Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.2-50 dated 2013-04-20 and 0.2-70 dated 2013-05-22
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
phytools-0.2-50/phytools/man/applyEdgeLengths.Rd |only
phytools-0.2-70/phytools/DESCRIPTION | 8
phytools-0.2-70/phytools/MD5 | 234 +++---
phytools-0.2-70/phytools/NAMESPACE | 13
phytools-0.2-70/phytools/R/contMap.R | 77 +-
phytools-0.2-70/phytools/R/densityMap.R | 40 -
phytools-0.2-70/phytools/R/estDiversity.R | 6
phytools-0.2-70/phytools/R/evol.vcv.R | 28
phytools-0.2-70/phytools/R/fastAnc.R | 6
phytools-0.2-70/phytools/R/make.simmap.R | 290 ++++++--
phytools-0.2-70/phytools/R/phylomorphospace.R | 17
phytools-0.2-70/phytools/R/read.simmap.R | 707 ++++++++------------
phytools-0.2-70/phytools/R/rerootingMethod.R | 6
phytools-0.2-70/phytools/R/utilities.R | 157 +++-
phytools-0.2-70/phytools/man/add.color.bar.Rd | 2
phytools-0.2-70/phytools/man/add.everywhere.Rd | 13
phytools-0.2-70/phytools/man/add.random.Rd | 4
phytools-0.2-70/phytools/man/allFurcTrees.Rd | 18
phytools-0.2-70/phytools/man/anc.Bayes.Rd | 12
phytools-0.2-70/phytools/man/anc.ML.Rd | 10
phytools-0.2-70/phytools/man/anc.trend.Rd | 25
phytools-0.2-70/phytools/man/applyBranchLengths.Rd |only
phytools-0.2-70/phytools/man/ave.rates.Rd | 6
phytools-0.2-70/phytools/man/bind.tip.Rd | 4
phytools-0.2-70/phytools/man/bmPlot.Rd | 34
phytools-0.2-70/phytools/man/branching.diffusion.Rd | 25
phytools-0.2-70/phytools/man/brownie.lite.Rd | 9
phytools-0.2-70/phytools/man/brownieREML.Rd | 29
phytools-0.2-70/phytools/man/contMap.Rd | 15
phytools-0.2-70/phytools/man/countSimmap.Rd | 14
phytools-0.2-70/phytools/man/densityMap.Rd | 12
phytools-0.2-70/phytools/man/describe.simmap.Rd | 4
phytools-0.2-70/phytools/man/drop.clade.Rd | 12
phytools-0.2-70/phytools/man/drop.tip.simmap.Rd | 17
phytools-0.2-70/phytools/man/estDiversity.Rd | 6
phytools-0.2-70/phytools/man/evol.rate.mcmc.Rd | 6
phytools-0.2-70/phytools/man/evol.vcv.Rd | 40 -
phytools-0.2-70/phytools/man/evolvcv.lite.Rd | 16
phytools-0.2-70/phytools/man/exhaustiveMP.Rd | 18
phytools-0.2-70/phytools/man/expm.Rd | 6
phytools-0.2-70/phytools/man/export.as.xml.Rd | 6
phytools-0.2-70/phytools/man/fancyTree.Rd | 62 -
phytools-0.2-70/phytools/man/fastAnc.Rd | 4
phytools-0.2-70/phytools/man/fastBM.Rd | 20
phytools-0.2-70/phytools/man/fastMRCA.Rd | 12
phytools-0.2-70/phytools/man/findMRCA.Rd | 4
phytools-0.2-70/phytools/man/fitBayes.Rd | 4
phytools-0.2-70/phytools/man/fitDiversityModel.Rd | 26
phytools-0.2-70/phytools/man/gammatest.Rd | 12
phytools-0.2-70/phytools/man/getCladesofSize.Rd |only
phytools-0.2-70/phytools/man/getDescendants.Rd | 10
phytools-0.2-70/phytools/man/getExtant.Rd | 10
phytools-0.2-70/phytools/man/getSisters.Rd | 6
phytools-0.2-70/phytools/man/getStates.Rd | 6
phytools-0.2-70/phytools/man/lambda.transform.Rd | 14
phytools-0.2-70/phytools/man/likMlambda.Rd | 12
phytools-0.2-70/phytools/man/ls.tree.Rd | 10
