Title: Read and Analyze PLEXOS Solutions
Diff between rplexos versions 0.12.1 dated 2015-02-04 and 0.13 dated 2015-03-18
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
rplexos-0.12.1/rplexos/inst/web |only
rplexos-0.12.1/rplexos/man/plexos_close.Rd |only
rplexos-0.13/rplexos/DESCRIPTION | 15
rplexos-0.13/rplexos/LICENSE | 4
rplexos-0.13/rplexos/MD5 | 99 -
rplexos-0.13/rplexos/NAMESPACE | 91 -
rplexos-0.13/rplexos/R/RcppExports.R | 22
rplexos-0.13/rplexos/R/auxiliary.R | 261 ++--
rplexos-0.13/rplexos/R/debug.R |only
rplexos-0.13/rplexos/R/globalVariables.R | 18
rplexos-0.13/rplexos/R/help.R | 45
rplexos-0.13/rplexos/R/log_parser.R | 173 +-
rplexos-0.13/rplexos/R/parallel.R |only
rplexos-0.13/rplexos/R/plexos_open.R | 300 +---
rplexos-0.13/rplexos/R/process_folder.R | 203 ++-
rplexos-0.13/rplexos/R/process_input.R | 636 +++++-----
rplexos-0.13/rplexos/R/process_solution.R | 1288 ++++++++++-----------
rplexos-0.13/rplexos/R/query.R | 1198 ++++++++++---------
rplexos-0.13/rplexos/R/query_summary.R |only
rplexos-0.13/rplexos/R/zzz.R | 29
rplexos-0.13/rplexos/README.md | 36
rplexos-0.13/rplexos/build/vignette.rds |binary
rplexos-0.13/rplexos/inst/doc/rplexos.R | 6
rplexos-0.13/rplexos/inst/doc/rplexos.Rmd | 19
rplexos-0.13/rplexos/inst/doc/rplexos.html | 514 ++++----
rplexos-0.13/rplexos/man/get_query.Rd |only
rplexos-0.13/rplexos/man/is_sample_stats.Rd | 44
rplexos-0.13/rplexos/man/list_folders.Rd | 32
rplexos-0.13/rplexos/man/plexos_open.Rd | 56
rplexos-0.13/rplexos/man/process_folder.Rd | 104 -
rplexos-0.13/rplexos/man/query_class_member.Rd |only
rplexos-0.13/rplexos/man/query_config.Rd | 50
rplexos-0.13/rplexos/man/query_log.Rd | 53
rplexos-0.13/rplexos/man/query_master.Rd | 242 +--
rplexos-0.13/rplexos/man/query_master_each.Rd |only
rplexos-0.13/rplexos/man/query_phase.Rd |only
rplexos-0.13/rplexos/man/query_property.Rd | 50
rplexos-0.13/rplexos/man/query_sql.Rd |only
rplexos-0.13/rplexos/man/query_time.Rd |only
rplexos-0.13/rplexos/man/rplexos.Rd | 51
rplexos-0.13/rplexos/man/start_debug_rplexos.Rd |only
rplexos-0.13/rplexos/man/start_parallel_rplexos.Rd |only
rplexos-0.13/rplexos/man/valid_columns.Rd | 30
rplexos-0.13/rplexos/src/RcppExports.cpp | 4
rplexos-0.13/rplexos/src/process_xml.cpp | 22
rplexos-0.13/rplexos/vignettes/rplexos.Rmd | 131 --
46 files changed, 2969 insertions(+), 2857 deletions(-)
Title: Robust Variance Meta-Regression
Diff between robumeta versions 1.5 dated 2015-01-12 and 1.6 dated 2015-03-18
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +++-
R/robumeta.R | 4 +++-
4 files changed, 14 insertions(+), 10 deletions(-)
Title: Statistical Experiments on Batch Computing Clusters
Diff between BatchExperiments versions 1.4 dated 2014-10-31 and 1.4.1 dated 2015-03-18
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
DESCRIPTION | 10 +-
MD5 | 79 ++++++++---------
NAMESPACE | 3
NEWS | 14 ++-
R/Algorithm.R | 2
R/Problem.R | 4
R/database.R | 33 ++++---
R/findExperiments.R | 12 ++
R/generateProblemInstance.R | 9 +
R/getExperimentParts.R |only
R/helpers.R | 13 ++
R/reduceResultsExperiments.R | 27 +++--
R/reduceResultsExperimentsParallel.R | 38 ++------
inst |only
man/BatchExperiments.Rd | 3
man/ExperimentJob.Rd | 3
man/addAlgorithm.Rd | 3
man/addExperiments.Rd | 3
man/addProblem.Rd | 3
man/findExperiments.Rd | 11 +-
