Title: Evolutionary Transcriptomics Analyses
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes. The aim of this tool is to provide a transcriptome analysis environment for answering questions regarding the evolution of biological processes.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between myTAI versions 0.4.0 dated 2016-05-04 and 0.5.0 dated 2017-03-14
DESCRIPTION | 17 MD5 | 196 ++++----- NAMESPACE | 6 NEWS.md | 34 + R/EarlyConservationTest.R | 13 R/FlatLineTest.R | 12 R/GroupDiffs.R | 2 R/MatchMap.R | 23 - R/PlotBarRE.R | 2 R/PlotCategoryExpr.R | 4 R/PlotContribution.R | 136 +++--- R/PlotCorrelation.R | 92 +++- R/PlotMeans.R | 270 +++++++----- R/PlotMedians.R |only R/PlotPattern.R | 3 R/PlotRE.R | 266 +++++++----- R/PlotSelectedAgeDistr.R | 18 R/PlotSignature.R |only R/PlotVars.R |only R/RcppExports.R | 2 R/ReductiveHourglassTest.R | 21 R/TAI.R | 2 R/TPI.R |only R/custom.myTAI.cols.R |only README.md | 63 +- build/vignette.rds |binary inst/doc/Advanced.R | 245 ++++------- inst/doc/Advanced.Rmd | 107 ----- inst/doc/Advanced.html | 104 ---- inst/doc/Enrichment.Rmd | 11 inst/doc/Enrichment.html | 15 inst/doc/Expression.Rmd | 4 inst/doc/Expression.html | 15 inst/doc/Intermediate.R | 317 ++++++--------- inst/doc/Intermediate.Rmd | 133 +----- inst/doc/Intermediate.html | 165 +++---- inst/doc/Introduction.R | 398 ++++++++++++------ inst/doc/Introduction.Rmd | 695 +++++++++++++++++++++++---------- inst/doc/Introduction.html | 504 ++++++++++++++--------- inst/doc/Taxonomy.html | 11 man/CollapseReplicates.Rd | 1 man/CombinatorialSignificance.Rd | 7 man/DiffGenes.Rd | 7 man/DivergenceExpressionSetExample.Rd | 7 man/EarlyConservationTest.Rd | 9 man/EnrichmentTest.Rd | 7 man/Expressed.Rd | 1 man/FlatLineTest.Rd | 19 man/GroupDiffs.Rd | 9 man/MatchMap.Rd | 7 man/PhyloExpressionSetExample.Rd | 7 man/PlotBarRE.Rd | 9 man/PlotCategoryExpr.Rd | 7 man/PlotContribution.Rd | 25 - man/PlotCorrelation.Rd | 24 - man/PlotDistribution.Rd | 7 man/PlotEnrichment.Rd | 7 man/PlotGeneSet.Rd | 7 man/PlotGroupDiffs.Rd | 7 man/PlotMeans.Rd | 89 ++-- man/PlotMedians.Rd |only man/PlotPattern.Rd | 10 man/PlotRE.Rd | 83 +-- man/PlotReplicateQuality.Rd | 1 man/PlotSelectedAgeDistr.Rd | 7 man/PlotSignature.Rd |only man/PlotVars.Rd |only man/RE.Rd | 7 man/REMatrix.Rd | 7 man/ReductiveHourglassTest.Rd | 17 man/SelectGeneSet.Rd | 7 man/TAI.Rd | 7 man/TDI.Rd | 7 man/TPI.Rd |only man/age.apply.Rd | 7 man/bar.colors.Rd | 1 man/bootMatrix.Rd | 7 man/ecScore.Rd | 7 man/geom.mean.Rd | 1 man/harm.mean.Rd | 1 man/is.ExpressionSet.Rd | 1 man/omitMatrix.Rd | 1 man/pMatrix.Rd | 7 man/pStrata.Rd | 1 man/pTAI.Rd | 7 man/pTDI.Rd | 7 man/rhScore.Rd | 7 man/taxid.Rd | 1 man/taxonomy.Rd | 7 man/tf.Rd | 7 src/RcppExports.cpp | 96 ++-- src/rcpp_funcs.cpp | 22 - src/registerDynamicSymbol.c |only tests/testthat/test-MatchMap.R | 1 tests/testthat/test-PlotContribution.R | 11 tests/testthat/test-PlotMeans.R | 5 tests/testthat/test-PlotRE.R | 4 vignettes/Advanced.Rmd | 107 ----- vignettes/Enrichment.Rmd | 11 vignettes/Expression.Rmd | 4 vignettes/Figures |only vignettes/Intermediate.Rmd | 133 +----- vignettes/Introduction.Rmd | 695 +++++++++++++++++++++++---------- 103 files changed, 3004 insertions(+), 2477 deletions(-)
Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar
functionality to 'xtable', but does more, with a simpler interface.
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 0.1.0 dated 2017-03-12 and 0.1.1 dated 2017-03-14
DESCRIPTION | 10 MD5 | 18 NEWS.md | 5 R/screen.R | 16 inst/doc/design-principles.Rmd | 3 inst/doc/design-principles.html | 1262 ++++++++++++++++----------------- inst/doc/introduction-to-huxtable.html | 687 ++++++++--------- tests/testthat/functions.R | 4 tests/testthat/test-output.R | 9 vignettes/design-principles.Rmd | 3 10 files changed, 1015 insertions(+), 1002 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors in GLMs of Li and Clyde (2015)
<http://arxiv.org/abs/1503.06913>. Other model
selection criteria include AIC, BIC and Empirical Bayes estimates of g.
Sampling probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an efficient MCMC algorithm
samples models using the BAS tree structure as an efficient hash table.
Uniform priors over all models or beta-binomial prior distributions on
model size are allowed, and for large p truncated priors on the model
space may be used. The user may force variables to always be included.
Details behind the sampling algorithm are provided in
Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049>.
This material is based upon work supported by the National Science
Foundation under Grant DMS-1106891. Any opinions, findings, and
conclusions or recommendations expressed in this material are those of
the author(s) and do not necessarily reflect the views of the
National Science Foundation.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.4.3 dated 2017-02-21 and 1.4.4 dated 2017-03-14
DESCRIPTION | 6 - MD5 | 28 +++---- NEWS.md | 18 ++++- R/bas.R | 6 + R/bas.gglm.R | 5 + R/coefficients.R | 62 ++++++++++++----- R/confint.coef.R | 4 - R/plot.bma.R | 4 - R/predict.bma.R | 59 ++++++++++++---- inst/doc/BAS-vignette.R | 11 ++- inst/doc/BAS-vignette.Rmd | 51 ++++++++++---- inst/doc/BAS-vignette.html | 161 ++++++++++++++++++++++++--------------------- man/coefficients.bma.Rd | 26 ++++++- man/predict.bma.Rd | 18 +++-- vignettes/BAS-vignette.Rmd | 51 ++++++++++---- 15 files changed, 341 insertions(+), 169 deletions(-)
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 1.0.8 dated 2017-01-13 and 1.0.9 dated 2017-03-14
DESCRIPTION | 9 +- MD5 | 146 ++++++++++++++++++++++--------------------- NAMESPACE | 2 R/xCheckParallel.r | 2 R/xDAGpropagate.r |only R/xEnrichConciser.r | 2 R/xEnrichViewer.r | 4 - R/xEnricherGenes.r | 103 ++++-------------------------- R/xEnricherYours.r | 43 ++++++++---- R/xGRsampling.r | 12 +-- R/xGRviaGeneAnno.r | 12 +-- R/xGRviaGenomicAnno.r | 6 - R/xGRviaGenomicAnnoAdv.r | 12 +-- R/xSNPscores.r | 2 R/xSocialiser.r | 2 R/xSocialiserGenes.r | 102 +++--------------------------- R/xSocialiserSNPs.r | 4 - R/xSymbol2GeneID.r |only inst/NEWS | 18 ++++- inst/xCheckParallel.html | 1 inst/xDAGpropagate.html |only inst/xEnricherGenes.html | 57 ++++++++++------ inst/xEnricherYours.html | 16 +++- inst/xGRviaGeneAnno.html | 30 +++++--- inst/xSocialiser.html | 2 inst/xSocialiserGenes.html | 36 +++++----- inst/xSocialiserSNPs.html | 13 +-- inst/xSymbol2GeneID.html |only man/xCheckParallel.Rd | 2 man/xCircos.Rd | 1 man/xColormap.Rd | 1 man/xConverter.Rd | 1 man/xDAGanno.Rd | 1 man/xDAGpropagate.Rd |only man/xDAGsim.Rd | 1 man/xEnrichBarplot.Rd | 1 man/xEnrichCompare.Rd | 1 man/xEnrichConciser.Rd | 3 man/xEnrichDAGplot.Rd | 1 man/xEnrichDAGplotAdv.Rd | 1 man/xEnrichNetplot.Rd | 1 man/xEnrichViewer.Rd | 1 man/xEnricher.Rd | 1 man/xEnricherGenes.Rd | 56 ++++++++++------ man/xEnricherSNPs.Rd | 1 man/xEnricherYours.Rd | 15 +++- man/xFunArgs.Rd | 1 man/xGR.Rd | 1 man/xGR2GeneScores.Rd | 1 man/xGR2nGenes.Rd | 1 man/xGRsampling.Rd | 1 man/xGRscores.Rd | 1 man/xGRviaGeneAnno.Rd | 31 +++++---- man/xGRviaGenomicAnno.Rd | 1 man/xGRviaGenomicAnnoAdv.Rd | 1 man/xLiftOver.Rd | 1 man/xRDataLoader.Rd | 1 man/xRd2HTML.Rd | 1 man/xRdWrap.Rd | 1 man/xSM2DF.Rd | 1 man/xSNP2GeneScores.Rd | 1 man/xSNP2nGenes.Rd | 1 man/xSNPlocations.Rd | 1 man/xSNPscores.Rd | 1 man/xSocialiser.Rd | 3 man/xSocialiserDAGplot.Rd | 1 man/xSocialiserDAGplotAdv.Rd | 1 man/xSocialiserGenes.Rd | 35 +++++----- man/xSocialiserNetplot.Rd | 1 man/xSocialiserSNPs.Rd | 14 +--- man/xSparseMatrix.Rd | 1 man/xSubneterGR.Rd | 1 man/xSubneterGenes.Rd | 1 man/xSubneterSNPs.Rd | 1 man/xSymbol2GeneID.Rd |only man/xVisKernels.Rd | 1 man/xVisNet.Rd | 1 77 files changed, 365 insertions(+), 469 deletions(-)
Title: Hidden Markov Model for Solar Geolocation Archival Tags
Description: Estimate positions of animal from data collected by solar geolocation archival tags.
