aut, cre] (<https://orcid.org/0000-0002-8579-5695>),
Luca Scrucca [aut] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Alessio Serafini <srf.alessio@gmail.com>
Diff between ppgmmga versions 1.0 dated 2018-10-14 and 1.0.1 dated 2018-10-15
DESCRIPTION | 8 MD5 | 17 - NEWS.md |only README.md | 45 ++ inst/CITATION | 2 inst/doc/ppgmmga.R | 6 inst/doc/ppgmmga.Rmd | 6 inst/doc/ppgmmga.html | 824 +++++++++++++++++++++++++++---------------------- src/approximations.cpp | 2 vignettes/ppgmmga.Rmd | 6 10 files changed, 533 insertions(+), 383 deletions(-)
Title: Lipid Annotation for LC-MS/MS DIA Data
Description: Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation and intensity rules.
Author: M Isabel Alcoriza-Balaguer, J Carlos Garcia-Canaveras
Maintainer: M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
Diff between LipidMS versions 0.1.0 dated 2018-07-12 and 1.0.0 dated 2018-10-15
LipidMS-0.1.0/LipidMS/data/mix_neg_Ce20.rda |only LipidMS-0.1.0/LipidMS/data/mix_neg_Ce40.rda |only LipidMS-0.1.0/LipidMS/data/mix_neg_fullMS.rda |only LipidMS-0.1.0/LipidMS/data/mix_pos_Ce20.rda |only LipidMS-0.1.0/LipidMS/data/mix_pos_Ce40.rda |only LipidMS-0.1.0/LipidMS/data/mix_pos_fullMS.rda |only LipidMS-0.1.0/LipidMS/data/serum_neg_Ce20.rda |only LipidMS-0.1.0/LipidMS/data/serum_neg_Ce40.rda |only LipidMS-0.1.0/LipidMS/data/serum_neg_fullMS.rda |only LipidMS-0.1.0/LipidMS/data/serum_pos_Ce20.rda |only LipidMS-0.1.0/LipidMS/data/serum_pos_Ce40.rda |only LipidMS-0.1.0/LipidMS/data/serum_pos_fullMS.rda |only LipidMS-0.1.0/LipidMS/man/joinAdducts.Rd |only LipidMS-0.1.0/LipidMS/man/mix_neg_Ce20.Rd |only LipidMS-0.1.0/LipidMS/man/mix_neg_Ce40.Rd |only LipidMS-0.1.0/LipidMS/man/mix_neg_fullMS.Rd |only LipidMS-0.1.0/LipidMS/man/mix_pos_Ce20.Rd |only LipidMS-0.1.0/LipidMS/man/mix_pos_Ce40.Rd |only LipidMS-0.1.0/LipidMS/man/mix_pos_fullMS.Rd |only LipidMS-0.1.0/LipidMS/man/removeAdducts.Rd |only LipidMS-0.1.0/LipidMS/man/removeDGs.Rd |only LipidMS-0.1.0/LipidMS/man/serum_neg_Ce20.Rd |only LipidMS-0.1.0/LipidMS/man/serum_neg_Ce40.Rd |only LipidMS-0.1.0/LipidMS/man/serum_neg_fullMS.Rd |only LipidMS-0.1.0/LipidMS/man/serum_pos_Ce20.Rd |only LipidMS-0.1.0/LipidMS/man/serum_pos_Ce40.Rd |only LipidMS-0.1.0/LipidMS/man/serum_pos_fullMS.Rd |only LipidMS-1.0.0/LipidMS/DESCRIPTION | 17 - LipidMS-1.0.0/LipidMS/MD5 | 237 +++++++------- LipidMS-1.0.0/LipidMS/NAMESPACE | 112 +++--- LipidMS-1.0.0/LipidMS/R/assignDB.R |only LipidMS-1.0.0/LipidMS/R/chainFrags.R | 235 +++++++------- LipidMS-1.0.0/LipidMS/R/checkClass.R | 85 +++-- LipidMS-1.0.0/LipidMS/R/checkIntensityRules.R | 58 +-- LipidMS-1.0.0/LipidMS/R/coelutingFrags.R | 55 ++- LipidMS-1.0.0/LipidMS/R/combineChains.R | 114 ++++--- LipidMS-1.0.0/LipidMS/R/createLipidDB.R | 2 LipidMS-1.0.0/LipidMS/R/crossTables.R | 80 ++++ LipidMS-1.0.0/LipidMS/R/dataProcessing.R | 160 +++++---- LipidMS-1.0.0/LipidMS/R/findCandidates.R | 46 +- LipidMS-1.0.0/LipidMS/R/getInclusionList.R | 8 LipidMS-1.0.0/LipidMS/R/idBAneg.R | 185 ++++++++--- LipidMS-1.0.0/LipidMS/R/idCEpos.R | 137 ++++++-- LipidMS-1.0.0/LipidMS/R/idCLneg.R | 149 ++++++--- LipidMS-1.0.0/LipidMS/R/idCarpos.R | 133 ++++++-- LipidMS-1.0.0/LipidMS/R/idCerneg.R | 132 ++++++-- LipidMS-1.0.0/LipidMS/R/idCerpos.R | 134 ++++++-- LipidMS-1.0.0/LipidMS/R/idDGpos.R | 140 ++++++-- LipidMS-1.0.0/LipidMS/R/idFAHFAneg.R | 129 +++++-- LipidMS-1.0.0/LipidMS/R/idFAneg.R | 131 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPCneg.R | 139 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPCpos.R | 140 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPEneg.R | 136 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPEpos.R | 137 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPGneg.R | 136 