man/generateProblemInstance.Rd | 8 +
man/getAlgorithm.Rd | 4
man/getAlgorithmIds.Rd | 4
man/getExperimentParts.Rd |only
man/getIndex.Rd | 3
man/getJobs.ExperimentRegistry.Rd | 8 +
man/getProblem.Rd | 4
man/getProblemIds.Rd | 4
man/getResultVars.Rd | 3
man/makeDesign.Rd | 3
man/makeExperimentRegistry.Rd | 3
man/reduceResultsExperiments.Rd | 13 ++
man/reduceResultsExperimentsParallel.Rd | 20 +++-
man/removeAlgorithm.Rd | 3
man/removeExperiments.Rd | 3
man/removeProblem.Rd | 3
man/summarizeExperiments.Rd | 3
tests/testthat/helpers.R | 1
tests/testthat/test_findExperiments.R | 23 ++++
tests/testthat/test_reduceResults.R | 12 ++
tests/testthat/test_reduceResultsExperimentsParallel.R | 12 ++
tests/testthat/test_summarizeExperiments.R | 7 +
42 files changed, 283 insertions(+), 131 deletions(-)
Permanent link
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Diff between ncvreg versions 3.2-0 dated 2014-07-12 and 3.3-0 dated 2015-03-18
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny
ncvreg-3.2-0/ncvreg/R/coxCVL.R |only
ncvreg-3.2-0/ncvreg/man/ncvreg_fit.Rd |only
ncvreg-3.3-0/ncvreg/DESCRIPTION | 17
ncvreg-3.3-0/ncvreg/MD5 | 61 +--
ncvreg-3.3-0/ncvreg/NAMESPACE | 31 -
ncvreg-3.3-0/ncvreg/NEWS | 11
ncvreg-3.3-0/ncvreg/R/cv.ncvreg.R | 89 +++-
ncvreg-3.3-0/ncvreg/R/cv.ncvsurv.R | 31 +
ncvreg-3.3-0/ncvreg/R/logLik.R | 11
ncvreg-3.3-0/ncvreg/R/loss.R | 23 +
ncvreg-3.3-0/ncvreg/R/ncvreg.R | 53 +-
ncvreg-3.3-0/ncvreg/R/ncvreg_fit.R | 69 ---
ncvreg-3.3-0/ncvreg/R/ncvsurv.R | 19 -
ncvreg-3.3-0/ncvreg/R/perm.ncvreg.R | 8
ncvreg-3.3-0/ncvreg/R/plot.cv.ncvreg.R | 6
ncvreg-3.3-0/ncvreg/R/predict.R | 16
ncvreg-3.3-0/ncvreg/R/predict.surv.R |only
ncvreg-3.3-0/ncvreg/R/setupLambdaCox.R | 12
ncvreg-3.3-0/ncvreg/R/summary.cv.ncvsurv.R |only
ncvreg-3.3-0/ncvreg/data/Lung.RData |only
ncvreg-3.3-0/ncvreg/inst/tests/par.R |only
ncvreg-3.3-0/ncvreg/inst/tests/surv.R | 322 +++++++++--------
ncvreg-3.3-0/ncvreg/inst/tests/test.R | 521 +++++++++++++++--------------
ncvreg-3.3-0/ncvreg/man/Lung.Rd |only
ncvreg-3.3-0/ncvreg/man/cv.ncvreg.Rd | 27 +
ncvreg-3.3-0/ncvreg/man/cv.ncvsurv.Rd |only
ncvreg-3.3-0/ncvreg/man/heart.Rd | 20 -
ncvreg-3.3-0/ncvreg/man/ncvreg-package.Rd | 11
ncvreg-3.3-0/ncvreg/man/ncvreg.Rd | 4
ncvreg-3.3-0/ncvreg/man/ncvsurv.Rd |only
ncvreg-3.3-0/ncvreg/man/perm.ncvreg.Rd | 2
ncvreg-3.3-0/ncvreg/man/plot.cv.ncvreg.Rd | 2
ncvreg-3.3-0/ncvreg/man/plot.ncvreg.Rd | 2
ncvreg-3.3-0/ncvreg/man/predict.Rd | 2
ncvreg-3.3-0/ncvreg/man/prostate.Rd | 18 -
ncvreg-3.3-0/ncvreg/src/cox-dh.c | 84 +---
36 files changed, 783 insertions(+), 689 deletions(-)
Title: Multivariate Normality Tests
Diff between MVN versions 3.8 dated 2015-01-28 and 3.9 dated 2015-03-18
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
R/hzTest.R | 4 ++++
R/mardiaTest.R | 4 ++++
R/mvOutlier.R | 8 ++++++--
R/roystonTest.R | 6 +++++-
inst/CITATION | 4 ++--
inst/doc/MVN.pdf |binary
man/mvOutlier.Rd | 6 +++++-
9 files changed, 38 insertions(+), 18 deletions(-)
Title: Batch Computing with R
Diff between BatchJobs versions 1.5 dated 2014-10-30 and 1.6 dated 2015-03-18
Description: Provides Map, Reduce and Filter variants to generate jobs on batch
computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine.
Multicore and SSH systems are also supported. For further details see the
project web page.
