Title: Functional Clustering Algorithms
Description: Unified framework to cluster functional data according to one of
seven models. All models are based on the projection of the curves onto a basis.
The main function funcit() calls wrapper functions for the existing algorithms,
so that input parameters are the same. A list is returned with each entry
representing the same or extended output for the corresponding method. Method
specific as well as general visualization tools are available.
Author: Christina Yassouridis [aut, cre],
Dominik Ernst [ctb],
Madison Giacofci [ctb],
Sophie Lambert-Lacroix [ctb],
Guillemette Marot [ctb],
Franck Picard [ctb],
Nicoleta Serban [ctb],
Huijing Jiang [ctb],
Gareth James [ctb],
Catherine Sugar [ctb],
Hans-Georg Mueller [ctb],
Jie Peng [ctb],
Chiou Jeng-Min [ctb],
Pai-Ling Li [ctb]
Maintainer: Christina Yassouridis <c_ya02@yahoo.de>
Diff between funcy versions 0.8.5 dated 2016-05-11 and 0.8.6 dated 2017-02-09
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 30 ++++++++++++------------------ R/classes.R | 2 +- R/distclust.R | 2 +- R/funPrinComp.R | 4 ++-- R/functions.R | 6 +++++- R/plot.R | 22 +++++++++++++++++----- R/plotFSCM.R | 2 +- R/xecute.R | 2 +- man/fpca.Rd | 9 +++++++-- man/funcit.Rd | 2 +- man/funcyCtrl-class.Rd | 6 ++++-- man/plotFuncy.Rd | 12 ++++++++++-- 14 files changed, 79 insertions(+), 54 deletions(-)
Title: Repeatability Estimation for Gaussian and Non-Gaussian Data
Description: R functions for estimating repeatability (intra-class
correlation) from gaussian, binary, proportion and count data.
Author: Holger Schielzeth <holger.schielzeth@uni-jena.de>,
Martin Stoffel <martin.adam.stoffel@gmail.com>,
Shinichi Nakagawa <s.nakagawa@unsw.edu.au>
Maintainer: Martin Stoffel <martin.adam.stoffel@gmail.com>
Diff between rptR versions 0.9.0 dated 2016-09-23 and 0.9.1 dated 2017-02-09
DESCRIPTION | 10 - MD5 | 54 ++++---- NEWS.md |only R/internals.R | 123 ++++++++++++++++-- R/plot.rpt.R | 4 R/print.rpt.R | 13 + R/rpt.R | 54 +++++++- R/rptBinary.R | 110 ++++++++++------ R/rptGaussian.R | 236 +++++++++++++++++++++++++----------- R/rptPoisson.R | 58 +++++--- R/rptProportion.R | 60 +++++---- README.md | 2 build/vignette.rds |binary inst/doc/rptR.R | 9 + inst/doc/rptR.Rmd | 84 ++++++++---- inst/doc/rptR.html | 177 +++++++++++++++++---------- man/bootstrap_nongaussian.Rd | 2 man/group_vars.Rd |only man/permut_nongaussian.Rd | 2 man/plot.rpt.Rd | 4 man/print.rpt.Rd | 9 + man/rpt.Rd | 56 +++++++- man/rptBinary.Rd | 19 ++ man/rptGaussian.Rd | 24 ++- man/rptPoisson.Rd | 19 ++ man/rptProportion.Rd | 19 ++ tests/testthat/test-rptBinary.R | 3 tests/testthat/test-rptProportion.R | 3 vignettes/rptR.Rmd | 84 ++++++++---- 29 files changed, 874 insertions(+), 364 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 3.2 dated 2017-02-03 and 3.3 dated 2017-02-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 9 +++++++++ configure | 18 ++++++++++++++++-- configure.ac | 4 +++- src/emf+.h | 8 ++++---- src/emf.h | 17 ++++++++++------- src/fontmetrics.h | 11 +++++++++-- 8 files changed, 62 insertions(+), 27 deletions(-)
Title: Verbose Assertions for Tabular Data (Data.frames and
Data.tables)
Description: Simple, flexible, assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, assertable is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, assertable includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.
Author: Grant Nguyen
Maintainer: Grant Nguyen <gngu@uw.edu>
Diff between assertable versions 0.2.0 dated 2017-01-27 and 0.2.1 dated 2017-02-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/assert_ids.R | 6 ++++-- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Creating Continuously Integrated Package Repositories from
Manifests
Description: Repository based tools for department and analysis level
reproducibility. 'GRANBase' allows creation of custom branched, continuous
integration-ready R repositories, including incremental testing of only packages
which have changed versions since the last repository build.
Author: Gabriel Becker[aut,cre], Cory Barr [cre,ctb]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between GRANBase versions 1.2.0 dated 2016-10-24 and 1.2.1 dated 2017-02-09
DESCRIPTION | 6 +- MD5 | 16 +++--- NEWS | 5 + R/GRANonGRAN.R | 4 - R/Utilities.R | 9 +-- R/buildBranchesInRepo.R | 15 ----- R/makeGRANRepos.R | 114 +++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/GRAN-Overview.pdf |binary 9 files changed, 83 insertions(+), 86 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. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <doi:10.1198/106186008X319331> and
Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.