Author: Eldar Rakhimberdiev <eldar@nioz.nl> with contributions from Anatoly
Saveliev and Julia Karagicheva
Maintainer: Eldar Rakhimberdiev <eldar@nioz.nl>
Diff between FLightR versions 0.4.5 dated 2016-12-15 and 0.4.6 dated 2017-03-14
DESCRIPTION | 13 ++++---- MD5 | 29 +++++++++++-------- R/data_import.R | 36 +++++++++++++++++++++--- R/data_preparation.R | 33 +++++++++++++++------- R/new_plotting_functions.R | 27 +++++++++++++++++- R/run_particle_filter.R | 30 ++++++++++++++------ R/summary_functions.R | 8 ++--- README.md | 26 ++++++++++------- build |only inst/CITATION | 50 +++++++++++++++++++++++++++++----- inst/doc |only man/find.stationary.location.Rd | 2 - man/get.tags.data.Rd | 4 -- man/plot_slopes_by_location.Rd | 8 +++-- tests/testthat/test_data_processing.R | 2 - vignettes |only 16 files changed, 198 insertions(+), 70 deletions(-)
Title: R Interface to a 'PostGIS' Database
Description: Provides an interface between R and
'PostGIS'-enabled 'PostgreSQL' databases to transparently transfer
spatial data. Both vector (points, lines, polygons) and raster
data are supported in read and write modes. Also provides
convenience functions to execute common procedures in
'PostgreSQL/PostGIS'.
Author: Mathieu Basille [aut],
David Bucklin [aut, cre]
Maintainer: David Bucklin <dbucklin@ufl.edu>
Diff between rpostgis versions 1.1.1 dated 2017-01-18 and 1.2.0 dated 2017-03-14
DESCRIPTION | 10 ++--- MD5 | 79 +++++++++++++++++++++++------------------------ NEWS | 18 ++++++++++ R/all_db_wrapper_fns.R | 19 +++++------ R/dbUtils_notExported.R | 33 ++++++++++++++++--- R/dbWriteDataFrame.R | 9 ++--- R/pgGetGeom.R | 75 ++++++++++++++++++++++++++++++++++++++++++-- R/pgInsert.R | 29 ++++++++++++++--- R/pgInsertize.R | 4 +- R/rpostgis-package.R | 3 - man/dbAddKey.Rd | 7 +--- man/dbAsDate.Rd | 7 +--- man/dbBuildTableQuery.Rd | 1 man/dbColumn.Rd | 7 +--- man/dbComment.Rd | 7 +--- man/dbConnCheck.Rd | 1 man/dbDrop.Rd | 26 +++++++-------- man/dbExistsTable.Rd | 9 ++--- man/dbIndex.Rd | 7 +--- man/dbSchema.Rd | 7 +--- man/dbTableInfo.Rd | 1 man/dbTableNameFix.Rd | 1 man/dbVacuum.Rd | 7 +--- man/dbVersion.Rd | 1 man/dbWriteDataFrame.Rd | 10 ++--- man/pgGetBoundary.Rd | 1 man/pgGetGeom.Rd | 25 ++++++++++++-- man/pgGetGeomQ.Rd |only man/pgGetLines.Rd | 1 man/pgGetPolys.Rd | 1 man/pgGetPts.Rd | 1 man/pgGetRast.Rd | 1 man/pgInsert.Rd | 16 +++++++-- man/pgInsertizeGeom.Rd | 3 - man/pgListGeom.Rd | 1 man/pgMakePts.Rd | 7 +--- man/pgPostGIS.Rd | 1 man/pgSRID.Rd | 1 man/pgWriteRast.Rd | 7 +--- man/roe_gps_data.Rd | 3 - man/rpostgis.Rd | 1 41 files changed, 287 insertions(+), 161 deletions(-)
Title: Multivariate VAM Fitting
Description: Fits a multivariate value-added model (VAM), see Broatch and Lohr (2012) <doi:10.3102/1076998610396900>, with normally distributed test scores and a binary outcome indicator. A pseudo-likelihood approach, Wolfinger (1993) <doi:10.1080/00949659308811554>, is used for the estimation of this joint generalized linear mixed model. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
Author: Andrew T. Karl, Jennifer Broatch, and Jennifer Green
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between RealVAMS versions 0.3-2 dated 2015-07-21 and 0.3-3 dated 2017-03-14
RealVAMS-0.3-2/RealVAMS/src/R_mstep.cpp |only RealVAMS-0.3-3/RealVAMS/DESCRIPTION | 15 +-- RealVAMS-0.3-3/RealVAMS/MD5 | 34 ++++--- RealVAMS-0.3-3/RealVAMS/NAMESPACE | 13 ++- RealVAMS-0.3-3/RealVAMS/NEWS | 6 + RealVAMS-0.3-3/RealVAMS/R/RealVAMS.R | 5 - RealVAMS-0.3-3/RealVAMS/R/plot.RealVAMS.R |only RealVAMS-0.3-3/RealVAMS/R/print.RealVAMS.R |only RealVAMS-0.3-3/RealVAMS/R/print.summary.RealVAMS.R |only RealVAMS-0.3-3/RealVAMS/R/summary.RealVAMS.R |only RealVAMS-0.3-3/RealVAMS/R/vp_cp.R | 81 ++++++++++++------ RealVAMS-0.3-3/RealVAMS/man/R_mstep2.Rd | 4 RealVAMS-0.3-3/RealVAMS/man/RealVAMS-package.Rd | 23 ++--- RealVAMS-0.3-3/RealVAMS/man/RealVAMS.Rd | 86 ++++++++++---------- RealVAMS-0.3-3/RealVAMS/man/example.outcome.data.Rd | 15 ++- RealVAMS-0.3-3/RealVAMS/man/example.score.data.Rd | 14 ++- RealVAMS-0.3-3/RealVAMS/man/plot.Rd |only RealVAMS-0.3-3/RealVAMS/man/print.Rd |only RealVAMS-0.3-3/RealVAMS/man/summary.Rd |only RealVAMS-0.3-3/RealVAMS/src/Makevars | 3 RealVAMS-0.3-3/RealVAMS/src/Makevars.win | 6 - RealVAMS-0.3-3/RealVAMS/src/R_mstep_cpp.cpp |only RealVAMS-0.3-3/RealVAMS/src/init.c |only 23 files changed, 180 insertions(+), 125 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.5.2 dated 2016-12-27 and 1.5.4 dated 2017-03-14
DESCRIPTION | 8 +- MD5 | 49 +++++++------ NAMESPACE | 1 R/03-geojob-obj.R | 19 ++++- R/check.R | 24 +++++- R/download-geojob.R | 20 ++++- R/query-webdata-times.R | 9 +- R/query-webdata-variables.R | 4 - R/result.R | 43 +++++++---- R/successful.R | 123 ++++++++++++++-------------------- R/times-webdata.R | 2 R/waitUntilFinished.R | 32 +++++++- README.md | 11 ++- inst/doc/geoknife.html | 11 --- inst/doc/plot_geotiff.html | 4 - inst/extdata/completed_request.xml |only inst/unnamed-chunk-7-1.png |only man/check-geojob.Rd | 6 + man/download.Rd | 10 ++ man/geojob-methods.Rd | 3 man/result-methods.Rd | 12 ++- man/successful-methods.Rd | 17 +--- man/wait.Rd | 15 +++- tests/testthat/test-download_result.R | 15 ++++ tests/testthat/test-geoknife_utils.R | 44 +++++++++++- tests/testthat/test-query_webdata.R |only tests/testthat/test-times_webdata.R | 16 ++++ 27 files changed, 330 insertions(+), 168 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The 'cmsaf' R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators ('cdo'). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The 'cmsaf' R-package is tested for CM SAF NetCDF data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided 'levbox_mergetime()'
function. The 'cmsaf' R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
Scripts for an easy application of the functions are provided at the CM SAF homepage
(<http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html>).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.7.1 dated 2016-11-28 and 1.7.2 dated 2017-03-14
DESCRIPTION | 8 ++++---- MD5 | 26 ++++++++++++++------------ NAMESPACE | 3 ++- R/box_mergetime.R | 29 +++++++++++++++-------------- R/extract.level.R |only R/levbox_mergetime.R | 1 + R/selmon.R | 22 +++++++++++----------- R/seltime.R | 1 - R/selyear.R | 2 +- R/timmean.R | 26 +++++++++++++------------- R/trend.R | 2 +- R/yearsum.R | 2 +- man/cmsaf.subc.Rd | 2 +- man/extract.level.Rd |only man/extract.period.Rd | 4 +++- 15 files changed, 67 insertions(+), 61 deletions(-)
Title: Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis
Description: Provides functions for the Bayesian analysis of extreme value
models. The 'rust' package <https://cran.r-project.org/package=rust> is
used to simulate a random sample from the required posterior distribution.
