Title: EasieR XML data collection
Diff between XML2R versions 0.0.5 dated 2014-03-03 and 0.0.6 dated 2014-03-09
Description: XML2R is a framework that reduces the effort required to transform
XML content into number of tables while preserving parent to child
relationships.
Author: Carson Sievert
Maintainer: Carson Sievert
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 6 ++++++
R/utils.R | 2 +-
4 files changed, 14 insertions(+), 8 deletions(-)
Title: Fisheries stock assessment simulation testing with Stock
Synthesis
Diff between ss3sim versions 0.8.0 dated 2014-01-22 and 0.8.2 dated 2014-03-09
Description: The ss3sim package develops a framework for fisheries stock
assessment simulation testing with Stock Synthesis 3 (SS3).
Author: Sean Anderson [aut, cre],
Cole Monnahan [aut],
Kelli Johnson [aut],
Kotaro Ono [aut],
Juan Valero [aut],
Curry Cunningham [aut],
Felipe Hurtado-Ferro [aut],
Roberto Licandeo [aut],
Carey McGilliard [aut],
Melissa Muradian [ctb],
Cody Szuwalski [aut],
Katyana Vert-pre [aut],
Athol Whitten [aut]
Maintainer: Sean Anderson
ss3sim-0.8.0/ss3sim/vignettes/scalar_dat.rda |only
ss3sim-0.8.0/ss3sim/vignettes/ts_dat.rda |only
ss3sim-0.8.2/ss3sim/DESCRIPTION | 8
ss3sim-0.8.2/ss3sim/MD5 | 43 ++--
ss3sim-0.8.2/ss3sim/R/get_recdevs.r | 5
ss3sim-0.8.2/ss3sim/R/run_ss3sim.r | 23 +-
ss3sim-0.8.2/ss3sim/R/scalar_dat.r |only
ss3sim-0.8.2/ss3sim/R/ss3sim_base.r | 21 --
ss3sim-0.8.2/ss3sim/R/ts_dat.r |only
ss3sim-0.8.2/ss3sim/README.md | 132 ++++++++-----
ss3sim-0.8.2/ss3sim/build/vignette.rds |binary
ss3sim-0.8.2/ss3sim/data |only
ss3sim-0.8.2/ss3sim/inst/CITATION | 10
ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.R | 22 +-
ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.Rnw | 191 +++++++++----------
ss3sim-0.8.2/ss3sim/inst/doc/ss3sim-vignette.pdf |binary
ss3sim-0.8.2/ss3sim/inst/extdata/eg-cases/R1-cod.txt |only
ss3sim-0.8.2/ss3sim/inst/ss3-tests |only
ss3sim-0.8.2/ss3sim/inst/tests/test-user-recdevs.R |only
ss3sim-0.8.2/ss3sim/man/get_recdevs.Rd | 5
ss3sim-0.8.2/ss3sim/man/run_ss3sim.Rd | 28 ++
ss3sim-0.8.2/ss3sim/man/scalar_dat.Rd |only
ss3sim-0.8.2/ss3sim/man/ss3sim_base.Rd | 10
ss3sim-0.8.2/ss3sim/man/ts_dat.Rd |only
ss3sim-0.8.2/ss3sim/vignettes/refs.bib | 18 -
ss3sim-0.8.2/ss3sim/vignettes/solarized-light.css |only
ss3sim-0.8.2/ss3sim/vignettes/ss3sim-vignette.Rnw | 191 +++++++++----------
27 files changed, 402 insertions(+), 305 deletions(-)
Title: Analyze and Gaussianize skewed, heavy-tailed data
Diff between LambertW versions 0.2.9.9 dated 2012-01-07 and 0.2.9.9.5 dated 2014-03-09
Description: The Lambert W framework is a new generalized way to analyze skewed, heavy-tailed data. Lambert W random variables (RV) are based on an input/output framework where the input is a RV X with distribution F(x), and the output Y = func(X) has similar properties as X (but slightly skewed or heavy-tailed). Then this transformed RV Y has a Lambert W x F distribution - for details see References. This package contains functions to perform a Lambert W analysis of skewed and heavy-tailed data: data can be simulated, parameters can be estimated from real world data, quantiles can be computed, and results plotted/printed in a 'nice' way. Probably the most important function is 'Gaussianize', which works the same way as the R function 'scale' but actually makes your data Gaussian. An optional modular toolkit implementation allows users to define their own Lambert W x 'my favorite distribution' and use it for their analysis.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
DESCRIPTION | 16 +--
MD5 | 46 ++++-----
NAMESPACE | 5 +
R/MLE_LambertW_new.R | 200 ++++++++++++++++++++--------------------
R/create_LambertW_input.R | 4
R/plot.LambertW_fit.R | 196 +++++++++++++++++++--------------------
R/plot.LambertW_input.R | 71 ++++++--------
R/plot.LambertW_output.R | 203 ++++++++++++++++++++---------------------
man/Gaussianize.Rd | 115 +++++++++++------------
man/IGMM.Rd | 10 +-
man/LambertW-methods.Rd | 51 ++++++----
man/LambertW-package.Rd | 10 +-
man/LambertW_output-methods.Rd | 71 +++++++-------
man/MLE_LambertW.Rd | 139 ++++++++++++++--------------
man/U-methods.Rd | 8 +
man/create_LambertW_output.Rd | 20 ++--
man/delta_01.Rd | 72 +++++++-------
man/delta_GMM.Rd | 5 -
man/delta_Taylor.Rd | 14 ++
man/gamma_01.Rd | 70 +++++++-------
man/gamma_GMM.Rd | 7 +
man/gamma_Taylor.Rd | 4
man/loglik-utils.Rd | 21 +++-
man/p_1.Rd | 144 +++++++++++++++--------------
24 files changed, 790 insertions(+), 712 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
Diff between aroma.affymetrix versions 2.11.1 dated 2013-10-18 and 2.12.0 dated 2014-03-09
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the disk space that limits the number of arrays that can be analyzed.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson
aroma.affymetrix-2.11.1/aroma.affymetrix/inst/NEWS |only
aroma.affymetrix-2.12.0/aroma.affymetrix/DESCRIPTION | 38 -
aroma.affymetrix-2.12.0/aroma.affymetrix/MD5 | 314 +++++----
aroma.affymetrix-2.12.0/aroma.affymetrix/NAMESPACE | 5
aroma.affymetrix-2.12.0/aroma.affymetrix/NEWS |only
aroma.affymetrix-2.12.0/aroma.affymetrix/R/999.AromaAffymetrix.R | 41 -
aroma.affymetrix-2.12.0/aroma.affymetrix/R/999.DEPRECATED.R | 162 -----
