Title: A collection of handy, useful functions
Description: A set of little functions that have been found
useful to do little odds and ends
Author: Jared P. Lander
Maintainer: Jared P. Lander
Diff between useful versions 1.1.6 dated 2012-09-29 and 1.1.8 dated 2014-01-20
useful-1.1.6/useful/man/plot.ts.Rd |only useful-1.1.8/useful/DESCRIPTION | 23 ++---- useful-1.1.8/useful/LICENSE |only useful-1.1.8/useful/MD5 | 93 +++++++++++++++------------ useful-1.1.8/useful/NAMESPACE | 12 ++- useful-1.1.8/useful/NEWS | 13 +++ useful-1.1.8/useful/R/binary.flip.r | 2 useful-1.1.8/useful/R/buildFormula.r | 2 useful-1.1.8/useful/R/buildMatrix.r |only useful-1.1.8/useful/R/comparisons.r | 2 useful-1.1.8/useful/R/corner.r | 2 useful-1.1.8/useful/R/formatters.r |only useful-1.1.8/useful/R/hartigan.r | 4 - useful-1.1.8/useful/R/intervals.r |only useful-1.1.8/useful/R/kmeansPlotting.r | 7 +- useful-1.1.8/useful/R/regex.r | 2 useful-1.1.8/useful/R/shiftColumn.r | 2 useful-1.1.8/useful/R/subspecials.r | 3 useful-1.1.8/useful/R/tsPlot.r | 14 ++-- useful-1.1.8/useful/R/useful-package.r | 2 useful-1.1.8/useful/man/ComputeHartigan.Rd | 16 ++-- useful-1.1.8/useful/man/FitKMeans.Rd | 36 ++++------ useful-1.1.8/useful/man/ForceDataFrame.Rd |only useful-1.1.8/useful/man/MapToInterval.Rd | 12 +-- useful-1.1.8/useful/man/PlotHartigan.Rd | 25 +++---- useful-1.1.8/useful/man/binary.flip.Rd | 8 +- useful-1.1.8/useful/man/bottomleft.Rd | 22 +++--- useful-1.1.8/useful/man/bottomright.Rd | 23 +++--- useful-1.1.8/useful/man/build.formula.Rd | 17 ++-- useful-1.1.8/useful/man/build.x.Rd |only useful-1.1.8/useful/man/build.y.Rd |only useful-1.1.8/useful/man/compare.list.Rd | 10 +- useful-1.1.8/useful/man/corner.Rd | 40 +++++------ useful-1.1.8/useful/man/fortify.acf.Rd | 10 +- useful-1.1.8/useful/man/fortify.kmeans.Rd | 23 +++--- useful-1.1.8/useful/man/fortify.ts.Rd | 11 +-- useful-1.1.8/useful/man/interval.check.Rd |only useful-1.1.8/useful/man/left.Rd | 22 +++--- useful-1.1.8/useful/man/multiple.Rd |only useful-1.1.8/useful/man/multiple.comma.Rd |only useful-1.1.8/useful/man/multiple.dollar.Rd |only useful-1.1.8/useful/man/multiple.identity.Rd |only useful-1.1.8/useful/man/multiple_format.Rd |only useful-1.1.8/useful/man/plot.acf.Rd | 12 +-- useful-1.1.8/useful/man/plot.kmeans.Rd | 23 +++--- useful-1.1.8/useful/man/plotTimesSeries.Rd |only useful-1.1.8/useful/man/right.Rd | 22 +++--- useful-1.1.8/useful/man/shift.column.Rd | 16 ++-- useful-1.1.8/useful/man/subOut.Rd | 19 ++--- useful-1.1.8/useful/man/subSpecials.Rd | 24 +++--- useful-1.1.8/useful/man/topleft.Rd | 22 +++--- useful-1.1.8/useful/man/topright.Rd | 22 +++--- useful-1.1.8/useful/man/ts.plotter.Rd | 12 +-- useful-1.1.8/useful/man/useful.Rd | 2 useful-1.1.8/useful/man/vplayout.Rd | 12 +-- 55 files changed, 332 insertions(+), 312 deletions(-)
Title: Testing Homoscedasticity, Multivariate Normality, and Missing
Completely at Random
Description: For detailed description see Jamshidian, M. Jalal, S., and Jansen, C. (2014). "MissMech: An R Package for Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random (MCAR)," Journal of Statistical Software, 56(6), 1-31. URL http://www.jstatsoft.org/v56/i06/.