Author: Bernd Bischl
Maintainer: Bernd Bischl
DESCRIPTION | 17 +-
MD5 | 221 ++++++++++++++++-----------------
NAMESPACE | 6
NEWS | 14 ++
R/Exports.R | 13 +
R/Registry.R | 73 +++++++++-
R/Resources.R | 4
R/Worker.R | 8 -
R/addJob.R | 12 -
R/batchApply.R | 70 ++++++----
R/batchMapResults.R | 2
R/batchReduceResults.R | 2
R/clusterFunctionsMulticore.R | 8 -
R/clusterFunctionsSLURM.R | 4
R/conf.R | 22 +--
R/database.R | 131 ++++++++++---------
R/filenames.R | 55 +++++++-
R/findStatus.R | 86 +++++++-----
R/grepLogs.R | 2
R/helpers.R | 17 ++
R/installPackagesOnSSHWorkers.R | 2
R/killJobs.R | 2
R/resetJobs.R | 2
R/showLog.R | 4
R/showStatus.R | 28 ++--
R/submitJobs.R | 2
R/sweepRegistry.R | 2
R/testJob.R | 3
R/waitForJobs.R | 10 -
R/zzz.R | 2
inst/CITATION | 38 +++--
man/BatchJobs.Rd | 3
man/addRegistryPackages.Rd | 3
man/addRegistrySourceDirs.Rd | 3
man/addRegistrySourceFiles.Rd | 3
man/applyJobFunction.Rd | 3
man/batchExpandGrid.Rd | 3
man/batchExport.Rd | 3
man/batchMap.Rd | 3
man/batchMapQuick.Rd | 3
man/batchMapResults.Rd | 3
man/batchReduce.Rd | 3
man/batchReduceResults.Rd | 3
man/batchUnexport.Rd | 3
man/callFunctionOnSSHWorkers.Rd | 3
man/cfBrewTemplate.Rd | 3
man/cfHandleUnknownSubmitError.Rd | 3
man/cfKillBatchJob.Rd | 3
man/cfReadBrewTemplate.Rd | 3
man/configuration.Rd | 3
man/copyRequiredJobFiles.Rd | 3
man/dbCreateJobDefTable.Rd | 3
man/dbGetJobs.Rd | 3
man/debugMulticore.Rd | 3
man/debugSSH.Rd | 3
man/filterResults.Rd | 3
man/findJobs.Rd | 3
man/findState.Rd | 49 ++++---
man/getConfig.Rd | 3
man/getErrorMessages.Rd | 3
man/getJob.Rd | 3
man/getJobIds.Rd | 3
man/getJobInfo.Rd | 3
man/getJobNr.Rd | 3
man/getJobParamDf.Rd | 3
man/getJobResources.Rd | 3
man/getJobs.Rd | 3
man/getLogFiles.Rd | 3
man/getResources.Rd | 3
man/getSSHWorkersInfo.Rd | 3
man/grepLogs.Rd | 3
man/installPackagesOnSSHWorkers.Rd | 3
man/killJobs.Rd | 5
man/loadConfig.Rd | 3
man/loadExports.Rd | 11 +
man/loadRegistry.Rd | 9 +
man/loadResult.Rd | 3
man/loadResults.Rd | 3
man/makeClusterFunctions.Rd | 3
man/makeClusterFunctionsInteractive.Rd | 3
man/makeClusterFunctionsLSF.Rd | 3
man/makeClusterFunctionsLocal.Rd | 3
man/makeClusterFunctionsMulticore.Rd | 14 +-
man/makeClusterFunctionsSGE.Rd | 3
man/makeClusterFunctionsSLURM.Rd | 3
man/makeClusterFunctionsSSH.Rd | 3
man/makeClusterFunctionsTorque.Rd | 3
man/makeJob.Rd | 3
man/makeRegistry.Rd | 3
man/makeSSHWorker.Rd | 3
man/makeSubmitJobResult.Rd | 3
man/reduceResults.Rd | 3
man/removeRegistry.Rd |only
man/removeRegistryPackages.Rd | 3
man/removeRegistrySourceDirs.Rd | 3
man/removeRegistrySourceFiles.Rd | 3
man/resetJobs.Rd | 3
man/sanitizePath.Rd | 3
man/setConfig.Rd | 3
man/setJobFunction.Rd | 3
man/setJobNames.Rd | 3
man/showClusterStatus.Rd | 3
man/showLog.Rd | 3
man/showStatus.Rd | 14 +-
man/sourceRegistryFiles.Rd | 3
man/submitJobs.Rd | 3
man/sweepRegistry.Rd | 3
man/testJob.Rd | 3
man/updateRegistry.Rd | 3
man/waitForJobs.Rd | 3
tests/testthat/test_export.R | 11 +
tests/testthat/test_makeRegistry.R | 11 +
112 files changed, 769 insertions(+), 433 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Diff between BAMMtools versions 2.0.2 dated 2014-07-10 and 2.0.4 dated 2015-03-18
Description: 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: Pascal Title
DESCRIPTION | 17 ++---
MD5 | 89 ++++++++++++++++-------------
R/NU.branching.times.R |only
R/addBAMMlegend.R |only
R/addBAMMshifts.R | 12 ++-
R/assignColorBreaks.R | 121 ++++++++++++++++++++++++++++++++++++----
R/barLegend.R | 29 ++++++++-
R/cohorts.R | 27 ++++++--
R/colorMap.R | 61 +++++++++++++++-----
R/credibleShiftSet.R | 4 +
R/distinctShiftConfigurations.R | 4 +
R/dtRates.R | 11 ++-
R/getBestShiftConfiguration.R | 6 -
R/getCladeRates.R | 4 +
R/getEventData.R | 25 ++++++--
R/getJenksBreaks.R |only
R/getRateThroughTimeMatrix.R | 14 +++-
R/getStartStopTimes.R | 17 +++--
R/plot.bammdata.R | 110 ++++++++++++++++++++++++++++--------
R/plot.bammshifts.R | 4 -