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPIneg.R | 136 ++++++-- LipidMS-1.0.0/LipidMS/R/idLPSneg.R | 137 ++++++-- LipidMS-1.0.0/LipidMS/R/idMGpos.R | 134 ++++++-- LipidMS-1.0.0/LipidMS/R/idNEG.R | 159 ++++++--- LipidMS-1.0.0/LipidMS/R/idPCneg.R | 138 ++++++-- LipidMS-1.0.0/LipidMS/R/idPCpos.R | 151 ++++++--- LipidMS-1.0.0/LipidMS/R/idPEneg.R | 143 ++++++-- LipidMS-1.0.0/LipidMS/R/idPEpos.R | 142 ++++++-- LipidMS-1.0.0/LipidMS/R/idPGneg.R | 136 ++++++-- LipidMS-1.0.0/LipidMS/R/idPIneg.R | 141 ++++++-- LipidMS-1.0.0/LipidMS/R/idPOS.R | 132 +++++--- LipidMS-1.0.0/LipidMS/R/idPSneg.R | 150 ++++++--- LipidMS-1.0.0/LipidMS/R/idSMpos.R | 133 ++++++-- LipidMS-1.0.0/LipidMS/R/idSphPneg.R | 162 ++++++--- LipidMS-1.0.0/LipidMS/R/idSphPpos.R | 163 ++++++---- LipidMS-1.0.0/LipidMS/R/idSphneg.R | 162 ++++++--- LipidMS-1.0.0/LipidMS/R/idSphpos.R | 166 ++++++---- LipidMS-1.0.0/LipidMS/R/idTGpos.R | 175 +++++++--- LipidMS-1.0.0/LipidMS/R/internal.R | 373 +++++++++++------------ LipidMS-1.0.0/LipidMS/R/organizeResults.R | 174 +++++++--- LipidMS-1.0.0/LipidMS/R/searchIsotopes.R |only LipidMS-1.0.0/LipidMS/build |only LipidMS-1.0.0/LipidMS/data/MS1_neg.rda |only LipidMS-1.0.0/LipidMS/data/MS1_pos.rda |only LipidMS-1.0.0/LipidMS/data/MSMS1_neg.rda |only LipidMS-1.0.0/LipidMS/data/MSMS1_pos.rda |only LipidMS-1.0.0/LipidMS/data/MSMS2_neg.rda |only LipidMS-1.0.0/LipidMS/data/MSMS2_pos.rda |only LipidMS-1.0.0/LipidMS/data/badb.rda |binary LipidMS-1.0.0/LipidMS/data/datalist | 18 - LipidMS-1.0.0/LipidMS/inst |only LipidMS-1.0.0/LipidMS/man/MS1_neg.Rd |only LipidMS-1.0.0/LipidMS/man/MS1_pos.Rd |only LipidMS-1.0.0/LipidMS/man/MSMS1_neg.Rd |only LipidMS-1.0.0/LipidMS/man/MSMS1_pos.Rd |only LipidMS-1.0.0/LipidMS/man/MSMS2_neg.Rd |only LipidMS-1.0.0/LipidMS/man/MSMS2_pos.Rd |only LipidMS-1.0.0/LipidMS/man/assignDB.Rd |only LipidMS-1.0.0/LipidMS/man/badb.Rd | 3 LipidMS-1.0.0/LipidMS/man/chainFrags.Rd | 34 +- LipidMS-1.0.0/LipidMS/man/checkClass.Rd | 47 ++ LipidMS-1.0.0/LipidMS/man/checkIntRules.Rd | 16 LipidMS-1.0.0/LipidMS/man/checkIntensityRules.Rd | 35 -- LipidMS-1.0.0/LipidMS/man/coelutingFrags.Rd | 30 + LipidMS-1.0.0/LipidMS/man/coelutionScore.Rd |only LipidMS-1.0.0/LipidMS/man/combineChains.Rd | 27 - LipidMS-1.0.0/LipidMS/man/crossAdducts.Rd |only LipidMS-1.0.0/LipidMS/man/crossTables.Rd | 16 LipidMS-1.0.0/LipidMS/man/dataProcessing.Rd | 84 ++--- LipidMS-1.0.0/LipidMS/man/findCandidates.Rd | 34 +- LipidMS-1.0.0/LipidMS/man/frags.Rd | 2 LipidMS-1.0.0/LipidMS/man/getInclusionList.Rd | 7 LipidMS-1.0.0/LipidMS/man/idBAneg.Rd | 64 ++- LipidMS-1.0.0/LipidMS/man/idCEpos.Rd | 63 ++- LipidMS-1.0.0/LipidMS/man/idCLneg.Rd | 74 ++-- LipidMS-1.0.0/LipidMS/man/idCarpos.Rd | 62 ++- LipidMS-1.0.0/LipidMS/man/idCerneg.Rd | 66 ++-- LipidMS-1.0.0/LipidMS/man/idCerpos.Rd | 67 ++-- LipidMS-1.0.0/LipidMS/man/idDGpos.Rd | 69 ++-- LipidMS-1.0.0/LipidMS/man/idFAHFAneg.Rd | 64 ++- LipidMS-1.0.0/LipidMS/man/idFAneg.Rd | 61 ++- LipidMS-1.0.0/LipidMS/man/idLPCneg.Rd | 65 ++-- LipidMS-1.0.0/LipidMS/man/idLPCpos.Rd | 63 ++- LipidMS-1.0.0/LipidMS/man/idLPEneg.Rd | 65 ++-- LipidMS-1.0.0/LipidMS/man/idLPEpos.Rd | 63 ++- LipidMS-1.0.0/LipidMS/man/idLPGneg.Rd | 63 ++- LipidMS-1.0.0/LipidMS/man/idLPIneg.Rd | 63 ++- LipidMS-1.0.0/LipidMS/man/idLPSneg.Rd | 63 ++- LipidMS-1.0.0/LipidMS/man/idMGpos.Rd | 61 ++- LipidMS-1.0.0/LipidMS/man/idNEG.Rd | 55 ++- LipidMS-1.0.0/LipidMS/man/idPCneg.Rd | 67 ++-- LipidMS-1.0.0/LipidMS/man/idPCpos.Rd | 80 ++-- LipidMS-1.0.0/LipidMS/man/idPEneg.Rd | 71 ++-- LipidMS-1.0.0/LipidMS/man/idPEpos.Rd | 69 ++-- LipidMS-1.0.0/LipidMS/man/idPGneg.Rd | 71 ++-- LipidMS-1.0.0/LipidMS/man/idPIneg.Rd | 75 ++-- LipidMS-1.0.0/LipidMS/man/idPOS.Rd | 52 ++- LipidMS-1.0.0/LipidMS/man/idPSneg.Rd | 76 ++-- LipidMS-1.0.0/LipidMS/man/idSMpos.Rd | 66 ++-- LipidMS-1.0.0/LipidMS/man/idSphPneg.Rd | 70 ++-- LipidMS-1.0.0/LipidMS/man/idSphPpos.Rd | 68 ++-- LipidMS-1.0.0/LipidMS/man/idSphneg.Rd | 70 ++-- LipidMS-1.0.0/LipidMS/man/idSphpos.Rd | 71 ++-- LipidMS-1.0.0/LipidMS/man/idTGpos.Rd | 82 +++-- LipidMS-1.0.0/LipidMS/man/organizeResults.Rd | 34 +- LipidMS-1.0.0/LipidMS/man/searchIsotopes.Rd |only LipidMS-1.0.0/LipidMS/vignettes |only 142 files changed, 5877 insertions(+), 3023 deletions(-)
