Title: Multi-States Semi-Markov Models
Diff between SemiMarkov versions 1.2 dated 2013-05-13 and 1.3 dated 2014-04-09
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol
DESCRIPTION | 23 -
MD5 | 30 +-
NAMESPACE | 2
R/SemiMarkov.R | 622 ++++++++++++++++++++++++++++++++--------------
data/asthma.rda |binary
man/asthma.rd | 2
man/hazard.Rd | 2
man/param.init.Rd | 2
man/plot.hazard.Rd | 2
man/print.hazard.Rd | 2
man/print.semiMarkov.Rd | 2
man/semiMarkov.Rd | 20 -
man/summary.hazard.Rd | 2
man/summary.semiMarkov.Rd | 2
man/table.state.rd | 2
tests/test.R | 1
16 files changed, 487 insertions(+), 229 deletions(-)
Title: yaImpute: An R Package for k-NN Imputation
Diff between yaImpute versions 1.0-20 dated 2013-11-27 and 1.0-21 dated 2014-04-09
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston
DESCRIPTION | 12 +++---
MD5 | 22 ++++++------
NEWS | 17 ++++++++-
R/asciigridimpute.R | 82 ++++++++++++++++++++++++++---------------------
R/grmsd.R | 15 ++++++--
R/yai.R | 58 +++++++++++++++++++++++++--------
R/yaiVarImp.R | 8 ++--
data/MoscowMtStJoe.RData |binary
data/TallyLake.RData |binary
man/asciigridimpute.Rd | 30 ++++++++++-------
man/yai.Rd | 38 +++++++++++++++++----
man/yaiVarImp.Rd | 6 ++-
12 files changed, 193 insertions(+), 95 deletions(-)
Title: spsmooth: An Extension Package for 'mgcv'.
Diff between spsmooth versions 1.1-0 dated 2013-05-16 and 1.1-3 dated 2014-04-09
Description: Produces Slepian smoother basis objects for use in Generalized Additive Models, as estimated by package:mgcv.
Author: Wesley Burr, with contributions from Karim Rahim
Maintainer: Wesley Burr
spsmooth-1.1-0/spsmooth/gnugpl2.txt |only
spsmooth-1.1-0/spsmooth/src/Makevars.in |only
spsmooth-1.1-3/spsmooth/DESCRIPTION | 16 ++++++++--------
spsmooth-1.1-3/spsmooth/LICENSE |only
spsmooth-1.1-3/spsmooth/MD5 | 11 +++++------
spsmooth-1.1-3/spsmooth/R/spmgcv.R | 14 ++++++++++++++
spsmooth-1.1-3/spsmooth/man/spsmooth-package.Rd | 7 ++++---
spsmooth-1.1-3/spsmooth/src/Makevars.win | 2 +-
8 files changed, 32 insertions(+), 18 deletions(-)
Title: classes and methods for spatial data
Diff between sp versions 1.0-14 dated 2013-10-24 and 1.0-15 dated 2014-04-09
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb]
Maintainer: Edzer Pebesma
sp-1.0-14/sp/tests/Examples |only
sp-1.0-15/sp/ChangeLog |only
sp-1.0-15/sp/DESCRIPTION | 8
sp-1.0-15/sp/MD5 | 64
sp-1.0-15/sp/NAMESPACE | 2
sp-1.0-15/sp/R/CRS-methods.R | 18
sp-1.0-15/sp/R/Class-SpatialPoints.R | 1
sp-1.0-15/sp/R/Class-SpatialPointsDataFrame.R | 2
sp-1.0-15/sp/R/Spatial-methods.R | 6
sp-1.0-15/sp/R/SpatialGrid-methods.R | 48
sp-1.0-15/sp/R/SpatialLinesDataFrame-methods.R | 2
sp-1.0-15/sp/R/SpatialPoints-methods.R | 14
sp-1.0-15/sp/R/SpatialPointsDataFrame-methods.R | 19
sp-1.0-15/sp/R/disaggregate.R | 209 -
sp-1.0-15/sp/R/image.R | 49
sp-1.0-15/sp/R/merge.R | 16
sp-1.0-15/sp/R/rbind.R | 6
sp-1.0-15/sp/R/spsample.R | 36
sp-1.0-15/sp/R/zerodist.R | 60
sp-1.0-15/sp/build/vignette.rds |binary
