Title: Various plotting functions
Diff between plotrix versions 3.5-10 dated 2014-11-09 and 3.5-11 dated 2015-01-20
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
NEWS | 4 ++++
3 files changed, 11 insertions(+), 7 deletions(-)
Title: Functions for Optimal Non-bipartite Matching
Diff between nbpMatching versions 1.4.0 dated 2013-04-17 and 1.4.4 dated 2015-01-20
Description: This package provides functions for performing nonbipartite
matching and matched randomization. A "bipartite" matching utilizes two
separate groups, e.g. smokers being matched to nonsmokers or cases being
matched to controls. A "nonbipartite" matching creates mates from one big
group, e.g. 100 hospitals being randomized for a two-arm cluster randomized
trial or 5000 children who have been exposed to various levels of
secondhand smoke and are being paired to form a greater exposure vs. lesser
exposure comparison. At the core of a nonbipartite matching is a NxN
distance matrix for N potential mates. The distance between two units
expresses a measure of similarity or quality as mates (the lower the
better). The 'gendistance()' and 'distancematrix()' functions assist in
creating this. The 'nonbimatch()' function creates the matching that
minimizes the total sum of distances between mates; hence, it is referred
to as an "optimal" matching. The 'assign.grp()' function aids in performing
a matched randomization. Note the package can also perform bipartite
matching using the prevent option in 'gendistance()'.
Author: Cole Beck [aut, cre], Bo Lu [aut], Robert Greevy [aut]
Maintainer: Cole Beck
DESCRIPTION | 39 +
MD5 | 55 +-
NAMESPACE | 24 -
R/assign.grp.R | 38 +
R/distancematrix.R | 69 ++-
R/fill.missing.R | 36 +
R/gendistance.R | 174 ++++++-
R/make.phantoms.R | 38 +
R/nbpmatching-package.R |only
R/nonbimatch.R | 75 ++-
R/qom.R | 70 ++-
R/quantile.R | 24 -
R/utils.R | 45 +
man/assign.grp.Rd | 49 --
man/distancematrix.Rd | 89 ++-
man/fill.missing.Rd | 66 +-
man/gendistance.Rd | 143 +++---
man/get.sets.Rd | 45 -
man/make.phantoms.Rd | 66 +-
man/nbpMatching-internal.Rd | 19
man/nbpMatching-package.Rd | 55 +-
man/nonbimatch.Rd | 67 +-
man/qom.Rd | 90 ++-
man/quantile.Rd | 43 -
man/scalar.dist.Rd | 36 -
src/fcorematch.f | 1003 +++++++++++++++++++++-----------------------
src/mwrap.f | 2
tests |only
28 files changed, 1462 insertions(+), 998 deletions(-)
Title: Various Options and Add-ins for Lattice
Diff between loa versions 0.2.21 dated 2015-01-13 and 0.2.22 dated 2015-01-20
Description: This package, Lattice Options and Add-ins (or loa), contains various plots and
functions that make use of the lattice/trellis plotting framework. The plots (which include
loaPlot, GoogleMap and trianglePlot) use panelPal, a function that extends lattice and hexbin
package methods to automate plot subscripting and panel-to-panel and panel-to key
synchronization/management. See ?loa for further details.
Author: Karl Ropkins
Maintainer: Karl Ropkins
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
inst/CITATION | 16 +++++++++-------
man/loa-package.Rd | 4 ++--
4 files changed, 21 insertions(+), 19 deletions(-)
Title: Modeling and Inferring Gene Networks
Diff between GeneNet versions 1.2.11 dated 2014-11-16 and 1.2.12 dated 2015-01-20
Description: GeneNet is a package for analyzing gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and
Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 6 ++++++
man/ggm.make.igraph.Rd | 2 +-
4 files changed, 14 insertions(+), 8 deletions(-)
Title: Sequential Event Interval Analysis
Diff between eventInterval versions 1.0-1 dated 2014-01-17 and 1.2 dated 2015-01-20
Description: Functions for analysis of rate changes in sequential events
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 14 +++++++-------
MD5 | 10 +++++-----
NEWS | 4 ++++
R/EIglm.R | 12 +++++-------
man/EIglm.Rd | 23 ++++++++++++++++++++---
man/eventInterval-package.Rd | 7 ++++---
6 files changed, 45 insertions(+), 25 deletions(-)
Title: Predicting Causal Direction from Dependency Features
Diff between D2C versions 1.1 dated 2014-12-16 and 1.2.1 dated 2015-01-20
Description: The relationship between statistical dependency and causality lies
at the heart of all statistical approaches to causal inference. The D2C
package implements a supervised machine learning approach to infer the
existence of a directed causal link between two variables in multivariate
settings with n>2 variables. The approach relies on the asymmetry of some
conditional (in)dependence relations between the members of the Markov
blankets of two variables causally connected. The D2C algorithm predicts
the existence of a direct causal link between two variables in a
multivariate setting by (i) creating a set of of features of the
relationship based on asymmetric descriptors of the multivariate dependency
and (ii) using a classifier to learn a mapping between the features and the
presence of a causal link
Author: Gianluca Bontempi, Catharina Olsen, Maxime Flauder
Maintainer: Catharina Olsen
D2C-1.1/D2C/CHANGES |only
D2C-1.1/D2C/R/D2c.Data.R |only
D2C-1.1/D2C/R/D2c.network.R |only
D2C-1.1/D2C/man/D2C.descriptor-class.Rd |only
D2C-1.2.1/D2C/DESCRIPTION | 12 +--
D2C-1.2.1/D2C/MD5 | 39 ++++++----
D2C-1.2.1/D2C/NAMESPACE | 24 +++++-
D2C-1.2.1/D2C/R/classes.R |only
D2C-1.2.1/D2C/R/d2c.R | 45 ++---------
D2C-1.2.1/D2C/R/util.R | 68 +++++++++++++++++-
D2C-1.2.1/D2C/build |only
D2C-1.2.1/D2C/data/alarm.RData |only
D2C-1.2.1/D2C/data/datalist | 2
D2C-1.2.1/D2C/inst |only
D2C-1.2.1/D2C/man/BER.Rd |only
D2C-1.2.1/D2C/man/alarm.Rd |only
D2C-1.2.1/D2C/man/dataset.Rd |only
D2C-1.2.1/D2C/man/example.Rd | 6 +
D2C-1.2.1/D2C/man/initialize-D2C-method.Rd | 5 +
D2C-1.2.1/D2C/man/initialize-D2C.descriptor-method.Rd | 1
D2C-1.2.1/D2C/man/initialize-DAG.network-method.Rd | 2
D2C-1.2.1/D2C/man/initialize-simulatedDAG-method.Rd | 10 ++
D2C-1.2.1/D2C/man/predict-D2C-method.Rd | 1
D2C-1.2.1/D2C/man/true.net.Rd |only
D2C-1.2.1/D2C/man/update-simulatedDAG-method.Rd |only
D2C-1.2.1/D2C/man/updateD2C-D2C-method.Rd |only
D2C-1.2.1/D2C/vignettes |only
27 files changed, 148 insertions(+), 67 deletions(-)
Title: Completing Ranks
Diff between crank versions 1.0-6 dated 2014-11-09 and 1.0-7 dated 2015-01-20
Description: Functions for completing and recalculating rankings.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 14 +++++++-------
MD5 | 2 +-
2 files changed, 8 insertions(+), 8 deletions(-)
Title: Baseline Correction of Spectra
Diff between baseline versions 1.1-3 dated 2014-02-21 and 1.1-4 dated 2015-01-20
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters.
