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Title: Gini methodology-based correlation and clustering analysis of
microarray and RNA-Seq gene expression data
Diff between rsgcc versions 1.0.1 dated 2012-03-14 and 1.0.2 dated 2012-06-15
Description: This package provides functions for calcluating the Gini
correlation coefficient (GCC), the Pearson's product moment
correlation coefficient (PCC), the Kendall tau rank correlation
coefficient (KCC), the Spearman's rank correlation coefficient
(SCC) and the Tukey's biweight correlation coefficient (BiWt).
It can also been implemented to perform correlation and
clustering analysises on the microarray and RNA-Seq gene
expression data. Additionally, this package can be applied for
further constructing gene co-expression networks (GCNs).
Author: Chuang Ma, Xiangfeng Wang
Maintainer: Chuang Ma
DESCRIPTION | 33 +++++++++++------------
MD5 | 30 ++++++++++-----------
R/rsgcc.R | 14 +++++-----
R/rsgccgui.R | 16 ++++++++++-
data/rsgcc.rda |binary
man/cor.matrix.Rd | 71 +++++++++++++++++++++++++++++++++++++--------------
man/cor.pair.Rd | 34 ++++++++++++++++--------
man/data.Rd | 17 ++----------
man/gcc.corfinal.Rd | 12 +++++---
man/gcc.dist.Rd | 4 +-
man/gcc.hclust.Rd | 9 +++---
man/gcc.heatmap.Rd | 4 +-
man/gcc.tsheatmap.Rd | 4 +-
man/getsgene.Rd | 4 +-
man/rsgcc-package.Rd | 18 ++++++------
man/rsgcc.gui.Rd | 8 ++---
16 files changed, 163 insertions(+), 115 deletions(-)
Title: R code for Stock Synthesis
Diff between r4ss versions 1.16 dated 2011-06-29 and 1.17 dated 2012-06-15
Description: Functions for reading output, plotting, exploring and
manipulating input files for Richard Methot's Stock Synthesis
fisheries stock assessment modeling platform.
Author: Ian Taylor, Ian Stewart, Allan Hicks, Tommy Garrison, Andre
Punt, John Wallace, Chantel Wetzel, and other contributors
Maintainer: Ian Taylor
r4ss-1.16/r4ss/R/SSmakesims.R |only
r4ss-1.16/r4ss/R/SSplotpars.R |only
r4ss-1.16/r4ss/R/SSrunsims.R |only
r4ss-1.16/r4ss/R/addSSsumarize.R |only
r4ss-1.16/r4ss/man/SSmakesims.Rd |only
r4ss-1.16/r4ss/man/SSrunsims.Rd |only
r4ss-1.17/r4ss/DESCRIPTION | 12
r4ss-1.17/r4ss/MD5 |only
r4ss-1.17/r4ss/NAMESPACE |only
r4ss-1.17/r4ss/R/IOTCmove.R | 100 +-
r4ss-1.17/r4ss/R/RebuildPlot.R | 91 +-
r4ss-1.17/r4ss/R/SSFishGraph.R | 226 ++---
r4ss-1.17/r4ss/R/SS_changepars.R | 208 ++--
r4ss-1.17/r4ss/R/SS_fitbiasramp.R | 547 ++++++------
r4ss-1.17/r4ss/R/SS_html.R |only
r4ss-1.17/r4ss/R/SS_makedatlist.R | 16
r4ss-1.17/r4ss/R/SS_output.R | 243 +++--
r4ss-1.17/r4ss/R/SS_parlines.R | 124 +-
r4ss-1.17/r4ss/R/SS_plots.R | 43
r4ss-1.17/r4ss/R/SS_plots_test.R |only
r4ss-1.17/r4ss/R/SS_profile.R | 182 ++--
r4ss-1.17/r4ss/R/SS_readdat.R | 11
r4ss-1.17/r4ss/R/SS_readforecast.R | 69 -
r4ss-1.17/r4ss/R/SS_recdevs.R | 266 +++---