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 1.2-0 dated 2017-02-06 and 1.2-1 dated 2017-02-09
DESCRIPTION | 13 ++++++++----- MD5 | 26 +++++++++++++------------- inst/NEWS | 14 ++++++++++++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary src/IndependenceTest.c | 4 ++-- src/Node.c | 6 +++--- src/Predict.c | 12 ++++++++---- src/RandomForest.c | 2 +- src/Splits.c | 25 +++++++++++++++++++------ src/Splits.h | 2 +- src/SurrogateSplits.c | 9 +++++---- src/Utils.c | 9 ++++----- src/Utils.h | 2 +- 14 files changed, 79 insertions(+), 45 deletions(-)
Title: Genomic Data Retrieval
Description: Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' (Yates et al. (2016) <doi:10.1093/nar/gkv1157>) databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between biomartr versions 0.2.1 dated 2016-12-15 and 0.3.0 dated 2017-02-09
DESCRIPTION | 13 +-- MD5 | 109 ++++++++++++++--------------- NEWS.md | 9 ++ R/getENSEMBL.Seq.R | 5 + R/getENSEMBLGENOMES.Seq.R | 10 ++ R/getKingdomAssemblySummary.R | 5 + R/getMetaGenomeSummary.R | 5 + R/getSummaryFile.R | 5 + README.md | 42 +++++++---- inst/CITATION |only inst/doc/Database_Retrieval.html | 4 - inst/doc/Evolutionary_Transcriptomics.html | 4 - inst/doc/Functional_Annotation.html | 4 - inst/doc/Introduction.html | 4 - inst/doc/MetaGenome_Retrieval.html | 4 - inst/doc/Sequence_Retrieval.R | 6 + inst/doc/Sequence_Retrieval.Rmd | 11 ++ inst/doc/Sequence_Retrieval.html | 12 ++- man/biomart.Rd | 7 - man/download.database.Rd | 7 - man/download.database.all.Rd | 7 - man/getAttributes.Rd | 7 - man/getCDS.Rd | 7 - man/getDatasets.Rd | 7 - man/getFilters.Rd | 7 - man/getGFF.Rd | 7 - man/getGO.Rd | 7 - man/getGenome.Rd | 7 - man/getGroups.Rd | 7 - man/getKingdomAssemblySummary.Rd | 7 - man/getKingdoms.Rd | 7 - man/getMarts.Rd | 7 - man/getMetaGenomeAnnotations.Rd | 7 - man/getMetaGenomeSummary.Rd | 7 - man/getMetaGenomes.Rd | 7 - man/getProteome.Rd | 7 - man/getSubgroups.Rd | 7 - man/getSummaryFile.Rd | 7 - man/is.genome.available.Rd | 1 man/listDatabases.Rd | 7 - man/listGenomes.Rd | 1 man/listGroups.Rd | 7 - man/listKingdoms.Rd | 7 - man/listMetaGenomes.Rd | 7 - man/listSubgroups.Rd | 7 - man/meta.retrieval.Rd | 1 man/meta.retrieval.all.Rd | 1 man/organismAttributes.Rd | 7 - man/organismBM.Rd | 7 - man/organismFilters.Rd | 7 - man/read_cds.Rd | 7 - man/read_genome.Rd | 7 - man/read_gff.Rd | 7 - man/read_proteome.Rd | 7 - man/refseqOrganisms.Rd | 1 vignettes/Sequence_Retrieval.Rmd | 11 ++ 56 files changed, 265 insertions(+), 227 deletions(-)
Title: Geographic Information System Application
Description: A geographic information system (GIS) graphical user interface (GUI) that
provides data viewing, management, and analysis tools.
Author: Jason C. Fisher [aut, cre]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between RSurvey versions 0.8-3 dated 2015-02-20 and 0.9.0 dated 2017-02-09
RSurvey-0.8-3/RSurvey/NEWS |only RSurvey-0.8-3/RSurvey/R/AddAxis.R |only RSurvey-0.8-3/RSurvey/R/Autocrop.R |only RSurvey-0.8-3/RSurvey/R/AutocropRegion.R |only RSurvey-0.8-3/RSurvey/R/BuildPackage.R |only RSurvey-0.8-3/RSurvey/R/CutoutPolygon.R |only RSurvey-0.8-3/RSurvey/R/ImportPackage.R |only RSurvey-0.8-3/RSurvey/R/LoadPackages.R |only RSurvey-0.8-3/RSurvey/R/OpenRSurvey.R |only RSurvey-0.8-3/RSurvey/R/POSIXct2Character.R |only RSurvey-0.8-3/RSurvey/R/Plot2d.R |only RSurvey-0.8-3/RSurvey/R/ProcessData.R |only RSurvey-0.8-3/RSurvey/R/SetInterpolation.R |only RSurvey-0.8-3/RSurvey/data |only RSurvey-0.8-3/RSurvey/inst/extdata/ex.polygon.1.ply |only RSurvey-0.8-3/RSurvey/inst/extdata/ex.polygon.2.ply |only RSurvey-0.8-3/RSurvey/man/AddAxis.Rd |only RSurvey-0.8-3/RSurvey/man/Autocrop.Rd |only RSurvey-0.8-3/RSurvey/man/AutocropRegion.Rd |only RSurvey-0.8-3/RSurvey/man/BuildPackage.Rd |only RSurvey-0.8-3/RSurvey/man/CutoutPolygon.Rd |only RSurvey-0.8-3/RSurvey/man/ImportPackage.Rd |only RSurvey-0.8-3/RSurvey/man/LoadPackages.Rd |only RSurvey-0.8-3/RSurvey/man/OpenRSurvey.Rd |only RSurvey-0.8-3/RSurvey/man/POSIXct2Character.Rd |only RSurvey-0.8-3/RSurvey/man/Plot2d.Rd |only RSurvey-0.8-3/RSurvey/man/ProcessData.Rd |only RSurvey-0.8-3/RSurvey/man/RSurvey-package.Rd |only RSurvey-0.8-3/RSurvey/man/SetInterpolation.Rd |only RSurvey-0.8-3/RSurvey/man/ex.data.Rd |only RSurvey-0.8-3/RSurvey/man/ex.project.Rd |only RSurvey-0.9.0/RSurvey/DESCRIPTION | 35 