Title: Batch computing with R.
Diff between BatchJobs versions 1.2 dated 2014-02-06 and 1.3 dated 2014-07-09
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
BatchJobs-1.2/BatchJobs/inst/tests |only
BatchJobs-1.3/BatchJobs/DESCRIPTION | 15
BatchJobs-1.3/BatchJobs/LICENSE | 5
BatchJobs-1.3/BatchJobs/MD5 | 334 +++++-----
BatchJobs-1.3/BatchJobs/NAMESPACE | 6
BatchJobs-1.3/BatchJobs/NEWS | 32
BatchJobs-1.3/BatchJobs/R/Exports.R | 4
BatchJobs-1.3/BatchJobs/R/Job.R | 10
BatchJobs-1.3/BatchJobs/R/Registry.R | 83 +-
BatchJobs-1.3/BatchJobs/R/Resources.R | 15
BatchJobs-1.3/BatchJobs/R/Worker.R | 23
BatchJobs-1.3/BatchJobs/R/WorkerLinux.R | 32
BatchJobs-1.3/BatchJobs/R/applyJobFunction.R | 12
BatchJobs-1.3/BatchJobs/R/batchApply.R | 17
BatchJobs-1.3/BatchJobs/R/batchExpandGrid.R | 18
BatchJobs-1.3/BatchJobs/R/batchMap.R | 39 -
BatchJobs-1.3/BatchJobs/R/batchMapQuick.R | 40 -
BatchJobs-1.3/BatchJobs/R/batchMapResults.R | 28
BatchJobs-1.3/BatchJobs/R/batchReduce.R | 27
BatchJobs-1.3/BatchJobs/R/batchReduceResults.R | 29
BatchJobs-1.3/BatchJobs/R/buffer.R | 18
BatchJobs-1.3/BatchJobs/R/callFunctionOnSSHWorkers.R | 30
BatchJobs-1.3/BatchJobs/R/checkIdValid.R | 3
BatchJobs-1.3/BatchJobs/R/clusterFunctions.R | 18
BatchJobs-1.3/BatchJobs/R/clusterFunctionsHelpers.R | 44 -
BatchJobs-1.3/BatchJobs/R/clusterFunctionsInteractive.R | 26
BatchJobs-1.3/BatchJobs/R/clusterFunctionsLSF.R | 32
BatchJobs-1.3/BatchJobs/R/clusterFunctionsLocal.R | 16
BatchJobs-1.3/BatchJobs/R/clusterFunctionsMulticore.R | 14
BatchJobs-1.3/BatchJobs/R/clusterFunctionsSGE.R | 25
BatchJobs-1.3/BatchJobs/R/clusterFunctionsSLURM.R | 28
BatchJobs-1.3/BatchJobs/R/clusterFunctionsSSH.R | 28
BatchJobs-1.3/BatchJobs/R/clusterFunctionsTorque.R | 28
BatchJobs-1.3/BatchJobs/R/conf.R | 80 +-
BatchJobs-1.3/BatchJobs/R/database.R | 157 ++--
BatchJobs-1.3/BatchJobs/R/debugMulticore.R | 16
BatchJobs-1.3/BatchJobs/R/debugSSH.R | 30
BatchJobs-1.3/BatchJobs/R/doJob.R | 205 ++----
BatchJobs-1.3/BatchJobs/R/filenames.R | 40 -
BatchJobs-1.3/BatchJobs/R/filterResults.R | 10
BatchJobs-1.3/BatchJobs/R/findJobs.R | 20
BatchJobs-1.3/BatchJobs/R/getErrorMessages.R | 2
BatchJobs-1.3/BatchJobs/R/getJob.R | 34 -
BatchJobs-1.3/BatchJobs/R/getJobInfo.R | 22
BatchJobs-1.3/BatchJobs/R/getSSHWorkersInfo.R | 4
BatchJobs-1.3/BatchJobs/R/grepLogs.R | 20
BatchJobs-1.3/BatchJobs/R/helpers.R | 81 +-
BatchJobs-1.3/BatchJobs/R/installPackagesOnSSHWorkers.R | 24
BatchJobs-1.3/BatchJobs/R/killJobs.R | 30
BatchJobs-1.3/BatchJobs/R/loadResult.R | 6
BatchJobs-1.3/BatchJobs/R/loadResults.R | 16
BatchJobs-1.3/BatchJobs/R/reduceResults.R | 68 +-
BatchJobs-1.3/BatchJobs/R/resetJobs.R | 10
BatchJobs-1.3/BatchJobs/R/scheduleWorkerJobs.R | 6
BatchJobs-1.3/BatchJobs/R/sendMail.R | 49 -
BatchJobs-1.3/BatchJobs/R/setJobFunction.R | 16
BatchJobs-1.3/BatchJobs/R/setJobNames.R | 8
BatchJobs-1.3/BatchJobs/R/showClusterStatus.R | 4
BatchJobs-1.3/BatchJobs/R/showLog.R | 12
BatchJobs-1.3/BatchJobs/R/showStatus.R | 15