The functionality of 'revdbayes' is similar to the 'evdbayes' package
<https://cran.r-project.org/package=evdbayes>, which uses Markov Chain
Monte Carlo ('MCMC') methods for posterior simulation. See the 'revdbayes'
website for more information, documentation and examples.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between revdbayes versions 1.0.0 dated 2016-11-23 and 1.1.0 dated 2017-03-14
DESCRIPTION | 21 - MD5 | 69 ++-- NAMESPACE | 32 + NEWS.md |only R/bayesplot.R |only R/distributions.R |only R/misc.R | 42 +- R/plot_evpred.R |only R/predictive.R |only R/priors.R | 155 ++++++--- R/revdbayes.R | 49 +- R/rposterior.R | 466 +++++++++++++++++++++++++++- R/rprior.R |only R/sample_diagnostics.R | 169 ++++++++-- README.md | 2 build/vignette.rds |binary inst/doc/revdbayes-predictive-vignette.R |only inst/doc/revdbayes-predictive-vignette.Rmd |only inst/doc/revdbayes-predictive-vignette.html |only inst/doc/revdbayes-vignette.R | 4 inst/doc/revdbayes-vignette.Rmd | 18 - inst/doc/revdbayes-vignette.html | 71 +--- man/binpost.Rd |only man/gev.Rd |only man/gom.Rd | 12 man/gp.Rd |only man/oxford.Rd | 1 man/plot.evpost.Rd | 89 ++++- man/plot.evpred.Rd |only man/portpirie.Rd | 3 man/pp_check.evpost.Rd |only man/predict.evpost.Rd |only man/quantile_to_gev.Rd |only man/rDir.Rd |only man/rainfall.Rd | 1 man/revdbayes.Rd | 17 - man/rpost.Rd | 139 +++++++- man/rprior_prob.Rd |only man/rprior_quant.Rd |only man/set_bin_prior.Rd |only man/set_prior.Rd | 50 +-- man/summary.evpost.Rd | 20 - man/venice.Rd | 5 vignettes/revdbayes-predictive-vignette.Rmd |only vignettes/revdbayes-vignette.Rmd | 18 - vignettes/revdbayes.bib | 36 +- 46 files changed, 1216 insertions(+), 273 deletions(-)
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a shared random effect.
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <chadrien@ncc.go.jp>
Diff between mexhaz versions 1.1 dated 2016-05-10 and 1.2 dated 2017-03-14
mexhaz-1.1/mexhaz/R/predMexhaz.R |only mexhaz-1.1/mexhaz/man/predMexhaz.Rd |only mexhaz-1.1/mexhaz/src/DeltaBs1.c |only mexhaz-1.1/mexhaz/src/DeltaBs23.c |only mexhaz-1.1/mexhaz/src/DeltaPwCst.c |only mexhaz-1.1/mexhaz/src/IntBs1.c |only mexhaz-1.1/mexhaz/src/IntBs23.c |only mexhaz-1.1/mexhaz/src/IntPwCst.c |only mexhaz-1.2/mexhaz/DESCRIPTION | 12 mexhaz-1.2/mexhaz/MD5 | 59 +- mexhaz-1.2/mexhaz/NAMESPACE | 12 mexhaz-1.2/mexhaz/NEWS | 65 ++ mexhaz-1.2/mexhaz/R/mexhaz.R | 685 ++++++++++++++++------------- mexhaz-1.2/mexhaz/R/plot.predMexhaz.R | 19 mexhaz-1.2/mexhaz/R/points.predMexhaz.R | 19 mexhaz-1.2/mexhaz/R/predict.mexhaz.r |only mexhaz-1.2/mexhaz/R/ranef.mexhaz.R |only mexhaz-1.2/mexhaz/R/update.mexhaz.R |only mexhaz-1.2/mexhaz/data/simdatn2.RData |only mexhaz-1.2/mexhaz/man/mexhaz-package.Rd | 48 +- mexhaz-1.2/mexhaz/man/mexhaz.Rd | 169 ++++--- mexhaz-1.2/mexhaz/man/plot.predMexhaz.Rd | 34 - mexhaz-1.2/mexhaz/man/points.predMexhaz.Rd | 33 - mexhaz-1.2/mexhaz/man/predict.mexhaz.Rd |only mexhaz-1.2/mexhaz/man/print.predMexhaz.Rd | 4 mexhaz-1.2/mexhaz/man/ranef.Rd |only mexhaz-1.2/mexhaz/man/ranef.mexhaz.Rd |only mexhaz-1.2/mexhaz/man/simdatn2.Rd |only mexhaz-1.2/mexhaz/man/summary.mexhaz.Rd | 7 mexhaz-1.2/mexhaz/man/update.mexhaz.Rd |only mexhaz-1.2/mexhaz/src/DeltaBs0R.c |only mexhaz-1.2/mexhaz/src/DeltaBs1R.c |only mexhaz-1.2/mexhaz/src/DeltaBs23R.c |only mexhaz-1.2/mexhaz/src/DeltaNsR.c |only mexhaz-1.2/mexhaz/src/DeltaWeibR.c |only mexhaz-1.2/mexhaz/src/FrailtyAdapt.c | 121 ++--- mexhaz-1.2/mexhaz/src/HazardBs0C.c |only mexhaz-1.2/mexhaz/src/HazardBs0R.c |only mexhaz-1.2/mexhaz/src/HazardBs1C.c |only mexhaz-1.2/mexhaz/src/HazardBs1R.c |only mexhaz-1.2/mexhaz/src/HazardBs23C.c |only mexhaz-1.2/mexhaz/src/HazardBs23R.c |only mexhaz-1.2/mexhaz/src/HazardNsC.c |only mexhaz-1.2/mexhaz/src/HazardNsR.c |only mexhaz-1.2/mexhaz/src/SplineFunc.c |only mexhaz-1.2/mexhaz/src/SplineFunc.h |only mexhaz-1.2/mexhaz/src/init.c |only 47 files changed, 761 insertions(+), 526 deletions(-)
Title: Integrative Clustering for Heterogeneous Biomedical Datasets
Description: Integrative context-dependent clustering for heterogeneous
biomedical datasets. Identifies local clustering structures in related
datasets, and a global clusters that exist across the datasets.
Author: Evelina Gabasova
Maintainer: Evelina Gabasova <egabasova@gmail.com>
Diff between clusternomics versions 0.1.0 dated 2016-08-01 and 0.1.1 dated 2017-03-14
DESCRIPTION | 15 +--- LICENSE | 2 MD5 | 23 +++---- R/clusternomics.R | 63 +++++++++++++++++++- README.md | 11 +++ build/vignette.rds |binary inst/doc/using-clusternomics.R | 11 +++ inst/doc/using-clusternomics.Rmd | 27 +++++++- inst/doc/using-clusternomics.html | 56 +++++++++++------ man/contextCluster.Rd | 4 + tests/testthat/test.clusternomics.globalBehaviour.R | 25 +++++++ tools |only vignettes/using-clusternomics.Rmd | 27 +++++++- 13 files changed, 213 insertions(+), 51 deletions(-)
Title: Computing Word Alignment Using IBM Model 1 (and Symmetrization)
for a Given Parallel Corpus and Its Evaluation
Description: For a given Sentence-Aligned Parallel Corpus, it aligns words for each sentence pair. It considers one-to-many and symmetrization alignments. Moreover, it evaluates the quality of word alignment based on this package and some other software. It also builds an automatic dictionary of two languages based on given parallel corpus.
