Title: Extending 'Dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.4.0 dated 2017-01-21 and 1.5.0 dated 2017-03-24
dendextend-1.4.0/dendextend/man/is.dendlist.Rd |only dendextend-1.4.0/dendextend/man/is.dendrogram.Rd |only dendextend-1.4.0/dendextend/man/is.dist.Rd |only dendextend-1.4.0/dendextend/man/is.hclust.Rd |only dendextend-1.4.0/dendextend/man/is.phylo.Rd |only dendextend-1.5.0/dendextend/ChangeLog | 131 ++++++++++- dendextend-1.5.0/dendextend/DESCRIPTION | 8 dendextend-1.5.0/dendextend/MD5 | 108 ++++----- dendextend-1.5.0/dendextend/NAMESPACE | 9 dendextend-1.5.0/dendextend/NEWS | 16 + dendextend-1.5.0/dendextend/NEWS.md | 16 + dendextend-1.5.0/dendextend/R/cor_bakers_gamma.R | 18 - dendextend-1.5.0/dendextend/R/cor_cophenetic.R | 28 +- dendextend-1.5.0/dendextend/R/cutree.dendrogram.R | 29 -- dendextend-1.5.0/dendextend/R/dendlist.R | 9 dendextend-1.5.0/dendextend/R/distinct_edges.R | 38 --- dendextend-1.5.0/dendextend/R/entanglement.R | 25 -- dendextend-1.5.0/dendextend/R/find_dend.R |only dendextend-1.5.0/dendextend/R/find_k.R | 6 dendextend-1.5.0/dendextend/R/ggdend.R | 29 -- dendextend-1.5.0/dendextend/R/highlight_branches.R | 13 - dendextend-1.5.0/dendextend/R/is.functions.R | 55 +--- dendextend-1.5.0/dendextend/R/labels.R | 38 --- dendextend-1.5.0/dendextend/R/labels_colors.R | 22 - dendextend-1.5.0/dendextend/R/nleaves.R | 53 +--- dendextend-1.5.0/dendextend/R/rotate.R | 68 +---- dendextend-1.5.0/dendextend/R/set.dendrogram.R | 47 --- dendextend-1.5.0/dendextend/R/tanglegram.R | 73 ------ dendextend-1.5.0/dendextend/R/unbranch.R | 20 - dendextend-1.5.0/dendextend/R/untangle.R | 51 +--- dendextend-1.5.0/dendextend/build/vignette.rds |binary dendextend-1.5.0/dendextend/inst/doc/Cluster_Analysis.html | 16 - dendextend-1.5.0/dendextend/inst/doc/FAQ.html | 4 dendextend-1.5.0/dendextend/inst/doc/Quick_Introduction.html | 4 dendextend-1.5.0/dendextend/inst/doc/introduction.html | 84 +++---- dendextend-1.5.0/dendextend/man/click_rotate.Rd | 5 dendextend-1.5.0/dendextend/man/cor_bakers_gamma.Rd | 14 - dendextend-1.5.0/dendextend/man/cor_cophenetic.Rd | 20 - dendextend-1.5.0/dendextend/man/cutree-methods.Rd | 37 +-- dendextend-1.5.0/dendextend/man/dend_diff.Rd | 9 dendextend-1.5.0/dendextend/man/entanglement.Rd | 12 - dendextend-1.5.0/dendextend/man/find_dend.Rd |only dendextend-1.5.0/dendextend/man/find_k.Rd | 9 dendextend-1.5.0/dendextend/man/ggdend.Rd | 23 + dendextend-1.5.0/dendextend/man/highlight_branches.Rd | 18 - dendextend-1.5.0/dendextend/man/highlight_distinct_edges.Rd | 13 - dendextend-1.5.0/dendextend/man/is_some_class.Rd |only dendextend-1.5.0/dendextend/man/labels-assign.Rd | 7 dendextend-1.5.0/dendextend/man/labels_colors.Rd | 4 dendextend-1.5.0/dendextend/man/ladderize.Rd | 4 dendextend-1.5.0/dendextend/man/nleaves.Rd | 2 dendextend-1.5.0/dendextend/man/nnodes.Rd | 2 dendextend-1.5.0/dendextend/man/rotate.Rd | 13 - dendextend-1.5.0/dendextend/man/set.Rd | 38 --- dendextend-1.5.0/dendextend/man/shuffle.Rd | 2 dendextend-1.5.0/dendextend/man/tanglegram.Rd | 98 +++----- dendextend-1.5.0/dendextend/man/unbranch.Rd | 8 dendextend-1.5.0/dendextend/man/untangle.Rd | 23 + dendextend-1.5.0/dendextend/tests/testthat/test-untangle.R | 23 + 59 files changed, 622 insertions(+), 780 deletions(-)
Title: Common Plots for Analysis
Description: Example 'ggplot2' plots we have found useful, under a standardized
calling interface.
Author: Nina Zumel, John Mount
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 0.2.2 dated 2017-02-17 and 0.2.3 dated 2017-03-24
DESCRIPTION | 10 ++-- MD5 | 72 +++++++++++++++++----------------- NAMESPACE | 1 R/ROC.R | 54 ++++++++++++++++--------- R/ScatterHist.R | 37 +++++++++-------- R/ScatterHistC.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/WVPlots_concept.html | 8 +-- inst/doc/WVPlots_examples.html | 14 +++--- man/BinaryYScatterPlot.Rd | 1 man/ClevelandDotPlot.Rd | 1 man/ConditionalSmoothedScatterPlot.Rd | 1 man/DiscreteDistribution.Rd | 1 man/DoubleDensityPlot.Rd | 1 man/DoubleHistogramPlot.Rd | 1 man/GainCurvePlot.Rd | 1 man/GainCurvePlotC.Rd | 1 man/GainCurvePlotWithNotation.Rd | 1 man/PRPlot.Rd | 1 man/PlotDistCountNormal.Rd | 1 man/PlotDistDensityBeta.Rd | 1 man/PlotDistDensityNormal.Rd | 1 man/PlotDistHistBeta.Rd | 1 man/ROCPlot.Rd | 1 man/ROCPlotPair.Rd | 1 man/ROCPlotPair2.Rd | 1 man/ScatterBoxPlot.Rd | 1 man/ScatterBoxPlotH.Rd | 1 man/ScatterHist.Rd | 1 man/ScatterHistC.Rd | 1 man/ScatterHistN.Rd | 1 man/ShadedDensity.Rd | 1 man/WVPlots.Rd | 1 man/calcPR.Rd | 1 man/graphROC.Rd |only man/reexports.Rd | 9 +++- tools |only 38 files changed, 120 insertions(+), 114 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include Sql Server, Oracle,
PostgreSql, Amazon RedShift, and Microsoft PDW.
Author: Martijn J. Schuemie [aut, cre],
Marc A. Suchard [aut],
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.2.0 dated 2017-01-16 and 1.3.0 dated 2017-03-24
DESCRIPTION | 10 MD5 | 63 +-- NEWS | 19 + R/HelperFunctions.R | 57 +-- R/RenderSql.R | 31 + README.md | 9 build/vignette.rds |binary inst/csv/replacementPatterns.csv | 579 +++++++++++++++++++--------------- inst/doc/UsingSqlRender.Rmd | 26 + inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary java/SqlRender.jardesc | 4 java/org/ohdsi/sql/MainClass.java |only java/org/ohdsi/sql/SqlRender.java | 26 + java/org/ohdsi/sql/SqlSplit.java | 121 +++---- java/org/ohdsi/sql/SqlTranslate.java | 185 +++++++++- java/org/ohdsi/sql/StringUtils.java | 24 + java/org/ohdsi/sql/TestSqlRender.java | 26 + man/camelCaseToSnakeCase.Rd | 1 man/createRWrapperForSql.Rd | 1 man/loadRenderTranslateSql.Rd | 1 man/readSql.Rd | 1 man/renderSql.Rd | 1 man/renderSqlFile.Rd | 1 man/snakeCaseToCamelCase.Rd | 1 man/splitSql.Rd | 1 man/translateSql.Rd | 20 - man/translateSqlFile.Rd | 7 man/writeSql.Rd | 1 tests/testthat/test-helperFunctions.R | 4 tests/testthat/test-renderSql.R | 16 tests/testthat/test-translateSql.R | 315 ++++++++++++------ vignettes/UsingSqlRender.Rmd | 26 + 33 files changed, 1031 insertions(+), 546 deletions(-)
Title: Format Significance Summaries for Reports
Description: Succinctly format significance summaries of
various models and tests. The main purpose is unified reporting and planning
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 0.1.4 dated 2017-02-16 and 0.1.5 dated 2017-03-24
DESCRIPTION | 10 +- MD5 | 115 +++++++++++++++++----------------- NEWS.md | 8 +- R/AUCTest.R | 12 +++ R/ChiSqTest.R | 8 ++ R/CorTest.R | 6 + R/EmpiricalFns.R | 2 R/FTest.R | 10 ++ R/TTest.R | 8 ++ R/fns.R | 28 ++++++-- README.md | 2 build/vignette.rds |binary inst/doc/lmExample.R |only inst/doc/lmExample.Rmd |only inst/doc/lmExample.html |only inst/doc/sigrFormatting.html | 4 - man/calcAUC.Rd | 1 man/calcDeviance.Rd | 1 man/calcSSE.Rd | 3 man/estimateDifferenceZeroCrossing.Rd | 1 man/getRenderingFormat.Rd | 1 man/permTestAUC.Rd | 1 man/permutationScoreModel.Rd | 1 man/print.sigr_statistic.Rd | 1 man/render.Rd | 1 man/render.sigr_aucpairtest.Rd | 1 man/render.sigr_aucpermtest.Rd | 1 man/render.sigr_aucresamptest.Rd | 1 man/render.sigr_chisqtest.Rd | 1 man/render.sigr_cortest.Rd | 1 man/render.sigr_emptest.Rd | 1 man/render.sigr_fishertest.Rd | 1 man/render.sigr_ftest.Rd | 1 man/render.sigr_permtest.Rd | 1 man/render.sigr_significance.Rd | 1 man/render.sigr_ttest.Rd | 1 man/resampleScoreModel.Rd | 1 man/resampleScoreModelPair.Rd | 1 man/resampleTestAUC.Rd | 1 man/sigr.Rd | 1 man/testAUCpair.Rd | 1 man/wrapChiSqTest.Rd | 1 man/wrapChiSqTest.data.frame.Rd | 1 man/wrapChiSqTest.glm.Rd | 1 man/wrapChiSqTestImpl.Rd | 1 man/wrapCorTest.Rd | 1 man/wrapCorTest.data.frame.Rd | 1 man/wrapCorTest.htest.Rd | 1 man/wrapFTest.Rd | 1 man/wrapFTest.data.frame.Rd | 1 man/wrapFTest.lm.Rd | 1 man/wrapFTestImpl.Rd | 1 man/wrapFisherTest.Rd | 1 man/wrapFisherTest.data.frame.Rd | 1 man/wrapFisherTest.htest.Rd | 1 man/wrapSignificance.Rd | 1 man/wrapTTest.Rd | 1 man/wrapTTest.data.frame.Rd | 1 man/wrapTTest.htest.Rd | 1 tools |only vignettes/lmExample.Rmd |only 61 files changed, 140 insertions(+), 118 deletions(-)
Title: Analyzing Archival Tagging Data
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Author: Robert Bauer
Maintainer: Robert Bauer <robert.bauer@ird.fr>
Diff between RchivalTag versions 0.0.1 dated 2017-03-21 and 0.0.2 dated 2017-03-24
ChangeLog |only DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- R/hist_tad.r | 3 +-- inst/doc/RchivalTag.pdf |binary man/classify_DayTime.Rd | 15 +++++++++++++++ man/hist_tad.Rd | 14 +++++++++++++- man/hist_tat.Rd | 14 +++++++++++++- man/plot_geopos.Rd | 2 +- man/ts2histos.Rd | 13 ++++++++++++- 10 files changed, 68 insertions(+), 18 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multivalue sets ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a Boolean algorithm that results in a