BatchJobs-1.3/BatchJobs/R/sourceRegistryFiles.R | 23
BatchJobs-1.3/BatchJobs/R/submitJobs.R | 109 +--
BatchJobs-1.3/BatchJobs/R/sweepRegistry.R | 4
BatchJobs-1.3/BatchJobs/R/syncRegistry.R | 10
BatchJobs-1.3/BatchJobs/R/testJob.R | 37 -
BatchJobs-1.3/BatchJobs/R/updateRegistry.R | 20
BatchJobs-1.3/BatchJobs/R/waitForJobs.R | 22
BatchJobs-1.3/BatchJobs/R/writeRscripts.R | 30
BatchJobs-1.3/BatchJobs/R/zzz.R | 12
BatchJobs-1.3/BatchJobs/inst/etc/BatchJobs_global_config.R | 6
BatchJobs-1.3/BatchJobs/man/BatchJobs.Rd | 7
BatchJobs-1.3/BatchJobs/man/applyJobFunction.Rd | 12
BatchJobs-1.3/BatchJobs/man/batchExpandGrid.Rd | 38 -
BatchJobs-1.3/BatchJobs/man/batchMap.Rd | 29
BatchJobs-1.3/BatchJobs/man/batchMapQuick.Rd | 93 +-
BatchJobs-1.3/BatchJobs/man/batchMapResults.Rd | 64 -
BatchJobs-1.3/BatchJobs/man/batchReduce.Rd | 35 -
BatchJobs-1.3/BatchJobs/man/batchReduceResults.Rd | 54 -
BatchJobs-1.3/BatchJobs/man/callFunctionOnSSHWorkers.Rd | 91 +-
BatchJobs-1.3/BatchJobs/man/cfBrewTemplate.Rd | 32
BatchJobs-1.3/BatchJobs/man/cfHandleUnknownSubmitError.Rd | 25
BatchJobs-1.3/BatchJobs/man/cfKillBatchJob.Rd | 27
BatchJobs-1.3/BatchJobs/man/cfReadBrewTemplate.Rd | 14
BatchJobs-1.3/BatchJobs/man/configuration.Rd | 1
BatchJobs-1.3/BatchJobs/man/copyRequiredJobFiles.Rd | 11
BatchJobs-1.3/BatchJobs/man/dbCreateJobDefTable.Rd | 4
BatchJobs-1.3/BatchJobs/man/dbGetJobs.Rd | 7
BatchJobs-1.3/BatchJobs/man/debugMulticore.Rd | 15
BatchJobs-1.3/BatchJobs/man/debugSSH.Rd | 38 -
BatchJobs-1.3/BatchJobs/man/filterResults.Rd | 26
BatchJobs-1.3/BatchJobs/man/findJobs.Rd | 32
BatchJobs-1.3/BatchJobs/man/findState.Rd | 49 -
BatchJobs-1.3/BatchJobs/man/getConfig.Rd | 4
BatchJobs-1.3/BatchJobs/man/getErrorMessages.Rd | 16
BatchJobs-1.3/BatchJobs/man/getJob.Rd | 17
BatchJobs-1.3/BatchJobs/man/getJobIds.Rd | 4
BatchJobs-1.3/BatchJobs/man/getJobInfo.Rd | 50 -
BatchJobs-1.3/BatchJobs/man/getJobNr.Rd | 4
BatchJobs-1.3/BatchJobs/man/getJobResources.Rd | 18
BatchJobs-1.3/BatchJobs/man/getJobs.Rd | 19
BatchJobs-1.3/BatchJobs/man/getLogFiles.Rd | 9
BatchJobs-1.3/BatchJobs/man/getResources.Rd | 4
BatchJobs-1.3/BatchJobs/man/getSSHWorkersInfo.Rd | 18
BatchJobs-1.3/BatchJobs/man/grepLogs.Rd | 35 -
BatchJobs-1.3/BatchJobs/man/installPackagesOnSSHWorkers.Rd | 42 -
BatchJobs-1.3/BatchJobs/man/killJobs.Rd | 38 -
BatchJobs-1.3/BatchJobs/man/loadConfig.Rd | 8
BatchJobs-1.3/BatchJobs/man/loadExports.Rd | 13
BatchJobs-1.3/BatchJobs/man/loadRegistry.Rd | 9
BatchJobs-1.3/BatchJobs/man/loadResult.Rd | 21
BatchJobs-1.3/BatchJobs/man/loadResults.Rd | 41 -
BatchJobs-1.3/BatchJobs/man/makeClusterFunctions.Rd | 112 +--
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsInteractive.Rd | 25
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsLSF.Rd | 37 -
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsLocal.Rd | 17
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsMulticore.Rd | 61 -
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsSGE.Rd | 35 -
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsSLURM.Rd | 37 -