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCdfFile.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCelFile.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCelSet.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCelSet.getAverageFile.R | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCelSetReporter.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCnChpFile.R | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixCnChpSet.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixPgfFile.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AffymetrixProbeTabFile.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ArrayExplorer.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ChipEffectFile.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ChipEffectSet.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ChipEffectSet.getBaseline.R | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/R/CnagCfhFile.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/CnagCfhSet.R | 5
aroma.affymetrix-2.12.0/aroma.affymetrix/R/DChipCdfBinFile.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/DChipDcpFile.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/R/DChipDcpSet.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/DChipQuantileNormalization.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/FirmaModel.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/GenericReporter.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/GenomeInformation.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/Model.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ProbeAffinityFile.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/QualityAssessmentModel.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/QuantileNormalization.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ResidualFile.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/ResidualSet.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/SmoothMultiarrayModel.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/SnpInformation.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/SpatialReporter.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/R/TransformReport.R | 3
aroma.affymetrix-2.12.0/aroma.affymetrix/R/WeightsFile.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/WeightsSet.R | 1
aroma.affymetrix-2.12.0/aroma.affymetrix/R/pdInfo2Cdf.R | 27
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UFL.R | 96 ++-
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,UGP.R | 102 +--
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,default,UGP+UFL.R | 28
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na32 |only
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/buildScripts/chipTypes/GenomeWideSNP_6/na33 |only
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/R/launchUtils.R | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/launch.R | 23
aroma.affymetrix-2.12.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R | 15
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AdditiveCovariatesNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffineCnPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffinePlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffineSnpPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixCdfFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixCelFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixCelSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixCelSetReporter.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixCnChpSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixFileSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixFileSetReporter.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixPgfFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AffymetrixProbeTabFile.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AlleleSummation.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AllelicCrosstalkCalibration.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AromaChipTypeAnnotationFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ArrayExplorer.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AvgCnPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AvgPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/AvgSnpPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/BackgroundCorrection.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/BaseCountNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/BasePositionNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ChipEffectFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ChipEffectGroupMerge.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ChipEffectSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ChipEffectTransform.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CnChipEffectFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CnChipEffectSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CnProbeAffinityFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CnagCfhFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CnagCfhSet.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CrlmmParametersFile.