Author: Mortaza Jamshidian, Siavash Jalal, and Camden Jansen
Maintainer: Mortaza Jamshidian
Diff between MissMech versions 1.0 dated 2013-07-06 and 1.0.1 dated 2014-01-20
DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- inst |only man/MissMech-package.Rd | 12 +++++++----- man/TestMCARNormality.Rd | 6 +++--- 5 files changed, 19 insertions(+), 16 deletions(-)
Title: Gaussian, Poisson, and Binomial Hierarchical Modeling
Description: Rgbp is an R package that utilizes approximate Bayesian machinery to provide a method of estimating two-level hierarchical models for Gaussian, Poisson, and Binomial data in a fast and computationally efficient manner. The main products of this package are point and interval estimates for the true parameters, whose good frequency properties can be validated via its repeated sampling procedure called frequency method checking. It is found that such Bayesian-frequentist reconciliation allows Rgbp to have attributes desirable both sides of the aisle, working well in small samples and yielding good coverage probabilities for its interval estimates.
Author: Joseph Kelly, Hyungsuk Tak, and Carl Morris
Maintainer: Joseph Kelly
Diff between Rgbp versions 1.0.3 dated 2013-12-02 and 1.0.4 dated 2014-01-20
DESCRIPTION | 8 MD5 | 16 R/br.R | 1165 ++++++++++++++++++++++++++++++++++++++++++---------- R/coverage.R | 129 ++++- R/gbp.R | 17 R/gr.R | 71 +-- man/coverage.Rd | 2 man/gbp-internal.Rd | 4 man/gbp.default.Rd | 20 9 files changed, 1150 insertions(+), 282 deletions(-)
Title: raster: Geographic data analysis and modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans
Diff between raster versions 2.2-5 dated 2014-01-01 and 2.2-12 dated 2014-01-20
ChangeLog | 14 ++- DESCRIPTION | 22 +++- MD5 | 105 +++++++++++----------- R/AAAClasses.R | 2 R/aggregate_sp.R | 46 ++++++--- R/bind.R | 31 ++++++ R/cellStats.R | 79 +++++++++++++--- R/cellValues.R | 2 R/compareCRS.R | 13 +- R/cover.R | 2 R/coverPolygons.R | 1 R/cropSpatial.R | 5 - R/dataType.R | 2 R/disaggregate.R | 2 R/distance.R | 2 R/extractPolygons.R | 219 +++++++++++++++++++++++++---------------------- R/gdalFormats.R | 6 + R/hdrBIL.R | 11 -- R/hdrEnvi.R | 8 - R/hdrRaster.R | 23 ++++ R/hdrSAGA.R | 33 +++---- R/indexReplace.R | 4 R/inifile.R | 67 ++++++-------- R/intersect_sp.R | 6 - R/isLonLat.R | 2 R/meta.R |only R/print.R | 32 +++++- R/projectRaster.R | 32 ++---- R/raster.R | 6 - R/rasterFromBIL.R | 9 - R/rasterFromRasterFile.R | 40 ++++++++ R/rasterFromSAGA.R | 2 R/rasterToPolygons.R | 34 +------ R/readCells.R | 3 R/resample.R | 16 ++- R/sampleRandom.R | 8 - R/union_sp.R | 11 +- R/writeAllRaster.R | 13 +- R/writeRaster.R | 8 + R/writeStartStopRaster.R | 17 ++- R/writeValues.R | 66 +++++++------- R/zonal.R | 90 ++++++++++++++----- inst/doc/Raster.pdf |binary inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary man/Raster-classes.Rd | 3 man/aggregate.Rd | 5 - man/cellStats.Rd | 5 - man/drawExtent.Rd | 13 +- man/freq.Rd | 2 man/layerize.Rd | 2 man/raster-package.Rd | 3 man/which.minmax.Rd | 3 man/zonal.Rd | 6 - 54 files changed, 693 insertions(+), 443 deletions(-)
