Title: Conversion of R regression output to LaTeX or HTML tables.
Diff between texreg versions 1.20 dated 2013-02-08 and 1.21 dated 2013-02-19
Description: texreg converts coefficients, standard errors,
significance stars, and goodness-of-fit statistics of
statistical models into LaTeX tables or HTML tables/MS Word
documents or to nicely formatted screen output for the R
console for easy model comparison. A list of several models can
be combined in a single table. The output is highly
customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld
DESCRIPTION | 20 ++--
MD5 | 25 +++---
NAMESPACE | 1
R/extract.R | 178 ++++++++++++--------------------------------
R/internal.R | 98 +++++++++++++++++++-----
R/texreg.R | 130 ++++++++++++++++++++++----------
inst/CITATION | 8 -
inst/doc/texreg.Rnw | 52 ++++++++----
inst/doc/texreg.pdf |binary
man/extract-methods.Rd | 5 +
man/extract.Rd | 27 ++++--
man/texreg.Rd | 33 +++++---
vignettes/texreg.Rnw | 52 ++++++++----
vignettes/texreg.Rnw.backup |only
14 files changed, 362 insertions(+), 267 deletions(-)
Title: Taxonomic information from around the web.
Diff between taxize versions 0.0.4 dated 2013-01-31 and 0.0.5 dated 2013-02-19
Description: Taxonomic information from around the web.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Carl
Boettiger [aut], Ignasi Bartomeus [aut]
Maintainer: Scott Chamberlain
taxize-0.0.4/taxize/tests |only
taxize-0.0.5/taxize/DESCRIPTION | 9 +++++----
taxize-0.0.5/taxize/MD5 | 20 ++++++++++----------
taxize-0.0.5/taxize/NEWS | 6 ++++++
taxize-0.0.5/taxize/R/get_tsn.R | 1 +
taxize-0.0.5/taxize/R/itis.R | 9 +++++----
taxize-0.0.5/taxize/R/tax_name.R | 16 ++++++++++------
taxize-0.0.5/taxize/R/tnrs.R | 10 ++++++++--
taxize-0.0.5/taxize/inst/tests/test-tax_name.R | 7 ++++---
taxize-0.0.5/taxize/inst/tests/test-ubio_namebank.R |only
taxize-0.0.5/taxize/man/getfullhierarchyfromtsn.Rd | 2 +-
taxize-0.0.5/taxize/man/tnrs.Rd | 13 +++++++++++--
12 files changed, 61 insertions(+), 32 deletions(-)
Title: classes and methods for spatio-temporal data
Diff between spacetime versions 1.0-3 dated 2012-12-25 and 1.0-4 dated 2013-02-19
Description: A package with classes and methods for spatio-temporal
data. In particular, space-time regular lattices, sparse
lattices, irregular data, and simple trajectories are
supported. Utility functions are provided for plotting data as
map sequences (lattice or animation) or multiple time series;
for spatial and temporal selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [cre, aut], Benedikt Graeler [ctb], Tom Gottfried
[ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma
DESCRIPTION | 11 +++---
MD5 | 39 +++++++++++------------
NAMESPACE | 8 ++--
R/ST-methods.R | 9 ++---
R/STFDF-methods.R | 23 ++++++++++---
R/STIDF-methods.R | 7 ++--
R/STSDF-methods.R | 10 ++++-
R/STTDF-methods.R | 57 ++++++++++++++++++++++++++++++++++
R/raster.R | 2 -
R/stplot.R | 16 +++++++--
inst/doc/jss816.Rnw | 12 ++++---
inst/doc/jss816.pdf |binary
inst/doc/pg.R |only
inst/doc/sto.Rnw | 6 +++
inst/doc/sto.pdf |binary
inst/doc/stpg.Rnw | 3 +
inst/doc/stpg.pdf |binary
man/STTDF-class.Rd | 1
tests/Examples/spacetime-Ex.Rout.save | 10 +++--
tests/raster.Rout.save | 4 +-
tests/wind.Rout.save | 3 +
21 files changed, 161 insertions(+), 60 deletions(-)
Title: Functions for estimation and inference of selection in
age-structured populations
Diff between lmf versions 1.0 dated 2012-05-20 and 1.1 dated 2013-02-19
Description: This R package provide methods for estimation and
statistical inference on directional and fluctuating selection
in age-structured populations.
