Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model equation 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.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 1.9 dated 2016-07-01 and 2.0 dated 2016-07-28
sommer-1.9/sommer/R/AI2.R |only sommer-1.9/sommer/R/AI3.R |only sommer-1.9/sommer/R/EMMAM.R |only sommer-1.9/sommer/man/AI2.Rd |only sommer-1.9/sommer/man/AI3.Rd |only sommer-1.9/sommer/man/EMMAM.Rd |only sommer-2.0/sommer/CHANGELOG | 19 ++ sommer-2.0/sommer/DESCRIPTION | 13 - sommer-2.0/sommer/MD5 | 99 ++++++------ sommer-2.0/sommer/NAMESPACE | 4 sommer-2.0/sommer/R/AI.R | 79 +++++---- sommer-2.0/sommer/R/EMMA.R | 50 +++++- sommer-2.0/sommer/R/MAI.R |only sommer-2.0/sommer/R/MAI2.R |only sommer-2.0/sommer/R/MAIhelp.R |only sommer-2.0/sommer/R/MEMMA.R |only sommer-2.0/sommer/R/MMERM.R | 246 ++++++++++++++++++++++++++++++- sommer-2.0/sommer/R/MNR.R |only sommer-2.0/sommer/R/NR.R | 22 +- sommer-2.0/sommer/R/NR22.R | 75 ++++++--- sommer-2.0/sommer/R/TP.prep.R | 1 sommer-2.0/sommer/R/ai2help.R |only sommer-2.0/sommer/R/eigenGWAS.R | 1 sommer-2.0/sommer/R/hits.R | 33 ++-- sommer-2.0/sommer/R/map.plot.R | 3 sommer-2.0/sommer/R/mmer.R | 169 ++++++++++++++------- sommer-2.0/sommer/R/mmer2.R | 176 ++++++++++++---------- sommer-2.0/sommer/R/mmerSNOW.R | 253 ++++++++++++++------------------ sommer-2.0/sommer/R/score.calc.R | 1 sommer-2.0/sommer/R/score.calcMV.R |only sommer-2.0/sommer/inst/CITATION | 4 sommer-2.0/sommer/inst/doc/sommer.R | 30 +++ sommer-2.0/sommer/inst/doc/sommer.Rmd | 84 ++++++++-- sommer-2.0/sommer/inst/doc/sommer.pdf |binary sommer-2.0/sommer/man/CPdata.Rd | 27 ++- sommer-2.0/sommer/man/HDdata.Rd | 2 sommer-2.0/sommer/man/MAI.Rd |only sommer-2.0/sommer/man/MAI2.Rd |only sommer-2.0/sommer/man/MEMMA.Rd |only sommer-2.0/sommer/man/MMERM.Rd | 47 +++++ sommer-2.0/sommer/man/MNR.Rd |only sommer-2.0/sommer/man/NR.Rd | 4 sommer-2.0/sommer/man/NR22.Rd | 4 sommer-2.0/sommer/man/PolyData.Rd | 8 - sommer-2.0/sommer/man/TP.prep.Rd | 7 sommer-2.0/sommer/man/Technow_data.Rd | 18 -- sommer-2.0/sommer/man/ai2help.Rd |only sommer-2.0/sommer/man/atcg1234.Rd | 2 sommer-2.0/sommer/man/cornHybrid.Rd | 5 sommer-2.0/sommer/man/eigenGWAS.Rd | 4 sommer-2.0/sommer/man/hits.Rd | 34 ++-- sommer-2.0/sommer/man/map.plot.Rd | 14 - sommer-2.0/sommer/man/mmer.Rd | 89 +++++++++-- sommer-2.0/sommer/man/mmer2.Rd | 17 +- sommer-2.0/sommer/man/mmerSNOW.Rd | 6 sommer-2.0/sommer/man/phase.F1.Rd | 7 sommer-2.0/sommer/man/score.calcMV.Rd |only sommer-2.0/sommer/man/sommer-package.Rd | 23 +- sommer-2.0/sommer/vignettes/sommer.Rmd | 9 - sommer-2.0/sommer/vignettes/sommer.html | 126 ++++++--------- 60 files changed, 1196 insertions(+), 619 deletions(-)
Title: Model-Based Clustering for Multivariate Partial Ranking Data
Description: Implementation of a model-based clustering algorithm for
ranking data. Multivariate rankings as well as partial rankings are taken
into account. This algorithm is based on an extension of the Insertion
Sorting Rank (ISR) model for ranking data, which is a meaningful and
effective model parametrized by a position parameter (the modal ranking,
quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity
of the rank population is modelled by a mixture of ISR, whereas conditional
independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez, Julien Jacques
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between Rankcluster versions 0.93.1 dated 2016-01-12 and 0.94 dated 2016-07-28
DESCRIPTION | 12 ++-- MD5 | 28 +++++------ R/Rankcluster-package.R | 4 - R/rankclust.R | 38 +++++++++------ build/vignette.rds |binary data/APA.rda |binary data/big4.rda |binary data/eurovision.rda |binary data/quiz.rda |binary data/sports.rda |binary data/words.rda |binary inst/doc/Rankcluster.pdf |binary man/Rankcluster-package.Rd | 6 +- man/rankclust.Rd | 2 src/RankCluster.cpp | 110 ++++++++++++++++++++++----------------------- 15 files changed, 103 insertions(+), 97 deletions(-)
Title: Goodness of Fit Tests for Logistic Regression Models
Description: Functions to assess the goodness of fit of binary, multinomial and ordinal logistic models.
Included are the Hosmer-Lemshow tests (binary, multinomial and ordinal) and the Lipsitz and
Pulkstenis-Robinson tests (ordinal).
Author: Matthew Jay [aut, cre]
Maintainer: Matthew Jay <matthew.jay.15@ucl.ac.uk>
Diff between generalhoslem versions 1.0.1 dated 2016-07-10 and 1.2.0 dated 2016-07-28
DESCRIPTION | 20 +++---- MD5 | 17 ++++-- NAMESPACE | 4 + R/lipsitz.test.R |only R/logitgof.R | 112 ++++++++++++++++++++++++------------------- R/pulkrob.chisq.R |only R/pulkrob.deviance.R |only build/partial.rdb |binary man/generalhoslem-package.Rd | 6 +- man/lipsitz.test.Rd |only man/logitgof.Rd | 94 +++++++++++++++++++----------------- man/pulkrob.chisq.Rd |only 12 files changed, 144 insertions(+), 109 deletions(-)
Title: Interface to Popular R Functions for Data Science Pipelines
Description:
Interface to popular R functions with formulas, such as 'lm', so they
can be included painlessly in data science pipelines implemented by 'magrittr'
with the operator %>%.