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsSSH.Rd | 26
BatchJobs-1.3/BatchJobs/man/makeClusterFunctionsTorque.Rd | 36 -
BatchJobs-1.3/BatchJobs/man/makeJob.Rd | 30
BatchJobs-1.3/BatchJobs/man/makeRegistry.Rd | 124 +--
BatchJobs-1.3/BatchJobs/man/makeSSHWorker.Rd | 83 +-
BatchJobs-1.3/BatchJobs/man/makeSubmitJobResult.Rd | 35 -
BatchJobs-1.3/BatchJobs/man/reduceResults.Rd | 141 ++--
BatchJobs-1.3/BatchJobs/man/resetJobs.Rd | 41 -
BatchJobs-1.3/BatchJobs/man/setConfig.Rd | 11
BatchJobs-1.3/BatchJobs/man/setJobFunction.Rd | 37 -
BatchJobs-1.3/BatchJobs/man/setJobNames.Rd | 18
BatchJobs-1.3/BatchJobs/man/showClusterStatus.Rd | 14
BatchJobs-1.3/BatchJobs/man/showLog.Rd | 37 -
BatchJobs-1.3/BatchJobs/man/showStatus.Rd | 36 -
BatchJobs-1.3/BatchJobs/man/sourceRegistryFiles.Rd | 12
BatchJobs-1.3/BatchJobs/man/submitJobs.Rd | 118 +--
BatchJobs-1.3/BatchJobs/man/sweepRegistry.Rd | 48 -
BatchJobs-1.3/BatchJobs/man/testJob.Rd | 40 -
BatchJobs-1.3/BatchJobs/man/updateRegistry.Rd | 7
BatchJobs-1.3/BatchJobs/man/waitForJobs.Rd | 49 -
BatchJobs-1.3/BatchJobs/tests/run-all.R | 3
BatchJobs-1.3/BatchJobs/tests/testthat |only
140 files changed, 2364 insertions(+), 2317 deletions(-)
Title: Weather Forecast Verification Utilities.
Diff between verification versions 1.39 dated 2014-06-02 and 1.40 dated 2014-07-09
Description: This package contains utilities for verification of
discrete,continuous, probabilistic forecasts and forecast
expressed as parametric distributions.
Author: NCAR - Research Applications Laboratory
Maintainer: Eric Gilleland
DESCRIPTION | 6 ++---
MD5 | 4 +--
R/predcomptests.R | 55 +++++++++++++++++++++++++++++++++++++++++++++++++-----
3 files changed, 55 insertions(+), 10 deletions(-)
Title: Iterated Racing Procedures
Diff between irace versions 1.04 dated 2013-06-09 and 1.05 dated 2014-07-09
Description: Iterated racing for automatic algorithm configuration
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste,
Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez
irace-1.04/irace/svn_version |only
irace-1.05/irace/BUGS |only
irace-1.05/irace/DESCRIPTION | 12
irace-1.05/irace/MD5 | 60 +-
irace-1.05/irace/NAMESPACE | 3
irace-1.05/irace/NEWS | 50 ++
irace-1.05/irace/R/cluster.R | 20
irace-1.05/irace/R/generation.R | 265 ++++++------
irace-1.05/irace/R/irace.R | 490 ++++++++++++-----------
irace-1.05/irace/R/main.R | 102 ++--
irace-1.05/irace/R/model.R | 6
irace-1.05/irace/R/race-wrapper.R | 161 ++++---
irace-1.05/irace/R/race.R | 52 +-
irace-1.05/irace/R/readConfiguration.R | 119 +++--
irace-1.05/irace/R/readParameters.R | 105 +++-
irace-1.05/irace/R/tnorm.R | 25 -
irace-1.05/irace/R/utils.R | 171 ++++++--
irace-1.05/irace/R/version.R | 2
irace-1.05/irace/README | 19
irace-1.05/irace/inst/bin/parallel-irace | 17
irace-1.05/irace/inst/examples/acotsp/tune-conf | 83 ---
irace-1.05/irace/inst/examples/hook-run-python |only
irace-1.05/irace/inst/examples/sge-cluster |only
irace-1.05/irace/inst/examples/tune-main-cluster | 11