Author: Thomas Kvalnes
Maintainer: Thomas Kvalnes
DESCRIPTION | 9
MD5 | 86 ++--
NAMESPACE | 12
R/atCfn.R | 24 -
R/boot.lmf.R | 830 ++++++++++++++++++++++-----------------------
R/ci.boot.lmf.R | 136 +++----
R/eigenl.R | 56 +--
R/fs.R | 100 ++---
R/inv.R | 18
R/lm.extract.R | 46 +-
R/lmf-internal.R | 250 ++++++-------
R/lmf.R | 546 ++++++++++++++---------------
R/lnL.M.R | 86 ++--
R/nearPD.R | 184 ++++-----
R/nfs.R | 60 +--
R/plot.boot.lmf.R | 194 +++++-----
R/plot.lmf.R | 284 +++++++--------
R/print.boot.lmf.R | 42 +-
R/print.ci.boot.lmf.R | 96 ++---
R/print.lmf.R | 66 +--
R/print.summary.boot.lmf.R | 422 +++++++++++-----------
R/print.summary.lmf.R | 212 +++++------
R/procomp.R | 12
R/promat.R | 32 -
R/rmnorm.R | 48 +-
R/se.R | 16
R/summary.boot.lmf.R | 776 +++++++++++++++++++++---------------------
R/summary.lmf.R | 234 ++++++------
data/sparrowdata.rda |binary
man/atCfn.Rd | 2
man/boot.lmf.Rd | 2
man/ci.boot.lmf.Rd | 2
man/eigenl.Rd | 2
man/fs.Rd | 2
man/lmf-package.Rd | 8
man/lmf.Rd | 2
man/lnL.M.Rd | 2
man/nfs.Rd | 2
man/plot.boot.lmf.Rd | 1
man/plot.lmf.Rd | 1
man/projection.Rd | 2
man/sparrowdata.Rd | 2
man/summary.boot.lmf.Rd | 2
man/summary.lmf.Rd | 2
44 files changed, 2462 insertions(+), 2449 deletions(-)
Title: Everyone's Statistical Software
Diff between Zelig versions 4.1-2 dated 2013-01-24 and 4.1-3 dated 2013-02-19
Description: Zelig is an easy-to-use program that can estimate, and
help interpret the results of, an enormous range of statistical
models. It literally is ``everyone's statistical software''
because Zelig's simple unified framework incorporates everyone
else's (R) code. We also hope it will become ``everyone's
statistical software'' for applications and teaching, and so
have designed Zelig so that anyone can easily use it or add
their programs to it. Zelig also comes with infrastructure
that facilitates the use of any existing method, such as by
allowing multiply imputed data for any model, and mimicking the
program Clarify (for Stata) that takes the raw output of
existing statistical procedures and translates them into
quantities of direct interest.