Title: Exemplar data sets for SGP analyses
Description: The package SGPdata contains three data sets utilized by the SGP Package as exemplars for users to set up their own data for SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner
Diff between SGPdata versions 7.0-0.0 dated 2013-04-11 and 8.0-0.0 dated 2014-01-20
SGPdata-7.0-0.0/SGPdata/LICENSE |only SGPdata-7.0-0.0/SGPdata/README.md |only SGPdata-8.0-0.0/SGPdata/DESCRIPTION | 34 +++++++++++-------------- SGPdata-8.0-0.0/SGPdata/MD5 | 14 ++++------ SGPdata-8.0-0.0/SGPdata/data/datalist | 1 SGPdata-8.0-0.0/SGPdata/data/sgpData_LONG.rda |binary SGPdata-8.0-0.0/SGPdata/inst/CITATION | 8 ++--- SGPdata-8.0-0.0/SGPdata/inst/NEWS | 5 +++ SGPdata-8.0-0.0/SGPdata/man/SGPdata-package.Rd | 6 ++-- 9 files changed, 34 insertions(+), 34 deletions(-)
Title: Data sets, functions and examples from the book:"Modern
Industrial Statistics" by Kenett, Zacks and Amberti
Description: This R package is providing all the data sets and statistical analysis applications used in Modern Industrial Statistics, with applications using R, MINITAB and JMP by R.S. Kenett and S. Zacks with contributions by D. Amberti, John Wiley and Sons, 2013, which is a second revised and expanded revision of Modern Industrial Statistics: Design and Control of Quality and Reliability, R. Kenett and S. Zacks, Duxbury/Wadsworth Publishing, 1998.
Author: Daniele Amberti
Maintainer: Daniele Amberti
Diff between mistat versions 1.0 dated 2013-09-26 and 1.0-2 dated 2014-01-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + inst/scripts/ch11.R | 8 ++++---- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans
Diff between geosphere versions 1.2-28 dated 2012-04-01 and 1.3-8 dated 2014-01-20
geosphere-1.2-28/geosphere/R/zzz.R |only geosphere-1.3-8/geosphere/ChangeLog | 5 ++ geosphere-1.3-8/geosphere/DESCRIPTION | 28 ++++++++----- geosphere-1.3-8/geosphere/MD5 | 41 ++++++++++---------- geosphere-1.3-8/geosphere/R/areaPolygon.R | 3 - geosphere-1.3-8/geosphere/R/centroid.R | 24 ++++++----- geosphere-1.3-8/geosphere/R/destPointRhumb.R | 4 - geosphere-1.3-8/geosphere/R/dist2Line.R | 18 ++++---- geosphere-1.3-8/geosphere/R/dist2gc.R | 4 - geosphere-1.3-8/geosphere/R/distCosines.R | 19 +++++++-- geosphere-1.3-8/geosphere/R/distVincentyEllipsoid.R | 9 +--- geosphere-1.3-8/geosphere/R/gcIntermediate.R | 1 geosphere-1.3-8/geosphere/R/geomean.R | 18 ++++---- geosphere-1.3-8/geosphere/R/geomedian.R |only geosphere-1.3-8/geosphere/R/greatCircle.R | 5 -- geosphere-1.3-8/geosphere/R/makePoly.R | 6 -- geosphere-1.3-8/geosphere/R/span.R | 2 geosphere-1.3-8/geosphere/build |only geosphere-1.3-8/geosphere/inst/doc/geosphere.R |only geosphere-1.3-8/geosphere/inst/doc/geosphere.Rnw | 2 geosphere-1.3-8/geosphere/inst/doc/geosphere.pdf |binary geosphere-1.3-8/geosphere/man/dist2line.Rd | 7 +-- geosphere-1.3-8/geosphere/man/geomean.Rd | 9 +++- geosphere-1.3-8/geosphere/vignettes |only 24 files changed, 117 insertions(+), 88 deletions(-)
Title: Aranda-Ordaz (AO) transformation families
Description: This package implements AO transformations for binary response variables in Generalized Linear Models (GLMs) and bounded response variables in Quantile Regression (QR) models. The Maximum Likelihood Estimate (MLE) of the transformation parameter is obtained using the profile log likelihood method
Author: Hakim-Moulay Dehbi (with contributions from Mario Cortina-Borja and Marco Geraci)
Maintainer: "Dehbi, Hakim-Moulay"
Diff between AOfamilies versions 1.0 dated 2012-10-18 and 1.01 dated 2014-01-20
AOfamilies-1.0/AOfamilies/R/AOfamilies.r |only AOfamilies-1.01/AOfamilies/DESCRIPTION | 20 +-- AOfamilies-1.01/AOfamilies/MD5 | 34 +++-- AOfamilies-1.01/AOfamilies/NAMESPACE | 2 AOfamilies-1.01/AOfamilies/R/AOfamiliesv3.R |only AOfamilies-1.01/AOfamilies/man/AOfamilies-package.Rd | 2 AOfamilies-1.01/AOfamilies/man/ao.asym.Rd | 10 - AOfamilies-1.01/AOfamilies/man/ao.glm.Rd | 110 +----------------- AOfamilies-1.01/AOfamilies/man/ao.glm.default.Rd |only AOfamilies-1.01/AOfamilies/man/ao.glm.fit.Rd | 23 ++- AOfamilies-1.01/AOfamilies/man/ao.glm.formula.Rd |only AOfamilies-1.01/AOfamilies/man/ao.qr.Rd | 96 +-------------- AOfamilies-1.01/AOfamilies/man/ao.qr.default.Rd |only AOfamilies-1.01/AOfamilies/man/ao.qr.fit.Rd | 36 ++--- AOfamilies-1.01/AOfamilies/man/ao.qr.formula.Rd |only AOfamilies-1.01/AOfamilies/man/ao.sym.Rd | 10 - AOfamilies-1.01/AOfamilies/man/fitted.ao.qr.Rd | 14 -- AOfamilies-1.01/AOfamilies/man/print.ao.qr.Rd | 12 - AOfamilies-1.01/AOfamilies/man/print.fitted.ao.qr.Rd | 16 -- AOfamilies-1.01/AOfamilies/man/print.summary.ao.qr.Rd | 15 -- AOfamilies-1.01/AOfamilies/man/summary.ao.qr.Rd | 13 -- 21 files changed, 93 insertions(+), 320 deletions(-)
Title: Maximum Likelihood Difference Scaling
Description: Difference scaling is a method for scaling perceived
supra-threshold differences. The package contains functions that
allow the user to design and run a difference scaling experiment,
to fit the resulting data by maximum likelihood and test the
internal validity of the estimated scale.