minimal causal combination which explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/shared/jquery-AUTHORS.txt),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 2.5 dated 2016-11-10 and 2.6 dated 2017-03-24
QCA-2.5/QCA/R/plot1.R |only QCA-2.5/QCA/inst/staticdocs/plot1-1.svg |only QCA-2.5/QCA/inst/staticdocs/plot1-2.svg |only QCA-2.5/QCA/inst/staticdocs/plot1-3.svg |only QCA-2.5/QCA/inst/staticdocs/plot1-4.svg |only QCA-2.5/QCA/inst/staticdocs/plot1.html |only QCA-2.5/QCA/man/plot1.Rd |only QCA-2.5/QCA/src/m2.c |only QCA-2.5/QCA/src/superSubset.c |only QCA-2.6/QCA/DESCRIPTION | 10 - QCA-2.6/QCA/MD5 | 127 ++++++------ QCA-2.6/QCA/NAMESPACE | 8 QCA-2.6/QCA/R/Xplot.R |only QCA-2.6/QCA/R/allExpressions.R | 11 - QCA-2.6/QCA/R/createMatrix.R | 59 +++++- QCA-2.6/QCA/R/deMorgan.R | 7 QCA-2.6/QCA/R/eqmcc.R | 2 QCA-2.6/QCA/R/export.R | 2 QCA-2.6/QCA/R/factorize.R | 24 +- QCA-2.6/QCA/R/getNoflevels.R | 14 + QCA-2.6/QCA/R/makeChart.R | 9 QCA-2.6/QCA/R/pof.R | 8 QCA-2.6/QCA/R/recode.R | 8 QCA-2.6/QCA/R/solveChart.R | 21 -- QCA-2.6/QCA/R/sortMatrix.R | 6 QCA-2.6/QCA/R/string.R | 17 + QCA-2.6/QCA/R/superSubset.R | 118 ++++-------- QCA-2.6/QCA/R/translate.R | 5 QCA-2.6/QCA/inst/ChangeLog | 17 + QCA-2.6/QCA/inst/gui/server.R | 2 QCA-2.6/QCA/inst/gui/www/js/maincode.js | 137 ++++++++------ QCA-2.6/QCA/inst/gui/www/js/raphael.export.js |only QCA-2.6/QCA/inst/gui/www/js/utils.js | 7 QCA-2.6/QCA/inst/staticdocs/CV.html | 4 QCA-2.6/QCA/inst/staticdocs/LegacyDatasets.html | 4 QCA-2.6/QCA/inst/staticdocs/Lipset.html | 4 QCA-2.6/QCA/inst/staticdocs/QCA-internal.html | 4 QCA-2.6/QCA/inst/staticdocs/QCA.package.html | 4 QCA-2.6/QCA/inst/staticdocs/RS.html | 4 QCA-2.6/QCA/inst/staticdocs/SOPexpression.html | 4 QCA-2.6/QCA/inst/staticdocs/XYplot.html | 4 QCA-2.6/QCA/inst/staticdocs/Xplot-1.svg |only QCA-2.6/QCA/inst/staticdocs/Xplot-2.svg |only QCA-2.6/QCA/inst/staticdocs/Xplot-3.svg |only QCA-2.6/QCA/inst/staticdocs/Xplot-4.svg |only QCA-2.6/QCA/inst/staticdocs/Xplot.html |only QCA-2.6/QCA/inst/staticdocs/calibrate.html | 4 QCA-2.6/QCA/inst/staticdocs/chartFunctions.html | 4 QCA-2.6/QCA/inst/staticdocs/deMorgan.html | 4 QCA-2.6/QCA/inst/staticdocs/eqmcc.html | 4 QCA-2.6/QCA/inst/staticdocs/export.html | 4 QCA-2.6/QCA/inst/staticdocs/factorize.html | 4 QCA-2.6/QCA/inst/staticdocs/findTh.html | 4 QCA-2.6/QCA/inst/staticdocs/fuzzyops.html | 4 QCA-2.6/QCA/inst/staticdocs/implicantMatrixFunctions.html | 25 +- QCA-2.6/QCA/inst/staticdocs/index.html | 10 - QCA-2.6/QCA/inst/staticdocs/intersection.html | 4 QCA-2.6/QCA/inst/staticdocs/pof.html | 4 QCA-2.6/QCA/inst/staticdocs/recode.html | 4 QCA-2.6/QCA/inst/staticdocs/retention.html | 4 QCA-2.6/QCA/inst/staticdocs/runGUI.html | 4 QCA-2.6/QCA/inst/staticdocs/subsetsAndSupersets.html | 18 + QCA-2.6/QCA/inst/staticdocs/truthTable.html | 8 QCA-2.6/QCA/man/QCA-internal.Rd | 3 QCA-2.6/QCA/man/QCA.package.Rd | 28 +- QCA-2.6/QCA/man/Xplot.Rd |only QCA-2.6/QCA/man/eqmcc.Rd | 7 QCA-2.6/QCA/man/implicantMatrixFunctions.Rd | 26 +- QCA-2.6/QCA/man/subsetsAndSupersets.Rd | 10 - QCA-2.6/QCA/man/truthTable.Rd | 3 QCA-2.6/QCA/src/QCA.c |only QCA-2.6/QCA/src/registerDynamicSymbol.c |only QCA-2.6/QCA/src/solveChart.c | 100 +++++++--- QCA-2.6/QCA/src/truthTable.c | 4 74 files changed, 555 insertions(+), 390 deletions(-)
Title: High Frequency Portfolio Analytics by PortfolioEffect
Description: R interface to PortfolioEffect cloud service for backtesting
high frequency trading (HFT) strategies, intraday portfolio analysis
and optimization. Includes auto-calibrating model pipeline for market
microstructure noise, risk factors, price jumps/outliers, tail risk
(high-order moments) and price fractality (long memory). Constructed
portfolios could use client-side market data or access HF intraday price
history for all major US Equities. See <https://www.portfolioeffect.com/>
for more information on the PortfolioEffect high frequency portfolio
analytics platform.
Author: Andrey Kostin [aut, cre],
Aleksey Zemnitskiy [aut],
Oleg Nechaev [aut],
Craig Otis and others [ctb, cph] (OpenFAST library),
Daniel Lemire, Muraoka Taro and others [ctb, cph] (JavaFastPFOR
library),
Joe Walnes, Jorg Schaible and others [ctb, cph] (XStream library),
Dain Sundstrom [ctb, cph] (Snappy library),
Extreme! Lab, Indiana University [ctb, cph] (XPP3 library),
The Apache Software Foundation [ctb, cph] (Apache Log4j and Commons
Lang libraries),
Google, Inc. [ctb, cph] (GSON library),
Free Software Foundation [ctb, cph] (GNU Trove and GNU Crypto
libraries)
Maintainer: Andrey Kostin <andrey.kostin@portfolioeffect.com>
Diff between PortfolioEffectHFT versions 1.7 dated 2016-09-17 and 1.8 dated 2017-03-24
PortfolioEffectHFT-1.7/PortfolioEffectHFT/man/util_summary.Rd |only PortfolioEffectHFT-1.8/PortfolioEffectHFT/DESCRIPTION | 10 PortfolioEffectHFT-1.8/PortfolioEffectHFT/MD5 | 43 +-- PortfolioEffectHFT-1.8/PortfolioEffectHFT/NAMESPACE | 1 PortfolioEffectHFT-1.8/PortfolioEffectHFT/NEWS | 10 PortfolioEffectHFT-1.8/PortfolioEffectHFT/R/forecast.R | 2 PortfolioEffectHFT-1.8/PortfolioEffectHFT/R/metric.R | 13 - PortfolioEffectHFT-1.8/PortfolioEffectHFT/R/plot.R | 52 +++- PortfolioEffectHFT-1.8/PortfolioEffectHFT/R/portfolio.R | 34 +-- PortfolioEffectHFT-1.8/PortfolioEffectHFT/R/position.R | 35 +-- PortfolioEffectHFT-1.8/PortfolioEffectHFT/R/util.R | 112 ++++++---- PortfolioEffectHFT-1.8/PortfolioEffectHFT/build/vignette.rds |binary PortfolioEffectHFT-1.8/PortfolioEffectHFT/demo/holding_period_risks_demo.R | 6 PortfolioEffectHFT-1.8/PortfolioEffectHFT/demo/lf_hf_strategy_demo.R | 4 PortfolioEffectHFT-1.8/PortfolioEffectHFT/demo/txnCosts_demo.R | 2 PortfolioEffectHFT-1.8/PortfolioEffectHFT/inst/doc/PortfolioEffectHFT.pdf |binary PortfolioEffectHFT-1.8/PortfolioEffectHFT/inst/java/portfolioeffect-quant-client-1.0.jar |binary PortfolioEffectHFT-1.8/PortfolioEffectHFT/man/create_metric.Rd | 4 PortfolioEffectHFT-1.8/PortfolioEffectHFT/man/optimization_run.Rd | 10 PortfolioEffectHFT-1.8/PortfolioEffectHFT/man/portfolio-class.Rd | 17 + PortfolioEffectHFT-1.8/PortfolioEffectHFT/man/portfolio_availableSymbols.Rd | 13 - PortfolioEffectHFT-1.8/PortfolioEffectHFT/man/position-class.Rd | 2 PortfolioEffectHFT-1.8/PortfolioEffectHFT/man/util_plot2df.Rd | 2 23 files changed, 223 insertions(+), 149 deletions(-)
More information about PortfolioEffectHFT at CRAN
Permanent link
Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: Provides efficient tools for population genomics data analysis,
able to process individual loci, large sets of loci, or whole genomes. PopGenome not only
implements a wide range of population genetics statistics, but also facilitates the easy
implementation of new algorithms by other researchers. PopGenome is optimized for speed via
the seamless integration of C code.
Author: Bastian Pfeifer [aut, cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Bastian Pfeifer <Bastian.Pfeifer@uni-duesseldorf.de>
Diff between PopGenome versions 2.2.2 dated 2017-03-15 and 2.2.3 dated 2017-03-24
DESCRIPTION | 8 MD5 | 14 build/vignette.rds |binary inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary inst/doc/Integration_of_new_Methods.pdf |binary inst/doc/Whole_genome_analyses_using_VCF_files.pdf | 408 ++++++++---------- src/Makevars | 2 src/Makevars.win | 2 8 files changed, 210 insertions(+), 224 deletions(-)
Title: Comprehensive Research Synthesis Tools for Systematic Reviews
and Meta-Analysis
Description: Functionalities for facilitating systematic reviews, data
extractions, and meta-analyses. It includes a GUI (graphical user interface)
to help screen the abstracts and titles of bibliographic data; tools to assign
screening effort across multiple collaborators/reviewers and to assess inter-
reviewer reliability; tools to help automate the download and retrieval of
journal PDF articles from online databases; figure and image extractions
from PDFs; web scraping of citations; automated and manual data extraction
from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items for
Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools
to fill gaps in incomplete or missing study parameters; generation of random
effects sizes for Hedges' d, log response ratio, odds ratio, and correlation
coefficients for Monte Carlo experiments; covariance equations for modelling
dependencies among multiple effect sizes (e.g., effect sizes with a common
control); and finally summaries that replicate analyses and outputs from
widely used but no longer updated meta-analysis software. Funding for this
package was supported by National Science Foundation (NSF) grants
DBI-1262545 and DEB-1451031.
