Title: SRMA Analysis of Array-based Sequencing Data
Diff between SRMA versions 1.0.0-1 dated 2012-02-18 and 1.0.0-2 dated 2012-04-12
Description: SRMA is an R package for sequence base calling using
Affymetrix custom resequencing arrays. It includes R
implementations of the Sequencing Robust Multi-array Analysis
methods that were developed to accurately identify all single
nucleotide variants in candidate gene sequences.
Author: Wenyi Wang
Maintainer: Wenyi Wang
SRMA-1.0.0-1/SRMA/R/write.srma.R |only
SRMA-1.0.0-1/SRMA/man/write.srma.Rd |only
SRMA-1.0.0-2/SRMA/DESCRIPTION | 8 ++++----
SRMA-1.0.0-2/SRMA/MD5 | 22 +++++++++++-----------
SRMA-1.0.0-2/SRMA/R/post.process.R | 13 ++++++-------
SRMA-1.0.0-2/SRMA/R/writeVCF.R |only
SRMA-1.0.0-2/SRMA/data/.Rapp.history |only
SRMA-1.0.0-2/SRMA/data/ref.info.rda |binary
SRMA-1.0.0-2/SRMA/data/reorg.dat.rda |binary
SRMA-1.0.0-2/SRMA/data/sd.adj.dat.rda |binary
SRMA-1.0.0-2/SRMA/doc/SRMA_Manual.pdf |binary
SRMA-1.0.0-2/SRMA/man/SRMAResults-class.Rd | 2 +-
SRMA-1.0.0-2/SRMA/man/get.delta.sigma.qn.Rd | 8 +++++---
SRMA-1.0.0-2/SRMA/man/post.process.Rd | 4 ++--
SRMA-1.0.0-2/SRMA/man/writeVCF.Rd |only
15 files changed, 29 insertions(+), 28 deletions(-)
Title: Supplemental S-PLUS functionality in R
Diff between splus2R versions 1.1-0 dated 2011-10-17 and 1.1-1 dated 2012-04-12
Description: Currently there are many functions in S-PLUS that are
missing in R. To facilitate the conversion of S-PLUS packages
to R packages, this package provides some missing S-PLUS
functionality in R.
Author: William Constantine, Tim Hesterberg, Knut Wittkowski, Tingting
Song
Maintainer: William Constantine
splus2R-1.1-0/splus2R/.project |only
splus2R-1.1-1/splus2R/DESCRIPTION | 8 -
splus2R-1.1-1/splus2R/MD5 | 22 ++--
splus2R-1.1-1/splus2R/R/Swrappers.R | 84 ++++++++--------
splus2R-1.1-1/splus2R/R/showStructure.R | 91 ++++++++++--------
splus2R-1.1-1/splus2R/R/sigseriesS3.R | 2
splus2R-1.1-1/splus2R/R/sigseriesS4.R | 6 -
splus2R-1.1-1/splus2R/R/splus2R_pkg.R | 2
splus2R-1.1-1/splus2R/man/colIds.Rd | 46 ++-------
splus2R-1.1-1/splus2R/man/ifelse1.Rd | 2
splus2R-1.1-1/splus2R/man/is.numeric.atomic.vector.Rd | 32 +++---
splus2R-1.1-1/splus2R/man/stdev.Rd | 6 -
splus2R-1.1-1/splus2R/man/subscript2d.Rd | 8 -
13 files changed, 155 insertions(+), 154 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.0 dated 2012-04-11 and 0.3.0.1 dated 2012-04-12
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 3.0.1). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
ChangeLog | 11
DESCRIPTION | 10
MD5 | 14
inst/NEWS | 7
inst/include/RcppArmadilloConfig.h | 2
inst/include/armadillo | 4
inst/include/armadillo_bits/arma_version.hpp | 2
inst/include/armadillo_bits/unwrap.hpp | 957 ++++++++++++++++++---------
8 files changed, 700 insertions(+), 307 deletions(-)
Title: Projected Spatial Gaussian Process (psgp) methods
Diff between psgp versions 0.3-0 dated 2012-01-24 and 0.3-1 dated 2012-04-12
Description: Implements projected sparse Gaussian process kriging for
the intamap package
Author: Ben Ingram
Maintainer: Remi Barillec
DESCRIPTION | 6 -
MD5 | 22 ++--
inst/doc/InstallationInstructions.pdf |binary
src/Makevars | 47 +++++----
src/RInterface.cpp | 8 -
src/gaussianProcesses/PSGP.cpp | 2
src/optimisation/SCGModelTrainer.cpp | 2
src/psgp_common.cpp | 160 +++++++++++++++++-----------------
src/psgp_common.h | 11 --
src/psgp_data.h | 7 -
src/psgp_settings.h | 1
src/sensor_metadata_parser.h | 9 +
12 files changed, 134 insertions(+), 141 deletions(-)
Title: GUI tool for analyzing 2D DIGE data
Diff between digeR versions 1.2 dated 2009-08-20 and 1.3 dated 2012-04-12
Description: An easy to use Graphical User Interfact for spots
correlation analysis, score plot, classification, feature
selection and power analysis for 2D DIGE experiment data.
