Title: R Package for Fitting the Multinomial Probit Model
Diff between MNP versions 2.6-3 dated 2011-12-07 and 2.6-4 dated 2013-06-09
Description: MNP is a publicly available R package that fits the
Bayesian multinomial probit model via Markov chain Monte Carlo.
The multinomial probit model is often used to analyze the
discrete choices made by individuals recorded in survey data.
Examples where the multinomial probit model may be useful
include the analysis of product choice by consumers in market
research and the analysis of candidate or party choice by
voters in electoral studies. The MNP software can also fit the
model with different choice sets for each individual, and
complete or partial individual choice orderings of the
available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm
that is developed by Imai and van Dyk (2005). ``A Bayesian
Analysis of the Multinomial Probit Model Using the Data
Augmentation,'' Journal of Econometrics, Vol. 124, No. 2
(February), pp. 311-334. Detailed examples are given in Imai
and van Dyk (2005). ``MNP: R Package for Fitting the
Multinomial Probit Model.'' Journal of Statistical Software,
Vol. 14, No. 3 (May), pp. 1-32.
Author: Kosuke Imai
Maintainer: Kosuke Imai
DESCRIPTION | 49 ++++++++++++++++++++++++++-----------------------
MD5 | 10 +++++-----
MNP.pdf |binary
R/mnp.R | 4 ++--
R/onAttach.R | 7 ++++---
R/xmatrix.mnp.R | 2 +-
6 files changed, 38 insertions(+), 34 deletions(-)
Title: eXtensible Time Series
Diff between xts versions 0.9-3 dated 2013-01-20 and 0.9-4 dated 2013-06-09
Description: Provide for uniform handling of R's different time-based
data classes by extending zoo, maximizing native format
information preservation and allowing for user level
customization and extension, while simplifying cross-class
interoperability.
Author: Jeffrey A. Ryan, Joshua M. Ulrich
Maintainer: Jeffrey A. Ryan
DESCRIPTION | 9 ++++----
MD5 | 44 ++++++++++++++++++++++---------------------
R/bind.R | 2 -
R/index.R | 8 +++++--
R/indexClass.R | 4 +++
R/merge.R | 4 ++-
R/parse8601.R | 6 ++---
R/rollapply.xts.R | 14 +++++++------
R/toperiod.R | 4 +--
R/xts.methods.R | 4 +--
inst/api_example/DESCRIPTION | 2 -
inst/doc/xts-faq.R |only
inst/doc/xts-faq.pdf |binary
inst/doc/xts.R |only
inst/doc/xts.pdf |binary
inst/include/xts.h | 10 ++++++++-
inst/include/xtsAPI.h | 43 ++++++++++++++++++++++++++++++++++++++++++
man/merge.Rd | 6 ++++-
man/xts-package.Rd | 2 -
src/init.c | 13 ++++++++----
src/period.max.f | 2 -
src/period.sum.f | 2 -
src/rbind.c | 1
src/xts.h | 10 ++++++++-
24 files changed, 137 insertions(+), 53 deletions(-)
Title: Simulating trees under the birth-death model
Diff between TreeSim versions 1.8 dated 2013-04-16 and 1.9 dated 2013-06-09
Description: The package simulates phylogenetic trees where (i) all
tips are sampled at one time point or (ii) tips are sampled
sequentially through time. (i) For sampling at one time point,
simulations are performed under a constant-rate birth-death
process, conditioned on having a fixed number of final tips
(sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and
number of tips (sim.bd.taxa.age). When conditioning on the
number of final tips, the method allows for shifts in rates and
mass extinction events during the birth-death process
(sim.rateshift.taxa).sim.bd.age (and sim.rateshift.taxa without
extinction) allow the speciation rate to change in a
density-dependent way. The LTT plots of the simulations can be
displayed using LTT.plot, LTT.plot.gen and LTT.average.root.
TreeSim further samples appropriately trees with n final tips
from a set of trees generated by the common sampling algorithm
stopping when a fixed number m>>n of leaves is first reached
(sim.gsa.taxa). This latter method is appropriate for m-tip
trees generated under a big class of models (details in the
sim.gsa.taxa man page). For incomplete phylogeny, the missing
speciation events can be added through simulations (corsim).
(ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for
serially sampled trees, where the trees are conditioned on
either the number of sampled tips or the age. Furthermore, for
a multitype-branching process with sequential sampling, trees
on a fixed number of tips can be simulated using
sim.bdtypes.stt.taxa.
