Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.14.0 dated 2015-10-25 and 3.0.0 dated 2016-01-09
aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustGcrma.AffymetrixCelFile.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustGcrma.AffymetrixCelSet.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustOptical.AffymetrixCelFile.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/bgAdjustRma.AffymetrixCelFile.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/nbrOfArrays.AffymetrixCnChpSet.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/nbrOfArrays.CnagCfhSet.Rd |only aroma.affymetrix-2.14.0/aroma.affymetrix/man/nbrOfArrays.DChipDcpSet.Rd |only aroma.affymetrix-3.0.0/aroma.affymetrix/DESCRIPTION | 15 aroma.affymetrix-3.0.0/aroma.affymetrix/MD5 | 283 ++-- aroma.affymetrix-3.0.0/aroma.affymetrix/NAMESPACE | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/NEWS | 28 aroma.affymetrix-3.0.0/aroma.affymetrix/R/999.DEPRECATED.R | 41 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AbstractProbeSequenceNormalization.R | 216 +-- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AdditiveCovariatesNormalization.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 9 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 32 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfCellIndices.R | 12 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.getSubsetOfUnits.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCdfFile.writeCdfByExcludingCells.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.BG.R | 652 ---------- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.R | 70 - aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.allocateFromCdf.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.createFrom.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeAffine.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeQuantile.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.BG.R | 172 -- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.NORM.R | 43 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 168 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 13 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 31 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCnChpSet.extras.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixCsvGenomeInformation.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixFileSet.getIdentifier.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixPgfFile.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AffymetrixTsvFile.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 291 ++-- aroma.affymetrix-3.0.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/AromaUfcFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ChipEffectFile.fromDataFile.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ChipEffectNnn.extractChromosomalDataFrame.R | 30 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnProbeAffinityFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnagCfhFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/CnagCfhSet.R | 33 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipDcpSet.R | 31 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipGenomeInformation.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipQuantileNormalization.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/DChipSnpInformation.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ExonChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ExonRmaPlm.calculateWeights.R | 12 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FirmaFile.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FirmaModel.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FragmentEquivalentClassNormalization.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/FragmentLengthNormalization.R | 245 ++- aroma.affymetrix-3.0.0/aroma.affymetrix/R/GcContentNormalization.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/GcRmaBackgroundCorrection.R | 362 +++++ aroma.affymetrix-3.0.0/aroma.affymetrix/R/GenericReporter.