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/CrlmmParametersSet.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/DChipCdfBinFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/DChipDcpFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/DChipDcpSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/DChipGenomeInformation.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/DChipQuantileNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/DChipSnpInformation.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ExonChipEffectFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ExonChipEffectSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ExonProbeAffinityFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ExonRmaPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/FirmaFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/FirmaModel.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/FirmaSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/FragmentEquivalentClassNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/FragmentLengthNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/GcContentNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/GcContentNormalization2.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/GenericReporter.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/GenomeInformation.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/HetLogAddCnPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/HetLogAddPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/HetLogAddSnpPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/LinearModelProbeSequenceNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/MatNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/MatSmoothing.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/MbeiCnPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/MbeiPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/MbeiSnpPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/Model.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/MultiArrayUnitModel.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/Non-documented_objects.Rd | 315 +++-------
aroma.affymetrix-2.12.0/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/OpticalBackgroundCorrection.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ParameterCelFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ParameterCelSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ProbeAffinityFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ProbeLevelModel.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ProbeLevelTransform.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ProbeLevelTransform3.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/QualityAssessmentFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/QualityAssessmentModel.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/QualityAssessmentSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/QuantileNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ReseqCrosstalkCalibration.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ResidualFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ResidualSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/RmaBackgroundCorrection.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/RmaCnPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/RmaPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/RmaSnpPlm.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ScaleNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/ScaleNormalization3.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SingleArrayUnitModel.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SmoothMultiarrayModel.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SmoothRmaModel.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SnpChipEffectFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SnpChipEffectGroupMerge.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SnpChipEffectSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SnpInformation.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SnpProbeAffinityFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/SpatialReporter.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/TransformReport.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/UgpGenomeInformation.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/UnitModel.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/UnitTypeScaleNormalization.Rd | 2
aroma.affymetrix-2.12.0/aroma.affymetrix/man/WeightsFile.Rd | 4
aroma.affymetrix-2.12.0/aroma.affymetrix/man/WeightsSet.Rd | 6
aroma.affymetrix-2.12.0/aroma.affymetrix/man/pdInfo2Cdf.Rd | 93 +-
158 files changed, 761 insertions(+), 958 deletions(-)
Permanent link
Title: Segregation measures for multitype spatial point patterns
Diff between spatialsegregation versions 2.38 dated 2012-05-10 and 2.40 dated 2014-03-09
More information about spatialsegregation at CRAN
Description: Summaries for measuring segregation/mingling in multitype spatial point patterns with graph based neighbourhood description.
Included indices: Mingling, Shannon, Simpson (also the non-spatial)
Included functionals: Mingling, Shannon, Simpson, ISAR, MCI.
