Title: A collection of handy, useful functions
Diff between useful versions 1.1.6 dated 2012-09-29 and 1.1.8 dated 2014-01-20
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
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
Diff between MissMech versions 1.0 dated 2013-07-06 and 1.0.1 dated 2014-01-20
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
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
Diff between Rgbp versions 1.0.3 dated 2013-12-02 and 1.0.4 dated 2014-01-20
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
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
Diff between raster versions 2.2-5 dated 2014-01-01 and 2.2-12 dated 2014-01-20
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
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
Diff between SGPdata versions 7.0-0.0 dated 2013-04-11 and 8.0-0.0 dated 2014-01-20
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
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
Diff between mistat versions 1.0 dated 2013-09-26 and 1.0-2 dated 2014-01-20
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
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 1 +
inst/scripts/ch11.R | 8 ++++----
4 files changed, 12 insertions(+), 11 deletions(-)
Title: Spherical Trigonometry
Diff between geosphere versions 1.2-28 dated 2012-04-01 and 1.3-8 dated 2014-01-20
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans
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
Diff between AOfamilies versions 1.0 dated 2012-10-18 and 1.01 dated 2014-01-20
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"
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
Diff between MLDS versions 0.4.1 dated 2012-10-17 and 0.4.3 dated 2014-01-20
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
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
Diff between MLCM versions 0.3 dated 2013-09-02 and 0.4 dated 2014-01-20
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
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
Diff between flexsurv versions 0.2 dated 2013-05-15 and 0.3 dated 2014-01-20
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
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.
Diff between DataCombine versions 0.1.12 dated 2014-01-10 and 0.1.13 dated 2014-01-20
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
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
Diff between BiodiversityR versions 2.3-6 dated 2013-06-28 and 2.4-1 dated 2014-01-20
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
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.
Diff between sequenza versions 1.0.3 dated 2013-12-12 and 1.0.4 dated 2014-01-20
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
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
Diff between RProtoBuf versions 0.3.2 dated 2013-12-16 and 0.4.0 dated 2014-01-20
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
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 -
RProtoBuf-0.4.0/RProtoBuf/DESCRIPTION | 18
RProtoBuf-0.4.0/RProtoBuf/MD5 | 194
RProtoBuf-0.4.0/RProtoBuf/NAMESPACE | 5
RProtoBuf-0.4.0/RProtoBuf/R/00classes.R | 12
RProtoBuf-0.4.0/RProtoBuf/R/completion.R | 22
RProtoBuf-0.4.0/RProtoBuf/R/containing_type.R | 6
RProtoBuf-0.4.0/RProtoBuf/R/merge.R | 4
RProtoBuf-0.4.0/RProtoBuf/R/read.R | 14
RProtoBuf-0.4.0/RProtoBuf/R/rexp_obj.R |only
RProtoBuf-0.4.0/RProtoBuf/R/serialize_pb.R |only
RProtoBuf-0.4.0/RProtoBuf/R/size.R | 2
RProtoBuf-0.4.0/RProtoBuf/R/wrapper_CodedInputStream.R | 19
RProtoBuf-0.4.0/RProtoBuf/R/wrapper_EnumDescriptor.R | 3
RProtoBuf-0.4.0/RProtoBuf/TODO | 109
RProtoBuf-0.4.0/RProtoBuf/build/vignette.rds |binary
RProtoBuf-0.4.0/RProtoBuf/cleanup | 9
RProtoBuf-0.4.0/RProtoBuf/configure | 731 +--
RProtoBuf-0.4.0/RProtoBuf/configure.win |only
RProtoBuf-0.4.0/RProtoBuf/inst/NEWS.Rd | 62
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-intro.R |only
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-intro.Rnw | 2196 +++++++++
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-intro.pdf |binary
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-quickref.R |only
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-quickref.Rnw | 131
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-quickref.pdf |binary
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-unitTests.R | 44
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-unitTests.Rnw | 54
RProtoBuf-0.4.0/RProtoBuf/inst/doc/RProtoBuf-unitTests.pdf |binary
RProtoBuf-0.4.0/RProtoBuf/inst/opencpu |only
RProtoBuf-0.4.0/RProtoBuf/inst/proto/addressbook.proto | 1
RProtoBuf-0.4.0/RProtoBuf/inst/proto/rexp.proto |only
RProtoBuf-0.4.0/RProtoBuf/inst/python |only
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/data/encoding.proto |only
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.addressbook.R | 27
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.bool.R |only
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.extremevalues.R |only
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.int32.R |only
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.int64.R | 10
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.messages.R |only
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.serialize.R | 46
RProtoBuf-0.4.0/RProtoBuf/inst/unitTests/runit.serialize_pb.R |only
RProtoBuf-0.4.0/RProtoBuf/man/ArrayInputStream-class.Rd | 15
RProtoBuf-0.4.0/RProtoBuf/man/ZeroCopyInputStream-class.Rd | 5
RProtoBuf-0.4.0/RProtoBuf/man/serialize_pb.Rd |only
RProtoBuf-0.4.0/RProtoBuf/man/size.Rd | 13
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionCopyingInputStream.cpp | 44
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionCopyingInputStream.h | 38
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionCopyingOutputStream.cpp | 30
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionCopyingOutputStream.h | 38
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionInputStream.cpp | 48
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionInputStream.h | 22
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionOutputStream.cpp | 47
RProtoBuf-0.4.0/RProtoBuf/src/ConnectionOutputStream.h | 22
RProtoBuf-0.4.0/RProtoBuf/src/DescriptorPoolLookup.cpp | 115
RProtoBuf-0.4.0/RProtoBuf/src/DescriptorPoolLookup.h | 50
RProtoBuf-0.4.0/RProtoBuf/src/Makevars.in | 3
RProtoBuf-0.4.0/RProtoBuf/src/Makevars.win |only
RProtoBuf-0.4.0/RProtoBuf/src/RSourceTree.cpp | 97
RProtoBuf-0.4.0/RProtoBuf/src/RSourceTree.h | 28
RProtoBuf-0.4.0/RProtoBuf/src/RWarningErrorCollector.cpp | 14
RProtoBuf-0.4.0/RProtoBuf/src/RWarningErrorCollector.h | 17
RProtoBuf-0.4.0/RProtoBuf/src/RconnectionCopyingInputStream.cpp | 63
RProtoBuf-0.4.0/RProtoBuf/src/RconnectionCopyingInputStream.h | 26
RProtoBuf-0.4.0/RProtoBuf/src/RcppMacros.h | 20
RProtoBuf-0.4.0/RProtoBuf/src/Rcppsupport.h | 176
RProtoBuf-0.4.0/RProtoBuf/src/S4_classes.h | 405 -
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
Diff between psych versions 1.3.12 dated 2013-12-12 and 1.4.1 dated 2014-01-20
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
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
Diff between fcros versions 1.0 dated 2013-07-29 and 1.1 dated 2014-01-20
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
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(-)