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 14
MD5 | 52 +-
R/baseline.fillPeaks.R | 162 +++-----
R/baseline.rfbaseline.R | 34 -
R/baselineGUI.R | 566 ++++++++++++++--------------
R/globals.R | 7
R/optimWizard.R | 796 ++++++++++++++++++++--------------------
R/optimisation.R | 826 ++++++++++++++++++++++--------------------
R/plotBaseline.R | 232 ++++++-----
R/plotOptim.R | 730 ++++++++++++++++++-------------------
man/baseline-package.Rd | 8
man/baseline.Rd | 4
man/baseline.als.Rd | 2
man/baseline.fillPeaks.Rd | 6
man/baseline.irls.Rd | 4
man/baseline.lowpass.Rd | 4
man/baseline.medianWindow.Rd | 4
man/baseline.modpolyfit.Rd | 4
man/baseline.peakDetection.Rd | 4
man/baseline.rfbaseline.Rd | 4
man/baseline.rollingBall.Rd | 4
man/baselineGUI.Rd | 8
man/custom.baseline.Rd | 2
man/doOptim.Rd | 1
man/milk.Rd | 2
man/optimWizard.Rd | 3
man/plotBaseline.Rd | 3
27 files changed, 1813 insertions(+), 1673 deletions(-)
Title: Random Forest for SNPs to Prevent X-chromosome SNP Importance
Bias
Diff between snpRF versions 0.3 dated 2014-12-31 and 0.4 dated 2015-01-20
Description: A modification of Breiman and Cutler's classification random forests modified for SNP (Single Nucleotide Polymorphism) data (based on randomForest v4.6-7) to prevent X-chromosome SNP variable importance bias compared to autosomal SNPs by simulating the process of X chromosome inactivation. Classification is based on a forest of trees using random subsets of SNPs and other variables as inputs.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew
Wiener. Modifications of randomForest v 4.6-7 for SNPs by Greg Jenkins based on a
method developed by Stacey Winham, Greg Jenkins and Joanna Biernacka.
Maintainer: Greg Jenkins
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/MDSplot.R | 2 +-
R/margin.R | 7 ++++---
R/predict.snpRF.R | 2 +-
5 files changed, 14 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-09 1.0.7
2014-09-16 1.0.6
2014-06-29 1.0.5
2014-05-15 1.0.3
2014-03-20 1.0.2
2014-02-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-10 1.7.6
2014-09-19 1.7.5
2014-09-16 1.7.4
2014-06-30 1.7.3
2014-05-16 1.7.2
2014-03-20 1.7.1
2014-02-21 1.7.0
Title: Pretty Descriptive Stats
Diff between prettyR versions 2.0-8 dated 2014-05-25 and 2.1 dated 2015-01-20
Description: Functions for conventionally formatting descriptive stats,
reshaping data frames and formatting R output as HTML.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 14 +--
MD5 | 25 +++--
NAMESPACE | 1
NEWS | 8 +
R/brkdn.R | 13 +--
R/describe.R | 203 +++++++++++++++++-------------------------------
R/print.xtab.R | 23 ++---
man/Mode.Rd | 15 +--
man/brkdn.Rd | 4
man/describe.Rd | 39 ++++-----
man/describe.factor.Rd | 15 ---
man/describe.logical.Rd | 8 -
man/describe.numeric.Rd | 8 -
man/print.desc.Rd |only
14 files changed, 157 insertions(+), 219 deletions(-)
Title: Tools for Descriptive Statistics
Diff between DescTools versions 0.99.8.1 dated 2014-09-22 and 0.99.9 dated 2015-01-20
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains as well functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Markus Huerzeler, Wallace W. Hui, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Yongyi Min, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell
DescTools-0.99.8.1/DescTools/R/AreaIdent.R |only
DescTools-0.99.8.1/DescTools/R/DescFactFact.R |only
DescTools-0.99.8.1/DescTools/R/Explore.R |only
DescTools-0.99.8.1/DescTools/R/FormatFix.R |only
DescTools-0.99.8.1/DescTools/R/FormatSig.R |only
DescTools-0.99.8.1/DescTools/R/Kappam.R |only
DescTools-0.99.8.1/DescTools/R/Min.R |only
DescTools-0.99.8.1/DescTools/R/Mround.R |only
DescTools-0.99.8.1/DescTools/R/Sec.R |only
DescTools-0.99.8.1/DescTools/R/WhichCharacters.R |only
DescTools-0.99.8.1/DescTools/R/WhichFactors.R |only
DescTools-0.99.8.1/DescTools/R/WhichFlags.R |only
DescTools-0.99.8.1/DescTools/R/WhichNumerics.R |only
DescTools-0.99.8.1/DescTools/data/d.world.rda |only
DescTools-0.99.8.1/DescTools/man/Explore.Rd |only
DescTools-0.99.8.1/DescTools/man/FormatFix.Rd |only
DescTools-0.99.8.1/DescTools/man/FormatSig.Rd |only
DescTools-0.99.8.1/DescTools/man/Mround.Rd |only
DescTools-0.99.8.1/DescTools/man/PwApply.Rd |only
DescTools-0.99.8.1/DescTools/man/WhichFlags.Rd |only
DescTools-0.99.8.1/DescTools/man/XLGetWorkbook.Rd |only
DescTools-0.99.8.1/DescTools/man/d.world.Rd |only
DescTools-0.99.9/DescTools/DESCRIPTION | 19
DescTools-0.99.9/DescTools/MD5 | 544 +++++++------
DescTools-0.99.9/DescTools/NAMESPACE | 2
DescTools-0.99.9/DescTools/NEWS | 101 ++
DescTools-0.99.9/DescTools/R/AddMonths.R | 47 -
DescTools-0.99.9/DescTools/R/Agree.R |only
DescTools-0.99.9/DescTools/R/AscToChar.R | 1
DescTools-0.99.9/DescTools/R/Assocs.R | 53 -
DescTools-0.99.9/DescTools/R/BinomCI.R | 244 +++--
DescTools-0.99.9/DescTools/R/BinomDiffCI.R | 4
DescTools-0.99.9/DescTools/R/BinomRatioCI.R |only