Author: Marc J. Lajeunesse [aut, cre]
Maintainer: Marc J. Lajeunesse <lajeunesse@usf.edu>
Diff between metagear versions 0.3 dated 2017-01-03 and 0.4 dated 2017-03-24
metagear-0.3/metagear/R/MA_phylogenetic.R |only metagear-0.3/metagear/R/MA_utils.R |only metagear-0.3/metagear/inst/doc/metagear_basic_vignette_v0.31.pdf |only metagear-0.3/metagear/inst/doc/metagear_basic_vignette_v0.31.pdf.asis |only metagear-0.3/metagear/vignettes/metagear_basic_vignette_v0.31.Rmd |only metagear-0.3/metagear/vignettes/metagear_basic_vignette_v0.31.pdf.asis |only metagear-0.4/metagear/DESCRIPTION | 14 metagear-0.4/metagear/MD5 | 125 ++--- metagear-0.4/metagear/NAMESPACE | 1 metagear-0.4/metagear/NEWS.md | 12 metagear-0.4/metagear/R/PDF_extractImages.R | 9 metagear-0.4/metagear/R/PDF_utils.R | 5 metagear-0.4/metagear/R/abstract_screener.R | 10 metagear-0.4/metagear/R/effort_redistribute.R | 90 ++++ metagear-0.4/metagear/R/figure_split.R |only metagear-0.4/metagear/R/figure_utils.R | 37 + metagear-0.4/metagear/R/plot_PRISMA.R | 63 ++ metagear-0.4/metagear/R/plot_PRISMA_utils.R | 217 ++++++++-- metagear-0.4/metagear/README.md |only metagear-0.4/metagear/build/vignette.rds |binary metagear-0.4/metagear/inst/doc/metagear_basic_vignette_v0.4.pdf |only metagear-0.4/metagear/inst/doc/metagear_basic_vignette_v0.4.pdf.asis |only metagear-0.4/metagear/man/Kam_et_al_2003_Fig2.Rd | 1 metagear-0.4/metagear/man/Kortum_and_Acymyan_2013_Fig4.Rd | 1 metagear-0.4/metagear/man/MA_effectsTable.Rd | 1 metagear-0.4/metagear/man/PDF_download.Rd | 1 metagear-0.4/metagear/man/PDF_extractImages.Rd | 1 metagear-0.4/metagear/man/PDFs_collect.Rd | 1 metagear-0.4/metagear/man/abstract_screener.Rd | 5 metagear-0.4/metagear/man/browse_DOI.Rd | 1 metagear-0.4/metagear/man/chachi.Rd | 1 metagear-0.4/metagear/man/covariance_commonControl.Rd | 1 metagear-0.4/metagear/man/effort_distribute.Rd | 1 metagear-0.4/metagear/man/effort_initialize.Rd | 1 metagear-0.4/metagear/man/effort_merge.Rd | 1 metagear-0.4/metagear/man/effort_redistribute.Rd | 1 metagear-0.4/metagear/man/effort_summary.Rd | 1 metagear-0.4/metagear/man/example_references_metagear.Rd | 1 metagear-0.4/metagear/man/figure_add.Rd | 1 metagear-0.4/metagear/man/figure_barPlot.Rd | 1 metagear-0.4/metagear/man/figure_detectAllPoints.Rd | 1 metagear-0.4/metagear/man/figure_detectAxis.Rd | 1 metagear-0.4/metagear/man/figure_display.Rd | 1 metagear-0.4/metagear/man/figure_displayDetectedPoints.Rd | 1 metagear-0.4/metagear/man/figure_displayDetections.Rd | 1 metagear-0.4/metagear/man/figure_extractDetectedPoints.Rd | 1 metagear-0.4/metagear/man/figure_read.Rd | 1 metagear-0.4/metagear/man/figure_removeOutlyingPoints.Rd | 1 metagear-0.4/metagear/man/figure_scatterPlot.Rd | 1 metagear-0.4/metagear/man/figure_splitPlot.Rd |only metagear-0.4/metagear/man/figure_transformByColors.Rd | 1 metagear-0.4/metagear/man/figure_transformToBinary.Rd | 1 metagear-0.4/metagear/man/figure_write.Rd | 1 metagear-0.4/metagear/man/impute_SD.Rd | 1 metagear-0.4/metagear/man/impute_missingness.Rd | 1 metagear-0.4/metagear/man/isPDF.Rd | 1 metagear-0.4/metagear/man/metagear-package.Rd | 7 metagear-0.4/metagear/man/plot_PRISMA.Rd | 30 + metagear-0.4/metagear/man/random_N.Rd | 1 metagear-0.4/metagear/man/random_OR.Rd | 1 metagear-0.4/metagear/man/random_RR.Rd | 1 metagear-0.4/metagear/man/random_d.Rd | 1 metagear-0.4/metagear/man/random_missingness.Rd | 1 metagear-0.4/metagear/man/random_pairedN.Rd | 1 metagear-0.4/metagear/man/random_r.Rd | 1 metagear-0.4/metagear/man/replicate_MetaWin2.0.Rd | 1 metagear-0.4/metagear/man/scrape_bibliography.Rd | 1 metagear-0.4/metagear/tests/testthat/test-effort_redistribute.R | 2 metagear-0.4/metagear/vignettes/metagear_basic_vignette_v0.4.Rmd |only metagear-0.4/metagear/vignettes/metagear_basic_vignette_v0.4.pdf.asis |only 70 files changed, 505 insertions(+), 163 deletions(-)
Title: Compute, Handle, Plot and Model Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut, cre],
Rich FitzJohn [aut],
Jun Cai [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between incidence versions 1.1.1 dated 2017-02-15 and 1.1.2 dated 2017-03-24
incidence-1.1.1/incidence/README.md |only incidence-1.1.2/incidence/DESCRIPTION | 8 incidence-1.1.2/incidence/MD5 | 23 - incidence-1.1.2/incidence/NEWS.md | 15 incidence-1.1.2/incidence/R/incidence.R | 249 +++++++------- incidence-1.1.2/incidence/R/subset.R | 23 + incidence-1.1.2/incidence/build/vignette.rds |binary incidence-1.1.2/incidence/inst/doc/customize_plot.html | 18 - incidence-1.1.2/incidence/inst/doc/incidence_class.html | 4 incidence-1.1.2/incidence/inst/doc/overview.html | 36 +- incidence-1.1.2/incidence/man/incidence.Rd | 11 incidence-1.1.2/incidence/tests/testthat/test-incidence.R | 4 incidence-1.1.2/incidence/tests/testthat/test-subset.R | 39 +- 13 files changed, 244 insertions(+), 186 deletions(-)
Title: Incremental Decomposition Methods
Description: Incremental Multiple Correspondence Analysis and Principal
Component Analysis.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide
Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.7.1 dated 2016-10-26 and 1.8.0 dated 2017-03-24
DESCRIPTION | 8 +++---- MD5 | 37 ++++++++++++++++---------------- R/add_eig.r | 56 ++++++++++++++++++++++++------------------------- R/add_es.R | 18 +++++++++------ R/add_svd.R | 57 +++++++++++++++++++------------------------------- R/do_es.r | 21 +++++++++++------- R/h_exact_mca.r | 52 ++++++++++++++++++++++++++++++--------------- R/i_mca.r | 11 ++++++--- R/i_pca.r | 59 ++++++++++++++++++++++++++++++++++++---------------- R/mat_split.r | 34 ++++++++++++++++++++--------- R/old_add_eig.R |only R/r_live_mca.r | 41 ++++++++++++++++++++++-------------- R/update.i_mca.R | 33 +++++++++++++++++------------ R/update.i_pca.R | 39 +++++++++++++++++++++++----------- man/add_es.Rd | 24 +++++---------------- man/i_mca.Rd | 8 +++---- man/i_pca.Rd | 16 +++++++------- man/idm.Rd | 4 +-- man/update.i_mca.Rd | 18 +++++++-------- man/update.i_pca.Rd | 7 +++--- 20 files changed, 308 insertions(+), 235 deletions(-)
Title: Provides Easy Downloading Capabilities for the UK Parliament API
Description: Description: Provides functions to download data from the <http://www.data.parliament.uk/> APIs. Because of the structure of the API, there is a named function for each type of available data for ease of use, as well as some functions designed to retrieve specific pieces of commonly used data. Functions for each new API will be added as and when they become available.
Author: Evan Odell [aut, cre]
Maintainer: Evan Odell <evanodell91@gmail.com>
Diff between hansard versions 0.3.4 dated 2016-12-13 and 0.4.0 dated 2017-03-24
hansard-0.3.4/hansard/R/hansard.r |only hansard-0.3.4/hansard/R/hansard_basic.R |only hansard-0.3.4/hansard/R/lords_vote_record.R |only hansard-0.3.4/hansard/man/hansard_basic.Rd |only hansard-0.3.4/hansard/man/lords_vote_record.Rd |only hansard-0.4.0/hansard/DESCRIPTION | 17 hansard-0.4.0/hansard/MD5 | 159 +++--- hansard-0.4.0/hansard/NAMESPACE | 15 hansard-0.4.0/hansard/NEWS.md | 63 ++ hansard-0.4.0/hansard/R/all_answered_questions.R | 106 ++-- hansard-0.4.0/hansard/R/bills.R | 167 +++--- hansard-0.4.0/hansard/R/commons_answered_questions.R | 159 ++---- hansard-0.4.0/hansard/R/commons_divisions.R | 390 ++++----------- hansard-0.4.0/hansard/R/commons_oral_question_times.R | 141 ++--- hansard-0.4.0/hansard/R/commons_oral_questions.R | 255 ++------- hansard-0.4.0/hansard/R/commons_terms.R | 92 ++- hansard-0.4.0/hansard/R/commons_written_questions.R | 173 ++---- hansard-0.4.0/hansard/R/constituencies.R | 92 +-- hansard-0.4.0/hansard/R/early_day_motions.R | 183 ++----- hansard-0.4.0/hansard/R/election_results.R | 98 +-- hansard-0.4.0/hansard/R/elections.R | 87 +-- hansard-0.4.0/hansard/R/epetition.R | 179 ++---- hansard-0.4.0/hansard/R/hansard.R |only hansard-0.4.0/hansard/R/hansard_generic.R | 22 hansard-0.4.0/hansard/R/hansard_tidy.R |only hansard-0.4.0/hansard/R/lord_vote_record.R |only hansard-0.4.0/hansard/R/lords_amendments.R | 71 +- hansard-0.4.0/hansard/R/lords_attendance.R | 110 +--- hansard-0.4.0/hansard/R/lords_divisions.R | 301 +++-------- hansard-0.4.0/hansard/R/lords_written_questions.R | 122 ++-- hansard-0.4.0/hansard/R/members.R | 355 +++++++------ hansard-0.4.0/hansard/R/members_search.R | 50 + hansard-0.4.0/hansard/R/mp_edms.R | 173 ++++-- hansard-0.4.0/hansard/R/mp_questions.R | 164 +++--- hansard-0.4.0/hansard/R/mp_vote_record.R | 202 ++++--- hansard-0.4.0/hansard/R/papers_laid.R | 89 ++- hansard-0.4.0/hansard/R/publication_logs.R | 73 ++ hansard-0.4.0/hansard/R/research_briefings.R | 305 ++++------- hansard-0.4.0/hansard/R/research_briefings_lists.R |only hansard-0.4.0/hansard/R/sessions_info.R | 101 ++- hansard-0.4.0/hansard/R/tv_programmes.R | 177 +++++- hansard-0.4.0/hansard/README.md | 13 hansard-0.4.0/hansard/build/vignette.rds |binary hansard-0.4.0/hansard/inst/doc/introduction.R | 92 +-- hansard-0.4.0/hansard/inst/doc/introduction.Rmd | 201 ++----- hansard-0.4.0/hansard/inst/doc/introduction.html | 175 ++---- hansard-0.4.0/hansard/man/all_answered_questions.Rd | 17 hansard-0.4.0/hansard/man/bills.Rd | 37 - hansard-0.4.0/hansard/man/commons_answered_questions.Rd | 26 - hansard-0.4.0/hansard/man/commons_division_date.Rd | 13 hansard-0.4.0/hansard/man/commons_divisions.Rd | 44 - hansard-0.4.0/hansard/man/commons_oral_question_times.Rd | 16 hansard-0.4.0/hansard/man/commons_oral_questions.Rd | 37 - hansard-0.4.0/hansard/man/commons_terms.Rd | 23 hansard-0.4.0/hansard/man/commons_written_questions.Rd | 26 - hansard-0.4.0/hansard/man/constituencies.Rd | 17 hansard-0.4.0/hansard/man/early_day_motions.Rd | 30 - hansard-0.4.0/hansard/man/election_results.Rd | 13 hansard-0.4.0/hansard/man/elections.Rd | 12 hansard-0.4.0/hansard/man/epetition.Rd | 27 - hansard-0.4.0/hansard/man/hansard.Rd | 13 hansard-0.4.0/hansard/man/hansard_generic.Rd | 5 hansard-0.4.0/hansard/man/hansard_tidy.Rd |only hansard-0.4.0/hansard/man/lord_vote_record.Rd |only hansard-0.4.0/hansard/man/lords_amendments.Rd | 16 hansard-0.4.0/hansard/man/lords_attendance.Rd | 17 hansard-0.4.0/hansard/man/lords_divisions.Rd | 28 - hansard-0.4.0/hansard/man/lords_written_questions.Rd | 23 hansard-0.4.0/hansard/man/members.Rd | 36 - hansard-0.4.0/hansard/man/members_search.Rd | 7 hansard-0.4.0/hansard/man/mp_edms.Rd | 22 hansard-0.4.0/hansard/man/mp_questions.Rd | 16 hansard-0.4.0/hansard/man/mp_vote_record.Rd | 30 - hansard-0.4.0/hansard/man/papers_laid.Rd | 21 hansard-0.4.0/hansard/man/publication_logs.Rd | 16 hansard-0.4.0/hansard/man/research_briefings.Rd | 39 - hansard-0.4.0/hansard/man/research_briefings_lists.Rd |only hansard-0.4.0/hansard/man/sessions_info.Rd | 21 hansard-0.4.0/hansard/man/tv_programmes.Rd | 34 + hansard-0.4.0/hansard/tests |only hansard-0.4.0/hansard/vignettes/introduction.Rmd | 201 ++----- 81 files changed, 2846 insertions(+), 3209 deletions(-)
Title: Estimating Structural Invariants of Graphical Models
Description: Efficient methods for constructing confidence intervals of monotone
graph invariants, as well as testing for monotone graph properties. Many
packages are available to estimate precision matrices, this package serves as a
tool to extract structural properties from their induced graphs. By iteratively
bootstrapping on only the relevant edge set, we are able to obtain the optimal
interval size.
Author: Manbir Gulati, Junwei Lu, and Han Liu
Maintainer: Manbir Gulati <manbirgulati@gmail.com>
Diff between GraphKit versions 0.4 dated 2017-02-21 and 0.5 dated 2017-03-24
GraphKit-0.4/GraphKit/data/datalist |only GraphKit-0.5/GraphKit/DESCRIPTION | 17 - GraphKit-0.5/GraphKit/MD5 | 33 +- GraphKit-0.5/GraphKit/NAMESPACE | 14 - GraphKit-0.5/GraphKit/R/Graph.R | 27 -- GraphKit-0.5/GraphKit/R/RcppExports.R | 4 GraphKit-0.5/GraphKit/data/Xs.rda |binary GraphKit-0.5/GraphKit/data/cov.hat.rda |binary GraphKit-0.5/GraphKit/data/t.hat.rda |binary GraphKit-0.5/GraphKit/man/GraphKit.Rd | 37 +-- GraphKit-0.5/GraphKit/man/Xs.Rd | 29 +- GraphKit-0.5/GraphKit/man/cov.hat.Rd | 29 +- GraphKit-0.5/GraphKit/man/graph_invar.Rd | 73 +++--- GraphKit-0.5/GraphKit/man/graph_prop.Rd | 79 +++--- GraphKit-0.5/GraphKit/man/t.hat.Rd | 29 +- GraphKit-0.5/GraphKit/src/Graph.cpp | 356 +++++++++++++++++++++++++++++- GraphKit-0.5/GraphKit/src/RcppExports.cpp | 7 GraphKit-0.5/GraphKit/src/init.c | 2 18 files changed, 539 insertions(+), 197 deletions(-)
Title: Fuzzy Logic Toolkit for R
Description: Design and simulate fuzzy logic systems using Type 1 Fuzzy Logic.
This toolkit includes with graphical user interface (GUI) and an adaptive neuro-
fuzzy inference system (ANFIS). This toolkit is a continuation from the previous
package ('FuzzyToolkitUoN'). Produced by the Intelligent Modelling & Analysis
Group, University of Nottingham.