irace-1.05/irace/inst/examples/tune-main-tmp | 12
irace-1.05/irace/inst/templates/forbidden.tmpl |only
irace-1.05/irace/inst/templates/hook-run.tmpl | 2
irace-1.05/irace/inst/templates/parameters.tmpl | 6
irace-1.05/irace/inst/templates/tune-conf.tmpl | 18
irace-1.05/irace/man/hook.evaluate.default.Rd |only
irace-1.05/irace/man/hook.run.default.Rd |only
irace-1.05/irace/man/irace-package.Rd | 4
irace-1.05/irace/man/irace.cmdline.Rd | 8
33 files changed, 1079 insertions(+), 744 deletions(-)
Title: Estimation and comparison of dynamic treatment regimes
Diff between DTR versions 1.3 dated 2014-03-03 and 1.5 dated 2014-07-09
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials
Author: Xinyu Tang [aut, cre],
Maria Melguizo [aut]
Maintainer: Xinyu Tang
DTR-1.3/DTR/R/contrast.chr.R |only
DTR-1.3/DTR/R/contrast.logrank.R |only
DTR-1.3/DTR/R/contrast.ph.R |only
DTR-1.3/DTR/R/contrast.wald.R |only
DTR-1.3/DTR/man/contrast.chr.Rd |only
DTR-1.3/DTR/man/contrast.logrank.Rd |only
DTR-1.3/DTR/man/contrast.ph.Rd |only
DTR-1.3/DTR/man/contrast.wald.Rd |only
DTR-1.5/DTR/DESCRIPTION | 10 +-
DTR-1.5/DTR/MD5 | 78 +++++++++----------
DTR-1.5/DTR/NAMESPACE | 2
DTR-1.5/DTR/R/CHRestimate.R | 23 +++--
DTR-1.5/DTR/R/LDTestimate.R | 18 ++++
DTR-1.5/DTR/R/PHfit.R | 144 ++++++++++++++++++------------------
DTR-1.5/DTR/R/WRSEestimate.R | 17 ++++
DTR-1.5/DTR/R/contrast_chr.R |only
DTR-1.5/DTR/R/contrast_logrank.R |only
DTR-1.5/DTR/R/contrast_ph.R |only
DTR-1.5/DTR/R/contrast_wald.R |only
DTR-1.5/DTR/R/plot.CHR.R | 2
DTR-1.5/DTR/R/plot.DTR.R | 41 ++++++++--
DTR-1.5/DTR/R/simPHdata.R | 3
DTR-1.5/DTR/data/PHdata.RData |binary
DTR-1.5/DTR/inst/NEWS.Rd | 17 ++++
DTR-1.5/DTR/man/CHRdata.Rd | 5 -
DTR-1.5/DTR/man/CHRestimate.Rd | 17 ++--
DTR-1.5/DTR/man/DTR-package.Rd | 19 ++--
DTR-1.5/DTR/man/DTR.object.Rd | 9 ++
DTR-1.5/DTR/man/LDTdata.Rd | 4 -
DTR-1.5/DTR/man/LDTestimate.Rd | 7 -
DTR-1.5/DTR/man/LRdata.Rd | 4 -
DTR-1.5/DTR/man/PHdata.Rd | 5 -
DTR-1.5/DTR/man/PHfit.Rd | 19 ++--
DTR-1.5/DTR/man/WRSEdata.Rd | 5 -
DTR-1.5/DTR/man/WRSEestimate.Rd | 7 -
DTR-1.5/DTR/man/contrast_chr.Rd |only
DTR-1.5/DTR/man/contrast_logrank.Rd |only
DTR-1.5/DTR/man/contrast_ph.Rd |only
DTR-1.5/DTR/man/contrast_wald.Rd |only
DTR-1.5/DTR/man/plot.CHR.Rd | 5 -
DTR-1.5/DTR/man/plot.DTR.Rd | 14 ++-
DTR-1.5/DTR/man/simCHRdata.Rd | 2
DTR-1.5/DTR/man/simLDTdata.Rd | 3
DTR-1.5/DTR/man/simLRdata.Rd | 6 -
DTR-1.5/DTR/man/simPHdata.Rd | 4 -
DTR-1.5/DTR/man/simWRSEdata.Rd | 4 -
DTR-1.5/DTR/man/summary.CHR.Rd | 7 -
DTR-1.5/DTR/man/summary.DTR.Rd | 5 -
48 files changed, 291 insertions(+), 215 deletions(-)
Title: Video comparison tool
Diff between VideoComparison versions 0.9-4 dated 2013-12-10 and 0.11 dated 2014-07-09
More information about VideoComparison at CRAN
Description: It will take the vectors of motion for two videos
(coming from a variant of shotdetect code allowing to store
detailed motion vectors in json format, for instance) and it
will look for comparing taking out the common chunk.