phytools-0.2-70/phytools/man/ltt.Rd | 18
phytools-0.2-70/phytools/man/ltt95.Rd | 8
phytools-0.2-70/phytools/man/make.era.map.Rd | 10
phytools-0.2-70/phytools/man/make.simmap.Rd | 28
phytools-0.2-70/phytools/man/map.overlap.Rd | 12
phytools-0.2-70/phytools/man/matchNodes.Rd | 4
phytools-0.2-70/phytools/man/mergeMappedStates.Rd |only
phytools-0.2-70/phytools/man/minSplit.Rd | 21
phytools-0.2-70/phytools/man/mrp.supertree.Rd | 14
phytools-0.2-70/phytools/man/multi.mantel.Rd | 9
phytools-0.2-70/phytools/man/multiC.Rd | 8
phytools-0.2-70/phytools/man/nodeHeights.Rd | 14
phytools-0.2-70/phytools/man/optim.phylo.ls.Rd | 30
phytools-0.2-70/phytools/man/orderMappedEdge.Rd | 4
phytools-0.2-70/phytools/man/paintSubTree.Rd | 20
phytools-0.2-70/phytools/man/paste.tree.Rd | 20
phytools-0.2-70/phytools/man/pbtree.Rd | 16
phytools-0.2-70/phytools/man/pgls.Ives.Rd | 11
phytools-0.2-70/phytools/man/phenogram.Rd | 30
phytools-0.2-70/phytools/man/phyl.RMA.Rd | 6
phytools-0.2-70/phytools/man/phyl.cca.Rd | 6
phytools-0.2-70/phytools/man/phyl.pairedttest.Rd | 42 -
phytools-0.2-70/phytools/man/phyl.pca.Rd | 8
phytools-0.2-70/phytools/man/phyl.resid.Rd | 10
phytools-0.2-70/phytools/man/phyl.vcv.Rd | 4
phytools-0.2-70/phytools/man/phylANOVA.Rd | 32
phytools-0.2-70/phytools/man/phyloDesign.Rd | 6
phytools-0.2-70/phytools/man/phylomorphospace.Rd | 16
phytools-0.2-70/phytools/man/phylomorphospace3d.Rd | 16
phytools-0.2-70/phytools/man/phylosig.Rd | 20
phytools-0.2-70/phytools/man/plotBranchbyTrait.Rd | 4
phytools-0.2-70/phytools/man/plotSimmap.Rd | 22
phytools-0.2-70/phytools/man/plotThresh.Rd | 4
phytools-0.2-70/phytools/man/plotTree.Rd | 10
phytools-0.2-70/phytools/man/posterior.evolrate.Rd | 6
phytools-0.2-70/phytools/man/read.newick.Rd | 12
phytools-0.2-70/phytools/man/read.simmap.Rd | 8
phytools-0.2-70/phytools/man/reorderSimmap.Rd | 10
phytools-0.2-70/phytools/man/repPhylo.Rd | 6
phytools-0.2-70/phytools/man/reroot.Rd | 6
phytools-0.2-70/phytools/man/rerootingMethod.Rd | 4
phytools-0.2-70/phytools/man/rescaleSimmap.Rd | 8
phytools-0.2-70/phytools/man/roundBranches.Rd | 4
phytools-0.2-70/phytools/man/rstate.Rd | 4
phytools-0.2-70/phytools/man/sampleFrom.Rd | 14
phytools-0.2-70/phytools/man/sim.corrs.Rd | 14
phytools-0.2-70/phytools/man/sim.history.Rd | 20
phytools-0.2-70/phytools/man/sim.ratebystate.Rd | 2
phytools-0.2-70/phytools/man/sim.rates.Rd | 18
phytools-0.2-70/phytools/man/splitTree.Rd | 10
phytools-0.2-70/phytools/man/splitplotTree.Rd | 4
phytools-0.2-70/phytools/man/starTree.Rd | 12
phytools-0.2-70/phytools/man/strahlerNumber.Rd | 4
phytools-0.2-70/phytools/man/threshBayes.Rd | 16
phytools-0.2-70/phytools/man/threshDIC.Rd | 4
phytools-0.2-70/phytools/man/threshState.Rd | 4
phytools-0.2-70/phytools/man/to.matrix.Rd | 2
phytools-0.2-70/phytools/man/treeSlice.Rd | 12
phytools-0.2-70/phytools/man/untangle.Rd | 4
phytools-0.2-70/phytools/man/vcvPhylo.Rd | 8
phytools-0.2-70/phytools/man/write.simmap.Rd | 24
