Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
ordered observations)
Diff between zoo versions 1.7-6 dated 2011-11-02 and 1.7-7 dated 2012-02-10
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre], Gabor Grothendieck [aut], Jeffrey A.
Ryan [aut], Felix Andrews [ctb]
Maintainer: Achim Zeileis
DESCRIPTION | 24 ++++++++++------------
MD5 | 37 ++++++++++++++++++-----------------
NEWS | 18 +++++++++++++++++
R/merge.zoo.R | 2 -
R/rollapply.R | 10 ++++-----
R/yearmon.R | 4 +--
inst/doc/zoo-design.pdf |binary
inst/doc/zoo-faq.Rnw | 45 +++++++++++++++++++++++++++++++++++++++----
inst/doc/zoo-faq.pdf |binary
inst/doc/zoo-quickref.pdf |binary
inst/doc/zoo-read.pdf |binary
inst/doc/zoo.pdf |binary
man/zooreg.Rd | 2 -
src/coredata.c | 2 -
src/init.c | 2 -
src/lag.c | 2 -
tests/Examples |only
tests/bugfixes.R | 6 +++++
tests/bugfixes.Rout.save | 14 ++++++++++++-
tests/vignette-zoo.Rout.save | 2 -
20 files changed, 121 insertions(+), 49 deletions(-)
Title: Multivariate Permutation Tests
Diff between flip versions 1.1 dated 2011-11-19 and 1.2 dated 2012-02-10
Description: It implements univariate and multivariate permutation
test, also allowing for multiplicity control.
Author: Livio Finos
Maintainer: Livio Finos
.dropbox |only
DESCRIPTION | 11 +-
MD5 | 32 +++---
NAMESPACE | 2
R/Padjust.R | 42 +++++---
R/dependence.R | 35 +++---
R/dependenceNA.R |only
R/dependenceW.R |only
R/flip-object.R | 10 -
R/flip.R | 76 ++++++++++----
R/npc.R | 38 ++++---
R/permSpace.R |only
R/rotation.R | 39 ++++---
R/symmetry.R | 27 +++--
R/utilities.R | 249 +++++++++++++-----------------------------------
desktop.ini |only
man/flip-package.Rd | 18 ++-
man/flip.Rd | 44 +++++---
man/multiplicity.Rd | 50 +++++++--
man/permutationSpace.Rd | 4
20 files changed, 347 insertions(+), 330 deletions(-)
Title: Multiresolution Kriging based on Markov random fields
Diff between LatticeKrig versions 1.2.1 dated 2011-09-09 and 1.4 dated 2012-02-10
Description: Functions for the interpolation of large spatial datasets.
This pacakge uses a "fixed rank Kriging" approach using a large
number of basis functions and provides spatial estimates that
are comparable to standard families of covariance functions and
estimates that are close to interpolating the observations (a
small nugget variance.) The covariance model for this method
approximates the Matern but also allows for a multi-resolution
model and supports efficient computation of the profile
likelihood for estimating covariance parameters. Also included
are generic methods for prediction and plotting of the
estimated surface.
Author: Douglas Nychka, Dorit Hammerling, Stephen Sain, and Tia Lerud
Maintainer: Doug Nychka
LatticeKrig-1.2.1/LatticeKrig/LICENSE |only
LatticeKrig-1.2.1/LatticeKrig/R/MLE.LKrig.R |only
LatticeKrig-1.2.1/LatticeKrig/man/BACK |only
LatticeKrig-1.2.1/LatticeKrig/tests/LKbasis.test.Rout |only
LatticeKrig-1.2.1/LatticeKrig/tests/LKrig.test.Rout |only
LatticeKrig-1.4/LatticeKrig/DESCRIPTION | 26
LatticeKrig-1.4/LatticeKrig/MD5 | 58 -