Then, provided you have some image's hashes it will compare
their signature in order to make up the decision about
chunk similarity of two video files.
Author: Silvia Espinosa, Joaquin Ordieres, Antonio Bello, Jose Maria Perez
Maintainer: Joaquin Ordieres
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NAMESPACE | 1 +
man/VideoComparison-package.Rd | 4 ++--
src/VideoDistance.cpp | 2 +-
6 files changed, 16 insertions(+), 12 deletions(-)
Permanent link
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-3 dated 2014-04-22 and 1.3-4 dated 2014-07-09
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 12 +--
MD5 | 14 +--
inst/NEWS | 140 +++++++++++++++--------------------
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
man/contrMat.Rd | 2
tests/Examples/multcomp-Ex.Rout.save | 6 -
8 files changed, 79 insertions(+), 95 deletions(-)
Title: Interactive web-maps based on the Leaflet JavaScript library
Diff between leafletR versions 0.2-0 dated 2014-04-28 and 0.2-1 dated 2014-07-09
Description: Display your spatial data on interactive web-maps using the open-source JavaScript library Leaflet. The package provides basic web-mapping functionality to combine vector data and online map tiles from different sources.
Author: Christian Graul
Maintainer: Christian Graul
DESCRIPTION | 10 +-
MD5 | 26 +++--
NAMESPACE | 2
R/baseMap.R |only
R/dfToGeoJSON.R | 7 -
R/leaflet.R | 18 ++--
R/leafletInt.R | 211 +++++++++++++++++++++++++++++++++++++++++++----
R/print.leafletr.style.R |only
R/styleCat.R | 3
R/styleGrad.R | 3
R/styleSingle.R | 16 ++-
R/toGeoJSON.R | 2
inst/NEWS | 17 +++
man/leaflet.Rd | 4
man/leafletR-package.Rd | 4
15 files changed, 272 insertions(+), 51 deletions(-)
Title: Classes for Relational Data
Diff between network versions 1.9.0 dated 2014-01-14 and 1.10.2 dated 2014-07-09
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb]
Maintainer: Carter T. Butts
network-1.10.2/network/ChangeLog | 18
network-1.10.2/network/DESCRIPTION | 16
network-1.10.2/network/MD5 | 49 -
network-1.10.2/network/NAMESPACE | 2
network-1.10.2/network/R/access.R | 176 ++--
network-1.10.2/network/R/assignment.R |only
network-1.10.2/network/R/coercion.R | 13
network-1.10.2/network/R/constructors.R | 40 -
network-1.10.2/network/R/operators.R | 16
network-1.10.2/network/R/plot.R | 27
network-1.10.2/network/build/vignette.rds |binary
network-1.10.2/network/inst/doc/networkVignette.R | 66 -
network-1.10.2/network/inst/doc/networkVignette.Rnw | 5
network-1.10.2/network/inst/doc/networkVignette.pdf |binary
network-1.10.2/network/man/edgeset.constructors.Rd | 2
network-1.10.2/network/man/network-package.Rd | 10
network-1.10.2/network/man/network.Rd | 2
network-1.10.2/network/man/network.extraction.Rd | 4
network-1.10.2/network/man/network.naedgecount.Rd | 2
network-1.10.2/network/man/plot.network.Rd | 2
network-1.10.2/network/src/access.c | 686 +++++++++----------
network-1.10.2/network/src/access.h | 5
network-1.10.2/network/tests/general.tests.R | 17
network-1.10.2/network/tests/pathological.tests.R |only
network-1.10.2/network/tests/plot_tests.R | 23
network-1.10.2/network/vignettes/networkVignette.Rnw | 5
network-1.9.0/network/vignettes/jssmod.cls |only
27 files changed, 640 insertions(+), 546 deletions(-)
Title: Bayesian Model Averaging with INLA
Diff between INLABMA versions 0.1-4 dated 2014-04-15 and 0.1-5 dated 2014-07-09
Description: Spatial Econometrics models using Bayesian Model Averaging
on models fitted with INLA. The INLA package can be obtained from
http://www.r-inla.org . We recommend the testing version, which can be
downloaded by running:
source("http://www.math.ntnu.no/inla/givemeINLA-testing.R")
Author: Virgilio Gomez Rubio
Maintainer: Virgilio Gomez Rubio
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/BMArho.R | 28 ++++++++++++++++++----------
R/leroux.R | 2 +-
4 files changed, 26 insertions(+), 18 deletions(-)
Title: R code for Stock Synthesis
Diff between r4ss versions 1.20 dated 2013-03-15 and 1.22 dated 2014-07-09
Description: Functions for reading output, plotting, exploring and
manipulating input files for Stock Synthesis fisheries stock
assessment modeling platform, developed by Richard Methot.