Author: Jon Garibaldi, Chao Chen, Tajul Razak
Maintainer: Jon Garibaldi <fuzzyr@cs.nott.ac.uk>
Diff between FuzzyR versions 2.0 dated 2016-09-28 and 2.1 dated 2017-03-24
FuzzyR-2.0/FuzzyR/man/anfis.addnode.Rd |only FuzzyR-2.0/FuzzyR/man/anfis.optimise.gradient.Rd |only FuzzyR-2.0/FuzzyR/man/anfis.optimise.lse.Rd |only FuzzyR-2.1/FuzzyR/DESCRIPTION | 14 - FuzzyR-2.1/FuzzyR/MD5 | 32 +- FuzzyR-2.1/FuzzyR/NAMESPACE | 3 FuzzyR-2.1/FuzzyR/R/ANFIS.R | 192 ++++++++--------- FuzzyR-2.1/FuzzyR/R/FuzzyInferenceSystem.R | 227 ++++++++++++++++---- FuzzyR-2.1/FuzzyR/R/FuzzyMF.R | 152 +++++++++---- FuzzyR-2.1/FuzzyR/R/FuzzyOperation.R | 252 ++++++++++++++++++++++ FuzzyR-2.1/FuzzyR/R/Utilities.R | 259 ++++++++++------------- FuzzyR-2.1/FuzzyR/man/anfis.builder.Rd | 2 FuzzyR-2.1/FuzzyR/man/evalmf.Rd | 2 FuzzyR-2.1/FuzzyR/man/fuzzyr.accuracy.Rd |only FuzzyR-2.1/FuzzyR/man/fuzzyr.match.fun.Rd |only FuzzyR-2.1/FuzzyR/man/gbell.fuzzification.Rd | 2 FuzzyR-2.1/FuzzyR/man/gbellmf.Rd | 2 FuzzyR-2.1/FuzzyR/man/genmf.Rd | 16 + FuzzyR-2.1/FuzzyR/man/km.da.Rd |only FuzzyR-2.1/FuzzyR/man/singletonmf.Rd | 2 20 files changed, 803 insertions(+), 354 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between curl versions 2.3 dated 2016-11-24 and 2.4 dated 2017-03-24
curl-2.3/curl/man/form_file.Rd |only curl-2.4/curl/DESCRIPTION | 16 +-- curl-2.4/curl/MD5 | 86 ++++++++++--------- curl-2.4/curl/NAMESPACE | 2 curl-2.4/curl/NEWS | 8 + curl-2.4/curl/R/curl.R | 18 ++-- curl-2.4/curl/R/fetch.R | 2 curl-2.4/curl/R/form.R | 35 ++++++-- curl-2.4/curl/R/handle.R | 4 curl-2.4/curl/build/vignette.rds |binary curl-2.4/curl/cleanup |only curl-2.4/curl/data/curl_symbols.rda |binary curl-2.4/curl/inst/doc/intro.R | 5 - curl-2.4/curl/inst/doc/intro.Rmd | 36 ++++---- curl-2.4/curl/inst/doc/intro.html | 100 ++++++++++++----------- curl-2.4/curl/man/curl.Rd | 8 - curl-2.4/curl/man/curl_download.Rd | 1 curl-2.4/curl/man/curl_escape.Rd | 1 curl-2.4/curl/man/curl_fetch.Rd | 1 curl-2.4/curl/man/curl_options.Rd | 1 curl-2.4/curl/man/handle.Rd | 1 curl-2.4/curl/man/handle_cookies.Rd | 1 curl-2.4/curl/man/ie_proxy.Rd | 1 curl-2.4/curl/man/multi.Rd | 1 curl-2.4/curl/man/multipart.Rd |only curl-2.4/curl/man/nslookup.Rd | 1 curl-2.4/curl/man/parse_date.Rd | 1 curl-2.4/curl/man/parse_headers.Rd | 1 curl-2.4/curl/src/Makevars.win | 10 +- curl-2.4/curl/src/curl-common.h | 4 curl-2.4/curl/src/curl.c | 60 ++++++++----- curl-2.4/curl/src/form.c | 34 +++++-- curl-2.4/curl/src/init.c | 2 curl-2.4/curl/src/interrupt.c | 6 - curl-2.4/curl/src/multi.c | 12 +- curl-2.4/curl/tests/testthat/helper-version.R | 2 curl-2.4/curl/tests/testthat/test-blockopen.R |only curl-2.4/curl/tests/testthat/test-certificates.R | 3 curl-2.4/curl/tests/testthat/test-cookies.R | 4 curl-2.4/curl/tests/testthat/test-gc.R | 8 - curl-2.4/curl/tests/testthat/test-handle.R | 2 curl-2.4/curl/tests/testthat/test-nonblocking.R | 35 +++++++- curl-2.4/curl/tests/testthat/test-post.R | 8 + curl-2.4/curl/tools/symbols-in-versions | 27 ++++++ curl-2.4/curl/tools/winlibs.R | 4 curl-2.4/curl/vignettes/intro.Rmd | 36 ++++---- 46 files changed, 359 insertions(+), 229 deletions(-)
Title: Bayesian Kernel Machine Regression
Description: Implementation of a statistical approach
for estimating the joint health effects of multiple
concurrent exposures.
Author: Jennifer F. Bobb [aut, cre]
Maintainer: Jennifer F. Bobb <jenniferfederbobb@gmail.com>
Diff between bkmr versions 0.1.0 dated 2016-07-01 and 0.2.0 dated 2017-03-24
DESCRIPTION | 11 - MD5 | 88 +++++----- NAMESPACE | 6 NEWS.md |only R/CalcPIPs.R | 1 R/CalcR2.R | 22 +- R/ComputeMixtureSummaries.R | 52 ++--- R/ComputePostmeanHnew.R | 190 +++++++++++++++++++-- R/ExtractEsts.R | 32 ++- R/InvestigatePrior_rm.R | 2 R/PredictorResponseFunctions.R | 97 +++++++---- R/SamplePred.R |only R/SimData.R | 37 +++- R/TracePlot.R | 1 R/argval_ListInput.R | 2 R/argval_ParamInput.R | 2 R/argval_controlParams.R | 2 R/base.r | 14 - R/bkmr_main_functions.R | 235 ++++++++++++++++++-------- R/bkmr_parameter_update_functions.R | 26 ++ R/bkmr_r_parameter_helper_functions.R | 296 +++++++++++++++++----------------- R/print_verbose.R | 6 R/zzz.R | 16 - README.md |only man/CalcGroupPIPs.Rd | 1 man/CalcPIPs.Rd | 1 man/CalcWithinGroupPIPs.Rd | 1 man/ComputePostmeanHnew.Rd | 19 +- man/ComputePostmeanHnew.approx.Rd |only man/ComputePostmeanHnew.exact.Rd |only man/ExtractEsts.Rd | 1 man/ExtractPIPs.Rd | 4 man/ExtractSamps.Rd | 1 man/InvestigatePrior.Rd | 4 man/OverallRiskSummaries.Rd | 16 + man/PlotPriorFits.Rd | 1 man/PredictorResponseBivar.Rd | 8 man/PredictorResponseBivarLevels.Rd | 8 man/PredictorResponseUnivar.Rd | 12 - man/SamplePred.Rd |only man/SimData.Rd | 15 - man/SingVarIntSummaries.Rd | 12 + man/SingVarRiskSummaries.Rd | 12 + man/SummarySamps.Rd | 1 man/TracePlot.Rd | 4 man/kmbayes.Rd | 35 ++-- man/print.bkmrfit.Rd |only man/set_verbose_opts.Rd | 1 man/summary.bkmrfit.Rd |only 49 files changed, 840 insertions(+), 455 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS, see <http://nomads.ncep.noaa.gov/> for more information) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <danny.c.bowman@gmail.com>
Diff between rNOMADS versions 2.3.3 dated 2017-02-23 and 2.3.5 dated 2017-03-24
DESCRIPTION | 8 +++--- MD5 | 14 +++++----- NEWS | 9 ++++++ R/GetDODS.R | 13 +++++++-- R/RNomadsTools.R | 10 +++---- R/ReadGrib.R | 59 ++++++++++++++++++++++++++++++++++++--------- man/BuildProfile.Rd | 6 +++- man/GetDODSModelRunInfo.Rd | 6 +++- 8 files changed, 92 insertions(+), 33 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 1.2 dated 2017-03-07 and 1.3 dated 2017-03-24
DESCRIPTION | 8 +++--- MD5 | 6 ++--- R/GSED.R | 60 ++++++++++++++++++++++++++++++++++++++++++++++++---- man/GSED-package.Rd | 4 +-- 4 files changed, 65 insertions(+), 13 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.
Author: Marie-Laure Delignette-Muller [aut],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurélie Siberchicot [aut, cre]
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.0-8 dated 2017-01-31 and 1.0-9 dated 2017-03-24
DESCRIPTION | 22 +++++++++---------- MD5 | 35 +++++++++++++++--------------- build/vignette.rds |binary data/danishmulti.rda |binary data/danishuni.rda |binary data/dataFAQlog1.rda |binary data/dataFAQscale1.rda |binary data/dataFAQscale2.rda |binary data/endosulfan.rda |binary data/fluazinam.rda |binary data/groundbeef.rda |binary data/salinity.rda |binary data/smokedfish.rda |binary data/toxocara.rda |binary inst/NEWS | 4 +++ inst/doc/FAQ.Rmd | 48 ++++++++++++++++++++++++++++++++++++++++++ tests/t-bootdist.R | 2 - tests/t-fitdist-customoptim.R |only vignettes/FAQ.Rmd | 48 ++++++++++++++++++++++++++++++++++++++++++ 19 files changed, 130 insertions(+), 29 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Package DoE.base creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 0.29 dated 2016-09-28 and 0.30 dated 2017-03-24
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/ICFT.R | 15 ++++++++++++--- R/oa.design.R | 2 +- R/utilities.for.children.R | 4 +++- inst/NEWS | 12 ++++++++++++ man/ICFTs.Rd | 12 +++++++----- 7 files changed, 46 insertions(+), 21 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to convert DICOM-format files to NIfTI-1 format.
Author: Jon Clayden, based on dcm2niix by Chris Rorden
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 0.2.0 dated 2017-01-13 and 0.3.0 dated 2017-03-24
divest-0.2.0/divest/src/Makevars |only divest-0.3.0/divest/DESCRIPTION | 10 - divest-0.3.0/divest/MD5 | 29 +-- divest-0.3.0/divest/NAMESPACE | 2 divest-0.3.0/divest/NEWS | 13 + divest-0.3.0/divest/R/read.R | 45 ++++- divest-0.3.0/divest/R/zzz.R | 7 divest-0.3.0/divest/cleanup | 2 divest-0.3.0/divest/configure |only divest-0.3.0/divest/configure.ac |only divest-0.3.0/divest/man/readDicom.Rd | 23 ++ divest-0.3.0/divest/src/Makevars.in |only divest-0.3.0/divest/src/Makevars.win |only divest-0.3.0/divest/src/dcm2niix/nii_dicom.cpp | 92 ++++------ divest-0.3.0/divest/src/dcm2niix/nii_dicom.h | 26 +- divest-0.3.0/divest/src/dcm2niix/nii_dicom_batch.cpp | 168 ++++++++++++++----- divest-0.3.0/divest/src/dcm2niix/nii_dicom_batch.h | 4 divest-0.3.0/divest/src/main.cpp | 34 ++- 18 files changed, 301 insertions(+), 154 deletions(-)
Title: Fitting Distributions to Given Data or Known Quantiles
Description: Collection of functions for fitting distributions to given data or
by known quantiles. Two main functions fit.perc() and fit.cont() provide
users a GUI that allows to choose a most appropriate distribution without
any knowledge of the R syntax. Note, this package is a part of the 'rrisk'
project.
Author: Natalia Belgorodski [aut] (STAT-UP Statistical Consulting),
Matthias Greiner [aut, cre] (Federal Institute for Risk Assessment,
Germany),
Kristin Tolksdorf [aut] (Federal Institute for Risk Assessment,
Germany),
Katharina Schueller [aut] (STAT-UP Statistical Consulting),
Matthias Flor [ctb] (Federal Institute for Risk Assessment, Germany),
Lutz Göhring [ctb] (Lutz Göhring Consulting)
Maintainer: Matthias Greiner <matthias.greiner@bfr.bund.de>
Diff between rriskDistributions versions 2.1.1 dated 2016-04-22 and 2.1.2 dated 2017-03-24
DESCRIPTION | 10 ++--- MD5 | 65 +++++++++++++++++++------------------- README.md | 8 ++-- man/fit.cont.Rd | 1 man/fit.perc.Rd | 1 man/get.beta.par.Rd | 7 +--- man/get.cauchy.par.Rd | 7 +--- man/get.chisq.par.Rd | 7 +--- man/get.chisqnc.par.Rd | 7 +--- man/get.exp.par.Rd | 7 +--- man/get.f.par.Rd | 7 +--- man/get.gamma.par.Rd | 7 +--- man/get.gompertz.par.Rd | 9 ++--- man/get.hyper.par.Rd | 7 +--- man/get.lnorm.par.Rd | 7 +--- man/get.logis.par.Rd | 7 +--- man/get.nbinom.par.Rd | 7 +--- man/get.norm.par.Rd | 7 +--- man/get.norm.sd.Rd | 7 +--- man/get.pert.par.Rd | 9 ++--- man/get.pois.par.Rd | 7 +--- man/get.t.par.Rd | 7 +--- man/get.tnorm.par.Rd | 7 +--- man/get.triang.par.Rd | 9 ++--- man/get.unif.par.Rd | 1 man/get.weibull.par.Rd | 7 +--- man/plotDiagnostics.perc.Rd | 1 man/rriskDistributions-package.Rd | 3 - man/rriskFitdist.cont.Rd | 1 man/rriskFitdist.perc.Rd | 1 man/rriskMLEdist.Rd | 1 man/rriskMMEdist.Rd | 1 man/useFitdist.Rd | 1 tools |only 34 files changed, 106 insertions(+), 135 deletions(-)
More information about rriskDistributions at CRAN
Permanent link
Title: Stock Assessment Graphs Database Web Services
Description: R interface to access the web services of the ICES Stock Assessment
Graphs database <http://sg.ices.dk>.