LatticeKrig-1.4/LatticeKrig/R/BACK |only
LatticeKrig-1.4/LatticeKrig/R/LKrig.MRF.precision.R | 22
LatticeKrig-1.4/LatticeKrig/R/LKrig.R | 39
LatticeKrig-1.4/LatticeKrig/R/LKrig.basis.R | 60 -
LatticeKrig-1.4/LatticeKrig/R/LKrig.coef.R | 21
LatticeKrig-1.4/LatticeKrig/R/LKrig.cov.R | 36
LatticeKrig-1.4/LatticeKrig/R/LKrig.cov.plot.R |only
LatticeKrig-1.4/LatticeKrig/R/LKrig.lnPlike.R | 26
LatticeKrig-1.4/LatticeKrig/R/LKrig.precision.R | 70 -
LatticeKrig-1.4/LatticeKrig/R/LKrig.setup.R | 42
LatticeKrig-1.4/LatticeKrig/R/LKrig.sim.R | 30
LatticeKrig-1.4/LatticeKrig/R/MLE.search.LKrig.R |only
LatticeKrig-1.4/LatticeKrig/R/Matern2LKrig.R |only
LatticeKrig-1.4/LatticeKrig/R/Wbasis.R | 25
LatticeKrig-1.4/LatticeKrig/R/predict.LKrig.R | 21
LatticeKrig-1.4/LatticeKrig/R/print.LKrig.R | 21
LatticeKrig-1.4/LatticeKrig/R/surface.LKrig.R | 21
LatticeKrig-1.4/LatticeKrig/R/zzz.R | 24
LatticeKrig-1.4/LatticeKrig/data |only
LatticeKrig-1.4/LatticeKrig/look |only
LatticeKrig-1.4/LatticeKrig/man/LKrig.Ctable.Rd |only
LatticeKrig-1.4/LatticeKrig/man/LKrig.Rd | 549 ++++++----
LatticeKrig-1.4/LatticeKrig/man/LKrig.basis.Rd | 145 ++
LatticeKrig-1.4/LatticeKrig/man/LKrig.internal.Rd | 25
LatticeKrig-1.4/LatticeKrig/man/MLE.search.LKrig.Rd |only
LatticeKrig-1.4/LatticeKrig/man/NorthAmericanRainfall.Rd |only
LatticeKrig-1.4/LatticeKrig/man/Wendland.basis.Rd | 15
LatticeKrig-1.4/LatticeKrig/tests/LKrig.precision.test.R |only
LatticeKrig-1.4/LatticeKrig/tests/LKrig.precision.test.Rout.save |only
LatticeKrig-1.4/LatticeKrig/tests/LKrig.test.Rout.save |only
37 files changed, 941 insertions(+), 335 deletions(-)
Title: Harrell Miscellaneous
Diff between Hmisc versions 3.9-1 dated 2012-01-14 and 3.9-2 dated 2012-02-10
Description: The Hmisc library contains many functions useful for data
analysis, high-level graphics, utility operations, functions
for computing sample size and power, importing datasets,
imputing missing values, advanced table making, variable
clustering, character string manipulation, conversion of S
objects to LaTeX code, and recoding variables. Please submit
bug reports to 'http://biostat.mc.vanderbilt.edu/trac/Hmisc'.
Author: Frank E Harrell Jr
Maintainer: Charles Dupont
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/summary.formula.s | 36 +++++++++++++++++++-----------------
3 files changed, 25 insertions(+), 23 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
...
Diff between foreign versions 0.8-48 dated 2011-12-07 and 0.8-49 dated 2012-02-10
Description: Functions for reading and writing data stored by
statistical packages such as Minitab, S, SAS, SPSS, Stata,
Systat, ..., and for reading and writing dBase files.
Author: R-core members, Saikat DebRoy, Roger Bivand
Maintainer: R-core
ChangeLog | 5 +++++
DESCRIPTION | 22 +++++++++++-----------
MD5 | 10 +++++-----
R/read.dta.R | 2 ++
src/stataread.c | 7 +++----
tests/spss.Rout.save | 13 ++++++++-----
6 files changed, 34 insertions(+), 25 deletions(-)
Title: Variational Bayes Latent Position Cluster Model for networks.