R/plot.credibleshiftset.R | 72 ++++++++++++-----------
R/plotRateThroughTime.R | 12 +++
R/segMap.R | 43 +++++++-------
R/setBAMMpriors.R | 37 +++++++++---
R/setPhyloTreeCoords.R | 40 ++++++-------
R/setPolarTreeCoords.R | 47 +++++++--------
R/speciesByRatesMatrix.R | 42 +++++++------
R/traitDependentBAMM.R |only
R/transparentColor.R | 6 -
R/writeEventData.R |only
data/events.fishes.rda |only
data/fishes.rda |only
data/traits.fishes.rda |only
man/BAMMtools-data.Rd | 14 +++-
man/BAMMtools-internal.Rd | 2
man/BAMMtools-package.Rd | 4 -
man/addBAMMlegend.Rd |only
man/addBAMMshifts.Rd | 6 -
man/assignColorBreaks.Rd | 27 ++++++--
man/cohorts.Rd | 10 ++-
man/getBranchShiftPriors.Rd | 2
man/getJenksBreaks.Rd |only
man/plot.bammdata.Rd | 61 ++++++++++++++------
man/plot.bammshifts.Rd | 15 ++++
man/plot.credibleshiftset.Rd | 24 ++++++-
man/plotRateThroughTime.Rd | 4 -
man/setBAMMpriors.Rd | 2
man/speciesByRatesMatrix.Rd | 36 +++++------
man/traitDependentBAMM.Rd |only
man/writeEventData.Rd |only
src/jenksBrks.c |only
src/treetraverse.c | 23 ++++---
52 files changed, 756 insertions(+), 328 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-09 1.1
2011-05-22 1.0
Title: Spatial and Space-Time Point Pattern Analysis
Diff between splancs versions 2.01-36 dated 2014-10-03 and 2.01-37 dated 2015-03-18
Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
Author: Roger Bivand [cre],
Barry Rowlingson [aut],
Peter Diggle [aut],
Giovanni Petris [ctb],
Stephen Eglen [ctb]
Maintainer: Roger Bivand
ChangeLog | 20 ++++++++++++++++++++
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NAMESPACE | 4 ++++
inst/ChangeLog | 20 ++++++++++++++++++++
src/ptinpoly.c | 2 +-
6 files changed, 55 insertions(+), 11 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Diff between fanc versions 1.13 dated 2013-08-06 and 1.22 dated 2015-03-18
Description: An R package "fanc" computes the penalized maximum
likelihood estimates of factor loadings and unique variances
for various tuning parameters. The pathwise coordinate descent
along with EM algorithm is used. This package also includes a
new graphical tool which outputs path diagram, goodness-of-fit
indices and model selection criteria for each regularization
parameter. The user can change the regularization parameter by
manipulating scrollbars, which is helpful to find a suitable
value of regularization parameter.
Author: Kei Hirose, Michio Yamamoto
Maintainer: Kei Hirose
fanc-1.13/fanc/src/fancC_v1.12.c |only
fanc-1.13/fanc/src/profiling.h |only
fanc-1.22/fanc/DESCRIPTION | 15
fanc-1.22/fanc/MD5 | 25
fanc-1.22/fanc/NAMESPACE | 6
fanc-1.22/fanc/R/fanc.R | 431 +++++------
fanc-1.22/fanc/R/out.fanc.R | 274 +------
fanc-1.22/fanc/R/plot.fanc.R | 1391 ++++++++++++++++++++++----------------
fanc-1.22/fanc/R/select.fanc.R |only
fanc-1.22/fanc/man/fanc.Rd | 16
fanc-1.22/fanc/man/out.fanc.Rd | 18
fanc-1.22/fanc/man/plot.fanc.Rd | 16
fanc-1.22/fanc/man/select.fanc.Rd |only
fanc-1.22/fanc/src/ezprof.c |only
fanc-1.22/fanc/src/ezprof.h |only
fanc-1.22/fanc/src/fanc.c |only
fanc-1.22/fanc/src/zeroin.c |only
fanc-1.22/fanc/src/zeroin.h |only
18 files changed, 1105 insertions(+), 1087 deletions(-)
Title: Business Analytics using R and Shiny
Diff between radiant versions 0.1.71 dated 2015-03-16 and 0.1.75 dated 2015-03-18
Description:
A platform-independent browser-based interface for business analytics in R, based on the Shiny package.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs
radiant-0.1.71/radiant/inst/base/tools/help/LICENSE |only
radiant-0.1.71/radiant/inst/quant/tools/help/LICENSE |only
radiant-0.1.75/radiant/DESCRIPTION | 10
radiant-0.1.75/radiant/LICENSE |only
radiant-0.1.75/radiant/MD5 | 185 +++++-----
radiant-0.1.75/radiant/R/aaa.R | 49 --
radiant-0.1.75/radiant/R/compare_means.R | 4
radiant-0.1.75/radiant/R/compare_props.R | 4
radiant-0.1.75/radiant/R/conjoint.R | 4
radiant-0.1.75/radiant/R/conjoint_profiles.R | 8