Author: Colin Millar [aut, cre],
Scott Large [aut],
Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesSAG versions 1.2-0 dated 2016-12-07 and 1.2-1 dated 2017-03-24
DESCRIPTION | 22 ++++++++++------------ MD5 | 36 ++++++++++++++++++------------------ NEWS | 6 ++++++ R/findKey.R | 3 +-- R/getFishStockReferencePoints.R | 2 +- R/getGraph.R | 8 ++++---- R/getSAG.R | 3 +-- R/getSAGGraphs.R | 12 ++++++------ R/getSummaryTable.R | 2 +- R/icesSAG-package.R | 9 ++++++--- R/utilities.R | 16 +++++++++++----- man/findKey.Rd | 7 +++---- man/getFishStockReferencePoints.Rd | 9 ++++----- man/getGraphs.Rd | 22 +++++++++++----------- man/getListStocks.Rd | 7 +++---- man/getSAG.Rd | 3 +-- man/getSAGGraphs.Rd | 14 +++++++------- man/getSummaryTable.Rd | 9 ++++----- man/icesSAG-package.Rd | 16 +++++++++------- 19 files changed, 107 insertions(+), 99 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Mike Bostock [cph] (d3.js)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.3.2 dated 2016-11-04 and 0.3.3 dated 2017-03-24
ggiraph-0.3.2/ggiraph/R/geom_bar_interactive.r |only ggiraph-0.3.3/ggiraph/DESCRIPTION | 10 ggiraph-0.3.3/ggiraph/MD5 | 113 +++---- ggiraph-0.3.3/ggiraph/NAMESPACE | 3 ggiraph-0.3.3/ggiraph/NEWS | 12 ggiraph-0.3.3/ggiraph/R/geom_boxplot_interactive.R | 5 ggiraph-0.3.3/ggiraph/R/geom_path_interactive.R | 6 ggiraph-0.3.3/ggiraph/R/geom_polygon_interactive.R | 6 ggiraph-0.3.3/ggiraph/R/geom_rect_interactive.R | 7 ggiraph-0.3.3/ggiraph/R/geom_segment_interactive.R | 3 ggiraph-0.3.3/ggiraph/R/geom_text_interactive.R | 13 ggiraph-0.3.3/ggiraph/R/ggiraph.R | 58 +-- ggiraph-0.3.3/ggiraph/R/zz_geom_bar_interactive.r |only ggiraph-0.3.3/ggiraph/README.md | 16 - ggiraph-0.3.3/ggiraph/build/vignette.rds |binary ggiraph-0.3.3/ggiraph/inst/doc/an_introduction.Rmd | 10 ggiraph-0.3.3/ggiraph/inst/doc/an_introduction.html | 38 +- ggiraph-0.3.3/ggiraph/inst/doc/custom_animation_effects.Rmd | 5 ggiraph-0.3.3/ggiraph/inst/doc/custom_animation_effects.html | 36 +- ggiraph-0.3.3/ggiraph/inst/doc/shiny_usage.R | 6 ggiraph-0.3.3/ggiraph/inst/doc/shiny_usage.Rmd | 18 - ggiraph-0.3.3/ggiraph/inst/doc/shiny_usage.html | 23 + ggiraph-0.3.3/ggiraph/inst/doc/sizing.R |only ggiraph-0.3.3/ggiraph/inst/doc/sizing.Rmd |only ggiraph-0.3.3/ggiraph/inst/doc/sizing.html |only ggiraph-0.3.3/ggiraph/inst/htmlwidgets/ggiraph.js | 131 +------- ggiraph-0.3.3/ggiraph/inst/htmlwidgets/lib/styles-0.0.1/styles.css | 13 ggiraph-0.3.3/ggiraph/inst/htmlwidgets/lib/styles-0.0.1/styles.js | 154 ++++++++++ ggiraph-0.3.3/ggiraph/inst/rmd |only ggiraph-0.3.3/ggiraph/inst/shiny/DT/server.R | 2 ggiraph-0.3.3/ggiraph/inst/shiny/DT/ui.R | 16 - ggiraph-0.3.3/ggiraph/inst/shiny/crimes/server.R | 1 ggiraph-0.3.3/ggiraph/inst/shiny/crimes/ui.R | 4 ggiraph-0.3.3/ggiraph/man/drawDetails.interactive_points_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/drawDetails.interactive_polygon_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/drawDetails.interactive_polyline_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/drawDetails.interactive_rect_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/drawDetails.interactive_segments_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/drawDetails.interactive_text_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_bar_interactive.Rd | 3 ggiraph-0.3.3/ggiraph/man/geom_boxplot_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_map_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_path_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_point_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_polygon_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_rect_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_segment_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/geom_text_interactive.Rd | 1 ggiraph-0.3.3/ggiraph/man/ggiraph.Rd | 6 ggiraph-0.3.3/ggiraph/man/ggiraphOutput.Rd | 1 ggiraph-0.3.3/ggiraph/man/interactive_points_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/interactive_polygon_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/interactive_polyline_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/interactive_rect_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/interactive_segments_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/interactive_text_grob.Rd | 1 ggiraph-0.3.3/ggiraph/man/renderggiraph.Rd | 1 ggiraph-0.3.3/ggiraph/vignettes/an_introduction.Rmd | 10 ggiraph-0.3.3/ggiraph/vignettes/custom_animation_effects.Rmd | 5 ggiraph-0.3.3/ggiraph/vignettes/shiny_usage.Rmd | 18 - ggiraph-0.3.3/ggiraph/vignettes/sizing.Rmd |only 61 files changed, 440 insertions(+), 333 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat. 'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records. As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.65 dated 2017-01-23 and 0.66 dated 2017-03-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/handle_ucipm.R | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-03 1.0
Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.16.4 dated 2017-03-20 and 2.16.6 dated 2017-03-24
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- inst/doc/rbamtools.pdf |binary src/gap_list.h | 4 ++-- src/samtools/bam.c | 12 ++++++------ src/samtools/bam_aux.c | 2 +- src/samtools/bam_import.c | 14 +++++++------- src/samtools/bam_index.c | 12 ++++++------ src/samtools/bam_sort.c | 4 ++-- src/samtools/bgzf.c | 12 ++++++------ src/samtools/faidx.c | 18 +++++++++--------- src/samtools/ksort.h | 2 +- src/samtools/kstring.c | 6 +++--- src/samtools/kstring.h | 4 ++-- src/samtools/razf.c | 16 ++++++++-------- src/samtools/sam.c | 10 +++++----- src/samtools/sam_header.c | 4 ++-- 17 files changed, 79 insertions(+), 79 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Author: Stéphane Dray, Guillaume Blanchet, Daniel Borcard, Guillaume Guenard,
Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Diff between adespatial versions 0.0-7 dated 2016-12-13 and 0.0-8 dated 2017-03-24
DESCRIPTION | 12 - MD5 | 113 +++++++----- NAMESPACE | 14 + R/WRperiodogram.R | 12 - R/aem.R |only R/aem.build.binary.R |only R/aem.time.R |only R/aem.weight.edges.R |only R/aem.weight.time.R |only R/bacProdxy.R |only R/dist.ldc.R | 135 +++++++------- R/forward.sel.R | 2 R/mastigouche.R |only R/moranNP.randtest.R | 2 R/msr.R | 14 + R/ortho.AIC.R | 2 R/rotation.R |only R/scalogram.R | 2 R/stimodels.R | 423 +++++++++++++++++++++------------------------- R/utils-aem.R |only build/vignette.rds |binary data/bacProdxy.rda |only data/mastigouche.rda |only inst/doc/tutorial.html | 57 +++--- man/Cperiodogram.Rd | 7 man/LCBD.comp.Rd | 7 man/WRperiodogram.Rd | 16 + man/aem.Rd |only man/aem.build.binary.Rd |only man/aem.time.Rd |only man/aem.weight.edges.Rd |only man/bacProdxy.Rd |only man/beta.div.Rd | 7 man/beta.div.comp.Rd | 7 man/chooseCN.Rd | 1 man/create.dbMEM.model.Rd | 9 man/createlistw.Rd | 7 man/dbmem.Rd | 9 man/dist.ldc.Rd | 132 +++++++------- man/forward.sel.Rd | 7 man/forward.sel.par.Rd | 9 man/give.thresh.Rd | 1 man/global.rtest.Rd | 7 man/mastigouche.Rd |only man/mem.Rd | 12 - man/mfpa.Rd | 9 man/moran.bounds.Rd | 7 man/moran.randtest.Rd | 7 man/moranNP.randtest.Rd | 7 man/mspa.Rd | 9 man/msr.Rd | 20 +- man/mst.nb.Rd | 7 man/multispati.Rd | 16 - man/ortho.AIC.Rd | 9 man/orthobasis.poly.Rd | 7 man/plot.orthobasisSp.Rd | 7 man/rotation.Rd |only man/scalogram.Rd | 10 - man/stimodels.Rd | 24 +- man/test.W.Rd | 7 man/trichoptera.Rd | 1 man/variogmultiv.Rd | 7 src/WRperiodogram.c | 2 src/WRperiodogram.h | 2 src/betadiv.c | 60 +++--- src/buildbinary.c |only src/init.c |only src/stipermute.c |only 68 files changed, 627 insertions(+), 617 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for Bayesian estimation of
antigen-driven selection in immunoglobulin (Ig) sequences, providing an
intuitive means of analyzing selection by quantifying the degree of
selective pressure. Also provides tools to profile mutations in Ig
sequences, build models of somatic hypermutation (SHM) in Ig sequences,
and make model-dependent distance comparisons of Ig repertoires.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.1.4 dated 2016-08-05 and 0.1.5 dated 2017-03-24