RSurvey-0.9.0/RSurvey/LICENSE.note |only RSurvey-0.9.0/RSurvey/MD5 | 171 +-- RSurvey-0.9.0/RSurvey/NAMESPACE | 80 - RSurvey-0.9.0/RSurvey/NEWS.md |only RSurvey-0.9.0/RSurvey/R/BuildHistogram.R | 388 ++++---- RSurvey-0.9.0/RSurvey/R/CheckEntry.R | 25 RSurvey-0.9.0/RSurvey/R/ChooseColor.R | 391 ++++---- RSurvey-0.9.0/RSurvey/R/ChoosePch.R | 183 ++- RSurvey-0.9.0/RSurvey/R/Data.R | 161 ++- RSurvey-0.9.0/RSurvey/R/DefineGrid.R |only RSurvey-0.9.0/RSurvey/R/EditData.R | 929 +++++++++----------- RSurvey-0.9.0/RSurvey/R/EditFunction.R | 673 +++++++------- RSurvey-0.9.0/RSurvey/R/EditText.R | 268 ++--- RSurvey-0.9.0/RSurvey/R/EvalFunction.R | 33 RSurvey-0.9.0/RSurvey/R/ExportData.R | 621 ++++++------- RSurvey-0.9.0/RSurvey/R/Format.R | 457 ++++----- RSurvey-0.9.0/RSurvey/R/FormatDateTime.R | 444 ++++----- RSurvey-0.9.0/RSurvey/R/GetBitmapImage.R | 53 + RSurvey-0.9.0/RSurvey/R/GetFile.R | 167 ++- RSurvey-0.9.0/RSurvey/R/ImportDataset.R |only RSurvey-0.9.0/RSurvey/R/ImportSpreadsheet.R | 466 +++++----- RSurvey-0.9.0/RSurvey/R/ImportText.R | 749 +++++++--------- RSurvey-0.9.0/RSurvey/R/LaunchGui.R |only RSurvey-0.9.0/RSurvey/R/ManagePackages.R |only RSurvey-0.9.0/RSurvey/R/ManagePolygons.R | 769 ++++++++-------- RSurvey-0.9.0/RSurvey/R/ManageVariables.R | 634 ++++++------- RSurvey-0.9.0/RSurvey/R/Plot3d.R | 312 +++--- RSurvey-0.9.0/RSurvey/R/ProgressBar.R | 108 +- RSurvey-0.9.0/RSurvey/R/Rename.R | 140 +-- RSurvey-0.9.0/RSurvey/R/RestoreSession.R | 45 RSurvey-0.9.0/RSurvey/R/Search.R | 210 ++-- RSurvey-0.9.0/RSurvey/R/SetAxesLimits.R | 338 +++---- RSurvey-0.9.0/RSurvey/R/SetConfiguration.R | 462 +++++---- RSurvey-0.9.0/RSurvey/R/SetCrs.R |only RSurvey-0.9.0/RSurvey/R/SetPlotAnnotation.R |only RSurvey-0.9.0/RSurvey/R/SetPolygonLimits.R | 145 +-- RSurvey-0.9.0/RSurvey/R/SetSortOrder.R | 174 ++- RSurvey-0.9.0/RSurvey/R/zzz.R | 30 RSurvey-0.9.0/RSurvey/README.md | 92 + RSurvey-0.9.0/RSurvey/inst/CITATION |only RSurvey-0.9.0/RSurvey/inst/extdata/ex.data.csv | 4 RSurvey-0.9.0/RSurvey/inst/extdata/ex.polygon.1.txt |only RSurvey-0.9.0/RSurvey/inst/extdata/ex.polygon.2.txt |only RSurvey-0.9.0/RSurvey/inst/images/README.md | 13 RSurvey-0.9.0/RSurvey/inst/images/rlogo.gif |binary RSurvey-0.9.0/RSurvey/man/BuildHistogram.Rd | 61 - RSurvey-0.9.0/RSurvey/man/CheckEntry.Rd | 39 RSurvey-0.9.0/RSurvey/man/ChooseColor.Rd | 44 RSurvey-0.9.0/RSurvey/man/ChoosePch.Rd | 46 RSurvey-0.9.0/RSurvey/man/Data.Rd | 92 + RSurvey-0.9.0/RSurvey/man/DefineGrid.Rd |only RSurvey-0.9.0/RSurvey/man/EditData.Rd | 135 +- RSurvey-0.9.0/RSurvey/man/EditFunction.Rd | 94 +- RSurvey-0.9.0/RSurvey/man/EditText.Rd | 65 - RSurvey-0.9.0/RSurvey/man/EvalFunction.Rd | 49 - RSurvey-0.9.0/RSurvey/man/ExportData.Rd | 105 +- RSurvey-0.9.0/RSurvey/man/Format.Rd | 58 - RSurvey-0.9.0/RSurvey/man/FormatDateTime.Rd | 55 - RSurvey-0.9.0/RSurvey/man/GetBitmapImage.Rd | 92 + RSurvey-0.9.0/RSurvey/man/GetFile.Rd | 86 + RSurvey-0.9.0/RSurvey/man/ImportDataset.Rd |only RSurvey-0.9.0/RSurvey/man/ImportSpreadsheet.Rd | 49 - RSurvey-0.9.0/RSurvey/man/ImportText.Rd | 133 +- RSurvey-0.9.0/RSurvey/man/LaunchGui.Rd |only RSurvey-0.9.0/RSurvey/man/ManagePackages.Rd |only RSurvey-0.9.0/RSurvey/man/ManagePolygons.Rd | 94 +- RSurvey-0.9.0/RSurvey/man/ManageVariables.Rd | 101 +- RSurvey-0.9.0/RSurvey/man/Plot3d.Rd | 115 +- RSurvey-0.9.0/RSurvey/man/ProgressBar.Rd | 116 +- RSurvey-0.9.0/RSurvey/man/Rename.Rd | 48 - RSurvey-0.9.0/RSurvey/man/RestoreSession.Rd | 52 - RSurvey-0.9.0/RSurvey/man/Search.Rd | 64 - RSurvey-0.9.0/RSurvey/man/SetAxesLimits.Rd | 63 - RSurvey-0.9.0/RSurvey/man/SetConfiguration.Rd | 97 -- RSurvey-0.9.0/RSurvey/man/SetCrs.Rd |only RSurvey-0.9.0/RSurvey/man/SetPlotAnnotation.Rd |only RSurvey-0.9.0/RSurvey/man/SetPolygonLimits.Rd | 49 - RSurvey-0.9.0/RSurvey/man/SetSortOrder.Rd | 67 - 110 files changed, 6122 insertions(+), 5717 deletions(-)
Title: Text Generation from Data
Description: Linguistic Descriptions of Complex Phenomena (LDCP) is an architecture and methodology that allows us to model complex phenomena, interpreting input data, and generating automatic text reports customized to the user needs (see <doi:10.1016/j.ins.2016.11.002> and <doi:10.1007/s00500-016-2430-5>). The proposed package contains a set of methods that facilitates the development of LDCP systems. It main goal is increasing the visibility and practical use of this research line.