sp-1.0-15/sp/inst/ChangeLog | 3525 ++++++++++++--------
sp-1.0-15/sp/inst/doc/csdacm.pdf |binary
sp-1.0-15/sp/inst/doc/intro_sp.pdf |binary
sp-1.0-15/sp/inst/doc/over.pdf |binary
sp-1.0-15/sp/man/GridTopology-class.Rd | 2
sp-1.0-15/sp/man/as.SpatialPolygons.GridTopology.Rd | 6
sp-1.0-15/sp/man/coordinates.Rd | 10
sp-1.0-15/sp/man/image.Rd | 8
sp-1.0-15/sp/man/spsample.Rd | 9
sp-1.0-15/sp/man/zerodist.Rd | 6
sp-1.0-15/sp/src/init.c | 1
sp-1.0-15/sp/src/sp.h | 1
sp-1.0-15/sp/src/zerodist.c | 63
sp-1.0-15/sp/tests/zerodist.Rout.save | 21
34 files changed, 2557 insertions(+), 1655 deletions(-)
Title: Multivariate Normal and t Distributions
Diff between mvtnorm versions 0.9-9997 dated 2014-01-17 and 0.9-9998 dated 2014-04-09
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch,
Fabian Scheipl, Bjoern Bornkamp, Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/mvnorm.R | 19 +++++++++++++------
build/vignette.rds |binary
inst/NEWS | 7 +++++--
inst/doc/MVT_Rnews.pdf |binary
6 files changed, 27 insertions(+), 17 deletions(-)
Title: Fitting exact conditional logistic regression with lasso and
elastic net penalties.
Diff between clogitL1 versions 1.1 dated 2013-09-24 and 1.2 dated 2014-04-09
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
Author: Stephen Reid and Robert Tibshirani
Maintainer: Stephen Reid
DESCRIPTION | 6 +++---
MD5 | 20 ++++++++++----------
NAMESPACE | 3 ++-
man/clogitL1-package.Rd | 2 +-
man/clogitL1.Rd | 2 +-
man/cv.clogitL1.Rd | 2 +-
man/plot.clogitL1.Rd | 2 +-
man/plot.cv.clogitL1.Rd | 2 +-
man/print.clogitL1.Rd | 2 +-
man/summary.clogitL1.Rd | 2 +-
man/summary.cv.clogitL1.Rd | 2 +-
11 files changed, 23 insertions(+), 22 deletions(-)
Title: ADMB for R Using Scripts or GUI
Diff between PBSadmb versions 0.66.87 dated 2013-05-15 and 0.68.104 dated 2014-04-09
Description: R Support for ADMB (Automatic Differentiation Model Builder)
Author: Jon T. Schnute
Maintainer: Rowan Haigh
PBSadmb-0.66.87/PBSadmb/inst/win/installWin.txt |only
PBSadmb-0.66.87/PBSadmb/man/installADMB.Rd |only
PBSadmb-0.68.104/PBSadmb/DESCRIPTION | 20
PBSadmb-0.68.104/PBSadmb/MD5 | 51
PBSadmb-0.68.104/PBSadmb/NAMESPACE | 13
PBSadmb-0.68.104/PBSadmb/R/PBSadmb.r | 2056 +++++++++---------
PBSadmb-0.68.104/PBSadmb/R/zzz.r | 7
PBSadmb-0.68.104/PBSadmb/inst/doc/ChangeLog.txt | 30
PBSadmb-0.68.104/PBSadmb/inst/doc/PBSadmbIntro.pdf |only
PBSadmb-0.68.104/PBSadmb/inst/doc/admb-re.pdf |binary
PBSadmb-0.68.104/PBSadmb/inst/doc/admb.pdf |binary
PBSadmb-0.68.104/PBSadmb/inst/doc/autodif.pdf |binary
PBSadmb-0.68.104/PBSadmb/inst/examples/ADpaths |only
PBSadmb-0.68.104/PBSadmb/inst/examples/ADpaths.txt |only
PBSadmb-0.68.104/PBSadmb/inst/examples/simple.pin | 2
PBSadmb-0.68.104/PBSadmb/inst/examples/simple_mc.pin | 2
PBSadmb-0.68.104/PBSadmb/inst/examples/simple_pbs.pin | 2
PBSadmb-0.68.104/PBSadmb/inst/examples/simple_pbs.r | 8
PBSadmb-0.68.104/PBSadmb/inst/examples/vonb.r | 8
PBSadmb-0.68.104/PBSadmb/inst/win/admbWin.txt | 64
PBSadmb-0.68.104/PBSadmb/man/admb.Rd | 33