Author: Roberto Bertolusso
Maintainer: Roberto Bertolusso <rbertolusso@rice.edu>
Diff between intubate versions 0.99.1 dated 2016-07-26 and 0.99.2 dated 2016-07-28
intubate-0.99.1/intubate/R/MASS.R |only intubate-0.99.1/intubate/R/graphics.R |only intubate-0.99.1/intubate/R/stats.R |only intubate-0.99.2/intubate/ChangeLog | 12 + intubate-0.99.2/intubate/DESCRIPTION | 9 - intubate-0.99.2/intubate/MD5 | 66 +++++++++- intubate-0.99.2/intubate/NAMESPACE | 10 + intubate-0.99.2/intubate/R/function_formula_data.R |only intubate-0.99.2/intubate/R/function_model_data.R |only intubate-0.99.2/intubate/R/function_object_data.R |only intubate-0.99.2/intubate/R/function_x_data.R |only intubate-0.99.2/intubate/R/non_standard_cases.R |only intubate-0.99.2/intubate/man/intubate-package.Rd | 79 +++++++++++-- intubate-0.99.2/intubate/man/ntbt_aggregate.Rd | 8 - intubate-0.99.2/intubate/man/ntbt_alias.Rd |only intubate-0.99.2/intubate/man/ntbt_barchart.Rd |only intubate-0.99.2/intubate/man/ntbt_bwplot.Rd |only intubate-0.99.2/intubate/man/ntbt_cch.Rd |only intubate-0.99.2/intubate/man/ntbt_cloud.Rd |only intubate-0.99.2/intubate/man/ntbt_contourplot.Rd |only intubate-0.99.2/intubate/man/ntbt_coxph.Rd |only intubate-0.99.2/intubate/man/ntbt_cppls.Rd |only intubate-0.99.2/intubate/man/ntbt_densityplot.Rd |only intubate-0.99.2/intubate/man/ntbt_dotplot.Rd |only intubate-0.99.2/intubate/man/ntbt_finegray.Rd |only intubate-0.99.2/intubate/man/ntbt_function_formula_data.Rd |only intubate-0.99.2/intubate/man/ntbt_gam.Rd |only intubate-0.99.2/intubate/man/ntbt_getInitial.Rd |only intubate-0.99.2/intubate/man/ntbt_glm.Rd | 26 +--- intubate-0.99.2/intubate/man/ntbt_gls.Rd |only intubate-0.99.2/intubate/man/ntbt_histogram.Rd |only intubate-0.99.2/intubate/man/ntbt_levelplot.Rd |only intubate-0.99.2/intubate/man/ntbt_lmList.Rd |only intubate-0.99.2/intubate/man/ntbt_lme.Rd |only intubate-0.99.2/intubate/man/ntbt_logtrans.Rd |only intubate-0.99.2/intubate/man/ntbt_model.matrix.Rd |only intubate-0.99.2/intubate/man/ntbt_multinom.Rd |only intubate-0.99.2/intubate/man/ntbt_mvr.Rd |only intubate-0.99.2/intubate/man/ntbt_nlme.Rd |only intubate-0.99.2/intubate/man/ntbt_nlsList.Rd |only intubate-0.99.2/intubate/man/ntbt_nnet.Rd |only intubate-0.99.2/intubate/man/ntbt_oneway.Rd |only intubate-0.99.2/intubate/man/ntbt_parallelplot.Rd |only intubate-0.99.2/intubate/man/ntbt_pcr.Rd |only intubate-0.99.2/intubate/man/ntbt_plsr.Rd |only intubate-0.99.2/intubate/man/ntbt_pyears.Rd |only intubate-0.99.2/intubate/man/ntbt_qq.Rd |only intubate-0.99.2/intubate/man/ntbt_qqmath.Rd |only intubate-0.99.2/intubate/man/ntbt_regsubsets.Rd |only intubate-0.99.2/intubate/man/ntbt_rpart.Rd |only intubate-0.99.2/intubate/man/ntbt_splom.Rd |only intubate-0.99.2/intubate/man/ntbt_stripchart.Rd | 6 intubate-0.99.2/intubate/man/ntbt_stripplot.Rd |only intubate-0.99.2/intubate/man/ntbt_survConcordance.Rd |only intubate-0.99.2/intubate/man/ntbt_survSplit.Rd |only intubate-0.99.2/intubate/man/ntbt_survexp.Rd |only intubate-0.99.2/intubate/man/ntbt_survfit.Rd |only intubate-0.99.2/intubate/man/ntbt_tmd.Rd |only intubate-0.99.2/intubate/man/ntbt_wireframe.Rd |only intubate-0.99.2/intubate/man/ntbt_xyplot.Rd |only 60 files changed, 165 insertions(+), 51 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides immunoglobulin (Ig) sequence lineage reconstruction,
diversity profiling, and amino acid property analysis. Also provides
core functionality for other tools in the Change-O suite.