Author: Matt Owen
Maintainer: Matt Owen
Zelig-4.1-2/Zelig/R/sim.relogit.R |only
Zelig-4.1-2/Zelig/man/sim.relogit.Rd |only
Zelig-4.1-3/Zelig/DESCRIPTION | 11 +-
Zelig-4.1-3/Zelig/MD5 | 41 ++++----
Zelig-4.1-3/Zelig/NAMESPACE | 3
Zelig-4.1-3/Zelig/R/names.relogit.R | 6 -
Zelig-4.1-3/Zelig/R/plots.R | 44 ++++++--
Zelig-4.1-3/Zelig/R/relogit.R | 9 +
Zelig-4.1-3/Zelig/R/summary.R | 137 ++++++++++++++++++++++++----
Zelig-4.1-3/Zelig/inst/doc/gamma.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/logit.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/ls.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/manual-bayes.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/manual-gee.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/manual.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/normal.pdf |binary
Zelig-4.1-3/Zelig/inst/doc/twosls.pdf |binary
Zelig-4.1-3/Zelig/man/plot.ci.Rd | 15 ++-
Zelig-4.1-3/Zelig/man/plot.pooled.sim.Rd | 15 ++-
Zelig-4.1-3/Zelig/man/summary.MI.Rd | 4
Zelig-4.1-3/Zelig/tests/MatchIt.R |only
Zelig-4.1-3/Zelig/tests/plot-ci.R | 18 +++
Zelig-4.1-3/Zelig/tests/relogit.R |only
Zelig-4.1-3/Zelig/tests/summary.MI.R |only
24 files changed, 237 insertions(+), 66 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.11 dated 2013-01-31 and 0.9.12 dated 2013-02-19
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 11 +--
MD5 | 54 ++++++++--------
NAMESPACE | 4 -
NEWS | 9 ++
R/main.r | 107 +++++++++++++++++++-------------
inst/doc/SNPRelateTutorial.Rnw | 4 -
inst/doc/SNPRelateTutorial.pdf |binary
man/SNPRelate-package.Rd | 4 -
man/snpgdsCutTree.Rd | 2
man/snpgdsExampleFileName.Rd | 4 -
man/snpgdsHCluster.Rd | 2
man/snpgdsIBDMLE.Rd | 2
man/snpgdsIBDMoM.Rd | 4 -
man/snpgdsIBDSelection.Rd | 2
man/snpgdsIBS.Rd | 2
man/snpgdsIBSNum.Rd | 2
man/snpgdsPCA.Rd | 2
man/snpgdsPCASampLoading.Rd | 1
man/snpgdsPairIBD.Rd | 2
man/snpgdsVCF2GDS.Rd | 39 ++++++++++-
src/CoreGDSLink.cpp | 133 ++++++++++++++++++++++++++++++++++------
src/CoreGDSLink.h | 88 +++++++++++++++++++++++++-
src/dGenGWAS.cpp | 66 +++++++++----------
src/dGenGWAS.h | 20 +++---
src/dType.h | 71 +++++++++++++++------
src/genIBD.cpp | 2
src/main.cpp | 9 ++
vignettes/SNPRelateTutorial.Rnw | 4 -
28 files changed, 467 insertions(+), 183 deletions(-)
Title: spatial and spatio-temporal geostatistical modelling, prediction
and simulation
Diff between gstat versions 1.0-15 dated 2013-01-08 and 1.0-16 dated 2013-02-19
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
Author: Edzer Pebesma [aut, cre], Benedikt Graeler [ctb]
Maintainer: Edzer Pebesma
DESCRIPTION | 13
MD5 | 53 +-
NAMESPACE | 2
R/krige.R | 22
R/krige0.R | 511 ++++++++++-----------
R/stVariogramModels.R | 324 +++++++------
R/variogramST.R | 88 ++-
data/vv.rda |binary
demo/00Index | 1
demo/lnsim.R |only
demo/stkrige.R | 425 +++++++++--------
inst/doc/gstat.pdf |binary
inst/doc/prs.pdf |binary
inst/doc/st.Rnw | 902 +++++++++++++++++++-------------------
inst/doc/st.pdf |binary
man/fit.StVariogram.Rd | 100 +---
man/fit.variogram.gls.Rd | 2
man/krige.Rd | 412 ++++++++---------
man/krigeST.Rd |only
man/ossfim.Rd | 2
man/plot.gstatVariogram.Rd | 2
man/variogram.Rd | 31 -
man/variogramSurface.Rd | 129 ++---
man/vgmST.Rd |only
src/sem.c | 11
tests/Examples/gstat-Ex.Rout.save | 241 ++++++----
tests/unproj.Rout.save | 4
tests/windst.R | 10
tests/windst.Rout.save | 14
29 files changed, 1687 insertions(+), 1612 deletions(-)
Title: CoreArray Genomic Data Structure (GDS) R Interface
Diff between gdsfmt versions 0.9.11 dated 2013-01-26 and 0.9.12 dated 2013-02-19
