Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.4 dated 2016-10-12 and 1.0.5 dated 2016-11-23
DESCRIPTION | 16 - MD5 | 184 +++++++++-------- NAMESPACE | 7 R/xCircos.r | 21 + R/xColormap.r |only R/xConverter.r | 2 R/xEnrichBarplot.r | 23 +- R/xEnrichCompare.r | 28 +- R/xEnrichConciser.r | 5 R/xEnrichDAGplot.r | 4 R/xEnrichDAGplotAdv.r | 4 R/xEnrichNetplot.r | 4 R/xEnricher.r | 23 +- R/xEnricherGenes.r | 4 R/xEnricherSNPs.r | 4 R/xEnricherYours.r | 14 - R/xGR.r |only R/xGR2GeneScores.r |only R/xGR2nGenes.r |only R/xGRsampling.r | 6 R/xGRscores.r |only R/xGRviaGeneAnno.r | 43 ++-- R/xGRviaGenomicAnno.r | 95 ++++---- R/xGRviaGenomicAnnoAdv.r | 75 +++--- R/xLiftOver.r | 10 R/xRDataLoader.r | 19 + R/xSNP2GeneScores.r | 44 ++-- R/xSNP2nGenes.r | 61 ++++- R/xSNPlocations.r | 8 R/xSNPscores.r | 8 R/xSocialiser.r | 2 R/xSocialiserGenes.r | 8 R/xSocialiserSNPs.r | 10 R/xSubneterGR.r |only R/xSubneterGenes.r | 34 +-- R/xSubneterSNPs.r | 18 - R/xVisNet.r | 2 data/ImmunoBase.RData |binary inst/CITATION | 4 inst/NEWS | 14 + inst/xCircos.html | 23 +- inst/xColormap.html |only inst/xEnrichBarplot.html | 16 - inst/xEnrichCompare.html | 18 + inst/xEnrichConciser.html | 4 inst/xEnrichDAGplot.html | 4 inst/xEnrichDAGplotAdv.html | 4 inst/xEnrichNetplot.html | 4 inst/xEnricher.html | 8 inst/xEnricherGenes.html | 11 - inst/xEnricherSNPs.html | 11 - inst/xEnricherYours.html | 8 inst/xGR.html |only inst/xGR2GeneScores.html |only inst/xGR2nGenes.html |only inst/xGRsampling.html | 7 inst/xGRscores.html |only inst/xGRviaGeneAnno.html | 30 +- inst/xGRviaGenomicAnno.html | 440 +---------------------------------------- inst/xGRviaGenomicAnnoAdv.html | 433 +--------------------------------------- inst/xLiftOver.html | 7 inst/xRDataLoader.html | 21 - inst/xSNP2GeneScores.html | 23 +- inst/xSNP2nGenes.html | 18 - inst/xSNPlocations.html | 10 inst/xSNPscores.html | 10 inst/xSocialiserGenes.html | 10 inst/xSocialiserSNPs.html | 9 inst/xSubneterGR.html |only inst/xSubneterGenes.html | 18 - inst/xSubneterSNPs.html | 28 +- man/xCircos.Rd | 23 +- man/xColormap.Rd |only man/xEnrichBarplot.Rd | 14 - man/xEnrichCompare.Rd | 16 - man/xEnrichConciser.Rd | 6 man/xEnrichDAGplot.Rd | 4 man/xEnrichDAGplotAdv.Rd | 4 man/xEnrichNetplot.Rd | 4 man/xEnricher.Rd | 8 man/xEnricherGenes.Rd | 11 - man/xEnricherSNPs.Rd | 11 - man/xEnricherYours.Rd | 8 man/xGR.Rd |only man/xGR2GeneScores.Rd |only man/xGR2nGenes.Rd |only man/xGRsampling.Rd | 7 man/xGRscores.Rd |only man/xGRviaGeneAnno.Rd | 30 +- man/xGRviaGenomicAnno.Rd | 294 +-------------------------- man/xGRviaGenomicAnnoAdv.Rd | 287 +------------------------- man/xLiftOver.Rd | 7 man/xRDataLoader.Rd | 21 - man/xSNP2GeneScores.Rd | 23 +- man/xSNP2nGenes.Rd | 18 - man/xSNPlocations.Rd | 10 man/xSNPscores.Rd | 10 man/xSocialiserGenes.Rd | 10 man/xSocialiserSNPs.Rd | 9 man/xSubneterGR.Rd |only man/xSubneterGenes.Rd | 18 - man/xSubneterSNPs.Rd | 28 +- 102 files changed, 830 insertions(+), 2030 deletions(-)
Title: Implementation of Smart SVA
Description: Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures variation of unknown sources (batch effects) for high-dimensional genomic data. The algorithm is based on the popular 'SVA' package and proposes a revision on it that achieves more than 10 times faster running time while trading no accuracy loss in return.
Author: Jun Chen <Chen.Jun2@mayo.edu>, Ehsan Behnam <behnamgh@usc.edu>
Maintainer: Jun Chen <Chen.Jun2@mayo.edu>
Diff between SmartSVA versions 0.1.0 dated 2016-11-13 and 0.1.1 dated 2016-11-23
DESCRIPTION | 19 +++---- MD5 | 12 +++- NAMESPACE | 7 ++ R/RcppExports.R |only R/SmartSVA.R | 134 ++++++++++++++++++++++++++++++++++++++++++++++++++++ man/smartsva.Rd | 31 ++++-------- man/smartsva.cpp.Rd |only src |only 8 files changed, 167 insertions(+), 36 deletions(-)
Title: Interface to the Search 'API' for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search 'API' (<http://api.plos.org/>) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.6.0 dated 2016-07-21 and 0.6.4 dated 2016-11-23
DESCRIPTION | 12 +- MD5 | 28 +++--- NAMESPACE | 5 - NEWS.md | 15 +++ R/fulltext.R | 8 + R/highbrow.r | 4 R/plosword.R | 4 R/plot_throughtime.R | 4 R/rplos-package.R | 23 ++--- R/searchplos.R | 4 R/zzz.R | 4 build/vignette.rds |binary man/rplos-defunct.Rd | 3 man/rplos.Rd | 14 +-- tests/testthat/test-fulltext.R | 172 +++++++++++++++++++++++++++++++++++++---- 15 files changed, 228 insertions(+), 72 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.1-0 dated 2016-11-21 and 1.1-1 dated 2016-11-23
party-1.1-0/party/tests/Rplots.pdf |only party-1.1-1/party/DESCRIPTION | 8 ++++---- party-1.1-1/party/MD5 | 31 +++++++++++++++---------------- party-1.1-1/party/inst/NEWS | 5 +++++ party-1.1-1/party/inst/doc/MOB.pdf |binary party-1.1-1/party/inst/doc/party.pdf |binary party-1.1-1/party/src/Convenience.c | 2 +- party-1.1-1/party/src/Distributions.c | 2 +- party-1.1-1/party/src/IndependenceTest.c | 2 +- party-1.1-1/party/src/LinearStatistic.c | 2 +- party-1.1-1/party/src/Node.c | 2 +- party-1.1-1/party/src/Predict.c | 2 +- party-1.1-1/party/src/S3Classes.c | 2 +- party-1.1-1/party/src/Splits.c | 2 +- party-1.1-1/party/src/SurrogateSplits.c | 2 +- party-1.1-1/party/src/TestStatistic.c | 2 +- party-1.1-1/party/src/TreeGrow.c | 8 +++++--- 17 files changed, 39 insertions(+), 33 deletions(-)
Title: Functions for Reading Ontologies into R
Description: Functions for reading ontologies into R as lists and manipulating sets of ontological terms.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyIndex versions 2.2 dated 2016-10-28 and 2.3 dated 2016-11-23
ontologyIndex-2.2/ontologyIndex/man/get_OBO.Rd |only ontologyIndex-2.2/ontologyIndex/man/get_OWL.Rd |only ontologyIndex-2.2/ontologyIndex/man/owl_list_attributes.Rd |only ontologyIndex-2.2/ontologyIndex/man/owl_properties.Rd |only ontologyIndex-2.3/ontologyIndex/DESCRIPTION | 10 ontologyIndex-2.3/ontologyIndex/MD5 | 44 - ontologyIndex-2.3/ontologyIndex/NAMESPACE | 12 ontologyIndex-2.3/ontologyIndex/R/data.R | 260 +++------- ontologyIndex-2.3/ontologyIndex/R/descendants.R | 44 + ontologyIndex-2.3/ontologyIndex/R/generic.R | 4 ontologyIndex-2.3/ontologyIndex/R/sets.R | 89 +++ ontologyIndex-2.3/ontologyIndex/data/mpo.RData |binary ontologyIndex-2.3/ontologyIndex/inst/doc/intro-to-ontologyX.R | 3 ontologyIndex-2.3/ontologyIndex/inst/doc/intro-to-ontologyX.Rmd | 16 ontologyIndex-2.3/ontologyIndex/inst/doc/intro-to-ontologyX.html | 15 ontologyIndex-2.3/ontologyIndex/inst/doc/reading-ontologies.R | 21 ontologyIndex-2.3/ontologyIndex/inst/doc/reading-ontologies.Rmd | 61 +- ontologyIndex-2.3/ontologyIndex/inst/doc/reading-ontologies.html | 111 +++- ontologyIndex-2.3/ontologyIndex/man/get_ontology.Rd | 20 ontologyIndex-2.3/ontologyIndex/man/get_relation_names.Rd |only ontologyIndex-2.3/ontologyIndex/man/get_term_frequencies.Rd | 2 ontologyIndex-2.3/ontologyIndex/man/get_term_info_content.Rd | 2 ontologyIndex-2.3/ontologyIndex/man/ontology_index.Rd | 17 ontologyIndex-2.3/ontologyIndex/man/propagate_relations.Rd |only ontologyIndex-2.3/ontologyIndex/vignettes/intro-to-ontologyX.Rmd | 16 ontologyIndex-2.3/ontologyIndex/vignettes/reading-ontologies.Rmd | 61 +- 26 files changed, 440 insertions(+), 368 deletions(-)
Title: General Purpose 'Oai-PMH' Services Client
Description: A general purpose client to work with any 'OAI-PMH'
(Open Archives Initiative Protocol for 'Metadata' Harvesting) service.