radiant-0.1.75/radiant/R/correlation.R | 2
radiant-0.1.75/radiant/R/full_factor.R | 2
radiant-0.1.75/radiant/R/glm_reg.R | 17
radiant-0.1.75/radiant/R/hier_clus.R | 7
radiant-0.1.75/radiant/R/kmeans_clus.R | 2
radiant-0.1.75/radiant/R/mds.R | 4
radiant-0.1.75/radiant/R/merge.R | 28 -
radiant-0.1.75/radiant/R/pmap.R | 8
radiant-0.1.75/radiant/R/pre_factor.R | 2
radiant-0.1.75/radiant/R/radiant.R | 87 +++-
radiant-0.1.75/radiant/R/regression.R | 9
radiant-0.1.75/radiant/R/sample_size.R | 6
radiant-0.1.75/radiant/R/sampling.R | 3
radiant-0.1.75/radiant/R/single_mean.R | 4
radiant-0.1.75/radiant/R/single_prop.R | 4
radiant-0.1.75/radiant/README.md | 47 +-
radiant-0.1.75/radiant/inst/base/global.R | 21 -
radiant-0.1.75/radiant/inst/base/tools/app/about.md | 47 +-
radiant-0.1.75/radiant/inst/base/tools/app/quit.R | 2
radiant-0.1.75/radiant/inst/base/tools/app/report.R | 8
radiant-0.1.75/radiant/inst/base/tools/data/pivot.R | 31 -
radiant-0.1.75/radiant/inst/base/tools/help/figures/pivot.png |binary
radiant-0.1.75/radiant/inst/examples/radiant_rcode.R | 68 ++-
radiant-0.1.75/radiant/inst/examples/single_mean.Rmd | 2
radiant-0.1.75/radiant/inst/marketing/server.R | 4
radiant-0.1.75/radiant/inst/marketing/tools/analysis/conjoint_profiles_ui.R | 4
radiant-0.1.75/radiant/inst/marketing/tools/analysis/full_factor_ui.R | 4
radiant-0.1.75/radiant/inst/marketing/tools/analysis/kmeans_clus_ui.R | 9
radiant-0.1.75/radiant/inst/marketing/tools/analysis/pmap_ui.R | 8
radiant-0.1.75/radiant/inst/marketing/tools/help/figures |only
radiant-0.1.75/radiant/inst/quant/tools/help/figures |only
radiant-0.1.75/radiant/inst/quant/ui.R | 2
radiant-0.1.75/radiant/man/changedata.Rd | 12
radiant-0.1.75/radiant/man/city.Rd | 17
radiant-0.1.75/radiant/man/computer.Rd | 9
radiant-0.1.75/radiant/man/diamonds.Rd | 9
radiant-0.1.75/radiant/man/getdata.Rd | 9
radiant-0.1.75/radiant/man/glm_reg.Rd | 2
radiant-0.1.75/radiant/man/hier_clus.Rd | 4
radiant-0.1.75/radiant/man/mac_launcher.Rd | 20 -
radiant-0.1.75/radiant/man/mergedata.Rd | 2
radiant-0.1.75/radiant/man/mp3.Rd | 7
radiant-0.1.75/radiant/man/newspaper.Rd | 9
radiant-0.1.75/radiant/man/plot.compare_means.Rd | 4
radiant-0.1.75/radiant/man/plot.compare_props.Rd | 4
radiant-0.1.75/radiant/man/plot.conjoint.Rd | 4
radiant-0.1.75/radiant/man/plot.glm_predict.Rd | 6
radiant-0.1.75/radiant/man/plot.glm_reg.Rd | 6
radiant-0.1.75/radiant/man/plot.hier_clus.Rd | 4
radiant-0.1.75/radiant/man/plot.pmap.Rd | 4
radiant-0.1.75/radiant/man/plot.regression.Rd | 4
radiant-0.1.75/radiant/man/plot.single_mean.Rd | 4
radiant-0.1.75/radiant/man/plot.single_prop.Rd | 4
radiant-0.1.75/radiant/man/predict.glm_reg.Rd | 8
radiant-0.1.75/radiant/man/predict.regression.Rd | 7
radiant-0.1.75/radiant/man/radiant.Rd | 5
radiant-0.1.75/radiant/man/rndnames.Rd | 9
radiant-0.1.75/radiant/man/sample_size.Rd | 2
radiant-0.1.75/radiant/man/save_glm_resid.Rd | 4
radiant-0.1.75/radiant/man/save_membership.Rd | 4
radiant-0.1.75/radiant/man/set_class.Rd | 4
radiant-0.1.75/radiant/man/shopping.Rd | 9
radiant-0.1.75/radiant/man/sig_stars.Rd | 3
radiant-0.1.75/radiant/man/sshh.Rd | 7
radiant-0.1.75/radiant/man/sshhr.Rd | 7
radiant-0.1.75/radiant/man/summary.compare_means.Rd | 4
radiant-0.1.75/radiant/man/summary.compare_props.Rd | 4
radiant-0.1.75/radiant/man/summary.conjoint.Rd | 4
radiant-0.1.75/radiant/man/summary.conjoint_profiles.Rd | 4
radiant-0.1.75/radiant/man/summary.correlation.Rd | 4
radiant-0.1.75/radiant/man/summary.full_factor.Rd | 4
radiant-0.1.75/radiant/man/summary.glm_reg.Rd | 6
radiant-0.1.75/radiant/man/summary.hier_clus.Rd | 4
radiant-0.1.75/radiant/man/summary.mds.Rd | 4
radiant-0.1.75/radiant/man/summary.pmap.Rd | 4
radiant-0.1.75/radiant/man/summary.pre_factor.Rd | 4
radiant-0.1.75/radiant/man/summary.regression.Rd | 4
radiant-0.1.75/radiant/man/summary.sample_size.Rd | 6
radiant-0.1.75/radiant/man/summary.sampling.Rd | 4