r4ss-1.17/r4ss/R/SS_splitdat.R | 130 +-
r4ss-1.17/r4ss/R/SS_writedat.R | 4
r4ss-1.17/r4ss/R/SS_writeforecast.R | 82 -
r4ss-1.17/r4ss/R/SS_writestarter.R | 5
r4ss-1.17/r4ss/R/SSgetMCMC.R | 2
r4ss-1.17/r4ss/R/SSgetoutput.R | 16
r4ss-1.17/r4ss/R/SSplotBiology.R | 123 ++
r4ss-1.17/r4ss/R/SSplotCatch.R | 581 ++++++-------
r4ss-1.17/r4ss/R/SSplotComparisons.R | 160 ++-
r4ss-1.17/r4ss/R/SSplotComps.R | 482 ++++++----
r4ss-1.17/r4ss/R/SSplotData.R | 24
r4ss-1.17/r4ss/R/SSplotDiscard.R | 29
r4ss-1.17/r4ss/R/SSplotIndices.R | 106 +-
r4ss-1.17/r4ss/R/SSplotMnwt.R | 35
r4ss-1.17/r4ss/R/SSplotMovementMap.R | 176 ++-
r4ss-1.17/r4ss/R/SSplotMovementRates.R | 83 +
r4ss-1.17/r4ss/R/SSplotNumbers.R | 107 +-
r4ss-1.17/r4ss/R/SSplotPars.R |only
r4ss-1.17/r4ss/R/SSplotRecdevs.R | 63 -
r4ss-1.17/r4ss/R/SSplotRecdist.R | 24
r4ss-1.17/r4ss/R/SSplotSPR.R | 38
r4ss-1.17/r4ss/R/SSplotSelex.R | 1233 +++++++++++++++++-----------
r4ss-1.17/r4ss/R/SSplotSpawnrecruit.R | 19
r4ss-1.17/r4ss/R/SSplotTags.R | 109 +-
r4ss-1.17/r4ss/R/SSplotTimeseries.R | 18
r4ss-1.17/r4ss/R/SSplotYield.R | 28
r4ss-1.17/r4ss/R/SSsummarize.R | 111 +-
r4ss-1.17/r4ss/R/SStableComparisons.R | 124 +-
r4ss-1.17/r4ss/R/TSCplot.R |only
r4ss-1.17/r4ss/R/addSSsummarize.R |only
r4ss-1.17/r4ss/R/bubble3.R | 52 -
r4ss-1.17/r4ss/R/hist2d.R |only
r4ss-1.17/r4ss/R/make_multifig.R | 477 +++++-----
r4ss-1.17/r4ss/R/mcmc.nuisance.R | 6
r4ss-1.17/r4ss/R/mcmc.out.R | 9
r4ss-1.17/r4ss/R/movepars.R | 698 +++++++--------
r4ss-1.17/r4ss/R/plotCI.R | 56 -
r4ss-1.17/r4ss/R/rich.colors.short.R | 18
r4ss-1.17/r4ss/R/sel.line.R | 183 ++--
r4ss-1.17/r4ss/R/selfit.R | 537 ++++++------
r4ss-1.17/r4ss/R/selfit_spline.R |only
r4ss-1.17/r4ss/R/stackpoly.R | 2
r4ss-1.17/r4ss/R/update_r4ss_files.R | 154 +--
r4ss-1.17/r4ss/man/IOTCmove.Rd | 59 -
r4ss-1.17/r4ss/man/RebuildPlot.Rd | 8
r4ss-1.17/r4ss/man/SS_fitbiasramp.Rd | 19
r4ss-1.17/r4ss/man/SS_html.Rd |only
r4ss-1.17/r4ss/man/SS_makedatlist.Rd | 111 +-
r4ss-1.17/r4ss/man/SS_output.Rd | 5
r4ss-1.17/r4ss/man/SS_plots.Rd | 30
r4ss-1.17/r4ss/man/SS_plots_test.Rd |only
r4ss-1.17/r4ss/man/SS_profile.Rd | 22
r4ss-1.17/r4ss/man/SS_readctl.Rd | 43
r4ss-1.17/r4ss/man/SS_readdat.Rd | 36
r4ss-1.17/r4ss/man/SS_readforecast.Rd | 44
r4ss-1.17/r4ss/man/SS_readstarter.Rd | 36
r4ss-1.17/r4ss/man/SS_splitdat.Rd | 14
r4ss-1.17/r4ss/man/SS_writectl.Rd | 36
r4ss-1.17/r4ss/man/SS_writedat.Rd | 44
r4ss-1.17/r4ss/man/SS_writeforecast.Rd | 44
r4ss-1.17/r4ss/man/SS_writestarter.Rd | 41
r4ss-1.17/r4ss/man/SSgetMCMC.Rd | 36
r4ss-1.17/r4ss/man/SSgetoutput.Rd | 37
r4ss-1.17/r4ss/man/SSplotBiology.Rd | 36
r4ss-1.17/r4ss/man/SSplotCatch.Rd | 36
r4ss-1.17/r4ss/man/SSplotComparisons.Rd | 64 -
r4ss-1.17/r4ss/man/SSplotComps.Rd | 38
r4ss-1.17/r4ss/man/SSplotData.Rd | 36
r4ss-1.17/r4ss/man/SSplotDiscard.Rd | 47 -