The 'OAI-PMH' protocol is described at
<http://www.openarchives.org/OAI/openarchivesprotocol.html>.
Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord',
'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and
'ListSets'.
Author: Scott Chamberlain [aut, cre],
Michal Bojanowski [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between oai versions 0.2.0 dated 2016-02-06 and 0.2.2 dated 2016-11-23
oai-0.2.0/oai/R/tbldf.R |only oai-0.2.0/oai/man/tsum.Rd |only oai-0.2.2/oai/DESCRIPTION | 20 +-- oai-0.2.2/oai/MD5 | 73 +++++------ oai-0.2.2/oai/NAMESPACE | 17 -- oai-0.2.2/oai/NEWS.md |only oai-0.2.2/oai/R/count_identifiers.R | 6 oai-0.2.2/oai/R/get_record.R | 61 +++++++-- oai-0.2.2/oai/R/handle_errors.R | 2 oai-0.2.2/oai/R/list_identifiers.R | 28 +--- oai-0.2.2/oai/R/list_metadataformats.R | 2 oai-0.2.2/oai/R/list_records.R | 28 ++-- oai-0.2.2/oai/R/list_sets.R | 2 oai-0.2.2/oai/R/oai-package.R | 31 ++-- oai-0.2.2/oai/R/oai_available.R |only oai-0.2.2/oai/R/record_parsers.R |only oai-0.2.2/oai/R/zzz.R | 88 ++++++------- oai-0.2.2/oai/README.md | 109 ++++++++-------- oai-0.2.2/oai/build/vignette.rds |binary oai-0.2.2/oai/inst/doc/oai_vignette.Rmd | 117 ++++++++---------- oai-0.2.2/oai/inst/doc/oai_vignette.html | 117 ++++++++---------- oai-0.2.2/oai/inst/vign/oai_vignette.Rmd | 4 oai-0.2.2/oai/inst/vign/oai_vignette.md | 111 ++++++++--------- oai-0.2.2/oai/man/count_identifiers.Rd | 7 + oai-0.2.2/oai/man/dumpers.Rd | 2 oai-0.2.2/oai/man/get_records.Rd | 48 +++++-- oai-0.2.2/oai/man/list_identifiers.Rd | 18 -- oai-0.2.2/oai/man/list_records.Rd | 22 +-- oai-0.2.2/oai/man/oai-package.Rd | 25 ++- oai-0.2.2/oai/man/oai_available.Rd |only oai-0.2.2/oai/src |only oai-0.2.2/oai/tests/testthat/test-count_identifiers.R | 10 - oai-0.2.2/oai/tests/testthat/test-dumpers.R | 18 +- oai-0.2.2/oai/tests/testthat/test-get_records.R | 45 ++++-- oai-0.2.2/oai/tests/testthat/test-handle_errors.R | 21 +-- oai-0.2.2/oai/tests/testthat/test-id.R | 6 oai-0.2.2/oai/tests/testthat/test-list_identifiers.R | 12 - oai-0.2.2/oai/tests/testthat/test-list_records.R | 2 oai-0.2.2/oai/tests/testthat/test-list_sets.R | 2 oai-0.2.2/oai/tests/testthat/test-providers.R | 2 oai-0.2.2/oai/vignettes/oai_vignette.Rmd | 117 ++++++++---------- 41 files changed, 604 insertions(+), 569 deletions(-)
Title: Distributed-Lag Structural Equation Modelling
Description: Inference functionalities for structural equation models with second-order polynomial and gamma lag shapes.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <magrini@disia.unifi.it>
Diff between dlsem versions 1.4 dated 2016-10-03 and 1.5 dated 2016-11-23
dlsem-1.4/dlsem/data/agres.rda |only dlsem-1.4/dlsem/man/agres.Rd |only dlsem-1.4/dlsem/man/pathAnal.Rd |only dlsem-1.5/dlsem/DESCRIPTION | 15 dlsem-1.5/dlsem/MD5 | 49 - dlsem-1.5/dlsem/NAMESPACE | 9 dlsem-1.5/dlsem/R/dlsem.r | 1084 +++++++++++---------------- dlsem-1.5/dlsem/build/vignette.rds |binary dlsem-1.5/dlsem/data/industry.rda |only dlsem-1.5/dlsem/inst/doc/dlsem_tutorial.R | 59 - dlsem-1.5/dlsem/inst/doc/dlsem_tutorial.Rnw | 326 ++++---- dlsem-1.5/dlsem/inst/doc/dlsem_tutorial.pdf |binary dlsem-1.5/dlsem/man/EM.imputation.Rd | 8 dlsem-1.5/dlsem/man/applyDiff.Rd | 4 dlsem-1.5/dlsem/man/causalEff.Rd |only dlsem-1.5/dlsem/man/dlsem-package.Rd | 8 dlsem-1.5/dlsem/man/dlsem.Rd | 140 +-- dlsem-1.5/dlsem/man/edgeCoeff.Rd | 15 dlsem-1.5/dlsem/man/fitIndices.Rd | 16 dlsem-1.5/dlsem/man/industry.Rd |only dlsem-1.5/dlsem/man/isIndep.Rd | 13 dlsem-1.5/dlsem/man/lagPlot.Rd | 21 dlsem-1.5/dlsem/man/unirootTest.Rd | 8 dlsem-1.5/dlsem/vignettes/dlsem_tutorial.Rnw | 326 ++++---- dlsem-1.5/dlsem/vignettes/figures/dag0.pdf |binary dlsem-1.5/dlsem/vignettes/figures/dag1.pdf |binary dlsem-1.5/dlsem/vignettes/figures/lagsh1.pdf |binary dlsem-1.5/dlsem/vignettes/figures/lagsh2.pdf |binary dlsem-1.5/dlsem/vignettes/figures/lagsh3.pdf |only 29 files changed, 989 insertions(+), 1112 deletions(-)
Title: Functions of Complex or Real Variable
Description: Extension of several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.
Author: Albert Dorador and Uffe Høgsbro Thygesen
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>
Diff between complexplus versions 1.0 dated 2016-08-16 and 2.0 dated 2016-11-23
complexplus-1.0/complexplus/R/Det.R |only complexplus-2.0/complexplus/DESCRIPTION | 10 +++++----- complexplus-2.0/complexplus/MD5 | 10 +++++----- complexplus-2.0/complexplus/NAMESPACE | 1 + complexplus-2.0/complexplus/R/DetV2.R |only complexplus-2.0/complexplus/R/matlog.R | 2 +- complexplus-2.0/complexplus/man/Det.Rd | 8 +++++++- 7 files changed, 19 insertions(+), 12 deletions(-)
Title: STK++ Core Library Integration to R using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of
C++ classes for statistics, clustering, linear algebra, arrays (with an
Eigen-like API), regression, dimension reduction, etc. The integration of
the library to R is using Rcpp.
The rtkore package includes the header files from the STK++ core library.
All files contain only templated classes and/or inlined functions.
STK++ is licensed under the GNU LGPL version 2 or later. rtkore
(the stkpp integration into R) is licensed under the
GNU GPL version 2 or later. See file LICENSE.note for details.