radiant-0.1.75/radiant/man/summary.single_mean.Rd | 4
radiant-0.1.75/radiant/man/summary.single_prop.Rd | 4
radiant-0.1.75/radiant/man/titanic.Rd | 7
radiant-0.1.75/radiant/man/titanic_pred.Rd | 7
radiant-0.1.75/radiant/man/toothpaste.Rd | 9
radiant-0.1.75/radiant/man/win_launcher.Rd | 18
radiant-0.1.75/radiant/tests/run-all.R | 4
96 files changed, 550 insertions(+), 482 deletions(-)
Title: Person Fit
Diff between PerFit versions 1.3 dated 2015-03-13 and 1.3.1 dated 2015-03-18
Description: Several person-fit statistics (PFSs) are offered. These statistics allow assessing whether
individual response patterns to tests or questionnaires are (im)plausible given
the other respondents in the sample or given a specified item response theory model. Some PFSs apply to
dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs
(personal biserial correlation, caution index, (normed) number of Guttman errors,
agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
R/PrintPerFit.R | 44 ++++----------------------------------------
man/PerFit-package.Rd | 4 ++--
man/lz.Rd | 8 +++-----
man/print.PerFit.Rd | 26 ++------------------------
6 files changed, 22 insertions(+), 82 deletions(-)
Title: Johnson Transformation for Normality
Diff between jtrans versions 0.1 dated 2013-07-24 and 0.2.1 dated 2015-03-18
Description: Transforming univariate non-normal data to normality using Johnson
families of distributions. Johnson family is a comprehensive distribution
family that accommodates many kinds of non-normal distributions. A bunch of
distributions with various parameters will be fit and the corresponding
p-values under a user-specified normality test will be given. The final
transformation will be the one with the largest p-value under the given
normality test.
Author: Yuchen Wang [aut, cre]
Maintainer: Yuchen Wang
jtrans-0.1/jtrans/R/fit_sb.R |only
jtrans-0.1/jtrans/R/fit_sl.R |only
jtrans-0.1/jtrans/R/fit_su.R |only
jtrans-0.2.1/jtrans/DESCRIPTION | 29 ++++---
jtrans-0.2.1/jtrans/MD5 | 20 ++--
jtrans-0.2.1/jtrans/NAMESPACE | 11 ++
jtrans-0.2.1/jtrans/R/fit_functions.R |only
jtrans-0.2.1/jtrans/R/jtrans.R | 109 +++++++++++++++------------
jtrans-0.2.1/jtrans/R/predict.R |only
jtrans-0.2.1/jtrans/R/qtls.R | 3
jtrans-0.2.1/jtrans/R/transeq.R |only
jtrans-0.2.1/jtrans/man/fit_functions.Rd | 67 +++++++++-------
jtrans-0.2.1/jtrans/man/jtrans.Rd | 96 +++++++++++++----------
jtrans-0.2.1/jtrans/man/predict_functions.Rd |only
jtrans-0.2.1/jtrans/man/transeq.Rd |only
15 files changed, 198 insertions(+), 137 deletions(-)
Title: Detection of Fixations in Eye-Tracking Data
Diff between saccades versions 0.1 dated 2014-10-04 and 0.1-1 dated 2015-03-18
Description: Functions for detecting eye fixations in raw eye-tracking
data. The detection is done using a velocity-based algorithm for
saccade detection proposed by Ralf Engbert and Reinhold Kliegl in
2003. The algorithm labels segments as saccades when the velocity of
the eye movement exceeds a certain threshold. Anything between two
saccades is considered a fixation. Thus the algorithm is not
appropriate for data containing episodes of smooth pursuit eye
movements.
Author: Titus von der Malsburg [aut, cph, cre]
Maintainer: Titus von der Malsburg
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/saccade_recognition.R | 12 ++++++------
man/detect.fixations.Rd | 2 +-
4 files changed, 14 insertions(+), 14 deletions(-)
Title: Adaptive, Sine-Multitaper Power Spectral Density Estimation
Diff between psd versions 0.4-1 dated 2014-04-16 and 1.0-0 dated 2015-03-18
Description: Produces power spectral density estimates through iterative
refinement of the optimal number of sine-tapers at each frequency. This
optimization procedure is based on the method of Riedel and Sidorenko
(1995), which minimizes the Mean Square Error (sum of variance and bias)
at each frequency, but modified for computational stability.