Included neighbourhoods: Geometric, k-nearest neighbours, Gabriel, Delaunay.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala
spatialsegregation-2.38/spatialsegregation/.cproject |only
spatialsegregation-2.38/spatialsegregation/.project |only
spatialsegregation-2.38/spatialsegregation/R/tests.R |only
spatialsegregation-2.38/spatialsegregation/change.log |only
spatialsegregation-2.38/spatialsegregation/toadd.txt |only
spatialsegregation-2.40/spatialsegregation/DESCRIPTION | 19 ++++------
spatialsegregation-2.40/spatialsegregation/MD5 | 12 ++----
spatialsegregation-2.40/spatialsegregation/NAMESPACE | 4 +-
spatialsegregation-2.40/spatialsegregation/R/bivariate_tests.R |only
spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-exposurepps.Rd | 10 +++++
spatialsegregation-2.40/spatialsegregation/man/spatialsegregation-segregationFun.Rd | 6 +--
11 files changed, 29 insertions(+), 22 deletions(-)
Permanent link
Title: Spatial Graph based Clustering Summaries for spatial point
patterns
Diff between SGCS versions 1.7 dated 2012-04-08 and 2.0 dated 2014-03-09
Description: Graph based clustering summaries for spatial point patterns. Includes Connectivity function,
Cumulative connectivity function and clustering function, plus the triplet intensity function T (and some other).
Author: Tuomas Rajala
Maintainer: Tuomas Rajala
SGCS-1.7/SGCS/.cproject |only
SGCS-1.7/SGCS/.project |only
SGCS-1.7/SGCS/R/test_components.R |only
SGCS-1.7/SGCS/change.log |only
SGCS-1.7/SGCS/src/test_comp.cpp |only
SGCS-2.0/SGCS/DESCRIPTION | 15 ++++++------
SGCS-2.0/SGCS/MD5 | 38 ++++++++++++++++----------------
SGCS-2.0/SGCS/NAMESPACE | 4 +--
SGCS-2.0/SGCS/R/Kfun.R |only
SGCS-2.0/SGCS/R/clustfun.R | 18 +++++++++++----
SGCS-2.0/SGCS/R/fun.R | 44 +++++++++++++++++++++++++++++---------
SGCS-2.0/SGCS/man/SGCS-funs.Rd | 21 ++++++++++++++----
SGCS-2.0/SGCS/man/SGCS-package.Rd | 1
SGCS-2.0/SGCS/src/Clustfun.cpp | 4 ++-
SGCS-2.0/SGCS/src/Confun.cpp | 3 ++
SGCS-2.0/SGCS/src/Confun.h | 1
SGCS-2.0/SGCS/src/Fun.cpp | 25 ++++++++++++++++++++-
SGCS-2.0/SGCS/src/Fun.h | 5 +++-
SGCS-2.0/SGCS/src/Graph.cpp | 4 +--
SGCS-2.0/SGCS/src/Kfun.cpp |only
SGCS-2.0/SGCS/src/Kfun.h |only
SGCS-2.0/SGCS/src/Pp.cpp | 40 ++++++++++++++++++----------------
SGCS-2.0/SGCS/src/Pp.h | 5 ++--
SGCS-2.0/SGCS/src/Tfun.cpp | 4 ++-
SGCS-2.0/SGCS/src/rfun.cpp | 22 ++++++++++---------
25 files changed, 168 insertions(+), 86 deletions(-)
Title: Detect and Test Regular Sequences and Subsequences
Diff between regsubseq versions 0.10 dated 2007-09-30 and 0.12 dated 2014-03-09
Description: For a sequence of event occurence times, we are interested in
finding subsequences in it that are too "regular". We define regular as being
significantly different from a homogeneous Poisson process. The departure from
the Poisson process is measured using a L1 distance. See Di and Perlman 2007
for more details.