Author: Yue Fan, Thomas Brendan Murphy, R. William G. Watson
Maintainer: Yue Fan
digeR-1.2/digeR/data/Thumbs.db |only
digeR-1.2/digeR/data/cover.jpg |only
digeR-1.2/digeR/data/gel.jpg |only
digeR-1.2/digeR/data/prostate.txt |only
digeR-1.3/digeR/DESCRIPTION | 8
digeR-1.3/digeR/MD5 |only
digeR-1.3/digeR/NAMESPACE |only
digeR-1.3/digeR/R/digeR.R | 2244 ++++++++++++++---------------
digeR-1.3/digeR/inst/doc/digeR-package.pdf |binary
digeR-1.3/digeR/inst/doc/digeR.pdf |binary
digeR-1.3/digeR/inst/extdata |only
digeR-1.3/digeR/man/digeR-package.Rd | 6
12 files changed, 1129 insertions(+), 1129 deletions(-)
Title: A suite of functions to back-fit fixed effects and forward-fit
random effects, as well as other miscellaneous functions.
Diff between LMERConvenienceFunctions versions 1.6.7 dated 2011-12-13 and 1.6.8.2 dated 2012-04-12
More information about LMERConvenienceFunctions at CRAN
Description: Functions to back-fit fixed effects (on F or t values and,
potentially, log-likelihood ratio testing) and to forward-fit
random effects (using log-likelihood ratio testing). Note that
the back- and forward-fitting of generalized linear
mixed-effects regression (\code{glmer}s) models is not yet
supported. The package also includes a function to compute
ANOVAs with upper- and lower-bound p-values (anti-conservative
and conservative, respectively), a function to graph model
criticism plots, functions to trim data on model residuals or
on a response variable (per subject), a function to perform
posthoc analyses (with or without MCMC p-values), a function to
generate (dynamic) 3d plots of (i) predicted values of an LMER
model for interactions between two numeric variables,(ii) the
raw data as a function of two numeric variable, and (iii)
kernel density estimates (densities) of two numeric variables.