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/GenomeInformation.AFFX.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/LimmaBackgroundCorrection.R | 148 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/MatNormalization.R | 190 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/MatSmoothing.R | 7 aroma.affymetrix-3.0.0/aroma.affymetrix/R/OpticalBackgroundCorrection.R | 159 +- aroma.affymetrix-3.0.0/aroma.affymetrix/R/Package.XTRA.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ParameterCelFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ParameterCelSet.R | 8 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelModel.calculateWeights.R | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ProbeLevelTransform3.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/QualityAssessmentFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/QuantileNormalization.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ReseqCrosstalkCalibration.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ResidualFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/RmaBackgroundCorrection.R | 183 ++ aroma.affymetrix-3.0.0/aroma.affymetrix/R/RmaPlm.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ScaleNormalization.R | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/R/ScaleNormalization3.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SmoothMultiarrayModel.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SmoothMultiarrayModel.fit.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpChipEffectFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpChipEffectSet.exportTotalAndFracB.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpInformation.R | 9 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SnpProbeAffinityFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/SpatialRowColumnNormalization.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/Transform.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UflSnpInformation.R | 31 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UgpGenomeInformation.R | 11 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UnitModel.fitCnProbes.R | 54 aroma.affymetrix-3.0.0/aroma.affymetrix/R/UnitTypeScaleNormalization.R | 4 aroma.affymetrix-3.0.0/aroma.affymetrix/R/WeightsFile.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/R/bpmapCluster2Cdf.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/createExonByTranscriptCdf.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/env2Cdf.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/findByCdf2.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/R/profileCGH.writeRegions.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/R/randomSeed.R |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/annotationData/dataSets/HapMap,testSet/all,fullnames.txt.md5 |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/annotationData/genomes/Human/Human,chromosomes.txt.md5 |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/annotationData/samples/HapMap270.saf.md5 |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R | 75 - aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/futures |only aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R | 119 - aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R | 119 - aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R | 3 aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R | 58 aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R | 6 aroma.affymetrix-3.0.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/CnagCfhSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/DChipDcpSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/FirmaSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/man/Non-documented_objects.Rd | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ParameterCelSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/ResidualSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/RmaBackgroundCorrection.Rd | 5 aroma.affymetrix-3.0.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/WeightsSet.Rd | 2 aroma.affymetrix-3.0.0/aroma.affymetrix/man/calculateParametersGsb.AffymetrixCelSet.Rd | 10 aroma.affymetrix-3.0.0/aroma.affymetrix/man/getHeader.AffymetrixCelFile.Rd | 1 aroma.affymetrix-3.0.0/aroma.affymetrix/man/randomSeed.Rd |only aroma.affymetrix-3.0.0/aroma.affymetrix/tests/AffymetrixCdfFile.R | 9 aroma.affymetrix-3.0.0/aroma.affymetrix/tests/AffymetrixCelFile.R |only aroma.affymetrix-3.0.0/aroma.affymetrix/tests/AffymetrixCelSet.R | 15 140 files changed, 2112 insertions(+), 2197 deletions(-)