Diff between VBLPCM versions 1.3 dated 2012-01-30 and 2.0 dated 2012-02-10
Description: A package to fit and simulate latent position and cluster
models for statistical networks using a Variational Bayes
approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend
DESCRIPTION | 10 -
MD5 | 50 +++---
NAMESPACE | 13 -
R/KL.R | 35 ++--
R/VBLPCM.R | 42 +++--
R/covs.R | 49 +-----
R/log_like_forces.R | 16 --
R/plot_network.R | 11 -
R/predict.R | 32 +++-
R/start.R | 80 ++++++++--
R/vb_bic.R | 26 ++-
man/VBLPCM-package.Rd | 27 +--
man/gof.vblpcm.Rd | 4
man/log_like_forces.Rd | 8 -
man/predict.vblpcm.Rd | 3
man/vblpcmBIC.Rd | 7
man/vblpcmcovs.Rd | 10 -
man/vblpcmstart.Rd | 10 -
src/KL_funcs.c | 374 ++++++++++++++++++++++++++++++++++++-------------
src/VBLPCM.c | 140 +++++++++++++-----
src/bb.c | 34 +++-
src/funcs.c | 1
src/headers.h | 12 +
src/likelihoods.c | 74 ++++++---
src/log_like_forces.c | 10 -
src/optim.c | 52 ++++--
26 files changed, 740 insertions(+), 390 deletions(-)
Title: Siena - Simulation Investigation for Empirical Network Analysis
Diff between RSiena versions 1.0.12.198 dated 2012-02-04 and 1.0.12.201 dated 2012-02-10
Description: Fits models to longitudinal networks
Author: Various
Maintainer: RSiena developers
DESCRIPTION | 10 ++--
MD5 | 34 ++++++++--------
R/initializeFRAN.r | 4 -
R/phase1.r | 3 -
R/phase3.r | 61 +++++++++++++++++++++++-------
changeLog | 53 ++++++++++++++++++++++++++
inst/doc/RSiena_Manual.pdf |binary
man/RSiena-package.Rd | 4 -
src/model/EpochSimulation.cpp | 26 +++++-------
src/model/variables/DependentVariable.cpp | 19 ++++-----
src/siena07internals.cpp | 10 +---
src/siena07internals.h | 10 +---
src/siena07models.cpp | 10 +---
src/siena07setup.cpp | 21 +++-------
src/siena07setup.h | 7 +--
src/siena07utilities.cpp | 20 ++++-----
src/siena07utilities.h | 8 +--
tests/scripts.R | 17 +++-----
18 files changed, 193 insertions(+), 124 deletions(-)
Title: Order Restricted Clustering for Microarray Experiments
Diff between ORCME versions 1.0 dated 2011-11-23 and 1.1 dated 2012-02-10
Description: This package provides clustering of genes with similar
dose response (or time course) profiles. It implements the
method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Martin Otava
DESCRIPTION | 17 +++++++------
MD5 | 12 ++++-----
NEWS | 2 -
data/doseData.rda |binary
data/geneData.rda |binary
man/doseData.Rd | 39 ++++++++++++++++++++++--------
man/geneData.Rd | 68 +++++++++++++++++++++++++++++++++++++++++-------------
7 files changed, 96 insertions(+), 42 deletions(-)
Title: Export tables to LaTeX or HTML
Diff between xtable versions 1.6-0 dated 2011-10-12 and 1.7-0 dated 2012-02-10
Description: Coerce data to LaTeX and HTML tables
Author: David B. Dahl
Maintainer: Charles Roosen
xtable-1.6-0/xtable/data/tli.txt.bz2 |only
xtable-1.7-0/xtable/DESCRIPTION | 12
xtable-1.7-0/xtable/MD5 | 22
xtable-1.7-0/xtable/NAMESPACE | 9
xtable-1.7-0/xtable/NEWS | 30
xtable-1.7-0/xtable/R/print.xtable.R | 990 ++++++++++++++-----------
xtable-1.7-0/xtable/R/table.attributes.R | 6
xtable-1.7-0/xtable/R/toLatex.R |only
xtable-1.7-0/xtable/data/tli.txt.gz |only
xtable-1.7-0/xtable/inst/doc/xtableGallery.pdf |binary
xtable-1.7-0/xtable/inst/doc/xtableGallery.snw | 118 ++
xtable-1.7-0/xtable/man/print.xtable.Rd | 163 ++--
xtable-1.7-0/xtable/man/toLatex.Rd |only
xtable-1.7-0/xtable/man/xtable.Rd | 27
14 files changed, 855 insertions(+), 522 deletions(-)
Title: Detection of disease-associated SNP interactions in case-parent
trio data
Diff between trio versions 1.4.23 dated 2012-02-06 and 1.4.24 dated 2012-02-10
Description: Testing SNPs and SNP interactions with a genotypic TDT.
This package furthermore contains functions for computing
pairwise values of LD measures and for identifying LD blocks,
as well as functions for setting up matched case pseudo-control
genotype data for case-parent trios in order to run trio logic
regreesion, to impute missing genotypes in trios, or to
simulate case-parent trios with disease risk dependent on SNP
interaction.
Author: Holger Schwender, Qing Li, Ingo Ruczinski
Maintainer: Holger Schwender
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/getLD.R | 20 +++++++++++++++-----
R/getLDlarge.R | 9 ++++++---
inst/doc/trio.pdf |binary
man/findLDblocks.Rd | 11 +++++++----
man/plot.getLD.Rd | 6 +++---
7 files changed, 41 insertions(+), 25 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.9-4 dated 2011-12-20 and 0.9-5 dated 2012-02-10
Description: Unmarked fits hierarchical models of animal abundance and
occurrence to data collected using survey methods such as point
counts, site occupancy sampling, distance sampling, removal
sampling, and double observer sampling. Parameters governing
the state and observation processes can be modeled as functions
of covariates.