DescTools-0.99.9/DescTools/R/BubbleLegend.R |only
DescTools-0.99.9/DescTools/R/CCC.R |only
DescTools-0.99.9/DescTools/R/CartToPol.R | 2
DescTools-0.99.9/DescTools/R/CartToSph.R |only
DescTools-0.99.9/DescTools/R/CharToAsc.R | 6
DescTools-0.99.9/DescTools/R/Closest.R | 28
DescTools-0.99.9/DescTools/R/CoefVar.R |only
DescTools-0.99.9/DescTools/R/CohenD.R |only
DescTools-0.99.9/DescTools/R/CohenKappa.R | 3
DescTools-0.99.9/DescTools/R/CollapseTable.R |only
DescTools-0.99.9/DescTools/R/ConDisPairs.R | 2
DescTools-0.99.9/DescTools/R/CorCI.R | 26
DescTools-0.99.9/DescTools/R/CramerV.R | 6
DescTools-0.99.9/DescTools/R/CronbachAlpha.R | 6
DescTools-0.99.9/DescTools/R/CutQ.R | 14
DescTools-0.99.9/DescTools/R/DenseRank.R |only
DescTools-0.99.9/DescTools/R/Desc.character.R | 3
DescTools-0.99.9/DescTools/R/Desc.data.frame.R | 23
DescTools-0.99.9/DescTools/R/Desc.factor.R | 10
DescTools-0.99.9/DescTools/R/Desc.flags.R | 5
DescTools-0.99.9/DescTools/R/Desc.formula.R | 15
DescTools-0.99.9/DescTools/R/Desc.integer.R | 5
DescTools-0.99.9/DescTools/R/Desc.list.R | 26
DescTools-0.99.9/DescTools/R/Desc.ordered.R | 8
DescTools-0.99.9/DescTools/R/Desc.table.R | 174 ++--
DescTools-0.99.9/DescTools/R/DescFactNum.R | 4
DescTools-0.99.9/DescTools/R/DescTools-internal.R | 424 +++++++---
DescTools-0.99.9/DescTools/R/DescToolsOptions.R | 40
DescTools-0.99.9/DescTools/R/DescWrd.data.frame.R | 15
DescTools-0.99.9/DescTools/R/DescWrd.default.R | 5
DescTools-0.99.9/DescTools/R/DescWrd.list.R |only
DescTools-0.99.9/DescTools/R/DunnTest.R |only
DescTools-0.99.9/DescTools/R/DunnTest.default.R |only
DescTools-0.99.9/DescTools/R/DunnTest.formula.R |only
DescTools-0.99.9/DescTools/R/DunnettTest.R |only
DescTools-0.99.9/DescTools/R/DunnettTest.default.R |only
DescTools-0.99.9/DescTools/R/DunnettTest.formula.R |only
DescTools-0.99.9/DescTools/R/EtaSq.R | 123 --
DescTools-0.99.9/DescTools/R/EtaSq.aovlist.R |only
DescTools-0.99.9/DescTools/R/EtaSq.lm.R |only
DescTools-0.99.9/DescTools/R/Exec.R |only
DescTools-0.99.9/DescTools/R/FctArgs.R | 3
DescTools-0.99.9/DescTools/R/Fibonacci.R | 32
DescTools-0.99.9/DescTools/R/FindCorr.R |only
DescTools-0.99.9/DescTools/R/Flags.R | 2
DescTools-0.99.9/DescTools/R/Format.R |only
DescTools-0.99.9/DescTools/R/Format.default.R |only
DescTools-0.99.9/DescTools/R/Format.matrix.R |only
DescTools-0.99.9/DescTools/R/Freq.R | 11
DescTools-0.99.9/DescTools/R/GetCurrPP.R | 27
DescTools-0.99.9/DescTools/R/GetCurrWrd.R | 32
DescTools-0.99.9/DescTools/R/GetCurrXL.R | 17
DescTools-0.99.9/DescTools/R/GetNewPP.R | 33
DescTools-0.99.9/DescTools/R/GetNewWrd.R | 48 -
DescTools-0.99.9/DescTools/R/GetNewXL.R | 25
DescTools-0.99.9/DescTools/R/HmsToSec.R | 16
DescTools-0.99.9/DescTools/R/HodgesLehmann.R | 50 +
DescTools-0.99.9/DescTools/R/Hour.R | 3
DescTools-0.99.9/DescTools/R/HuberM.R | 33
DescTools-0.99.9/DescTools/R/ICC.R | 227 ++---
DescTools-0.99.9/DescTools/R/IdentifyA.R |only
DescTools-0.99.9/DescTools/R/ImportDlg.R | 4
DescTools-0.99.9/DescTools/R/Impute.R |only
DescTools-0.99.9/DescTools/R/Interval.R | 21
DescTools-0.99.9/DescTools/R/IsNumeric.R |only
DescTools-0.99.9/DescTools/R/IsPrime.R | 2
DescTools-0.99.9/DescTools/R/IsWhole.R | 2
DescTools-0.99.9/DescTools/R/IsZero.R |only
DescTools-0.99.9/DescTools/R/JarqueBeraTest.R | 10
DescTools-0.99.9/DescTools/R/KappaM.R |only
DescTools-0.99.9/DescTools/R/KendallW.R | 109 +-
DescTools-0.99.9/DescTools/R/Kurt.R | 38
DescTools-0.99.9/DescTools/R/LOCF.default.R | 2
DescTools-0.99.9/DescTools/R/Large.R | 2
DescTools-0.99.9/DescTools/R/LastDayOfMonth.R |only
DescTools-0.99.9/DescTools/R/Lc.R | 26
DescTools-0.99.9/DescTools/R/Lc.default.R |only
DescTools-0.99.9/DescTools/R/Lc.formula.R |only
DescTools-0.99.9/DescTools/R/MeanCI.R | 79 +
DescTools-0.99.9/DescTools/R/MeanSE.R | 5
DescTools-0.99.9/DescTools/R/Midx.R | 4
DescTools-0.99.9/DescTools/R/Minute.R |only
DescTools-0.99.9/DescTools/R/OddsRatio.R | 22
DescTools-0.99.9/DescTools/R/Outlier.R | 7
DescTools-0.99.9/DescTools/R/Overlap.R |only
DescTools-0.99.9/DescTools/R/PairApply.R | 2
DescTools-0.99.9/DescTools/R/PalDescTools.R | 36
DescTools-0.99.9/DescTools/R/PartitionBy.R |only
DescTools-0.99.9/DescTools/R/PasswordDlg.R | 2
DescTools-0.99.9/DescTools/R/PlotBubble.R | 15
DescTools-0.99.9/DescTools/R/PlotBubble.default.R |only
DescTools-0.99.9/DescTools/R/PlotBubble.formula.R |only
DescTools-0.99.9/DescTools/R/PlotCirc.R | 24
DescTools-0.99.9/DescTools/R/PlotCorr.R | 4
DescTools-0.99.9/DescTools/R/PlotDesc.default.R | 2
DescTools-0.99.9/DescTools/R/PlotDesc.factor.R | 15
DescTools-0.99.9/DescTools/R/PlotDesc.integer.R | 2
DescTools-0.99.9/DescTools/R/PlotDesc.ordered.R | 10
DescTools-0.99.9/DescTools/R/PlotDesc.table.R | 46 -
DescTools-0.99.9/DescTools/R/PlotDescFactNum.R | 4
DescTools-0.99.9/DescTools/R/PlotFct.R | 6
DescTools-0.99.9/DescTools/R/PlotPar.R | 5
DescTools-0.99.9/DescTools/R/PlotPyramid.R | 5