Author: Andrew J. Barbour and Robert L. Parker, with contributions from David
Myer
Maintainer: Andrew J. Barbour
psd-0.4-1/psd/inst/Examples/benchmarking.R |only
psd-0.4-1/psd/inst/Examples/profiling.R |only
psd-0.4-1/psd/vignettes/framed.sty |only
psd-0.4-1/psd/vignettes/mathsyms.tex |only
psd-0.4-1/psd/vignettes/tbl_norms.tex |only
psd-0.4-1/psd/vignettes/tbl_specprogs.tex |only
psd-1.0-0/psd/DESCRIPTION | 42
psd-1.0-0/psd/MD5 | 181 ++-
psd-1.0-0/psd/NAMESPACE | 54 -
psd-1.0-0/psd/R/RcppExports.R |only
psd-1.0-0/psd/R/func_envir.R | 154 +--
psd-1.0-0/psd/R/func_norm.R | 73 -
psd-1.0-0/psd/R/func_pilot.R |only
psd-1.0-0/psd/R/func_psdcore.R | 648 +++++++------
psd-1.0-0/psd/R/func_pspectrum.R | 317 ++----
psd-1.0-0/psd/R/func_riedsid.R | 248 ++---
psd-1.0-0/psd/R/func_spec.R | 93 +
psd-1.0-0/psd/R/func_specprops.R | 75 -
psd-1.0-0/psd/R/func_tapers.R | 545 ++++++-----
psd-1.0-0/psd/R/func_utils.R | 302 ++----
psd-1.0-0/psd/R/func_whiten.R | 136 +-
psd-1.0-0/psd/R/psd-package.R | 60 -
psd-1.0-0/psd/R/zzz.R | 23
psd-1.0-0/psd/README.md |only
psd-1.0-0/psd/build/vignette.rds |binary
psd-1.0-0/psd/demo/ctap.R | 15
psd-1.0-0/psd/inst/CITATION | 2
psd-1.0-0/psd/inst/Examples/_benchmarking.R |only
psd-1.0-0/psd/inst/Examples/_profiling.R |only
psd-1.0-0/psd/inst/Examples/_resample.R |only
psd-1.0-0/psd/inst/Examples/benchmarking_data.rda |only
psd-1.0-0/psd/inst/Examples/current_benchmarking_data.rda |only
psd-1.0-0/psd/inst/Examples/fix_R |only
psd-1.0-0/psd/inst/Examples/rdex_confint.R | 6
psd-1.0-0/psd/inst/Examples/rdex_constraintapers.R | 14
psd-1.0-0/psd/inst/Examples/rdex_normalization.R | 6
psd-1.0-0/psd/inst/Examples/rdex_parabolicweights.R | 57 -
psd-1.0-0/psd/inst/Examples/rdex_pilotspec.R | 7
psd-1.0-0/psd/inst/Examples/rdex_prewhiten.R | 6
psd-1.0-0/psd/inst/Examples/rdex_psdcore.R | 10
psd-1.0-0/psd/inst/Examples/rdex_psdenv.R | 6
psd-1.0-0/psd/inst/Examples/rdex_pspectrum.R | 14
psd-1.0-0/psd/inst/Examples/rdex_riedsid.R | 13
psd-1.0-0/psd/inst/Examples/rdex_spec.R | 6
psd-1.0-0/psd/inst/Examples/rdex_spectralproperties.R | 6
psd-1.0-0/psd/inst/Examples/rdex_splinegrad.R | 6
psd-1.0-0/psd/inst/Examples/rdex_tapers.R | 17
psd-1.0-0/psd/inst/Examples/rdex_utilities.R | 70 -
psd-1.0-0/psd/inst/Examples/run.rdev |only
psd-1.0-0/psd/inst/NEWS.Rd | 73 +
psd-1.0-0/psd/inst/WISHLIST | 25
psd-1.0-0/psd/inst/doc/REFS.bib | 40
psd-1.0-0/psd/inst/doc/fftw.R | 164 +--
psd-1.0-0/psd/inst/doc/fftw.Rnw | 64 -
psd-1.0-0/psd/inst/doc/fftw.pdf |binary
psd-1.0-0/psd/inst/doc/normalization.R | 22
psd-1.0-0/psd/inst/doc/normalization.Rnw | 47
psd-1.0-0/psd/inst/doc/normalization.pdf |binary
psd-1.0-0/psd/inst/doc/psd_overview.R | 329 +++---
psd-1.0-0/psd/inst/doc/psd_overview.Rnw | 671 ++++++--------
psd-1.0-0/psd/inst/doc/psd_overview.pdf |binary
psd-1.0-0/psd/man/Tohoku.Rd | 43
psd-1.0-0/psd/man/as.tapers.Rd | 104 +-
psd-1.0-0/psd/man/ctap_loess.Rd |only
psd-1.0-0/psd/man/ctap_simple_rcpp.Rd |only
psd-1.0-0/psd/man/hfsnm.Rd | 26
psd-1.0-0/psd/man/magnet.Rd | 44
psd-1.0-0/psd/man/modulo_floor.Rd |only
psd-1.0-0/psd/man/parabolic_weights.Rd | 116 +-
psd-1.0-0/psd/man/pgram_compare.Rd |only
psd-1.0-0/psd/man/pilot_spec.Rd | 119 +-
psd-1.0-0/psd/man/prewhiten.Rd | 195 +---
psd-1.0-0/psd/man/psd-environment.Rd | 189 ++-
psd-1.0-0/psd/man/psd-normalization.Rd | 101 +-
psd-1.0-0/psd/man/psd-package.Rd | 137 +-
psd-1.0-0/psd/man/psd-utilities.Rd | 295 ++----
psd-1.0-0/psd/man/psdcore.Rd | 144 +--
psd-1.0-0/psd/man/pspectrum.Rd | 99 +-
psd-1.0-0/psd/man/rcpp_ctap_simple.Rd |only
psd-1.0-0/psd/man/resample_fft_rcpp.Rd |only
psd-1.0-0/psd/man/riedsid.Rd | 132 +-
psd-1.0-0/psd/man/spec-methods.Rd | 49 -