Author: Jason Vander Heiden [aut, cre],
Namita Gupta [aut],
Susanna Marquez [ctb],
Daniel Gadala-Maria [ctb],
Roy Jiang [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between alakazam versions 0.2.3 dated 2016-02-22 and 0.2.4 dated 2016-07-28
alakazam-0.2.3/alakazam/R/GeneUsage.R |only alakazam-0.2.3/alakazam/inst/extdata |only alakazam-0.2.3/alakazam/inst/staticdocs |only alakazam-0.2.3/alakazam/man/getSeqDistance.Rd |only alakazam-0.2.3/alakazam/man/getSeqMatrix.Rd |only alakazam-0.2.3/alakazam/man/multiggplot.Rd |only alakazam-0.2.3/alakazam/man/testSeqEqual.Rd |only alakazam-0.2.4/alakazam/DESCRIPTION | 32 alakazam-0.2.4/alakazam/MD5 | 161 ++- alakazam-0.2.4/alakazam/NAMESPACE | 39 alakazam-0.2.4/alakazam/NEWS.md | 53 + alakazam-0.2.4/alakazam/R/Alakazam.R | 132 +- alakazam-0.2.4/alakazam/R/AminoAcids.R | 35 alakazam-0.2.4/alakazam/R/Classes.R |only alakazam-0.2.4/alakazam/R/Core.R | 77 - alakazam-0.2.4/alakazam/R/Data.R |only alakazam-0.2.4/alakazam/R/Diversity.R | 294 +----- alakazam-0.2.4/alakazam/R/Gene.R |only alakazam-0.2.4/alakazam/R/Lineage.R | 81 - alakazam-0.2.4/alakazam/R/RcppExports.R |only alakazam-0.2.4/alakazam/R/Sequence.R | 636 +++----------- alakazam-0.2.4/alakazam/R/Topology.R |only alakazam-0.2.4/alakazam/README.md | 52 - alakazam-0.2.4/alakazam/build/vignette.rds |binary alakazam-0.2.4/alakazam/data/ExampleDb.rda |only alakazam-0.2.4/alakazam/data/ExampleTrees.rda |binary alakazam-0.2.4/alakazam/inst/CITATION | 4 alakazam-0.2.4/alakazam/inst/doc/AminoAcids-Vignette.R | 17 alakazam-0.2.4/alakazam/inst/doc/AminoAcids-Vignette.Rmd | 55 - alakazam-0.2.4/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-0.2.4/alakazam/inst/doc/Diversity-Vignette.R | 44 alakazam-0.2.4/alakazam/inst/doc/Diversity-Vignette.Rmd | 87 + alakazam-0.2.4/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-0.2.4/alakazam/inst/doc/Lineage-Vignette.R | 66 - alakazam-0.2.4/alakazam/inst/doc/Lineage-Vignette.Rmd | 99 +- alakazam-0.2.4/alakazam/inst/doc/Lineage-Vignette.pdf |binary alakazam-0.2.4/alakazam/inst/doc/Topology-Vignette.R |only alakazam-0.2.4/alakazam/inst/doc/Topology-Vignette.Rmd |only alakazam-0.2.4/alakazam/inst/doc/Topology-Vignette.pdf |only alakazam-0.2.4/alakazam/inst/markr |only alakazam-0.2.4/alakazam/man/ABBREV_AA.Rd | 2 alakazam-0.2.4/alakazam/man/ChangeoClone-class.Rd | 4 alakazam-0.2.4/alakazam/man/DEFAULT_COLORS.Rd | 6 alakazam-0.2.4/alakazam/man/DiversityCurve-class.Rd | 10 alakazam-0.2.4/alakazam/man/DiversityTest-class.Rd | 23 alakazam-0.2.4/alakazam/man/EdgeTest-class.Rd |only alakazam-0.2.4/alakazam/man/ExampleDb.Rd |only alakazam-0.2.4/alakazam/man/ExampleTrees.Rd | 16 alakazam-0.2.4/alakazam/man/IMGT_REGIONS.Rd | 2 alakazam-0.2.4/alakazam/man/IUPAC_CODES.Rd | 2 alakazam-0.2.4/alakazam/man/MRCATest-class.Rd |only alakazam-0.2.4/alakazam/man/alakazam.Rd | 72 - alakazam-0.2.4/alakazam/man/aminoAcidProperties.Rd | 16 alakazam-0.2.4/alakazam/man/buildPhylipLineage.Rd | 20 alakazam-0.2.4/alakazam/man/bulk.Rd | 2 alakazam-0.2.4/alakazam/man/calcCoverage.Rd | 13 alakazam-0.2.4/alakazam/man/calcDiversity.Rd | 2 alakazam-0.2.4/alakazam/man/charge.Rd | 10 alakazam-0.2.4/alakazam/man/collapseDuplicates.Rd | 29 alakazam-0.2.4/alakazam/man/countClones.Rd | 8 alakazam-0.2.4/alakazam/man/countGenes.Rd | 45 alakazam-0.2.4/alakazam/man/estimateAbundance.Rd | 14 alakazam-0.2.4/alakazam/man/extractVRegion.Rd | 14 alakazam-0.2.4/alakazam/man/getAAMatrix.Rd | 2 alakazam-0.2.4/alakazam/man/getDNAMatrix.Rd | 2 alakazam-0.2.4/alakazam/man/getMRCA.Rd |only alakazam-0.2.4/alakazam/man/getPathLengths.Rd |only alakazam-0.2.4/alakazam/man/getSegment.Rd | 28 alakazam-0.2.4/alakazam/man/gridPlot.Rd |only alakazam-0.2.4/alakazam/man/isValidAASeq.Rd | 4 alakazam-0.2.4/alakazam/man/makeChangeoClone.Rd | 16 alakazam-0.2.4/alakazam/man/makeTempDir.Rd | 7 alakazam-0.2.4/alakazam/man/maskSeqEnds.Rd | 3 alakazam-0.2.4/alakazam/man/maskSeqGaps.Rd | 3 alakazam-0.2.4/alakazam/man/pairwiseDist.Rd |only alakazam-0.2.4/alakazam/man/pairwiseEqual.Rd |only alakazam-0.2.4/alakazam/man/permuteLabels.Rd |only alakazam-0.2.4/alakazam/man/plotAbundance.Rd | 12 alakazam-0.2.4/alakazam/man/plotDiversityCurve.Rd | 16 alakazam-0.2.4/alakazam/man/plotEdgeTest.Rd |only alakazam-0.2.4/alakazam/man/plotMRCATest.Rd |only alakazam-0.2.4/alakazam/man/plotSubtrees.Rd |only alakazam-0.2.4/alakazam/man/rarefyDiversity.Rd | 25 alakazam-0.2.4/alakazam/man/readChangeoDb.Rd | 21 alakazam-0.2.4/alakazam/man/seqDist.Rd |only alakazam-0.2.4/alakazam/man/seqEqual.Rd |only alakazam-0.2.4/alakazam/man/sortGenes.Rd |only alakazam-0.2.4/alakazam/man/summarizeSubtrees.Rd |only alakazam-0.2.4/alakazam/man/tableEdges.Rd |only alakazam-0.2.4/alakazam/man/testDiversity.Rd | 22 alakazam-0.2.4/alakazam/man/testEdges.Rd |only alakazam-0.2.4/alakazam/man/testMRCA.Rd |only alakazam-0.2.4/alakazam/man/translateDNA.Rd | 14 alakazam-0.2.4/alakazam/man/translateStrings.Rd | 4 alakazam-0.2.4/alakazam/man/writeChangeoDb.Rd | 9 alakazam-0.2.4/alakazam/src |only alakazam-0.2.4/alakazam/vignettes/AminoAcids-Vignette.Rmd | 49 - alakazam-0.2.4/alakazam/vignettes/Diversity-Vignette.Rmd | 81 - alakazam-0.2.4/alakazam/vignettes/Lineage-Vignette.Rmd | 67 - alakazam-0.2.4/alakazam/vignettes/Topology-Vignette.Rmd |only 100 files changed, 1144 insertions(+), 1515 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: The reproducer R package includes data analysis functions and data
sets (e.g., related to software defect prediction) to streamline reproducible
research in software engineering.