DescTools-0.99.9/DescTools/R/PlotRCol.R | 5
DescTools-0.99.9/DescTools/R/PlotTernary.R |only
DescTools-0.99.9/DescTools/R/PlotVenn.R | 122 +-
DescTools-0.99.9/DescTools/R/PlotWeb.R | 8
DescTools-0.99.9/DescTools/R/PolToCart.R | 2
DescTools-0.99.9/DescTools/R/PolarGrid.R | 2
DescTools-0.99.9/DescTools/R/PostHocTest.aov.R | 31
DescTools-0.99.9/DescTools/R/PostHocTest.matrix.R |only
DescTools-0.99.9/DescTools/R/PostHocTest.table.R |only
DescTools-0.99.9/DescTools/R/Prec.R |only
DescTools-0.99.9/DescTools/R/Quarter.R | 2
DescTools-0.99.9/DescTools/R/Ray.R | 42 -
DescTools-0.99.9/DescTools/R/RndPairs.R |only
DescTools-0.99.9/DescTools/R/RoundM.R |only
DescTools-0.99.9/DescTools/R/ScheffeTest.aov.R | 1
DescTools-0.99.9/DescTools/R/SecToHms.R | 24
DescTools-0.99.9/DescTools/R/Second.R |only
DescTools-0.99.9/DescTools/R/SelectVarDlg.data.frame.R | 4
DescTools-0.99.9/DescTools/R/SelectVarDlg.default.R | 3
DescTools-0.99.9/DescTools/R/Skew.R | 41
DescTools-0.99.9/DescTools/R/Small.R | 2
DescTools-0.99.9/DescTools/R/Sort.data.frame.R | 4
DescTools-0.99.9/DescTools/R/SphToCart.R |only
DescTools-0.99.9/DescTools/R/Stamp.R |only
DescTools-0.99.9/DescTools/R/Str.R | 2
DescTools-0.99.9/DescTools/R/StrLeft.R |only
DescTools-0.99.9/DescTools/R/StrPad.R | 17
DescTools-0.99.9/DescTools/R/StrRight.R |only
DescTools-0.99.9/DescTools/R/StrVal.R | 14
DescTools-0.99.9/DescTools/R/SysInfo.R | 1
DescTools-0.99.9/DescTools/R/TheilU.R | 4
DescTools-0.99.9/DescTools/R/Trim.R | 14
DescTools-0.99.9/DescTools/R/TukeyBiweight.R | 21
DescTools-0.99.9/DescTools/R/Untable.R | 41
DescTools-0.99.9/DescTools/R/Untable.data.frame.R |only
DescTools-0.99.9/DescTools/R/Untable.default.R |only
DescTools-0.99.9/DescTools/R/WrdInsTab.R | 10
DescTools-0.99.9/DescTools/R/WrdKill.R |only
DescTools-0.99.9/DescTools/R/WrdPlot.R | 13
DescTools-0.99.9/DescTools/R/WrdTable.Freq.R | 11
DescTools-0.99.9/DescTools/R/WrdTable.R | 2
DescTools-0.99.9/DescTools/R/WrdTable.default.R | 41
DescTools-0.99.9/DescTools/R/WrdText.R | 31
DescTools-0.99.9/DescTools/R/XLGetRange.R | 17
DescTools-0.99.9/DescTools/R/XLKill.R |only
DescTools-0.99.9/DescTools/R/YuenTTest.R |only
DescTools-0.99.9/DescTools/R/YuenTTest.default.R |only
DescTools-0.99.9/DescTools/R/YuenTTest.formula.R |only
DescTools-0.99.9/DescTools/R/ZeroIfNA.R |only
DescTools-0.99.9/DescTools/R/Zodiac.R | 2
DescTools-0.99.9/DescTools/R/aovlDetails.R |only
DescTools-0.99.9/DescTools/R/aovlErrorTerms.R |only
DescTools-0.99.9/DescTools/R/createCOMReference.R |only
DescTools-0.99.9/DescTools/R/dBenf.R |only
DescTools-0.99.9/DescTools/R/dRevGumbel.R |only
DescTools-0.99.9/DescTools/R/identify.formula.R | 24
DescTools-0.99.9/DescTools/R/lines.smooth.spline.R |only
DescTools-0.99.9/DescTools/R/pBenf.R |only
DescTools-0.99.9/DescTools/R/pRevGumbel.R |only
DescTools-0.99.9/DescTools/R/plot.Lclist.R |only
DescTools-0.99.9/DescTools/R/print.Assocs.R | 3
DescTools-0.99.9/DescTools/R/print.DunnTest.R |only
DescTools-0.99.9/DescTools/R/print.ICC.R | 6
DescTools-0.99.9/DescTools/R/print.PostHocTest.R | 19
DescTools-0.99.9/DescTools/R/qBenf.R |only
DescTools-0.99.9/DescTools/R/qRevGumbel.R |only
DescTools-0.99.9/DescTools/R/qRevGumbelExp.R |only
DescTools-0.99.9/DescTools/R/rBenf.R |only
DescTools-0.99.9/DescTools/R/rRevGumbel.R |only
DescTools-0.99.9/DescTools/R/z%overlaps%.R | 8
DescTools-0.99.9/DescTools/data/d.countries.rda |only
DescTools-0.99.9/DescTools/data/d.prefix.rda |only
DescTools-0.99.9/DescTools/demo/plots.R | 2
DescTools-0.99.9/DescTools/inst/CITATION |only
DescTools-0.99.9/DescTools/inst/doc/DescTools.pdf |binary
DescTools-0.99.9/DescTools/inst/doc/DescToolsCompanion.pdf |binary
DescTools-0.99.9/DescTools/man/AddMonths.Rd | 8
DescTools-0.99.9/DescTools/man/Agree.Rd |only
DescTools-0.99.9/DescTools/man/AllDuplicated.Rd | 5
DescTools-0.99.9/DescTools/man/AndersonDarlingTest.Rd | 2
DescTools-0.99.9/DescTools/man/AreaIdent.Rd | 10
DescTools-0.99.9/DescTools/man/Assocs.Rd | 5
DescTools-0.99.9/DescTools/man/Benf.Rd |only
DescTools-0.99.9/DescTools/man/Between.Rd | 12
DescTools-0.99.9/DescTools/man/BinomCI.Rd | 24
DescTools-0.99.9/DescTools/man/BinomDiffCI.Rd | 2
DescTools-0.99.9/DescTools/man/BinomRatioCI.rd |only
DescTools-0.99.9/DescTools/man/BoxCoxLambda.Rd | 6
DescTools-0.99.9/DescTools/man/BubbleLegend.Rd |only
DescTools-0.99.9/DescTools/man/CCC.Rd |only
DescTools-0.99.9/DescTools/man/CartToPol.Rd | 23
DescTools-0.99.9/DescTools/man/Closest.Rd | 15
DescTools-0.99.9/DescTools/man/CochranArmitageTest.Rd | 5
DescTools-0.99.9/DescTools/man/CoefVar.Rd |only
DescTools-0.99.9/DescTools/man/CohenD.Rd |only
DescTools-0.99.9/DescTools/man/CohenKappa.Rd | 45 -
DescTools-0.99.9/DescTools/man/CollapseTable.Rd |only
DescTools-0.99.9/DescTools/man/ColorLegend.Rd | 7
DescTools-0.99.9/DescTools/man/ConnLines.Rd | 5
DescTools-0.99.9/DescTools/man/Contrasts.Rd | 17
DescTools-0.99.9/DescTools/man/CramerV.Rd | 20