Author: Ian Taylor, Ian Stewart, Allan Hicks, Tommy Garrison, Andre
Punt, John Wallace, Chantel Wetzel, James Thorson, Yukio Takeuchi,
and other contributors
Maintainer: Ian Taylor
r4ss-1.20/r4ss/R/hist2d.R |only
r4ss-1.20/r4ss/man/RebuildPlot.Rd |only
r4ss-1.20/r4ss/man/SSplotRetroDevs.Rd |only
r4ss-1.20/r4ss/man/hist2d.Rd |only
r4ss-1.22/r4ss/DESCRIPTION | 23
r4ss-1.22/r4ss/MD5 | 296 +-
r4ss-1.22/r4ss/NAMESPACE | 18
r4ss-1.22/r4ss/R/IOTCmove.R | 124 -
r4ss-1.22/r4ss/R/NegLogInt_Fn.R |only
r4ss-1.22/r4ss/R/PinerPlot.R |only
r4ss-1.22/r4ss/R/RebuildPlot.R | 147 -
r4ss-1.22/r4ss/R/SSFishGraph.R | 241 +-
r4ss-1.22/r4ss/R/SS_RunJitter.R |only
r4ss-1.22/r4ss/R/SS_changepars.R | 241 +-
r4ss-1.22/r4ss/R/SS_doRetro.R | 48
r4ss-1.22/r4ss/R/SS_fitbiasramp.R | 640 ++---
r4ss-1.22/r4ss/R/SS_html.R | 27
r4ss-1.22/r4ss/R/SS_makedatlist.R | 60
r4ss-1.22/r4ss/R/SS_output.R | 3369 ++++++++++++++--------------
r4ss-1.22/r4ss/R/SS_parlines.R | 176 -
r4ss-1.22/r4ss/R/SS_plots.R | 308 ++
r4ss-1.22/r4ss/R/SS_profile.R | 403 ++-
r4ss-1.22/r4ss/R/SS_readctl.R | 18
r4ss-1.22/r4ss/R/SS_readdat.R | 38
r4ss-1.22/r4ss/R/SS_readforecast.R | 15
r4ss-1.22/r4ss/R/SS_readstarter.R | 13
r4ss-1.22/r4ss/R/SS_recdevs.R | 296 +-
r4ss-1.22/r4ss/R/SS_splitdat.R | 158 -
r4ss-1.22/r4ss/R/SS_write_length.fit.R | 21
r4ss-1.22/r4ss/R/SS_writectl.R | 17
r4ss-1.22/r4ss/R/SS_writedat.R | 19
r4ss-1.22/r4ss/R/SS_writeforecast.R | 21
r4ss-1.22/r4ss/R/SS_writestarter.R | 25
r4ss-1.22/r4ss/R/SSbootstrap.R | 15
r4ss-1.22/r4ss/R/SSchangeYears.R |only
r4ss-1.22/r4ss/R/SSgetMCMC.R | 31
r4ss-1.22/r4ss/R/SSgetoutput.R | 37
r4ss-1.22/r4ss/R/SSmakeMmatrix.R |only
r4ss-1.22/r4ss/R/SSplotBiology.R | 935 ++++---
r4ss-1.22/r4ss/R/SSplotCatch.R | 747 +++---
r4ss-1.22/r4ss/R/SSplotCohorts.R | 477 ++-
r4ss-1.22/r4ss/R/SSplotComparisons.R | 471 +++
r4ss-1.22/r4ss/R/SSplotComps.R | 2695 +++++++++++-----------
r4ss-1.22/r4ss/R/SSplotData.R | 56
r4ss-1.22/r4ss/R/SSplotDiscard.R | 48
r4ss-1.22/r4ss/R/SSplotIndices.R | 73
r4ss-1.22/r4ss/R/SSplotMCMC_ExtraSelex.R | 19
r4ss-1.22/r4ss/R/SSplotMnwt.R | 54
r4ss-1.22/r4ss/R/SSplotMovementMap.R | 187 -
r4ss-1.22/r4ss/R/SSplotMovementRates.R | 53
r4ss-1.22/r4ss/R/SSplotNumbers.R | 63
r4ss-1.22/r4ss/R/SSplotPars.R | 883 +++----
r4ss-1.22/r4ss/R/SSplotProfile.R | 86
r4ss-1.22/r4ss/R/SSplotRecdevs.R | 31
r4ss-1.22/r4ss/R/SSplotRecdist.R | 37
r4ss-1.22/r4ss/R/SSplotRetroDevs.R | 2
r4ss-1.22/r4ss/R/SSplotRetroRecruits.R |only
r4ss-1.22/r4ss/R/SSplotSPR.R | 48
r4ss-1.22/r4ss/R/SSplotSelex.R | 1604 +++++++------
r4ss-1.22/r4ss/R/SSplotSpawnrecruit.R | 40