Title: Efficient Designs for Discrete Choice Experiments
Description: Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Crabbe M, Akinc D and Vandebroek M (2014) <doi:10.1016/j.trb.2013.11.008>.
Author: Frits Traets [aut, cre]
Maintainer: Frits Traets <frits.traets@kuleuven.be>
Diff between idefix versions 0.2.4 dated 2018-01-17 and 0.3.1 dated 2018-10-15
idefix-0.2.4/idefix/man/Charbin.Rd |only idefix-0.2.4/idefix/man/SeqKL.Rd |only idefix-0.3.1/idefix/DESCRIPTION | 15 idefix-0.3.1/idefix/MD5 | 54 - idefix-0.3.1/idefix/NAMESPACE | 4 idefix-0.3.1/idefix/R/Fullsets_ucpp.R |only idefix-0.3.1/idefix/R/RcppExports.R |only idefix-0.3.1/idefix/R/data.R | 32 idefix-0.3.1/idefix/R/efficiency_algorithms.R | 843 +++++++++++++-------- idefix-0.3.1/idefix/R/efficiency_criterions.R | 116 +- idefix-0.3.1/idefix/R/efficiency_criterions_ucpp.R |only idefix-0.3.1/idefix/R/estimation_support.R | 380 ++++++--- idefix-0.3.1/idefix/R/generation.R | 135 +++ idefix-0.3.1/idefix/R/idefix.R |only idefix-0.3.1/idefix/R/importance_sampling.R | 236 ++++- idefix-0.3.1/idefix/R/shiny_support.R | 647 +++++++--------- idefix-0.3.1/idefix/build/partial.rdb |binary idefix-0.3.1/idefix/data/example_design2.RData |only idefix-0.3.1/idefix/data/nochoice_design.RData |only idefix-0.3.1/idefix/man/Datatrans.Rd | 68 - idefix-0.3.1/idefix/man/Decode.Rd | 67 - idefix-0.3.1/idefix/man/ImpsampMNL.Rd | 90 +- idefix-0.3.1/idefix/man/Modfed.Rd | 122 +-- idefix-0.3.1/idefix/man/Profiles.Rd | 6 idefix-0.3.1/idefix/man/RespondMNL.Rd | 17 idefix-0.3.1/idefix/man/SeqDB.Rd | 115 +- idefix-0.3.1/idefix/man/SurveyApp.Rd | 138 ++- idefix-0.3.1/idefix/man/example_design.Rd | 2 idefix-0.3.1/idefix/man/example_design2.Rd |only idefix-0.3.1/idefix/man/idefix-package.Rd |only idefix-0.3.1/idefix/man/nochoice_design.Rd |only idefix-0.3.1/idefix/src |only 32 files changed, 1939 insertions(+), 1148 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports
Cox-PH, proportional odds, and accelerated failure time models. Allows for
semi and fully parametric models (parametric only for accelerated failure
time models) and Bayesian parametric models. Includes functions for easy visual
diagnostics of model fits and imputation of censored data.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 2.0.8 dated 2018-07-14 and 2.0.9 dated 2018-10-15
DESCRIPTION | 8 ++++---- MD5 | 33 ++++++++++++++++++--------------- NAMESPACE | 3 +++ NEWS | 6 ++++++ R/clusterBootstrap.R |only R/ic_bayes.R | 3 ++- R/ic_par.R | 2 ++ R/ic_sp.R | 4 +++- R/internal_utilities.R | 15 ++++++++++++++- R/referenceClasses.R | 5 ++++- R/user_utilities.R | 4 ++-- inst/doc/icenReg.Rnw | 2 +- inst/doc/icenReg.pdf |binary man/ic_sp.Rd | 2 +- man/ir_clustBoot.Rd |only man/simIC_cluster.Rd |only man/survCIs.Rd | 4 ++-- src/icenReg_files/basicUtilities.cpp | 2 +- vignettes/icenReg.Rnw | 2 +- 19 files changed, 64 insertions(+), 31 deletions(-)
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani, Maria Brigida Ferraro, Alessio Serafini
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 1.1.3 dated 2018-03-21 and 2.0 dated 2018-10-15