Author: Patricia Conde-Clemente [aut, cre], Jose M. Alonso [aut], Gracian Trivino [aut]
Maintainer: Patricia Conde-Clemente <patricia.condeclemente@gmail.com>
Diff between rLDCP versions 1.0.0 dated 2016-12-23 and 1.0.1 dated 2017-02-09
DESCRIPTION | 8 +- MD5 | 9 +- NEWS.md | 1 inst/CITATION | 129 +++++++++++++++++------------------ inst/extdata/comfortableroomdata.csv |only inst/ldcpSchema.xsd | 4 - 6 files changed, 76 insertions(+), 75 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from <http://www.bnlearn.com>.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 4.0 dated 2016-05-16 and 4.1 dated 2017-02-09
bnlearn-4.0/bnlearn/src/contincency.tables.c |only bnlearn-4.1/bnlearn/Changelog | 30 + bnlearn-4.1/bnlearn/DESCRIPTION | 10 bnlearn-4.1/bnlearn/MD5 | 240 +++++------ bnlearn-4.1/bnlearn/NAMESPACE | 5 bnlearn-4.1/bnlearn/R/arc.strength.R | 2 bnlearn-4.1/bnlearn/R/backend-indep.R | 2 bnlearn-4.1/bnlearn/R/choose.direction.R | 11 bnlearn-4.1/bnlearn/R/custom.fit.R | 11 bnlearn-4.1/bnlearn/R/cv.R | 12 bnlearn-4.1/bnlearn/R/fast-iamb.R | 4 bnlearn-4.1/bnlearn/R/fast.lm.R |only bnlearn-4.1/bnlearn/R/fit.R | 180 +++----- bnlearn-4.1/bnlearn/R/frontend-bn.R | 24 + bnlearn-4.1/bnlearn/R/frontend-bootstrap.R | 57 -- bnlearn-4.1/bnlearn/R/frontend-fit.R | 33 + bnlearn-4.1/bnlearn/R/frontend-graph.R | 5 bnlearn-4.1/bnlearn/R/frontend-nodes.R | 41 + bnlearn-4.1/bnlearn/R/frontend-plot.R | 2 bnlearn-4.1/bnlearn/R/frontend-predict.R | 35 + bnlearn-4.1/bnlearn/R/frontend-print.R | 8 bnlearn-4.1/bnlearn/R/frontend-score.R | 21 bnlearn-4.1/bnlearn/R/frontend-simulation.R | 24 - bnlearn-4.1/bnlearn/R/globals.R | 31 + bnlearn-4.1/bnlearn/R/graphviz.R | 2 bnlearn-4.1/bnlearn/R/grow-shrink.R | 4 bnlearn-4.1/bnlearn/R/hill-climbing.R | 7 bnlearn-4.1/bnlearn/R/hiton-pc.R | 4 bnlearn-4.1/bnlearn/R/impute.R |only bnlearn-4.1/bnlearn/R/incremental-association.R | 4 bnlearn-4.1/bnlearn/R/inter-iamb.R | 4 bnlearn-4.1/bnlearn/R/lattice.R | 2 bnlearn-4.1/bnlearn/R/learning-algorithms.R | 4 bnlearn-4.1/bnlearn/R/maxmin-pc.R | 4 bnlearn-4.1/bnlearn/R/scores.R | 14 bnlearn-4.1/bnlearn/R/simulation.R | 6 bnlearn-4.1/bnlearn/R/tabu.R | 12 bnlearn-4.1/bnlearn/R/utils-cluster.R | 9 bnlearn-4.1/bnlearn/R/utils-graph.R | 70 +++ bnlearn-4.1/bnlearn/R/utils-misc.R | 95 ++-- bnlearn-4.1/bnlearn/R/utils-sanitization.R | 487 +++++++++++++++++------ bnlearn-4.1/bnlearn/man/alarm.Rd | 3 bnlearn-4.1/bnlearn/man/arc.strength.Rd | 4 bnlearn-4.1/bnlearn/man/bn.class.Rd | 22 - bnlearn-4.1/bnlearn/man/bn.cv.Rd | 49 +- bnlearn-4.1/bnlearn/man/bn.fit.Rd | 9 bnlearn-4.1/bnlearn/man/bn.fit.methods.Rd | 51 -- bnlearn-4.1/bnlearn/man/bn.kcv.class.Rd | 3 bnlearn-4.1/bnlearn/man/bnboot.Rd | 3 bnlearn-4.1/bnlearn/man/bnlearn-package.Rd | 10 bnlearn-4.1/bnlearn/man/choose.direction.Rd | 4 bnlearn-4.1/bnlearn/man/clgaussian-test.Rd | 2 bnlearn-4.1/bnlearn/man/cpdag.Rd | 2 bnlearn-4.1/bnlearn/man/foreign.Rd | 12 bnlearn-4.1/bnlearn/man/graph.Rd | 2 bnlearn-4.1/bnlearn/man/graphgen.Rd | 4 bnlearn-4.1/bnlearn/man/graphviz.plot.Rd | 7 bnlearn-4.1/bnlearn/man/hailfinder.Rd | 3 bnlearn-4.1/bnlearn/man/impute.Rd |only bnlearn-4.1/bnlearn/man/insurance.Rd | 3 bnlearn-4.1/bnlearn/man/mb.Rd | 9 bnlearn-4.1/bnlearn/man/parallel.Rd | 4 bnlearn-4.1/bnlearn/man/plot.bn.Rd | 5 bnlearn-4.1/bnlearn/man/plot.bn.strength.Rd | 5 bnlearn-4.1/bnlearn/man/rbn.Rd | 2 bnlearn-4.1/bnlearn/man/score.Rd | 15 bnlearn-4.1/bnlearn/man/strength.plot.Rd | 10 bnlearn-4.1/bnlearn/src/acyclic.c | 64 +-- bnlearn-4.1/bnlearn/src/allsubs.test.c | 2 bnlearn-4.1/bnlearn/src/arcs2amat.c | 22 - bnlearn-4.1/bnlearn/src/averaging.c | 48 +- bnlearn-4.1/bnlearn/src/bayesian.network.c | 2 bnlearn-4.1/bnlearn/src/bootstrap.c | 18 bnlearn-4.1/bnlearn/src/cache.structure.c | 26 - bnlearn-4.1/bnlearn/src/cg.assumptions.c | 10 bnlearn-4.1/bnlearn/src/cg.loglikelihood.c | 93 +--- bnlearn-4.1/bnlearn/src/cg.mutual.information.c | 5 bnlearn-4.1/bnlearn/src/common.c | 140 ++++-- bnlearn-4.1/bnlearn/src/configurations.c | 22 - bnlearn-4.1/bnlearn/src/contingency.tables.c |only bnlearn-4.1/bnlearn/src/covariance.c | 193 +++++++-- bnlearn-4.1/bnlearn/src/cpdag.c | 283 +++++++------ bnlearn-4.1/bnlearn/src/ctest.c | 50 +- bnlearn-4.1/bnlearn/src/data.frame.c | 41 + bnlearn-4.1/bnlearn/src/dedup.c | 30 - bnlearn-4.1/bnlearn/src/dirichlet.posterior.c | 2 bnlearn-4.1/bnlearn/src/discrete.monte.carlo.c | 10 bnlearn-4.1/bnlearn/src/discrete.tests.c | 12 bnlearn-4.1/bnlearn/src/enums.c | 48 ++ bnlearn-4.1/bnlearn/src/fast.lm.c |only bnlearn-4.1/bnlearn/src/filter.arcs.c | 30 - bnlearn-4.1/bnlearn/src/fitted.c | 4 bnlearn-4.1/bnlearn/src/gaussian.loglikelihood.c | 35 - bnlearn-4.1/bnlearn/src/gaussian.monte.carlo.c | 48 +- bnlearn-4.1/bnlearn/src/graph.generation.c | 2 bnlearn-4.1/bnlearn/src/graph.priors.c | 134 +++++- bnlearn-4.1/bnlearn/src/hc.cache.lookup.c | 2 bnlearn-4.1/bnlearn/src/include/blas.h | 24 - bnlearn-4.1/bnlearn/src/include/bn.h | 2 bnlearn-4.1/bnlearn/src/include/covariance.h | 30 - bnlearn-4.1/bnlearn/src/include/fitted.h |only bnlearn-4.1/bnlearn/src/include/matrix.h | 2 bnlearn-4.1/bnlearn/src/include/rcore.h | 1 bnlearn-4.1/bnlearn/src/include/scores.h | 34 + bnlearn-4.1/bnlearn/src/include/sets.h | 2 bnlearn-4.1/bnlearn/src/include/tests.h | 10 bnlearn-4.1/bnlearn/src/is.dag.c | 8 bnlearn-4.1/bnlearn/src/is.row.equal.c | 14 bnlearn-4.1/bnlearn/src/least.squares.c |only bnlearn-4.1/bnlearn/src/linear.algebra.c | 187 ++++++-- bnlearn-4.1/bnlearn/src/linear.correlation.c | 14 bnlearn-4.1/bnlearn/src/loss.c | 75 +-- bnlearn-4.1/bnlearn/src/map.lw.c | 27 - bnlearn-4.1/bnlearn/src/mi.matrix.c | 102 ++-- bnlearn-4.1/bnlearn/src/path.c | 8 bnlearn-4.1/bnlearn/src/pdag2dag.c | 18 bnlearn-4.1/bnlearn/src/per.node.score.c | 219 +++++----- bnlearn-4.1/bnlearn/src/predict.c | 50 +- bnlearn-4.1/bnlearn/src/rbn.c | 91 ++-- bnlearn-4.1/bnlearn/src/roundrobin.test.c | 14 bnlearn-4.1/bnlearn/src/sanitization.c | 44 -- bnlearn-4.1/bnlearn/src/score.delta.c | 179 +++++--- bnlearn-4.1/bnlearn/src/shrinkage.c | 16 bnlearn-4.1/bnlearn/src/strings.c | 8 bnlearn-4.1/bnlearn/src/wishart.posterior.c | 102 ++-- 125 files changed, 2716 insertions(+), 1700 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science:
modeling of loss distributions; risk theory and ruin theory;
simulation of compound models, discrete mixtures and compound
hierarchical models; credibility theory. Support for many additional
probability distributions to model insurance loss amounts and loss
frequency: 19 continuous heavy tailed distributions; the
Poisson-inverse Gaussian discrete distribution; zero-truncated and
zero-modified extensions of the standard discrete distributions.