Author: Kenneth Knoblauch and Laurence T. Maloney,
based in part on C code written by Laurence T. Maloney
and J. N. Yang
Maintainer: Ken Knoblauch
Diff between MLDS versions 0.4.1 dated 2012-10-17 and 0.4.3 dated 2014-01-20
MLDS-0.4.1/MLDS/MLDS-Ex.pdf |only MLDS-0.4.3/MLDS/DESCRIPTION | 28 +++++++++++++++------------- MLDS-0.4.3/MLDS/MD5 | 17 +++++++++-------- MLDS-0.4.3/MLDS/R/plot.mlds.R | 30 ++++++++++++++++++------------ MLDS-0.4.3/MLDS/R/runQuadExperiment.R | 2 +- MLDS-0.4.3/MLDS/R/runTriadExperiment.R | 2 +- MLDS-0.4.3/MLDS/build |only MLDS-0.4.3/MLDS/inst/NEWS | 7 +++++++ MLDS-0.4.3/MLDS/inst/doc/MLDS.R |only MLDS-0.4.3/MLDS/inst/doc/MLDS.pdf |binary MLDS-0.4.3/MLDS/man/plot.mlds.Rd | 15 ++++++++------- 11 files changed, 59 insertions(+), 42 deletions(-)
Title: Maximum Likelihood Conjoint Measurement
Description: Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along 2 or more dimensions and the observer is required to compare the stimuli along one of them. This package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact.
Author: Ken Knoblauch [aut, cre],
Laurence T. Maloney [aut]
Maintainer: Ken Knoblauch
Diff between MLCM versions 0.3 dated 2013-09-02 and 0.4 dated 2014-01-20
DESCRIPTION | 18 +++++++++++------- MD5 | 8 ++++---- R/plot.mlcm.R | 12 ++++++------ inst/NEWS | 5 ++++- man/plot.mlcm.Rd | 11 ++++++----- 5 files changed, 31 insertions(+), 23 deletions(-)
Title: Flexible parametric survival models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Easily extensible to fit user-defined parametric distributions.
Author: Christopher Jackson
Maintainer: Christopher Jackson
Diff between flexsurv versions 0.2 dated 2013-05-15 and 0.3 dated 2014-01-20
DESCRIPTION | 17 +-- MD5 | 40 ++++---- NAMESPACE | 1 R/GenF.R | 208 ++++++++++++++++++++++++++++++--------------- R/GenGamma.R | 183 ++++++++++++++++++++++++++++----------- R/Gompertz.R | 107 +++++++++++++---------- R/deriv.R | 112 +++++++++++++++--------- R/flexsurvreg.R | 166 +++++++++++++++++++++++------------ R/spline.R | 32 ++++-- R/utils.R | 19 ++-- inst/NEWS | 53 +++++++++++ man/GenGamma.Rd | 2 man/Gompertz.Rd | 4 man/flexsurv-package.Rd | 9 + man/flexsurvreg.Rd | 122 ++++++++++++++++---------- man/flexsurvspline.Rd | 16 ++- man/qgeneric.Rd | 35 ++++--- man/summary.flexsurvreg.Rd | 5 - tests/flexsurv.R | 21 +++- tests/spline.R | 3 tests/utils.R | 70 ++++++++++----- 21 files changed, 815 insertions(+), 410 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Description: R tools for combining and cleaning data sets, including filling in
missing observations with data from another data frame and creating
lag/lead variables.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
Diff between DataCombine versions 0.1.12 dated 2014-01-10 and 0.1.13 dated 2014-01-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 6 ++++++ R/MoveFront.R | 34 +++++++++++++++++++++++++++++----- README.md | 2 +- man/MoveFront.Rd | 35 +++++++++++++++++++++++++++++++---- 6 files changed, 76 insertions(+), 19 deletions(-)
Title: GUI for biodiversity, suitability and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt
Diff between BiodiversityR versions 2.3-6 dated 2013-06-28 and 2.4-1 dated 2014-01-20
DESCRIPTION | 31 MD5 | 47 NAMESPACE | 4 R/BiodiversityRGUI.R | 1 R/ensemble.accepted.categories.R |only R/ensemble.batch.R | 487 +--- R/ensemble.drop1.R | 797 +++---- R/ensemble.dummy.variables.R |only R/ensemble.formulae.R | 4 R/ensemble.habitat.change.R |only R/ensemble.mean.R |only R/ensemble.raster.R | 2789 +++++++++------------------ R/ensemble.simplified.categories.R |only R/ensemble.strategy.R | 162 - R/ensemble.test.R | 3723 ++++++++++++++++++++----------------- R/ensemble.test.gbm.R | 104 - R/ensemble.test.nnet.R | 103 - R/ensemble.test.splits.R | 616 ++---- R/ensemble.weights.R | 72 R/evaluation.strip.data.R | 452 ++++ R/evaluation.strip.plot.R | 48 R/renyiplot.R | 19 man/ensemble.Rd | 318 +-- man/ensemble.batch.Rd |only man/ensemble.dummy.variables.Rd |only man/ensemble.raster.Rd | 447 +--- man/evaluation.strip.Rd | 81 man/renyiresult.Rd | 23 28 files changed, 4925 insertions(+), 5403 deletions(-)
Title: Analysis and visualization of tumor sequencing data.