fclust-1.1.3/fclust/R/FKM.med.noise.R |only fclust-1.1.3/fclust/R/MPC.R |only fclust-1.1.3/fclust/R/PC.R |only fclust-1.1.3/fclust/R/PE.R |only fclust-1.1.3/fclust/R/SIL.F.R |only fclust-1.1.3/fclust/R/SIL.R |only fclust-1.1.3/fclust/R/XB.R |only fclust-2.0/fclust/DESCRIPTION | 20 fclust-2.0/fclust/MD5 | 196 +++-- fclust-2.0/fclust/NAMESPACE | 23 fclust-2.0/fclust/NEWS.md |only fclust-2.0/fclust/R/ARI.F.R |only fclust-2.0/fclust/R/FKM.R | 662 +++++++++++--------- fclust-2.0/fclust/R/FKM.ent.R | 667 +++++++++++--------- fclust-2.0/fclust/R/FKM.ent.noise.R | 784 ++++++++++++++--------- fclust-2.0/fclust/R/FKM.gk.R | 785 ++++++++++++++--------- fclust-2.0/fclust/R/FKM.gk.ent.R | 786 +++++++++++++---------- fclust-2.0/fclust/R/FKM.gk.ent.noise.R | 896 +++++++++++++++------------ fclust-2.0/fclust/R/FKM.gk.noise.R | 898 ++++++++++++++++----------- fclust-2.0/fclust/R/FKM.gkb.R | 840 ++++++++++++++----------- fclust-2.0/fclust/R/FKM.gkb.ent.R | 838 ++++++++++++++----------- fclust-2.0/fclust/R/FKM.gkb.ent.noise.R | 953 ++++++++++++++++------------- fclust-2.0/fclust/R/FKM.gkb.noise.R | 953 ++++++++++++++++------------- fclust-2.0/fclust/R/FKM.med.R | 694 ++++++++++++--------- fclust-2.0/fclust/R/FKM.med_noise.R |only fclust-2.0/fclust/R/FKM.noise.R | 773 +++++++++++++---------- fclust-2.0/fclust/R/FKM.pf.R | 673 +++++++++++--------- fclust-2.0/fclust/R/FKM.pf.noise.R | 790 ++++++++++++++---------- fclust-2.0/fclust/R/Fclust.R | 868 +++++++++++++------------- fclust-2.0/fclust/R/Fclust.compare.R |only fclust-2.0/fclust/R/Fclust.index.R | 144 ++-- fclust-2.0/fclust/R/Hraw.R | 71 +- fclust-2.0/fclust/R/JACCARD.F.R |only fclust-2.0/fclust/R/MPC_mod.R |only fclust-2.0/fclust/R/NEFRC.R |only fclust-2.0/fclust/R/NEFRC.noise.R |only fclust-2.0/fclust/R/PC_mod.R |only fclust-2.0/fclust/R/PE_mod.R |only fclust-2.0/fclust/R/RI.F.R |only fclust-2.0/fclust/R/RcppExports.R |only fclust-2.0/fclust/R/SIL.F_mod.R |only fclust-2.0/fclust/R/SIL_mod.R |only fclust-2.0/fclust/R/VAT.R | 73 +- fclust-2.0/fclust/R/VCV.R | 255 +++---- fclust-2.0/fclust/R/VCV2.R | 197 ++--- fclust-2.0/fclust/R/VIFCR.R | 221 +++--- fclust-2.0/fclust/R/XB_mod.R |only fclust-2.0/fclust/R/cl.memb.H.R | 57 - fclust-2.0/fclust/R/cl.memb.R | 41 - fclust-2.0/fclust/R/cl.memb.t.R | 81 +- fclust-2.0/fclust/R/cl.size.H.R | 41 - fclust-2.0/fclust/R/cl.size.R | 39 - fclust-2.0/fclust/R/plot.fclust.R | 398 +++++++----- fclust-2.0/fclust/R/print.fclust.R | 53 - fclust-2.0/fclust/R/summary.fclust.R | 153 ++-- fclust-2.0/fclust/R/zzz.R |only fclust-2.0/fclust/data/NBA.rda |only fclust-2.0/fclust/data/houseVotes.rda |only fclust-2.0/fclust/data/synt.data2.rda |only fclust-2.0/fclust/man/ARI.F.Rd |only fclust-2.0/fclust/man/FKM.Rd | 135 ++-- fclust-2.0/fclust/man/FKM.ent.Rd | 151 ++-- fclust-2.0/fclust/man/FKM.ent.noise.Rd | 143 ++-- fclust-2.0/fclust/man/FKM.gk.Rd | 135 ++-- fclust-2.0/fclust/man/FKM.gk.ent.Rd | 146 ++-- fclust-2.0/fclust/man/FKM.gk.ent.noise.Rd | 154 ++-- fclust-2.0/fclust/man/FKM.gk.noise.Rd | 141 ++-- fclust-2.0/fclust/man/FKM.gkb.Rd | 140 ++-- fclust-2.0/fclust/man/FKM.gkb.ent.Rd | 152 ++-- fclust-2.0/fclust/man/FKM.gkb.ent.noise.Rd | 160 ++-- fclust-2.0/fclust/man/FKM.gkb.noise.Rd | 148 ++-- fclust-2.0/fclust/man/FKM.med.Rd | 148 ++-- fclust-2.0/fclust/man/FKM.med.noise.Rd | 137 ++-- fclust-2.0/fclust/man/FKM.noise.Rd | 125 +-- fclust-2.0/fclust/man/FKM.pf.Rd | 142 ++-- fclust-2.0/fclust/man/FKM.pf.noise.Rd | 148 ++-- fclust-2.0/fclust/man/Fclust.Rd | 64 - fclust-2.0/fclust/man/Fclust.compare.Rd |only fclust-2.0/fclust/man/Fclust.index.Rd | 80 +- fclust-2.0/fclust/man/Hraw.Rd | 82 +- fclust-2.0/fclust/man/JACCARD.F.Rd |only fclust-2.0/fclust/man/MPC.Rd | 72 +- fclust-2.0/fclust/man/Mc.Rd | 158 ++-- fclust-2.0/fclust/man/NBA.Rd |only fclust-2.0/fclust/man/NEFRC.Rd |only fclust-2.0/fclust/man/NEFRC.noise.Rd |only fclust-2.0/fclust/man/PC.Rd | 72 +- fclust-2.0/fclust/man/PE.Rd | 74 +- fclust-2.0/fclust/man/RI.F.Rd |only fclust-2.0/fclust/man/SIL.F.Rd | 84 +- fclust-2.0/fclust/man/SIL.Rd | 84 +- fclust-2.0/fclust/man/VAT.Rd | 66 +- fclust-2.0/fclust/man/VCV.Rd | 84 +- fclust-2.0/fclust/man/VCV2.Rd | 82 +- fclust-2.0/fclust/man/VIFCR.Rd | 68 +- fclust-2.0/fclust/man/XB.Rd | 86 +- fclust-2.0/fclust/man/butterfly.Rd | 56 - fclust-2.0/fclust/man/cl.memb.H.Rd | 62 - fclust-2.0/fclust/man/cl.memb.Rd | 62 - fclust-2.0/fclust/man/cl.memb.t.Rd | 68 +- fclust-2.0/fclust/man/cl.size.H.Rd | 60 - fclust-2.0/fclust/man/cl.size.Rd | 58 - fclust-2.0/fclust/man/houseVotes.Rd |only fclust-2.0/fclust/man/plot.fclust.Rd | 107 +-- fclust-2.0/fclust/man/print.fclust.Rd | 54 - fclust-2.0/fclust/man/summary.fclust.Rd | 52 - fclust-2.0/fclust/man/synt.data.Rd | 64 + fclust-2.0/fclust/man/synt.data2.Rd |only fclust-2.0/fclust/man/unemployment.Rd | 58 - fclust-2.0/fclust/src |only 110 files changed, 10654 insertions(+), 8431 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops.
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>
Diff between dslabs versions 0.5.0 dated 2018-10-11 and 0.5.1 dated 2018-10-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- data/tissue_gene_expression.rda |binary inst/script/make-tissue-gene-expression.R | 9 ++++++--- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Dendroclimatological
Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are two core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. The second one is compare_methods(),
which effectively compares several linear and nonlinear regression algorithms.
Author: Jernej Jevsenak [aut, cre], Tom Levanic [ctb]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 1.0.0 dated 2018-07-06 and 1.0.1 dated 2018-10-15
DESCRIPTION | 6 MD5 | 30 +- NAMESPACE | 3 NEWS.md | 9 R/compare_methods.R | 32 ++- R/daily_response.R | 161 ++++++++++++++- R/glimpse_daily_data.R |only inst/CITATION | 16 + inst/doc/Examples_daily_response.R | 43 ++-- inst/doc/Examples_daily_response.Rmd | 66 +++--- inst/doc/Examples_daily_response.html | 189 ++++++++++-------- inst/doc/compare_methods_vignette.html | 342 ++++++++++++++++----------------- man/compare_methods.Rd | 4 man/daily_response.Rd | 25 +- man/glimpse_daily_data.Rd |only tests/testthat/test_general.R | 16 - vignettes/Examples_daily_response.Rmd | 66 +++--- 17 files changed, 634 insertions(+), 374 deletions(-)
Title: Reproducibility of Gene Expression Clusters
Description: This is a function for validating microarray clusters via reproducibility,
based on the paper referenced below.
Author: Amy Kapp <Amy_Kapp@hotmail.com> and Rob Tibshirani <tibs@stanford.edu>
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between clusterRepro versions 0.5-1.1 dated 2009-03-01 and 0.9 dated 2018-10-15
DESCRIPTION | 21 +++++++++++++-------- MD5 |only NAMESPACE | 1 + 3 files changed, 14 insertions(+), 8 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <http://jmlr.org/papers/v18/15-481.html>). Both Cayley, footrule, Kendall, and Spearman distances are supported in the models. The rank data to be analyzed can be the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen, Valeria Vitelli, Marta Crispino, Qinghua Liu
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 0.1.0 dated 2018-10-08 and 0.1.1 dated 2018-10-15