DescTools-0.99.9/DescTools/man/CronbachAlpha.Rd | 11
DescTools-0.99.9/DescTools/man/CutQ.Rd | 11
DescTools-0.99.9/DescTools/man/DateFunctions.Rd | 27
DescTools-0.99.9/DescTools/man/DenseRank.Rd |only
DescTools-0.99.9/DescTools/man/Desc.Rd | 1
DescTools-0.99.9/DescTools/man/Desc.data.frame.Rd | 10
DescTools-0.99.9/DescTools/man/Desc.flags.Rd | 30
DescTools-0.99.9/DescTools/man/Desc.table.Rd | 10
DescTools-0.99.9/DescTools/man/DescTools-package.Rd | 227 +++--
DescTools-0.99.9/DescTools/man/DescWrd.Rd | 9
DescTools-0.99.9/DescTools/man/DunnTest.Rd |only
DescTools-0.99.9/DescTools/man/DunnettTest.Rd |only
DescTools-0.99.9/DescTools/man/Entropy.Rd | 2
DescTools-0.99.9/DescTools/man/EtaSq.Rd | 81 +
DescTools-0.99.9/DescTools/man/Exec.Rd |only
DescTools-0.99.9/DescTools/man/Fibonacci.Rd | 40
DescTools-0.99.9/DescTools/man/FindCorr.Rd |only
DescTools-0.99.9/DescTools/man/FisherZ.Rd | 48 -
DescTools-0.99.9/DescTools/man/Format.Rd |only
DescTools-0.99.9/DescTools/man/GetNewWrd.Rd | 56 +
DescTools-0.99.9/DescTools/man/GetNewXL.Rd | 12
DescTools-0.99.9/DescTools/man/GetPairs.Rd | 3
DescTools-0.99.9/DescTools/man/GoodmanKruskalTauA.Rd | 5
DescTools-0.99.9/DescTools/man/HmsToSec.Rd | 6
DescTools-0.99.9/DescTools/man/HoeffD.Rd | 9
DescTools-0.99.9/DescTools/man/HotellingsT.Rd | 11
DescTools-0.99.9/DescTools/man/HuberM.Rd | 25
DescTools-0.99.9/DescTools/man/ICC.Rd | 60 -
DescTools-0.99.9/DescTools/man/IsDichotomous.Rd | 2
DescTools-0.99.9/DescTools/man/IsOdd.Rd | 2
DescTools-0.99.9/DescTools/man/IsWhole.Rd | 35
DescTools-0.99.9/DescTools/man/JarqueBeraTest.Rd | 32
DescTools-0.99.9/DescTools/man/Kappam.Rd | 28
DescTools-0.99.9/DescTools/man/KendallW.Rd | 23
DescTools-0.99.9/DescTools/man/KrippAlpha.Rd | 38
DescTools-0.99.9/DescTools/man/Lambda.Rd | 33
DescTools-0.99.9/DescTools/man/Large.Rd | 14
DescTools-0.99.9/DescTools/man/Lc.Rd | 49 -
DescTools-0.99.9/DescTools/man/LogLin.Rd | 20
DescTools-0.99.9/DescTools/man/LogSt.Rd | 2
DescTools-0.99.9/DescTools/man/MHChisqTest.Rd | 4
DescTools-0.99.9/DescTools/man/MeanCI.Rd | 46 -
DescTools-0.99.9/DescTools/man/MeanDiffCI.Rd | 2
DescTools-0.99.9/DescTools/man/MeanSE.Rd | 11
DescTools-0.99.9/DescTools/man/Midx.Rd | 18
DescTools-0.99.9/DescTools/man/MultinomCI.Rd | 18
DescTools-0.99.9/DescTools/man/Ndec.Rd | 3
DescTools-0.99.9/DescTools/man/OddsRatio.Rd | 7
DescTools-0.99.9/DescTools/man/Outlier.Rd | 6
DescTools-0.99.9/DescTools/man/PairApply.Rd |only
DescTools-0.99.9/DescTools/man/PartCor.Rd | 2
DescTools-0.99.9/DescTools/man/PartitionBy.Rd |only
DescTools-0.99.9/DescTools/man/PasswordDlg.Rd | 8
DescTools-0.99.9/DescTools/man/Permn.Rd | 6
DescTools-0.99.9/DescTools/man/PlotBubble.Rd | 43 -
DescTools-0.99.9/DescTools/man/PlotCorr.Rd | 15
DescTools-0.99.9/DescTools/man/PlotDesc.Rd | 10
DescTools-0.99.9/DescTools/man/PlotFdist.Rd | 2
DescTools-0.99.9/DescTools/man/PlotPolar.Rd | 2
DescTools-0.99.9/DescTools/man/PlotTernary.Rd |only
DescTools-0.99.9/DescTools/man/PlotVenn.Rd | 12
DescTools-0.99.9/DescTools/man/PlotWeb.Rd | 24
DescTools-0.99.9/DescTools/man/PostHocTest.Rd | 16
DescTools-0.99.9/DescTools/man/RevGumbel.Rd |only
DescTools-0.99.9/DescTools/man/RndPairs.Rd |only
DescTools-0.99.9/DescTools/man/RoundM.Rd |only
DescTools-0.99.9/DescTools/man/ScheffeTest.Rd | 2
DescTools-0.99.9/DescTools/man/Skew.Rd | 44 -
DescTools-0.99.9/DescTools/man/SomersDelta.Rd | 8
DescTools-0.99.9/DescTools/man/Stamp.Rd |only
DescTools-0.99.9/DescTools/man/StrCountW.Rd | 4
DescTools-0.99.9/DescTools/man/StrPad.Rd | 6
DescTools-0.99.9/DescTools/man/StrRight.Rd |only
DescTools-0.99.9/DescTools/man/StrVal.Rd | 25
DescTools-0.99.9/DescTools/man/StuartTauC.Rd | 6
DescTools-0.99.9/DescTools/man/SysInfo.Rd | 10
DescTools-0.99.9/DescTools/man/TheilU.Rd | 18
DescTools-0.99.9/DescTools/man/Trim.Rd | 14
DescTools-0.99.9/DescTools/man/TukeyBiweight.Rd | 18
DescTools-0.99.9/DescTools/man/UncertCoef.Rd | 2
DescTools-0.99.9/DescTools/man/UnitConv.Rd | 110 +-
DescTools-0.99.9/DescTools/man/Untable.Rd | 19
DescTools-0.99.9/DescTools/man/Winsorize.Rd | 3
DescTools-0.99.9/DescTools/man/WrdInsTab.Rd | 7
DescTools-0.99.9/DescTools/man/WrdPlot.Rd | 5
DescTools-0.99.9/DescTools/man/WrdTable.Rd | 14
DescTools-0.99.9/DescTools/man/WrdText.Rd | 28
DescTools-0.99.9/DescTools/man/XLGetRange.Rd | 42 -
DescTools-0.99.9/DescTools/man/XLView.Rd | 9
DescTools-0.99.9/DescTools/man/YuenTTest.Rd |only
DescTools-0.99.9/DescTools/man/ZeroIfNA.Rd |only
DescTools-0.99.9/DescTools/man/d.countries.Rd |only
DescTools-0.99.9/DescTools/man/d.pizza.Rd | 15
DescTools-0.99.9/DescTools/man/identify.formula.Rd | 16
DescTools-0.99.9/DescTools/man/lines.loess.Rd | 19
DescTools-0.99.9/DescTools/man/overlaps.Rd | 31
333 files changed, 3478 insertions(+), 2089 deletions(-)
Title: Clinical Significance Functions
Diff between clinsig versions 1.0-4 dated 2013-04-14 and 1.0-5 dated 2015-01-20
Description: Functions for calculating clinical significance.