Author: Antoine Tremblay
Maintainer: Antoine Tremblay, Dalhousie University
LMERConvenienceFunctions-1.6.7/LMERConvenienceFunctions/R/posthoc.fnc.R |only
LMERConvenienceFunctions-1.6.7/LMERConvenienceFunctions/man/posthoc.fnc.Rd |only
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/DESCRIPTION | 28 +
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/MD5 | 54 +--
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/NEWS | 39 +-
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/R/bfFixefLMER_F.fnc.R | 4
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/R/bfFixefLMER_t.fnc.R | 27 +
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/R/fitLMER.fnc.R | 11
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/R/mcposthoc.fnc.R | 172 ++++++----
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/R/plotLMER3d.fnc.R | 17
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/R/plotRaw3d.fnc.R | 13
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/LMERConvenienceFunctions-package.Rd | 9
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/bfFixefLMER_F.fnc.Rd | 12
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/bfFixefLMER_t.fnc.Rd | 14
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/cd.Rd | 2
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/cdf.Rd | 2
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/cdup.Rd | 2
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/cn.Rd | 2
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/f.Rd | 2
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/ffRanefLMER.fnc.Rd | 8
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/fitLMER.fnc.Rd | 21 -
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/mcp.fnc.Rd | 4
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/mcposthoc.fnc.Rd | 156 ++++-----
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/pamer.fnc.Rd | 6
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/perSubjectTrim.fnc.Rd | 13
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/plotDensity3d.fnc.Rd | 4
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/plotLMER3d.fnc.Rd | 23 -
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/plotRaw3d.fnc.Rd | 9
LMERConvenienceFunctions-1.6.8.2/LMERConvenienceFunctions/man/romr.fnc.Rd | 6
29 files changed, 386 insertions(+), 274 deletions(-)
Permanent link
Title: Censored Regression (Tobit) Models
Diff between censReg versions 0.5-8 dated 2012-03-04 and 0.5-10 dated 2012-04-12
Description: Estimation of censored regression (Tobit) models with
cross-section and panel data
Author: Arne Henningsen
Maintainer: Arne Henningsen
censReg-0.5-10/censReg/DESCRIPTION | 10
censReg-0.5-10/censReg/MD5 | 33
censReg-0.5-10/censReg/NAMESPACE | 6
censReg-0.5-10/censReg/NEWS | 10
censReg-0.5-10/censReg/R/censReg.R | 7
censReg-0.5-10/censReg/R/margEff.censReg.R |only
censReg-0.5-10/censReg/R/print.summary.margEff.censReg.R |only
censReg-0.5-10/censReg/R/summary.margEff.censReg.R |only
censReg-0.5-10/censReg/inst/doc/censReg.Rnw | 48 +
censReg-0.5-10/censReg/inst/doc/censReg.Rnw.backup |only
censReg-0.5-10/censReg/inst/doc/censReg.bib | 41 -
censReg-0.5-10/censReg/inst/doc/censReg.pdf |binary
censReg-0.5-10/censReg/man/censReg.Rd | 3
censReg-0.5-10/censReg/man/margEff.censReg.Rd |only
censReg-0.5-10/censReg/tests/censRegPanelLargerTest.Rout.save | 5
censReg-0.5-10/censReg/tests/censRegPanelTest.R | 9
censReg-0.5-10/censReg/tests/censRegPanelTest.Rout.save | 106 ++
censReg-0.5-10/censReg/tests/censRegTest.R | 22
censReg-0.5-10/censReg/tests/censRegTest.Rout.save | 402 +++++++++-
censReg-0.5-8/censReg/INDEX |only
censReg-0.5-8/censReg/censReg.Rproj |only
21 files changed, 658 insertions(+), 44 deletions(-)
Title: X12 - wrapper function and structure for batch processing
Diff between x12 versions 1.0-0 dated 2012-04-02 and 1.0-1 dated 2012-04-12
Description: A wrapper function and GUI for the X12 binaries
Author: Alexander Kowarik
Maintainer: Alexander Kowarik
DESCRIPTION | 8 +-
MD5 | 43 +++++------
R/crossVal-methods.R | 4 -
R/plot-methods.R | 32 ++++++++
data/AirPassengersX12.RData |binary
data/AirPassengersX12Batch.RData |binary
man/X12-methods.Rd | 54 ++++++++++++--
man/crossVal-methods.Rd | 75 +++++++++++++++++++-
man/getP-methods.Rd | 3
man/loadP-methods.Rd | 3
man/plot-methods.Rd | 113 +++++++++++++++++++++++++++---
man/plotRsdAcf-methods.Rd | 40 ++++++++++
man/plotSeasFac-methods.Rd | 42 +++++++++++
man/plotSpec-methods.Rd | 38 +++++++++-
man/prev-methods.Rd | 25 +++++-
man/summary-methods.Rd |only
man/x12.Rd | 10 +-
man/x12BaseInfo-class.Rd | 7 +
man/x12Batch-class.Rd | 10 +-
man/x12List-class.Rd | 12 +--
man/x12Output-class.Rd | 61 +++++++++-------
man/x12Parameter-class.Rd | 145 +++++++++++++++++++++++----------------
man/x12Single-class.Rd | 42 ++++++-----
23 files changed, 596 insertions(+), 171 deletions(-)
Title: An R Package for the Calculation and Visualization of Student
Growth Percentiles & Percentile Growth Trajectories.