phytools-0.2-70/phytools/man/writeAncestors.Rd | 2
phytools-0.2-70/phytools/man/writeNexus.Rd | 2
120 files changed, 1548 insertions(+), 1343 deletions(-)
Title: Exploring water quality monitoring data
Diff between wq versions 0.3-8 dated 2012-09-09 and 0.3-9 dated 2013-05-22
Description: Functions to assist in the processing and exploration of
data from monitoring programs for aquatic ecosystems. The name
"wq" stands for "water quality" and reflects a focus on time
series data for physical and chemical properties of water, as
well as the plankton. The package is intended for programs that
sample approximately monthly at discrete stations, a feature of
many legacy data sets. Although our emphasis is on aquatic
ecosystems, most of the functions should be useful for analysis
of similar-frequency time series regardless of the subject
matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby
ChangeLog | 6 +++++-
DESCRIPTION | 9 +++++----
MD5 | 19 +++++++++++++------
R/plotSeason.R | 4 ++--
R/plotTsAnom.R | 16 ++++++++--------
inst/CITATION | 2 +-
inst/doc |only
man/wq-package.Rd | 4 ++--
vignettes |only
9 files changed, 36 insertions(+), 24 deletions(-)
Title: Automate parallelization of function calls by means of dynamic
code analysis
Diff between parallelize.dynamic versions 0.9 dated 2013-05-08 and 0.9-1 dated 2013-05-22
More information about parallelize.dynamic at CRAN
Description: Passing a given function name or a call to the
parallelize/parallelize_call functions analyses and executes
the code, if possible in parallel. Parallel code execution can
be performed locally or on remote batch queuing systems.
Author: Stefan Boehringer
Maintainer: Stefan Boehringer
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/Rdata.R | 14 ++++++++++++--
R/Rparallel.R | 4 +++-
R/Rparallel.back.R | 3 ++-
R/Rsystem.R | 16 ++++++++--------
6 files changed, 33 insertions(+), 20 deletions(-)
Permanent link
Title: Sample size calculations for longitudinal data
Diff between longpower versions 1.0-4 dated 2013-01-23 and 1.0-7 dated 2013-05-22
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue
DESCRIPTION | 14 +++---
MD5 | 31 +++++++-------
NAMESPACE | 2
R/lmmpower.R | 4 -
README.markdown |only
inst/CITATION | 2
inst/doc/longpower.R |only
inst/doc/longpower.Rnw | 90 ++++++++++++++++++++++--------------------
inst/doc/longpower.bib |only
inst/doc/longpower.pdf |binary
man/diggle.linear.power.Rd | 74 +++++++++-------------------------
man/edland.linear.power.Rd | 12 -----
man/liu.liang.linear.power.Rd | 31 +-------------
man/lmmpower-methods.Rd | 50 ++---------------------
man/longpower-package.Rd | 16 ++-----
man/power.mmrm.Rd | 10 ----
man/power.mmrm.ar1.Rd | 44 ++++++++++++--------
man/print.power.longtest.Rd | 5 --
18 files changed, 143 insertions(+), 242 deletions(-)
Title: Genetic diversity partition statistics and Informative locus
selection using Fst, Gst, Dest(Jost Chao) G'st and In.