Author: Neda Daneshagr and Majid Sarmad.
Maintainer: Neda Daneshgar<ne_da978@stu-mail.um.ac.ir>
Diff between word.alignment versions 1.0.4 dated 2016-12-30 and 1.0.5 dated 2017-03-14
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- R/Symmetrization.R | 63 ++++++++++++++++++++---------------------- R/mydictionary.R | 10 +++--- R/prepareData.R | 2 - R/squareN.R | 2 - R/word_alignIBM1.R | 15 ++++------ man/Symmetrization.Rd | 2 - man/word.alignment-package.Rd | 4 +- 9 files changed, 60 insertions(+), 62 deletions(-)
More information about word.alignment at CRAN
Permanent link
Title: Simultaneous Inference for Diversity Indices
Description: Provides estimation of simultaneous bootstrap and asymptotic confidence intervals for diversity indices, namely the Shannon and the Simpson index. Several pre--specified multiple comparison types are available to choose. Further user--defined contrast matrices are applicable. In addition, simboot estimates adjusted as well as unadjusted p--values for two of the three proposed bootstrap methods. Further simboot allows for comparing biological diversities of two or more groups while simultaneously testing a user-defined selection of Hill numbers of orders q, which are considered as appropriate and useful indices for measuring diversity.
Author: Ralph Scherer, Philip Pallmann
Maintainer: Ralph Scherer <shearer.ra76@gmail.com>
Diff between simboot versions 0.2-5 dated 2014-04-15 and 0.2-6 dated 2017-03-14
DESCRIPTION | 12 - MD5 | 14 +- NAMESPACE | 4 NEWS | 4 R/mcpHill.R | 4 README.md | 3 man/sbdiv.Rd | 386 ++++++++++++++++++++++++++++----------------------------- man/simboot.Rd | 4 8 files changed, 219 insertions(+), 212 deletions(-)
Title: Sigmoid Functions for Machine Learning
Description: Several different sigmoid functions are implemented, including a wrapper function, SoftMax preprocessing and inverse functions.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between sigmoid versions 0.2.0 dated 2016-08-14 and 0.2.1 dated 2017-03-14
DESCRIPTION | 8 +++---- MD5 | 34 +++++++++++++++++------------- NAMESPACE | 4 +++ R/sigmoid.R | 39 +++++++++++++++++++++++++++++++++++ README.md | 6 +---- build/vignette.rds |binary inst/doc/sigmoid.html | 32 ++++++++++++++-------------- man/Gompertz.Rd | 1 man/SoftMax.Rd | 1 man/SoftPlus.Rd |only man/inverse_Gompertz.Rd | 1 man/leakly_relu.Rd |only man/logistic.Rd | 1 man/logit.Rd | 1 man/relu.Rd |only man/relu_output_to_derivative.Rd |only man/sigmoid.Rd | 1 man/sigmoid_output_to_derivative.Rd | 1 man/softplus_output_to_derivative.Rd |only man/tanh_output_to_derivative.Rd | 1 tools |only 21 files changed, 85 insertions(+), 46 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files. In
addition, various risk estimation methods are included. Note that the package
includes a graphical user interface that allows to use various methods of this
package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.0.0 dated 2017-01-04 and 5.0.1 dated 2017-03-14
DESCRIPTION | 8 MD5 | 31 R/0classes.r | 2 R/GUIfunctions.R | 35 build/vignette.rds |binary inst/doc/sdcApp.Rmd | 10 inst/doc/sdcApp.html | 936 ++++++++++------- inst/doc/sdc_guidelines.pdf |binary inst/shiny/sdcApp/controllers/reactive_expressions.R | 8 inst/shiny/sdcApp/controllers/ui_about.R | 2 inst/shiny/sdcApp/controllers/ui_import_data.R | 2 inst/shiny/sdcApp/controllers/ui_modify_data.R | 25 inst/shiny/sdcApp/controllers/ui_results_categorical.R | 12 inst/shiny/sdcApp/controllers/ui_setup_sdc.R | 46 inst/shiny/sdcApp/server.R | 4 src/init.c |only vignettes/sdcApp.Rmd | 10 17 files changed, 709 insertions(+), 422 deletions(-)
Title: Functions for the Logitnormal Distribution
Description: Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.
Author: Thomas Wutzler
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between logitnorm versions 0.8.33 dated 2016-11-10 and 0.8.34 dated 2017-03-14
logitnorm-0.8.33/logitnorm/README.md |only logitnorm-0.8.34/logitnorm/DESCRIPTION | 14 +++++++------- logitnorm-0.8.34/logitnorm/MD5 | 9 +++++---- logitnorm-0.8.34/logitnorm/NEWS.md |only logitnorm-0.8.34/logitnorm/build/vignette.rds |binary logitnorm-0.8.34/logitnorm/inst/doc/logitnorm.html | 2 +- logitnorm-0.8.34/logitnorm/tools |only 7 files changed, 13 insertions(+), 12 deletions(-)
Title: A Very Basic Templating Engine
Description: Replace parameters in strings and/or text files with specified
values.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between infuser versions 0.2.5 dated 2016-10-12 and 0.2.6 dated 2017-03-14
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/helpers.R | 2 +- build/vignette.rds |binary inst/doc/getting_started.html | 6 +++--- man/infuse.Rd | 1 - man/print.infuse.Rd | 1 - man/print_requested_params.Rd | 1 - man/read_template.Rd | 1 - man/trim.Rd | 1 - man/variables_requested.Rd | 1 - 11 files changed, 19 insertions(+), 25 deletions(-)
Title: Easily Gate or Select Points on a Scatter Plot
Description: Allows user to choose/gate a region on the plot and returns points
within it.
Author: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <wj241@cam.ac.uk>
Diff between gatepoints versions 0.1.2 dated 2016-12-16 and 0.1.3 dated 2017-03-14
DESCRIPTION | 8 ++--- MD5 | 14 +++++----- README.md | 6 ++-- build/vignette.rds |binary inst/doc/gatepoints.html | 64 ++++++++++++++++++++++++++++++----------------- man/fhs.Rd | 1 man/gatepoints.Rd | 1 tools |only 8 files changed, 57 insertions(+), 37 deletions(-)
Title: Evolutionary Parameter Estimation for 'Repast Simphony' Models
Description: The EvoPER, Evolutionary Parameter Estimation for 'Repast Simphony'
Agent-Based framework (<https://repast.github.io/>), provides optimization
driven parameter estimation methods based on evolutionary computation
techniques which could be more efficient and require, in some cases,
fewer model evaluations than other alternatives relying on experimental design.