Support for phase-type distributions commonly used to compute ruin
probabilities.
Author: Vincent Goulet [cre, aut],
Sébastien Auclair [ctb],
Christophe Dutang [aut],
Xavier Milhaud [ctb],
Tommy Ouellet [ctb],
Louis-Philippe Pouliot [ctb],
Mathieu Pigeon [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 2.0-0 dated 2016-11-12 and 2.1-0 dated 2017-02-09
actuar-2.0-0/actuar/R/SpecialIntegrals.R |only actuar-2.0-0/actuar/man/SpecialIntegrals.Rd |only actuar-2.0-0/actuar/src/expint.c |only actuar-2.0-0/actuar/src/gammaint.c |only actuar-2.1-0/actuar/DESCRIPTION | 11 - actuar-2.1-0/actuar/MD5 | 94 ++++++------- actuar-2.1-0/actuar/NAMESPACE | 9 - actuar-2.1-0/actuar/R/betaint.R |only actuar-2.1-0/actuar/inst/NEWS.Rd | 29 +++- actuar-2.1-0/actuar/inst/doc/actuar.R | 4 actuar-2.1-0/actuar/inst/doc/actuar.Rnw | 16 +- actuar-2.1-0/actuar/inst/doc/actuar.pdf |binary actuar-2.1-0/actuar/inst/doc/coverage.R | 24 +-- actuar-2.1-0/actuar/inst/doc/coverage.Rnw | 1 actuar-2.1-0/actuar/inst/doc/coverage.pdf |binary actuar-2.1-0/actuar/inst/doc/credibility.R | 26 +-- actuar-2.1-0/actuar/inst/doc/credibility.Rnw | 3 actuar-2.1-0/actuar/inst/doc/credibility.pdf |binary actuar-2.1-0/actuar/inst/doc/distributions.Rnw | 142 +++++++++++---------- actuar-2.1-0/actuar/inst/doc/distributions.pdf |binary actuar-2.1-0/actuar/inst/doc/modeling.R | 74 +++++----- actuar-2.1-0/actuar/inst/doc/modeling.Rnw | 9 - actuar-2.1-0/actuar/inst/doc/modeling.pdf |binary actuar-2.1-0/actuar/inst/doc/risk.R | 50 +++---- actuar-2.1-0/actuar/inst/doc/risk.Rnw | 7 - actuar-2.1-0/actuar/inst/doc/risk.pdf |binary actuar-2.1-0/actuar/inst/doc/simulation.R | 36 ++--- actuar-2.1-0/actuar/inst/doc/simulation.Rnw | 15 +- actuar-2.1-0/actuar/inst/doc/simulation.pdf |binary actuar-2.1-0/actuar/man/InverseExponential.Rd | 2 actuar-2.1-0/actuar/man/InverseGamma.Rd | 2 actuar-2.1-0/actuar/man/InverseTransformedGamma.Rd | 2 actuar-2.1-0/actuar/man/InverseWeibull.Rd | 2 actuar-2.1-0/actuar/man/betaint.Rd |only actuar-2.1-0/actuar/src/actuar.h | 15 +- actuar-2.1-0/actuar/src/dpq.c | 64 --------- actuar-2.1-0/actuar/src/init.c | 9 + actuar-2.1-0/actuar/src/invexp.c | 2 actuar-2.1-0/actuar/src/invgamma.c | 2 actuar-2.1-0/actuar/src/invgauss.c | 47 +++--- actuar-2.1-0/actuar/src/invtrgamma.c | 2 actuar-2.1-0/actuar/src/invweibull.c | 2 actuar-2.1-0/actuar/src/names.c | 6 actuar-2.1-0/actuar/vignettes/actuar.Rnw | 16 +- actuar-2.1-0/actuar/vignettes/actuar.bib | 114 +++++++++------- actuar-2.1-0/actuar/vignettes/coverage.Rnw | 1 actuar-2.1-0/actuar/vignettes/credibility.Rnw | 3 actuar-2.1-0/actuar/vignettes/distributions.Rnw | 142 +++++++++++---------- actuar-2.1-0/actuar/vignettes/modeling.Rnw | 9 - actuar-2.1-0/actuar/vignettes/risk.Rnw | 7 - actuar-2.1-0/actuar/vignettes/simulation.Rnw | 15 +- 51 files changed, 502 insertions(+), 512 deletions(-)
Title: Probability of Sharing Rare Variants among Relatives
Description: Computes estimates of the probability of related individuals sharing a rare variant.
Author: Alexandre Bureau, Ingo Ruczinski, Samuel G. Younkin
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>
Diff between RVsharing versions 1.6.0 dated 2016-06-17 and 1.7.0 dated 2017-02-09
DESCRIPTION | 10 ++-- MD5 | 18 ++++--- NAMESPACE | 2 R/RVgene.R | 95 ++++++++++++++++++++++++++++++++------- R/RVgene_allshare.R |only R/functions.R | 1 man/GeneDropSim.allsubsets.fn.Rd | 4 - man/RVgene.Rd | 6 +- man/RVgene_allshare.Rd |only man/RVsharing.Rd | 6 +- man/RVsharingProb.rd | 7 +- 11 files changed, 108 insertions(+), 41 deletions(-)
Title: Heart Rate Variability Analysis of ECG Data
Description: Allows users to import data files containing heartbeat positions in the most broadly used formats, to remove outliers or points with unacceptable physiological values present in the time series, to plot HRV data, and to perform time domain, frequency domain and nonlinear HRV analysis.