Diff between SGP versions 0.8-0.0 dated 2012-01-10 and 0.9-0.0 dated 2012-04-12
Description: Functions to calculate student growth percentiles and
percentile growth projections/trajectories for students using
large scale, longitudinal assessment data. Functions use
quantile regression to estimate the conditional density
associated with each student's achievement history. Percentile
growth projections/trajectories are calculated using the
coefficient matrices derived from the quantile regression
analyses and specify what percentile growth is required for
students to reach future achievement targets.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 42
MD5 | 76
NAMESPACE | 2
R/abcSGP.R | 49
R/analyzeSGP.R | 1673 ++++++++----------
R/baselineSGP.R | 19
R/bubblePlot.R | 76
R/bubblePlot_Styles.R | 3196 +++++++++++++++++++++++++++---------
R/capwords.R |only
R/combineSGP.R | 573 +++---
R/growthAchievementPlot.R | 512 ++---
R/growthAchievementPlot_Styles.R |only
R/outputSGP.R | 201 +-
R/prepareSGP.R | 342 ++-
R/sqliteSGP.R |only
R/startParallel.R |only
R/stopParallel.R |only
R/studentGrowthPercentiles.R | 121 -
R/studentGrowthPlot.R | 18
R/studentGrowthPlot_Styles.R | 71
R/studentGrowthProjections.R | 90 -
R/summarizeSGP.R | 670 +++++--
R/visualizeSGP.R | 755 ++++----
data/SGPstateData.rda |binary
inst/CITATION | 8
inst/NEWS | 51
man/SGP-package.Rd | 8
man/SGPstateData.Rd | 2
man/abcSGP.Rd | 80
man/analyzeSGP.Rd | 164 +
man/bubblePlot_Styles.Rd | 12
man/combineSGP.Rd | 13
man/growthAchievementPlot.Rd | 10
man/growthAchievementPlot_Styles.Rd |only
man/outputSGP.Rd | 30
man/prepareSGP.Rd | 9
man/studentGrowthPercentiles.Rd | 16
man/studentGrowthPlot.Rd | 7
man/studentGrowthPlot_Styles.Rd | 6
man/studentGrowthProjections.Rd | 14
man/summarizeSGP.Rd | 129 +
man/visualizeSGP.Rd | 126 -
42 files changed, 5819 insertions(+), 3352 deletions(-)
Title: Statistical Disclosure Control methods for the generation of
public- and scientific-use files.