Author: Lech Madeyski [cre, aut, ctb],
Marian Jureczko [ctb] (Data contributor),
Barbara Kitchenham [ctb] (Data and code contributor),
David Budgen [ctb] (Data contributor),
Pearl Brereton [ctb] (Data contributor),
Jacky Keung [ctb] (Data contributor),
Stuart Charters [ctb] (Data contributor),
Shirley Gibbs [ctb] (Data contributor),
Amnart Pohthong [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.1.5 dated 2016-05-14 and 0.1.6 dated 2016-07-28
reproducer-0.1.5/reproducer/man/cloudOfWords.Rd |only reproducer-0.1.6/reproducer/DESCRIPTION | 16 reproducer-0.1.6/reproducer/MD5 | 25 reproducer-0.1.6/reproducer/NAMESPACE | 9 reproducer-0.1.6/reproducer/NEWS.md | 20 reproducer-0.1.6/reproducer/R/MadeyskiKitchenhamMetaAnalysis.R | 649 ++++++++++ reproducer-0.1.6/reproducer/R/data.R | 24 reproducer-0.1.6/reproducer/R/reproducer.R | 74 - reproducer-0.1.6/reproducer/data/KitchenhamMadeyski.SimulatedCrossoverDataSets.rda |only reproducer-0.1.6/reproducer/inst/CITATION | 3 reproducer-0.1.6/reproducer/man/KitchenhamMadeyski.SimulatedCrossoverDataSets.Rd |only reproducer-0.1.6/reproducer/man/getEffectSizesABBA.Rd |only reproducer-0.1.6/reproducer/man/getEffectSizesABBAIgnoringPeriodEffect.Rd |only reproducer-0.1.6/reproducer/man/getSimulationData.Rd |only reproducer-0.1.6/reproducer/man/percentageInaccuracyOfLargeSampleVarianceApproximation.Rd |only reproducer-0.1.6/reproducer/man/plotOutcomesForIndividualsInEachSequenceGroup.Rd |only reproducer-0.1.6/reproducer/man/proportionOfSignificantTValuesUsingCorrectAnalysis.Rd |only reproducer-0.1.6/reproducer/man/proportionOfSignificantTValuesUsingIncorrectAnalysis.Rd |only reproducer-0.1.6/reproducer/man/reproduceSimulationResultsBasedOn500Reps1000Obs.Rd |only 19 files changed, 729 insertions(+), 91 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [aut],
Kohei Watanabe [ctb],
Benjamin Lauderdale [ctb],
Adam Obeng [ctb],
Pablo Barberá [ctb],
Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.9.7-17 dated 2016-06-21 and 0.9.8 dated 2016-07-28
DESCRIPTION | 18 - MD5 | 99 ++++--- NAMESPACE | 4 NEWS.md | 29 ++ R/collocations.R | 157 ++++++------ R/converters.R | 8 R/corpus.R | 6 R/describe-texts.R | 2 R/dfm-classes.R | 2 R/dfm-main.R | 42 +-- R/dfm-methods.R | 17 - R/dfm-weighting.R | 2 R/dictionaries.R | 155 +++++++++--- R/encoding.R | 20 - R/joinTokens.R | 16 - R/kwic.R | 12 R/ngrams.R | 4 R/phrases.R | 7 R/selectFeatures.R | 16 - R/settings.R | 4 R/stopwords.R | 6 R/textfile.R | 81 ++---- R/textmodel-NB.R | 484 +++++++++++++++++++------------------- R/textmodel-generics.R | 8 R/textmodel-wordfish.R | 8 R/textmodel-wordscores.R | 2 R/tokenize.R | 52 ++-- R/tokenize_outtakes.R | 2 R/util.R |only R/wordstem.R | 2 README.md | 40 +-- build/vignette.rds |binary inst/doc/LitVignette.html | 43 ++- inst/doc/quickstart.html | 142 ++++++----- man/applyDictionary.Rd | 2 man/collocations.Rd | 36 +- man/dictionary.Rd | 19 + man/textmodel_NB.Rd | 6 tests/data/dictionaries |only tests/testthat.R | 2 tests/testthat/data/glob |only tests/testthat/data/tar |only tests/testthat/data/yoshi.ykd |only tests/testthat/testCollocations.R |only tests/testthat/testDictionaries.R | 80 ++++++ tests/testthat/testKwic.R | 48 +++ tests/testthat/testTextfile.R |only tests/testthat/testTextfile2.R |only tests/testthat/testUtil.R |only 49 files changed, 1017 insertions(+), 666 deletions(-)
Title: Half-Normal Plots with Simulation Envelopes
Description: Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
Author: Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral <rafael_moral@yahoo.com.br>
Diff between hnp versions 1.2 dated 2016-03-08 and 1.2-1 dated 2016-07-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/hnp.Rd | 18 +++++++++--------- man/newhnp.Rd | 10 +++++----- man/orange.Rd | 2 +- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Diff between extraDistr versions 1.7.2 dated 2016-06-24 and 1.8.0 dated 2016-07-28
DESCRIPTION | 8 - MD5 | 109 +++++++++---------- NAMESPACE | 3 NEWS.md | 14 ++ R/RcppExports.R | 12 ++ R/discrete-laplace-distribution.R |only R/gev-distribution.R | 2 R/laplace-distribution.R | 5 man/DiscreteLaplace.Rd |only man/GEV.Rd | 2 man/Laplace.Rd | 5 src/RcppExports.cpp | 42 +++++++ src/bernoulli-distribution.cpp | 7 - src/beta-binomial-distribution.cpp | 11 + src/beta-negative-binomial-distribution.cpp | 17 +- src/bhattacharjee-distribution.cpp | 2 src/birnbaum-saunders-distribution.cpp | 2 src/bivariate-normal-distribution.cpp | 4 src/bivariate-poisson-distribution.cpp | 5 src/categorical-distribution.cpp | 2 src/dirichlet-multinomial-distribution.cpp | 70 +++++++----- src/discrete-laplace-distribution.cpp |only src/discrete-uniform-distribution.cpp | 2 src/discrete-weibull-distribution.cpp | 2 src/frechet-distribution.cpp | 3 src/gamma-poisson-distribution.cpp | 12 +- src/gev-distribution.cpp | 3 src/gompertz-distribution.cpp | 3 src/gpd-distribution.cpp | 3 src/gumbel-distribution.cpp | 3 src/half-normal-distribution.cpp | 2 src/huber-distribution.cpp | 2 src/kumaraswamy-distribution.cpp | 3 src/laplace-distribution.cpp | 9 + src/logarithmic-series-distribution.cpp | 2 src/lomax-distribution.cpp | 3 src/mixture-of-normal-distributions.cpp | 2 src/mixture-of-poisson-distributions.cpp | 2 src/multinomial-distribution.cpp | 77 +++++++------ src/multivariate-hypergeometric-distribution.cpp | 8 - src/pareto-distribution.cpp | 3 src/power-distribution.cpp | 3 src/rayleigh-distribution.cpp | 3 src/shared.cpp | 25 +++- src/shared.h | 6 - src/slash-distribution.cpp | 4 src/triangular-distribution.cpp | 5 src/truncated-normal-distribution.cpp | 10 - src/wald-distribution.cpp | 10 + src/zero-inflated-binomial-distribution.cpp | 2 src/zero-inflated-negative-binomial-distribution.cpp | 2 src/zero-inflated-poisson-distribution.cpp | 2 tests/testthat/test-discrete.R | 1 tests/testthat/test-inappropriate-parameters.R | 42 +++++-- tests/testthat/test-infinity.R | 4 tests/testthat/test-multivariate-distributions.R | 35 ++++++ tests/testthat/test-non-negative.R | 6 - 57 files changed, 411 insertions(+), 215 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.10.0-2 dated 2016-06-24 and 2.11.0 dated 2016-07-28
StanHeaders-2.10.0-2/StanHeaders/inst/include/stan/math/prim/arr/fun/dist.hpp |only StanHeaders-2.10.0-2/StanHeaders/inst/include/stan/math/prim/scal/fun.hpp |only StanHeaders-2.10.0-2/StanHeaders/inst/include/stan/math/rev/mat/functor.hpp |only StanHeaders-2.11.0/StanHeaders/DESCRIPTION | 8 StanHeaders-2.11.0/StanHeaders/MD5 | 180 ++++++---- StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/ast.hpp | 12 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/ast_def.cpp | 23 + StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/generator.hpp | 39 +- StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_def.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_def.hpp | 12 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions.hpp | 5 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions_def.cpp | 26 + StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar.hpp | 8 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar_def.hpp | 9 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar.hpp | 12 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp | 29 + StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp | 3 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/base_nuts.hpp | 5 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/diag_e_xhmc.