r4ss-1.17/r4ss/man/SSplotIndices.Rd | 48 -
r4ss-1.17/r4ss/man/SSplotMCMC_ExtraSelex.Rd | 42
r4ss-1.17/r4ss/man/SSplotMnwt.Rd | 42
r4ss-1.17/r4ss/man/SSplotMovementMap.Rd | 52 -
r4ss-1.17/r4ss/man/SSplotMovementRates.Rd | 69 +
r4ss-1.17/r4ss/man/SSplotNumbers.Rd | 39
r4ss-1.17/r4ss/man/SSplotPars.Rd | 40
r4ss-1.17/r4ss/man/SSplotRecdevs.Rd | 42
r4ss-1.17/r4ss/man/SSplotRecdist.Rd | 38
r4ss-1.17/r4ss/man/SSplotSPR.Rd | 36
r4ss-1.17/r4ss/man/SSplotSelex.Rd | 113 +-
r4ss-1.17/r4ss/man/SSplotSpawnrecruit.Rd | 36
r4ss-1.17/r4ss/man/SSplotTags.Rd | 58 -
r4ss-1.17/r4ss/man/SSplotTimeseries.Rd | 36
r4ss-1.17/r4ss/man/SSplotYield.Rd | 30
r4ss-1.17/r4ss/man/SSsummarize.Rd | 50 -
r4ss-1.17/r4ss/man/SStableComparisons.Rd | 46 -
r4ss-1.17/r4ss/man/TSCplot.Rd |only
r4ss-1.17/r4ss/man/addSSsummarize.Rd | 60 -
r4ss-1.17/r4ss/man/bubble3.Rd | 42
r4ss-1.17/r4ss/man/hist2d.Rd |only
r4ss-1.17/r4ss/man/make_multifig.Rd | 40
r4ss-1.17/r4ss/man/mcmc.nuisance.Rd | 28
r4ss-1.17/r4ss/man/mcmc.out.Rd | 42
r4ss-1.17/r4ss/man/mountains.Rd | 4
r4ss-1.17/r4ss/man/plotCI.Rd | 44
r4ss-1.17/r4ss/man/r4ss-package.Rd | 8
r4ss-1.17/r4ss/man/rich.colors.short.Rd | 47 -
r4ss-1.17/r4ss/man/selfit.Rd | 3
r4ss-1.17/r4ss/man/selfit_spline.Rd |only
r4ss-1.17/r4ss/man/stackpoly.Rd | 36
124 files changed, 5756 insertions(+), 4579 deletions(-)
Title: Bayesian nonparametric modeling in R
Diff between DPpackage versions 1.1-4 dated 2012-01-03 and 1.1-5 dated 2012-06-15
Description: This package contains functions to perform inference via
simulation from the posterior distributions for Bayesian
nonparametric and semiparametric models. Although the name of
the package was motivated by the Dirichlet Process prior, the
package considers and will consider other priors on functional
spaces. So far, DPpackage includes models considering Dirichlet
Processes, Dependent Dirichlet Processes, Dependent Poisson-
Dirichlet Processes, Hierarchical Dirichlet Processes, Polya
Trees, Linear Dependent Tailfree Processes, Mixtures of
Triangular distributions, Random Bernstein polynomials priors
and Dependent Bernstein Polynomials. The package also includes
models considering Penalized B-Splines. Currently the package
includes semiparametric models for marginal and conditional
density estimation, ROC curve analysis, interval censored data,
binary regression models, generalized linear mixed models, IRT
type models, and generalized additive models. The package also
contains functions to compute Pseudo-Bayes factors for model
comparison, and to elicitate the precision parameter of the
Dirichlet Process. To maximize computational efficiency, the
actual sampling for each model is done in compiled FORTRAN. The
functions return objects which can be subsequently analyzed
with functions provided in the coda package.