Author: Antonio Prestes Garcia [aut, cre],
Alfonso Rodriguez-Paton [aut, ths]
Maintainer: Antonio Prestes Garcia <antonio.pgarcia@alumnos.upm.es>
Diff between evoper versions 0.3.0 dated 2016-11-26 and 0.4.0 dated 2017-03-14
evoper-0.3.0/evoper/man/predatorprey.plot.Rd |only evoper-0.4.0/evoper/DESCRIPTION | 11 evoper-0.4.0/evoper/MD5 | 218 + evoper-0.4.0/evoper/NAMESPACE | 31 evoper-0.4.0/evoper/NEWS | 48 evoper-0.4.0/evoper/R/abm-acor.R |only evoper-0.4.0/evoper/R/abm-ees1.R |only evoper-0.4.0/evoper/R/abm-ees2.R |only evoper-0.4.0/evoper/R/abm-pso.R |only evoper-0.4.0/evoper/R/abm-saa.R |only evoper-0.4.0/evoper/R/class-estimates.R |only evoper-0.4.0/evoper/R/class-objective.R |only evoper-0.4.0/evoper/R/class-options.R |only evoper-0.4.0/evoper/R/evoper.R | 2429 --------------------- evoper-0.4.0/evoper/R/experiments.R |only evoper-0.4.0/evoper/R/helper-functions.R |only evoper-0.4.0/evoper/R/test-functions.R |only evoper-0.4.0/evoper/man/Estimates-class.Rd | 5 evoper-0.4.0/evoper/man/Magnitude.Rd | 2 evoper-0.4.0/evoper/man/ObjectiveFunction-class.Rd | 2 evoper-0.4.0/evoper/man/Options-class.Rd | 6 evoper-0.4.0/evoper/man/OptionsACOR-class.Rd | 2 evoper-0.4.0/evoper/man/OptionsEES1-class.Rd | 2 evoper-0.4.0/evoper/man/OptionsEES2-class.Rd | 2 evoper-0.4.0/evoper/man/OptionsFactory.Rd | 2 evoper-0.4.0/evoper/man/OptionsPSO-class.Rd | 4 evoper-0.4.0/evoper/man/OptionsSAA-class.Rd | 4 evoper-0.4.0/evoper/man/PlainFunction-class.Rd | 2 evoper-0.4.0/evoper/man/RepastFunction-class.Rd | 2 evoper-0.4.0/evoper/man/abm.acor.Rd | 2 evoper-0.4.0/evoper/man/abm.ees1.Rd | 2 evoper-0.4.0/evoper/man/abm.ees2.Rd | 2 evoper-0.4.0/evoper/man/abm.pso.Rd | 2 evoper-0.4.0/evoper/man/abm.saa.Rd | 2 evoper-0.4.0/evoper/man/acor.F.Rd | 2 evoper-0.4.0/evoper/man/acor.N.Rd | 2 evoper-0.4.0/evoper/man/acor.S.Rd | 2 evoper-0.4.0/evoper/man/acor.W.Rd | 2 evoper-0.4.0/evoper/man/acor.archive.Rd | 2 evoper-0.4.0/evoper/man/acor.lthgaussian.Rd | 2 evoper-0.4.0/evoper/man/acor.probabilities.Rd | 2 evoper-0.4.0/evoper/man/acor.sigma.Rd | 2 evoper-0.4.0/evoper/man/acor.updateants.Rd | 2 evoper-0.4.0/evoper/man/acor.weigth.Rd | 2 evoper-0.4.0/evoper/man/bestFitness.Rd | 2 evoper-0.4.0/evoper/man/bestSolution.Rd | 2 evoper-0.4.0/evoper/man/cbuf.Rd | 2 evoper-0.4.0/evoper/man/compare.algorithms1.Rd |only evoper-0.4.0/evoper/man/contourplothelper.Rd | 21 evoper-0.4.0/evoper/man/ees1.challenge.Rd | 2 evoper-0.4.0/evoper/man/ees1.explore.Rd | 6 evoper-0.4.0/evoper/man/ees1.mating.Rd | 2 evoper-0.4.0/evoper/man/ees1.mating1.Rd | 2 evoper-0.4.0/evoper/man/ees1.mutation.Rd | 6 evoper-0.4.0/evoper/man/ees1.recombination.Rd | 2 evoper-0.4.0/evoper/man/ees1.selection.Rd | 2 evoper-0.4.0/evoper/man/enforceBounds.Rd | 2 evoper-0.4.0/evoper/man/es.evaluate.Rd | 2 evoper-0.4.0/evoper/man/f0.adtn.rosenbrock2.Rd | 2 evoper-0.4.0/evoper/man/f0.bohachevsky.Rd |only evoper-0.4.0/evoper/man/f0.bohachevsky4.Rd |only evoper-0.4.0/evoper/man/f0.cigar.Rd |only evoper-0.4.0/evoper/man/f0.cigar4.Rd |only evoper-0.4.0/evoper/man/f0.griewank.Rd |only evoper-0.4.0/evoper/man/f0.griewank4.Rd |only evoper-0.4.0/evoper/man/f0.nlnn.rosenbrock2.Rd | 2 evoper-0.4.0/evoper/man/f0.periodtuningpp.Rd | 24 evoper-0.4.0/evoper/man/f0.periodtuningpp12.Rd |only evoper-0.4.0/evoper/man/f0.periodtuningpp24.Rd |only evoper-0.4.0/evoper/man/f0.periodtuningpp48.Rd |only evoper-0.4.0/evoper/man/f0.periodtuningpp72.Rd |only evoper-0.4.0/evoper/man/f0.rosenbrock2.Rd | 2 evoper-0.4.0/evoper/man/f0.rosenbrock4.Rd |only evoper-0.4.0/evoper/man/f0.rosenbrockn.Rd |only evoper-0.4.0/evoper/man/f0.schaffer.Rd |only evoper-0.4.0/evoper/man/f0.schaffer4.Rd |only evoper-0.4.0/evoper/man/f0.schwefel.Rd |only evoper-0.4.0/evoper/man/f0.schwefel4.Rd |only evoper-0.4.0/evoper/man/f0.test.Rd | 2 evoper-0.4.0/evoper/man/f1.adtn.rosenbrock2.Rd | 2 evoper-0.4.0/evoper/man/f1.bohachevsky.Rd |only evoper-0.4.0/evoper/man/f1.cigar.Rd |only evoper-0.4.0/evoper/man/f1.griewank.Rd |only evoper-0.4.0/evoper/man/f1.nlnn.rosenbrock2.Rd | 2 evoper-0.4.0/evoper/man/f1.rosenbrock2.Rd | 2 evoper-0.4.0/evoper/man/f1.rosenbrockn.Rd |only evoper-0.4.0/evoper/man/f1.schaffer.Rd |only evoper-0.4.0/evoper/man/f1.schwefel.Rd |only evoper-0.4.0/evoper/man/f1.test.Rd | 2 evoper-0.4.0/evoper/man/fixdfcolumns.Rd | 2 evoper-0.4.0/evoper/man/getFitness.Rd | 2 evoper-0.4.0/evoper/man/getSolution.Rd | 2 evoper-0.4.0/evoper/man/gm.mean.Rd | 2 evoper-0.4.0/evoper/man/gm.sd.Rd | 2 evoper-0.4.0/evoper/man/histplothelper.Rd | 2 evoper-0.4.0/evoper/man/initSolution.Rd | 2 evoper-0.4.0/evoper/man/lowerBound.Rd | 2 evoper-0.4.0/evoper/man/naiveperiod.Rd | 2 evoper-0.4.0/evoper/man/partSolutionSpace.Rd | 2 evoper-0.4.0/evoper/man/predatorprey.Rd | 2 evoper-0.4.0/evoper/man/predatorprey.plot0.Rd |only evoper-0.4.0/evoper/man/predatorprey.plot1.Rd |only evoper-0.4.0/evoper/man/pso.Velocity.Rd | 2 evoper-0.4.0/evoper/man/pso.best.Rd | 2 evoper-0.4.0/evoper/man/pso.chi.Rd | 2 evoper-0.4.0/evoper/man/pso.lbest.Rd | 2 evoper-0.4.0/evoper/man/pso.neighborhood.K2.Rd | 2 evoper-0.4.0/evoper/man/pso.neighborhood.K4.Rd | 2 evoper-0.4.0/evoper/man/pso.neighborhood.KN.Rd | 2 evoper-0.4.0/evoper/man/pso.printbest.Rd | 2 evoper-0.4.0/evoper/man/random.wheel.Rd |only evoper-0.4.0/evoper/man/saa.bolt.Rd | 2 evoper-0.4.0/evoper/man/saa.neighborhood.Rd | 2 evoper-0.4.0/evoper/man/saa.neighborhood1.Rd | 2 evoper-0.4.0/evoper/man/saa.neighborhoodH.Rd | 2 evoper-0.4.0/evoper/man/saa.neighborhoodN.Rd | 2 evoper-0.4.0/evoper/man/saa.tbyk.Rd | 2 evoper-0.4.0/evoper/man/saa.tcte.Rd | 2 evoper-0.4.0/evoper/man/saa.texp.Rd | 2 evoper-0.4.0/evoper/man/scatterplotlothelper.Rd | 4 evoper-0.4.0/evoper/man/show.comp1.Rd |only evoper-0.4.0/evoper/man/slope.Rd | 2 evoper-0.4.0/evoper/man/slopes.Rd | 2 evoper-0.4.0/evoper/man/sortSolution.Rd | 2 evoper-0.4.0/evoper/man/summarize.comp1.Rd |only evoper-0.4.0/evoper/man/upperBound.Rd | 2 evoper-0.4.0/evoper/man/xmeanci1.Rd | 2 evoper-0.4.0/evoper/man/xmeanci2.Rd | 2 evoper-0.4.0/evoper/man/xyplothelper.Rd | 4 evoper-0.4.0/evoper/tests |only 130 files changed, 331 insertions(+), 2638 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel and David Giménez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.2.3 dated 2017-02-17 and 3.2.4 dated 2017-03-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/chisq.test2.R | 7 +++++-- R/compare.i.R | 6 +++--- R/compareGroups.default.R | 4 ++-- inst/doc/changelog | 2 ++ inst/doc/compareGroups_vignette.html | 2 +- man/compareGroups-internal.Rd | 4 ++-- man/compareGroups-package.Rd | 4 ++-- man/compareGroups.Rd | 4 +++- 10 files changed, 33 insertions(+), 26 deletions(-)