Author: Leandro Rodriguez-Linares [aut, cre],
Xose Vila [aut],
Maria Jose Lado [aut],
Arturo Mendez [aut],
Abraham Otero [aut],
Constantino Antonio Garcia [aut],
Matti Lassila [ctb]
Maintainer: Leandro Rodriguez-Linares <leandro@uvigo.es>
Diff between RHRV versions 4.2.2 dated 2016-11-15 and 4.2.3 dated 2017-02-09
RHRV-4.2.2/RHRV/inst/doc/RHRV-quickstart.R |only RHRV-4.2.2/RHRV/inst/doc/RHRV-quickstart.Rnw |only RHRV-4.2.2/RHRV/inst/doc/RHRV-quickstart.pdf |only RHRV-4.2.2/RHRV/vignettes/Makefile |only RHRV-4.2.2/RHRV/vignettes/RHRV-quickstart.Rnw |only RHRV-4.2.2/RHRV/vignettes/figures/quickstart-concordance.tex |only RHRV-4.2.2/RHRV/vignettes/figures/quickstart-plottingFreqFourier.pdf |only RHRV-4.2.2/RHRV/vignettes/figures/quickstart-plottingFreqWavelet.pdf |only RHRV-4.2.2/RHRV/vignettes/figures/quickstart-plottingHR.pdf |only RHRV-4.2.2/RHRV/vignettes/figures/quickstart-plottingNIHR.pdf |only RHRV-4.2.3/RHRV/DESCRIPTION | 16 +++---- RHRV-4.2.3/RHRV/MD5 | 22 +++------- RHRV-4.2.3/RHRV/build/vignette.rds |binary RHRV-4.2.3/RHRV/inst/doc/RHRV-quickstart.Rmd |only RHRV-4.2.3/RHRV/inst/doc/RHRV-quickstart.html |only RHRV-4.2.3/RHRV/man/RHRV-package.Rd | 4 - RHRV-4.2.3/RHRV/vignettes/RHRV-quickstart.Rmd |only RHRV-4.2.3/RHRV/vignettes/figures/basicHRVData.pdf |binary RHRV-4.2.3/RHRV/vignettes/figures/basicHRVData.png |only 19 files changed, 18 insertions(+), 24 deletions(-)
Title: A Shiny GUI for some Parameter Estimation Examples
Description: Allows specification and fitting of some parameter
estimation examples inspired by time-resolved spectroscopy via
a Shiny GUI.
Author: Joris Snellenburg [cre, aut],
Katharine Mullen [aut],
Ivo van Stokkum [aut]
Maintainer: Joris Snellenburg <j.snellenburg@vu.nl>
Diff between paramGUI versions 2.1 dated 2017-02-06 and 2.1.1 dated 2017-02-09
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: A Flexible and Robust Sys.sleep() Replacement
Description: Provides a near drop-in replacement for base::Sys.sleep() that allows more types of input
to produce delays in the execution of code and can silence/prevent typical sources of error.
Author: Russell S. Pierce [aut, cre],
Timothy Gann [aut]
Maintainer: Russell S. Pierce <russell.s.pierce@gmail.com>
Diff between naptime versions 1.2.0 dated 2016-12-01 and 1.2.2 dated 2017-02-09
ChangeLog | 4 ++++ DESCRIPTION | 16 ++++++++-------- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/naptime.R | 12 +++--------- README.md | 18 ++++++++++++++++-- inst/doc/naptime.Rmd | 2 +- inst/doc/naptime.html | 6 +++--- man/naptime.Rd | 2 +- vignettes/naptime.Rmd | 2 +- 11 files changed, 52 insertions(+), 35 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical work-flow--procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and re-weighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine. Choirat [aut],
Christopher Gandrud [aut, cre],
James Honaker [aut],
Kosuke Imai [aut],
Gary King [aut],
Olivia Lau [aut]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>
Diff between Zelig versions 5.0-14 dated 2017-01-31 and 5.0-15 dated 2017-02-09
Zelig-5.0-14/Zelig/NEWS |only Zelig-5.0-15/Zelig/DESCRIPTION | 16 - Zelig-5.0-15/Zelig/MD5 | 104 ++++---- Zelig-5.0-15/Zelig/NAMESPACE | 2 Zelig-5.0-15/Zelig/NEWS.md |only Zelig-5.0-15/Zelig/R/assertions.R | 17 + Zelig-5.0-15/Zelig/R/create-json.R | 13 - Zelig-5.0-15/Zelig/R/model-exp.R | 14 - Zelig-5.0-15/Zelig/R/model-gamma-survey.R | 5 Zelig-5.0-15/Zelig/R/model-gamma.R | 18 - Zelig-5.0-15/Zelig/R/model-gee.R | 10 Zelig-5.0-15/Zelig/R/model-lognorm.R | 14 - Zelig-5.0-15/Zelig/R/model-oprobit-bayes.R | 8 Zelig-5.0-15/Zelig/R/model-quantile.R | 11 Zelig-5.0-15/Zelig/R/model-relogit.R | 19 + Zelig-5.0-15/Zelig/R/model-survey.R | 103 ++++---- Zelig-5.0-15/Zelig/R/model-timeseries.R | 13 - Zelig-5.0-15/Zelig/R/model-weibull.R | 30 +- Zelig-5.0-15/Zelig/R/model-zelig.R | 112 ++++++-- Zelig-5.0-15/Zelig/R/plots.R | 6 Zelig-5.0-15/Zelig/R/utils.R | 89 +++++-- Zelig-5.0-15/Zelig/R/wrappers.R | 28 ++ Zelig-5.0-15/Zelig/man/Zelig-class.Rd | 6 Zelig-5.0-15/Zelig/man/Zelig-timeseries-class.Rd | 2 Zelig-5.0-15/Zelig/man/createJSON.Rd | 7 Zelig-5.0-15/Zelig/man/factorize.Rd |only Zelig-5.0-15/Zelig/man/from_zelig_model.Rd |only Zelig-5.0-15/Zelig/man/is_timeseries.Rd |only Zelig-5.0-15/Zelig/man/reduce.Rd | 2 Zelig-5.0-15/Zelig/man/strip_package_name.Rd |only Zelig-5.0-15/Zelig/tests/testthat.R | 1 Zelig-5.0-15/Zelig/tests/testthat/test-arima.R | 69 +++++ Zelig-5.0-15/Zelig/tests/testthat/test-assertions.R | 7 Zelig-5.0-15/Zelig/tests/testthat/test-bayesdiagnostics.R |only Zelig-5.0-15/Zelig/tests/testthat/test-createJSON.R |only Zelig-5.0-15/Zelig/tests/testthat/test-exp.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-gamma.R |only Zelig-5.0-15/Zelig/tests/testthat/test-gammasurvey.R |only Zelig-5.0-15/Zelig/tests/testthat/test-logitbayes.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-logitsurvey.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-lognom.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-ls.R | 36 ++ Zelig-5.0-15/Zelig/tests/testthat/test-negbin.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-normal.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-normalsurvey.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-plots.R | 14 + Zelig-5.0-15/Zelig/tests/testthat/test-poisson.R | 18 + Zelig-5.0-15/Zelig/tests/testthat/test-poissonbayes.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-poissonsurvey.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-probit.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-probitbayes.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-probitsurvey.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-relogit.R |only Zelig-5.0-15/Zelig/tests/testthat/test-survey.R |only Zelig-5.0-15/Zelig/tests/testthat/test-tobit.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-tobitbayes.R | 4 Zelig-5.0-15/Zelig/tests/testthat/test-weibull.R |only Zelig-5.0-15/Zelig/tests/testthat/test-weights.R |only Zelig-5.0-15/Zelig/tests/testthat/test-wrappers.R | 7 Zelig-5.0-15/Zelig/tests/testthat/test-zelig.R | 177 ++++++++++++++ 60 files changed, 780 insertions(+), 254 deletions(-)
Title: Meta-Analysis of Region-Based Tests of Rare DNA Variants
Description: Computes necessary information to meta analyze region-based
tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and
performs meta analysis.
