Title: yaImpute: An R Package for k-NN Imputation
Diff between yaImpute versions 1.0-21 dated 2014-04-09 and 1.0-22 dated 2014-07-10
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston
DESCRIPTION | 12 ++---
MD5 | 16 +++---
NEWS | 7 ++
R/asciigridimpute.R | 2
R/grmsd.R | 10 ++--
R/impute.R | 110 ++++++++++++++++++++++++-----------------------
R/yai.R | 4 -
data/MoscowMtStJoe.RData |binary
data/TallyLake.RData |binary
9 files changed, 87 insertions(+), 74 deletions(-)
Title: Geostatistics using SpatialPoints and rasters
Diff between geostatsp versions 0.9.7 dated 2014-02-27 and 0.9.9 dated 2014-07-10
Description: This package provides to geostatistical modelling facilities using raster and SpatialPoints objects.
Author: Patrick Brown
Maintainer: Patrick Brown
geostatsp-0.9.7/geostatsp/R/as.im.RasterLayer.R |only
geostatsp-0.9.7/geostatsp/man/as.im.Rd |only
geostatsp-0.9.9/geostatsp/DESCRIPTION | 12
geostatsp-0.9.9/geostatsp/MD5 | 54 -
geostatsp-0.9.9/geostatsp/NAMESPACE | 4
geostatsp-0.9.9/geostatsp/R/asImRaster.R |only
geostatsp-0.9.9/geostatsp/R/informationLgm.R | 5
geostatsp-0.9.9/geostatsp/R/krige.R | 12
geostatsp-0.9.9/geostatsp/R/lgm.R | 61 +
geostatsp-0.9.9/geostatsp/R/logLikGradient.R | 4
geostatsp-0.9.9/geostatsp/R/loglikLgm.R | 141 ++-
geostatsp-0.9.9/geostatsp/R/maternGmrfPrec.R | 893 ++++++++++++++---------
geostatsp-0.9.9/geostatsp/R/profLlgm.R | 2
geostatsp-0.9.9/geostatsp/R/simLgcp.R | 4
geostatsp-0.9.9/geostatsp/R/stackRasterList.R | 14
geostatsp-0.9.9/geostatsp/data/gambiaUTM.RData |binary
geostatsp-0.9.9/geostatsp/data/loaloa.RData |binary
geostatsp-0.9.9/geostatsp/data/murder.RData |binary
geostatsp-0.9.9/geostatsp/data/nn32.RData |binary
geostatsp-0.9.9/geostatsp/data/rongelapUTM.RData |binary
geostatsp-0.9.9/geostatsp/data/swissRain.RData |binary
geostatsp-0.9.9/geostatsp/data/torontoPop.RData |binary
geostatsp-0.9.9/geostatsp/data/wheat.RData |binary
geostatsp-0.9.9/geostatsp/man/RFsimulate.Rd | 15
geostatsp-0.9.9/geostatsp/man/asImRaster.Rd |only
geostatsp-0.9.9/geostatsp/man/krige.Rd | 4
geostatsp-0.9.9/geostatsp/man/maternGmrfPrec.Rd | 13
geostatsp-0.9.9/geostatsp/man/stackRasterList.Rd | 20
geostatsp-0.9.9/geostatsp/tests/RFsimulate.R | 6
geostatsp-0.9.9/geostatsp/tests/lgm.R | 5
30 files changed, 793 insertions(+), 476 deletions(-)
Title: Statistical experiments on batch computing clusters.
Diff between BatchExperiments versions 1.1 dated 2014-02-07 and 1.2 dated 2014-07-10
More information about BatchExperiments at CRAN
Description: Extends the BatchJobs package to run statistical experiments on
batch computing clusters. For further details see the project web page.