Title: Bayesian Exponential Random Graph Models
Description: Set of tools to analyse Bayesian exponential random graph models.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Florian Maire [ctb],
Nial Friel [ctb]
Maintainer: Alberto Caimo <acaimo.stats@gmail.com>
Diff between Bergm versions 3.0.1 dated 2014-11-24 and 4.0.0 dated 2017-03-14
Bergm-3.0.1/Bergm/R/abergm.R |only Bergm-3.0.1/Bergm/R/bbeta.R |only Bergm-3.0.1/Bergm/R/bbeta.output.R |only Bergm-3.0.1/Bergm/R/bergmS.R |only Bergm-3.0.1/Bergm/R/bergmS.output.R |only Bergm-3.0.1/Bergm/man/Bergm-package.Rd |only Bergm-3.0.1/Bergm/man/abergm.Rd |only Bergm-3.0.1/Bergm/man/bbeta.Rd |only Bergm-3.0.1/Bergm/man/bbeta.output.Rd |only Bergm-3.0.1/Bergm/man/bergmS.Rd |only Bergm-3.0.1/Bergm/man/bergmS.output.Rd |only Bergm-4.0.0/Bergm/DESCRIPTION | 22 ++- Bergm-4.0.0/Bergm/MD5 | 29 +---- Bergm-4.0.0/Bergm/NAMESPACE | 26 ++-- Bergm-4.0.0/Bergm/R/bergm.R | 168 ++++++++++++++++++++--------- Bergm-4.0.0/Bergm/R/bergm.output.R | 178 +++++++++++++++---------------- Bergm-4.0.0/Bergm/R/bgof.R | 96 ++++++++++++++++ Bergm-4.0.0/Bergm/R/calibrate.bergm.R |only Bergm-4.0.0/Bergm/man/bergm.Rd | 133 ++++++++++------------- Bergm-4.0.0/Bergm/man/bergm.output.Rd | 42 ++++--- Bergm-4.0.0/Bergm/man/bgof.Rd | 127 ++++++++++++++-------- Bergm-4.0.0/Bergm/man/calibrate.bergm.Rd |only 22 files changed, 510 insertions(+), 311 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: 'ggplot2' is an excellent and flexible package for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.1.1 dated 2016-12-05 and 0.1.2 dated 2017-03-14
DESCRIPTION | 25 ++++++------- MD5 | 90 +++++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS.md | 19 +++++++++ R/geom_exec.R | 2 - R/get_palette.R |only R/ggbarplot.R | 5 +- R/ggboxplot.R | 6 ++- R/ggdensity.R | 4 +- R/ggdotplot.R | 3 + R/ggerrorplot.R | 3 + R/gghistogram.R | 4 +- R/ggpar.R | 85 +++++++++++++++++++++++++++++--------------- R/ggscatter.R | 11 +++-- R/ggstripchart.R | 3 + R/ggviolin.R | 3 + R/utilities.R | 70 ++++++++++++++++++++++++++++++++---- README.md | 8 ++-- man/desc_statby.Rd | 1 man/diff_express.Rd | 1 man/geom_exec.Rd | 1 man/get_palette.Rd |only man/ggbarplot.Rd | 1 man/ggboxplot.Rd | 2 - man/ggdensity.Rd | 1 man/ggdotchart.Rd | 1 man/ggdotplot.Rd | 1 man/ggecdf.Rd | 1 man/ggerrorplot.Rd | 1 man/gghistogram.Rd | 1 man/ggline.Rd | 1 man/ggmaplot.Rd | 1 man/ggpar.Rd | 42 +++++++++++++-------- man/ggpie.Rd | 1 man/ggqqplot.Rd | 1 man/ggscatter.Rd | 16 +++++--- man/ggstripchart.Rd | 1 man/ggtext.Rd | 1 man/ggviolin.Rd | 1 man/show_line_types.Rd | 1 man/show_point_shapes.Rd | 1 man/stat_chull.Rd | 1 man/stat_conf_ellipse.Rd | 1 man/stat_mean.Rd | 1 man/theme_pubr.Rd | 3 - tools |only 46 files changed, 267 insertions(+), 160 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data for Report
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features are
1) CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Produce pdf, rtf, text report files.
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between ncar versions 0.3.1 dated 2017-02-03 and 0.3.3 dated 2017-03-14
ncar-0.3.1/ncar/LICENSE |only ncar-0.3.1/ncar/R/IndiNCA.R |only ncar-0.3.1/ncar/R/NCA.R |only ncar-0.3.1/ncar/R/data.R |only ncar-0.3.1/ncar/R/runCDISC.R |only ncar-0.3.1/ncar/data |only ncar-0.3.1/ncar/man/IndiNCA.Rd |only ncar-0.3.1/ncar/man/NCA.Rd |only ncar-0.3.1/ncar/man/ncar_0.3.1-package.Rd |only ncar-0.3.1/ncar/man/runCDISC.Rd |only ncar-0.3.3/ncar/DESCRIPTION | 42 +++++-------- ncar-0.3.3/ncar/MD5 | 70 ++++++++++++---------- ncar-0.3.3/ncar/NAMESPACE | 25 +------- ncar-0.3.3/ncar/R/AUC.R | 77 ++++++++---------------- ncar-0.3.3/ncar/R/BasicUtil.R |only ncar-0.3.3/ncar/R/BestSlope.R | 77 ++++++++---------------- ncar-0.3.3/ncar/R/IntAUC.R | 81 ++++++++------------------ ncar-0.3.3/ncar/R/Interpol.R | 93 +++++++++--------------------- ncar-0.3.3/ncar/R/LinAUC.R | 46 +++----------- ncar-0.3.3/ncar/R/LogAUC.R | 67 ++++++--------------- ncar-0.3.3/ncar/R/Round.R | 28 +-------- ncar-0.3.3/ncar/R/Slope.R | 73 ++++++++--------------- ncar-0.3.3/ncar/R/Unit.R |only ncar-0.3.3/ncar/R/pdfNCA.R |only ncar-0.3.3/ncar/R/rtfNCA.R |only ncar-0.3.3/ncar/R/sNCA.R |only ncar-0.3.3/ncar/R/sysdata.rda |binary ncar-0.3.3/ncar/R/tabNCA.R |only ncar-0.3.3/ncar/R/txtNCA.R |only ncar-0.3.3/ncar/inst/NEWS.Rd |only ncar-0.3.3/ncar/inst/doc/ncar-manual.pdf |binary ncar-0.3.3/ncar/man/AUC.Rd | 72 +++++++++-------------- ncar-0.3.3/ncar/man/BasicUtil.Rd |only ncar-0.3.3/ncar/man/BestSlope.Rd | 85 +++++++++++---------------- ncar-0.3.3/ncar/man/IntAUC.Rd | 88 +++++++++++----------------- ncar-0.3.3/ncar/man/Interpol.Rd | 86 ++++++++++----------------- ncar-0.3.3/ncar/man/LinAUC.Rd | 72 ++++++++++------------- ncar-0.3.3/ncar/man/LogAUC.Rd | 74 ++++++++++------------- ncar-0.3.3/ncar/man/Round.Rd | 63 ++++++++------------ ncar-0.3.3/ncar/man/RptCfg.Rd | 68 ++++++++++----------- ncar-0.3.3/ncar/man/Slope.Rd | 70 ++++++++++------------ ncar-0.3.3/ncar/man/Unit.Rd |only ncar-0.3.3/ncar/man/ncar-package.Rd |only ncar-0.3.3/ncar/man/pdfNCA.Rd |only ncar-0.3.3/ncar/man/rtfNCA.Rd |only ncar-0.3.3/ncar/man/sNCA.Rd |only ncar-0.3.3/ncar/man/tabNCA.Rd |only ncar-0.3.3/ncar/man/txtNCA.Rd |only ncar-0.3.3/ncar/tests/Test.R | 43 +++++++++---- 49 files changed, 543 insertions(+), 857 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-19 1.4
2015-04-17 1.3
2014-08-30 1.2
2014-06-06 1.1
2013-10-20 1.0.1
2013-04-05 1.0.0
2013-02-10 0.9.0
2012-11-20 0.4.0
2012-05-31 0.3.1
2012-05-10 0.3.0
2012-03-15 0.2.1
2012-02-09 0.2.0
2012-01-04 0.1.3
2011-12-06 0.1.2
2011-11-14 0.1
Title: Wrap R Functions for Debugging and Ease of Use
Description: Provides 'DebugFnW()' to capture function context on error for
debugging, and 'let()' which converts non-standard evaluation interfaces to
standard evaluation interfaces.
'DebugFnW()' captures the calling function and arguments prior to the
call causing the exception, while
the classic `options(error=dump.frames)` form captures at the
moment of the exception
itself (thus function arguments may not be at their starting values).