Author: Arie Voorman, Jennifer Brody, Han Chen, Thomas Lumley, Brian Davis
Maintainer: Brian Davis <Brian.Davis281@gmail.com>
Diff between seqMeta versions 1.6.6 dated 2016-09-26 and 1.6.7 dated 2017-02-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/pchisqsum2.R | 8 ++++---- README.md | 9 +++++++-- 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.2.0 dated 2016-12-24 and 0.2.1 dated 2017-02-09
ChangeLog | 43 +++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 15 ++++++++------- MD5 | 24 ++++++++++++------------ R/anytime.R | 18 +++++++++++++++--- R/init.R | 13 ++++--------- build/partial.rdb |binary inst/NEWS.Rd | 21 ++++++++++++++++++--- man/anytime.Rd | 12 ++++++------ man/getFormats.Rd | 9 ++++----- man/iso8601.Rd | 8 ++++---- src/anytime.cpp | 41 +++++++++++++++++++++-------------------- tests/allFormats.R | 2 ++ tests/simpleTests.R | 6 ++++++ 13 files changed, 143 insertions(+), 69 deletions(-)
Title: Evaluate Treatment Selection Biomarkers
Description: A suite of descriptive and inferential methods designed to evaluate one or more biomarkers for their ability to guide patient treatment recommendations. Package includes functions to assess the calibration of risk models; and plot, evaluate, and compare markers.
Author: Marshall Brown and Holly Janes
Maintainer: Marshall Brown <mdbrown@fhcrc.org>
Diff between TreatmentSelection versions 1.2.0 dated 2016-01-15 and 2.0.3 dated 2017-02-09
TreatmentSelection-1.2.0/TreatmentSelection/R/CDFdeltaPLOT_gg.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/CDFdeltaPLOT_gg_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/Theta.cutoff.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/boot.sample.case.control.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/boot.sample.cohort.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/boot.sample.stratified.case.control.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/cover.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/eval.trtsel.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/expit.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.F.case.control.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.F.cohort.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.F.stratified.case.control.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.plot.ci_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.risk.t0.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.risk.t1.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.case.control.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.cohort.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/get.summary.measures.stratified.case.control.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/logit.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/logit.one.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/myplotcompare.trtsel_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/one.boot.plot.compare.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/one.boot.plot_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/predcurvePLOT_gg.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/predcurvePLOT_gg_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/print.calibrate.trtsel.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/print.compare.trtsel.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/print.eval.trtsel.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/shade.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/shade_gg.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/sum.I.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/test.Null.warning.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOT_gg.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOT_gg_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOTcompare_gg.R |only TreatmentSelection-1.2.0/TreatmentSelection/R/trteffectPLOTcompare_gg_disc.R |only TreatmentSelection-1.2.0/TreatmentSelection/man/eval.trtsel.Rd |only TreatmentSelection-1.2.0/TreatmentSelection/man/print.compare.trtsel.rd |only TreatmentSelection-2.0.3/TreatmentSelection/DESCRIPTION | 13 TreatmentSelection-2.0.3/TreatmentSelection/MD5 | 131 - TreatmentSelection-2.0.3/TreatmentSelection/NAMESPACE | 38 TreatmentSelection-2.0.3/TreatmentSelection/NEWS | 8 TreatmentSelection-2.0.3/TreatmentSelection/R/CDFdeltaPLOT.R | 243 ++- TreatmentSelection-2.0.3/TreatmentSelection/R/SelectionImpactPLOT_gg.R | 26 TreatmentSelection-2.0.3/TreatmentSelection/R/TreatmentSelection-package.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/boot.sample.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/calibrate.trtsel.R | 329 ++-- TreatmentSelection-2.0.3/TreatmentSelection/R/compare.trtsel.R | 343 +++- TreatmentSelection-2.0.3/TreatmentSelection/R/estimate_measures.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/evaluate.trtsel.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/get.F.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/get.coef.R | 26 TreatmentSelection-2.0.3/TreatmentSelection/R/get.plot.ci.R | 41 TreatmentSelection-2.0.3/TreatmentSelection/R/get.risk.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/get.summary.measures.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/is.trtsel.R | 10 TreatmentSelection-2.0.3/TreatmentSelection/R/myplotcompare.trtsel.R | 158 +- TreatmentSelection-2.0.3/TreatmentSelection/R/one.boot.compare.R | 185 ++ TreatmentSelection-2.0.3/TreatmentSelection/R/one.boot.eval.R | 111 + TreatmentSelection-2.0.3/TreatmentSelection/R/one.boot.plot.R | 243 +++ TreatmentSelection-2.0.3/TreatmentSelection/R/plot.trtsel.R | 153 +- TreatmentSelection-2.0.3/TreatmentSelection/R/predcurvePLOT.R | 223 ++- TreatmentSelection-2.0.3/TreatmentSelection/R/print.trtsel.R | 385 +++++ TreatmentSelection-2.0.3/TreatmentSelection/R/subroutines.