Author: Jim Lemon
Maintainer: Jim Lemon
clinsig-1.0-4/clinsig/INDEX |only
clinsig-1.0-5/clinsig/DESCRIPTION | 14 +++++++-------
clinsig-1.0-5/clinsig/MD5 | 5 ++---
clinsig-1.0-5/clinsig/man/clinsig.Rd | 4 ++--
4 files changed, 11 insertions(+), 12 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Diff between aroma.affymetrix versions 2.12.0 dated 2014-03-09 and 2.13.0 dated 2015-01-20
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the disk space that limits the number of arrays that can be analyzed.
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
31.doASCRMAv2,PairedPSCBS.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/Sc03b_MF_v04 |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/BatchJobs |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/setup/launch-addons.sh |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/setup/launch-replication.sh |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/setup/launch-system.sh |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/DESCRIPTION | 36
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/MD5 | 556
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/NAMESPACE | 31
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/NEWS | 5641 +++++-----
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/021.dynamic_imports.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AbstractProbeSequenceNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AdditiveCovariatesNormalization.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffinePlm.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R | 53
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.COUNTS.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.MONOCELL.R | 30
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 35
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.UNIQUE.R | 34
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.computeAffinities.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleCellPairs.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs2.R | 37
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getAlleleProbePairs3.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getCellQuartets.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getProbeSequenceData.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupCellMap.R | 62
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.readDataFrame.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCdfFile.writeCdfByExcludingCells.R | 32
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.BG.R | 15
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.PLOT.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.R | 22
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.allocateFromCdf.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.createFrom.R | 15
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeAffine.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelFile.normalizeQuantile.R | 7
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.BG.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.NORM.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.PLOT.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.extractAffyBatch.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.extractFeatureSet.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.extractMatrix.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.importFromDChip.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.justSNPRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSet.writeSgr.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCelSetTuple.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixCnChpSet.extras.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixFileSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixNetAffxCsvFile.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AffymetrixPgfFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AlleleSummation.R | 11
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.PLOT.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AllelicCrosstalkCalibration.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AromaCellMatchScoreFile.importFromBpmap.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AromaCellSequenceFile.importFromBpmap.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/AvgPlm.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/BaseCountNormalization.R | 11
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/BasePositionNormalization.getFit.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectFile.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectFile.TOFULL.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectFile.fromDataFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectGroupMerge.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.STATS.R | 50
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.TOFULL.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.extractExpressionSet.R | 48
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.extractTheta.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChipEffectSet.xam.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ChromosomalModel.getPositionChipTypeUnit.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectFile.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.importFromApt.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.importFromDChip.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnChipEffectSet.writeWig.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnPlm.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnProbeAffinityFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CnagCfhSet.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CopyNumberChromosomalModel.applyCCF.R | 68
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CrlmmModel.EXT.R | 24
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CrlmmModel.R | 26
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/CrlmmParametersSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/DChipDcpSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/DChipDcpSet.extras.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/DChipQuantileNormalization.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonChipEffectFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonChipEffectSet.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonProbeAffinityFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonRmaPlm.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ExonRmaPlm.calculateWeights.R | 21
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FirmaFile.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FirmaModel.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FirmaSet.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FragmentEquivalentClassNormalization.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/FragmentLengthNormalization.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/GcContentNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/GcContentNormalization2.plotCovariateEffects.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/HetLogAddPlm.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/LimmaBackgroundCorrection.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MatNormalization.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MatSmoothing.R | 17
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MbeiPlm.R | 7
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/MultiArrayUnitModel.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/OpticalBackgroundCorrection.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ParameterCelFile.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ParameterCelSet.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelModel.calculateResiduals.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelModel.calculateWeights.R | 17
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelModel.fit.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ProbeLevelTransform3.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/QualityAssessmentFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/QualityAssessmentModel.R | 27
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ReseqCrosstalkCalibration.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ResidualFile.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ResidualSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/RmaBackgroundCorrection.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/RmaPlm.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ScaleNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/ScaleNormalization3.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SingleArrayUnitModel.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SingleArrayUnitModel.fit.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SmoothMultiarrayModel.fit.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectFile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectFile.extractTotalAndFracB.R | 34