Description: This package provides tools to analyze NGS data, including cellularity and ploidy estimation; mutation and copy number detection and quantification;
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero
Diff between sequenza versions 1.0.3 dated 2013-12-12 and 1.0.4 dated 2014-01-20
DESCRIPTION | 10 +- MD5 | 27 +++---- NAMESPACE | 23 ++++-- NEWS | 8 +- R/next.R | 128 +++++++++++++++++++++++++++-------- R/workflows.R | 176 +++++++++++++++++++++++++++++++++++++++++++++---- exec/sequenza-utils.py | 6 - inst/doc/sequenza.R | 67 +++++++++++------- inst/doc/sequenza.Rnw | 41 +++++++++-- inst/doc/sequenza.bib | 17 ++++ inst/doc/sequenza.pdf |binary man/varscan.Rd |only man/workflows.Rd | 13 +++ vignettes/sequenza.Rnw | 41 +++++++++-- vignettes/sequenza.bib | 17 ++++ 15 files changed, 464 insertions(+), 110 deletions(-)
Title: R Interface to the Protocol Buffers API
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal RPC protocols and file formats.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel
Diff between RProtoBuf versions 0.3.2 dated 2013-12-16 and 0.4.0 dated 2014-01-20
RProtoBuf-0.3.2/RProtoBuf/R/exceptions.R |only RProtoBuf-0.3.2/RProtoBuf/src/SocketCopyingInputStream.cpp |only RProtoBuf-0.3.2/RProtoBuf/src/SocketCopyingInputStream.h |only RProtoBuf-0.3.2/RProtoBuf/src/ZeroCopyInputStreamWrapper.h |only RProtoBuf-0.3.2/RProtoBuf/src/ZeroCopyOutputStreamWrapper.h |only RProtoBuf-0.3.2/RProtoBuf/src/connections.h |only RProtoBuf-0.3.2/RProtoBuf/src/exceptions.cpp |only RProtoBuf-0.3.2/RProtoBuf/src/sisocks.h |only RProtoBuf-0.3.2/RProtoBuf/vignettes/Makefile |only RProtoBuf-0.3.2/RProtoBuf/vignettes/Makefile.in |only RProtoBuf-0.3.2/RProtoBuf/vignettes/RProtoBuf |only RProtoBuf-0.3.2/RProtoBuf/vignettes/RProtoBuf-intro.tex |only RProtoBuf-0.3.2/RProtoBuf/vignettes/RProtoBuf-quickref |only RProtoBuf-0.3.2/RProtoBuf/vignettes/RProtoBuf-quickref.tex |only RProtoBuf-0.3.2/RProtoBuf/vignettes/RProtoBuf-unitTests.tex |only RProtoBuf-0.3.2/RProtoBuf/vignettes/unitTests |only RProtoBuf-0.3.2/RProtoBuf/vignettes/unitTests-results |only RProtoBuf-0.4.0/RProtoBuf/ChangeLog | 234 - 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RProtoBuf-0.4.0/RProtoBuf/src/ZeroCopyInputStreamWrapper.cpp | 38 RProtoBuf-0.4.0/RProtoBuf/src/ZeroCopyOutputStreamWrapper.cpp | 38 RProtoBuf-0.4.0/RProtoBuf/src/extensions.cpp | 46 RProtoBuf-0.4.0/RProtoBuf/src/extractors.cpp | 216 RProtoBuf-0.4.0/RProtoBuf/src/fieldtypes.h | 57 RProtoBuf-0.4.0/RProtoBuf/src/lookup.cpp | 295 - RProtoBuf-0.4.0/RProtoBuf/src/mutators.cpp | 2206 +++++----- RProtoBuf-0.4.0/RProtoBuf/src/rprotobuf.cpp | 392 - RProtoBuf-0.4.0/RProtoBuf/src/rprotobuf.h | 331 - RProtoBuf-0.4.0/RProtoBuf/src/streams.cpp | 524 +- RProtoBuf-0.4.0/RProtoBuf/src/wrapper_ArrayInputStream.cpp | 11 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_ArrayOutputStream.cpp | 10 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_Descriptor.cpp | 344 - RProtoBuf-0.4.0/RProtoBuf/src/wrapper_EnumDescriptor.cpp | 146 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_EnumValueDescriptor.cpp | 33 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_FieldDescriptor.cpp | 152 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_FileDescriptor.cpp | 149 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_Message.cpp | 2126 ++++----- RProtoBuf-0.4.0/RProtoBuf/src/wrapper_MethodDescriptor.cpp | 59 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_ServiceDescriptor.cpp | 181 RProtoBuf-0.4.0/RProtoBuf/src/wrapper_ZeroCopyInputStream.cpp | 82 RProtoBuf-0.4.0/RProtoBuf/vignettes/RProtoBuf-intro.Rnw | 2196 +++++++++ RProtoBuf-0.4.0/RProtoBuf/vignettes/RProtoBuf-quickref.Rnw | 131 RProtoBuf-0.4.0/RProtoBuf/vignettes/RProtoBuf-unitTests.Rnw | 54 RProtoBuf-0.4.0/RProtoBuf/vignettes/inactive |only 109 files changed, 10171 insertions(+), 4935 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
Diff between psych versions 1.3.12 dated 2013-12-12 and 1.4.1 dated 2014-01-20
DESCRIPTION | 12 +- MD5 | 234 ++++++++++++++++++++++---------------------- NAMESPACE | 7 + R/ICLUST.R | 8 + R/ICLUST.cluster.R | 2 R/ICLUST.diagram.R | 2 R/VSS.R | 1 R/VSSem.R | 4 R/alpha.R | 67 ++++++------ R/circ.simulation.R | 2 R/cluster.cor.R | 80 ++++++++++++++- R/cor.ci.R | 12 +- R/corr.test.R | 3 R/cosiner.R | 2 R/cosinor.R | 2 R/describe.R | 79 +++++++++++--- R/describe.by.R | 2 R/df2latex.R | 141 +++++++++++++++++++++++++- R/error.bars.by.R | 2 R/fa.R | 62 +++++------ R/fa.diagram.R | 10 + R/fa.parallel.R | 110 ++++++++++++-------- R/fa.parallel.poly.R | 8 - R/fa.poly.R | 26 ++-- R/factor.minres.R | 4 R/factor.scores.R | 11 +- R/factor.wls.R | 4 R/irt.2p.R | 2 R/irt.discrim.R | 2 R/misc.R | 23 ++++ R/mixed.cor.R | 1 R/model.fit.R | 2 R/omega.R | 14 +- R/omega.diagram.R | 5 R/pairs.panels.R | 15 +- R/phi2poly.R | 2 R/plot.irt.R | 4 R/polychoric.R | 100 +++++++++++++----- R/principal.R | 2 R/print.psych.R | 17 +++ R/r.test.R | 2 R/reverse.code.R | 2 R/schmid.R | 7 - R/score.alpha.r | 2 R/score.irt.poly.R | 4 R/score.items.R | 20 ++- R/sim.congeneric.R | 42 ++++--- R/sim.item.R | 9 - R/sim.parallel.r | 2 R/sim.structural.R | 2 R/simulation.circ.R | 2 