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/test.Null.R | 63 TreatmentSelection-2.0.3/TreatmentSelection/R/timetoevent_subroutines.R |only TreatmentSelection-2.0.3/TreatmentSelection/R/trteffectPLOT.R | 475 +++++- TreatmentSelection-2.0.3/TreatmentSelection/R/trtsel.R | 345 +++- TreatmentSelection-2.0.3/TreatmentSelection/R/trtsel.boot.R | 86 - TreatmentSelection-2.0.3/TreatmentSelection/README.md | 11 TreatmentSelection-2.0.3/TreatmentSelection/data/surv_tsdata.rda |only TreatmentSelection-2.0.3/TreatmentSelection/inst/check.R |only TreatmentSelection-2.0.3/TreatmentSelection/inst/example/checkSubCohortEstimation.R | 15 TreatmentSelection-2.0.3/TreatmentSelection/inst/example/tutorial.Rmd | 318 ++-- TreatmentSelection-2.0.3/TreatmentSelection/inst/example/tutorial.html | 738 ++++++---- TreatmentSelection-2.0.3/TreatmentSelection/inst/example/tutorial_reference.html |only TreatmentSelection-2.0.3/TreatmentSelection/inst/todo.Rmd |only TreatmentSelection-2.0.3/TreatmentSelection/man/TreatmentSelection-package.Rd | 67 TreatmentSelection-2.0.3/TreatmentSelection/man/calibrate.trtsel.Rd | 152 +- TreatmentSelection-2.0.3/TreatmentSelection/man/compare.Rd |only TreatmentSelection-2.0.3/TreatmentSelection/man/compare.trtsel.Rd | 265 +-- TreatmentSelection-2.0.3/TreatmentSelection/man/evaluate.trtsel.Rd |only TreatmentSelection-2.0.3/TreatmentSelection/man/is.trtsel.Rd | 23 TreatmentSelection-2.0.3/TreatmentSelection/man/plot.trtsel.Rd | 217 +- TreatmentSelection-2.0.3/TreatmentSelection/man/print.calibrate.trtsel.Rd | 23 TreatmentSelection-2.0.3/TreatmentSelection/man/print.compare.trtsel.Rd |only TreatmentSelection-2.0.3/TreatmentSelection/man/print.eval.trtsel.Rd | 22 TreatmentSelection-2.0.3/TreatmentSelection/man/print.trtsel.Rd | 23 TreatmentSelection-2.0.3/TreatmentSelection/man/print.trtsel_summary_measures.Rd |only TreatmentSelection-2.0.3/TreatmentSelection/man/surv_tsdata.Rd |only TreatmentSelection-2.0.3/TreatmentSelection/man/trtsel.Rd | 239 +-- TreatmentSelection-2.0.3/TreatmentSelection/man/trtsel_measures.Rd |only TreatmentSelection-2.0.3/TreatmentSelection/man/tsdata.Rd | 50 TreatmentSelection-2.0.3/TreatmentSelection/man/tsdata_cc.Rd | 50 TreatmentSelection-2.0.3/TreatmentSelection/man/tsdata_scc.Rd | 60 95 files changed, 4188 insertions(+), 1720 deletions(-)
More information about TreatmentSelection at CRAN
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Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <http://www.ncbi.nlm.nih.gov/pubmed>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.7 dated 2017-01-05 and 1.0.8 dated 2017-02-09
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/pubtator_function.R | 12 +++++++----- data/GeneToEntrez.rda |binary data/HGNC2UniprotID.rda |binary data/HGNCdata.rda |binary data/common_words_new.rda |binary 7 files changed, 18 insertions(+), 16 deletions(-)
Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly maximizing the log likelihood function. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>
Diff between ziphsmm versions 1.0.2 dated 2017-01-27 and 1.0.3 dated 2017-02-09
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- R/hsmmsim2.R | 48 +++++++++++++++++++++++++++++++++++++------ R/package.R | 4 +-- man/hsmmsim2.Rd | 48 +++++++++++++++++++++++++++++++++++++------ man/package-ziphsmm.Rd | 4 +-- src/rcpparma_hello_world.cpp | 22 +++++++++++-------- 7 files changed, 111 insertions(+), 35 deletions(-)
Title: Multi-Locus Random-SNP-Effect Mixed Linear Model for Genome-Wide
Association Studies and Linkage Analyses
Description: Conduct multi-locus GWAS and multi-locus QTL mapping under the framework of random-SNP-effect mixed linear model (mrMLM). First, each position (or marker) on the genome is scanned by mrMLM algorithm. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers (or QTL) that are potentially associated with the trait are included in a multi-locus model, their effects are estimated by empirical Bayes and true QTN or QTL are identified by likelihood ratio test.
Author: Wenlong Ren,Yuanli Ni,Shibo Wang,Yangjun Wen,Bo Huang and Yuanming Zhang
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between mrMLM versions 2.0 dated 2016-12-20 and 2.1 dated 2017-02-09
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 8 R/mrMLM.R | 3883 +++++++++++++++++++++---- inst/doc/Instruction.pdf |binary inst/extdata/GWAS_mrMLM_Character_Genotype.csv | 1158 +++---- man/mrMLM-package.Rd | 33 7 files changed, 4012 insertions(+), 1092 deletions(-)
Title: Query HaploReg and RegulomeDB
Description: A set of utilities for querying
HaploReg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>
and RegulomeDB <http://www.regulomedb.org> web-based tools. The package connects to
Haploreg or RegulomeDB, searches and downloads results, without
opening web pages, directly from R environment.
Results are stored in a data frame that can be directly used in various
kinds of downstream analyses.
Author: I. Y. Zhbannikov, K. G. Arbeev, A. I. Yashin
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between haploR versions 1.4.1 dated 2016-12-31 and 1.4.2 dated 2017-02-09
DESCRIPTION | 12 ++-- MD5 | 24 ++++----- R/haploreg.R | 35 +++++++------- R/haploregStudy.R | 6 +- R/regulome.R | 103 +++++++++++++++++++++++++----------------- README.md | 6 +- inst/NEWS | 2 inst/doc/haplor-vignette.Rmd | 12 ++-- inst/doc/haplor-vignette.html | 34 +++++++------ man/haploR-getStudyList.Rd | 6 +- man/haploR-queryHaploreg.Rd | 8 +-- man/haploR-queryRegulome.Rd | 15 ++++-- vignettes/haplor-vignette.Rmd | 12 ++-- 13 files changed, 155 insertions(+), 120 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.3.2 dated 2016-01-06 and 1.3.3 dated 2017-02-09
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- R/dunn.test.R | 11 ++++++----- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Conover-Iman Test of Multiple Comparisons Using Rank Sums
Description: Computes the Conover-Iman test (1979) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Conover-Iman test may be understood as a test for median difference. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
Author: Alexis Dinno <alexis.dinno@pdx.edu>
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between conover.test versions 1.1.1 dated 2016-01-06 and 1.1.2 dated 2017-02-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/conover.test.R | 11 ++++++----- 3 files changed, 12 insertions(+), 11 deletions(-)