Author: Tanja Stadler
Maintainer: Tanja Stadler
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/sim2.bd.fast.single.mrca.R | 6 +++++-
R/sim2.bd.fast.single.origin.R | 1 +
man/TreeSim-package.Rd | 4 ++--
man/corsim.Rd | 3 ++-
man/sim.bdsky.stt.Rd | 3 ++-
man/sim.bdtypes.stt.taxa.Rd | 3 ++-
8 files changed, 25 insertions(+), 17 deletions(-)
Title: Perceptual analysis, visualization and organization of spectral
color data in R
Diff between pavo versions 0.3-1 dated 2013-05-06 and 0.5 dated 2013-06-09
Description: A cohesive framework for parsing, analyzing and organizing
color from spectral data
Author: Rafael Maia [aut, cre], Chad Eliason [aut], Pierre-Paul Bitton
[aut]
Maintainer: Rafael Maia
DESCRIPTION | 6 +-
MD5 | 28 +++++-----
NEWS | 11 +++
R/coldist.R | 23 ++++++--
R/internal.R | 23 ++++++++
R/plot.rspec.r | 15 +++--
R/spec2rgb.R | 5 +
R/summary.rspec.R | 142 ++++++++++++++++++++++++++++++++++++---------------
R/tcsplot.R | 31 +++++++----
R/vismodel.R | 48 +++++++++++------
inst/CITATION | 8 +-
man/coldist.Rd | 3 -
man/summary.rspec.Rd | 17 +++---
man/tcsplot.Rd | 16 +++++
man/vismodel.Rd | 5 +
15 files changed, 275 insertions(+), 106 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.2 dated 2013-04-17 and 0.3 dated 2013-06-09
Description: Basic R package to access the data structures offered by
the BEFdata portal.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
rbefdata-0.2/rbefdata/R/bef.combineObjects.R |only
rbefdata-0.2/rbefdata/R/bef.getDataset.R |only
rbefdata-0.2/rbefdata/R/bef.getKeywords.R |only
rbefdata-0.2/rbefdata/R/bef.getMetadata.R |only
rbefdata-0.2/rbefdata/R/bef.getProposal.R |only
rbefdata-0.2/rbefdata/R/bef.getdata.R |only
rbefdata-0.2/rbefdata/R/bef.searchTematres.R |only
rbefdata-0.2/rbefdata/R/bef.searchTematresLower.R |only
rbefdata-0.2/rbefdata/R/bef.searchTematresUpper.R |only
rbefdata-0.2/rbefdata/man/bef.combineObjects.Rd |only
rbefdata-0.2/rbefdata/man/bef.getDataset.Rd |only
rbefdata-0.2/rbefdata/man/bef.getKeywords.Rd |only
rbefdata-0.2/rbefdata/man/bef.getMetadata.Rd |only
rbefdata-0.2/rbefdata/man/bef.getProposal.Rd |only
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rbefdata-0.2/rbefdata/man/bef.searchTematres.Rd |only
rbefdata-0.2/rbefdata/man/bef.searchTematresLower.Rd |only
rbefdata-0.2/rbefdata/man/bef.searchTematresUpper.Rd |only
rbefdata-0.3/rbefdata/DESCRIPTION | 37 ++++--
rbefdata-0.3/rbefdata/MD5 | 55 +++++-----
rbefdata-0.3/rbefdata/NAMESPACE | 12 ++
rbefdata-0.3/rbefdata/NEWS | 21 +++
rbefdata-0.3/rbefdata/R/bef.options.R | 4
rbefdata-0.3/rbefdata/R/bef.portal.get.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.attachment.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.dataset.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.dataset_list.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.keywords.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.metadata.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.proposal.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.broader_keywords.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.keywords.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.narrower_keywords.R |only
rbefdata-0.3/rbefdata/R/helper.R |only
rbefdata-0.3/rbefdata/R/rbefdata-defunct.R |only
rbefdata-0.3/rbefdata/R/zzz.R | 3
rbefdata-0.3/rbefdata/inst |only
rbefdata-0.3/rbefdata/man/bef.portal.get.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.attachment.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.dataset.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.dataset_list.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.keywords.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.metadata.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.proposal.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.broader_keywords.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.keywords.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.narrower_keywords.Rd |only
rbefdata-0.3/rbefdata/man/rbefdata-defunct.Rd |only
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51 files changed, 90 insertions(+), 42 deletions(-)
Title: Calculate observed and expected disease incidence counts from a
case file and population data.