Diff between diveRsity versions 1.4.6 dated 2013-04-01 and 1.5.0 dated 2013-05-22
Description: diveRsity is a package which allows the calculation of
both genetic diversity partition statistics, genetic
differentiation statistics and locus informativeness for
ancestry assignment. It also provides users with various option
to calculate bootstrapped 95% confidence intervals both across
loci, for pairwise population comparisons and to plot these
results interactively. V1.2 and up provides parallel computing
capabilities and pairwise results without bootstrapping. Weir
and Cockerham's 1984 F-statistics are now also calculated.
Various plotting features are also provided. Chi-square tests
of genetic heterogeneity are also provided. Functionality for
the calculation of various diversity parameters is also
possible for RAD-seq derived SNP data sets containing thousands
of marker loci.
Author: Kevin Keenan,
Maintainer: Kevin Keenan
diveRsity-1.4.6/diveRsity/R/diveRsity_v1.4.6.R |only
diveRsity-1.5.0/diveRsity/DESCRIPTION | 10 +++++-----
diveRsity-1.5.0/diveRsity/MD5 | 10 ++++++----
diveRsity-1.5.0/diveRsity/R/diveRsity_v1.5.0.R |only
diveRsity-1.5.0/diveRsity/data/pop_stats.rda |binary
diveRsity-1.5.0/diveRsity/inst/CITATION |only
diveRsity-1.5.0/diveRsity/inst/doc/diveRsity.R |only
diveRsity-1.5.0/diveRsity/inst/doc/diveRsity.pdf |binary
8 files changed, 11 insertions(+), 9 deletions(-)
Title: Logistic Regression
Diff between BayesLogit versions 0.2-2 dated 2013-05-07 and 0.2-4 dated 2013-05-22
Description: The BayesLogit package does posterior simulation for
binomial and multinomial logistic regression using the
Polya-Gamma latent variable technique. This method is fully
automatic, exact, and fast. A routine to efficiently sample
from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle
DESCRIPTION | 8 ++--
MD5 | 20 +++++------
inst/Dynamic/DESCRIPTION | 6 +--
inst/Static/DESCRIPTION | 4 +-
man/rpg.Rd | 10 ++---
src/Makevars | 4 +-
src/Matrix.h | 33 +++++++++----------
src/MatrixFrame.cpp | 4 ++
src/MatrixFrame.h | 79 ++++++++++++++++++++++++++++++++++++++++++++---
src/PolyaGamma.cpp | 28 ++++++++++++----
src/PolyaGamma.h | 2 -
11 files changed, 142 insertions(+), 56 deletions(-)
Title: Analysis of Multivariate Event Times
Diff between mets versions 0.2.2 dated 2013-05-21 and 0.2.3 dated 2013-05-22
Description: Implementation of various statistical models for
multivariate event history data. Including multivariate
cumulative incidence models, and bivariate random effects
probit models (Liability models)
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
DESCRIPTION | 8 ++++----
MD5 | 34 ++++++++++++++++++----------------
NAMESPACE | 16 ++++++++--------
R/bicomprisk.R | 2 +-
R/biprobit.R | 2 +-
R/biprobit.strata.R | 3 ++-
R/bptwin.R | 2 +-
R/fastreshape.R | 5 +++--
R/logLik.biprobit.R | 2 +-
R/mets-packages.R | 8 ++++++++
R/surv.boxarea.R | 2 +-
R/twinlm.R | 11 ++++++-----
R/twinsim.R | 15 ++++++++++++---
data/datalist | 1 +
data/migr.txt.gz |only
inst/tests/test_reshape.R | 29 ++++++++++++++++++-----------
man/fast.reshape.Rd | 2 +-
man/migr.Rd |only
man/twinlm.Rd | 9 +++++----
19 files changed, 91 insertions(+), 60 deletions(-)
Title: adephylo: exploratory analyses for the phylogenetic comparative
method.