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/model/model_header.hpp | 1 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/model/util.hpp | 16 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/services/arguments/categorical_argument.hpp | 5 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/services/init/initialize_state.hpp | 7 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/services/io/write_error_msg.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/src/stan/version.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/fwd/mat.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/fwd/mat/fun/squared_distance.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/fwd/mat/vectorize/apply_scalar_unary.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/arr.hpp | 1 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/arr/fun/log_sum_exp.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat.hpp | 3 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/Phi.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/abs.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/acos.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/asin.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/asinh.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/atan.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cbrt.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/ceil.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cos.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cosh.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_exp_quad.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_u_to_z.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/digamma.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/distance.hpp | 7 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/erf.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/erfc.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/exp.hpp | 47 +- StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/expm1.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/fabs.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/floor.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_Phi.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_cloglog.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_logit.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_sqrt.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/inv_square.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/lgamma.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log.hpp | 35 + StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log10.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1m_exp.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/log1p_exp.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/round.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sin.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sinh.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/sqrt.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/square.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/squared_distance.hpp | 47 ++ StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tan.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tanh.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/fun/tgamma.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/mat/vectorize/apply_scalar_unary.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal.hpp | 1 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi.hpp | 7 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/abs.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/digamma.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/divide.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_p.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_q.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_inc_beta.hpp | 3 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddz.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv.hpp | 7 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_cloglog.hpp | 6 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_logit.hpp | 6 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_sqrt.hpp | 8 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_square.hpp | 7 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/lgamma.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m.hpp | 5 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_exp.hpp | 5 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p_exp.hpp | 6 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/log_mix.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/square.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/fun/squared_distance.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_ccdf_log.hpp | 14 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf_log.hpp | 14 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/arr/functor/coupled_ode_system.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/core/precomputed_gradients.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat.hpp | 1 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp | 24 - StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat/fun/grad.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat/fun/sd.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat/fun/stan_print.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat/fun/variance.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/mat/vectorize/apply_scalar_unary.hpp | 4 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/scal.hpp | 1 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/scal/fun/grad_inc_beta.hpp | 2 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/scal/fun/squared_distance.hpp |only StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of_rec.hpp | 1 StanHeaders-2.11.0/StanHeaders/inst/include/stan/math/version.hpp | 2 112 files changed, 438 insertions(+), 290 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications as things
that can be generated and manipulated programmatically. Structural equation
models may be specified with reticular action model matrices or paths, linear
structural relations matrices or paths, or directly in matrix algebra. Fit
functions include full information maximum likelihood, maximum likelihood, and
weighted least squares. Example models include confirmatory factor, multiple
group, mixture distribution, categorical threshold, modern test theory,
differential equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.6.8 dated 2016-07-16 and 2.6.9 dated 2016-07-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/MxVersion.R | 2 +- inst/CITATION | 2 +- src/omxMLFitFunction.cpp | 9 +-------- 5 files changed, 11 insertions(+), 18 deletions(-)
Title: High-Dimensional Screening for Semiparametric Longitudinal
Regression
Description: Implements a screening procedure proposed by Wanghuan Chu, Runze Li
and Matthew Reimherr (2016) <DOI:10.1214/16-AOAS912> for varying coefficient
longitudinal models with ultra-high dimensional predictors . The effect of each
predictor is allowed to vary over time, approximated by a low-dimensional B-spline.
Within-subject correlation is handled using a generalized estimation equation
approach with structure specified by the user. Variance is allowed to change
over time, also approximated by a B-spline.