shazam-0.1.4/shazam/data/HS1FDistance.rda |only shazam-0.1.4/shazam/data/HS5FModel.rda |only shazam-0.1.4/shazam/data/IMGT_V_BY_REGIONS_NO_CDR3.rda |only shazam-0.1.4/shazam/data/IMGT_V_NO_CDR3.rda |only shazam-0.1.4/shazam/data/M1NDistance.rda |only shazam-0.1.4/shazam/data/MRS5NFModel.rda |only shazam-0.1.4/shazam/data/U5NModel.rda |only shazam-0.1.4/shazam/man/HS1FDistance.Rd |only shazam-0.1.4/shazam/man/HS5FModel.Rd |only shazam-0.1.4/shazam/man/M1NDistance.Rd |only shazam-0.1.4/shazam/man/MRS5NFModel.Rd |only shazam-0.1.4/shazam/man/U5NModel.Rd |only shazam-0.1.5/shazam/DESCRIPTION | 23 shazam-0.1.5/shazam/MD5 | 165 +- shazam-0.1.5/shazam/NAMESPACE | 26 shazam-0.1.5/shazam/NEWS.md | 91 + shazam-0.1.5/shazam/R/Baseline.R | 211 +- shazam-0.1.5/shazam/R/Core.R | 51 shazam-0.1.5/shazam/R/DistToNearest.R | 1052 +++++++++++- shazam-0.1.5/shazam/R/MutationProfiling.R | 758 ++++++++- shazam-0.1.5/shazam/R/RegionDefinitions.R | 16 shazam-0.1.5/shazam/R/Shazam.R | 63 shazam-0.1.5/shazam/R/Shmulate.R | 26 shazam-0.1.5/shazam/R/TargetingModels.R | 1221 ++++++++++++--- shazam-0.1.5/shazam/R/sysdata.rda |binary shazam-0.1.5/shazam/data/HH_S1F.rda |only shazam-0.1.5/shazam/data/HH_S5F.rda |only shazam-0.1.5/shazam/data/HKL_S1F.rda |only shazam-0.1.5/shazam/data/HKL_S5F.rda |only shazam-0.1.5/shazam/data/IMGT_V.rda |binary shazam-0.1.5/shazam/data/IMGT_V_BY_REGIONS.rda |binary shazam-0.1.5/shazam/data/MK_RS1NF.rda |only shazam-0.1.5/shazam/data/MK_RS5NF.rda |only shazam-0.1.5/shazam/data/U5N.rda |only shazam-0.1.5/shazam/inst/CITATION | 24 shazam-0.1.5/shazam/inst/doc/Baseline-Vignette.R | 38 shazam-0.1.5/shazam/inst/doc/Baseline-Vignette.Rmd | 81 shazam-0.1.5/shazam/inst/doc/Baseline-Vignette.pdf |binary shazam-0.1.5/shazam/inst/doc/DistToNearest-Vignette.R | 77 shazam-0.1.5/shazam/inst/doc/DistToNearest-Vignette.Rmd | 182 +- shazam-0.1.5/shazam/inst/doc/DistToNearest-Vignette.pdf |binary shazam-0.1.5/shazam/inst/doc/Targeting-Vignette.pdf |binary shazam-0.1.5/shazam/man/Baseline-class.Rd | 11 shazam-0.1.5/shazam/man/DensityThreshold-class.Rd |only shazam-0.1.5/shazam/man/GmmThreshold-class.Rd |only shazam-0.1.5/shazam/man/HH_S1F.Rd |only shazam-0.1.5/shazam/man/HH_S5F.Rd |only shazam-0.1.5/shazam/man/HKL_S1F.Rd |only shazam-0.1.5/shazam/man/HKL_S5F.Rd |only shazam-0.1.5/shazam/man/IMGT_SCHEMES.Rd | 9 shazam-0.1.5/shazam/man/MK_RS1NF.Rd |only shazam-0.1.5/shazam/man/MK_RS5NF.Rd |only shazam-0.1.5/shazam/man/MUTATION_SCHEMES.Rd | 3 shazam-0.1.5/shazam/man/MutationDefinition-class.Rd | 4 shazam-0.1.5/shazam/man/RegionDefinition-class.Rd | 4 shazam-0.1.5/shazam/man/TargetingModel-class.Rd | 9 shazam-0.1.5/shazam/man/U5N.Rd |only shazam-0.1.5/shazam/man/calcBaseline.Rd | 13 shazam-0.1.5/shazam/man/calcExpectedMutations.Rd | 16 shazam-0.1.5/shazam/man/calcObservedMutations.Rd | 81 shazam-0.1.5/shazam/man/calcTargetingDistance.Rd | 43 shazam-0.1.5/shazam/man/clearConsole.Rd | 1 shazam-0.1.5/shazam/man/collapseClones.Rd | 3 shazam-0.1.5/shazam/man/createBaseline.Rd | 9 shazam-0.1.5/shazam/man/createMutabilityMatrix.Rd | 35 shazam-0.1.5/shazam/man/createMutationDefinition.Rd | 1 shazam-0.1.5/shazam/man/createRegionDefinition.Rd | 1 shazam-0.1.5/shazam/man/createSubstitutionMatrix.Rd | 51 shazam-0.1.5/shazam/man/createTargetingMatrix.Rd | 3 shazam-0.1.5/shazam/man/createTargetingModel.Rd | 3 shazam-0.1.5/shazam/man/distToNearest.Rd | 70 shazam-0.1.5/shazam/man/editBaseline.Rd |only shazam-0.1.5/shazam/man/expectedMutations.Rd | 13 shazam-0.1.5/shazam/man/extendMutabilityMatrix.Rd | 5 shazam-0.1.5/shazam/man/extendSubstitutionMatrix.Rd | 1 shazam-0.1.5/shazam/man/findThreshold.Rd |only shazam-0.1.5/shazam/man/getBaselineStats.Rd | 11 shazam-0.1.5/shazam/man/getPlatform.Rd | 1 shazam-0.1.5/shazam/man/getnproc.Rd | 1 shazam-0.1.5/shazam/man/groupBaseline.Rd | 8 shazam-0.1.5/shazam/man/makeAverage1merMut.Rd |only shazam-0.1.5/shazam/man/makeAverage1merSub.Rd |only shazam-0.1.5/shazam/man/makeDegenerate5merMut.Rd |only shazam-0.1.5/shazam/man/makeDegenerate5merSub.Rd |only shazam-0.1.5/shazam/man/minNumMutationsTune.Rd |only shazam-0.1.5/shazam/man/minNumSeqMutationsTune.Rd |only shazam-0.1.5/shazam/man/observedMutations.Rd | 34 shazam-0.1.5/shazam/man/plotBaselineDensity.Rd | 5 shazam-0.1.5/shazam/man/plotBaselineSummary.Rd | 5 shazam-0.1.5/shazam/man/plotDensityThreshold.Rd |only shazam-0.1.5/shazam/man/plotGmmThreshold.Rd |only shazam-0.1.5/shazam/man/plotMutability.Rd | 5 shazam-0.1.5/shazam/man/plotTune.Rd |only shazam-0.1.5/shazam/man/shazam.Rd | 19 shazam-0.1.5/shazam/man/shmulateSeq.Rd | 7 shazam-0.1.5/shazam/man/shmulateTree.Rd | 9 shazam-0.1.5/shazam/man/slideWindowDb.Rd |only shazam-0.1.5/shazam/man/slideWindowSeq.Rd |only shazam-0.1.5/shazam/man/slideWindowTune.Rd |only shazam-0.1.5/shazam/man/slideWindowTunePlot.Rd |only shazam-0.1.5/shazam/man/summarizeBaseline.Rd | 25 shazam-0.1.5/shazam/man/testBaseline.Rd | 8 shazam-0.1.5/shazam/man/writeTargetingDistance.Rd | 3 shazam-0.1.5/shazam/vignettes/Baseline-Vignette.Rmd | 81 shazam-0.1.5/shazam/vignettes/DistToNearest-Vignette.Rmd | 182 +- 105 files changed, 4022 insertions(+), 876 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
Ruben Arslan [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
Eli Grey [ctb, cph] (FileSaver library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 1.3 dated 2016-12-21 and 1.4 dated 2017-03-24
rmarkdown-1.3/rmarkdown/tests/testthat/site/PageB.Rmd |only rmarkdown-1.4/rmarkdown/DESCRIPTION | 17 - rmarkdown-1.4/rmarkdown/MD5 | 143 +++++----- rmarkdown-1.4/rmarkdown/NAMESPACE | 3 rmarkdown-1.4/rmarkdown/R/draft.R | 2 rmarkdown-1.4/rmarkdown/R/html_dependencies.R | 17 + rmarkdown-1.4/rmarkdown/R/html_document.R | 17 - rmarkdown-1.4/rmarkdown/R/html_fragment.R | 3 rmarkdown-1.4/rmarkdown/R/html_paged.R | 2 rmarkdown-1.4/rmarkdown/R/html_resources.R | 2 rmarkdown-1.4/rmarkdown/R/knit_print.R | 17 + rmarkdown-1.4/rmarkdown/R/latex_dependencies.R | 19 + rmarkdown-1.4/rmarkdown/R/output_format.R | 15 - rmarkdown-1.4/rmarkdown/R/params.R | 62 +++- rmarkdown-1.4/rmarkdown/R/pdf_document.R | 17 - rmarkdown-1.4/rmarkdown/R/render.R | 9 rmarkdown-1.4/rmarkdown/R/render_site.R | 6 rmarkdown-1.4/rmarkdown/R/shiny_prerendered.R | 47 +++ rmarkdown-1.4/rmarkdown/R/util.R | 3 rmarkdown-1.4/rmarkdown/inst/NEWS | 33 ++ rmarkdown-1.4/rmarkdown/inst/rmd/h/default.html | 2 rmarkdown-1.4/rmarkdown/inst/rmd/h/navigation-1.1/tabsets.js | 50 +++ rmarkdown-1.4/rmarkdown/man/all_output_formats.Rd | 1 rmarkdown-1.4/rmarkdown/man/beamer_presentation.Rd | 1 rmarkdown-1.4/rmarkdown/man/default_output_format.Rd | 1 rmarkdown-1.4/rmarkdown/man/draft.Rd | 3 rmarkdown-1.4/rmarkdown/man/find_external_resources.Rd | 1 rmarkdown-1.4/rmarkdown/man/github_document.Rd | 1 rmarkdown-1.4/rmarkdown/man/html-dependencies.Rd | 15 - rmarkdown-1.4/rmarkdown/man/html_document.Rd | 22 - rmarkdown-1.4/rmarkdown/man/html_document_base.Rd | 1 rmarkdown-1.4/rmarkdown/man/html_fragment.Rd | 13 rmarkdown-1.4/rmarkdown/man/html_notebook.Rd | 1 rmarkdown-1.4/rmarkdown/man/html_notebook_metadata.Rd | 1 rmarkdown-1.4/rmarkdown/man/html_notebook_output.Rd | 7 rmarkdown-1.4/rmarkdown/man/html_vignette.Rd | 1 rmarkdown-1.4/rmarkdown/man/includes.Rd | 1 rmarkdown-1.4/rmarkdown/man/knit_params_ask.Rd | 1 rmarkdown-1.4/rmarkdown/man/knitr_options.Rd | 1 rmarkdown-1.4/rmarkdown/man/knitr_options_html.Rd | 1 rmarkdown-1.4/rmarkdown/man/knitr_options_pdf.Rd | 1 rmarkdown-1.4/rmarkdown/man/latex_dependency.Rd | 1 rmarkdown-1.4/rmarkdown/man/md_document.Rd | 1 rmarkdown-1.4/rmarkdown/man/metadata.Rd | 1 rmarkdown-1.4/rmarkdown/man/navbar_html.Rd | 2 rmarkdown-1.4/rmarkdown/man/odt_document.Rd | 1 rmarkdown-1.4/rmarkdown/man/output_format.Rd | 3 rmarkdown-1.4/rmarkdown/man/paged_table.Rd | 1 rmarkdown-1.4/rmarkdown/man/pandoc_args.Rd | 5 rmarkdown-1.4/rmarkdown/man/pandoc_available.Rd | 1 rmarkdown-1.4/rmarkdown/man/pandoc_convert.Rd | 1 rmarkdown-1.4/rmarkdown/man/pandoc_options.Rd | 1 rmarkdown-1.4/rmarkdown/man/pandoc_path_arg.Rd | 1 rmarkdown-1.4/rmarkdown/man/pandoc_self_contained_html.Rd | 1 rmarkdown-1.4/rmarkdown/man/pandoc_template.Rd | 1 rmarkdown-1.4/rmarkdown/man/parse_html_notebook.Rd | 1 rmarkdown-1.4/rmarkdown/man/pdf_document.Rd | 9 rmarkdown-1.4/rmarkdown/man/relative_to.Rd | 1 rmarkdown-1.4/rmarkdown/man/render_delayed.Rd | 1 rmarkdown-1.4/rmarkdown/man/render_supporting_files.Rd | 1 rmarkdown-1.4/rmarkdown/man/resolve_output_format.Rd | 1 rmarkdown-1.4/rmarkdown/man/rmarkdown_format.Rd | 8 rmarkdown-1.4/rmarkdown/man/rtf_document.Rd | 1 rmarkdown-1.4/rmarkdown/man/run.Rd | 1 rmarkdown-1.4/rmarkdown/man/shiny_prerendered_chunk.Rd | 1 rmarkdown-1.4/rmarkdown/man/shiny_prerendered_clean.Rd | 1 rmarkdown-1.4/rmarkdown/man/shiny_prerendered_server_start_code.Rd | 1 rmarkdown-1.4/rmarkdown/man/slidy_presentation.Rd | 9 rmarkdown-1.4/rmarkdown/man/tufte_handout.Rd | 1 rmarkdown-1.4/rmarkdown/man/word_document.Rd | 1 rmarkdown-1.4/rmarkdown/man/yaml_front_matter.Rd | 1 rmarkdown-1.4/rmarkdown/tests/testthat/site/PageB.rmd |only rmarkdown-1.4/rmarkdown/tests/testthat/test-params.R |only rmarkdown-1.4/rmarkdown/tests/testthat/test-site.R | 2 74 files changed, 415 insertions(+), 207 deletions(-)
Title: Toolkit for Corpus Analysis
Description: Library for corpus analysis using the Corpus Workbench as an
efficient back end for indexing and querying large corpora. The package offers
functionality to flexibly create partitions and to carry out basic statistical
operations (count, co-occurrences etc.). The original full text of documents
can be reconstructed and inspected at any time. Beyond that, the package
is intended to serve as an interface to packages implementing advanced
statistical procedures. Respective data structures (document term matrices, term
co-occurrence matrices etc.) can be created based on the indexed corpora.