R/splitHalf.R | 5 R/stats.by.r | 4 R/statsBy.boot.R | 4 R/statsBy.r | 2 R/summary.psych.R | 69 +++++++----- R/table2matrix.R | 6 - R/tetrachor.R | 147 +++++++++++++++++++++++++-- build/vignette.rds |binary data/Gleser.rda |only data/ability.rda |only inst/CITATION | 6 - inst/NEWS.Rd | 64 ++++++++++-- inst/doc/overview.R | 4 inst/doc/overview.Rnw | 42 +++---- inst/doc/overview.pdf |binary inst/doc/psych_for_sem.R | 80 +++++++-------- inst/doc/psych_for_sem.Rnw | 7 - inst/doc/psych_for_sem.pdf |binary man/00.psych-package.Rd | 6 - man/Gleser.Rd |only man/ICLUST.cluster.Rd | 3 man/Promax.Rd | 2 man/VSS.Rd | 8 - man/ability.Rd |only man/alpha.Rd | 8 + man/bfi.Rd | 6 - man/bifactor.Rd | 6 - man/circ.tests.Rd | 4 man/cluster.cor.Rd | 11 +- man/cluster.plot.Rd | 2 man/cor.ci.Rd | 2 man/cor.plot.Rd | 2 man/corFiml.Rd | 4 man/cubits.Rd | 23 ++-- man/describe.Rd | 22 +++- man/df2latex.Rd | 20 +++ man/error.bars.Rd | 2 man/error.bars.by.Rd | 9 + man/error.crosses.Rd | 10 - man/fa.Rd | 4 man/fa.diagram.Rd | 9 + man/fa.parallel.Rd | 16 ++- man/factor.residuals.Rd | 6 - man/factor.scores.Rd | 3 man/factor.stats.Rd | 2 man/factor2cluster.Rd | 2 man/guttman.Rd | 5 man/headtail.Rd | 4 man/iclust.diagram.Rd | 4 man/iqitems.Rd | 17 +-- man/misc.Rd | 50 +++++++-- man/mixed.cor.Rd | 2 man/msq.Rd | 9 + man/omega.Rd | 2 man/omega.graph.Rd | 5 man/phi2poly.Rd | 3 man/plot.psych.Rd | 2 man/polar.Rd | 2 man/score.alpha.Rd | 10 + man/score.irt.Rd | 7 - man/score.items.Rd | 29 +++-- man/sim.congeneric.Rd | 3 man/simulation.circ.Rd | 4 man/smc.Rd | 2 man/structure.diagram.Rd | 2 man/test.psych.Rd | 2 man/tetrachor.Rd | 18 ++- vignettes/overview.Rnw | 42 +++---- vignettes/psych_for_sem.Rnw | 7 - 120 files changed, 1398 insertions(+), 645 deletions(-)
Title: FCROS for detecting differentially expressed genes
Description: A fold change ranks ordering statistics based method
for detecting differentially expressed genes. The
variation in levels of fold change calculated using
several combinations on pairs from biological conditions
is used to associate statistics to genes.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele
Diff between fcros versions 1.0 dated 2013-07-29 and 1.1 dated 2014-01-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/fcros.R | 4 ++-- R/fcros2.R | 6 +++--- R/fcrosRMat.R | 6 +++--- R/fcrosTtest.R | 6 ++++-- man/fcros-package.Rd | 8 ++++---- man/fcros.Rd | 16 ++++++++-------- man/fcros2.Rd | 16 ++++++++-------- man/fcrosRMat.Rd | 11 +++++++---- man/fcrosTopN.Rd | 4 ++-- man/fcrosTtest.Rd | 3 ++- 12 files changed, 58 insertions(+), 52 deletions(-)