BayesMallows-0.1.0/BayesMallows/src/importance_sampling.h |only BayesMallows-0.1.1/BayesMallows/DESCRIPTION | 20 BayesMallows-0.1.1/BayesMallows/MD5 | 51 BayesMallows-0.1.1/BayesMallows/R/compute_mallows.R | 23 BayesMallows-0.1.1/BayesMallows/build/partial.rdb |binary BayesMallows-0.1.1/BayesMallows/inst/doc/BayesMallowsPackage.R | 12 BayesMallows-0.1.1/BayesMallows/inst/doc/BayesMallowsPackage.Rmd | 12 BayesMallows-0.1.1/BayesMallows/inst/doc/BayesMallowsPackage.html |24982 ---------- BayesMallows-0.1.1/BayesMallows/man/compute_mallows.Rd | 33 BayesMallows-0.1.1/BayesMallows/src/Makevars | 16 BayesMallows-0.1.1/BayesMallows/src/clustering.cpp | 8 BayesMallows-0.1.1/BayesMallows/src/clustering.h | 5 BayesMallows-0.1.1/BayesMallows/src/distfuns.cpp | 7 BayesMallows-0.1.1/BayesMallows/src/distfuns.h | 2 BayesMallows-0.1.1/BayesMallows/src/importance_sampling.cpp | 4 BayesMallows-0.1.1/BayesMallows/src/misc.h | 1 BayesMallows-0.1.1/BayesMallows/src/missing_data.cpp | 6 BayesMallows-0.1.1/BayesMallows/src/missing_data.h | 5 BayesMallows-0.1.1/BayesMallows/src/pairwise_comparisons.cpp | 2 BayesMallows-0.1.1/BayesMallows/src/pairwise_comparisons.h | 12 BayesMallows-0.1.1/BayesMallows/src/parameterupdates.cpp | 13 BayesMallows-0.1.1/BayesMallows/src/parameterupdates.h | 1 BayesMallows-0.1.1/BayesMallows/src/partitionfuns.cpp | 30 BayesMallows-0.1.1/BayesMallows/src/partitionfuns.h | 3 BayesMallows-0.1.1/BayesMallows/src/rmallows.cpp | 4 BayesMallows-0.1.1/BayesMallows/src/run_mcmc.cpp | 17 BayesMallows-0.1.1/BayesMallows/vignettes/BayesMallowsPackage.Rmd | 12 27 files changed, 141 insertions(+), 25140 deletions(-)
Title: Multidimensional Scaling of Asymmetric Data
Description: Multidimensional scaling models and methods for the visualization for asymmetric data <doi:10.1111/j.2044-8317.1996.tb01078.x>. An asymmetric matrix has the same number of rows and columns, and these rows and columns refer to the same set of objects. At least some elements in the upper-triangle are different from the corresponding elements in the lower triangle. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides the slide-vector model <doi:10.1007/BF02294474>, a scaling model with unique dimensions and the asymscal model for asymmetric multidimensional scaling. Furthermore, a heat map for skew-symmetric data, and the decomposition of asymmetry are provided for the analysis of asymmetric tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 1.2.5 dated 2018-02-01 and 2.0 dated 2018-10-15
asymmetry-1.2.5/asymmetry/R/onLoad.R |only asymmetry-1.2.5/asymmetry/inst/doc/asymmetricmds.R |only asymmetry-1.2.5/asymmetry/inst/doc/asymmetricmds.Rmd |only asymmetry-1.2.5/asymmetry/inst/doc/asymmetricmds.html |only asymmetry-1.2.5/asymmetry/inst/doc/index.html |only asymmetry-1.2.5/asymmetry/inst/java |only asymmetry-1.2.5/asymmetry/java |only asymmetry-2.0/asymmetry/DESCRIPTION | 16 +-- asymmetry-2.0/asymmetry/MD5 | 51 ++++------ asymmetry-2.0/asymmetry/NAMESPACE | 6 - asymmetry-2.0/asymmetry/R/asymscal.R | 30 +++--- asymmetry-2.0/asymmetry/R/hmap.R | 12 +- asymmetry-2.0/asymmetry/R/mdsunique.R | 86 +++++++++++++----- asymmetry-2.0/asymmetry/R/slidevector.R | 79 +++++++++++----- asymmetry-2.0/asymmetry/build/partial.rdb |binary asymmetry-2.0/asymmetry/build/vignette.rds |binary asymmetry-2.0/asymmetry/inst/doc/asymmetry.R | 23 ++++ asymmetry-2.0/asymmetry/inst/doc/asymmetry.Rmd | 33 +++++- asymmetry-2.0/asymmetry/inst/doc/asymmetry.html | 39 ++++++-- asymmetry-2.0/asymmetry/man/Englishtowns.Rd | 2 asymmetry-2.0/asymmetry/man/asymscal.Rd | 8 - asymmetry-2.0/asymmetry/man/hmap.Rd | 4 asymmetry-2.0/asymmetry/man/mdsunique.Rd | 7 - asymmetry-2.0/asymmetry/man/plot.skewsymmetry.Rd | 3 asymmetry-2.0/asymmetry/man/plot.slidevector.Rd | 12 +- asymmetry-2.0/asymmetry/man/skewsymmetry.Rd | 4 asymmetry-2.0/asymmetry/man/slidevector.Rd | 3 asymmetry-2.0/asymmetry/vignettes/asymmetry.Rmd | 33 +++++- 28 files changed, 294 insertions(+), 157 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation (Faux et al., 2016, <doi:10.3835/plantgenome2016.02.0013>).
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history (Chen et al., 2009, <doi:10.1101/gr.083634.108>).