Diff between sdcMicro versions 3.1.0 dated 2012-03-20 and 3.1.1 dated 2012-04-12
Description: Data from statistical agencies and other institutions are
mostly confidential. This package can be used for the
generation of anonymized (micro)data, i.e. for the generation
of public- and scientific-use files. The package sdcMicroGUI
includes a graphical user interface for the methods in this
package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl, Bernd
Prantner
Maintainer: Matthias Templ
sdcMicro-3.1.0/sdcMicro/.project |only
sdcMicro-3.1.0/sdcMicro/.project.svntmp |only
sdcMicro-3.1.1/sdcMicro/DESCRIPTION | 13 -
sdcMicro-3.1.1/sdcMicro/MD5 | 50 ++--
sdcMicro-3.1.1/sdcMicro/R/LocalRecProg.R |only
sdcMicro-3.1.1/sdcMicro/R/freqCalc.r | 11 -
sdcMicro-3.1.1/sdcMicro/data/CASCrefmicrodata.rda |binary
sdcMicro-3.1.1/sdcMicro/data/EIA.rda |binary
sdcMicro-3.1.1/sdcMicro/data/Tarragona.rda |binary
sdcMicro-3.1.1/sdcMicro/data/casc1.rda |binary
sdcMicro-3.1.1/sdcMicro/data/francdat.rda |binary
sdcMicro-3.1.1/sdcMicro/data/free1.rda |binary
sdcMicro-3.1.1/sdcMicro/data/microData.rda |binary
sdcMicro-3.1.1/sdcMicro/data/testdata.RData |binary
sdcMicro-3.1.1/sdcMicro/inst/doc/sdcMicroPaper.pdf |binary
sdcMicro-3.1.1/sdcMicro/man/freqCalc.Rd | 13 -
sdcMicro-3.1.1/sdcMicro/src/0Main.cpp | 7
sdcMicro-3.1.1/sdcMicro/src/Framework.h | 34 +++
sdcMicro-3.1.1/sdcMicro/src/LocalRecProg |only
sdcMicro-3.1.1/sdcMicro/src/Makevars.win | 2
sdcMicro-3.1.1/sdcMicro/src/Measure_Hierarchical.h | 19 -
sdcMicro-3.1.1/sdcMicro/src/Measure_Risk.h | 96 --------
sdcMicro-3.1.1/sdcMicro/src/Measure_Threshold.h | 12 -
sdcMicro-3.1.1/sdcMicro/src/Pram.h | 88 --------
sdcMicro-3.1.1/sdcMicro/src/Suda2.h | 229 ---------------------
sdcMicro-3.1.1/sdcMicro/src/freqCalc.h | 61 ++++-
26 files changed, 134 insertions(+), 501 deletions(-)
Title: R interface to the dieharder RNG test suite
Diff between RDieHarder versions 0.1.1 dated 2009-02-01 and 0.1.2 dated 2012-04-12
Description: The RDieHarder packages provides an R interface to the
dieharder suite of random number generators and tests that was
developed by Robert G. Brown and David Bauer, extending earlier
work by George Marsaglia and others.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
RDieHarder-0.1.1/RDieHarder/inst/doc/RDieHarder-data.pdf |only
RDieHarder-0.1.1/RDieHarder/inst/doc/RDieHarder-manpageexample.pdf |only
RDieHarder-0.1.1/RDieHarder/inst/doc/RDieHarder-r.rngs.pdf |only
RDieHarder-0.1.1/RDieHarder/inst/doc/Rplots.ps |only
RDieHarder-0.1.1/RDieHarder/inst/doc/auto |only
RDieHarder-0.1.1/RDieHarder/src/deprecated |only
RDieHarder-0.1.1/RDieHarder/src/histogram.c |only
RDieHarder-0.1.1/RDieHarder/src/rdieharder.c.unused |only
RDieHarder-0.1.1/RDieHarder/src/report.c.unused |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_2dsphere.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_3dsphere.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_birthdays.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_bitstream.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_count_1s_byte.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_count_1s_stream.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_craps.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_dna.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_operm5.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_opso.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_oqso.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_parking_lot.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_rank_32x32.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_rank_6x8.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_runs.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_squeeze.c |only