psd-1.0-0/psd/man/spec_confint.Rd | 76 -
psd-1.0-0/psd/man/spectral_properties.Rd | 118 +-
psd-1.0-0/psd/man/splineGrad.Rd | 49 -
psd-1.0-0/psd/man/tapers-constraints.Rd | 198 +---
psd-1.0-0/psd/man/tapers-methods.Rd | 47
psd-1.0-0/psd/src/Makevars |only
psd-1.0-0/psd/src/Makevars.win |only
psd-1.0-0/psd/src/RcppExports.cpp |only
psd-1.0-0/psd/src/ctap_simple.c | 105 --
psd-1.0-0/psd/src/ctap_simple_r.cpp |only
psd-1.0-0/psd/src/resample_fft.cpp |only
psd-1.0-0/psd/tests |only
psd-1.0-0/psd/vignettes/Makefile | 9
psd-1.0-0/psd/vignettes/README | 52 -
psd-1.0-0/psd/vignettes/REFS.bib | 40
psd-1.0-0/psd/vignettes/fftw.Rnw | 64 -
psd-1.0-0/psd/vignettes/fftw.synctex.gz |only
psd-1.0-0/psd/vignettes/normalization.Rnw | 47
psd-1.0-0/psd/vignettes/normalization.synctex.gz |only
psd-1.0-0/psd/vignettes/psd_overview.Rnw | 671 ++++++--------
psd-1.0-0/psd/vignettes/psd_overview.synctex.gz |only
psd-1.0-0/psd/vignettes/supp_mathsyms.tex |only
psd-1.0-0/psd/vignettes/supp_norms.tex |only
psd-1.0-0/psd/vignettes/supp_specprogs.tex |only
106 files changed, 3941 insertions(+), 3975 deletions(-)
Title: Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain
Diff between FuzzyStatProb versions 1.0 dated 2013-03-11 and 2.0 dated 2015-03-18
Description: An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain,
from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley
in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package FuzzyNumbers is used to represent the output probabilities.
Author: Author: Pablo J. Villacorta
Maintainer: Pablo J. Villacorta
FuzzyStatProb-1.0/FuzzyStatProb/man/FuzzyStatProb.Rd |only
FuzzyStatProb-2.0/FuzzyStatProb/DESCRIPTION | 35
FuzzyStatProb-2.0/FuzzyStatProb/MD5 | 22
FuzzyStatProb-2.0/FuzzyStatProb/NAMESPACE | 5
FuzzyStatProb-2.0/FuzzyStatProb/R/FuzzyStatProb-package.R | 2
FuzzyStatProb-2.0/FuzzyStatProb/R/initial-pop.R | 2
FuzzyStatProb-2.0/FuzzyStatProb/R/main.R | 859 ++++++++-----
FuzzyStatProb-2.0/FuzzyStatProb/R/memb-fn-reg.R | 24
FuzzyStatProb-2.0/FuzzyStatProb/R/objective-fn.R | 5
FuzzyStatProb-2.0/FuzzyStatProb/build |only
FuzzyStatProb-2.0/FuzzyStatProb/data |only
FuzzyStatProb-2.0/FuzzyStatProb/inst |only
FuzzyStatProb-2.0/FuzzyStatProb/man/fuzzyStationaryProb.Rd |only
FuzzyStatProb-2.0/FuzzyStatProb/man/robotMatrix.Rd |only
FuzzyStatProb-2.0/FuzzyStatProb/vignettes |only
15 files changed, 603 insertions(+), 351 deletions(-)
Title: Wrapper for FFTW3: Includes 1-D, Univariate and Multivariate,
and 2-D Transform
Diff between fftwtools versions 0.9-6 dated 2014-02-20 and 0.9-7 dated 2015-03-18
Description: Provides a wrapper for several FFTW functions. This package provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using FFTW3. The package includes the functions fftw and mvfftw which are designed to mimic the functionality of the R functions fft and mvfft. The FFT functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data.
Author: Karim Rahim
Maintainer: Karim Rahim
DESCRIPTION | 16 +++++++-------
MD5 | 8 +++----
R/fftwtools.R | 41 +++++++++++++++++++++++---------------
build/vignette.rds |binary
inst/doc/testTimeAndSimpleUse.pdf |binary
5 files changed, 37 insertions(+), 28 deletions(-)
Title: Differential Co-Expression and Differential Expression Analysis
Diff between decode versions 1.0 dated 2015-01-28 and 1.1 dated 2015-03-18
Description: Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.
Author: Thomas Lui [aut, cre]
Maintainer: Thomas Lui
DESCRIPTION | 12 +++++++-----
MD5 | 11 ++++++++---
R/Decode.r | 16 +++++++++-------
build |only
inst/doc |only
man/runDecode.Rd | 9 +++++++--
vignettes |only
7 files changed, 31 insertions(+), 17 deletions(-)