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
David Wilson [ctb],
Daniel Money [ctb],
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>)
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 0.8.1 dated 2018-10-12 and 0.8.2 dated 2018-10-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 5 +++++ R/Class-SimParam.R | 4 ++-- R/misc.R | 8 ++++++++ R/phenotypes.R | 12 ++---------- README.md | 6 +++--- inst/doc/intro.html | 6 +++--- src/optimize.cpp | 4 ++-- 9 files changed, 37 insertions(+), 32 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA (National Oceanic and Atmospheric Administration, <http://www.noaa.gov>), GEBCO (General Bathymetric Chart of the Oceans, <http://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>
Diff between marmap versions 1.0.1 dated 2018-09-22 and 1.0.2 dated 2018-10-15
DESCRIPTION | 8 +- MD5 | 46 ++++++++-------- R/dist2isobath.R | 28 +++++----- R/get.depth.R | 32 +++++------ R/get.sample.R | 28 +++++----- R/getNOAA.bathy.R | 18 +++--- R/palette.etopo.R | 2 R/print.buffer.R | 30 +++++----- R/space.pies.R | 126 ++++++++++++++++++++++----------------------- R/subsetBathy.R | 22 +++---- R/summary.bathy.R | 22 +++---- build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary man/etopo.Rd | 54 +++++++++++-------- man/fortify.bathy.Rd | 33 ++++++----- man/marmap.Rd | 4 - 24 files changed, 233 insertions(+), 220 deletions(-)
Title: Fetch 'Scholary' Full Text from 'Crossref'
Description: Text mining client for 'Crossref' (<https://crossref.org>). Includes
functions for getting getting links to full text of articles, fetching full
text articles from those links or Digital Object Identifiers ('DOIs'),
and text extraction from 'PDFs'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between crminer versions 0.1.4 dated 2017-08-12 and 0.2.0 dated 2018-10-15
DESCRIPTION | 23 +++++++++++++-------- LICENSE | 2 - MD5 | 41 +++++++++++++++++++------------------- NEWS.md | 13 ++++++++++++ R/as_tdmurl.R | 29 +++++++++++++++++++------- R/caching.R | 23 ++++++++++----------- R/crm_extract.R | 28 ++++++++++++++++++++----- R/crm_links.R | 14 +++++++++--- R/crm_pdf.R | 2 + R/crm_text.R | 4 ++- README.md | 7 +++--- inst/examples/raw-example.rds |only man/as_tdmurl.Rd | 14 ++++++++++-- man/crm_cache.Rd | 6 ++--- man/crm_extract.Rd | 16 ++++++++++++-- man/crm_links.Rd | 9 +++++++- man/crm_pdf.Rd | 2 + man/crm_text.Rd | 2 + tests/testthat/test-crm_extract.R | 17 ++++++++++++++- tests/testthat/test-crm_html.R | 3 +- tests/testthat/test-crm_plain.R | 6 +++-- tests/testthat/test-crm_text.R | 8 +++++++ 22 files changed, 192 insertions(+), 77 deletions(-)
Title: Extended Tools for Cosinor Analysis of Rhythms
Description: Statistical procedures for calculating population–mean cosinor, non–stationary cosinor, estimation of best–fitting period, tests of population rhythm differences and more. See Cornélissen, G. (2014). <doi:10.1186/1742-4682-11-16>.
Author: Augustin Mutak <mutak94@gmail.com>
Maintainer: Augustin Mutak <mutak94@gmail.com>
Diff between cosinor2 versions 0.2.0 dated 2018-10-01 and 0.2.1 dated 2018-10-15
DESCRIPTION | 6 MD5 | 10 - inst/doc/cosinor2.R | 15 +- inst/doc/cosinor2.Rmd | 15 +- inst/doc/cosinor2.html | 295 ++----------------------------------------------- vignettes/cosinor2.Rmd | 15 +- 6 files changed, 49 insertions(+), 307 deletions(-)
Title: Penalized Composite Link Model for Efficient Estimation of
Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data)
assuming that counts are Poisson distributed and that the underlying sequence
on a fine grid to be estimated is smooth. The method is based on the composite
link model and estimation is achieved by maximizing a penalized likelihood.
Smooth detailed sequences of counts and rates are so estimated from the binned
counts. Ungrouping binned data can be desirable for many reasons: Bins can be
too coarse to allow for accurate analysis; comparisons can be hindered when
different grouping approaches are used in different histograms; and the last
interval is often wide and open-ended and, thus, covers a lot of information
in the tail area. Age-at-death distributions grouped in age classes and
abridged life tables are examples of binned data. Because of modest assumptions,
the approach is suitable for many demographic and epidemiological applications.
For a detailed description of the method and applications see
Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Author: Marius D. Pascariu [aut, cre] (<https://orcid.org/0000-0002-2568-6489>),
Silvia Rizzi [aut],
Jonas Schoeley [aut] (<https://orcid.org/0000-0002-3340-8518>),
Maciej J. Danko [aut] (<https://orcid.org/0000-0002-7924-9022>)
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between ungroup versions 1.1.0 dated 2018-09-30 and 1.1.1 dated 2018-10-15
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/pclm_fit.R | 58 --------------------------------- R/utils.R | 73 ++++++++++++++++++++++++++++++++++++++---- build/partial.rdb |binary inst/doc/Intro.pdf |binary man/frac.Rd | 2 - man/seqlast.Rd | 2 - man/suggest.valid.out.step.Rd | 2 - man/validate.nlast.Rd | 8 ++-- 10 files changed, 87 insertions(+), 82 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.2.0 dated 2018-05-19 and 0.2.1 dated 2018-10-15