Author: Serge Iovleff [aut, cre],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff <serge.iovleff@stkpp.org>
Diff between rtkore versions 1.1.0 dated 2016-06-13 and 1.2.0 dated 2016-11-23
DESCRIPTION | 8 MD5 | 195 +++++++---- R/rtkore.R | 9 build/vignette.rds |binary inst/NEWS.Rd | 20 - inst/doc/rtkpp-QuickRef.R |only inst/doc/rtkpp-QuickRef.Rnw |only inst/doc/rtkpp-QuickRef.pdf |only inst/doc/rtkpp-Tips.R |only inst/doc/rtkpp-Tips.Rnw |only inst/doc/rtkpp-Tips.pdf |only inst/doc/rtkpp-arrays.R |only inst/doc/rtkpp-arrays.Rnw |only inst/doc/rtkpp-arrays.pdf |only inst/doc/rtkpp-introduction.R | 2 inst/doc/rtkpp-introduction.Rnw | 55 +-- inst/doc/rtkpp-introduction.pdf |binary inst/include/Algebra.h | 4 inst/include/DManager.h | 2 inst/include/STKpp.h | 1 inst/include/STatistiK.h | 4 inst/include/Sdk.h | 1 inst/projects/Algebra/include/STK_InvertFixedSizeMatrix.h |only inst/projects/Algebra/include/STK_InvertFixedSizeSymMatrix.h |only inst/projects/Algebra/include/STK_lapack_SymEigen.h | 4 inst/projects/Analysis/include/STK_Funct_betaRatio.h | 2 inst/projects/Analysis/include/STK_Funct_gammaRatio.h | 2 inst/projects/Arrays/include/STK_Array2DDiagonal.h | 33 - inst/projects/Arrays/include/STK_Array2DPoint.h | 12 inst/projects/Arrays/include/STK_Array2DSquare.h | 20 - inst/projects/Arrays/include/STK_ArrayBaseInitializer.h | 12 inst/projects/Arrays/include/STK_CAllocator.h | 3 inst/projects/Arrays/include/STK_ExprBaseDot.h | 4 inst/projects/Arrays/include/STK_IArray1D.h | 8 inst/projects/Arrays/include/STK_IArray2D.h | 47 ++ inst/projects/Arrays/include/STK_ITContainer2D.h | 37 +- inst/projects/DManager/include/STK_CvHandler.h |only inst/projects/DManager/include/STK_DataHandler.h | 2 inst/projects/DManager/include/STK_DataHandlerBase.h | 7 inst/projects/DManager/include/STK_IDataHandler.h | 2 inst/projects/DManager/include/STK_ReadWriteCsv.h | 45 ++ inst/projects/Rtkpp/include/STK_RVector.h | 9 inst/projects/STKernel/include/STK_Range.h | 31 + inst/projects/STKernel/include/STK_String.h | 2 inst/projects/STatistiK/include/STK_Kernel_Hamming.h | 8 inst/projects/STatistiK/include/STK_Law_Beta.h | 20 - inst/projects/STatistiK/include/STK_Law_Binomial.h | 8 inst/projects/STatistiK/include/STK_Law_Cauchy.h | 20 - inst/projects/STatistiK/include/STK_Law_ChiSquared.h | 20 - inst/projects/STatistiK/include/STK_Law_Exponential.h | 20 - inst/projects/STatistiK/include/STK_Law_FisherSnedecor.h | 20 - inst/projects/STatistiK/include/STK_Law_Gamma.h | 20 - inst/projects/STatistiK/include/STK_Law_Geometric.h | 18 - inst/projects/STatistiK/include/STK_Law_HyperGeometric.h | 16 inst/projects/STatistiK/include/STK_Law_LogNormal.h | 20 - inst/projects/STatistiK/include/STK_Law_Logistic.h | 20 - inst/projects/STatistiK/include/STK_Law_NegativeBinomial.h | 16 inst/projects/STatistiK/include/STK_Law_Normal.h | 20 - inst/projects/STatistiK/include/STK_Law_Poisson.h | 12 inst/projects/STatistiK/include/STK_Law_Student.h | 20 - inst/projects/STatistiK/include/STK_Law_Uniform.h | 2 inst/projects/STatistiK/include/STK_Law_UniformDiscrete.h | 2 inst/projects/STatistiK/include/STK_Law_Util.h | 2 inst/projects/STatistiK/include/STK_Law_Weibull.h | 20 - inst/projects/STatistiK/include/STK_RandBase.h | 59 +++ inst/projects/STatistiK/include/STK_Stat_Bivariate.h | 2 inst/projects/STatistiK/include/STK_Stat_ConfusionMatrix.h |only inst/projects/STatistiK/include/STK_Stat_Factor.h | 156 +++++--- inst/projects/STatistiK/include/STK_Stat_Functors.h | 4 inst/projects/STatistiK/include/STK_Stat_MultiFactor.h |only inst/projects/STatistiK/include/STK_Stat_Online.h | 3 inst/projects/STatistiK/include/STK_Stat_Transform.h | 3 inst/projects/Sdk/include/STK_IRunner.h | 61 +-- inst/projects/Sdk/include/STK_Macros.h | 7 inst/projects/Sdk/include/STK_MacrosVersion.h |only inst/projects/Sdk/include/STK_StaticAssert.h | 22 - inst/projects/StatModels/include/STK_IClusterModelBase.h |only man/rtkore-package.Rd | 7 vignettes/images |only vignettes/programs |only vignettes/rtkore.bib | 21 + vignettes/rtkpp-QuickRef.Rnw |only vignettes/rtkpp-Tips.Rnw |only vignettes/rtkpp-arrays.Rnw |only vignettes/rtkpp-introduction.Rnw | 55 +-- vignettes/rtkpp-preamble.tex |only 86 files changed, 791 insertions(+), 496 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Sydney E. Everhart [ctb, dtc],
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb],
Erik Sotka [ctb],
Brian J. Knaus [ctb],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.2.1 dated 2016-08-29 and 2.3.0 dated 2016-11-23
DESCRIPTION | 12 +- MD5 | 68 ++++++------ NAMESPACE | 2 NEWS | 47 ++++++++ R/Index_calculations.r | 19 +-- R/amova.r | 15 ++ R/bitwise.r | 2 R/bootstraping.R | 33 ++++- R/distances.r | 4 R/internal.r | 70 ++++++++++++ R/methods.r | 91 +++++++++++----- R/poppr.R | 2 R/sample_schemes.r | 13 +- R/visualizations.r | 59 +++++++--- R/zzz.r | 7 + README.md | 14 +- build/vignette.rds |binary inst/doc/algo.pdf |binary inst/doc/mlg.html | 74 ++++++------- inst/doc/poppr_manual.Rmd | 8 - inst/doc/poppr_manual.html | 225 ++++++++++++++++++---------------------- man/aboot.Rd | 23 +++- man/coercion-methods.Rd | 14 ++ man/genotype_curve.Rd | 26 +++- man/ia.Rd | 12 +- man/poppr-package.Rd | 2 man/poppr.amova.Rd | 16 ++ tests/test-all.R | 1 tests/testthat/test-bootclass.R |only tests/testthat/test-distpop.R | 2 tests/testthat/test-genclone.R | 8 + tests/testthat/test-plots.R | 18 +-- tests/testthat/test-snpclone.R |only tests/testthat/test-trees.R | 10 + vignettes/poppr_manual.Rmd | 8 - vignettes/the_bibliography.bib | 2 36 files changed, 602 insertions(+), 305 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.9-0 dated 2016-10-28 and 2.0-0 dated 2016-11-23
DESCRIPTION | 13 MD5 | 34 NAMESPACE | 4 R/TheilSen.R | 3 R/importAURN.R | 15 R/importKCL.R | 14 R/percentileRose.R | 27 R/polarPlot.R | 2148 ++++++++++++++++++++++++++++++----------------------- R/scatterPlot.R | 4 R/timePlot.R | 8 R/timeProp.R | 7 R/timeVariation.R | 25 R/utilities.R | 12 R/windRose.R | 532 +++++++------ man/importAURN.Rd | 6 man/importKCL.Rd | 4 man/polarPlot.Rd | 541 +++++++------ man/windRose.Rd | 412 +++++----- 18 files changed, 2143 insertions(+), 1666 deletions(-)
Title: A Simulation Tool to Determine the Required Sample Size for
Repertory Grid Studies
Description: Simulation tool to facilitate determination of
required sample size to achieve category saturation
for studies using multiple repertory grids in conjunction with
content analysis.