Author: Bernd Bischl
Maintainer: Michel Lang
BatchExperiments-1.1/BatchExperiments/inst |only
BatchExperiments-1.2/BatchExperiments/DESCRIPTION | 10
BatchExperiments-1.2/BatchExperiments/MD5 | 137 +++++-----
BatchExperiments-1.2/BatchExperiments/NAMESPACE | 3
BatchExperiments-1.2/BatchExperiments/NEWS | 4
BatchExperiments-1.2/BatchExperiments/R/Algorithm.R | 22 -
BatchExperiments-1.2/BatchExperiments/R/Experiment.R | 8
BatchExperiments-1.2/BatchExperiments/R/ExperimentRegistry.R | 14 -
BatchExperiments-1.2/BatchExperiments/R/Problem.R | 74 +----
BatchExperiments-1.2/BatchExperiments/R/addExperiments.R | 124 ++++-----
BatchExperiments-1.2/BatchExperiments/R/applyJobFunction.R | 40 +-
BatchExperiments-1.2/BatchExperiments/R/database.R | 32 +-
BatchExperiments-1.2/BatchExperiments/R/designs.R | 31 --
BatchExperiments-1.2/BatchExperiments/R/findExperiments.R | 34 +-
BatchExperiments-1.2/BatchExperiments/R/generateProblemInstance.R | 8
BatchExperiments-1.2/BatchExperiments/R/getAlgorithm.R | 6
BatchExperiments-1.2/BatchExperiments/R/getAlgorithmIds.R | 2
BatchExperiments-1.2/BatchExperiments/R/getIndex.R | 34 +-
BatchExperiments-1.2/BatchExperiments/R/getJob.R | 7
BatchExperiments-1.2/BatchExperiments/R/getJobInfo.R | 18 -
BatchExperiments-1.2/BatchExperiments/R/getProblem.R | 4
BatchExperiments-1.2/BatchExperiments/R/getProblemIds.R | 2
BatchExperiments-1.2/BatchExperiments/R/helpers.R |only
BatchExperiments-1.2/BatchExperiments/R/reduceResultsExperiments.R | 63 ++--
BatchExperiments-1.2/BatchExperiments/R/reduceResultsExperimentsParallel.R | 33 +-
BatchExperiments-1.2/BatchExperiments/R/removeAlgorithm.R | 16 -
BatchExperiments-1.2/BatchExperiments/R/removeExperiments.R | 10
BatchExperiments-1.2/BatchExperiments/R/removeProblem.R | 18 -
BatchExperiments-1.2/BatchExperiments/R/setJobFunction.R | 6
BatchExperiments-1.2/BatchExperiments/R/summarizeExperiments.R | 22 -
BatchExperiments-1.2/BatchExperiments/R/testJob.R | 8
BatchExperiments-1.2/BatchExperiments/R/updateExperimentRegistry.R | 6
BatchExperiments-1.2/BatchExperiments/R/zzz.R | 1
BatchExperiments-1.2/BatchExperiments/man/BatchExperiments.Rd | 7
BatchExperiments-1.2/BatchExperiments/man/ExperimentJob.Rd | 30 +-
BatchExperiments-1.2/BatchExperiments/man/addAlgorithm.Rd | 32 +-
BatchExperiments-1.2/BatchExperiments/man/addExperiments.Rd | 136 ++++-----
BatchExperiments-1.2/BatchExperiments/man/addProblem.Rd | 67 ++--
BatchExperiments-1.2/BatchExperiments/man/findExperiments.Rd | 69 ++---
BatchExperiments-1.2/BatchExperiments/man/generateProblemInstance.Rd | 8
BatchExperiments-1.2/BatchExperiments/man/getAlgorithm.Rd | 12
BatchExperiments-1.2/BatchExperiments/man/getAlgorithmIds.Rd | 9
BatchExperiments-1.2/BatchExperiments/man/getIndex.Rd | 76 ++---
BatchExperiments-1.2/BatchExperiments/man/getJobs.ExperimentRegistry.Rd | 22 -
BatchExperiments-1.2/BatchExperiments/man/getProblem.Rd | 8
BatchExperiments-1.2/BatchExperiments/man/getProblemIds.Rd | 9
BatchExperiments-1.2/BatchExperiments/man/getResultVars.Rd | 39 +-
BatchExperiments-1.2/BatchExperiments/man/makeDesign.Rd | 41 +-
BatchExperiments-1.2/BatchExperiments/man/makeExperimentRegistry.Rd | 121 ++++----
BatchExperiments-1.2/BatchExperiments/man/reduceResultsExperiments.Rd | 85 ++----
BatchExperiments-1.2/BatchExperiments/man/reduceResultsExperimentsParallel.Rd | 69 ++---
BatchExperiments-1.2/BatchExperiments/man/removeAlgorithm.Rd | 17 -
BatchExperiments-1.2/BatchExperiments/man/removeExperiments.Rd | 23 -
BatchExperiments-1.2/BatchExperiments/man/removeProblem.Rd | 17 -
BatchExperiments-1.2/BatchExperiments/man/summarizeExperiments.Rd | 44 +--
BatchExperiments-1.2/BatchExperiments/tests/run-all.R | 4
BatchExperiments-1.2/BatchExperiments/tests/testthat |only
57 files changed, 843 insertions(+), 899 deletions(-)
Permanent link
Title: Inference for model-free between-group parameters for censored
survival data.