hdme-0.2.0/hdme/R/set_radius.R |only hdme-0.2.1/hdme/DESCRIPTION | 6 hdme-0.2.1/hdme/MD5 | 103 - hdme-0.2.1/hdme/NAMESPACE | 32 hdme-0.2.1/hdme/NEWS.md | 36 hdme-0.2.1/hdme/R/RcppExports.R | 14 hdme-0.2.1/hdme/R/corrected_lasso_gaussian.R | 79 - hdme-0.2.1/hdme/R/corrected_lasso_glm.R | 119 -- hdme-0.2.1/hdme/R/cv_corrected_lasso.R | 180 +-- hdme-0.2.1/hdme/R/fit_corrected_lasso.R | 238 ++-- hdme-0.2.1/hdme/R/fit_gds.R | 70 - hdme-0.2.1/hdme/R/fit_gmu_lasso.R | 234 +-- hdme-0.2.1/hdme/R/fit_gmus.R | 154 +- hdme-0.2.1/hdme/R/fit_mus.R | 86 - hdme-0.2.1/hdme/R/gauss_loss.R | 24 hdme-0.2.1/hdme/R/gmu_lasso_binomial.R | 94 - hdme-0.2.1/hdme/R/helper_functions.R | 57 hdme-0.2.1/hdme/R/mus_glm.R | 100 - hdme-0.2.1/hdme/R/musalgorithm.R | 144 +- hdme-0.2.1/hdme/R/plot.corrected_lasso.R | 90 - hdme-0.2.1/hdme/R/plot.cv_corrected_lasso.R | 42 hdme-0.2.1/hdme/R/plot.gds.R | 54 hdme-0.2.1/hdme/R/plot.gmu_lasso.R | 52 hdme-0.2.1/hdme/R/plot.gmus.R | 100 - hdme-0.2.1/hdme/R/project_gradient.R | 42 hdme-0.2.1/hdme/R/project_onto_l1_ball.R | 18 hdme-0.2.1/hdme/README.md | 193 +-- hdme-0.2.1/hdme/build/partial.rdb |binary hdme-0.2.1/hdme/build/vignette.rds |binary hdme-0.2.1/hdme/inst/CITATION | 26 hdme-0.2.1/hdme/inst/REFERENCES.bib | 340 ++--- hdme-0.2.1/hdme/inst/doc/hdme-package.R | 470 ++++---- hdme-0.2.1/hdme/inst/doc/hdme-package.Rmd | 1054 +++++++++--------- hdme-0.2.1/hdme/inst/doc/hdme-package.html | 1054 ++++++++---------- hdme-0.2.1/hdme/man/cv_corrected_lasso.Rd | 140 +- hdme-0.2.1/hdme/man/fit_corrected_lasso.Rd | 180 +-- hdme-0.2.1/hdme/man/fit_gds.Rd | 76 - hdme-0.2.1/hdme/man/fit_gmu_lasso.Rd | 126 +- hdme-0.2.1/hdme/man/fit_gmus.Rd | 122 +- hdme-0.2.1/hdme/man/fit_mus.Rd | 108 - hdme-0.2.1/hdme/man/gmu_lasso_binomial.Rd | 62 - hdme-0.2.1/hdme/man/mus_glm.Rd | 50 hdme-0.2.1/hdme/man/musalgorithm.Rd | 40 hdme-0.2.1/hdme/man/plot.corrected_lasso.Rd | 76 - hdme-0.2.1/hdme/man/plot.cv_corrected_lasso.Rd | 32 hdme-0.2.1/hdme/man/plot.gds.Rd | 70 - hdme-0.2.1/hdme/man/plot.gmu_lasso.Rd | 70 - hdme-0.2.1/hdme/man/plot.gmus.Rd | 94 - hdme-0.2.1/hdme/src/Makevars | 5 hdme-0.2.1/hdme/src/Makevars.win | 6 hdme-0.2.1/hdme/tests/testthat.R | 8 hdme-0.2.1/hdme/tests/testthat/test_corrected_lasso.R | 68 - hdme-0.2.1/hdme/vignettes/hdme-package.Rmd | 1054 +++++++++--------- 53 files changed, 3883 insertions(+), 3809 deletions(-)
Title: Create FDA-Style Data and Program Definitions
Description: Creates a directory of archived files with a descriptive 'PDF'
document at the root level (i.e. 'define.pdf') containing tables
of definitions of data items and relative-path hyperlinks to
the documented files. Converts file extensions to 'txt' per FDA
expectations and converts 'CSV' files to 'SAS' Transport format.
Relies on data item descriptors stored as per R package 'spec'.
See 'package?define'. See also '?define'.
Requires a compatible installation of 'pdflatex',
e.g. <https://miktex.org/>.
Author: Tim Bergsma [aut, cre],
Scott Pivirotto [ctb]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between define versions 0.2.7 dated 2018-03-13 and 0.2.8 dated 2018-10-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/methods.R | 5 ++++- R/submission.R | 6 ++++-- man/as.tabular.define.Rd | 4 +++- 5 files changed, 18 insertions(+), 11 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (ICRAF),
Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting),
World Agroforesrtry Centre (ICRAF) [cph]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.103.7 dated 2018-05-15 and 1.103.8 dated 2018-10-15
DESCRIPTION | 10 MD5 | 34 - R/rdistq_fit.R | 2 build/vignette.rds |binary inst/doc/wildfire_example.html | 911 +++++++++++++----------------------- man/as.data.frame.mcSimulation.Rd | 7 man/chance_event.Rd | 4 man/decisionSupport.Rd | 7 man/eviSimulation.Rd | 7 man/hist.eviSimulation.Rd | 8 man/hist.welfareDecisionAnalysis.Rd | 4 man/make_CPT.Rd | 5 man/paramtnormci_fit.Rd | 4 man/plsr.mcSimulation.Rd | 5 man/random.Rd | 14 man/rtnorm90ci.Rd | 5 man/sample_simple_CPT.Rd | 4 man/summary.mcSimulation.Rd | 6 18 files changed, 412 insertions(+), 625 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Model Tropical Cyclone Wind Speeds
Description: Allows users to input tracking data for a hurricane
or other tropical storm, along with a data frame of grid points at which
to model wind speeds. Functions in this package will then calculate wind
speeds at each point based on wind model equations. This modeling framework
is currently set up to model winds for North American locations with
Atlantic basin storms. This work was supported
in part by grants from the National Institute of Environmental Health
Sciences (R00ES022631), the National Science Foundation (1331399), and the
Department of Energy (DE-FG02-08ER64644).
Author: Brooke Anderson [aut, cre],
Andrea Schumacher [aut],
Seth Guikema [aut],
Steven Quiring [aut],
Joshua Ferreri [aut],
Andrea Staid [ctb],
Michael Guo [ctb],
Lei Ming [ctb],
Laiyin Zhu [ctb]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>
Diff between stormwindmodel versions 0.1.0 dated 2017-01-09 and 0.1.1 dated 2018-10-15
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Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.0.7 dated 2018-09-27 and 1.0.8 dated 2018-10-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 ++++- R/ardlDlm.default.R | 16 ++++++++-------- man/dLagM-package.Rd | 4 ++-- 5 files changed, 22 insertions(+), 19 deletions(-)