Author: Mark Heckmann [aut, cre],
Lukas Burk [aut]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between gridsampler versions 0.5 dated 2016-09-03 and 0.6 dated 2016-11-23
gridsampler-0.5/gridsampler/vignettes/gridsampler.png |only gridsampler-0.6/gridsampler/DESCRIPTION | 11 - gridsampler-0.6/gridsampler/MD5 | 35 ++-- gridsampler-0.6/gridsampler/NAMESPACE | 1 gridsampler-0.6/gridsampler/NEWS.md | 6 gridsampler-0.6/gridsampler/R/utils.R | 1 gridsampler-0.6/gridsampler/README.md | 15 + gridsampler-0.6/gridsampler/inst/doc/index.R | 3 gridsampler-0.6/gridsampler/inst/doc/index.Rmd | 16 +- gridsampler-0.6/gridsampler/inst/doc/index.html | 18 +- gridsampler-0.6/gridsampler/inst/shiny/global.R | 14 + gridsampler-0.6/gridsampler/inst/shiny/server.R | 80 ++++++++-- gridsampler-0.6/gridsampler/inst/shiny/text/index.html | 18 +- gridsampler-0.6/gridsampler/inst/shiny/ui.R | 40 +++-- gridsampler-0.6/gridsampler/tests/testthat/test-sampling-code.R | 6 gridsampler-0.6/gridsampler/vignettes/gridsampler_pane_3a.png |binary gridsampler-0.6/gridsampler/vignettes/gridsampler_pane_3b.png |binary gridsampler-0.6/gridsampler/vignettes/gridsampler_panes.png |binary gridsampler-0.6/gridsampler/vignettes/index.Rmd | 16 +- 19 files changed, 198 insertions(+), 82 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 2.1.4 dated 2016-07-21 and 2.2.0 dated 2016-11-23
ggtern-2.1.4/ggtern/man/annotation-raster-tern.Rd |only ggtern-2.1.4/ggtern/man/calc_mahalanobis_distance.Rd |only ggtern-2.1.4/ggtern/man/convenience_functions.Rd |only ggtern-2.1.4/ggtern/man/coord-tern.Rd |only ggtern-2.1.4/ggtern/man/data_sets_Feldspar.Rd |only ggtern-2.1.4/ggtern/man/data_sets_Fragments.Rd |only ggtern-2.1.4/ggtern/man/data_sets_USDA.Rd |only ggtern-2.1.4/ggtern/man/getBreaks.Rd |only ggtern-2.1.4/ggtern/man/ggplotGrob.Rd |only ggtern-2.1.4/ggtern/man/modification-gridExtra.Rd |only ggtern-2.1.4/ggtern/man/plotconstruction.Rd |only ggtern-2.1.4/ggtern/man/scale_tern_continuous.Rd |only ggtern-2.1.4/ggtern/man/stat_density_tern.Rd |only ggtern-2.1.4/ggtern/man/suffix_arrow.Rd |only ggtern-2.1.4/ggtern/man/ternary-transformation.Rd |only ggtern-2.1.4/ggtern/man/themearrowlength.Rd |only ggtern-2.1.4/ggtern/man/themelegendposition.Rd |only ggtern-2.1.4/ggtern/man/themerotate.Rd |only ggtern-2.1.4/ggtern/man/themeshowhidearrows.Rd |only ggtern-2.1.4/ggtern/man/themeshowhidemask.Rd |only ggtern-2.1.4/ggtern/man/themeticksoutside.Rd |only ggtern-2.2.0/ggtern/DESCRIPTION | 26 - ggtern-2.2.0/ggtern/MD5 | 273 ++++++++-------- ggtern-2.2.0/ggtern/NAMESPACE | 30 + ggtern-2.2.0/ggtern/NEWS | 15 ggtern-2.2.0/ggtern/R/aes.R | 13 ggtern-2.2.0/ggtern/R/annotation-raster-tern.R | 9 ggtern-2.2.0/ggtern/R/annotation-tern.R | 1 ggtern-2.2.0/ggtern/R/calc-mahalanobis-distance.R | 3 ggtern-2.2.0/ggtern/R/calc-tern-tlr2xy.R | 9 ggtern-2.2.0/ggtern/R/coord-tern.R | 287 +++++++---------- ggtern-2.2.0/ggtern/R/depreciated.R | 22 - ggtern-2.2.0/ggtern/R/doc-data.R | 75 ++-- ggtern-2.2.0/ggtern/R/doc-theme-convenience.R | 52 +-- ggtern-2.2.0/ggtern/R/geom-Xisoprop.R | 12 ggtern-2.2.0/ggtern/R/geom-Xline.R | 37 +- ggtern-2.2.0/ggtern/R/geom-confidence-tern.R | 4 ggtern-2.2.0/ggtern/R/geom-crosshair-tern.R | 11 ggtern-2.2.0/ggtern/R/geom-density-tern.R | 16 ggtern-2.2.0/ggtern/R/geom-errorbarX.R | 13 ggtern-2.2.0/ggtern/R/geom-interpolate-tern.R | 3 ggtern-2.2.0/ggtern/R/geom-mask.R | 7 ggtern-2.2.0/ggtern/R/geom-point-swap.R | 1 ggtern-2.2.0/ggtern/R/geom-smooth-tern.R | 4 ggtern-2.2.0/ggtern/R/gg-internal.R | 14 ggtern-2.2.0/ggtern/R/ggtern-constructor.R | 8 ggtern-2.2.0/ggtern/R/ggtern-package.R | 16 ggtern-2.2.0/ggtern/R/labels-new.R | 7 ggtern-2.2.0/ggtern/R/labels-percent.R | 17 - ggtern-2.2.0/ggtern/R/legend-draw-tern.R | 3 ggtern-2.2.0/ggtern/R/modifications-gridExtra.R | 6 ggtern-2.2.0/ggtern/R/onLoad.R | 97 +++++ ggtern-2.2.0/ggtern/R/plot-build.R | 193 +++++------ ggtern-2.2.0/ggtern/R/plot-construction.R | 57 +++ ggtern-2.2.0/ggtern/R/plot.R | 2 ggtern-2.2.0/ggtern/R/position-.R | 1 ggtern-2.2.0/ggtern/R/position-jitter-tern.R | 5 ggtern-2.2.0/ggtern/R/position-nudge-tern.R | 1 ggtern-2.2.0/ggtern/R/save.R | 8 ggtern-2.2.0/ggtern/R/scales-tern.R | 58 +-- ggtern-2.2.0/ggtern/R/stat-confidence-tern.R | 7 ggtern-2.2.0/ggtern/R/stat-density-tern.R | 33 - ggtern-2.2.0/ggtern/R/stat-interpolate-methods.R | 18 - ggtern-2.2.0/ggtern/R/stat-interpolate-tern.R | 3 ggtern-2.2.0/ggtern/R/strip-unapproved.R | 86 ++--- ggtern-2.2.0/ggtern/R/tern-limits.R | 78 +++- ggtern-2.2.0/ggtern/R/theme-arrowlength.R | 36 +- ggtern-2.2.0/ggtern/R/theme-clockwise.R | 9 ggtern-2.2.0/ggtern/R/theme-defaults.R | 272 +++++++++++++--- ggtern-2.2.0/ggtern/R/theme-elements.R | 33 - ggtern-2.2.0/ggtern/R/theme-latex.R |only ggtern-2.2.0/ggtern/R/theme-legend-position.R | 2 ggtern-2.2.0/ggtern/R/theme-mesh.R | 64 +++ ggtern-2.2.0/ggtern/R/theme-noarrows.R | 7 ggtern-2.2.0/ggtern/R/theme-nomask.R | 7 ggtern-2.2.0/ggtern/R/theme-novar-tern.R | 18 - ggtern-2.2.0/ggtern/R/theme-rotate.R | 4 ggtern-2.2.0/ggtern/R/theme-showgrid.R | 5 ggtern-2.2.0/ggtern/R/theme-showlabels.R | 1 ggtern-2.2.0/ggtern/R/theme-showsecondary.R | 3 ggtern-2.2.0/ggtern/R/theme-showtitles.R | 5 ggtern-2.2.0/ggtern/R/theme-ticksoutside.R | 5 ggtern-2.2.0/ggtern/R/theme-zoom.R |only ggtern-2.2.0/ggtern/R/theme.R | 60 +-- ggtern-2.2.0/ggtern/R/utilities.R | 166 +++++++-- ggtern-2.2.0/ggtern/README.md | 40 ++ ggtern-2.2.0/ggtern/build/partial.rdb |binary ggtern-2.2.0/ggtern/demo/00Index | 2 ggtern-2.2.0/ggtern/demo/mask.R | 1 ggtern-2.2.0/ggtern/demo/points.R | 1 ggtern-2.2.0/ggtern/inst |only ggtern-2.2.0/ggtern/man/aes.Rd | 7 ggtern-2.2.0/ggtern/man/annotate.Rd | 7 ggtern-2.2.0/ggtern/man/annotation_raster_tern.Rd |only ggtern-2.2.0/ggtern/man/arrangeGrob.Rd |only ggtern-2.2.0/ggtern/man/breaks_tern.Rd |only ggtern-2.2.0/ggtern/man/coord_tern.Rd |only ggtern-2.2.0/ggtern/man/data_Feldspar.Rd |only ggtern-2.2.0/ggtern/man/data_Fragments.Rd |only ggtern-2.2.0/ggtern/man/data_USDA.Rd |only ggtern-2.2.0/ggtern/man/draw_key_tern.Rd | 4 ggtern-2.2.0/ggtern/man/geom_Xisoprop.Rd | 4 ggtern-2.2.0/ggtern/man/geom_Xline.Rd | 