Author: Yanming Di
Maintainer: Yanming Di
DESCRIPTION | 14 +++++++++-----
MD5 |only
NAMESPACE |only
R/sysdata.rda |binary
4 files changed, 9 insertions(+), 5 deletions(-)
Title: Algorithms and framework for Nonnegative Matrix Factorization
(NMF)
Diff between NMF versions 0.20 dated 2013-11-01 and 0.20.2 dated 2014-03-09
Description: This package provides a framework to perform Non-negative Matrix
Factorization (NMF). It implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux
DESCRIPTION | 39 +++-----
MD5 | 178 ++++++++++++++++++-------------------
NAMESPACE | 60 ++++++------
NEWS | 11 ++
R/NMF-class.R | 7 +
R/NMFSet-class.R | 2
R/NMFStrategy-class.R | 1
R/NMFStrategyIterative-class.R | 2
R/NMFStrategyOctave-class.R | 4
R/NMFplots.R | 21 ++--
R/aheatmap.R | 144 ++++++++++++++++++++---------
R/algorithms-brunet.R | 5 -
R/algorithms-snmf.R | 4
R/nmf.R | 2
R/options.R | 6 +
R/parallel.R | 83 +++++++++++++----
demo/aheatmap.R | 8 +
inst/doc/NMF-unitTests.Rnw | 197 ++++++++++++++++++++---------------------
inst/doc/NMF-unitTests.pdf |binary
inst/doc/NMF-vignette.R | 8 -
inst/doc/NMF-vignette.Rnw | 10 +-
inst/doc/NMF-vignette.pdf |binary
inst/doc/consensus.pdf |binary
inst/doc/heatmaps.pdf |binary
inst/m-files/brunet.m | 7 +
inst/tests/runit.interface.r | 6 -
man/Frobenius-nmf.Rd | 9 +
man/KL-nmf.Rd | 9 +
man/NMF-class.Rd | 9 +
man/NMF-package.Rd | 4
man/NMFOffset-class.Rd | 4
man/NMFStrategy.Rd | 3
man/NMFfit-class.Rd | 4
man/NMFfitX-class.Rd | 4
man/NMFfitX1-class.Rd | 4
man/NMFfitXn-class.Rd | 4
man/NMFns-class.Rd | 10 +-
man/NMFstd-class.Rd | 4
man/RNG.Rd | 4
man/aheatmap.Rd | 18 ++-
man/algorithmic.Rd | 18 ++-
man/assess.Rd | 4
man/basis-coef-methods.Rd | 4
man/basiscor.Rd | 4
man/connectivity.Rd | 4
man/dimnames.Rd | 9 -
man/esGolub.Rd | 4
man/fcnnls.Rd | 10 +-
man/fitted.Rd | 4
man/foreach.Rd | 20 ++++
man/grid.Rd | 6 -
man/heatmaps.Rd | 12 --
man/lsNMF-nmf.Rd | 6 -
man/nmf-compare.Rd | 4
man/nmf.Rd | 4
man/nmfAlgorithm.Rd | 4
man/nmfCheck.Rd | 4
man/nmfEstimateRank.Rd | 12 +-
man/nmfFormals.Rd | 4
man/nmfModel.Rd | 4
man/nmfReport.Rd | 4
man/nmfSeed.Rd | 4
man/nmfWrapper.Rd | 4
man/nmf_update_KL.Rd | 8 -
man/nmf_update_euclidean.Rd | 10 +-
man/nneg.Rd | 4
man/nsNMF-nmf.Rd | 18 ++-
man/offset-nmf.Rd | 16 +--
man/options.Rd | 12 ++
man/predict.Rd | 4
man/profplot.Rd | 4
man/purity.Rd | 10 +-
man/randomize.Rd | 4
man/rmatrix.Rd | 4
man/rnmf.Rd | 4
man/rss.Rd | 4
man/scale.NMF.Rd | 4
man/scores.Rd | 4
man/setNMFMethod.Rd | 4
man/silhouette.NMF.Rd | 8 +
man/smoothing.Rd | 4
man/stop-NMF.Rd | 12 +-
man/subset-NMF.Rd | 10 +-
man/syntheticNMF.Rd | 4
man/t.NMF.Rd | 4
man/types.Rd | 12 +-
man/utils.Rd | 4
tests/doRUnit.R | 5 -
vignettes/NMF-unitTests.Rnw | 197 ++++++++++++++++++++---------------------
vignettes/NMF-vignette.Rnw | 10 +-
90 files changed, 903 insertions(+), 529 deletions(-)
Title: gpairs: The Generalized Pairs Plot
Diff between gpairs versions 1.1 dated 2012-02-20 and 1.2 dated 2014-03-09
Description: Produces a generalized pairs (gpairs) plot.