RDieHarder-0.1.1/RDieHarder/src/run_diehard_sums.c |only
RDieHarder-0.1.1/RDieHarder/src/run_marsaglia_tsang_gcd.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_bitdist.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_lagged_sums.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_minimum_distance.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_operm.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_permutations.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_persist.c |only
RDieHarder-0.1.1/RDieHarder/src/run_rgb_timing.c |only
RDieHarder-0.1.1/RDieHarder/src/run_sts_monobit.c |only
RDieHarder-0.1.1/RDieHarder/src/run_sts_runs.c |only
RDieHarder-0.1.1/RDieHarder/src/run_sts_serial.c |only
RDieHarder-0.1.1/RDieHarder/src/run_user_template.c |only
RDieHarder-0.1.1/RDieHarder/src/table.c.unused |only
RDieHarder-0.1.1/RDieHarder/src/work.c |only
RDieHarder-0.1.1/RDieHarder/tests/longerRun.R |only
RDieHarder-0.1.1/RDieHarder/tests/longerRun.Rout.save |only
RDieHarder-0.1.2/RDieHarder/ChangeLog |only
RDieHarder-0.1.2/RDieHarder/DESCRIPTION | 22
RDieHarder-0.1.2/RDieHarder/MD5 |only
RDieHarder-0.1.2/RDieHarder/R/dieharder.R | 49 -
RDieHarder-0.1.2/RDieHarder/R/zzz.R | 19
RDieHarder-0.1.2/RDieHarder/cleanup | 4
RDieHarder-0.1.2/RDieHarder/inst/doc/RDieHarder.Rnw | 63 -
RDieHarder-0.1.2/RDieHarder/inst/doc/RDieHarder.pdf |binary
RDieHarder-0.1.2/RDieHarder/man/dieharder.Rd | 4
RDieHarder-0.1.2/RDieHarder/src/Makevars.in | 2
RDieHarder-0.1.2/RDieHarder/src/add_ui_rngs.c | 63 -
RDieHarder-0.1.2/RDieHarder/src/choose_rng.c |only
RDieHarder-0.1.2/RDieHarder/src/dieharder.c | 227 ++++-
RDieHarder-0.1.2/RDieHarder/src/dieharder.h | 78 +
RDieHarder-0.1.2/RDieHarder/src/dieharder_exit.c | 2
RDieHarder-0.1.2/RDieHarder/src/help.c | 210 ++---
RDieHarder-0.1.2/RDieHarder/src/list_rand.c | 12
RDieHarder-0.1.2/RDieHarder/src/list_rngs.c | 107 +-
RDieHarder-0.1.2/RDieHarder/src/list_tests.c | 44 -
RDieHarder-0.1.2/RDieHarder/src/output.c | 155 +--
RDieHarder-0.1.2/RDieHarder/src/output.h | 27
RDieHarder-0.1.2/RDieHarder/src/output_rnds.c | 47 -
RDieHarder-0.1.2/RDieHarder/src/parsecl.c | 391 +++++-----
RDieHarder-0.1.2/RDieHarder/src/rng_empty_random.c | 27
RDieHarder-0.1.2/RDieHarder/src/run_all_tests.c |only
RDieHarder-0.1.2/RDieHarder/src/run_test.c |only
RDieHarder-0.1.2/RDieHarder/src/startup.c | 68 -
RDieHarder-0.1.2/RDieHarder/src/time_rng.c |only
RDieHarder-0.1.2/RDieHarder/src/user_template.c | 14
RDieHarder-0.1.2/RDieHarder/src/user_template.h | 18
RDieHarder-0.1.2/RDieHarder/tests/RDieHarder.R | 2
RDieHarder-0.1.2/RDieHarder/tests/RDieHarder.Rout.save | 11
74 files changed, 940 insertions(+), 726 deletions(-)
Title: Package for analysis and visualization of metagenes
Diff between oposSOM versions 0.1-3 dated 2011-07-27 and 0.1-4 dated 2012-04-12
Description: This package translates microarray expression data into
metagenes and provides various visualizations and second level
analyses.
Author: Henry Wirth
Maintainer: Henry Wirth
DESCRIPTION | 8 ++++----
MD5 |only
data/datalist |only
data/tissues.RData |binary
man/oposSOM-package.Rd | 4 ++--
5 files changed, 6 insertions(+), 6 deletions(-)
Title: Normality test for multivariate variables
Diff between mvnormtest versions 0.1-7 dated 2009-02-10 and 0.1-9 dated 2012-04-12
Description: Generalization of shapiro-wilk test for multivariate
variables.