Author: Ian Fiske, Richard Chandler, Andy Royle, Marc Kery
Maintainer: Richard Chandler
unmarked-0.9-4/unmarked/inst/doc/colext-gof.pdf |only
unmarked-0.9-4/unmarked/inst/doc/unmarked.bib |only
unmarked-0.9-5/unmarked/DESCRIPTION | 19
unmarked-0.9-5/unmarked/MD5 | 89 +
unmarked-0.9-5/unmarked/NAMESPACE | 5
unmarked-0.9-5/unmarked/R/boot.R |only
unmarked-0.9-5/unmarked/R/colext.R | 498 +++++-----
unmarked-0.9-5/unmarked/R/pcountOpen.R | 17
unmarked-0.9-5/unmarked/R/ranef.R |only
unmarked-0.9-5/unmarked/R/unmarkedFit.R | 304 ------
unmarked-0.9-5/unmarked/R/unmarkedFrame.R | 78 +
unmarked-0.9-5/unmarked/inst/bench/bench.pcountOpen.R | 25
unmarked-0.9-5/unmarked/inst/csv/alfl.capRecap.csv |only
unmarked-0.9-5/unmarked/inst/csv/alfl.csv |only
unmarked-0.9-5/unmarked/inst/csv/alflCovs.csv |only
unmarked-0.9-5/unmarked/inst/doc/cap-recap.Rnw |only
unmarked-0.9-5/unmarked/inst/doc/cap-recap.pdf |only
unmarked-0.9-5/unmarked/inst/doc/colext.pdf |binary
unmarked-0.9-5/unmarked/inst/doc/distsamp.Rnw | 4
unmarked-0.9-5/unmarked/inst/doc/distsamp.pdf |binary
unmarked-0.9-5/unmarked/inst/doc/unmarked.Rnw | 71 +
unmarked-0.9-5/unmarked/inst/doc/unmarked.pdf |binary
unmarked-0.9-5/unmarked/inst/unitTests/runTests.R | 25
unmarked-0.9-5/unmarked/inst/unitTests/runit.gdistsamp.R | 10
unmarked-0.9-5/unmarked/inst/unitTests/runit.nonparboot.R |only
unmarked-0.9-5/unmarked/inst/unitTests/runit.pcountOpen.R | 60 +
unmarked-0.9-5/unmarked/inst/unitTests/runit.ranef.R |only
unmarked-0.9-5/unmarked/inst/unitTests/runit.unmarkedMultFrame.R | 120 ++
unmarked-0.9-5/unmarked/inst/unitTests/sim.gdistsamp.R | 1
unmarked-0.9-5/unmarked/inst/unitTests/sim.pcountOpen.r | 72 -
unmarked-0.9-5/unmarked/inst/unitTests/sim.ranef.R |only
unmarked-0.9-5/unmarked/man/colext.Rd | 7
unmarked-0.9-5/unmarked/man/distsamp.Rd | 13
unmarked-0.9-5/unmarked/man/extract-methods.Rd | 34
unmarked-0.9-5/unmarked/man/gdistsamp.Rd | 7
unmarked-0.9-5/unmarked/man/gmultmix.Rd | 44
unmarked-0.9-5/unmarked/man/multinomPois.Rd | 43
unmarked-0.9-5/unmarked/man/nonparboot-methods.Rd | 3
unmarked-0.9-5/unmarked/man/occu.Rd | 5
unmarked-0.9-5/unmarked/man/occuRN.Rd | 9
unmarked-0.9-5/unmarked/man/parboot.Rd | 41
unmarked-0.9-5/unmarked/man/pcount.Rd | 17
unmarked-0.9-5/unmarked/man/pcountOpen.Rd | 58 -
unmarked-0.9-5/unmarked/man/ranef-methods.Rd |only
unmarked-0.9-5/unmarked/man/unmarked-package.Rd | 40
unmarked-0.9-5/unmarked/man/unmarkedMultFrame.Rd | 2
unmarked-0.9-5/unmarked/man/unmarkedRanef-class.Rd |only
unmarked-0.9-5/unmarked/src/nll_pcountOpen.cpp | 94 +
unmarked-0.9-5/unmarked/src/nll_pcountOpen.h | 6
unmarked-0.9-5/unmarked/vignettes |only
50 files changed, 987 insertions(+), 834 deletions(-)
Title: Korean NLP Package
Diff between KoNLP versions 0.0-9.0 dated 2012-01-04 and 0.0-9.2 dated 2012-02-10
Description: Korean language processing package. Morphlogical analyzer,
POS tagger, Keystroke converter, Hangul automata...