r4ss-1.22/r4ss/R/SSplotSummaryF.R | 76
r4ss-1.22/r4ss/R/SSplotTags.R | 44
r4ss-1.22/r4ss/R/SSplotTimeseries.R | 53
r4ss-1.22/r4ss/R/SSplotYield.R | 30
r4ss-1.22/r4ss/R/SSsummarize.R | 82
r4ss-1.22/r4ss/R/SStableComparisons.R | 29
r4ss-1.22/r4ss/R/TSCplot.R | 76
r4ss-1.22/r4ss/R/addSSsummarize.R | 73
r4ss-1.22/r4ss/R/bubble3.R | 201 +
r4ss-1.22/r4ss/R/getADMBHessian.R |only
r4ss-1.22/r4ss/R/make_multifig.R | 569 ++--
r4ss-1.22/r4ss/R/mcmc.nuisance.R | 39
r4ss-1.22/r4ss/R/mcmc.out.R | 51
r4ss-1.22/r4ss/R/mountains.R | 30
r4ss-1.22/r4ss/R/movepars.R | 711 +++--
r4ss-1.22/r4ss/R/plotCI.R | 77
r4ss-1.22/r4ss/R/r4ss-package.R |only
r4ss-1.22/r4ss/R/read.admbFit.R |only
r4ss-1.22/r4ss/R/rich.colors.short.R | 30
r4ss-1.22/r4ss/R/sel.line.R | 205 -
r4ss-1.22/r4ss/R/selfit.R | 592 ++--
r4ss-1.22/r4ss/R/selfit_spline.R | 692 ++---
r4ss-1.22/r4ss/R/stackpoly.R | 26
r4ss-1.22/r4ss/R/update_r4ss_files.R | 201 +
r4ss-1.22/r4ss/README.md |only
r4ss-1.22/r4ss/man/DoProjectPlots.Rd |only
r4ss-1.22/r4ss/man/IOTCmove.Rd | 114
r4ss-1.22/r4ss/man/NegLogInt_Fn.Rd |only
r4ss-1.22/r4ss/man/PinerPlot.Rd |only
r4ss-1.22/r4ss/man/SSFishGraph.Rd | 59
r4ss-1.22/r4ss/man/SS_RunJitter.Rd |only
r4ss-1.22/r4ss/man/SS_changepars.Rd | 94
r4ss-1.22/r4ss/man/SS_doRetro.Rd | 109
r4ss-1.22/r4ss/man/SS_fitbiasramp.Rd | 145 -
r4ss-1.22/r4ss/man/SS_html.Rd | 87
r4ss-1.22/r4ss/man/SS_makedatlist.Rd | 314 +-
r4ss-1.22/r4ss/man/SS_output.Rd | 204 -
r4ss-1.22/r4ss/man/SS_parlines.Rd | 90
r4ss-1.22/r4ss/man/SS_plots.Rd | 629 ++---
r4ss-1.22/r4ss/man/SS_profile.Rd | 184 -
r4ss-1.22/r4ss/man/SS_readctl.Rd | 87
r4ss-1.22/r4ss/man/SS_readdat.Rd | 98
r4ss-1.22/r4ss/man/SS_readforecast.Rd | 90
r4ss-1.22/r4ss/man/SS_readstarter.Rd | 80
r4ss-1.22/r4ss/man/SS_recdevs.Rd | 105
r4ss-1.22/r4ss/man/SS_splitdat.Rd | 93
r4ss-1.22/r4ss/man/SS_write_length.fit.Rd | 87
r4ss-1.22/r4ss/man/SS_writectl.Rd | 95
r4ss-1.22/r4ss/man/SS_writedat.Rd | 95
r4ss-1.22/r4ss/man/SS_writeforecast.Rd | 103
r4ss-1.22/r4ss/man/SS_writestarter.Rd | 104
r4ss-1.22/r4ss/man/SSbootstrap.Rd | 55
r4ss-1.22/r4ss/man/SSgetMCMC.Rd | 146 -
r4ss-1.22/r4ss/man/SSgetoutput.Rd | 136 -
r4ss-1.22/r4ss/man/SSmakeMmatrix.Rd |only
r4ss-1.22/r4ss/man/SSplotBiology.Rd | 187 -
r4ss-1.22/r4ss/man/SSplotCatch.Rd | 269 --
r4ss-1.22/r4ss/man/SSplotCohorts.Rd | 215 -
r4ss-1.22/r4ss/man/SSplotComparisons.Rd | 508 +---
r4ss-1.22/r4ss/man/SSplotComps.Rd | 432 +--
r4ss-1.22/r4ss/man/SSplotData.Rd | 186 -
r4ss-1.22/r4ss/man/SSplotDiscard.Rd | 179 -
r4ss-1.22/r4ss/man/SSplotIndices.Rd | 274 --
r4ss-1.22/r4ss/man/SSplotMCMC_ExtraSelex.Rd | 107