More information about aroma.affymetrix at CRAN
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Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: "James P. Howard, II" <jh@jameshoward.us>
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Diff between phonics versions 0.5.4 dated 2015-12-27 and 0.6.2 dated 2016-01-09
DESCRIPTION | 8 +++---- MD5 | 41 ++++++++++++++++++++++++---------------- NAMESPACE | 4 +++ R/RcppExports.R | 4 +-- R/caverphone.R | 2 - R/lein.R | 2 - R/mra.R |only R/nysiis.R | 2 - R/rogerroot.R |only R/statcan.R | 2 - README.md | 4 +++ man/caverphone.Rd | 5 ++-- man/lein.Rd | 5 ++-- man/metaphone.Rd | 5 ++-- man/mra.Rd |only man/nysiis.Rd | 3 +- man/rogerroot.Rd |only man/soundex.Rd | 5 ++-- man/statcan.Rd | 5 ++-- src/metaphone.cpp | 2 - src/soundex.cpp | 2 - tests/testthat/mra-compare.csv |only tests/testthat/mra-encode.csv |only tests/testthat/rogerroot.csv |only tests/testthat/test-mra.R |only tests/testthat/test-rogerroot.R |only 26 files changed, 62 insertions(+), 39 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.6 dated 2016-01-08 and 1.1.7 dated 2016-01-09
DESCRIPTION | 6 +- MD5 | 4 - R/GDM_Table_Funcs.R | 134 ++++++++++++++++++++++++++-------------------------- 3 files changed, 72 insertions(+), 72 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.2 dated 2016-01-08 and 0.1.3 dated 2016-01-09
eyetrackingR-0.1.2/eyetrackingR/tests/testthat/clust_dat_output_lm.txt |only eyetrackingR-0.1.3/eyetrackingR/DESCRIPTION | 6 eyetrackingR-0.1.3/eyetrackingR/MD5 | 26 - eyetrackingR-0.1.3/eyetrackingR/NEWS.md | 3 eyetrackingR-0.1.3/eyetrackingR/inst/doc/divergence_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/growth_curve_analysis_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/onset_contingent_analysis_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/preparing_your_data_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/inst/doc/window_analysis_vignette.html | 4 eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tb_output_between_subj.txt | 193 ++++++--- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tb_output_interaction.txt | 197 ++++++---- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tb_output_within_subj.txt | 175 +++++--- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/tclust_tb_anal.txt |only eyetrackingR-0.1.3/eyetrackingR/tests/testthat/test_analyze_time_bins.R | 67 +-- eyetrackingR-0.1.3/eyetrackingR/tests/testthat/test_cluster_analysis.R | 39 + 15 files changed, 458 insertions(+), 268 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 2.10.0 dated 2015-12-07 and 2.10.2 dated 2016-01-09
secr-2.10.0/secr/vignettes/secr-datainput.html |only secr-2.10.0/secr/vignettes/secr-overview.html |only secr-2.10.2/secr/DESCRIPTION | 12 - secr-2.10.2/secr/MD5 | 72 ++++----- secr-2.10.2/secr/NAMESPACE | 2 secr-2.10.2/secr/NEWS | 26 +++ secr-2.10.2/secr/R/LLsurface.secr.R | 2 secr-2.10.2/secr/R/discretize.R | 51 +++++- secr-2.10.2/secr/R/join.R | 32 +--- secr-2.10.2/secr/R/make.capthist.R | 39 +++-- secr-2.10.2/secr/R/mask.check.R | 20 +- secr-2.10.2/secr/R/methods.R | 43 ++++- secr-2.10.2/secr/R/par.secr.fit.R | 5 secr-2.10.2/secr/R/pdot.R | 4 secr-2.10.2/secr/R/pmixProfileLL.R | 17 +- secr-2.10.2/secr/R/secr.design.MS.R | 8 - secr-2.10.2/secr/R/secr.fit.R | 7 secr-2.10.2/secr/R/secrloglik.R | 4 secr-2.10.2/secr/R/sim.capthist.R | 137 ++++++++++++------ secr-2.10.2/secr/R/sim.popn.R | 1 secr-2.10.2/secr/R/sim.secr.R | 11 + secr-2.10.2/secr/R/utility.R | 64 ++++++++ secr-2.10.2/secr/R/verify.R | 1 secr-2.10.2/secr/build/vignette.rds |binary secr-2.10.2/secr/inst/doc/secr-manual.pdf |binary secr-2.10.2/secr/inst/doc/secr-overview.R | 19 -- secr-2.10.2/secr/man/Parallel.Rd | 17 ++ secr-2.10.2/secr/man/contour.Rd | 2 secr-2.10.2/secr/man/discretize.Rd | 16 +- secr-2.10.2/secr/man/secr-package.Rd | 4 secr-2.10.2/secr/man/smooths.Rd | 4 secr-2.10.2/secr/src/detectfn.c | 155 +++++++++++++++++--- secr-2.10.2/secr/src/polygon.c | 23 +-- secr-2.10.2/secr/src/secr.c | 185 ++++++++++++------------- secr-2.10.2/secr/src/secr.h | 17 +- secr-2.10.2/secr/src/sighting.c | 115 ++++++++++----- secr-2.10.2/secr/src/trapping.c | 15 +- secr-2.10.2/secr/src/utils.c | 46 +++++- 38 files changed, 789 insertions(+), 387 deletions(-)
Title: Empirical Bayes Estimation and Inference in R
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 0.58 dated 2015-09-21 and 0.61 dated 2016-01-09
DESCRIPTION | 6 +++--- MD5 | 25 +++++++++++++------------ R/Bmix.R | 4 ++-- R/GLmix.R | 50 +++++++++++++++++++++++++++++++++----------------- R/KWDual.R | 2 +- R/Weibullmix.R | 5 +++-- R/predict.R | 1 - demo/00Index | 3 ++- demo/GLmix0.R |only inst/ChangeLog | 18 ++++++++++++++++++ man/Bmix.Rd | 2 +- man/GLmix.Rd | 9 ++++++--- man/KWDual.Rd | 2 +- man/medde.Rd | 4 ++-- 14 files changed, 85 insertions(+), 46 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.4 dated 2015-12-15 and 3.1.8 dated 2016-01-09
DESCRIPTION | 8 MD5 | 122 ++++++------- NAMESPACE | 12 + R/Methods-aux.R | 2 R/RCauto.R | 6 R/RFfit.R | 11 - R/RMmodels.R | 358 +++++++++++++++++++-------------------- R/basic.fctns.R | 3 R/convert.R | 23 +- R/fitgauss.R | 118 +++++++------ R/generatemodels.R | 31 ++- R/getNset.R | 18 + R/kriging.R | 76 ++++---- R/rf-plots.R | 20 +- R/rf.R | 5 configure.ac | 5 inst/CITATION | 2 inst/doc/multivariate_jss.pdf |binary man/Bayesian.Rd | 1 man/GaussianFields.Rd | 99 ++++++++-- man/RFboxcox.Rd | 2 man/RFgetModelInfo.Rd | 1 man/RFinterpolate.Rd | 2 man/RFloglikelihood.Rd | 10 - man/RFoptions.Rd | 12 - man/RMintern.Rd | 22 -- man/RMmatrix.Rd | 2 man/RMmodelsMultivariate.Rd | 28 ++- man/RMmodelsTrend.Rd | 3 man/RMmppplus.Rd | 12 - man/papers.jss14.Rd | 1 man/plot-method.Rd | 1 src/Huetchen.cc | 7 src/InternalCov.cc | 10 - src/KeyInfo.cc | 4 src/MLE.cc | 51 +++-- src/Makevars.in | 11 - src/Primitive.cc | 31 +++ src/RF.h | 146 +++++++--------- src/Specific.cc | 2 src/circulant.cc | 58 ++++-- src/direct.cc | 32 +-- src/extremes.cc | 8 src/families.cc | 13 + src/gauss.cc | 69 ++++++- src/gausslikeli.cc | 193 ++++++++------------- src/getNset.cc | 69 ++++--- src/hyperplan.cc | 4 src/initNerror.cc | 49 ++--- src/nugget.cc | 2 src/plusmalS.cc | 3 src/rf_interfaces.cc | 380 ++++++++++++++++++++++-------------------- src/sequential.cc | 4 src/shape_processes.h | 1 src/spectral.cc | 2 src/startGetNset.cc | 3 src/tbm.cc | 2 src/trend.cc | 13 - src/userinterfaces.cc | 2 src/variogramAndCo.cc | 73 +++++--- src/variogramAndCo.h | 12 - src/win_linux_aux.cc | 4 62 files changed, 1291 insertions(+), 983 deletions(-)
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.3 dated 2015-09-11 and 2.4 dated 2016-01-09
DESCRIPTION | 11 +++--- MD5 | 24 +++++++++----- NAMESPACE | 3 + R/OUshifts.R | 73 ++++++++++++++++++++++++++++++------------- R/testingTreeWithQuartetCF.r |only README.md | 13 +++++++ data/guidetree.rda |only data/quartetCF.rda |only man/OUshifts.Rd | 9 ++++- man/guidetree.Rd |only man/phyloglm.Rd | 2 - man/phylolm-package.Rd | 11 +++--- man/phylolm.Rd | 4 +- man/quartetCF.Rd |only man/stepwise.test.tree.Rd |only man/test.one.species.tree.Rd |only man/test.tree.preparation.Rd |only 17 files changed, 105 insertions(+), 45 deletions(-)
Title: LaTeX Wrappers for R Users
Description: Provides the functionality to write LaTeX code from within R
without having to learn LaTeX. Functionality also exists to create HTML
and Markdown code. While the functionality still exists to write
complete documents with lazyWeave, it is generally easier to do so with
with markdown and knitr. lazyWeave's main strength now is the ability
to design custom and complex tables for reporting results.