Author: Heewon Jeon
Maintainer: Heewon Jeon
KoNLP-0.0-9.0/KoNLP/man/makeTagList.Rd |only
KoNLP-0.0-9.2/KoNLP/DESCRIPTION | 13
KoNLP-0.0-9.2/KoNLP/MD5 | 36 +-
KoNLP-0.0-9.2/KoNLP/NAMESPACE | 3
KoNLP-0.0-9.2/KoNLP/NEWS | 7
KoNLP-0.0-9.2/KoNLP/R/KoAnalyzerRun.R | 177 ++++++-------
KoNLP-0.0-9.2/KoNLP/R/manageDic.R | 25 +
KoNLP-0.0-9.2/KoNLP/R/sysdata.rda |only
KoNLP-0.0-9.2/KoNLP/man/HangulAutomata.Rd | 2
KoNLP-0.0-9.2/KoNLP/man/MorphAnalyzer.Rd | 2
KoNLP-0.0-9.2/KoNLP/man/SimplePos09.Rd | 2
KoNLP-0.0-9.2/KoNLP/man/SimplePos22.Rd | 4
KoNLP-0.0-9.2/KoNLP/man/convertHangulStringToJamos.Rd | 2
KoNLP-0.0-9.2/KoNLP/man/convertHangulStringToKeyStrokes.Rd | 7
KoNLP-0.0-9.2/KoNLP/man/convertTag.Rd |only
KoNLP-0.0-9.2/KoNLP/man/detectInputEncoding.Rd | 4
KoNLP-0.0-9.2/KoNLP/man/doKoMorph.Rd | 2
KoNLP-0.0-9.2/KoNLP/man/extractNoun.Rd | 2
KoNLP-0.0-9.2/KoNLP/man/is.hangul.Rd | 12
KoNLP-0.0-9.2/KoNLP/man/is.jamo.Rd |only
KoNLP-0.0-9.2/KoNLP/man/reloadAllDic.Rd | 4
21 files changed, 160 insertions(+), 144 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Diff between ape versions 2.8 dated 2011-10-24 and 3.0 dated 2012-02-10
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree,
generalized skyline plots, estimation of absolute evolutionary
rates and clock-like trees using mean path lengths,
non-parametric rate smoothing and penalized likelihood.
Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR,
SDM, and triangle methods, and several methods handling
incomplete distance matrices (NJ*, BIONJ*, MVR*, and the
corresponding triangle method).
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre
Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer
Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian
Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis
DESCRIPTION | 8 -
MD5 | 96 ++++++++-------
NEWS | 64 ++++++++++
R/DNA.R | 4
R/PGLS.R | 271 +++++++++++++++++++++------------------------
R/ace.R | 2
R/chronopl.R | 102 +++++++++-------
R/clustal.R | 6
R/compute.brtime.R | 2
R/dbd.R |only
R/dist.topo.R | 94 ++++++++++++---
R/drop.tip.R | 8 -
R/is.ultrametric.R | 36 +++--
R/mantel.test.R | 19 +--
R/nodelabels.R | 11 +
R/plot.phylo.R | 37 ++----
R/rTrait.R | 6
R/read.nexus.R | 10 -
R/read.tree.R | 2
R/rtree.R | 12 -
R/vcv.phylo.R | 66 +++++-----
R/write.nexus.R | 54 ++------
R/yule.R | 19 +--
Thanks | 9 -
data/hivtree.newick.rda |binary
data/hivtree.table.txt.gz |binary
data/landplants.newick.rda |binary
data/opsin.newick.rda |binary
inst/doc/MoranI.pdf |binary
man/DNAbin.Rd | 3
man/ape-internal.Rd | 5
man/bionj.Rd | 7 -
man/boot.phylo.Rd | 6
man/chronopl.Rd | 21 ++-
man/dbd.Rd |only
man/fastme.Rd | 7 -
man/mantel.test.Rd | 2
man/nj.Rd | 7 -
man/nodelabels.Rd | 4
man/pcoa.Rd | 2
man/plot.phylo.Rd | 6
man/rTraitDisc.Rd | 9 +
man/read.nexus.Rd | 6
man/read.tree.Rd | 5
man/write.nexus.Rd | 10 -
src/BIONJ.c | 14 --
src/dist_dna.c | 77 ++++++++----
src/me.c | 14 --
src/me_ols.c | 4
src/newick.c | 14 --
50 files changed, 658 insertions(+), 503 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-09-26 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-01-13 1.0.0