Description: CoreArray project is to develop portable and scalable
storage technologies for bioinformatics data, allowing parallel
computing at the multicore and cluster levels.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 9
MD5 | 81 ++-
NEWS | 22 -
R/GDS.all.R | 228 ++++++----
inst/doc |only
inst/unitTests/runit.01.datatype.r | 8
inst/unitTests/runit.02.dataconvert.r | 15
inst/unitTests/runit.03.dimension.r | 15
inst/unitTests/runit.04.datareadwrite.r | 15
inst/unitTests/valid/standard.RData |binary
man/add.gdsn.Rd | 16
man/apply.gdsn.Rd | 14
man/assign.gdsn.Rd |only
man/cleanup.gds.Rd | 6
man/clusterApply.gdsn.Rd | 14
man/gdsfmt-package.Rd | 6
man/index.gdsn.Rd | 13
man/objdesp.gdsn.Rd | 2
man/print.gds.class.Rd | 3
man/print.gdsn.class.Rd | 3
src/CoreGDS.cpp | 172 ++++++-
src/dBase.cpp | 30 -
src/dBase.h | 18
src/dFile.cpp | 55 +-
src/dFile.h | 8
src/dParallel.cpp | 6
src/dParallel.h | 14
src/dPlatform.cpp | 4
src/dPlatform.h | 29 -
src/dSeq.cpp | 57 --
src/dSeq.h | 251 -----------
src/dStream.cpp | 41 +
src/dStream.h | 23 +
src/dStruct.cpp | 72 ++-
src/dStruct.h | 697 +++++++++++++++++++++++++++++---
src/dType.h | 214 ++++++++-
src/gdsfmt.cpp | 260 +++++++++--
vignettes |only
38 files changed, 1698 insertions(+), 723 deletions(-)
Title: EpiEstim: a package to estimate time varying reproduction
numbers from epidemic curves.
Diff between EpiEstim versions 1.0-0 dated 2012-06-07 and 1.1-0 dated 2013-02-19
Description: This package provides tools to quantify transmissibility
throughout an epidemic from the analysis of time series of
incidence.
Author: Anne Cori
Maintainer: Anne Cori
DESCRIPTION | 9
MD5 | 26
NAMESPACE | 10
R/EstimationR.R | 1360 ++++++++++++++++++++++++++--------------------
man/DiscrSI.Rd | 91 +--
man/EpiEstim-package.Rd | 104 +--
man/EstimateR.Rd | 253 ++++----
man/Flu1918.Rd | 90 +--
man/Flu2009.Rd | 78 +-
man/Measles1861.Rd | 70 +-
man/OverallInfectivity.Rd | 86 +-
man/SARS2003.Rd | 74 +-
man/Smallpox1972.Rd | 78 +-
man/WT.Rd |only
sync.x64.ffs_db |only
15 files changed, 1285 insertions(+), 1044 deletions(-)
Title: Projected Spatial Gaussian Process (psgp) methods
Diff between psgp versions 0.3-1 dated 2012-04-12 and 0.3-2 dated 2013-02-19
Description: Implements projected sparse Gaussian process kriging for
the intamap package
Author: Ben Ingram
Maintainer: Remi Barillec
DESCRIPTION | 12 +++++++-----
MD5 | 14 ++++++++------
NAMESPACE | 1 -
R/spatialPredict.R | 13 +++++++------
inst/doc/InstallationInstructions.pdf |binary
man/learnParameters.rd | 3 ---
man/makePrediction.rd | 1 -
src/covarianceFunctions/GaussianCF.cpp |only
src/covarianceFunctions/GaussianCF.h |only
9 files changed, 22 insertions(+), 22 deletions(-)
Title: procedures for automated interpolation
Diff between intamap versions 1.3-21 dated 2013-02-08 and 1.3-23 dated 2013-02-19
Description: A package that provides classes and methods for automated
spatial interpolation.
Author: Edzer Pebesma
Maintainer: Jon Olav Skoien
DESCRIPTION | 13 +++++------
MD5 | 12 +++++-----
R/pointKriging.R | 19 ++++++----------
R/spCopPred.R | 6 ++---
R/transGaussian.R | 19 +++++++---------
man/estimateParameters.Rd | 1
tests/unbiased.Rout.save | 54 +++++++++++++++++++++++-----------------------
7 files changed, 60 insertions(+), 64 deletions(-)
Title: Kriging methods for computer experiments
Diff between DiceKriging versions 1.5 dated 2012-11-30 and 1.5.1 dated 2013-02-19
Description: Estimation, validation and prediction of kriging models.
Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville.
Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant
CHANGELOG | 9 +++
DESCRIPTION | 9 ++-
MD5 | 17 +++----
R/checkNames.R | 18 +++----
R/kmStruct.R | 103 +++++++++++++++++++++++++------------------
inst/tests/test-checkNames.R |only
man/DiceKriging-package.Rd | 4 -
man/plot.km.Rd | 2
man/simulate.km.Rd |binary
man/update.km.Rd | 13 +++--
10 files changed, 103 insertions(+), 72 deletions(-)
Title: GeMTC network meta-analysis
Diff between gemtc versions 0.1-2 dated 2013-01-21 and 0.2 dated 2013-02-19
Description: An R package for performing network meta-analyses (mixed
treatment comparisons).
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef
gemtc-0.1-2/gemtc/R/mtc.R |only
gemtc-0.1-2/gemtc/R/mtc.rjava.R |only
gemtc-0.1-2/gemtc/inst/extdata/luades-thrombolytic.samples.gz |only
gemtc-0.1-2/gemtc/man/figures/parkinson-inconsistency.pdf |only
gemtc-0.1-2/gemtc/man/figures/parkinson-inconsistency.png |only
gemtc-0.1-2/gemtc/man/read.mtc.network.Rd |only
gemtc-0.1-2/gemtc/man/read.mtc.result.samples.Rd |only
gemtc-0.1-2/gemtc/man/write.mtc.network.Rd |only
gemtc-0.2/gemtc/DESCRIPTION | 17 -
gemtc-0.2/gemtc/MD5 | 56 +++--
gemtc-0.2/gemtc/NAMESPACE | 27 +-
gemtc-0.2/gemtc/NEWS |only
gemtc-0.2/gemtc/R/blobbogram.R |only
gemtc-0.2/gemtc/R/code.R |only
gemtc-0.2/gemtc/R/data.R |only
gemtc-0.2/gemtc/R/inits.R |only
gemtc-0.2/gemtc/R/ll.binom.logit.R |only
gemtc-0.2/gemtc/R/ll.normal.identity.R |only
gemtc-0.2/gemtc/R/minimum.diameter.spanning.tree.R |only
gemtc-0.2/gemtc/R/mtc.model.R |only
gemtc-0.2/gemtc/R/mtc.model.consistency.R |only
gemtc-0.2/gemtc/R/mtc.network.R |only
gemtc-0.2/gemtc/R/mtc.result.R |only
gemtc-0.2/gemtc/R/mtc.run.R |only
gemtc-0.2/gemtc/R/priors.R |only
gemtc-0.2/gemtc/R/rank.probability.R |only
gemtc-0.2/gemtc/R/relative.effect.R |only
gemtc-0.2/gemtc/inst/extdata/luades-smoking.samples.gz |binary
gemtc-0.2/gemtc/inst/gemtc.model.template.txt |only
gemtc-0.2/gemtc/inst/tests |only
gemtc-0.2/gemtc/man/blobbogram.Rd |only
gemtc-0.2/gemtc/man/figures/parkinson.pdf |only
gemtc-0.2/gemtc/man/figures/parkinson.png |only
gemtc-0.2/gemtc/man/gemtc-package.Rd | 38 +++
gemtc-0.2/gemtc/man/mtc.model.Rd | 36 ++-
gemtc-0.2/gemtc/man/mtc.network.Rd | 98 +++++++---
gemtc-0.2/gemtc/man/mtc.run.Rd | 82 +++-----
gemtc-0.2/gemtc/man/rank.probability.Rd | 17 -
gemtc-0.2/gemtc/man/relative.effect.Rd | 52 ++---
gemtc-0.2/gemtc/src/rank.c | 4
gemtc-0.2/gemtc/tests |only
41 files changed, 254 insertions(+), 173 deletions(-)