PBSadmb-0.68.104/PBSadmb/man/compAD.Rd | 16
PBSadmb-0.68.104/PBSadmb/man/convAD.Rd | 16
PBSadmb-0.68.104/PBSadmb/man/linkAD.Rd | 16
PBSadmb-0.68.104/PBSadmb/man/makeAD.Rd | 17
PBSadmb-0.68.104/PBSadmb/man/readADopts.Rd | 2
PBSadmb-0.68.104/PBSadmb/man/readADpaths.Rd |only
PBSadmb-0.68.104/PBSadmb/man/setADMBPath.Rd | 13
PBSadmb-0.68.104/PBSadmb/man/setupAD.Rd |only
PBSadmb-0.68.104/PBSadmb/man/suggestPath.Rd |only
PBSadmb-0.68.104/PBSadmb/vignettes |only
31 files changed, 1258 insertions(+), 1118 deletions(-)
Title: Utilities for producing maps
Diff between mapmisc versions 0.9.3 dated 2014-02-27 and 0.9.4 dated 2014-04-09
Description: This package contains various utilities for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 15 ++++++---------
MD5 | 24 ++++++++++++------------
R/colourScale.R | 2 +-
R/insetMap.R | 8 ++++----
R/legendBreaks.R | 17 +++++++++++------
R/map.new.R | 5 +++--
R/openmap.R | 2 +-
R/utils.R | 12 ++++++------
build/vignette.rds |binary
inst/doc/mapLayers.pdf |binary
inst/doc/mapmisc.pdf |binary
man/openmap.Rd | 8 +++-----
vignettes/Makefile | 11 +++++------
13 files changed, 52 insertions(+), 52 deletions(-)
Title: Dynamic NETworks via integrative analysis of digitised data in
terms of network, ontology and evolution
Diff between dnet versions 0.99.0 dated 2014-03-25 and 1.0.0 dated 2014-04-09
Description: The 'dnet' package is initiated to fill in the need of an open-source tool for digitised data in an integrative manner. More specifically, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang
DESCRIPTION | 18 +-
MD5 | 112 +++++++------
NAMESPACE | 13 +
R/dDAGannotate.r |only
R/dDAGinduce.r |only
R/dDAGlevel.r |only
R/dDAGreverse.r |only
R/dDAGroot.r |only
R/dDAGtip.r |only
R/dEnricher.r |only
R/dGSEA.r | 260 ++++++++++++++++++-------------
R/dGSEAview.r | 2
R/dGSEAwrite.r | 2
R/dNetInduce.r | 18 +-
R/dNetPipeline.r | 3
R/dRWR.r | 174 +++++++++++++++++---
R/visDAG.r |only
R/visGSEA.r | 2
inst/NEWS | 10 -
inst/staticdocs/CITATIONs.md | 2
inst/staticdocs/INSTALLATIONs.md | 62 ++++---
inst/staticdocs/INSTALLATIONs_tmp.md |only
inst/staticdocs/RData.md |only
inst/staticdocs/README.md | 23 +-
inst/staticdocs/demo/CLL.r | 4
inst/staticdocs/demo/Fang.r | 15 -
inst/staticdocs/demo/Hiratani.r | 6
inst/staticdocs/demo/List_demos.txt | 1
inst/staticdocs/demo/TCGA.r |only
inst/staticdocs/docs.r | 136 ++++++++++++++--
inst/staticdocs/images/dnet_workflow.png |only
inst/staticdocs/templates/navbar.html | 3
man/dBUMfit.Rd | 46 ++---
man/dBUMscore.Rd | 40 ++--
man/dCommSignif.Rd | 16 -
man/dContrast.Rd | 8
man/dDAGannotate.Rd |only
man/dDAGinduce.Rd |only
man/dDAGlevel.Rd |only
man/dDAGreverse.Rd |only
man/dDAGroot.Rd |only
man/dDAGtip.Rd |only
man/dEnricher.Rd |only
man/dFDRscore.Rd | 13 -
man/dGSEA.Rd | 207 ++++++++++++++++--------
man/dGSEAview.Rd | 14 -
man/dGSEAwrite.Rd | 9 -
man/dNetConfidence.Rd | 26 +--
man/dNetFind.Rd | 108 ++++++------
man/dNetInduce.Rd | 34 +---
man/dNetPipeline.Rd | 34 +---