Diff between surv2sampleComp versions 1.0-3 dated 2013-12-23 and 1.0-4 dated 2014-07-10
More information about surv2sampleComp at CRAN
Description: Performs inference of several model-free group contrast measures, which include difference/ratio of cumulative incidence rates at given time points, quantiles, and restricted mean survival times (RMST). Two kinds of covariate adjustment procedures (i.e., regression and augmentation) for inference of the metrics based on RMST are also included.
Author: Lu Tian, Hajime Uno
Maintainer: Hajime Uno
surv2sampleComp-1.0-3/surv2sampleComp/R/KM2-02-pert-ver004.R |only
surv2sampleComp-1.0-4/surv2sampleComp/DESCRIPTION | 8 ++++----
surv2sampleComp-1.0-4/surv2sampleComp/MD5 | 8 ++++----
surv2sampleComp-1.0-4/surv2sampleComp/NAMESPACE | 4 ++++
surv2sampleComp-1.0-4/surv2sampleComp/R/KM2-02-pert-ver005.R |only
surv2sampleComp-1.0-4/surv2sampleComp/man/surv2sampleComp-package.Rd | 4 ++--
6 files changed, 14 insertions(+), 10 deletions(-)
Permanent link
Title: Grain size analysis, textural classifications and distribution
of unconsolidated sediments
Diff between rysgran versions 2.0 dated 2012-03-20 and 2.1.0 dated 2014-07-10
Description: This package is a port to R of the SysGran program, written in Delphi by Camargo (2006). It contains functions for the analysis of grain size samples (in logarithmic (phi) and geometric (micrometers) scale) based on various methods, like Folk & Ward (1957) and Methods of Moments (Tanner, 1995), among others; textural classifications and distribution of unconsolidated sediments are shown in histograms, bivariated plots and ternary diagrams of Shepard (1954) and Pejrup (1988). English and Portuguese languages are supported in outputs
Author: Eliandro Ronael Gilbert, Mauricio Garcia de Camargo, Leonardo Sandrini-Neto
Maintainer: Eliandro Ronael Gilbert
rysgran-2.0/rysgran/R/others.methods.r |only
rysgran-2.1.0/rysgran/DESCRIPTION | 22 --
rysgran-2.1.0/rysgran/MD5 | 34 +--
rysgran-2.1.0/rysgran/R/class.mean.r | 12 -
rysgran-2.1.0/rysgran/R/class.percent.R | 47 ++--
rysgran-2.1.0/rysgran/R/flemming.plot.R |only
rysgran-2.1.0/rysgran/R/flemming.table.r |only
rysgran-2.1.0/rysgran/R/gran.stats.R | 75 ++++---
rysgran-2.1.0/rysgran/R/legend.bubbles.r | 4
rysgran-2.1.0/rysgran/R/other.methods.r |only
rysgran-2.1.0/rysgran/R/pejrup.plot.R | 12 -
rysgran-2.1.0/rysgran/R/rysgran.hist.R | 2
rysgran-2.1.0/rysgran/R/rysgran.plot.R | 261 ++++++++++++++++++++++++++-
rysgran-2.1.0/rysgran/R/rysgran.ternary.R | 226 ++++++++++++-----------
rysgran-2.1.0/rysgran/R/shepard.plot.R | 16 -
rysgran-2.1.0/rysgran/man/gran.stats.Rd | 82 ++++++++
rysgran-2.1.0/rysgran/man/legend.bubbles.Rd | 3
rysgran-2.1.0/rysgran/man/rysgran-package.Rd | 6
rysgran-2.1.0/rysgran/man/rysgran.plot.Rd | 7
rysgran-2.1.0/rysgran/man/rysgran.ternary.Rd | 18 +
20 files changed, 591 insertions(+), 236 deletions(-)
Title: Generation of regular factorial designs
Diff between planor versions 0.1-12 dated 2014-04-23 and 0.2-0 dated 2014-07-10
Description: planor is dedicated to the automatic generation of regular factorial designs, including fractional designs, orthogonal block designs, row-column designs and split-plots.