Author: Andreas Blaette
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between polmineR versions 0.7.1 dated 2017-02-27 and 0.7.2 dated 2017-03-24
polmineR-0.7.1/polmineR/R/comp_class.R |only polmineR-0.7.1/polmineR/R/compare_method.R |only polmineR-0.7.1/polmineR/R/cooccurrencesBundle_methods.R |only polmineR-0.7.1/polmineR/R/cooccurrencesReshaped_methods.R |only polmineR-0.7.1/polmineR/R/cooccurrences_methods.R |only polmineR-0.7.1/polmineR/inst/doc/vignette.Rnw |only polmineR-0.7.1/polmineR/inst/doc/vignette.pdf |only polmineR-0.7.1/polmineR/man/comp-class.Rd |only polmineR-0.7.1/polmineR/man/compare-method.Rd |only polmineR-0.7.1/polmineR/vignettes/vignette.Rnw |only polmineR-0.7.2/polmineR/DESCRIPTION | 53 - polmineR-0.7.2/polmineR/MD5 | 193 +++--- polmineR-0.7.2/polmineR/NAMESPACE | 21 polmineR-0.7.2/polmineR/NEWS | 14 polmineR-0.7.2/polmineR/R/CQI.R | 2 polmineR-0.7.2/polmineR/R/CQI.Rcpp.R | 108 +++ polmineR-0.7.2/polmineR/R/CQI.cqpserver.R | 2 polmineR-0.7.2/polmineR/R/CQI.perl.R | 2 polmineR-0.7.2/polmineR/R/CQI.rcqp.R | 2 polmineR-0.7.2/polmineR/R/Corpus_class.R | 12 polmineR-0.7.2/polmineR/R/RegistryFile.R |only polmineR-0.7.2/polmineR/R/as.DocumentTermMatrix_method.R | 4 polmineR-0.7.2/polmineR/R/as.markdown_method.R | 27 polmineR-0.7.2/polmineR/R/as.speeches_method.R | 2 polmineR-0.7.2/polmineR/R/blapply_method.R | 2 polmineR-0.7.2/polmineR/R/chisquare_method.R | 2 polmineR-0.7.2/polmineR/R/context_class.R | 59 -- polmineR-0.7.2/polmineR/R/context_method.R | 205 ++----- polmineR-0.7.2/polmineR/R/cooccurrences_class.R | 46 + polmineR-0.7.2/polmineR/R/cooccurrences_method.R | 406 +++----------- polmineR-0.7.2/polmineR/R/corpus_method.R | 9 polmineR-0.7.2/polmineR/R/count_method.R | 185 ++++-- polmineR-0.7.2/polmineR/R/cpos_method.R | 47 + polmineR-0.7.2/polmineR/R/decode_method.R | 2 polmineR-0.7.2/polmineR/R/dispersion_method.R | 2 polmineR-0.7.2/polmineR/R/dotplot_method.R | 2 polmineR-0.7.2/polmineR/R/encode_method.R | 24 polmineR-0.7.2/polmineR/R/enrich_method.R | 19 polmineR-0.7.2/polmineR/R/features_class.R |only polmineR-0.7.2/polmineR/R/features_method.R |only polmineR-0.7.2/polmineR/R/hits_class.R | 101 +-- polmineR-0.7.2/polmineR/R/html_method.R | 14 polmineR-0.7.2/polmineR/R/install.corpus_function.R |only polmineR-0.7.2/polmineR/R/kwic_class.R | 6 polmineR-0.7.2/polmineR/R/kwic_method.R | 92 +-- polmineR-0.7.2/polmineR/R/ll_method.R | 4 polmineR-0.7.2/polmineR/R/mail_method.R | 8 polmineR-0.7.2/polmineR/R/meta_method.R | 2 polmineR-0.7.2/polmineR/R/pAttributes_method.R | 36 + polmineR-0.7.2/polmineR/R/partitionBundle_method.R | 4 polmineR-0.7.2/polmineR/R/partitionBundle_methods.R | 3 polmineR-0.7.2/polmineR/R/partition_class.R | 4 polmineR-0.7.2/polmineR/R/partition_method.R | 60 -- polmineR-0.7.2/polmineR/R/pmi_method.R | 2 polmineR-0.7.2/polmineR/R/polmineR_package.R | 12 polmineR-0.7.2/polmineR/R/read_method.R | 2 polmineR-0.7.2/polmineR/R/registry.R | 84 -- polmineR-0.7.2/polmineR/R/sAttributes2cpos_method.R | 47 - polmineR-0.7.2/polmineR/R/sAttributes_method.R | 34 - polmineR-0.7.2/polmineR/R/size_method.R | 6 polmineR-0.7.2/polmineR/R/tTest.R | 2 polmineR-0.7.2/polmineR/R/templates_method.R | 102 +-- polmineR-0.7.2/polmineR/R/trim_method.R | 19 polmineR-0.7.2/polmineR/R/use_method.R | 20 polmineR-0.7.2/polmineR/R/utils.R | 4 polmineR-0.7.2/polmineR/R/view_method.R | 23 polmineR-0.7.2/polmineR/R/zzz.R | 77 ++ polmineR-0.7.2/polmineR/README.md | 28 polmineR-0.7.2/polmineR/build/vignette.rds |binary polmineR-0.7.2/polmineR/inst/doc/vignette.R | 281 ++++++--- polmineR-0.7.2/polmineR/inst/doc/vignette.Rmd |only polmineR-0.7.2/polmineR/inst/doc/vignette.html |only polmineR-0.7.2/polmineR/man/CQI.Rd | 5 polmineR-0.7.2/polmineR/man/Corpus-class.Rd | 2 polmineR-0.7.2/polmineR/man/RegistryFile-class.Rd |only polmineR-0.7.2/polmineR/man/as.markdown.Rd | 7 polmineR-0.7.2/polmineR/man/as.speeches-method.Rd | 2 polmineR-0.7.2/polmineR/man/blapply.Rd | 2 polmineR-0.7.2/polmineR/man/context-class.Rd | 2 polmineR-0.7.2/polmineR/man/context-method.Rd | 35 - polmineR-0.7.2/polmineR/man/cooccurrences-class.Rd | 22 polmineR-0.7.2/polmineR/man/cooccurrences.Rd | 63 +- polmineR-0.7.2/polmineR/man/cooccurrencesBundle-class.Rd | 7 polmineR-0.7.2/polmineR/man/cooccurrencesReshaped.Rd | 6 polmineR-0.7.2/polmineR/man/corpus-method.Rd | 2 polmineR-0.7.2/polmineR/man/count-method.Rd | 29 - polmineR-0.7.2/polmineR/man/cpos-method.Rd | 25 polmineR-0.7.2/polmineR/man/dispersion-method.Rd | 2 polmineR-0.7.2/polmineR/man/dotplot-method.Rd | 4 polmineR-0.7.2/polmineR/man/encode-method.Rd | 23 polmineR-0.7.2/polmineR/man/features-class.Rd |only polmineR-0.7.2/polmineR/man/features-method.Rd |only polmineR-0.7.2/polmineR/man/hits.Rd | 14 polmineR-0.7.2/polmineR/man/install.corpus.Rd |only polmineR-0.7.2/polmineR/man/mail-method.Rd | 4 polmineR-0.7.2/polmineR/man/pAttributes.Rd | 8 polmineR-0.7.2/polmineR/man/partition-class.Rd | 18 polmineR-0.7.2/polmineR/man/partition.Rd | 28 polmineR-0.7.2/polmineR/man/polmineR-package.Rd | 12 polmineR-0.7.2/polmineR/man/read-method.Rd | 2 polmineR-0.7.2/polmineR/man/registry.Rd | 19 polmineR-0.7.2/polmineR/man/sAttributes-method.Rd | 17 polmineR-0.7.2/polmineR/man/tTest.Rd | 2 polmineR-0.7.2/polmineR/man/templates.Rd | 26 polmineR-0.7.2/polmineR/man/textstatistics.Rd | 4 polmineR-0.7.2/polmineR/man/trim-method.Rd | 2 polmineR-0.7.2/polmineR/man/use.Rd | 4 polmineR-0.7.2/polmineR/vignettes/vignette.Rmd |only 108 files changed, 1505 insertions(+), 1422 deletions(-)
Title: Local Polynomial Estimators in Measurement Error Models
Description: Provide local polynomial estimators for nonparametric mean regression and nonparametric modal regression in the presence/absence of measurement error. Bandwidth selection is also provided for each estimator.
Author: Haiming Zhou <zhouh@niu.edu> and Xianzheng Huang <huang@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between lpme versions 1.0.1 dated 2014-12-19 and 1.1.0 dated 2017-03-24
lpme-1.0.1/lpme/R/bwSIMEX.R |only lpme-1.0.1/lpme/R/lpme.R |only lpme-1.0.1/lpme/man/bwSIMEX.Rd |only lpme-1.0.1/lpme/man/lpme.Rd |only lpme-1.0.1/lpme/src/lpme_gjasa.cpp |only lpme-1.0.1/lpme/src/lpme_gjasa.h |only lpme-1.0.1/lpme/src/lpme_gnew.cpp |only lpme-1.0.1/lpme/src/lpme_gnew.h |only lpme-1.1.0/lpme/DESCRIPTION | 18 ++-- lpme-1.1.0/lpme/MD5 | 37 +++++--- lpme-1.1.0/lpme/NAMESPACE | 10 +- lpme-1.1.0/lpme/R/meanreg.R |only lpme-1.1.0/lpme/R/meanreg_bwSIMEX.R |only lpme-1.1.0/lpme/R/modereg.R |only lpme-1.1.0/lpme/R/modereg_bw.R |only lpme-1.1.0/lpme/R/modereg_bwSIMEX.R |only lpme-1.1.0/lpme/R/wrappers.R | 106 +++++++++++++----------- lpme-1.1.0/lpme/inst |only lpme-1.1.0/lpme/man/meanreg.Rd |only lpme-1.1.0/lpme/man/meanreg_bwSIMEX.Rd |only lpme-1.1.0/lpme/man/modereg.Rd |only lpme-1.1.0/lpme/man/modereg_bw.Rd |only lpme-1.1.0/lpme/man/modereg_bwSIMEX.Rd |only lpme-1.1.0/lpme/src/lpme_common.cpp | 28 +++++- lpme-1.1.0/lpme/src/lpme_common.h | 11 ++ lpme-1.1.0/lpme/src/lpme_densityreg_fit.cpp |only lpme-1.1.0/lpme/src/lpme_meanreg_dfc.cpp |only lpme-1.1.0/lpme/src/lpme_meanreg_hz.cpp |only lpme-1.1.0/lpme/src/lpme_modereg_band1.cpp |only lpme-1.1.0/lpme/src/lpme_modereg_band2.cpp |only lpme-1.1.0/lpme/src/lpme_modereg_fit.cpp |only lpme-1.1.0/lpme/src/lpme_modereg_fit_approx.cpp |only lpme-1.1.0/lpme/src/registerDynamicSymbol.c |only 33 files changed, 134 insertions(+), 76 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 2.1 dated 2016-10-18 and 2.2 dated 2017-03-24
irace-2.1/irace/inst/examples/sge-cluster |only irace-2.2/irace/BUGS | 31 irace-2.2/irace/DESCRIPTION | 8 irace-2.2/irace/MD5 | 70 - irace-2.2/irace/NEWS | 75 + irace-2.2/irace/R/cluster.R | 158 +- irace-2.2/irace/R/generation.R | 12 irace-2.2/irace/R/irace.R | 97 - irace-2.2/irace/R/main.R | 76 + irace-2.2/irace/R/parameterAnalysis.R | 18 irace-2.2/irace/R/race-wrapper.R | 32 irace-2.2/irace/R/race.R | 194 +-- irace-2.2/irace/R/readConfiguration.R | 196 ++- irace-2.2/irace/R/testing.R | 28 irace-2.2/irace/R/utils.R | 10 irace-2.2/irace/R/version.R | 2 irace-2.2/irace/README.md | 79 - irace-2.2/irace/build/partial.rdb |only irace-2.2/irace/inst/doc/irace-package.R | 35 irace-2.2/irace/inst/doc/irace-package.Rnw | 704 ++++++++----- irace-2.2/irace/inst/doc/irace-package.pdf |binary irace-2.2/irace/inst/examples/batchmode-cluster |only irace-2.2/irace/inst/examples/hypervolume/target-evaluator | 2 irace-2.2/irace/inst/templates/scenario.txt.tmpl | 9 irace-2.2/irace/inst/templates/target-runner-windows.tmpl |only irace-2.2/irace/man/defaultScenario.Rd | 8 irace-2.2/irace/man/irace-package.Rd | 73 - irace-2.2/irace/man/target.evaluator.default.Rd | 50 irace-2.2/irace/man/target.runner.default.Rd | 58 - irace-2.2/irace/tests/testthat.R | 11 irace-2.2/irace/vignettes/NEWS.txt | 75 + irace-2.2/irace/vignettes/irace-output.Rdata |binary irace-2.2/irace/vignettes/irace-package.Rnw | 704 ++++++++----- irace-2.2/irace/vignettes/irace-package.bib | 48 34 files changed, 1850 insertions(+), 1013 deletions(-)
Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated.
Author: François Rousset [aut, cre, cph]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between Infusion versions 1.0.0 dated 2016-07-25 and 1.1.0 dated 2017-03-24
DESCRIPTION | 17 +- MD5 | 47 +++--- NAMESPACE | 11 - R/MSL.R | 39 +++-- R/Rmixmod.R | 47 ++++++ R/SLik.R | 8 - R/SLikSQuant.R | 34 ++-- R/add_simulation.R | 8 - R/calc_all_slices.R |only R/infer_surface.R | 4 R/jointDens.R | 352 ++++++++++++++++++++++++++++------------------- R/newParameters.R | 26 +-- R/plot.SLik.R | 70 +-------- R/plot.SLik_j.R |only R/project.R | 2 R/quantiles.R | 7 R/undocumentedFns.R | 6 inst/CITATION | 18 +- inst/NEWS.Rd |only man/Infusion-internal.Rd | 12 - man/MSL.Rd | 6 man/add.simulation.Rd | 5 man/infer_jointDens.Rd | 57 ++++--- man/options.Rd | 2 man/plot.SLik.Rd | 6 man/refine.SLik.Rd | 4 26 files changed, 444 insertions(+), 344 deletions(-)
More information about bridgesampling at CRAN
Permanent link
Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness. This is the 'lite' version of the more complete 'viridis' package
that can be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridisLite versions 0.1.3 dated 2016-03-12 and 0.2.0 dated 2017-03-24
DESCRIPTION | 14 ++++++-------- MD5 | 12 +++++++----- R/viridis.R | 41 ++++++++++++++++++++++++++++++++--------- README.md | 10 +++++++--- man/viridis.Rd | 21 ++++++++++++--------- man/viridis.map.Rd | 1 - tests |only 7 files changed, 64 insertions(+), 35 deletions(-)
Title: Large-Scale Bayesian Variable Selection Using Variational
Methods
Description: Fast algorithms for fitting Bayesian variable selection
models and computing Bayes factors, in which the outcome (or
response variable) is modeled using a linear regression or a
logistic regression. The algorithms are based on the variational
approximations described in "Scalable variational inference for
Bayesian variable selection in regression, and its accuracy in
genetic association studies" (P. Carbonetto & M. Stephens, 2012,
<DOI:10.1214/12-BA703>). This software has been applied to large
data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto, Matthew Stephens, David Gerard
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between varbvs versions 2.0.0 dated 2016-05-28 and 2.0-8 dated 2017-03-24
varbvs-2.0-8/varbvs/DESCRIPTION | 29 +++++-- varbvs-2.0-8/varbvs/MD5 | 68 ++++++++++++------ varbvs-2.0-8/varbvs/NAMESPACE | 7 + varbvs-2.0-8/varbvs/R/RcppExports.R |only varbvs-2.0-8/varbvs/R/misc.R | 12 --- varbvs-2.0-8/varbvs/R/plot.varbvs.R | 8 +- varbvs-2.0-8/varbvs/R/subset.varbvs.R |only varbvs-2.0-8/varbvs/R/varbvs.R | 14 ++- varbvs-2.0-8/varbvs/R/varbvsbin.R | 8 +- varbvs-2.0-8/varbvs/R/varbvsbinupdate.R | 2 varbvs-2.0-8/varbvs/R/varbvsbinz.R | 8 +- varbvs-2.0-8/varbvs/R/varbvsbinzupdate.R | 2 varbvs-2.0-8/varbvs/R/varbvsnorm.R | 9 +- varbvs-2.0-8/varbvs/R/varbvsnormupdate.R | 83 ++++++++++++++++------ varbvs-2.0-8/varbvs/README.md |only varbvs-2.0-8/varbvs/build |only varbvs-2.0-8/varbvs/inst/doc |only varbvs-2.0-8/varbvs/man/plot.varbvs.Rd | 11 ++ varbvs-2.0-8/varbvs/man/subset.varbvs.Rd |only varbvs-2.0-8/varbvs/man/varbvs.Rd | 2 varbvs-2.0-8/varbvs/src/RcppExports.cpp |only varbvs-2.0-8/varbvs/src/init.c |only varbvs-2.0-8/varbvs/src/misc.c | 2 varbvs-2.0-8/varbvs/src/misc.h | 2 varbvs-2.0-8/varbvs/src/varbvsnormupdate_rcpp.cpp |only varbvs-2.0-8/varbvs/src/varbvsr.c | 12 +-- varbvs-2.0-8/varbvs/src/varbvsr.h |only varbvs-2.0-8/varbvs/tests |only varbvs-2.0-8/varbvs/vignettes/cd.Rmd |only varbvs-2.0-8/varbvs/vignettes/cfw.Rmd |only varbvs-2.0-8/varbvs/vignettes/cytokine.Rmd |only varbvs-2.0-8/varbvs/vignettes/leukemia.Rmd |only varbvs-2.0.0/varbvs/vignettes/demo.cc.R |only varbvs-2.0.0/varbvs/vignettes/demo.cd.R |only varbvs-2.0.0/varbvs/vignettes/demo.cfw.R |only varbvs-2.0.0/varbvs/vignettes/demo.cytokine.R |only varbvs-2.0.0/varbvs/vignettes/demo.leukemia.R |only varbvs-2.0.0/varbvs/vignettes/demo.qtl.R |only 38 files changed, 184 insertions(+), 95 deletions(-)
Title: Fast n-Gram 'Tokenization'
Description: An n-gram is a sequence of n "words" taken, in order, from a
body of text. This is a collection of utilities for creating,
displaying, summarizing, and "babbling" n-grams. The
'tokenization' and "babbling" are handled by very efficient C
code, which can even be built as its own standalone library.