Diff between adephylo versions 1.1-3 dated 2012-10-31 and 1.1-4 dated 2013-05-22
Description: Multivariate tools to analyze comparative data, i.e. a
phylogeny and some traits measured for each taxa.
Author: Thibaut Jombart
Maintainer: Thibaut Jombart
ChangeLog | 12 +++
DESCRIPTION | 13 ++-
MD5 | 95 ++++++++++++++--------------
R/bullseye.R |only
R/dibas.R | 110 +++++++++++++++++++++++++++++++--
data/carni19.RData |binary
data/carni70.RData |binary
data/lizards.RData |binary
data/maples.RData |binary
data/mjrochet.RData |binary
data/palm.RData |binary
data/procella.RData |binary
data/tithonia.RData |binary
data/ungulates.RData |binary
inst/doc/adephylo.R |only
inst/doc/adephylo.pdf |binary
man/abouheif.Rd | 22 +++---
man/adephylo.package.Rd | 29 +++++---
man/bullseye.Rd |only
man/carni19.Rd | 9 +-
man/carni70.Rd | 10 ++-
man/dibas.Rd | 28 ++++++--
man/distRoot.Rd | 5 -
man/distTips.Rd | 9 +-
man/lizards.Rd | 10 +--
man/maples.Rd | 14 ++--
man/mjrochet.Rd | 19 +++--
man/orthobasis.Rd | 8 +-
man/orthogram.Rd | 56 ++++++++++++----
man/palm.Rd | 7 +-
man/ppca.Rd | 12 ++-
man/procella.Rd | 9 +-
man/proxTips.Rd | 7 +-
man/sp.tips.Rd | 6 -
man/table.phylo4d.Rd | 43 +++++++-----
man/tithonia.Rd | 4 -
man/treePart.Rd | 7 +-
man/ungulates.Rd | 4 -
vignettes/figs/adephylo-012.pdf |binary
vignettes/figs/adephylo-016.pdf |binary
vignettes/figs/adephylo-018.pdf |binary
vignettes/figs/adephylo-aboutest.pdf |binary
vignettes/figs/adephylo-figFourBas.pdf |binary
vignettes/figs/adephylo-lm1.pdf |binary
vignettes/figs/adephylo-loadings.pdf |binary
vignettes/figs/adephylo-orthobas1.pdf |binary
vignettes/figs/adephylo-pca1.pdf |binary
vignettes/figs/adephylo-pca2.pdf |binary
vignettes/figs/adephylo-phylo4d.pdf |binary
vignettes/figs/adephylo-resid.pdf |binary
50 files changed, 384 insertions(+), 164 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.13 dated 2013-02-26 and 0.9.14 dated 2013-05-22
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
SNPRelate-0.9.13/SNPRelate/R/main.r |only
SNPRelate-0.9.13/SNPRelate/src/main.cpp |only
SNPRelate-0.9.14/SNPRelate/DESCRIPTION | 8
SNPRelate-0.9.14/SNPRelate/MD5 | 82 +--
SNPRelate-0.9.14/SNPRelate/NEWS | 56 +-
SNPRelate-0.9.14/SNPRelate/R/IBD.r |only
SNPRelate-0.9.14/SNPRelate/R/IBS.r |only
SNPRelate-0.9.14/SNPRelate/R/LD.r |only
SNPRelate-0.9.14/SNPRelate/R/PCA.r |only
SNPRelate-0.9.14/SNPRelate/R/SNPRelate_Main.r |only
SNPRelate-0.9.14/SNPRelate/inst/CITATION | 10
SNPRelate-0.9.14/SNPRelate/inst/doc/SNPRelateTutorial.R |only
SNPRelate-0.9.14/SNPRelate/inst/doc/SNPRelateTutorial.Rnw | 9