`let()` rebinds (possibly unbound) names to names, which is different than
`with()` rebinds names to values.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 0.1.0 dated 2017-02-11 and 0.1.1 dated 2017-03-14
DESCRIPTION | 16 ++++++--- MD5 | 47 +++++++++++++------------- NEWS.md | 6 ++- R/DebugFn.R | 23 +++++++------ R/let.R | 69 +++++++++++++++++++++++++++++++++------ README.md | 9 +++++ build/vignette.rds |binary inst/doc/DebugFnW.Rmd | 6 ++- inst/doc/DebugFnW.html | 7 ++- inst/doc/let.R | 6 +++ inst/doc/let.Rmd | 26 ++++++++++++++ inst/doc/let.html | 26 +++++++++++++- man/DebugFn.Rd | 4 +- man/DebugFnE.Rd | 4 +- man/DebugFnW.Rd | 7 +-- man/DebugFnWE.Rd | 4 +- man/DebugPrintFn.Rd | 4 +- man/DebugPrintFnE.Rd | 4 +- man/buildNameCallback.Rd | 1 man/let.Rd | 6 ++- man/restrictToNameAssignments.Rd | 1 man/wrapr.Rd | 1 tools |only vignettes/DebugFnW.Rmd | 6 ++- vignettes/let.Rmd | 26 ++++++++++++++ 25 files changed, 235 insertions(+), 74 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between StereoMorph versions 1.6 dated 2017-02-13 and 1.6.1 dated 2017-03-14
StereoMorph-1.6.1/StereoMorph/DESCRIPTION | 8 - StereoMorph-1.6.1/StereoMorph/MD5 | 40 +++-- StereoMorph-1.6.1/StereoMorph/NAMESPACE | 2 StereoMorph-1.6.1/StereoMorph/R/alignShapesToMidline.R | 8 + StereoMorph-1.6.1/StereoMorph/R/calibrateCameras.R | 80 +++++----- StereoMorph-1.6.1/StereoMorph/R/extractFrames.R | 75 ++++++++- StereoMorph-1.6.1/StereoMorph/R/findCheckerboardCorners.R | 8 - StereoMorph-1.6.1/StereoMorph/R/reflectMissingShapes.R | 9 + StereoMorph-1.6.1/StereoMorph/R/testCalibration.R | 13 + StereoMorph-1.6.1/StereoMorph/inst/CITATION | 6 StereoMorph-1.6.1/StereoMorph/inst/extdata/Shapes_2D |only StereoMorph-1.6.1/StereoMorph/inst/extdata/Shapes_3D |only StereoMorph-1.6.1/StereoMorph/inst/extdata/apps/digitizeImages/server.R | 2 StereoMorph-1.6.1/StereoMorph/inst/extdata/apps/digitizeImages/session_parameters.txt | 2 StereoMorph-1.6.1/StereoMorph/inst/extdata/apps/digitizeImages/www/digitize_image.js | 31 ++- StereoMorph-1.6.1/StereoMorph/man/StereoMorph-package.Rd | 25 ++- StereoMorph-1.6.1/StereoMorph/man/TPSToShapes.Rd |only StereoMorph-1.6.1/StereoMorph/man/calibrateCameras.Rd | 13 - StereoMorph-1.6.1/StereoMorph/man/extractFrames.Rd |only StereoMorph-1.6.1/StereoMorph/man/writeLMToTPS.Rd |only StereoMorph-1.6.1/StereoMorph/src/StereoMorph_init.c |only StereoMorph-1.6/StereoMorph/src/Makevars |only StereoMorph-1.6/StereoMorph/src/Makevars.win |only 23 files changed, 215 insertions(+), 107 deletions(-)
Title: Fluid Use of Big Data in R
Description: Methods to get a grip on working with remote data sources ('SQL' databases,
'sparklyr' 'Spark' 2.0.0 and above) through 'dplyr'. Adds convenience functions to make such tasks more like
working with an in-memory 'data.frame'. Results do depend on which 'dplyr' data service you use.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between replyr versions 0.2.3 dated 2017-02-21 and 0.2.4 dated 2017-03-14
DESCRIPTION | 12 ++-- MD5 | 72 ++++++++++++++++------------- NAMESPACE | 2 NEWS.md | 6 ++ R/coalesce.R | 7 ++ R/copyToFrom.R | 84 +++++++++++++++++++++++++++------ R/filter.R | 2 R/inTest.R | 2 R/land.R | 30 ++++++++++-- R/renameRestrictCols.R | 4 - R/replyr.R | 4 - R/summary.R | 22 +++++++- R/uniqueValues.R | 16 +++--- README.md | 22 +++++--- build/vignette.rds |binary inst/doc/BizarroPipe.html | 11 ++-- inst/doc/NArm.html | 9 +-- inst/doc/ParametricExample.R | 21 +++----- inst/doc/ParametricExample.Rmd | 28 +++++------ inst/doc/ParametricExample.html | 30 +++++------- inst/doc/coalesce.R |only inst/doc/coalesce.Rmd |only inst/doc/coalesce.html |only inst/doc/letExample.html | 8 +-- inst/doc/replyr.R | 10 +++- inst/doc/replyr.Rmd | 17 +++++- inst/doc/replyr.html | 99 ++++++++++++++++++++-------------------- inst/doc/summary.R |only inst/doc/summary.Rmd |only inst/doc/summary.html |only man/grapes-land-grapes.Rd | 2 man/replyr.Rd | 4 - man/replyr_coalesce.Rd | 5 +- man/replyr_copy_to.Rd | 2 man/replyr_drop_table_name.Rd |only man/replyr_summary.Rd | 9 ++- man/replyr_uniqueValues.Rd | 2 vignettes/ParametricExample.Rmd | 28 +++++------ vignettes/coalesce.Rmd |only vignettes/replyr.Rmd | 17 +++++- vignettes/replyrs.png |only vignettes/summary.Rmd |only 42 files changed, 360 insertions(+), 227 deletions(-)
Title: Binning and Plotting of Linearly Referenced Data
Description: Short for 'linear binning', the linbin package provides functions
for manipulating, binning, and plotting linearly referenced data. Although
developed for data collected on river networks, it can be used with any interval
or point data referenced to a 1-dimensional coordinate system. Flexible bin
generation and batch processing makes it easy to compute and visualize variables
at multiple scales, useful for identifying patterns within and between variables
and investigating the influence of scale of observation on data interpretation.
Author: Ethan Z. Welty [aut, cre],
Christian E. Torgersen [ctb] (author support and guidance),
Samuel J. Brenkman [ctb] (elwha and quinault datasets),
Jeffrey J. Duda [ctb] (elwha dataset),
Jonathan B. Armstrong [ctb] (fishmotion dataset)
Maintainer: Ethan Z. Welty <ethan.welty+linbin@gmail.com>
Diff between linbin versions 0.1.1 dated 2015-11-17 and 0.1.2 dated 2017-03-14
DESCRIPTION | 10 ++-- MD5 | 84 ++++++++++++++++++++-------------------- NEWS.md |only R/datasets.R | 12 ++--- R/plot_events.R | 4 - R/sample_events.R | 9 ++-- README.md | 10 ++-- build/vignette.rds |binary inst/CITATION | 16 +++---- inst/doc/examples.R | 26 ++++++------ inst/doc/examples.Rmd | 34 ++++++++-------- inst/doc/examples.html | 56 ++++++++++++-------------- inst/doc/introduction.html | 34 +++++++--------- man/as_events.Rd | 6 +- man/build_function_call.Rd | 3 - man/crop_events.Rd | 1 man/cut_events.Rd | 1 man/elwha.Rd | 1 man/event_coverage.Rd | 1 man/event_gaps.Rd | 1 man/event_overlaps.Rd | 1 man/event_range.Rd | 1 man/events.Rd | 1 man/fill_event_gaps.Rd | 3 - man/find_intersecting_events.Rd | 1 man/fishmotion.Rd | 3 - man/if_else.Rd | 1 man/is_events.Rd | 1 man/is_not_integer.Rd | 1 man/netmap.Rd | 1 man/overlapping_events.Rd | 1 man/plot_events.Rd | 5 -- man/plot_events_single.Rd | 1 man/quinault.Rd | 1 man/read_events.Rd | 1 man/rgrep_exact.Rd | 1 man/sample_events.Rd | 1 man/sampling_functions.Rd | 3 - man/seq_events.Rd | 1 man/simple.Rd | 1 man/sorted_events.Rd | 3 - man/transform_events.Rd | 1 tools |only vignettes/examples.Rmd | 34 ++++++++-------- 44 files changed, 176 insertions(+), 201 deletions(-)
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 1.0.0 dated 2017-03-12 and 1.1.0 dated 2017-03-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/ecmback.r | 18 +++++++++++++++++- R/ecmpredict.r | 35 +++++++++++++++++------------------ man/Wilshire.Rd | 1 - man/durbinH.Rd | 1 - man/ecm.Rd | 1 - man/ecmback.Rd | 3 +-- man/ecmpredict.Rd | 7 +++---- man/lagpad.Rd | 1 - 10 files changed, 51 insertions(+), 42 deletions(-)
Title: A Universal Foreach Parallel Adaptor using the Future API of the
'future' Package
Description: Provides a '%dopar%' adaptor such that any type of futures can
be used as backends for the 'foreach' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 0.3.0 dated 2016-10-28 and 0.4.0 dated 2017-03-14
DESCRIPTION | 15 ++- MD5 | 33 ++++---- NAMESPACE | 3 NEWS | 122 +++++++++++++++++++++++-------- R/doFuture-package.R | 78 +++++++++++++++++-- R/doFuture.R | 160 ++++++++++++++++++++++++++++++++++------- R/utils.R |only build/vignette.rds |binary inst/tests2/foreach/examples.R | 17 ++-- inst/tests2/plyr/examples.R | 51 ++++++++++--- man/doFuture.Rd | 101 ++++++++++++++++++++++--- man/registerDoFuture.Rd | 1 tests/foreach,errors.R | 6 - tests/foreach,nested_dopar.R | 6 - tests/foreach.R | 8 +- tests/future.batchtools.R |only tests/incl/start,load-only.R | 3 tests/registerDoFuture.R | 11 +- tests/times.R |only 19 files changed, 480 insertions(+), 135 deletions(-)
Title: Fitting the copCAR Regression Model for Discrete Areal Data
Description: Provides tools for fitting the copCAR (Hughes, 2015)
<DOI:10.1080/10618600.2014.948178> regression model for discrete
areal data. Three types of estimation are supported (continuous
extension, composite marginal likelihood, and distributional transform),
for three types of outcomes (Bernoulli, negative binomial, and Poisson).