4 ggtern-2.2.0/ggtern/man/geom_confidence_tern.Rd | 10 ggtern-2.2.0/ggtern/man/geom_crosshair_tern.Rd | 8 ggtern-2.2.0/ggtern/man/geom_density_tern.Rd | 54 ++- ggtern-2.2.0/ggtern/man/geom_errorbarX.Rd | 11 ggtern-2.2.0/ggtern/man/geom_interpolate_tern.Rd | 21 - ggtern-2.2.0/ggtern/man/geom_point_swap.Rd | 7 ggtern-2.2.0/ggtern/man/geom_smooth_tern.Rd | 21 - ggtern-2.2.0/ggtern/man/ggplot.Rd | 3 ggtern-2.2.0/ggtern/man/ggplot_build.Rd | 11 ggtern-2.2.0/ggtern/man/ggplot_gtable.Rd | 7 ggtern-2.2.0/ggtern/man/ggsave.Rd | 4 ggtern-2.2.0/ggtern/man/ggtern.Rd | 21 + ggtern-2.2.0/ggtern/man/ggtern_labels.Rd | 9 ggtern-2.2.0/ggtern/man/ggtern_labels_arrow_suffix.Rd |only ggtern-2.2.0/ggtern/man/ggtern_package.Rd | 11 ggtern-2.2.0/ggtern/man/ggtern_themes.Rd | 101 ++++- ggtern-2.2.0/ggtern/man/label_formatter.Rd | 4 ggtern-2.2.0/ggtern/man/labels_tern.Rd |only ggtern-2.2.0/ggtern/man/mahalanobis_distance.Rd |only ggtern-2.2.0/ggtern/man/overloaded.Rd | 11 ggtern-2.2.0/ggtern/man/plot_construction.Rd |only ggtern-2.2.0/ggtern/man/position_jitter_tern.Rd | 5 ggtern-2.2.0/ggtern/man/position_nudge_tern.Rd | 3 ggtern-2.2.0/ggtern/man/predictdf2d.Rd |only ggtern-2.2.0/ggtern/man/rgb2hex.Rd |only ggtern-2.2.0/ggtern/man/scale_X_continuous.Rd |only ggtern-2.2.0/ggtern/man/strip_unapproved.Rd | 4 ggtern-2.2.0/ggtern/man/tern_limits.Rd | 29 + ggtern-2.2.0/ggtern/man/ternary_transformation.Rd |only ggtern-2.2.0/ggtern/man/theme.Rd |only ggtern-2.2.0/ggtern/man/theme_arrowlength.Rd |only ggtern-2.2.0/ggtern/man/theme_clockwise.Rd | 11 ggtern-2.2.0/ggtern/man/theme_complete.Rd | 39 +- ggtern-2.2.0/ggtern/man/theme_convenience_functions.Rd |only ggtern-2.2.0/ggtern/man/theme_elements.Rd | 90 ----- ggtern-2.2.0/ggtern/man/theme_latex.Rd |only ggtern-2.2.0/ggtern/man/theme_legendposition.Rd |only ggtern-2.2.0/ggtern/man/theme_mesh.Rd | 18 - ggtern-2.2.0/ggtern/man/theme_novar_tern.Rd | 9 ggtern-2.2.0/ggtern/man/theme_rotate.Rd |only ggtern-2.2.0/ggtern/man/theme_showarrows.Rd |only ggtern-2.2.0/ggtern/man/theme_showgrid.Rd | 3 ggtern-2.2.0/ggtern/man/theme_showlabels.Rd | 3 ggtern-2.2.0/ggtern/man/theme_showmask.Rd |only ggtern-2.2.0/ggtern/man/theme_showprimary.Rd | 5 ggtern-2.2.0/ggtern/man/theme_showtitles.Rd | 3 ggtern-2.2.0/ggtern/man/theme_ticksoutside.Rd |only ggtern-2.2.0/ggtern/man/theme_zoom_X.Rd |only ggtern-2.2.0/ggtern/man/transform_position_tern.Rd | 3 ggtern-2.2.0/ggtern/man/undocumented.Rd | 10 ggtern-2.2.0/ggtern/man/zzz-depreciated.Rd | 21 - 154 files changed, 1861 insertions(+), 1117 deletions(-)
Title: Flexible BUGS-Compatible System for Hierarchical Statistical
Modeling and Algorithm Development
Description: Flexible application of algorithms to models specified in the BUGS
language. Algorithms can be written in the NIMBLE language and made available to
any model.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-
Bergman, Duncan Temple Lang
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6-1 dated 2016-10-11 and 0.6-2 dated 2016-11-23
DESCRIPTION | 6 INSTALL | 6 MD5 | 285 ++++++++------- NAMESPACE | 9 NEWS | 27 + R/BUGS_BUGSdecl.R | 73 +++- R/BUGS_model.R | 257 +++++++++++--- R/BUGS_modelDef.R | 196 +++++----- R/BUGS_readBUGS.R | 3 R/MCEM_build.R | 375 +++++++++++--------- R/MCMC_autoBlock.R | 2 R/MCMC_build.R | 10 R/MCMC_comparisons.R | 7 R/MCMC_configuration.R | 18 - R/MCMC_conjugacy.R | 115 +++--- R/MCMC_samplers.R | 38 +- R/MCMC_suite.R | 86 ++-- R/MCMC_utils.R | 1 R/RCfunction_compile.R | 7 R/RCfunction_core.R | 40 ++ R/cppDefs_cppProject.R | 18 - R/cppDefs_nimbleFunction.R | 9 R/cppInterfaces_nimbleFunctions.R | 65 ++- R/cppInterfaces_otherTypes.R | 2 R/distributions_implementations.R | 4 R/distributions_inputList.R | 11 R/distributions_processInputList.R | 501 ++++++++++++++++++++++------ R/genCpp_eigenization.R | 13 R/genCpp_generateCpp.R | 15 R/genCpp_sizeProcessing.R | 30 + R/nimbleFunction_Rexecution.R | 92 ++++- R/nimbleFunction_compile.R | 3 R/nimbleFunction_core.R | 8 R/nimbleFunction_keywordProcessing.R | 71 +++ R/nimbleFunction_nodeFunction.R | 53 +- R/nimbleFunction_nodeFunctionNew.R | 74 +++- R/nimbleFunction_util.R | 14 R/nimbleProject.R | 107 +++-- R/options.R | 1 R/types_nodeFxnVector.R | 2 R/types_symbolTable.R | 15 README.md | 6 inst/CppCode/accessorClasses.cpp | 12 inst/CppCode/dists.cpp | 59 +-- inst/include/nimble/accessorClasses.h | 38 ++ inst/include/nimble/nodeFun.h | 13 inst/tests/test-checkDSL.R |only inst/tests/test-distributions.R | 31 + inst/tests/test-getBound.R |only inst/tests/test-getDistributionInfo.R |only inst/tests/test-getParam.R | 2 inst/tests/test-misc.R |only inst/tests/test_utils.R | 25 + man/BUGSdeclClass-class.Rd | 2 man/Categorical.Rd | 4 man/CmodelBaseClass-class.Rd | 2 man/CnimbleFunctionBase-class.Rd | 2 man/Constraint.Rd | 2 man/Dirichlet.Rd | 2 man/Exponential.Rd | 2 man/Interval.Rd | 2 man/MCMCconf-class.Rd | 2 man/MCMCsuite.Rd | 2 man/MCMCsuiteClass-class.Rd | 2 man/Multinomial.Rd | 4 man/Multivariate-t.Rd | 2 man/MultivariateNormal.Rd | 2 man/Rmatrix2mvOneVar.Rd | 2 man/RmodelBaseClass-class.Rd | 2 man/Wishart.Rd | 2 man/asRow.Rd | 2 man/autoBlock.Rd | 2 man/buildAuxiliaryFilter.Rd | 2 man/buildBootstrapFilter.Rd | 2 man/buildEnsembleKF.Rd | 2 man/buildLiuWestFilter.Rd | 2 man/buildMCEM.Rd | 20 - man/buildMCMC.Rd | 4 man/checkInterrupt.Rd | 2 man/codeBlockClass-class.Rd | 2 man/combine_MCMC_comparison_results.Rd | 2 man/compareMCMCs.Rd | 2 man/compileNimble.Rd | 7 man/configureMCMC.Rd | 2 man/decide.Rd | 2 man/decideAndJump.Rd | 2 man/declare.Rd | 2 man/deregisterDistributions.Rd | 2 man/distributionInfo.Rd |only man/getBUGSexampleDir.Rd | 2 man/getBound.Rd |only man/getDefinition.Rd | 2 man/getLoadingNamespace.Rd | 2 man/getNimbleOption.Rd | 2 man/getParam.Rd | 4 man/getsize.Rd | 2 man/identityMatrix.Rd | 2 man/initializeModel.Rd | 2 man/is.nf.Rd | 6 man/makeBoundInfo.Rd |only man/makeParamInfo.Rd | 2 man/make_MCMC_comparison_pages.Rd | 2 man/modelBaseClass-class.Rd | 108 +++++- man/modelDefClass-class.Rd | 2 man/modelValues.Rd | 2 man/modelValuesBaseClass-class.Rd | 2 man/modelValuesConf.Rd | 2 man/nfMethod.Rd | 2 man/nfVar.Rd | 