man/dNetReorder.Rd | 75 ++++----
man/dPvalAggregate.Rd | 23 +-
man/dRWR.Rd | 90 +++++-----
man/dSVDsignif.Rd | 24 +-
man/visColoralpha.Rd | 4
man/visColormap.Rd | 25 +-
man/visDAG.Rd |only
man/visGSEA.Rd | 20 +-
man/visHeatmap.Rd | 30 +--
man/visHeatmapAdv.Rd | 40 ++--
man/visNet.Rd | 19 --
man/visNetArc.Rd | 29 +--
man/visNetCircle.Rd | 28 +--
man/visNetMul.Rd | 17 --
man/visNetReorder.Rd | 21 +-
man/visTreeBootstrap.Rd | 177 ++++++++++-----------
67 files changed, 1191 insertions(+), 852 deletions(-)
Title: Three-way component analysis
Diff between ThreeWay versions 1.1.1 dated 2013-08-29 and 1.1.2 dated 2014-04-09
Description: Component analysis for three-way data arrays by means of Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models
Author: Maria Antonietta Del Ferraro, Henk A.L. Kiers, Paolo Giordani
Maintainer: Paolo Giordani
DESCRIPTION | 11 ++++------
MD5 | 45 ++++++++++++++++++++++----------------------
R/DimSelector.R | 23 ++++++++++------------
R/pcamean.R | 3 ++
data/Bus.rda |binary
data/TV.rda |binary
data/meaudret.rda |binary
inst |only
man/CP.Rd | 3 +-
man/CPdimensionalityplot.Rd | 6 ++---
man/CPfunc.Rd | 10 ++-------
man/CPfuncrep.Rd | 4 +--
man/DimSelector.Rd | 4 +--
man/LineCon.Rd | 4 +--
man/T1.Rd | 7 +++---
man/T2.Rd | 7 +++---
man/T2func.Rd | 9 +++-----
man/T2funcrep.Rd | 4 +--
man/T3.Rd | 7 +++---
man/T3dimensionalityplot.Rd | 4 +--
man/T3func.Rd | 4 +--
man/T3funcrep.Rd | 4 +--
man/pcamean.Rd | 4 +--
man/threewayanova.Rd | 2 -
24 files changed, 83 insertions(+), 82 deletions(-)
Title: Hierarchical and grouped time series
Diff between hts versions 4.1 dated 2014-03-07 and 4.2 dated 2014-04-09
Description: Methods for analysing and forecasting hierarchical and grouped time series.
Author: Rob J Hyndman, Earo Wang and Alan Lee with contributions from Roman A Ahmed and Han Lin Shang to earlier versions of the package
Maintainer: Rob J Hyndman
hts-4.1/hts/README.md |only
hts-4.2/hts/ChangeLog | 4 +++
hts-4.2/hts/DESCRIPTION | 6 ++---
hts-4.2/hts/MD5 | 17 +++++++--------
hts-4.2/hts/R/accuracy.gts.R | 8 ++-----
hts-4.2/hts/R/forecast.gts.R | 44 ++++++++++++++--------------------------
hts-4.2/hts/R/plot.gts.R | 6 +++--
hts-4.2/hts/build/vignette.rds |binary
hts-4.2/hts/inst/doc/hts.pdf |binary
hts-4.2/hts/man/accuracy.gts.Rd | 2 -
10 files changed, 39 insertions(+), 48 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining with R
Diff between FactoMineR versions 1.25 dated 2013-05-09 and 1.26 dated 2014-04-09
Description: an R package for exploratory data analysis
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson
FactoMineR-1.25/FactoMineR/FactoMineR-Ex.R |only
FactoMineR-1.26/FactoMineR/DESCRIPTION | 10 -
FactoMineR-1.26/FactoMineR/MD5 | 71 ++++-----
FactoMineR-1.26/FactoMineR/NAMESPACE | 5
FactoMineR-1.26/FactoMineR/R/AovSum.r | 2
FactoMineR-1.26/FactoMineR/R/CA.R | 3
FactoMineR-1.26/FactoMineR/R/HCPC.R | 32 ++--
FactoMineR-1.26/FactoMineR/R/HMFA.R | 2
FactoMineR-1.26/FactoMineR/R/MFA.R | 2