Author: John W. Emerson and Walton A. Green
Maintainer: John W. Emerson
DESCRIPTION | 13
MD5 | 10
NAMESPACE | 1
R/gpairs.R | 1341 ++++++++++++++++++++++++++++----------------------------
data/Leaves.rda |binary
man/gpairs.Rd | 4
6 files changed, 690 insertions(+), 679 deletions(-)
Title: Burns Statistics Financial
Diff between BurStFin versions 1.01 dated 2012-02-12 and 1.02 dated 2014-03-09
Description: A suite of functions for finance, including the estimation
of variance matrices via a statistical factor model or
Ledoit-Wolf shrinkage.
Author: Burns Statistics
Maintainer: Pat Burns
DESCRIPTION | 14 +++--
MD5 | 20 ++++----
NAMESPACE | 2
R/factor.model.stat.R | 115 ++++++++++++++++++++++++++---------------------
R/slideWeight.R |only
R/threeDarr.R | 4 -
R/var.add.benchmark.R | 7 +-
R/var.shrink.eqcor.R | 49 +++++++++++---------
inst/NEWS | 43 +++++++++++++++++
man/factor.model.stat.Rd | 31 +++++++++---
man/slideWeight.Rd |only
man/var.shrink.eqcor.Rd | 20 +++++---
12 files changed, 198 insertions(+), 107 deletions(-)
Title: R interface to the QuantLib library
Diff between RQuantLib versions 0.3.11 dated 2014-01-27 and 0.3.12 dated 2014-03-09
Description: The RQuantLib package makes parts of QuantLib visible to the R
user. Currently a number option pricing functions are included, both vanilla
and exotic, as well as a broad range of fixed-income functions. Also included
are general calendaring and holiday utilities. Further software contributions
are welcome.
The QuantLib project aims to provide a comprehensive software framework for
quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of
financial assets.
The Windows binary version is self-contained and does not require a QuantLib
(or Boost) installation.
RQuantLib uses the Rcpp R/C++ interface class library. See the Rcpp package
on CRAN (or R-Forge) for more information on Rcpp.
Note that while RQuantLib's code is licensed under the GPL (v2 or later),
QuantLib itself is released under a somewhat less restrictive Open Source
license (see QuantLib-License.txt).
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 31 ++++
DESCRIPTION | 10 -
MD5 | 18 +-
NAMESPACE | 4
R/inline.R | 47 +++---
configure | 378 ++++++++++++++++++++++++-------------------------
configure.in | 49 +++---
man/FittedBondCurve.Rd | 7
src/Makevars.in | 5
src/Makevars.win | 9 -
10 files changed, 304 insertions(+), 254 deletions(-)
Title: Methods for patient-centered network meta-analysis
Diff between pcnetmeta versions 1.0 dated 2014-01-18 and 1.1 dated 2014-03-09
Description: Provides functions to conduct network meta-analysis using arm-based method, which was proposed by Zhang et al (2013); contains functions to generate summary table for effect sizes (e.g., odds ratio, population-averaged event rate), plot network comparisons, and plot credible interval for population-averaged event rate.