4 man/nimArray.Rd | 2 man/nimCat.Rd | 2 man/nimCopy.Rd | 2 man/nimDim.Rd | 2 man/nimInteger.Rd | 2 man/nimMatrix.Rd | 2 man/nimNumeric.Rd | 2 man/nimPrint.Rd | 2 man/nimStop.Rd | 2 man/nimbleCode.Rd | 2 man/nimbleFunction.Rd | 5 man/nimbleFunctionBase-class.Rd | 2 man/nimbleFunctionList-class.Rd | 2 man/nimbleFunctionVirtual.Rd | 2 man/nimbleModel.Rd | 2 man/nimbleOptions.Rd | 2 man/nodeFunctions.Rd | 2 man/rankSample.Rd | 2 man/readBUGSmodel.Rd | 2 man/registerDistributions.Rd | 24 + man/rename_MCMC_comparison_method.Rd | 2 man/reshape_comparison_results.Rd | 2 man/resize.Rd | 2 man/run.time.Rd | 2 man/runMCMC.Rd | 2 man/samplers.Rd | 2 man/setAndCalculate.Rd | 2 man/setAndCalculateOne.Rd | 2 man/setSize.Rd | 2 man/setupOutputs.Rd | 2 man/simNodes.Rd | 2 man/simNodesMV.Rd | 2 man/singleVarAccessClass-class.Rd | 2 man/t.Rd | 2 man/testBUGSmodel.Rd | 2 man/updateMCMCcomparisonWithHighOrderESS.Rd | 2 man/valueInCompiledNimbleFunction.Rd | 2 man/values.Rd | 2 147 files changed, 2211 insertions(+), 994 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <http://doi.org/10.18637/jss.v074.i11>.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.3-0 dated 2016-10-24 and 1.3-1 dated 2016-11-23
DESCRIPTION | 10 - MD5 | 31 ++-- NEWS | 12 + R/compare.syn.r | 81 ++++++---- build/partial.rdb |only inst/doc/synthpop.R | 73 ++++----- inst/doc/synthpop.Rnw | 180 ++++++++++++------------ inst/doc/synthpop.pdf |binary man/compare.fit.synds.Rd | 2 man/compare.synds.Rd | 2 man/summary.fit.synds.Rd | 2 man/summary.synds.Rd | 2 man/syn.Rd | 2 man/synthpop-package.Rd | 9 - vignettes/Figure3Z.pdf |binary vignettes/synthpop.Rnw | 180 ++++++++++++------------ vignettes/synthpop.bib | 350 +++++++++++++++++++++++------------------------ 17 files changed, 503 insertions(+), 433 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut, cre],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between mboost versions 2.6-0 dated 2016-03-12 and 2.7-0 dated 2016-11-23
DESCRIPTION | 17 +++--- MD5 | 53 ++++++++++---------- NAMESPACE | 15 +++-- R/bl.R | 17 ++++++ R/btree.R | 18 +++---- R/crossvalidation.R | 7 +- R/family.R | 97 ++++++++++++++++++++++++++++++++++++++ R/mboost.R | 4 - R/plot.R | 49 ++++++++++++------- R/survival.R | 8 +-- R/varimp.R |only README.md |only build/vignette.rds |binary inst/CITATION | 4 - inst/NEWS.Rd | 56 +++++++++++++++++++++ inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost.Rnw | 2 inst/doc/mboost.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/doc/mboost_tutorial.R | 66 ++++++++++++++++--------- inst/doc/mboost_tutorial.Rnw | 26 +++++++--- inst/doc/mboost_tutorial.pdf |binary man/Family.Rd | 44 ++++++++++++++--- man/baselearners.Rd | 34 +++++++------ man/cvrisk.Rd | 19 +++++++ man/mboost_package.Rd | 14 ++++- man/varimp.Rd |only vignettes/mboost.Rnw | 2 vignettes/mboost_tutorial.Rnw | 26 +++++++--- 29 files changed, 434 insertions(+), 144 deletions(-)
Title: Gaussian Graphs Models Selection
Description: Graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: Annie Bouvier <Annie.Bouvier@inra.fr>
Diff between GGMselect versions 0.1-10 dated 2015-08-26 and 0.1-11 dated 2016-11-23
DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++----------------- NEWS | 9 +++++++++ inst/doc/Notice.pdf |binary src/critQE.c | 6 +++++- tests/bsch.Rout.save | 10 +++++----- tests/penInf.Rout.save | 10 +++++----- tests/sh9.2012.Rout.save | 10 +++++----- tests/shPUR.Rout.save | 10 +++++----- tests/test1Fast.Rout.save | 10 +++++----- tests/test1QE.Rout.save | 10 +++++----- tests/test2Fast.Rout.save | 10 +++++----- tests/test2QE.Rout.save | 10 +++++----- tests/test3Fast.Rout.save | 10 +++++----- tests/test3QE.Rout.save | 10 +++++----- tests/test5Fast.Rout.save | 10 +++++----- tests/test7Fast.Rout.save | 10 +++++----- tests/testMyFam.Rout.save | 10 +++++----- 18 files changed, 102 insertions(+), 89 deletions(-)
Title: Construction Methods of some Series of PBIB Designs
Description: Series of partially balanced incomplete block designs (PBIB) based on the combinatory method (S) introduced in (Imane Rezgui et al, 2014) <doi:10.3844/jmssp.2014.45.48>; and it gives their associated U-type design.
Author: Mohamed Laib, Imane Rezgui, Zebida Gheribi-Aoulmi and Herve Monod
Maintainer: Mohamed Laib <laib.med@gmail.com>
Diff between CombinS versions 1.1 dated 2015-02-24 and 1.1-1 dated 2016-11-23
CombinS-1.1-1/CombinS/DESCRIPTION | 23 ++++-- CombinS-1.1-1/CombinS/MD5 | 33 ++++---- CombinS-1.1-1/CombinS/NAMESPACE | 12 ++- CombinS-1.1-1/CombinS/R/CombS.R | 107 ++++++++++++++++++++--------- CombinS-1.1-1/CombinS/R/GPBIB4A.R | 91 ++++++++++++++++++------ CombinS-1.1-1/CombinS/R/GPBIB4B.R | 73 +++++++++++++------ CombinS-1.1-1/CombinS/R/GPBIB5.R | 74 +++++++++++++------- CombinS-1.1-1/CombinS/R/GPBIB7A.R | 75 ++++++++++++++------ CombinS-1.1-1/CombinS/R/GPBIB7B.R | 78 ++++++++++++++------- CombinS-1.1-1/CombinS/R/UType.R | 31 +++++++- CombinS-1.1-1/CombinS/man/CombS.Rd | 88 +++++++++++------------ CombinS-1.1-1/CombinS/man/GPBIB4A.Rd | 94 +++++++++++++------------ CombinS-1.1-1/CombinS/man/GPBIB4B.Rd | 88 ++++++++++++----------- CombinS-1.1-1/CombinS/man/GPBIB5.Rd | 89 ++++++++++++------------ CombinS-1.1-1/CombinS/man/GPBIB7A.Rd | 90 ++++++++++++------------ CombinS-1.1-1/CombinS/man/GPBIB7B.Rd | 90 ++++++++++++------------ CombinS-1.1-1/CombinS/man/UType.Rd | 52 +++++--------- CombinS-1.1/CombinS/man/CombinS-package.Rd |only 18 files changed, 723 insertions(+), 465 deletions(-)
Title: R Bindings for Selenium WebDriver
Description: The RSelenium package provides a set of R bindings for the
Selenium 2.0 WebDriver (see <https://seleniumhq.github.io/docs/wd.html>
for more information) using the JsonWireProtocol (see
<https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more
information). Selenium 2.0 WebDriver allows driving a web browser
natively as a user would either locally or on a remote machine using
the Selenium server it marks a leap forward in terms of web browser
automation. Selenium automates web browsers (commonly referred to as
browsers). Using RSelenium you can automate browsers locally or
remotely.