SNPRelate-0.9.14/SNPRelate/inst/doc/SNPRelateTutorial.pdf |binary
SNPRelate-0.9.14/SNPRelate/man/SNPRelate-package.Rd | 10
SNPRelate-0.9.14/SNPRelate/man/snpgdsCutTree.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsDiss.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsDrawTree.Rd | 8
SNPRelate-0.9.14/SNPRelate/man/snpgdsGDS2BED.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsGDS2Eigen.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsGDS2PED.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsGetGeno.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsHCluster.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDKING.Rd |only
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDMLE.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDMLELogLik.Rd | 5
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBDMoM.Rd | 10
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBS.Rd | 7
SNPRelate-0.9.14/SNPRelate/man/snpgdsIBSNum.Rd | 7
SNPRelate-0.9.14/SNPRelate/man/snpgdsIndInb.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsLDMat.Rd | 9
SNPRelate-0.9.14/SNPRelate/man/snpgdsLDpair.Rd | 7
SNPRelate-0.9.14/SNPRelate/man/snpgdsLDpruning.Rd | 11
SNPRelate-0.9.14/SNPRelate/man/snpgdsOption.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCA.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCACorr.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCASNPLoading.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsPCASampLoading.Rd | 6
SNPRelate-0.9.14/SNPRelate/man/snpgdsPairIBDMLELogLik.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsSNPList.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsSNPRateFreq.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsSampMissrate.Rd | 4
SNPRelate-0.9.14/SNPRelate/man/snpgdsSelectSNP.Rd | 2
SNPRelate-0.9.14/SNPRelate/man/snpgdsSummary.Rd | 2
SNPRelate-0.9.14/SNPRelate/src/SNPRelate.cpp |only
SNPRelate-0.9.14/SNPRelate/src/genIBS.cpp | 322 +++++++++++--
SNPRelate-0.9.14/SNPRelate/vignettes/SNPRelateTutorial.Rnw | 9
47 files changed, 446 insertions(+), 188 deletions(-)
Title: Solving biasing produced by tied values in cluster analysis.
Diff between recluster versions 1.9 dated 2013-03-29 and 2.1 dated 2013-05-22
Description: A high frequency of ties and zero values produces
hierarchical cluster dendrograms whose topology and bootstrap
supports are affected by the order of rows in the original
matrix. The recluster package evaluates the magnitude of this
bias and computes consensus trees after re-sampling the
original row order also applying this algorithm to a multiscale
bootstrap procedure.