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.exportTotalAndFracB.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractAlleleSet.R | 37
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpCnvQSet.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpQSet.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpChipEffectSet.extractTotalAndFreqB.R | 36
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpCnvQSet.extractTheta.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpInformation.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpPlm.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpProbeAffinityFile.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SnpQSet.extractTheta.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SpatialReporter.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/SpatialRowColumnNormalization.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/TransformReport.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/UnitModel.fitCnProbes.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/UnitTypeScaleNormalization.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/WeightsFile.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/WeightsSet.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/bpmapCluster2Cdf.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/createExonByTranscriptCdf.R | 66
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doCRMAv1.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doCRMAv2.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doFIRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doGCRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/doRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/env2Cdf.R | 38
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/fitPlasqUnit.R | 40
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/getPlasqTypes.R | 15
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/justRMA.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/pdInfo2Cdf.R | 24
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/profileCGH.writeRegions.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/readCdfGroupStrands.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/readCfnHeader.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/R/setupExampleData.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/buildScripts/chipTypes/HG-U133A |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp,Sty/11.doASCRMAv2,TCNs,500K.R | 30
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/addons/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,PSCBS.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/21.TCN,500K.R | 18
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN,paired.R | 24
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/archive/system/chipTypes/Mapping250K_Nsp,Sty/31.ASCN.R | 18
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R | 20
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/GenomeWideSNP_6/11.justSNPRMA_vs_oligo.R | 16
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_affyPLM.R | 107
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R | 120
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/12.doGCRMA_vs_gcrma.R | 99
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/21.justRMA_vs_affy.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/11.MatNormalization_vs_MAT.R | 9
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Hs_PromPR_v02/21.MatSmoothing_vs_MAT.R | 17
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/Mapping250K_Nsp/12.CRLMM_vs_oligo.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/Mapping10K_Xba142/11.doASCRMAv1,CBS,invalid.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R | 12
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/setup/99a.cleanupRootDirectories.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_5/21.doASCRMAv2.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/11.justSNPRMA.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plots.R | 7
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,singleArray.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HG-U133_Plus_2/11.doRMA,PLM,withPriors.R | 14
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/01c.installPackages.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/11.MatNormalization.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,QC.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,extras.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20101202,gcrma.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1,SmNorm.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/11.doCRMAv1.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/12.doASCRMAv1.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,FLN,zero.R | 3
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,QA.R | 107
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,extractAndWrite.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,CE.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,CBS,ref.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,PSCN.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,extract.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,plots.R | 1
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,singleArray.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/31.doASCRMAv1.ArrayExplorer.R | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping10K_Xba142/41.ACC,expectile.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/21.doASCRMAv1,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping250K_Sty/22.doASCRMAv2,singleArray.R |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/21.CRMA.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/31.ASCRMA.R | 5
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/41.BCN.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN,AS.R | 182
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/42.BPN.R | 8
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/61.TCN,XYbias.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/12.justSNPRMA,CRLMM.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,ArrayExplorer.R | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/11.GcRmaBackgroundCorrection.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/11.RmaBackgroundCorrection.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/12.QuantileNormalization.R | 10
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/CRMA,Mapping50K_Hind240,BiasCorrectedChrXY.R | 72
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/CRMAv2,Mapping50K_Hind240.R | 167
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-CRLMM |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-GCRMA |only
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tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/inst/vignettes/replication-RMA |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixPgfFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnagCfhFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CnagCfhSet.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/DChipDcpFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/DChipDcpSet.Rd | 4
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/FirmaFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/FirmaSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ParameterCelFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ParameterCelSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ResidualFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/ResidualSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/WeightsFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/WeightsSet.Rd | 6
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/extractExpressionSet.ChipEffectSet.Rd | 3
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/justRMA.Rd |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/setupExampleData.AromaAffymetrix.Rd |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/setupExampleData.Rd |only
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/man/writeImage.AffymetrixCelFile.Rd | 2
tmp/cranberry75635d8348c/aroma.affymetrix-2.13.0/aroma.affymetrix/tests |only
282 files changed, 4882 insertions(+), 4572 deletions(-)
Permanent link
Title: A General-Purpose Package for Dynamic Report Generation in R
Diff between knitr versions 1.8 dated 2014-11-11 and 1.9 dated 2015-01-20
Description: This package provides a general-purpose tool for dynamic report
generation in R, which can be used to deal with any type of (plain text)
files, including Sweave, HTML, Markdown, reStructuredText, AsciiDoc, and
Textile. R code is evaluated as if it were copied and pasted in an R
terminal thanks to the evaluate package (e.g., we do not need to explicitly
print() plots from ggplot2 or lattice). R code can be reformatted by the
formatR package so that long lines are automatically wrapped, with indent