Diff between diseasemapping versions 0.6 dated 2012-01-17 and 0.7.3 dated 2013-06-09
More information about diseasemapping at CRAN
Description: Tools for calculating rates and Standardized Incidence
Ratios from case and population data.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 22 +++++++++++++---------
MD5 | 41 ++++++++++++++++++++++-------------------
R/cancerRates.R | 8 +++-----
R/computeArea.r | 5 ++---
R/formatCases.R | 8 --------
R/getBreaks.R | 6 +++++-
R/getSMR.data.frame.R | 17 ++++++++++++++---
R/getStdRate.R | 24 +++++++-----------------
R/mergeBugsData.R | 1 +
data/casedata.RData |binary
data/datalist |only
data/kentucky.RData |only
data/popdata.RData |binary
data/referencepop.RData |binary
man/diseasemapping-package.Rd | 35 +++++++++++++++++++++++++++++++++++
man/expandCensus.Rd | 3 ++-
man/formatCases.Rd | 3 ++-
man/formatPopulation.Rd | 15 +++++++++------
man/getBreaks.Rd | 4 ++--
man/getSMR.Rd | 11 ++++++++---
man/getStdRate.Rd | 6 +++---
man/kentucky.Rd |only
man/referencepop.Rd | 9 ++++++---
23 files changed, 134 insertions(+), 84 deletions(-)
Permanent link
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.14 dated 2013-05-22 and 0.9.15 dated 2013-06-09
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8 -
MD5 | 106 +++++++++----------
NEWS | 7 +
R/IBD.r | 215 +++++++++++++++++++++++++---------------
R/SNPRelate_Main.r | 12 +-
inst/doc/SNPRelateTutorial.R | 125 ++++++++++++++---------
inst/doc/SNPRelateTutorial.Rnw | 65 +++++++++---
inst/doc/SNPRelateTutorial.pdf |binary
man/SNPRelate-package.Rd | 19 +--
man/snpgdsBED2GDS.Rd | 2
man/snpgdsCombineGeno.Rd | 2
man/snpgdsCreateGeno.Rd | 2
man/snpgdsCreateGenoSet.Rd | 2
man/snpgdsCutTree.Rd | 2
man/snpgdsDiss.Rd | 2
man/snpgdsDrawTree.Rd | 2
man/snpgdsErrMsg.Rd | 2
man/snpgdsExampleFileName.Rd | 2
man/snpgdsGDS2BED.Rd | 2
man/snpgdsGDS2Eigen.Rd | 2
man/snpgdsGDS2PED.Rd | 2
man/snpgdsGetGeno.Rd | 2
man/snpgdsHCluster.Rd | 2
man/snpgdsIBDKING.Rd | 101 +++++++++++-------
man/snpgdsIBDMLE.Rd | 11 +-
man/snpgdsIBDMLELogLik.Rd | 2
man/snpgdsIBDMoM.Rd | 13 ++
man/snpgdsIBDSelection.Rd | 38 +++----
man/snpgdsIBS.Rd | 2
man/snpgdsIBSNum.Rd | 2
man/snpgdsIndInb.Rd | 2
man/snpgdsIndInbCoef.Rd | 2
man/snpgdsLDMat.Rd | 2
man/snpgdsLDpair.Rd | 2
man/snpgdsLDpruning.Rd | 2
man/snpgdsOption.Rd | 2
man/snpgdsPCA.Rd | 72 ++++++++++---
man/snpgdsPCACorr.Rd | 2
man/snpgdsPCASNPLoading.Rd | 2
man/snpgdsPCASampLoading.Rd | 2
man/snpgdsPairIBD.Rd | 2
man/snpgdsPairIBDMLELogLik.Rd | 2
man/snpgdsSNPList.Rd | 2
man/snpgdsSNPListClass.Rd | 2
man/snpgdsSNPListIntersect.Rd | 2
man/snpgdsSNPListStrand.Rd | 2
man/snpgdsSNPRateFreq.Rd | 2
man/snpgdsSampMissrate.Rd | 2
man/snpgdsSelectSNP.Rd | 2
man/snpgdsSummary.Rd | 2
man/snpgdsVCF2GDS.Rd | 2
src/SNPRelate.cpp | 142 ++++++++++++--------------
src/genIBS.cpp | 35 +-----
vignettes/SNPRelateTutorial.Rnw | 65 +++++++++---
54 files changed, 669 insertions(+), 439 deletions(-)
Title: Iterated Racing Procedures
Diff between irace versions 1.03 dated 2013-01-15 and 1.04 dated 2013-06-09
Description: Iterated racing for automatic algorithm configuration
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Thomas Stützle,
Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez
DESCRIPTION | 13 +++++-----
MD5 | 27 +++++++++++----------
NAMESPACE | 1
NEWS | 7 +++++
R/irace.R | 2 -
R/main.R | 6 ++--
R/model.R | 2 -
R/race-wrapper.R | 51 +++++++++++++++++++++++++++++------------
R/version.R | 2 -
README | 9 ++++++-
inst/examples/acotsp/tune-conf | 5 +---
inst/examples/tune-main-tmp |only
inst/templates/tune-conf.tmpl | 5 +---
man/irace-package.Rd | 4 +--
svn_version | 2 -
15 files changed, 86 insertions(+), 50 deletions(-)