Author: Emily Goren <emily.goren@gmail.com> and John Hughes
<jphughesjr@gmail.com>
Maintainer: John Hughes <jphughesjr@gmail.com>
Diff between copCAR versions 2.0-1 dated 2017-02-21 and 2.0-2 dated 2017-03-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/copCAR.R | 15 ++++++++------- man/copCAR.Rd | 15 ++++++++------- 4 files changed, 23 insertions(+), 21 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' 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 0.3.0 dated 2017-02-09 and 0.4.0 dated 2017-03-14
biomartr-0.3.0/biomartr/R/getSubgroups.R |only biomartr-0.3.0/biomartr/R/listSubgroups.R |only biomartr-0.3.0/biomartr/inst/doc/Evolutionary_Transcriptomics.R |only biomartr-0.3.0/biomartr/inst/doc/Evolutionary_Transcriptomics.Rmd |only biomartr-0.3.0/biomartr/inst/doc/Evolutionary_Transcriptomics.html |only biomartr-0.3.0/biomartr/man/getSubgroups.Rd |only biomartr-0.3.0/biomartr/man/listSubgroups.Rd |only biomartr-0.3.0/biomartr/vignettes/Evolutionary_Transcriptomics.Rmd |only biomartr-0.4.0/biomartr/DESCRIPTION | 24 - biomartr-0.4.0/biomartr/MD5 | 138 +++--- biomartr-0.4.0/biomartr/NAMESPACE | 11 biomartr-0.4.0/biomartr/NEWS.md | 44 ++ biomartr-0.4.0/biomartr/R/biomart.R | 48 +- biomartr-0.4.0/biomartr/R/exists.ftp.file.R |only biomartr-0.4.0/biomartr/R/getAssemblyStats.R |only biomartr-0.4.0/biomartr/R/getAttributes.R | 62 ++ biomartr-0.4.0/biomartr/R/getCDS.R | 29 - biomartr-0.4.0/biomartr/R/getDatasets.R | 71 ++- biomartr-0.4.0/biomartr/R/getENSEMBL.Seq.R | 11 biomartr-0.4.0/biomartr/R/getENSEMBLGENOMES.Seq.R | 12 biomartr-0.4.0/biomartr/R/getENSEMBLGENOMESInfo.R |only biomartr-0.4.0/biomartr/R/getENSEMBLInfo.R |only biomartr-0.4.0/biomartr/R/getFilters.R | 57 ++ biomartr-0.4.0/biomartr/R/getGENOMEREPORT.R | 4 biomartr-0.4.0/biomartr/R/getGFF.R | 28 - biomartr-0.4.0/biomartr/R/getGenome.R | 27 - biomartr-0.4.0/biomartr/R/getGroups.R | 24 - biomartr-0.4.0/biomartr/R/getKingdoms.R | 2 biomartr-0.4.0/biomartr/R/getMarts.R | 31 - biomartr-0.4.0/biomartr/R/getProteome.R | 27 - biomartr-0.4.0/biomartr/R/getSubMarts.R |only biomartr-0.4.0/biomartr/R/listDatabases.R | 14 biomartr-0.4.0/biomartr/R/listGroups.R | 128 +++++- biomartr-0.4.0/biomartr/R/listKingdoms.R | 2 biomartr-0.4.0/biomartr/R/meta.retrieval.R | 128 +++++- biomartr-0.4.0/biomartr/R/meta.retrieval.all.R | 11 biomartr-0.4.0/biomartr/R/read_assemblystats.R |only biomartr-0.4.0/biomartr/R/read_cds.R | 2 biomartr-0.4.0/biomartr/R/read_genome.R | 2 biomartr-0.4.0/biomartr/R/read_proteome.R | 2 biomartr-0.4.0/biomartr/R/toupper_first_char.R |only biomartr-0.4.0/biomartr/R/utils.R | 9 biomartr-0.4.0/biomartr/README.md | 54 -- biomartr-0.4.0/biomartr/build/vignette.rds |binary biomartr-0.4.0/biomartr/inst/doc/BioMart_Examples.R |only biomartr-0.4.0/biomartr/inst/doc/BioMart_Examples.Rmd |only biomartr-0.4.0/biomartr/inst/doc/BioMart_Examples.html |only biomartr-0.4.0/biomartr/inst/doc/Database_Retrieval.R | 44 ++ biomartr-0.4.0/biomartr/inst/doc/Database_Retrieval.Rmd | 148 +------ biomartr-0.4.0/biomartr/inst/doc/Database_Retrieval.html | 116 +---- biomartr-0.4.0/biomartr/inst/doc/Functional_Annotation.R | 27 + biomartr-0.4.0/biomartr/inst/doc/Functional_Annotation.Rmd | 27 + biomartr-0.4.0/biomartr/inst/doc/Functional_Annotation.html | 57 ++ biomartr-0.4.0/biomartr/inst/doc/Introduction.html | 4 biomartr-0.4.0/biomartr/inst/doc/MetaGenome_Retrieval.R | 29 + biomartr-0.4.0/biomartr/inst/doc/MetaGenome_Retrieval.Rmd | 210 +++++++++- biomartr-0.4.0/biomartr/inst/doc/MetaGenome_Retrieval.html | 152 +++++++ biomartr-0.4.0/biomartr/inst/doc/Sequence_Retrieval.R | 6 biomartr-0.4.0/biomartr/inst/doc/Sequence_Retrieval.Rmd | 10 biomartr-0.4.0/biomartr/inst/doc/Sequence_Retrieval.html | 20 biomartr-0.4.0/biomartr/man/biomart.Rd | 28 - biomartr-0.4.0/biomartr/man/getAssemblyStats.Rd |only biomartr-0.4.0/biomartr/man/getENSEMBLGENOMESInfo.Rd |only biomartr-0.4.0/biomartr/man/getENSEMBLInfo.Rd |only biomartr-0.4.0/biomartr/man/getGENOMEREPORT.Rd |only biomartr-0.4.0/biomartr/man/getGroups.Rd | 2 biomartr-0.4.0/biomartr/man/getKingdoms.Rd | 2 biomartr-0.4.0/biomartr/man/listGroups.Rd | 20 biomartr-0.4.0/biomartr/man/listKingdoms.Rd | 2 biomartr-0.4.0/biomartr/man/meta.retrieval.Rd | 34 + biomartr-0.4.0/biomartr/man/meta.retrieval.all.Rd | 8 biomartr-0.4.0/biomartr/man/read_assemblystats.Rd |only biomartr-0.4.0/biomartr/tests/testthat/test-biomart.R | 4 biomartr-0.4.0/biomartr/tests/testthat/test-getAttributes.R | 4 biomartr-0.4.0/biomartr/tests/testthat/test-getDatasets.R | 2 biomartr-0.4.0/biomartr/tests/testthat/test-getFilters.R | 2 biomartr-0.4.0/biomartr/tests/testthat/test-getGroups().R |only biomartr-0.4.0/biomartr/tests/testthat/test-getKingdoms().R |only biomartr-0.4.0/biomartr/vignettes/BioMart_Examples.Rmd |only biomartr-0.4.0/biomartr/vignettes/Database_Retrieval.Rmd | 148 +------ biomartr-0.4.0/biomartr/vignettes/Functional_Annotation.Rmd | 27 + biomartr-0.4.0/biomartr/vignettes/MetaGenome_Retrieval.Rmd | 210 +++++++++- biomartr-0.4.0/biomartr/vignettes/Sequence_Retrieval.Rmd | 10 83 files changed, 1610 insertions(+), 745 deletions(-)