Author: Alejandro Jara
Maintainer: Alejandro Jara
DESCRIPTION | 42 +++---
MD5 | 6
R/PTlm.R | 356 ++++++++++++++++++++++++++++-----------------------------
man/LDDProc.Rd | 2
4 files changed, 204 insertions(+), 202 deletions(-)
Title: Topic models
Diff between topicmodels versions 0.1-5 dated 2012-04-17 and 0.1-6 dated 2012-06-15
Description: Provides an interface to the C code for Latent Dirichlet
Allocation (LDA) models and Correlated Topics Models (CTM) by
David M. Blei and co-authors and the C++ code for fitting LDA
models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
Author: Bettina Grün and Kurt Hornik
Maintainer: Bettina Grün
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 6 ++++++
data/AssociatedPress.rda |binary
inst/NEWS | 6 ++++++
inst/doc/topicmodels.pdf |binary
6 files changed, 21 insertions(+), 9 deletions(-)
Title: Spartan (Simulation Parameter Analysis R Toolkit ApplicatioN)
Diff between spartan versions 1.0 dated 2012-05-17 and 1.1 dated 2012-06-15
Description: Computer simulations are becoming a popular technique to
use in attempts to further our understanding of complex
systems. This package provides code for four techniques
described in available literature which aid the analysis of
simulation results, at both single and multiple timepoints in
the simulation run. The first technique addresses aleatory
uncertainty in the system caused through inherent
stochasticity, and determines the number of replicate runs
necessary to generate a representative result. The second
examines how robust asimulation is to parameter perturbation,
through the use of a one-at-a-time parameter analysis
technique. Thirdly, a latin hypercube based sensitivity
analysis technique is included which can elucidate non-linear
effects between parameters and indicate implications of
epistemic uncertainty with reference to the system being
modelled. Finally, a further sensitivity analysis technique,
the extended Fourier Amplitude Sampling Test (eFAST) has been
included to partition the variance in simulation results
between input parameters, to determine the parameters which
have a significant effect on simulation behaviour.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique
Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden
DESCRIPTION | 6
MD5 | 50 ++--
R/aa_analyse_all_sample_sizes.R | 51 ++--
R/aa_graphATestsForSampleSize.R | 4
R/aa_graphSampleSizeSummary.R | 82 ++++---
R/aa_sampleSizeSummary.R | 43 ++-
R/efast_generate_medians_for_all_parameter_subsets.R | 33 +-
R/efast_generate_sample.R | 215 +++++++++----------
R/efast_get_overall_medians.R | 91 ++++----
R/efast_graph_Results.R | 1
R/efast_run_Analysis.R | 198 +++++++++--------
R/efast_sd.R | 1
R/getMediansSubset.R | 1
R/lhc_generateLHCSummary.R | 91 ++++----
R/lhc_generatePRCoEffs.R | 91 ++++----
R/lhc_generate_lhc_sample.R | 61 +++--
R/lhc_graphMeasuresForParameterChange.R | 92 +++++---
R/lhc_process_sample_run_subsets.R | 27 +-
R/oat_analyseAllParams.R | 130 ++++++-----
R/oat_graphATestsForSampleSize.R | 94 ++++----