FactoMineR-1.26/FactoMineR/R/PCA.R | 3
FactoMineR-1.26/FactoMineR/R/RegBest.r | 2
FactoMineR-1.26/FactoMineR/R/dimdesc.r | 16 +-
FactoMineR-1.26/FactoMineR/R/plot.CA.R | 6
FactoMineR-1.26/FactoMineR/R/plot.GPA.R | 2
FactoMineR-1.26/FactoMineR/R/plot.HCPC.R | 2
FactoMineR-1.26/FactoMineR/R/plot.MCA.R | 6
FactoMineR-1.26/FactoMineR/R/plot.MFA.R | 18 +-
FactoMineR-1.26/FactoMineR/R/plot.PCA.R | 6
FactoMineR-1.26/FactoMineR/R/plotellipses.r | 16 +-
FactoMineR-1.26/FactoMineR/R/summary.FAMD.r | 15 +-
FactoMineR-1.26/FactoMineR/R/summary.MCA.r | 20 +-
FactoMineR-1.26/FactoMineR/R/summary.MFA.r | 15 +-
FactoMineR-1.26/FactoMineR/R/summary.PCA.r | 13 -
FactoMineR-1.26/FactoMineR/R/svd.triplet.R | 72 +++++++---
FactoMineR-1.26/FactoMineR/inst/doc/FactoMineR.pdf |binary
FactoMineR-1.26/FactoMineR/inst/doc/clustering_and_pricipal_component_methods.pdf |binary
FactoMineR-1.26/FactoMineR/man/AovSum.Rd | 6
FactoMineR-1.26/FactoMineR/man/coeffRV.Rd | 3
FactoMineR-1.26/FactoMineR/man/plot.CA.Rd | 2
FactoMineR-1.26/FactoMineR/man/plot.MCA.Rd | 4
FactoMineR-1.26/FactoMineR/man/plot.MFA.Rd | 2
FactoMineR-1.26/FactoMineR/man/plot.MFApartial.Rd | 2
FactoMineR-1.26/FactoMineR/man/plot.PCA.Rd | 2
FactoMineR-1.26/FactoMineR/man/summary.FAMD.Rd | 8 -
FactoMineR-1.26/FactoMineR/man/summary.MCA.Rd | 8 -
FactoMineR-1.26/FactoMineR/man/summary.MFA.Rd | 8 -
FactoMineR-1.26/FactoMineR/man/summary.PCA.Rd | 8 -
37 files changed, 237 insertions(+), 155 deletions(-)
Title: Likelihood inference in meta-analysis and meta-regression
models.
Diff between metaLik versions 0.40.0 dated 2014-01-31 and 0.41.0 dated 2014-04-09
Description: first- and higher-order likelihood inference in
meta-analysis and meta-regression models.
Author: Annamaria Guolo and Cristiano Varin
Maintainer: Cristiano Varin
DESCRIPTION | 6 ++--
MD5 | 14 ++++-----
NEWS | 9 +++++-
R/metaLik.R | 69 ++++++++++++++++++++++++++++++++-----------------
man/metaLik.Rd | 6 ++--
man/profile.metaLik.Rd | 10 +++++--
man/summary.metaLik.Rd | 16 +----------
man/test.metaLik.Rd | 15 ++++++----
8 files changed, 86 insertions(+), 59 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Diff between DoE.base versions 0.26 dated 2014-02-19 and 0.26-1 dated 2014-04-09
Description: This package creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides some utility functions used also by other DoE packages.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/printandsummary.design.R | 43 +++++++++++++++++++++++++------------------
inst/NEWS | 5 +++++
4 files changed, 37 insertions(+), 25 deletions(-)
Title: TSdbi extension for importing time series from web sources via
JSON
Diff between TSjson versions 2013.9-1 dated 2013-09-29 and 2014.4-1 dated 2014-04-09
Description: Provides methods for generics in the TSdbi package to
retrieve data from web data sources, importing them using Javascript
object notation. Direct connections or a proxy connection are
possible. (Only Statistics Canada connections are currently supported.)