Author: Runze Li [aut],
Wanghuan Chu [aut],
Liying Huang [aut, cre],
John Dziak [aut]
Maintainer: Liying Huang <lxh37@PSU.EDU>
Diff between VariableScreening versions 0.1.0 dated 2016-07-19 and 0.1.1 dated 2016-07-28
DESCRIPTION | 20 ++++++++++---------- MD5 | 6 +++--- R/screenlong.R | 3 +-- man/screenlong.Rd | 3 +-- 4 files changed, 15 insertions(+), 17 deletions(-)
More information about VariableScreening at CRAN
Permanent link
Title: Dynamic FBA : Dynamic Flux Balance Analysis
Description: Implements dynamic FBA technique proposed by Varma et al 1994.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>
Diff between sybilDynFBA versions 1.0.0 dated 2016-06-02 and 1.0.1 dated 2016-07-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/dynamicFBA.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful
and 'ready-to-publish' survival curves with the 'number at risk' table. Other
functions are also available for visual examinations of 'cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre],
Marcin Kosinski [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between survminer versions 0.2.1 dated 2016-04-23 and 0.2.2 dated 2016-07-28
DESCRIPTION | 20 +++++++++++--------- MD5 | 30 ++++++++++++++++++++---------- NAMESPACE | 3 +++ NEWS.md | 13 +++++++++++++ R/ggcoxdiagnostics.R |only R/ggcoxfunctional.R | 5 ++--- R/ggcoxzph.R | 9 ++++----- R/ggsurvplot.R | 36 +++++++++++++++++++++++++----------- README.md | 15 +++++++++++---- build |only inst |only man/ggcoxdiagnostics.Rd |only man/ggcoxfunctional.Rd | 5 ++--- man/ggcoxzph.Rd | 9 ++++----- man/ggsurvplot.Rd | 19 ++++++++++++------- vignettes |only 16 files changed, 107 insertions(+), 57 deletions(-)
Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima <jcadima@isa.utl.pt>
Diff between subselect versions 0.12-5 dated 2015-04-13 and 0.12-6 dated 2016-07-28
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 3 ++- build/vignette.rds |binary inst/CHANGELOG | 2 ++ 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Computation of Graphlet Orbit Counts in Sparse Graphs
Description: Implements orbit counting using a fast combinatorial approach.
Counts orbits of nodes and edges from edge matrix or data frame, or a
graph object from the graph package.
Author: Tomaz Hocevar [aut],
Janez Demsar [aut, cre]
Maintainer: Janez Demsar <janez.demsar@fri.uni-lj.si>
Diff between orca versions 1.1 dated 2015-03-10 and 1.1-1 dated 2016-07-28
DESCRIPTION | 16 ++++++++++------ MD5 | 6 +++--- inst/CITATION | 42 +++++++++++++++++++++++------------------- man/orca.Rd | 2 +- 4 files changed, 37 insertions(+), 29 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 4.0 dated 2016-05-20 and 4.1 dated 2016-07-28
DESCRIPTION | 9 ++-- MD5 | 22 ++++++---- NAMESPACE | 3 + R/RFI.R | 8 +++ R/Slope.R |only R/Slope3d.R |only R/Slope_Legend.R |only R/compute_energy_per_face.R | 96 ++++++++++++++++++++++---------------------- R/molaR_Batch.R | 65 +++++++++++++++++++++++++---- R/plyZClip.R |only build/molaR.pdf |binary man/Slope.Rd |only man/Slope3d.Rd |only man/Slope_Legend.Rd |only man/molaR_Batch.Rd | 10 +++- man/plyZClip.Rd |only 16 files changed, 144 insertions(+), 69 deletions(-)
Title: Test Bench for Missing Data Imputing Models/Methods Comparison
Description: Provides a Test bench for comparison of missing
data imputation models/methods. It compares imputing methods with reference
to RMSE, MAE or MAPE parameters. It allows to add new proposed methods to test
bench and to compare with other methods. The function 'append_method()' allows
to add multiple numbers of methods to the existing methods available in test bench.
Author: Neeraj Bokde
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Diff between imputeTestbench versions 1.2.0 dated 2016-06-19 and 2.0.2 dated 2016-07-28
DESCRIPTION | 8 MD5 | 24 +- NAMESPACE | 1 R/append_method.R | 2 R/impute_errors.R | 323 ++++++++++++++++++++++++--------- R/plot_errors.R | 62 +++++- inst/doc/imputeTestbench-Vignette.R | 9 inst/doc/imputeTestbench-Vignette.Rmd | 17 + inst/doc/imputeTestbench-Vignette.html | 43 +++- man/append_method.Rd | 2 man/impute_errors.Rd | 13 + man/plot_errors.Rd | 13 + vignettes/imputeTestbench-Vignette.Rmd | 17 + 13 files changed, 400 insertions(+), 134 deletions(-)
More information about imputeTestbench at CRAN
Permanent link
Title: Wrapper for the Gnu Scientific Library
Description:
An R wrapper for some of the functionality of the
Gnu Scientific Library.
Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and
multimin by Andrew Clausen
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 1.9-10.1 dated 2015-12-02 and 2.1-1 dated 2016-07-28
DESCRIPTION | 19 +-- MD5 | 79 ++++++++-------- R/ellint.R | 6 - R/legendre.R | 246 +++++++++++++++++++++++++++++++++++++------------- build/vignette.rds |binary configure | 3 configure.ac | 8 + inst/CITATION | 7 - inst/doc/gslpaper.pdf |binary man/Ellint.Rd | 4 man/Legendre.Rd | 35 ++++++- man/Psi.Rd | 2 man/Transport.Rd | 2 man/gsl-deprecated.Rd |only src/airy.c | 24 ++-- src/bessel.c | 110 +++++++++++----------- src/clausen.c | 2 src/coulomb.c | 28 ++--- src/coupling.c | 6 - src/dawson.c | 2 src/debye.c | 8 - src/dilog.c | 4 src/ellint.c | 27 ++--- src/elljac.c | 2 src/error.c | 12 +- src/expint.c | 26 ++--- src/fermi_dirac.c | 18 +-- src/gamma.c | 46 ++++----- src/gegenbauer.c | 10 +- src/hyperg.c | 20 ++-- src/laguerre.c | 8 - src/lambert.c | 4 src/legendre.c | 123 +++++++++++++++++++++---- src/log.c | 10 +- src/poly.c | 2 src/pow_int.c | 2 src/psi.c | 12 +- src/synchrotron.c | 4 src/transport.c | 8 - src/trig.c | 18 +-- src/zeta.c | 14 +- 41 files changed, 592 insertions(+), 369 deletions(-)
Title: Fit GLD Regression Model and GLD Quantile Regression Model to
Empirical Data
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDreg versions 1.0.3 dated 2015-07-04 and 1.0.4 dated 2016-07-28
DESCRIPTION | 10 +- MD5 | 18 +-- R/GLD.lm.R | 197 +++++++++++++++++++++--------------------- R/summaryGraphics.gld.lm.R | 13 +- man/GLD.lm.Rd | 23 ++++ man/GLD.lm.full.Rd | 4 man/GLD.quantreg.Rd | 4 man/GLDreg-package.Rd | 4 man/fun.plot.q.Rd | 4 man/summaryGraphics.gld.lm.Rd | 11 +- 10 files changed, 155 insertions(+), 133 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, and full details are given in the vignette accompanying this package and the references in the help files. The creation of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 2.3 dated 2016-06-15 and 2.4 dated 2016-07-28
CARBayesST-2.3/CARBayesST/R/print.carbayesST.R |only CARBayesST-2.3/CARBayesST/man/print.carbayesST.Rd |only CARBayesST-2.4/CARBayesST/DESCRIPTION | 8 CARBayesST-2.4/CARBayesST/MD5 | 76 ++- CARBayesST-2.4/CARBayesST/NAMESPACE | 7 CARBayesST-2.4/CARBayesST/R/binomial.CARadaptive.R | 27 - CARBayesST-2.4/CARBayesST/R/binomial.CARanova.R | 16 CARBayesST-2.4/CARBayesST/R/binomial.CARar.R | 16 CARBayesST-2.4/CARBayesST/R/binomial.CARlinear.R | 15 CARBayesST-2.4/CARBayesST/R/binomial.CARlocalised.R | 15 CARBayesST-2.4/CARBayesST/R/binomial.CARsepspatial.R | 15 CARBayesST-2.4/CARBayesST/R/coef.CARBayesST.R |only CARBayesST-2.4/CARBayesST/R/fitted.CARBayesST.R |only CARBayesST-2.4/CARBayesST/R/gaussian.CARadaptive.R | 19 CARBayesST-2.4/CARBayesST/R/gaussian.CARanova.R | 15 CARBayesST-2.4/CARBayesST/R/gaussian.CARar.R | 16 CARBayesST-2.4/CARBayesST/R/gaussian.CARlinear.R | 15 CARBayesST-2.4/CARBayesST/R/logLik.CARBayesST.R |only CARBayesST-2.4/CARBayesST/R/model.matrix.CARBayesST.R |only CARBayesST-2.4/CARBayesST/R/poisson.CARadaptive.R | 17 CARBayesST-2.4/CARBayesST/R/poisson.CARanova.R | 16 CARBayesST-2.4/CARBayesST/R/poisson.CARar.R | 16 CARBayesST-2.4/CARBayesST/R/poisson.CARlinear.R | 18 CARBayesST-2.4/CARBayesST/R/poisson.CARlocalised.R | 16 CARBayesST-2.4/CARBayesST/R/poisson.CARsepspatial.R | 16 CARBayesST-2.4/CARBayesST/R/print.CARBayesST.R |only CARBayesST-2.4/CARBayesST/R/residuals.CARBayesST.R |only CARBayesST-2.4/CARBayesST/build/vignette.rds |binary CARBayesST-2.4/CARBayesST/inst/doc/CARBayesST.R | 153 ++++---- CARBayesST-2.4/CARBayesST/inst/doc/CARBayesST.Rnw | 286 ++++++++------- CARBayesST-2.4/CARBayesST/inst/doc/CARBayesST.pdf |binary CARBayesST-2.4/CARBayesST/man/CARBayesST-package.Rd | 7 CARBayesST-2.4/CARBayesST/man/ST.CARadaptive.Rd | 12 CARBayesST-2.4/CARBayesST/man/ST.CARanova.Rd | 11 CARBayesST-2.4/CARBayesST/man/ST.CARar.Rd | 12 CARBayesST-2.4/CARBayesST/man/ST.CARlinear.Rd | 12 CARBayesST-2.4/CARBayesST/man/ST.CARlocalised.Rd | 11 CARBayesST-2.4/CARBayesST/man/ST.CARsepspatial.Rd | 9 CARBayesST-2.4/CARBayesST/man/coef.CARBayesST.Rd |only CARBayesST-2.4/CARBayesST/man/fitted.CARBayesST.Rd |only CARBayesST-2.4/CARBayesST/man/logLik.CARBayesST.Rd |only CARBayesST-2.4/CARBayesST/man/model.matrix.CARBayesST.Rd |only CARBayesST-2.4/CARBayesST/man/print.CARBayesST.Rd |only CARBayesST-2.4/CARBayesST/man/residuals.CARBayesST.Rd |only CARBayesST-2.4/CARBayesST/vignettes/CARBayesST.Rnw | 286 ++++++++------- CARBayesST-2.4/CARBayesST/vignettes/CARBayesST.bib | 105 ++--- 46 files changed, 732 insertions(+), 531 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Description: Implementation of the vine graphical model for building
high-dimensional probability distributions as a factorization of
bivariate copulas and marginal density functions. This package
provides S4 classes for vines (C-vines and D-vines) and methods
for inference, goodness-of-fit tests, density/distribution
function evaluation, and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut],
Joris Meys [ctb]
Maintainer: Yasser Gonzalez-Fernandez <ygonzalezfernandez@gmail.com>
Diff between vines versions 1.1.4 dated 2015-10-07 and 1.1.5 dated 2016-07-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 5 +++++ R/h.R | 2 +- R/hinverse.R | 2 +- tests/testthat.R | 2 +- 6 files changed, 16 insertions(+), 11 deletions(-)
Title: A Simple Web Framework for R
Description: A set of functions to ease the building of web APIs.