Author: Slawomir Jarek
Maintainer: Slawomir Jarek
DESCRIPTION | 10 +++++++---
MD5 |only
NAMESPACE |only
man/mshapiro.test.Rd | 2 +-
4 files changed, 8 insertions(+), 4 deletions(-)
Title: Generalized Boosted Regression Models
Diff between gbm versions 1.6-3.1 dated 2010-05-07 and 1.6-3.2 dated 2012-04-12
Description: This package implements extensions to Freund and
Schapire's AdaBoost algorithm and Friedman's gradient boosting
machine. Includes regression methods for least squares,
absolute loss, quantile regression, logistic, Poisson, Cox
proportional hazards partial likelihood, and AdaBoost
exponential loss.
Author: Greg Ridgeway
Maintainer: Greg Ridgeway
DESCRIPTION | 7 +++---
MD5 |only
NAMESPACE |only
R/gbm.R | 53 ++++++++++++++++++++++---------------------------
inst/doc/gbm.pdf |binary
man/quantile.rug.Rd | 1
man/shrink.gbm.Rd | 1
man/shrink.gbm.pred.Rd | 1
8 files changed, 28 insertions(+), 35 deletions(-)
Title: Colocalisation tests of two genetic traits
Diff between coloc versions 1.07 dated 2012-02-22 and 1.08 dated 2012-04-12
Description: Performs the colocalisation tests described in Plagnol et
al (2009) and Wallace et al (in preparation).
Author: Chris Wallace
Maintainer: Chris Wallace
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/coloc.test.R | 5 ++---
man/coloc.test.Rd | 4 ++--
5 files changed, 17 insertions(+), 13 deletions(-)
Title: Adjustment of Survey Respondent Weights
Diff between reweight versions 1.02 dated 2008-03-06 and 1.2.1 dated 2012-04-12
Description: Adjusts the weights of survey respondents so that the
marginal distributions of certain variables fit more closely to
those from a more precise source (e.g. Census Bureau's data).
Author: Feiming Chen
Maintainer: Feiming Chen
DESCRIPTION | 24 ++++++++++++++----------
MD5 |only
R/reweight.R | 8 ++++++--
data/pumswgt.rda |binary
inst/doc/reweight-presentation.pdf |binary
man/reweight.Rd | 12 +++++-------
6 files changed, 25 insertions(+), 19 deletions(-)
Title: Full feature implementation of hash/associated
arrays/dictionaries
Diff between hash versions 2.1.0 dated 2011-03-18 and 2.1.0.1 dated 2012-04-12
Description: This package implements a data structure similar to hashes
in Perl and dictionaries in Python but with a purposefully R
flavor. For objects of appreciable size, access using hashes
outperforms native named lists and vectors.
Author: Christopher Brown
Maintainer: Christopher Brown
DESCRIPTION | 7 +++----
MD5 |only
R/zzz.R | 5 +++--
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Bayesian semiparametric growth curve models that additionally
include multiple membership random effects.
Diff between growcurves versions 0.1 dated 2012-03-25 and 0.1.1 dated 2012-04-12
Description: Employs a Dirichlet Process (DP) prior on the set of
by-subject random effect parameters under repeated waves of
measurements to allow the number of random effect parameters
specified per subject, \code{q}, to be equal to the number of
measurement waves, \code{T}. Random effects are grouped by
subject and all \code{q} parameters receive the DP prior. An
additional set of random effects are included that utilize a
different grouping factor; e.g. treatment(s) exposure or
dosage. These additional random effects are mapped back to
subjects through a multiple membership weight matrix.
Author: Terrance Savitsky
Maintainer:
DESCRIPTION | 6 +++---
MD5 | 26 +++++++++++++-------------
NEWS | 4 ++--
R/dpgrow.R | 4 ++--
R/dpgrowmm.R | 12 ++++++------
R/dpgrowmult.R | 6 +++---
R/effectsplot.R | 4 ++--
R/growthCurve.R | 2 +-
R/help.R | 11 ++++++++---
R/mcmcPlots.R | 6 +++---
man/dpgrowmm.Rd | 6 +++---
man/growcurves-package.Rd | 14 +++++++++++---
src/DPre.cpp | 2 +-
src/mmCmiar.cpp | 2 +-
14 files changed, 59 insertions(+), 46 deletions(-)