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
TSjson-2013.9-1/TSjson/inst/doc/Guide.Stex |only
TSjson-2014.4-1/TSjson/DESCRIPTION | 13
TSjson-2014.4-1/TSjson/MD5 | 14 -
TSjson-2014.4-1/TSjson/NAMESPACE | 6
TSjson-2014.4-1/TSjson/NEWS | 13
TSjson-2014.4-1/TSjson/R/TSdbiMethods.R | 18 +
TSjson-2014.4-1/TSjson/man/TSdbiMethods.Rd | 20 +
TSjson-2014.4-1/TSjson/tests/0pythonRequirementsTests.R |only
TSjson-2014.4-1/TSjson/tests/statcan.R | 220 ++++++++--------
9 files changed, 176 insertions(+), 128 deletions(-)
Title: memory-efficient storage of large data on disk and fast access
functions
Diff between ff versions 2.2-12 dated 2013-10-16 and 2.2-13 dated 2014-04-09
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not unlike
data.frames and import/export filters for csv files.
ff objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and virtual
attributes. ff objects have well-defined hybrid copying semantics,
which gives rise to certain performance improvements through
virtualization. ff objects can be stored and reopened across R
sessions. ff files can be shared by multiple ff R objects
(using different data en/de-coding schemes) in the same process
or from multiple R processes to exploit parallelism. A wide choice of
finalizer options allows to work with 'permanent' files as well as
creating/removing 'temporary' ff files completely transparent to the
user. On certain OS/Filesystem combinations, creating the ff files
works without notable delay thanks to using sparse file allocation.
Several access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve good
performance even with large datasets, for example virtual matrix
transpose without touching a single byte on disk. Further, to reduce
disk I/O, 'logicals' and non-standard data types get stored native and
compact on binary flat files i.e. logicals take up exactly 2 bits to
represent TRUE, FALSE and NA.
Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and ram
objects and support for batch processing on ff objects (e.g. as.ram,
as.ff, ffapply). ff interfaces closely with functionality from package
'bit': chunked looping, fast bit operations and coercions between
different objects that can store subscript information ('bit',
'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows
to work interactively with selections of large datasets and quickly
modify selection criteria.
Further high-performance enhancements can be made available upon request.
Author: Daniel Adler
Maintainer: Jens Oehlschlägel
DESCRIPTION | 8 -
MD5 | 16 +--
NAMESPACE | 14 ++-
NEWS | 24 +++++
R/ff.R | 12 +-
man/clone.rd | 3
man/filename.rd | 5 -
src/ordermerge.c | 229 ++++++++++++++++++++++++++++++-------------------------
src/r_ff.c | 8 +
9 files changed, 187 insertions(+), 132 deletions(-)
Title: A S3 class for vectors of 64bit integers
Diff between bit64 versions 0.9-3 dated 2013-12-05 and 0.9-4 dated 2014-04-09
Description:
Package 'bit64' provides serializable S3 atomic 64bit (signed) integers
that can be used in vectors, matrices, arrays and data.frames. Methods are
available for coercion from and to logicals, integers, doubles, characters
and factors as well as many elementwise and summary functions. Many fast
algorithmic operations such as 'match' and 'order' support interactive data
exploration and manipulation and optionally leverage caching.
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel
DESCRIPTION | 8 +--
MD5 | 26 +++++------
NEWS | 11 +++++
R/cache.R | 6 +-
R/hash64.R | 4 -
R/highlevel64.R | 52 +++++++++++------------
R/integer64.R | 103 +++++++++++++++++++++++------------------------
R/sort64.R | 44 ++++++++++----------
R/sortuse64.R | 4 -
man/bit64-package.rd | 103 +++++++++++++++++++++++------------------------
man/match.integer64.rd | 2
man/ramsort.integer64.rd | 4 -
src/integer64.h | 6 +-
src/sortuse64.c | 2
14 files changed, 194 insertions(+), 181 deletions(-)
Title: A class for vectors of 1-bit booleans
Diff between bit versions 1.1-11 dated 2013-12-05 and 1.1-12 dated 2014-04-09
Description: bitmapped vectors of booleans (no NAs),
coercion from and to logicals, integers and integer subscripts;
fast boolean operators and fast summary statistics.