and spaces added, and comments preserved. A simple caching mechanism is
provided to cache results from computations for the first time and the
computations will be skipped the next time. Almost all common graphics
devices, including those in base R and add-on packages like Cairo,
cairoDevice and tikzDevice, are built-in with this package and it is
straightforward to switch between devices without writing any special
functions. The width and height as well as alignment of plots in the output
document can be specified in chunk options (the size of plots for graphics
devices is also supported). Multiple plots can be recorded in a single code
chunk, and it is also allowed to rearrange plots to the end of a chunk or
just keep the last plot. Warnings, messages and errors are written in the
output document by default (can be turned off). The large collection of
hooks in this package makes it possible for the user to control almost
everything in the R code input and output. Hooks can be used either to
format the output or to run R code fragments before or after a code chunk.
The language in code chunks is not restricted to R (there is simple support
to Python and shell scripts, etc). Many features are borrowed from or
inspired by Sweave, cacheSweave, pgfSweave, brew and decumar.
Author: Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Ashley Manton [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
knitr-1.8/knitr/NEWS |only
knitr-1.9/knitr/DESCRIPTION | 138 +++++++-----
knitr-1.9/knitr/MD5 | 242 +++++++++++-----------
knitr-1.9/knitr/NAMESPACE | 2
knitr-1.9/knitr/R/block.R | 22 +-
knitr-1.9/knitr/R/cache.R | 94 ++++++++
knitr-1.9/knitr/R/citation.R | 5
knitr-1.9/knitr/R/defaults.R | 4
knitr-1.9/knitr/R/engine.R | 42 +++
knitr-1.9/knitr/R/hooks-extra.R | 18 -
knitr-1.9/knitr/R/hooks-html.R | 6
knitr-1.9/knitr/R/hooks-latex.R | 4
knitr-1.9/knitr/R/hooks-md.R | 3
knitr-1.9/knitr/R/hooks.R | 17 +
knitr-1.9/knitr/R/output.R | 21 +
knitr-1.9/knitr/R/package.R | 2
knitr-1.9/knitr/R/pandoc.R | 6
knitr-1.9/knitr/R/parser.R | 1
knitr-1.9/knitr/R/table.R | 42 ++-
knitr-1.9/knitr/R/template.R | 3
knitr-1.9/knitr/R/themes-eclipse.R | 1
knitr-1.9/knitr/R/themes.R | 8
knitr-1.9/knitr/R/utils-conversion.R | 40 ++-
knitr-1.9/knitr/R/utils-rd2html.R | 5
knitr-1.9/knitr/R/utils-sweave.R | 7
knitr-1.9/knitr/R/utils-vignettes.R | 16 -
knitr-1.9/knitr/R/utils.R | 7
knitr-1.9/knitr/README.md | 41 ---
knitr-1.9/knitr/build/knitr.pdf |binary
knitr-1.9/knitr/build/vignette.rds |binary
knitr-1.9/knitr/inst/NEWS.Rd |only
knitr-1.9/knitr/inst/doc/datatables.Rmd | 8
knitr-1.9/knitr/inst/doc/datatables.html | 8
knitr-1.9/knitr/inst/doc/docco-classic.html | 3
knitr-1.9/knitr/inst/doc/docco-linear.html | 2
knitr-1.9/knitr/inst/doc/knit_expand.html | 4
knitr-1.9/knitr/inst/doc/knit_print.html | 4
knitr-1.9/knitr/inst/doc/knitr-html.html | 4
knitr-1.9/knitr/inst/doc/knitr-intro.Rmd | 4
knitr-1.9/knitr/inst/doc/knitr-intro.html | 20 -
knitr-1.9/knitr/inst/doc/knitr-markdown.html | 4
knitr-1.9/knitr/inst/doc/knitr-refcard.Rmd | 2
knitr-1.9/knitr/inst/doc/knitr-refcard.pdf |binary
knitr-1.9/knitr/inst/examples/download_count.csv |only
knitr-1.9/knitr/inst/examples/knitr-beamer.Rnw | 59 ++---
knitr-1.9/knitr/inst/examples/knitr-beamer.lyx | 126 +++++------
knitr-1.9/knitr/inst/examples/knitr-graphics.Rnw | 26 +-
knitr-1.9/knitr/inst/examples/knitr-graphics.lyx | 47 ++--
knitr-1.9/knitr/inst/examples/knitr-listings.Rnw | 8
knitr-1.9/knitr/inst/examples/knitr-listings.lyx | 2
knitr-1.9/knitr/inst/examples/knitr-manual.Rnw | 4
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knitr-1.9/knitr/inst/examples/knitr-minimal.lyx | 2
knitr-1.9/knitr/inst/examples/knitr-packages.bib | 32 +-
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knitr-1.9/knitr/inst/examples/knitr-subfloats.Rnw | 4
knitr-1.9/knitr/inst/examples/knitr-themes.Rnw | 4
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knitr-1.9/knitr/inst/examples/upload-github.R |only
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knitr-1.9/knitr/man/clean_cache.Rd |only
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knitr-1.9/knitr/man/image_uri.Rd | 1
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knitr-1.9/knitr/man/kable.Rd | 4
knitr-1.9/knitr/man/knit.Rd | 11 -
knitr-1.9/knitr/man/knit2html.Rd | 1
knitr-1.9/knitr/man/knit2pdf.Rd | 1
knitr-1.9/knitr/man/knit2wp.Rd | 10
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knitr-1.9/knitr/man/knit_filter.Rd | 13 -
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knitr-1.9/knitr/man/knit_hooks.Rd | 1
knitr-1.9/knitr/man/knit_meta.Rd | 1
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knitr-1.9/knitr/man/knit_print.Rd | 1
knitr-1.9/knitr/man/knit_rd.Rd | 5
knitr-1.9/knitr/man/knit_theme.Rd | 11 -
knitr-1.9/knitr/man/knitr-package.Rd | 3
knitr-1.9/knitr/man/load_cache.Rd |only
knitr-1.9/knitr/man/opts_chunk.Rd | 1
knitr-1.9/knitr/man/opts_knit.Rd | 1
knitr-1.9/knitr/man/opts_template.Rd | 1
knitr-1.9/knitr/man/output_hooks.Rd | 3
knitr-1.9/knitr/man/pandoc.Rd | 7
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knitr-1.9/knitr/man/plot_crop.Rd | 1
knitr-1.9/knitr/man/rand_seed.Rd | 1
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knitr-1.9/knitr/man/rocco.Rd | 1
knitr-1.9/knitr/man/rst2pdf.Rd | 1
knitr-1.9/knitr/man/set_alias.Rd | 1
knitr-1.9/knitr/man/set_header.Rd | 1
knitr-1.9/knitr/man/set_parent.Rd | 1
knitr-1.9/knitr/man/spin.Rd | 1
knitr-1.9/knitr/man/spin_child.Rd | 1
knitr-1.9/knitr/man/stitch.Rd | 1
knitr-1.9/knitr/man/vignette_engines.Rd | 1
knitr-1.9/knitr/man/wrap_rmd.Rd | 1
knitr-1.9/knitr/man/write_bib.Rd | 1
knitr-1.9/knitr/tests/testit/test-output.R | 11 +
knitr-1.9/knitr/tests/testit/test-table.R | 32 ++
knitr-1.9/knitr/vignettes/datatables.Rmd | 8
knitr-1.9/knitr/vignettes/knitr-intro.Rmd | 4
knitr-1.9/knitr/vignettes/knitr-refcard.Rmd | 2
125 files changed, 837 insertions(+), 540 deletions(-)
Title: Cairo-based cross-platform antialiased graphics device driver.
Diff between cairoDevice versions 2.20 dated 2014-02-22 and 2.21 dated 2015-01-20
Description: Cairo/GTK graphics device driver with output to screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces. Supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
R/cairoDevice.R | 12 ++++++------
R/zzz.R | 3 +--
man/Cairo.Rd | 10 +++++-----
man/asCairoDevice.Rd | 2 +-
src/cairoDevice.c | 7 +++++--
7 files changed, 27 insertions(+), 25 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Diff between vines versions 1.1.0 dated 2014-05-11 and 1.1.1 dated 2015-01-20
Description: Vines are graphical models for pair-copula constructions that represent high-dimensional distributions as a factorization of bivariate copulas and marginal density functions. This package contains S4 classes for vines (C-vines and D-vines) and methods for inference, goodness-of-fit tests, density/distribution function evaluation, and simulation.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez
DESCRIPTION | 10 +++++-----
MD5 | 50 +++++++++++++++++++++++++-------------------------
NAMESPACE | 2 +-
NEWS | 12 ++++++++----
R/Vine.R | 6 +++---
R/dimnames.R | 6 +++---
R/dvine.R | 4 ++--
R/h.R | 6 +++---
R/hinverse.R | 6 +++---
R/pvine.R | 6 +++---
R/rvine.R | 28 ++++++++++++++--------------
R/show.R | 16 ++++++++--------
R/vineFit.R | 4 ++--
R/vineFitML.R | 12 ++++++------
R/vineGoF.R | 4 ++--
R/vineIter.R | 22 +++++++++++-----------
R/vineOrder.R | 8 ++++----
R/vinePIT.R | 8 ++++----
R/vineParameters.R | 4 ++--
inst/CITATION | 13 ++++++-------
src/h.c | 4 ++--
src/h.h | 4 ++--
src/hinverse.c | 4 ++--
src/hinverse.h | 4 ++--
src/register.c | 4 ++--
tests/hfunctions.R | 12 ++++++------
26 files changed, 131 insertions(+), 128 deletions(-)
Title: Compute the Personalized Activity Index via flexible Bayesian
Negative Binomial model.
Diff between lmeNBBayes versions 1.2 dated 2014-01-24 and 1.3 dated 2015-01-20
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "A flexible mixed effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Kondo Y, Zhao Y and Petkau AJ. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which is modelled with infinite mixture of Beta distributions, very flexible distribution that theoretically allows any form. The package also has the option of single beta distribution for random effects. These mixed-effect models could be useful beyond the application of the safety monitoring. The inference is based on MCMC samples and this package contains a Gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNB, which contains the functions to compute the Personalized Activity Index in frequentist framework.
Author: Yumi Kondo
Maintainer: Yumi Kondo
DESCRIPTION | 13
MD5 | 15
NAMESPACE | 8
R/nbinDPmix_C.R | 5241 ++++++++++++++++++++++++-----------------------
man/getDIC.Rd | 88
man/getS.StatInMed.Rd |only
man/index_batch_Bayes.Rd | 97
man/lmeNBBayes.Rd | 160 +
src/nbinDPmix.c | 30
9 files changed, 3088 insertions(+), 2564 deletions(-)