Author: Hervé Monod, Annie Bouvier, André Kobilinsky
Maintainer: Annie Bouvier
planor-0.1-12/planor/R/bigm.R |only
planor-0.1-12/planor/src/bigm.cpp |only
planor-0.1-12/planor/tests/AB.R |only
planor-0.1-12/planor/tests/AB.Rout.save |only
planor-0.1-12/planor/tests/BU_mai2011_2.R |only
planor-0.1-12/planor/tests/BU_mai2011_2.Rout.save |only
planor-0.1-12/planor/vignettes/planorVignette.tex |only
planor-0.2-0/planor/ChangeLog | 5
planor-0.2-0/planor/DESCRIPTION | 19
planor-0.2-0/planor/MD5 | 67 -
planor-0.2-0/planor/NAMESPACE | 13
planor-0.2-0/planor/R/basep.R | 72 -
planor-0.2-0/planor/R/designkey.R | 22
planor-0.2-0/planor/R/keymatrix.R | 26
planor-0.2-0/planor/R/listofkeyrings.R | 3
planor-0.2-0/planor/R/planor.R | 193 +--
planor-0.2-0/planor/R/zzz.R | 5
planor-0.2-0/planor/inst/doc/PlanorInRmanual.pdf | 1403 ++++++++++------------
planor-0.2-0/planor/inst/doc/index.html | 10
planor-0.2-0/planor/inst/doc/planor-manual.pdf |binary
planor-0.2-0/planor/inst/doc/planorVignette.pdf |binary
planor-0.2-0/planor/man/planor-package.Rd | 10
planor-0.2-0/planor/src/planor.cpp | 117 -
planor-0.2-0/planor/tests/Kobi0.Rout.save | 12
planor-0.2-0/planor/tests/Kobi1.Rout.save | 12
planor-0.2-0/planor/tests/Kobi2.Rout.save | 12
planor-0.2-0/planor/tests/Kobi3.Rout.save | 12
planor-0.2-0/planor/tests/KobiRecursive.Rout.save | 12
planor-0.2-0/planor/tests/NewKobi1.Rout.save | 12
planor-0.2-0/planor/tests/Touzeau2.Rout.save | 12
planor-0.2-0/planor/tests/exsimple.Rout.save | 12
planor-0.2-0/planor/tests/generate.Rout.save | 20
planor-0.2-0/planor/tests/haies.Rout.save | 12
planor-0.2-0/planor/tests/mixkey.Rout.save | 12
planor-0.2-0/planor/tests/noineligible.Rout.save | 12
planor-0.2-0/planor/tests/testSummary.Rout.save | 12
planor-0.2-0/planor/vignettes/PlanorInRmanual.Rnw | 2
planor-0.2-0/planor/vignettes/planorVignette.Rnw | 6
38 files changed, 1024 insertions(+), 1113 deletions(-)
Title: Tools to determine DNA profile evidence.
Diff between likeLTD versions 5.3.3 dated 2014-05-07 and 5.4.0 dated 2014-07-10
Description: Tools to determine DNA profile Weight of Evidence.