Author: Lifeng Lin, Jing Zhang
Maintainer: Lifeng Lin
DESCRIPTION | 12 ++--
MD5 | 30 +++++-----
NAMESPACE | 2
R/ci.plot.R | 10 ++-
R/create.tab.R | 21 ++++---
R/nma.ab.R | 129 ++++++++++++++++++++++++++++-------------------
R/nma.networkplot.R | 4 -
data/Ara09.rda |binary
man/Ara09.Rd | 8 +-
man/Lam07.Rd | 6 +-
man/Lam07.Summary.Rd | 4 -
man/ci.plot.Rd | 11 ++--
man/create.tab.Rd | 19 +++---
man/nma.ab.Rd | 115 ++++++++++++++++++++++++++++-------------
man/nma.networkplot.Rd | 9 ++-
man/pcnetmeta-package.Rd | 22 +++++---
16 files changed, 248 insertions(+), 154 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-114 dated 2014-03-08 and 3.1-115 dated 2014-03-09
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core
nlme-3.1-114/nlme/man/lmeScale.Rd |only
nlme-3.1-115/nlme/ChangeLog | 13 +++++++++-
nlme-3.1-115/nlme/DESCRIPTION | 8 +++---
nlme-3.1-115/nlme/MD5 | 25 +++++++++-----------
nlme-3.1-115/nlme/NAMESPACE | 2 -
nlme-3.1-115/nlme/R/gls.R | 11 ++------
nlme-3.1-115/nlme/R/gnls.R | 11 ++------
nlme-3.1-115/nlme/R/lme.R | 31 +++----------------------
nlme-3.1-115/nlme/R/nlme.R | 12 +++------
nlme-3.1-115/nlme/man/glsControl.Rd | 21 +++++------------
nlme-3.1-115/nlme/man/gnlsControl.Rd | 23 ++++++------------
nlme-3.1-115/nlme/man/lme.Rd | 12 +++++----
nlme-3.1-115/nlme/man/lmeControl.Rd | 42 +++++++++++++++-------------------
nlme-3.1-115/nlme/man/nlmeControl.Rd | 43 +++++++++++++++--------------------
14 files changed, 103 insertions(+), 151 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 1.7-1282 dated 2014-03-07 and 1.7-1286 dated 2014-03-09
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumented variables, robust and multi-way clustered standard errors.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
lfe-1.7-1282/lfe/tests/Examples |only
lfe-1.7-1286/lfe/DESCRIPTION | 8
lfe-1.7-1286/lfe/MD5 | 20
lfe-1.7-1286/lfe/build/autoconf/install-sh | 668 ++++++++-------------------
lfe-1.7-1286/lfe/configure | 18
lfe-1.7-1286/lfe/inst/doc/identification.pdf |binary
lfe-1.7-1286/lfe/inst/doc/lfehow.pdf |binary
lfe-1.7-1286/lfe/inst/doc/speed.pdf |binary
lfe-1.7-1286/lfe/src/Makevars.in | 2
lfe-1.7-1286/lfe/src/Makevars.win |only
lfe-1.7-1286/lfe/src/lfe.c | 3
lfe-1.7-1286/lfe/tests/efcheck.R | 2
12 files changed, 230 insertions(+), 491 deletions(-)
Title: Efficient selection of undirected graphical models for
high-dimensional datasets
Diff between gRapHD versions 0.2.3 dated 2013-04-14 and 0.2.4 dated 2014-03-09
Description: gRapHD is designed for efficient selection of high-dimensional undirected
graphical models. The package provides tools for selecting trees, forests
and decomposable models minimizing information criteria such as AIC or BIC,
and for displaying the independence graphs of the models. It has also some
useful tools for analysing graphical structures. It supports the use of
discrete, continuous, or both types of variables.