R/oat_parameter_sampling.R | 47 ++--
R/oat_plotResultDistribution.R | 113 +++++----
R/oat_processParamSubsets.R | 53 +++-
R/pcor.mat.R | 8
R/pcor.rec.R | 15 -
R/pcor.test.R | 12 -
26 files changed, 946 insertions(+), 664 deletions(-)
Title: A collection of handy, useful functions
Diff between useful versions 1.1.4 dated 2012-03-20 and 1.1.5 dated 2012-06-15
Description: A set of little functions that have been found useful to
do little odds and ends
Author: Jared P. Lander
Maintainer:
DESCRIPTION | 9 +++++----
MD5 | 23 +++++++++++++++++++----
NAMESPACE | 17 +++++++++++++++++
NEWS | 20 ++++++++++++++------
R/binary.flip.r |only
R/kmeansPlotting.r |only
R/shiftColumn.r |only
R/tsPlot.r |only
man/binary.flip.Rd |only
man/fortify.acf.Rd |only
man/fortify.kmeans.Rd |only
man/fortify.ts.Rd |only
man/plot.acf.Rd |only
man/plot.kmeans.Rd |only
man/plot.ts.Rd |only
man/shift.column.Rd |only
man/ts.plotter.Rd |only
man/vplayout.Rd |only
test |only
useful.Rproj | 4 ++++
20 files changed, 59 insertions(+), 14 deletions(-)
Title: Maximum likelihood estimate of penetrance parameters
Diff between MLEP versions 0.0-1 dated 2011-12-25 and 0.0-3 dated 2012-06-15
Description: Programs for exploring the maximum likelihood estimates of
penetrance parameters for linkage analysis
Author: Yuki Sugaya
Maintainer: Yuki Sugaya
MLEP-0.0-1/MLEP/R/persp_penetrance.R |only
MLEP-0.0-1/MLEP/man/persp_penetrance.Rd |only
MLEP-0.0-1/MLEP/src/mlep_0.0.0.c |only
MLEP-0.0-3/MLEP/DESCRIPTION | 11 ++++++-----
MLEP-0.0-3/MLEP/INDEX |only
MLEP-0.0-3/MLEP/MD5 | 25 +++++++++++++------------
MLEP-0.0-3/MLEP/NAMESPACE | 2 +-
MLEP-0.0-3/MLEP/R/PerspPenetrance.R |only
MLEP-0.0-3/MLEP/R/fr.R | 9 ++-------
MLEP-0.0-3/MLEP/R/grr.R | 8 ++------
MLEP-0.0-3/MLEP/man/MLEP-package.Rd | 6 +++---
MLEP-0.0-3/MLEP/man/PerspPenetrance.Rd |only
MLEP-0.0-3/MLEP/man/fr.Rd | 10 +++-------
MLEP-0.0-3/MLEP/man/grr.Rd | 7 ++-----
MLEP-0.0-3/MLEP/man/mlep.Rd | 2 +-
MLEP-0.0-3/MLEP/man/polynomial.Rd | 5 ++---
MLEP-0.0-3/MLEP/src/mlep_0.0.2.c |only
17 files changed, 35 insertions(+), 50 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Diff between gMCP versions 0.7-9 dated 2012-05-07 and 0.7-10 dated 2012-06-15
Description: This package provides functions and a graphical user
interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests,
adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 6 +--
MD5 | 32 ++++++++++----------
NAMESPACE | 1
NEWS | 27 +++++++++++++---
R/analysis.R | 35 +++++++++++++++++++---
R/doRUnitTests.R |only
R/gMCP.R | 5 +--
inst/doc/AQuickStart.pdf |binary
inst/doc/gMCP.pdf |binary
inst/doc/gMCP/gMCP.Rnw | 25 +++++++++++++++
inst/doc/parametric.pdf |binary
inst/java-src/org/af/gMCP/gui/CreateGraphGUI.java | 6 +--
inst/java-src/org/af/gMCP/gui/MenuBarMGraph.java | 3 +
inst/java-src/org/af/gMCP/gui/RControl.java | 6 +++
man/doUnitTestsForGMCP.Rd |only
man/gMCP.Rd | 6 +++
man/generateBounds.Rd | 4 --
src/gMCP.c | 28 ++++++++++-------
18 files changed, 137 insertions(+), 47 deletions(-)