For further information see the likeLTD guide at the URL provided,
or the paper under citation.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele
DESCRIPTION | 8
MD5 | 21 -
NAMESPACE | 4
R/hypothesis.R | 4
R/maximize.R | 661 +++++++++++++++++++++++++++++++++++++++++----
R/objectives.R | 4
R/reports.R | 110 ++++++-
inst/doc/likeLTDguide.pdf |binary
inst/doc/usage.pdf |binary
man/evaluate.Rd |only
man/optimisation.params.Rd | 4
man/output.report.Rd | 5
12 files changed, 737 insertions(+), 84 deletions(-)
Title: Nonparametric maximum likelihood estimation for random effect
models
Diff between npmlreg versions 0.45-4 dated 2013-10-11 and 0.45-5 dated 2014-07-10
Description: Nonparametric maximum likelihood estimation or Gaussian
quadrature for overdispersed generalized linear models and
variance component models
Author: Jochen Einbeck, Ross Darnell and John Hinde
Maintainer: Jochen Einbeck
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
R/alldist.R | 8 ++++----
R/allvc.R | 13 ++++++++-----
build |only
data/hosp.rda |binary
data/irlsuicide.rda |binary
data/missouri.rda |binary
inst/doc/npmlreg-v.pdf |binary
man/alldist.Rd | 6 +++---
10 files changed, 28 insertions(+), 24 deletions(-)
Title: Hypergeometric tests
Diff between hypergea versions 0.99.5 dated 2014-06-22 and 1.0.1 dated 2014-07-10
Description: Package to perform (exact) hypergeometric tests on IxJ and 2x2x2 contingency tables using parallelised C code
Author: Markus Boenn
Maintainer: Markus Boenn
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
R/getOddsRatio.R | 2 +-
R/hypergea-internal.R | 5 ++---
man/getExpectedValues.Rd | 3 ---
man/getMargins.Rd | 3 ---
man/getOddsRatio.Rd | 24 +++++++++---------------
man/hypergeom.test.Rd | 6 ++----
src/hypergeom_2x2x2.cpp | 37 ++-----------------------------------
src/hypergeom_IxJ.cpp | 4 ++--
10 files changed, 31 insertions(+), 79 deletions(-)
Title: Variable selection for generalized linear mixed models by
L1-penalized estimation
Diff between glmmLasso versions 1.3.0 dated 2014-05-30 and 1.3.1 dated 2014-07-10
Description: Variable selection for generalized linear mixed models by L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll
DESCRIPTION | 8 +-
MD5 | 16 ++--
R/glmmLasso.r | 125 +++++++++++++++++++++++++++++--------
R/glmm_final.r | 8 +-
R/glmm_final.smooth.r | 32 ++++++---
R/glmm_final_multi_random.r | 6 -
R/glmm_final_multi_random_smooth.r | 14 +++-
R/likelihood.r | 5 +
man/glmmLasso.rd | 4 -
9 files changed, 161 insertions(+), 57 deletions(-)
Title: COndition SpecIfic sub-NEtwork
Diff between COSINE versions 2.0 dated 2014-03-27 and 2.1 dated 2014-07-10
Description: To identify the globally most discriminative subnetwork from gene
expression profiles using an optimization model and genetic algorithm
Author: Haisu Ma
Maintainer: Haisu Ma
DESCRIPTION | 10 +++----
MD5 | 48 +++++++++++++++++++++++++------------
NAMESPACE | 2 -
R/COSINE-internal.R | 2 -
R/DataSimu.R | 1
R/GA_search.R | 1
R/GA_search_PPI.R |only
R/Score_adjust_PPI.R |only
R/choose_lambda.R | 2 -
R/diff_gen_PPI.R |only
R/diff_gen_for3.R | 6 +++-
R/get_components_PPI.R |only
R/get_quantiles_PPI.R |only
R/random_network_sampling_PPI.R |only
data/PPI.rda |only
data/datalist | 11 +++++---
data/scaled_edge_score.rda |only
data/scaled_node_score.rda |only
data/set1_GA.rda |binary
data/set1_scaled_diff.rda |binary
data/set1_unscaled_diff.rda |binary
data/simulated_data.rda |binary
man/COSINE-package.Rd | 39 ++----------------------------
man/GA_search.Rd | 4 +--
man/GA_search_PPI.Rd |only
man/PPI.Rd |only
man/Score_adjust_PPI.Rd |only
man/choose_lambda.Rd | 4 +--
man/diff_gen_PPI.Rd |only
man/get_components_PPI.Rd |only
man/get_quantiles_PPI.Rd |only
man/random_network_sampling_PPI.Rd |only