With 'bit' vectors you can store true binary booleans {FALSE,TRUE} at the
expense of 1 bit only, on a 32 bit architecture this means factor 32 less
RAM and ~ factor 32 more speed on boolean operations. Due to overhead of
R calls, actual speed gain depends on the size of the vector: expect gains
for vectors of size > 10000 elements. Even for one-time boolean operations
it can pay-off to convert to bit, the pay-off is obvious, when such
components are used more than once.
Reading from and writing to bit is approximately as fast as accessing
standard logicals - mostly due to R's time for memory allocation. The package
allows to work with pre-allocated memory for return values by calling .Call()
directly: when evaluating the speed of C-access with pre-allocated vector
memory, coping from bit to logical requires only 70% of the time for copying
from logical to logical; and copying from logical to bit comes at a
performance penalty of 150%. the package now contains further classes for
representing logical selections: 'bitwhich' for very skewed selections and
'ri' for selecting ranges of values for chunked processing. All three index
classes can be used for subsetting 'ff' objects (ff-2.1-0 and higher).
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel
DESCRIPTION | 6 +-
MD5 | 22 ++++++----
NAMESPACE | 12 +++++
NEWS | 15 +++++++
R/attrutil.R | 5 --
R/bit.R | 118 +++++++++++++++++++++++---------------------------------
R/chunkutil.R | 3 -
R/clone.R |only
R/generics.R | 2
man/clone.rd |only
src/Makevars |only
src/bit.c | 14 +++---
src/chunkutil.c | 2
src/clone.c |only
14 files changed, 104 insertions(+), 95 deletions(-)
Title: Quandl Data Connection
Diff between Quandl versions 2.3.1 dated 2014-04-08 and 2.3.2 dated 2014-04-09
Description: This package interacts directly with the Quandl API to offer data
in a number of formats usable in R, as well as the ability to upload and
search.
Author: Raymond McTaggart, Gergely Daroczi
Maintainer: Raymond McTaggart
ChangeLog | 7 +++++++
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/Quandl.R | 2 +-
tests/test-all.R | 2 +-
5 files changed, 16 insertions(+), 9 deletions(-)
Title: Global Charcoal Database
Diff between GCD versions 3.0.1 dated 2014-03-12 and 3.0.2 dated 2014-04-09
Description: Global Charcoal database data and tools
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 5 +++++
R/potveg.R | 10 +++++-----
4 files changed, 17 insertions(+), 12 deletions(-)
Title: Dual empirical likelihood inference under density ratio models
in the presence of multiple samples
Diff between drmdel versions 1.2 dated 2014-01-07 and 1.3 dated 2014-04-09
Description: Dual empirical likelihood (DEL) inference under semiparametric density ratio models (DRM) in the presence of multiple samples, including population cumulative distribution function estimation, quantile estimation and comparison, density estimation, composite hypothesis testing for DRM parameters which encompasses testing for changes in population distribution functions as a special case, etc.
Author: Song Cai
Maintainer: Song Cai
drmdel-1.2/drmdel/man/mdeleCov.Rd |only
drmdel-1.3/drmdel/ChangeLog | 13
drmdel-1.3/drmdel/DESCRIPTION | 12
drmdel-1.3/drmdel/MD5 | 36 -
drmdel-1.3/drmdel/NAMESPACE | 2
drmdel-1.3/drmdel/R/drmdel.R | 637 +++++++++++++++++------------
drmdel-1.3/drmdel/inst/examples/examples.R | 121 ++---
drmdel-1.3/drmdel/man/cdfDRM.Rd | 31 -
drmdel-1.3/drmdel/man/densityDRM.Rd | 46 --
drmdel-1.3/drmdel/man/drmdel.Rd | 43 -
drmdel-1.3/drmdel/man/meleCov.Rd |only
drmdel-1.3/drmdel/man/quantileCompWald.Rd | 2
drmdel-1.3/drmdel/man/quantileDRM.Rd | 72 +--
drmdel-1.3/drmdel/man/summaryDRM.Rd | 13
drmdel-1.3/drmdel/src/basisFuncs.c | 2
drmdel-1.3/drmdel/src/basisFuncs.h | 2
drmdel-1.3/drmdel/src/drmdel.c | 62 +-
drmdel-1.3/drmdel/src/utilities.c | 2
drmdel-1.3/drmdel/src/utilities.h | 2
drmdel-1.3/drmdel/tests/drmdelTest.R | 121 ++---
20 files changed, 689 insertions(+), 530 deletions(-)
More information about cuttlefish.model at CRAN
Permanent link