Author: Gabriel Coelho Goncalves de Abreu
Maintainer: Gabriel Coelho Goncalves de Abreu
DESCRIPTION | 28 ++++++++++++----------------
MD5 | 6 +++---
NAMESPACE | 2 +-
R/functions.r | 2 +-
4 files changed, 17 insertions(+), 21 deletions(-)
Title: Straightforward BibTeX and BibLaTeX Bibliography Management
Diff between RefManageR versions 0.7.2 dated 2014-02-28 and 0.8.1 dated 2014-03-09
Description: RefManageR provides tools for importing and working with
bibliographic references. It greatly enhances the bibentry class by
providing a class BibEntry which stores BibTeX and BibLaTeX references,
supports UTF-8 encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. BibTeX and BibLaTeX .bib files
can be read into R and converted to BibEntry objects. Interfaces to NCBI's
Entrez, CrossRef, and Zotero are provided for importing references and
references can be created from locally stored PDFs using Poppler. Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with RMarkdown or RHTML.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean
DESCRIPTION | 11 ++++---
MD5 | 64 ++++++++++++++++++++++++++++---------------
R/05makeBibLatex.R | 6 +++-
R/07makeBibLatexAuthoryear.R | 6 +++-
R/BibEntryExtractOp.R | 2 -
R/NamesAssign.R | 2 -
R/ReadBib.R | 2 -
R/ReadCrossRef.R | 18 ++++++------
R/ReadPubMed.R | 24 +++++++++-------
R/RefManageR-package.R | 2 -
R/SearchBib.R | 3 +-
R/WriteBib.R | 4 +-
R/open.BibEntry.R | 21 ++++++--------
R/rmdCite.R | 2 -
R/toBibtex.R | 30 ++++++++++++--------
build |only
inst/NEWS |only
inst/doc |only
man/Cite.Rd | 2 -
man/GetPubMedRelated.Rd | 8 ++++-
man/LookupPubMedID.Rd | 2 -
man/ReadCrossRef.Rd | 27 +++++++++---------
man/RefManageR-package.Rd | 4 +-
man/SearchBib.Rd | 6 ++--
man/open.BibEntry.Rd | 2 -
vignettes |only
26 files changed, 149 insertions(+), 99 deletions(-)
Title: Targeted Maximum Likelihood Estimation
Diff between tmle versions 1.2.0-3 dated 2012-11-15 and 1.2.0-4 dated 2014-03-09
Description: tmle implements targeted maximum likelihood estimation, first described in van der Laan and Rubin, 2006 (Targeted Maximum Likelihood Learning, The International Journal of biostatistics, 2(1), 2006. This version adds the tmleMSM function to the package, for estimating the parameters of a marginal structural model (MSM) for a binary point treatment effect. The tmle function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. Effect estimation stratified by a binary mediating variable is also available. The population mean is calculated when there is missingness, and no variation in the treatment assignment. An ID argument can be used to identify repeated measures. Default settings call SuperLearner to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
Author: Susan Gruber, in collaboration with Mark van der Laan
Maintainer: Susan Gruber
DESCRIPTION | 38 ++++++++---------------------
LICENSE |only
MD5 | 31 ++++++++++++------------
NAMESPACE | 3 ++
NEWS | 4 +++
R/tmle.R | 59 +++++++++++++++++++++-------------------------
man/SL.glm.interaction.Rd | 2 -
man/calcParameters.Rd | 2 -
man/calcSigma.Rd | 10 ++++---
man/estimateG.Rd | 2 -
man/estimateQ.Rd | 2 -
man/summary.tmle.Rd | 2 -
man/summary.tmleMSM.Rd | 2 -
man/tmle-package.Rd | 2 -
man/tmle.Rd | 8 +++---
man/tmleMSM.Rd | 2 -
man/tmleNews.Rd | 2 -
17 files changed, 81 insertions(+), 90 deletions(-)
Title: Linked Micromap Plots for U. S. States
Diff between micromapST versions 1.0.2 dated 2014-01-11 and 1.0.3 dated 2014-03-09
Description: This package provides the users the ability to quickly create Linked
Micromap plots of the 50 U.S. states and District of Columbia (51 areas).
Linked Micromaps are visualizations of georeferenced data that link statistical
graphics to an organized series of small maps.
The Help description contains examples of how to use the micromapST function.
This package contains the US and State boundary files and FIPS/State conversion tables
used by the micromapST function and several data sets used in the micromapST examples.
Copyrighted 2013 and 2014 by Carr, Pearson and Pickle.
Author: Dan Carr
Maintainer: Jim Pearson
DESCRIPTION | 10
MD5 | 16
NEWS | 84 ++-
R/micromapST.r | 1115 +++++++++++++++++++++++++++----------------
R/panelFunctions.r | 117 +++-
man/micromapST-package.Rd | 19
man/micromapSTDefaults.Rd | 88 +--
man/micromapSTSetDefaults.Rd | 6
man/panelDesc.Rd | 29 -
9 files changed, 957 insertions(+), 527 deletions(-)