man/scaled_edge_score.Rd |only
man/scaled_node_score.Rd |only
34 files changed, 58 insertions(+), 72 deletions(-)
Title: Condition Number Regularized Covariance Estimation
Diff between CondReg versions 0.16 dated 2013-03-23 and 0.20 dated 2014-07-10
Description: Based on
\url{http://statistics.stanford.edu/~ckirby/techreports/GEN/2012/2012-10.pdf}
Author: Sang-Yun Oh
Maintainer: Sang-Yun Oh
CondReg-0.16/CondReg/data/condreg_data.rda |only
CondReg-0.16/CondReg/man/X.Rd |only
CondReg-0.16/CondReg/man/condreg_data.Rd |only
CondReg-0.16/CondReg/man/path_solver.Rd |only
CondReg-0.16/CondReg/man/sigma.Rd |only
CondReg-0.16/CondReg/tests |only
CondReg-0.20/CondReg/DESCRIPTION | 14 -
CondReg-0.20/CondReg/MD5 | 33 +-
CondReg-0.20/CondReg/NAMESPACE | 4
CondReg-0.20/CondReg/R/condreg.R | 307 +++++++++++++++++--------
CondReg-0.20/CondReg/data/simulationdata.RData |only
CondReg-0.20/CondReg/demo |only
CondReg-0.20/CondReg/man/R.Rd |only
CondReg-0.20/CondReg/man/condreg.Rd | 31 +-
CondReg-0.20/CondReg/man/crbulk.Rd | 15 -
CondReg-0.20/CondReg/man/datasnp.Rd |only
CondReg-0.20/CondReg/man/kgrid.Rd | 11
CondReg-0.20/CondReg/man/ml_solver.Rd | 16 -
CondReg-0.20/CondReg/man/path_backward.Rd |only
CondReg-0.20/CondReg/man/path_forward.Rd |only
CondReg-0.20/CondReg/man/pfweights.Rd |only
CondReg-0.20/CondReg/man/select_condreg.Rd | 30 +-
CondReg-0.20/CondReg/man/select_kmax.Rd | 11
CondReg-0.20/CondReg/man/transcost.Rd |only
24 files changed, 298 insertions(+), 174 deletions(-)
Title: Analysis and visualization of macroevolutionary dynamics on
phylogenetic trees
Diff between BAMMtools versions 1.0.1 dated 2014-03-07 and 2.0.2 dated 2014-07-10
Description: BAMMtools provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang
Maintainer: Dan Rabosky
DESCRIPTION | 8
MD5 | 113 ++++----
NAMESPACE | 2
R/addBAMMshifts.R | 8
R/as.phylo.branchprior.R |only
R/assignColorBreaks.R | 16 -
R/bammcolors.R |only
R/barLegend.R |only
R/bayesFactorBranches.R |only
R/cohorts.R |only
R/colorMap.R | 22 -
R/computeBayesFactors.R | 179 +++----------
R/credibleShiftSet.R | 198 +-------------
R/distinctShiftConfigurations.R | 33 +-
R/dtRates.R | 12
R/fxnDeps.R |only
R/getBestShiftConfiguration.R | 79 +++++
R/getBranchShiftPriors.R | 31 +-
R/getCohortMatrix.R | 46 ++-
R/getEventData.R | 2
R/getRateThroughTimeMatrix.R | 122 ++++++++
R/plot.bammdata.R | 208 ++++-----------
R/plot.bammshifts.R | 74 ++---
R/plot.credibleshiftset.R | 96 +++----
R/plotRateThroughTime.R | 32 +-
R/print.bammdata.R | 1
R/rateLegend.R | 5
R/setBAMMpriors.R | 19 -
R/subsetEventData.R | 4
R/subtreeBAMM.R | 502 +++++++++++++++++++++++--------------
R/summary.bammdata.R | 71 ++---
R/summary.branchprior.R | 7
R/summary.credibleshiftset.R | 9
R/testTimeVariableBranches.R |only
data/events.primates.rda |binary
data/events.whales.rda |binary
data/mcmc.primates.rda |binary
data/mcmc.whales.rda |binary
data/prior.primates.rda |binary
data/prior.whales.rda |binary
man/BAMMtools-internal.Rd | 4
man/BAMMtools-package.Rd | 6
man/addBAMMshifts.Rd | 22 +
man/assignColorBreaks.Rd | 5
man/bayesFactorBranches.Rd |only
man/cohorts.Rd |only
man/computeBayesFactors.Rd | 21 -
man/credibleShiftSet.Rd | 35 +-
man/distinctShiftConfigurations.Rd | 25 +
man/getBestShiftConfiguration.Rd | 23 -
man/getBranchShiftPriors.Rd | 15 -
man/getRateThroughTimeMatrix.Rd | 4
man/plot.bammdata.Rd | 46 ++-
man/plot.bammshifts.Rd | 4
man/plot.credibleshiftset.Rd | 2
man/plotRateThroughTime.Rd | 54 ++-
man/samplingProbs.Rd | 5
man/setBAMMpriors.Rd | 9
man/subsetEventData.Rd | 27 -
man/summary.bammdata.Rd | 5
man/summary.credibleshiftset.Rd | 2
man/testTimeVariableBranches.Rd |only
src/cohort_matrix.c |only
63 files changed, 1190 insertions(+), 1023 deletions(-)