Author: John Harrison <johndharrison0@gmail.com>
Maintainer: John Harrison <johndharrison0@gmail.com>
Diff between RSelenium versions 1.4.5 dated 2016-10-01 and 1.5.0 dated 2016-11-23
DESCRIPTION | 25 MD5 | 106 NAMESPACE | 27 NEWS | 16 R/errorHandler.R | 397 +-- R/remoteDriver.R | 1426 ++++++----- R/selKeys-data.R | 63 R/sysdata.rda |only R/util.R | 234 + R/webElement.R | 436 +-- README.md | 2 inst/apps/shinytestapp/reqplots.R | 38 inst/apps/shinytestapp/tests-saucelabs/runtest.R | 35 inst/apps/shinytestapp/tests-saucelabs/setup.r | 4 inst/apps/shinytestapp/tests-saucelabs/test-daterangeinput.r | 15 inst/apps/shinytestapp/tests-saucelabs/test-numericinput.r | 18 inst/apps/shinytestapp/tests-saucelabs/test-output.r | 18 inst/apps/shinytestapp/tests-saucelabs/test-selectinput.r | 3 inst/apps/shinytestapp/tests-saucelabs/test-sliderinput.r | 20 inst/apps/shinytestapp/tests/test-daterangeinput.r | 15 inst/apps/shinytestapp/tests/test-numericinput.r | 18 inst/apps/shinytestapp/tests/test-output.r | 21 inst/apps/shinytestapp/tests/test-selectinput.r | 6 inst/apps/shinytestapp/tests/test-sliderinput.r | 20 inst/apps/shinytestapp/ui.R | 44 inst/doc/RSelenium-basics.Rmd | 2 inst/doc/RSelenium-basics.html | 15 inst/doc/RSelenium-docker.html | 13 inst/doc/shinytesting.Rmd | 2 inst/doc/shinytesting.html | 2 inst/examples/serverUtils/checkForServer.R | 27 inst/examples/serverUtils/startServer.R | 29 inst/sauceTests/cleanBuild.R | 16 inst/sauceTests/runtest.R | 28 inst/sauceTests/setup.r | 4 inst/sauceTests/test-alerts.r | 55 inst/sauceTests/test-api-example.r | 79 man/checkForServer.Rd | 14 man/errorHandler-class.Rd | 92 man/getChromeProfile.Rd | 9 man/getFirefoxProfile.Rd | 8 man/makeFirefoxProfile.Rd | 13 man/phantom.Rd | 27 man/remoteDriver-class.Rd | 387 ++ man/selKeys.Rd | 11 man/startServer.Rd | 31 man/webElement-class.Rd | 84 tests/testthat/helper.R | 6 tests/testthat/test-api_example_tests.R | 55 tests/testthat/test-cookie_tests.R | 15 tests/testthat/test-executing_javascript_tests.R |only tests/testthat/test-page_loading_tests.R | 4 tests/testthat/test-util_function_tests.R | 6 vignettes/RSelenium-basics.Rmd | 2 vignettes/shinytesting.Rmd | 2 55 files changed, 2411 insertions(+), 1634 deletions(-)
Title: Exploring Machine Learning Better, Together
Description: 'OpenML.org' is an online machine learning platform where researchers can
automatically share data, machine learning tasks and experiments and organize them
online to work and collaborate more effectively.
We provide a R interface to the OpenML REST API in order to download and upload data
sets, tasks, flows and runs, see <http://www.openml.org/guide> for more information.
Author: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>,
Bernd Bischl <bernd_bischl@gmx.net>,
Dominik Kirchhoff <dom.kirchhoff@gmail.com>,
Michel Lang <michellang@gmail.com>,
Benjamin Hofner <benjamin.hofner@fau.de>,
Jakob Bossek <j.bossek@gmail.com>,
Pascal Kerschke <kerschke@uni-muenster.de>,
Joaquin Vanschoren <joaquin.vanschoren@gmail.com>
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between OpenML versions 1.0 dated 2016-11-12 and 1.1 dated 2016-11-23
DESCRIPTION | 15 +++++---- MD5 | 24 +++++++-------- NAMESPACE | 1 NEWS | 14 +++++++- R/convertOMLFlowToMlr.R | 4 +- R/convertOMLRunToBMR.R | 71 +++++++++++++++++++++++++++++++++++++++++++-- R/getOMLDataSetQualities.R | 2 - R/getOMLFlow.R | 4 +- R/listOMLTasks.R | 4 +- R/runTaskFlow.R | 2 - R/zzz.R | 12 ++++++- inst/doc/OpenML.pdf |binary man/convertOMLRunToBMR.Rd | 2 - 13 files changed, 120 insertions(+), 35 deletions(-)
Title: Miscellaneous Functions for Survival Data
Description: A collection of functions to help in the analysis of
right-censored survival data. These extend the methods available in
package:survival.
Author: Chris Dardis
Maintainer: Chris Dardis <christopherdardis@gmail.com>
Diff between survMisc versions 0.5.3 dated 2016-07-07 and 0.5.4 dated 2016-11-23
DESCRIPTION | 8 +++--- MD5 | 20 +++++++-------- R/COV.R | 8 ++++-- R/asWide.R | 6 +++- R/autoplotTAP.R | 3 +- R/autoplotTen.R | 68 +++++++++++++++++++++++++---------------------------- inst/NEWS.Rd | 9 +++++-- inst/doc/plots.pdf |binary man/COV.Rd | 6 ++++ man/asWide.Rd | 4 +++ man/autoplotTAP.Rd | 2 + 11 files changed, 78 insertions(+), 56 deletions(-)
Title: Send Push Notifications using Pushover
Description: Send push notifications to mobile devices or the desktop using Pushover. These notifications can display job status, results, scraped web data, or any other text or numeric data.
Author: Brian Connelly [aut, cre]
Maintainer: Brian Connelly <bdc@bconnelly.net>
Diff between pushoverr versions 0.1.4 dated 2014-11-06 and 1.0.0 dated 2016-11-23
pushoverr-0.1.4/pushoverr/NEWS |only pushoverr-0.1.4/pushoverr/R/PushoverMessage.R |only pushoverr-0.1.4/pushoverr/R/PushoverResponse.R |only pushoverr-0.1.4/pushoverr/R/cancel_receipt.R |only pushoverr-0.1.4/pushoverr/R/devices.R |only pushoverr-0.1.4/pushoverr/R/keys.R |only pushoverr-0.1.4/pushoverr/R/receipts.R |only pushoverr-0.1.4/pushoverr/R/sounds.R |only pushoverr-0.1.4/pushoverr/man/PushoverMessage-class.Rd |only pushoverr-0.1.4/pushoverr/man/PushoverMessage.Rd |only pushoverr-0.1.4/pushoverr/man/PushoverResponse-class.Rd |only pushoverr-0.1.4/pushoverr/man/PushoverResponse.Rd |only pushoverr-0.1.4/pushoverr/man/cancel_receipt.Rd |only pushoverr-0.1.4/pushoverr/man/content_value-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/headers-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/http_status_code-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/is.success-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/is.valid_token.Rd |only pushoverr-0.1.4/pushoverr/man/pushover_priorities.Rd |only pushoverr-0.1.4/pushoverr/man/receipt-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/request-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/send-PushoverMessage-method.Rd |only pushoverr-0.1.4/pushoverr/man/send_pushovermessage.Rd |only pushoverr-0.1.4/pushoverr/man/show-PushoverMessage-method.Rd |only pushoverr-0.1.4/pushoverr/man/show-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/status-PushoverResponse-method.Rd |only pushoverr-0.1.4/pushoverr/man/validate_PushoverMessage.Rd |only pushoverr-0.1.4/pushoverr/man/validate_PushoverResponse.Rd |only pushoverr-0.1.4/pushoverr/man/validate_key.Rd |only pushoverr-1.0.0/pushoverr/DESCRIPTION | 18 pushoverr-1.0.0/pushoverr/LICENSE | 2 pushoverr-1.0.0/pushoverr/MD5 | 90 ++-- pushoverr-1.0.0/pushoverr/NAMESPACE | 41 +- pushoverr-1.0.0/pushoverr/NEWS.md |only pushoverr-1.0.0/pushoverr/R/cancel_retries.R |only pushoverr-1.0.0/pushoverr/R/check_receipt.R |only pushoverr-1.0.0/pushoverr/R/get_devices.R |only pushoverr-1.0.0/pushoverr/R/get_group_info.R |only pushoverr-1.0.0/pushoverr/R/get_pushover_limits.R |only pushoverr-1.0.0/pushoverr/R/get_pushover_sounds.R |only pushoverr-1.0.0/pushoverr/R/group_rename.R |only pushoverr-1.0.0/pushoverr/R/group_subscription.R |only pushoverr-1.0.0/pushoverr/R/is.pushover_sound.R |only pushoverr-1.0.0/pushoverr/R/is.valid_app.R |only pushoverr-1.0.0/pushoverr/R/is.valid_device.R |only pushoverr-1.0.0/pushoverr/R/is.valid_receipt.R |only pushoverr-1.0.0/pushoverr/R/is.valid_user.R |only pushoverr-1.0.0/pushoverr/R/pushover.R | 183 +++++----- pushoverr-1.0.0/pushoverr/R/pushover_api.R |only pushoverr-1.0.0/pushoverr/R/pushoverr.R | 20 - pushoverr-1.0.0/pushoverr/R/set_pushover_app.R |only pushoverr-1.0.0/pushoverr/R/set_pushover_user.R |only pushoverr-1.0.0/pushoverr/R/stop_for_pushover_status.R |only pushoverr-1.0.0/pushoverr/R/update_glance.R |only pushoverr-1.0.0/pushoverr/R/verify_user.R |only pushoverr-1.0.0/pushoverr/README.md | 151 ++++---- pushoverr-1.0.0/pushoverr/man/cancel_retries.Rd |only pushoverr-1.0.0/pushoverr/man/check_receipt.Rd | 72 +-- pushoverr-1.0.0/pushoverr/man/get_devices.Rd | 46 +- pushoverr-1.0.0/pushoverr/man/get_group_info.Rd |only pushoverr-1.0.0/pushoverr/man/get_pushover_limits.Rd |only pushoverr-1.0.0/pushoverr/man/get_pushover_sounds.Rd | 21 - pushoverr-1.0.0/pushoverr/man/group_rename.Rd |only pushoverr-1.0.0/pushoverr/man/group_subscription.Rd |only pushoverr-1.0.0/pushoverr/man/is.pushover_sound.Rd |only pushoverr-1.0.0/pushoverr/man/is.valid_app.Rd |only pushoverr-1.0.0/pushoverr/man/is.valid_device.Rd | 24 - pushoverr-1.0.0/pushoverr/man/is.valid_receipt.Rd | 22 - pushoverr-1.0.0/pushoverr/man/is.valid_user.Rd |only pushoverr-1.0.0/pushoverr/man/pushover.Rd | 90 ++-- pushoverr-1.0.0/pushoverr/man/pushover_api.Rd |only pushoverr-1.0.0/pushoverr/man/pushoverr.Rd | 22 - pushoverr-1.0.0/pushoverr/man/set_pushover_app.Rd | 121 +----- pushoverr-1.0.0/pushoverr/man/set_pushover_user.Rd |only pushoverr-1.0.0/pushoverr/man/stop_for_pushover_status.Rd |only pushoverr-1.0.0/pushoverr/man/update_glance.Rd |only pushoverr-1.0.0/pushoverr/man/verify_user.Rd |only 77 files changed, 466 insertions(+), 457 deletions(-)
Title: Pumilio in R
Description: R package to query and get data out of a Pumilio sound archive system (http://ljvillanueva.github.io/pumilio/).