Author: Bart Smeets [aut, cre]
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between jug versions 0.1.2 dated 2016-05-10 and 0.1.3 dated 2016-07-28
jug-0.1.2/jug/man/parse_post_data.Rd |only jug-0.1.2/jug/man/parse_query.Rd |only jug-0.1.3/jug/DESCRIPTION | 19 +- jug-0.1.3/jug/MD5 | 45 ++--- jug-0.1.3/jug/NAMESPACE | 3 jug-0.1.3/jug/R/cors.R |only jug-0.1.3/jug/R/helpers.R | 64 +------ jug-0.1.3/jug/R/middleware_core.R | 10 - jug-0.1.3/jug/R/middleware_error.R | 33 +++ jug-0.1.3/jug/R/request.R | 22 +- jug-0.1.3/jug/R/test_request.R | 12 - jug-0.1.3/jug/inst/doc/jug.R | 10 - jug-0.1.3/jug/inst/doc/jug.Rmd | 134 ++++++++------- jug-0.1.3/jug/inst/doc/jug.html | 67 ++++--- jug-0.1.3/jug/man/cors.Rd |only jug-0.1.3/jug/man/parse_params.Rd |only jug-0.1.3/jug/man/simple_error_handler.Rd | 7 jug-0.1.3/jug/man/simple_error_handler_json.Rd |only jug-0.1.3/jug/man/use.Rd | 4 jug-0.1.3/jug/tests/testthat/test_cors.R |only jug-0.1.3/jug/tests/testthat/test_error_handling.R | 27 ++- jug-0.1.3/jug/tests/testthat/test_func_decoration.R | 24 ++ jug-0.1.3/jug/tests/testthat/test_get.R | 14 + jug-0.1.3/jug/tests/testthat/test_helpers.R | 33 ++- jug-0.1.3/jug/tests/testthat/test_multiple_mw_function.R | 20 ++ jug-0.1.3/jug/tests/testthat/test_post.R | 55 +++++- jug-0.1.3/jug/vignettes/jug.Rmd | 134 ++++++++------- 27 files changed, 467 insertions(+), 270 deletions(-)
Title: Create 'Formattable' Data Structures
Description: Provides functions to create formattable vectors and data frames.
'Formattable' vectors are printed with text formatting, and formattable
data frames are printed with multiple types of formatting in HTML
to improve the readability of data presented in tabular form rendered in
web pages.
Author: Kun Ren [aut, cre],
Kenton Russell [aut]
Maintainer: Kun Ren <ken@renkun.me>
Diff between formattable versions 0.1.5 dated 2015-12-03 and 0.2 dated 2016-07-28
formattable-0.1.5/formattable/inst/htmlwidgets/lib |only formattable-0.2/formattable/DESCRIPTION | 25 formattable-0.2/formattable/LICENSE | 4 formattable-0.2/formattable/MD5 | 147 - formattable-0.2/formattable/NAMESPACE | 195 - formattable-0.2/formattable/NEWS |only formattable-0.2/formattable/R/as.datatable.R |only formattable-0.2/formattable/R/formats.R | 417 +-- formattable-0.2/formattable/R/formattable.R | 1143 +++++----- formattable-0.2/formattable/R/formatter.R | 313 +- formattable-0.2/formattable/R/package.R | 56 formattable-0.2/formattable/R/render.R | 220 - formattable-0.2/formattable/R/style.R | 381 +-- formattable-0.2/formattable/R/transform.R | 130 - formattable-0.2/formattable/R/utils.R | 178 - formattable-0.2/formattable/README.md | 386 +-- formattable-0.2/formattable/build |only formattable-0.2/formattable/inst/doc |only formattable-0.2/formattable/inst/htmlwidgets/formattable_widget.js | 58 formattable-0.2/formattable/inst/htmlwidgets/formattable_widget.yaml | 10 formattable-0.2/formattable/man/accounting.Rd | 74 formattable-0.2/formattable/man/area.Rd |only formattable-0.2/formattable/man/as.datatable.Rd |only formattable-0.2/formattable/man/as.datatable.formattable.Rd |only formattable-0.2/formattable/man/as.htmlwidget.Rd | 42 formattable-0.2/formattable/man/as.htmlwidget.formattable.Rd | 126 - formattable-0.2/formattable/man/color_bar.Rd | 46 formattable-0.2/formattable/man/color_text.Rd | 36 formattable-0.2/formattable/man/color_tile.Rd | 36 formattable-0.2/formattable/man/comma.Rd | 72 formattable-0.2/formattable/man/csscolor.Rd | 56 formattable-0.2/formattable/man/currency.Rd | 88 formattable-0.2/formattable/man/digits.Rd | 50 formattable-0.2/formattable/man/format_table.Rd | 181 - formattable-0.2/formattable/man/formattable-package.Rd | 64 formattable-0.2/formattable/man/formattable.Date.Rd | 70 formattable-0.2/formattable/man/formattable.POSIXct.Rd | 70 formattable-0.2/formattable/man/formattable.POSIXlt.Rd | 70 formattable-0.2/formattable/man/formattable.Rd | 48 formattable-0.2/formattable/man/formattable.data.frame.Rd | 157 - formattable-0.2/formattable/man/formattable.default.Rd | 66 formattable-0.2/formattable/man/formattable.factor.Rd | 66 formattable-0.2/formattable/man/formattable.logical.Rd | 74 formattable-0.2/formattable/man/formattable.numeric.Rd | 78 formattable-0.2/formattable/man/formattableOutput.Rd | 38 formattable-0.2/formattable/man/formatter.Rd | 106 formattable-0.2/formattable/man/gradient.Rd | 84 formattable-0.2/formattable/man/icontext.Rd | 84 formattable-0.2/formattable/man/is.formattable.Rd | 46 formattable-0.2/formattable/man/normalize.Rd | 49 formattable-0.2/formattable/man/normalize_bar.Rd |only formattable-0.2/formattable/man/percent.Rd | 66 formattable-0.2/formattable/man/prefix.Rd | 62 formattable-0.2/formattable/man/proportion.Rd |only formattable-0.2/formattable/man/proportion_bar.Rd |only formattable-0.2/formattable/man/qrank.Rd | 50 formattable-0.2/formattable/man/renderFormattable.Rd | 40 formattable-0.2/formattable/man/scientific.Rd | 48 formattable-0.2/formattable/man/style.Rd | 98 formattable-0.2/formattable/man/suffix.Rd | 60 formattable-0.2/formattable/man/vmap.Rd | 64 formattable-0.2/formattable/tests/testthat.R | 8 formattable-0.2/formattable/tests/testthat/test-formats.R | 250 +- formattable-0.2/formattable/tests/testthat/test-formattable.R | 445 ++- formattable-0.2/formattable/tests/testthat/test-formatter.R | 128 - formattable-0.2/formattable/tests/testthat/test-render.R | 38 formattable-0.2/formattable/tests/testthat/test-style.R | 210 - formattable-0.2/formattable/tests/testthat/test-transform.R | 87 formattable-0.2/formattable/tests/testthat/test-utils.R | 40 formattable-0.2/formattable/vignettes |only 70 files changed, 3890 insertions(+), 3444 deletions(-)