r4ss-1.22/r4ss/man/SSplotMnwt.Rd | 178 -
r4ss-1.22/r4ss/man/SSplotMovementMap.Rd | 170 -
r4ss-1.22/r4ss/man/SSplotMovementRates.Rd | 178 -
r4ss-1.22/r4ss/man/SSplotNumbers.Rd | 215 -
r4ss-1.22/r4ss/man/SSplotPars.Rd | 190 -
r4ss-1.22/r4ss/man/SSplotProfile.Rd | 335 +-
r4ss-1.22/r4ss/man/SSplotRecdevs.Rd | 191 -
r4ss-1.22/r4ss/man/SSplotRecdist.Rd | 159 -
r4ss-1.22/r4ss/man/SSplotRetroRecruits.Rd |only
r4ss-1.22/r4ss/man/SSplotSPR.Rd | 185 -
r4ss-1.22/r4ss/man/SSplotSelex.Rd | 291 --
r4ss-1.22/r4ss/man/SSplotSpawnrecruit.Rd | 223 -
r4ss-1.22/r4ss/man/SSplotSummaryF.Rd | 90
r4ss-1.22/r4ss/man/SSplotTags.Rd | 222 -
r4ss-1.22/r4ss/man/SSplotTimeseries.Rd | 226 -
r4ss-1.22/r4ss/man/SSplotYield.Rd | 168 -
r4ss-1.22/r4ss/man/SSsummarize.Rd | 148 -
r4ss-1.22/r4ss/man/SStableComparisons.Rd | 162 -
r4ss-1.22/r4ss/man/TSCplot.Rd | 265 --
r4ss-1.22/r4ss/man/addSSsummarize.Rd | 295 --
r4ss-1.22/r4ss/man/bubble3.Rd | 201 -
r4ss-1.22/r4ss/man/getADMBHessian.Rd |only
r4ss-1.22/r4ss/man/make_multifig.Rd | 406 +--
r4ss-1.22/r4ss/man/mcmc.nuisance.Rd | 156 -
r4ss-1.22/r4ss/man/mcmc.out.Rd | 185 -
r4ss-1.22/r4ss/man/mountains.Rd | 134 -
r4ss-1.22/r4ss/man/movepars.Rd | 53
r4ss-1.22/r4ss/man/plotCI.Rd | 125 -
r4ss-1.22/r4ss/man/r4ss-package.Rd | 92
r4ss-1.22/r4ss/man/read.admbFit.Rd |only
r4ss-1.22/r4ss/man/rich.colors.short.Rd | 77
r4ss-1.22/r4ss/man/sel.line.Rd | 56
r4ss-1.22/r4ss/man/selfit.Rd | 56
r4ss-1.22/r4ss/man/selfit_spline.Rd | 76
r4ss-1.22/r4ss/man/stackpoly.Rd | 146 -
r4ss-1.22/r4ss/man/update_r4ss_files.Rd | 134 -
160 files changed, 16025 insertions(+), 14864 deletions(-)
Title: Family of Lasso Regression
Diff between flare versions 1.3.0 dated 2014-04-26 and 1.4.0 dated 2014-07-09
Description: The package "flare" provides the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan and Han Liu
Maintainer: Xingguo Li
DESCRIPTION | 8 +++----
MD5 | 36 ++++++++++++++++----------------
R/slim.R | 14 ++++++------
R/slim.dantzig.ladm.scr.R | 11 +++++----
R/slim.dantzig.ladm.scr2.R | 11 +++++----
R/slim.lad.ladm.scr.btr.R | 9 ++++----
R/slim.lasso.ladm.scr.R | 9 ++++----
R/slim.lq.ladm.scr.btr.R | 9 ++++----
R/slim.sqrt.ladm.scr.R | 9 ++++----
R/sugm.R | 13 ++++++-----
R/sugm.clime.ladm.scr.R | 14 ++++++++----
R/sugm.select.R | 13 +++++++----
R/sugm.tiger.ladm.scr.R | 9 ++++----
man/flare-internal.Rd | 22 +++++++++++++------
man/flare-package.Rd | 4 +--
man/slim.Rd | 4 +--
man/sugm.Rd | 2 -
src/sugm_clime_ladm_scr.c | 2 -
src/sugm_tiger_ladm_scr.c | 50 ---------------------------------------------
19 files changed, 111 insertions(+), 138 deletions(-)