Author: Luis J. Villanueva-Rivera
Maintainer: Luis J. Villanueva-Rivera <ljvillanueva@coquipr.com>
Diff between pumilioR versions 1.3 dated 2014-04-14 and 1.3.1 dated 2016-11-23
DESCRIPTION | 8 +- MD5 | 28 +++++----- NAMESPACE | 1 NEWS | 5 + R/getCollections.R | 2 R/getSites.R | 2 R/getSounds.R | 2 build/vignette.rds |binary inst/doc/pumiliosetup.Rmd | 4 - inst/doc/pumiliosetup.html | 126 ++++++++++++++++++++++++++------------------- man/checkVersion.Rd | 6 +- man/getFile.Rd | 17 ------ man/pumilioR.package.Rd | 4 - vignettes/pumiliosetup.Rmd | 4 - vignettes/pumiliosetup.md | 4 - 15 files changed, 114 insertions(+), 99 deletions(-)
Title: Phase II Clinical Trial Design for Multinomial Endpoints
Description: Provide multinomial design methods under intersection-union test (IUT) and union-intersection test (UIT) scheme for Phase II trial. The design types include : Minimax (minimize the maximum sample size), Optimal (minimize the expected sample size), Admissible (minimize the Bayesian risk) and Maxpower (maximize the exact power level).
Author: Yalin Zhu, Rui Qin
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>
Diff between ph2mult versions 0.1.0 dated 2016-08-21 and 0.1.1 dated 2016-11-23
ph2mult-0.1.0/ph2mult/vignettes |only ph2mult-0.1.1/ph2mult/DESCRIPTION | 7 - ph2mult-0.1.1/ph2mult/MD5 | 8 - ph2mult-0.1.1/ph2mult/R/searchfun_IUT.R | 31 ++-- ph2mult-0.1.1/ph2mult/man/IUT.design.Rd | 213 ++++++++++++++++---------------- 5 files changed, 129 insertions(+), 130 deletions(-)
Title: A Collection of Disease Outbreak Data
Description: Empirical or simulated disease outbreak data, provided either as
RData or as text files.
Author: Thibaut Jombart [aut],
Simon Frost [aut],
Pierre Nouvellet [aut],
Finlay Campbell [aut, cre]
Maintainer: Finlay Campbell <f.campbell15@imperial.ac.uk>
Diff between outbreaks versions 1.0.0 dated 2016-10-31 and 1.1.0 dated 2016-11-23
DESCRIPTION | 6 ++--- MD5 | 8 +++++- NEWS.md |only R/mers.korea.2015.R |only README.md | 52 ++++++++++++++++++++++++++++++++------------- data/mers.korea.2015.RData |only man/mers.korea.2015.Rd |only 7 files changed, 46 insertions(+), 20 deletions(-)
Title: Detecting Epistatic Selection with Partially Observed Genotype
Data
Description: An efficient multi-core package to reconstruct an underlying network of
genomic signatures of high-dimensional epistatic selection from
partially observed genotype data. The phenotype that we consider is viability.
The network captures the conditional dependent short- and long-range linkage
disequilibrium structure of genomes and thus reveals aberrant marker-marker
associations that are due to epistatic selection. We target on high-dimensional
genotype data where number of variables (markers) is larger than number of
sample sizes (p >> n). The computations is memory-optimized using the sparse
matrix output.
Author: Pariya Behrouzi, Danny Arends and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between epistasis versions 0.0.0-1 dated 2016-11-07 and 0.0.1-1 dated 2016-11-23
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++----------- NAMESPACE | 1 R/Gibbs_method.R | 4 +- R/episelect.R | 17 +++------- R/episim.R | 4 +- R/epistasis.R | 18 ++++++++++ R/initialize.R | 4 +- R/model.selection.R | 87 ++++++++++++++++++++++++++++++++++------------------ data/B73Ki11.RData |only data/CviCol.RData |binary man/B73Ki11.Rd |only man/CviCol.Rd | 10 +++++ man/R.approx.Rd | 7 +--- man/R.gibbs.Rd | 3 - man/cutoffs.Rd | 5 +- man/episelect.Rd | 45 +++++++++++++++++--------- man/episim.Rd | 9 +++-- man/epistasis.Rd | 13 ++++--- man/lower.upper.Rd | 3 - man/plot.episim.Rd | 1 man/print.epi.Rd |only 22 files changed, 172 insertions(+), 106 deletions(-)
Title: Coordinate-Descent Algorithm for Discrete Data
Description: Structure learning of Bayesian network using coordinate-descent
algorithm. This algorithm is designed for discrete network assuming a multinomial data set,
and we use a multi-logit model to do the regression.
The algorithm is described in Gu, Fu and Zhou (2016) <http://arxiv.org/abs/1403.2310>.
Author: Jiaying Gu [aut, cre]
Maintainer: Jiaying Gu <gujy.lola@gmail.com>
Diff between discretecdAlgorithm versions 0.0.1 dated 2016-08-11 and 0.0.2 dated 2016-11-23
DESCRIPTION | 8 MD5 | 23 R/CD-main.R | 64 + R/basic.R | 9 R/lambda.R | 2 README.md | 14 man/cd.run.Rd | 8 src/dCD.cpp | 1512 +++++++++++++++++----------------- src/dCD.h | 13 src/wrap.cpp | 18 tests/testthat/test-CD_run.R | 2 tests/testthat/test-cd_adaptive_run.R |only tests/testthat/test-get_summary.R | 6 13 files changed, 884 insertions(+), 795 deletions(-)
More information about discretecdAlgorithm at CRAN
Permanent link
Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between d3r versions 0.4.0 dated 2016-10-13 and 0.5.0 dated 2016-11-23
d3r-0.4.0/d3r/inst/www/d3/v3/dist/d3.v3.min.js |only d3r-0.4.0/d3r/inst/www/d3/v4/dist/d3.v4.min.js |only d3r-0.5.0/d3r/DESCRIPTION | 12 - d3r-0.5.0/d3r/MD5 | 23 +- d3r-0.5.0/d3r/NEWS.md |only d3r-0.5.0/d3r/R/dependencies.R | 35 +-- d3r-0.5.0/d3r/inst/examples/example_draw_igraph_with_layout.R | 40 ++- d3r-0.5.0/d3r/inst/www/d3/v3/dist/d3.min.js |only d3r-0.5.0/d3r/inst/www/d3/v4/API.md | 111 +++++----- d3r-0.5.0/d3r/inst/www/d3/v4/CHANGES.md | 6 d3r-0.5.0/d3r/inst/www/d3/v4/README.md | 12 + d3r-0.5.0/d3r/inst/www/d3/v4/dist/d3.min.js |only d3r-0.5.0/d3r/man/d3_dep_v3.Rd | 6 d3r-0.5.0/d3r/man/d3_dep_v4.Rd | 6 d3r-0.5.0/d3r/tests/testthat/test_deps.R | 6 15 files changed, 160 insertions(+), 97 deletions(-)