The babbler is a simple Markov chain. The package also offers
a vignette with complete example 'workflows' and information about
the utilities offered in the package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [aut]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between ngram versions 3.0.2 dated 2017-01-17 and 3.0.3 dated 2017-03-24
ChangeLog | 5 +++ DESCRIPTION | 6 ++-- LICENSE | 2 - MD5 | 25 ++++++++++--------- R/checks.r | 4 +-- R/ngram.r | 2 - README.md | 2 - inst/doc/ngram-guide.Rnw | 2 - inst/doc/ngram-guide.pdf |binary src/Makevars | 2 - src/ngram/src/rand/platform.h | 54 +++++++++++++++++++++++++++++++++++------- src/ngram_native.c |only vignettes/cover/cover.pdf |binary vignettes/ngram-guide.Rnw | 2 - 14 files changed, 74 insertions(+), 32 deletions(-)
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. Alternating optimization is
an iterative process where the genetic score weights, the environmental score weights,
and the main model parameters are estimated in turn assuming the other parameters to
be constant. This approach has greatly enhanced predictive power over traditional GxE
models which include only a single genetic variant and a single environmental
exposure. Gene x gene interactions (GxG) and environment x environment interactions
(ExE) can be incorporated into the genetic and environmental scores. Any standard
model formula can be used, it doesn't have to be a two-way interaction model.
Although this approach was made for GxE modelling, the genetic score doesn't need to
contain genetic variables and the environmental score doesn't need to contain
environmental variables, therefore this approach is highly flexible.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.0.0 dated 2017-02-13 and 1.0.1 dated 2017-03-24
DESCRIPTION | 33 +-- MD5 | 29 +- NAMESPACE | 1 R/LEGIT.R | 85 ++++++-- build/vignette.rds |binary inst/doc/LEGIT.html | 477 ++++++++++++++++++++++++++++++++-------------- man/LEGIT.Rd | 6 man/LEGIT_cv.Rd | 8 man/backward_step.Rd | 3 man/example_2way.Rd | 1 man/example_3way.Rd | 1 man/forward_step.Rd | 8 man/longitudinal_folds.Rd |only man/predict.LEGIT.Rd | 1 man/stepwise_search.Rd | 9 man/summary.LEGIT.Rd | 1 16 files changed, 448 insertions(+), 215 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 3.0.0 dated 2016-01-09 and 3.1.0 dated 2017-03-24
aroma.affymetrix-3.0.0/aroma.affymetrix/inst/testScripts/parallel |only aroma.affymetrix-3.1.0/aroma.affymetrix/DESCRIPTION | 20 aroma.affymetrix-3.1.0/aroma.affymetrix/MD5 | 526 aroma.affymetrix-3.1.0/aroma.affymetrix/NAMESPACE | 8 aroma.affymetrix-3.1.0/aroma.affymetrix/NEWS | 6392 +++++----- aroma.affymetrix-3.1.0/aroma.affymetrix/R/999.DEPRECATED.R | 16 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AbstractProbeSequenceNormalization.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 7 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCdfFile.PLOT.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 7 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupCellMap.R | 6 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelFile.PLOT.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelFile.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelFile.createFrom.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelFile.extractMatrix.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSet.BG.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSet.NORM.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSet.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSet.extractMatrix.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCelSetReporter.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R | 9 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.getSetsOfProbes.R | 31 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AromaCellMatchScoreFile.importFromBpmap.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AromaCellSequenceFile.importFromBpmap.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/AromaUnitTabularBinaryFile.AFFX.PLOT.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/ArrayExplorer.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/BasePositionNormalization.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/ChipEffectFile.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/ChipEffectFile.TOFULL.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/ChipEffectSet.xam.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/CnChipEffectFile.R | 6 aroma.affymetrix-3.1.0/aroma.affymetrix/R/CnagCfhSet.R | 8 aroma.affymetrix-3.1.0/aroma.affymetrix/R/CrlmmModel.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/DChipCdfBinFile.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/DChipDcpSet.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/DChipGenomeInformation.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/DChipSnpInformation.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/ExonChipEffectFile.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/FirmaModel.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/FragmentLengthNormalization.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/GcRmaBackgroundCorrection.R | 10 aroma.affymetrix-3.1.0/aroma.affymetrix/R/GenericReporter.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/LimmaBackgroundCorrection.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/MatNormalization.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/Model.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/OpticalBackgroundCorrection.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/ParameterCelFile.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/QualityAssessmentModel.R | 10 aroma.affymetrix-3.1.0/aroma.affymetrix/R/RmaBackgroundCorrection.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/SnpChipEffectFile.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/SnpChipEffectSet.extractTotalAndFreqB.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/R/SpatialReporter.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/R/TransformReport.R | 6 aroma.affymetrix-3.1.0/aroma.affymetrix/R/UnitModel.fitCnProbes.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UFL.R | 316 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UGP.R | 284 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Cytogenetics_Array/na28/Cytogenetics_Array,UGP,na28.R | 288 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na25/GenomeWideSNP_5,UFL,na25,GWS6.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GWS5,default,UGP+UFL,na26.R | 180 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UFL,na26.R | 208 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_5/na26/GenomeWideSNP_5,UGP,na26.R | 220 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UFL.R | 450 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UGP.R | 380 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,default,UGP+UFL.R | 190 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na25/GenomeWideSNP_6,UFL,na25.R | 180 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GWS6,default,UGP+UFL,na26.R | 178 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UFL,na26.R | 396 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na26/GenomeWideSNP_6,UGP,na26.R | 550 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GWS6,default,UGP+UFL,na27.1.R | 178 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UFL,na27.1.R | 312 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27.1/GenomeWideSNP_6,UGP,na27.1.R | 358 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na27/GenomeWideSNP_6,UGC,na27.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UFL,na30.R | 324 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na30/GenomeWideSNP_6,UGP,na30.R | 330 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UFL.R | 386 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,UGP.R | 344 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na31/GenomeWideSNP_6,default,UGP+UFL.R | 190 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UFL.R | 450 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,UGP.R | 366 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32/GenomeWideSNP_6,default,UGP+UFL.R | 190 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UFL.R | 450 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,UGP.R | 380 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33/GenomeWideSNP_6,default,UGP+UFL.R | 190 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na35 |only aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UFL,na30.R | 246 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/MOUSEDIVm520650/na30/MOUSEDIVm520650,UGP,na30.R | 282 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UFL,na26.R | 224 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba131/na26/Mapping10K_Xba131,UGP,na26.R | 248 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UFL,na26.R | 224 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping10K_Xba142/na26/Mapping10K_Xba142,UGP,na26.R | 248 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UFL,na26.R | 222 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na26/Mapping250K_Nsp,UGP,na26.R | 254 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na28/Mapping250K_Nsp,UGC,na28.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UFL,na31.R | 222 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Nsp/na31/Mapping250K_Nsp,UGP,na31.R | 256 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UFL,na26.R | 224 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na26/Mapping250K_Sty,UGP,na26.R | 254 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na28/Mapping250K_Sty,UGC,na28.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UFL,na31.R | 222 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping250K_Sty/na31/Mapping250K_Sty,UGP,na31.R | 254 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Hind240,UFL.R | 232 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/Mapping50K_Xba240,UGP.R | 222 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UFL,na26.R | 226 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Hind240/na26/Mapping50K_Hind240,UGP,na26.R | 252 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UFL.R | 274 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,UGP.R | 286 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UFL,na26.R | 224 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/Mapping50K_Xba240/na26/Mapping50K_Xba240,UGP,na26.R | 254 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,ACP.R | 324 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1,UGP.R | 364 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/downloadScripts/chipTypes/Mapping50K_Hind240,Xba240/HapMap,testSet,100K.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/R/downloadUtils.R | 686 - aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R | 851 - aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R | 74 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R | 6 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/11.UFL.R | 204 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/21.UGP.R | 202 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R | 193 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R | 193 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R | 219 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R | 219 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R | 253 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 221 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R | 189 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/31.doASCRMAv2,PairedPSCBS.R | 253 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 221 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/11.AllelicCrosstalkCalibration.R | 19 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/GenomeWideSNP_6/11.BasePositionNormalization.R | 19 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/11.OpticalBackgroundCorrection.R | 19 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/12.GcRmaBackgroundCorrection.R | 19 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/13.RmaBackgroundCorrection.R | 19 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/HG-U133_Plus_2/14.NormExpBackgroundCorrection.R | 19 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/Hs_PromPR_v02/11.MatNormalization.R | 21 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.AllelicCrosstalkCalibration.R | 28 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.BasePositionNormalization.R | 28 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/futures/Mapping10K_Xba142/11.UniqueCDF.R | 28 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R | 74 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R | 74 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/CytoScanHD_Array/21.doASCRMAv2,PSCN.R | 128 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01a.downloadAnnotationData.R | 3 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData,GEO.R |only aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R | 212 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/01b.downloadRawData.R | 82 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R | 70 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/01b.downloadRawData.R | 108 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/01b.downloadRawData.R | 74 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/vignettes/CRMAv2,Mapping50K_Hind240.R | 390 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/vignettes/replication-CRLMM/R/01b.downloadRawData.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/inst/vignettes/replication-GCRMA/R/01b.downloadRawData.R | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AdditiveCovariatesNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffineCnPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffinePlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffineSnpPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixCelSetReporter.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixFileSetReporter.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixPgfFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AlleleSummation.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AllelicCrosstalkCalibration.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ArrayExplorer.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AvgCnPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AvgPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/AvgSnpPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/BackgroundCorrection.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/BaseCountNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/BasePositionNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ChipEffectFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ChipEffectGroupMerge.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ChipEffectSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ChipEffectTransform.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CnagCfhFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CnagCfhSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/DChipDcpFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/DChipDcpSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/DChipGenomeInformation.Rd | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/man/DChipQuantileNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/DChipSnpInformation.Rd | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ExonRmaPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/FirmaFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/FirmaModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/FirmaSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/FragmentEquivalentClassNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/FragmentLengthNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/GcContentNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/GcContentNormalization2.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/GenericReporter.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/GenomeInformation.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/HetLogAddCnPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/HetLogAddPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/HetLogAddSnpPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/LinearModelProbeSequenceNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/MatNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/MatSmoothing.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/MbeiCnPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/MbeiPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/MbeiSnpPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/Model.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/MultiArrayUnitModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/Non-documented_objects.Rd | 4 aroma.affymetrix-3.1.0/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/OpticalBackgroundCorrection.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ParameterCelFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ParameterCelSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ProbeLevelModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ProbeLevelTransform.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ProbeLevelTransform3.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/QualityAssessmentModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/QuantileNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ReseqCrosstalkCalibration.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ResidualFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ResidualSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/RmaBackgroundCorrection.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/RmaCnPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/RmaPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/RmaSnpPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ScaleNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/ScaleNormalization3.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SingleArrayUnitModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SmoothMultiarrayModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SmoothRmaModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SnpChipEffectGroupMerge.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SnpInformation.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SnpPlm.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/SpatialReporter.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/TransformReport.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/UgpGenomeInformation.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/UnitModel.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/UnitTypeScaleNormalization.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/WeightsFile.Rd | 2 aroma.affymetrix-3.1.0/aroma.affymetrix/man/WeightsSet.Rd | 2 263 files changed, 14227 insertions(+), 12927 deletions(-)
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