Author: Benjamin Nutter
Maintainer: Benjamin Nutter <nutter@battelle.org>
Diff between lazyWeave versions 3.0.0 dated 2015-07-27 and 3.0.1 dated 2016-01-09
DESCRIPTION | 8 MD5 | 162 +++--- NAMESPACE | 90 +-- NEWS | 119 ++-- R/catconttable.R | 418 +++++++-------- R/cattable.R | 462 ++++++++--------- R/conttable.R | 390 +++++++------- R/is.significant.R | 74 +- R/lazy.build.R | 286 +++++----- R/lazy.citation.R | 116 ++-- R/lazy.counter.R | 276 +++++----- R/lazy.figure.R | 324 ++++++------ R/lazy.file.end.R | 44 - R/lazy.file.start.R | 262 ++++----- R/lazy.footnote.R | 154 ++--- R/lazy.insert.code.R | 80 +-- R/lazy.label.R | 54 +- R/lazy.landscape.R | 70 +- R/lazy.link.R | 118 ++-- R/lazy.list.R | 344 ++++++------- R/lazy.matrix.R | 282 +++++----- R/lazy.page.break.R | 68 +- R/lazy.page.number.R | 70 +- R/lazy.ref.R | 108 ++-- R/lazy.section.R | 352 ++++++------- R/lazy.table.R | 924 +++++++++++++++++------------------ R/lazy.text.R | 298 +++++------ R/lazy.text.format.R | 126 ++-- R/lazy.toc.R | 152 ++--- R/lazy.verbatim.end.R | 28 - R/lazy.verbatim.start.R | 78 +- R/lazy.write.R | 148 ++--- R/lazyWeave.R | 80 +-- R/mantel.test.R | 288 +++++----- R/map.size.R | 114 ++-- R/print.ctable.R | 242 ++++----- R/pvalString.R | 166 +++--- R/setHtmlOptions.R | 114 ++-- R/split_ctable.R | 56 +- R/univ.R | 350 ++++++------- R/write.ctable.r | 678 ++++++++++++------------- R/write.univ.R | 218 ++++---- R/zzz.R | 36 - README.md | 54 +- man/ComparisonTable.Rd | 396 +++++++-------- man/Delivery.rd | 68 +- man/Scout.rd | 48 - man/WritePrintCtable.Rd | 240 ++++----- man/is_significant.Rd | 76 +- man/lazy.build.Rd | 92 +-- man/lazy.citation.Rd | 86 +-- man/lazy.counter.Rd | 154 ++--- man/lazy.figure.Rd | 150 ++--- man/lazy.file.end.Rd | 36 - man/lazy.file.start.Rd | 156 ++--- man/lazy.footnote.Rd | 102 +-- man/lazy.insert.code.Rd | 72 +- man/lazy.landscape.Rd | 62 +- man/lazy.link.Rd | 68 +- man/lazy.list.Rd | 148 ++--- man/lazy.matrix.Rd | 174 +++--- man/lazy.page.break.Rd | 64 +- man/lazy.page.number.Rd | 58 +- man/lazy.ref.Rd | 82 +-- man/lazy.section.Rd | 160 +++--- man/lazy.table.Rd | 366 ++++++------- man/lazy.text.Rd | 136 ++--- man/lazy.text.format.Rd | 94 +-- man/lazy.toc.Rd | 104 +-- man/lazy.verbatim.start.Rd | 72 +- man/lazy.write.Rd | 72 +- man/lazyWeave.Rd | 88 +-- man/mantel.test.Rd | 126 ++-- man/map.size.Rd | 82 +-- man/pvalString.Rd | 106 ++-- man/setHtmlOptions.Rd | 122 ++-- man/univ.Rd | 184 +++--- man/write.univ.Rd | 224 ++++---- tests/testthat.R | 6 tests/testthat/test-is.significant.R | 28 - tests/testthat/test-lazy.citation.R | 48 - tests/testthat/test-lazy.counter.R | 4 82 files changed, 6620 insertions(+), 6615 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.7 dated 2015-10-28 and 1.8 dated 2016-01-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/C_CIT_V12.R | 4 +++- man/cit-package.Rd | 4 ++-- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Gaussian Approximation of Bayesian Binary Regression Models
Description: The main functions compute the expectation propagation approximation of a Bayesian probit/logit models with Gaussian prior. More information can be found in Chopin and Ridgway (2015). More models and priors should follow.
Author: James Ridgway
Maintainer: James Ridgway <james.ridgway@ensae.fr>
Diff between EPGLM versions 1.1 dated 2015-09-18 and 1.1.1 dated 2016-01-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/function.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)