Author: Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger
Vila, Gerard Talavera, Roger H.L. Dennis
Maintainer: Leonardo Dapporto
DESCRIPTION | 10 ++++-----
MD5 | 42 +++++++++++++++++++++++++---------------
NAMESPACE | 4 +--
R/recluster.boot.R | 2 -
R/recluster.col.R |only
R/recluster.cons.R | 31 ++++++++++++++++++++++-------
R/recluster.dist.R | 4 +--
R/recluster.expl.diss.R |only
R/recluster.group.colours.R |only
R/recluster.node.strength.R | 13 ++++++------
R/recluster.plot.col.R |only
R/recluster.plot.matrix.R |only
R/recluster.plot.sites.col.R |only
man/recluster.Rd | 42 +++++++++++++++++++++++++++++++---------
man/recluster.boot.Rd | 13 ++++++------
man/recluster.check.Rd | 2 -
man/recluster.col.Rd |only
man/recluster.cons.Rd | 38 ++++++++++++++++++++++++------------
man/recluster.dist.Rd | 13 ++++++++++--
man/recluster.expl.diss.Rd |only
man/recluster.group.col.Rd |only
man/recluster.hist.Rd | 4 +--
man/recluster.multi.Rd | 9 ++++----
man/recluster.node.strength.Rd | 15 ++++++++++++--
man/recluster.plot.Rd | 9 ++++----
man/recluster.plot.col.Rd |only
man/recluster.plot.matrix.Rd |only
man/recluster.plot.sites.col.Rd |only
28 files changed, 171 insertions(+), 80 deletions(-)
Title: Composite-likelihood based Analysis of Random Fields
Diff between CompRandFld versions 1.0.2 dated 2012-04-13 and 1.0.3 dated 2013-05-22
Description: The aim of this package is to collect a set of procedures
for the analysis of Random Fields by Composite Likelihood
methods. Spatial analysis often involves dealing with large
dataset. Therefore even simple studies may be too
computationally demanding. Composite likelihood based methods
are emerging as useful tools for mitigating such computational
problems and show satisfactory results when compared with other
techniques such as, for example the tapering method. Moreover,
composite likelihood (and related quantities) have some good
properties similar to those of the standard likelihood.
Author: Simone Padoan
Maintainer: Simone Padoan
CompRandFld-1.0.2/CompRandFld/R/zzz.r |only
CompRandFld-1.0.3/CompRandFld/DESCRIPTION | 22
CompRandFld-1.0.3/CompRandFld/MD5 | 91
CompRandFld-1.0.3/CompRandFld/R/CompositeLikelihood.r | 83
CompRandFld-1.0.3/CompRandFld/R/Covariogram.r | 22
CompRandFld-1.0.3/CompRandFld/R/Covmatrix.r |only
CompRandFld-1.0.3/CompRandFld/R/Distributions.r | 10
CompRandFld-1.0.3/CompRandFld/R/EmpiricalEstimators.r | 33
CompRandFld-1.0.3/CompRandFld/R/Fitting.r | 61
CompRandFld-1.0.3/CompRandFld/R/Kriging.r |only
CompRandFld-1.0.3/CompRandFld/R/Likelihood.r | 95
CompRandFld-1.0.3/CompRandFld/R/Simulation.r | 55
CompRandFld-1.0.3/CompRandFld/R/Statistics.r | 28
CompRandFld-1.0.3/CompRandFld/R/Utility.r | 284 +
CompRandFld-1.0.3/CompRandFld/R/WeightedLeastSquare.r | 68
CompRandFld-1.0.3/CompRandFld/data |only
CompRandFld-1.0.3/CompRandFld/inst/doc/CompRandFld-manual.pdf |binary
CompRandFld-1.0.3/CompRandFld/man/CheckCorrModel.Rd | 10
CompRandFld-1.0.3/CompRandFld/man/CheckInput.Rd | 23
CompRandFld-1.0.3/CompRandFld/man/CheckLikelihood.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/CheckModel.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/CheckType.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/CheckVarType.Rd | 6
CompRandFld-1.0.3/CompRandFld/man/CompLikelihood.Rd | 17
CompRandFld-1.0.3/CompRandFld/man/CorrelationParam.Rd | 10
CompRandFld-1.0.3/CompRandFld/man/Covariogram.Rd | 31
CompRandFld-1.0.3/CompRandFld/man/Covmatrix.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Dist2Dist.Rd | 10
CompRandFld-1.0.3/CompRandFld/man/EVariogram.Rd | 119
CompRandFld-1.0.3/CompRandFld/man/FitComposite.Rd | 348 +-
CompRandFld-1.0.3/CompRandFld/man/FitGev.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/GevLogLik.Rd | 8
CompRandFld-1.0.3/CompRandFld/man/HypoTest.Rd | 7
CompRandFld-1.0.3/CompRandFld/man/InitParam.Rd | 28
CompRandFld-1.0.3/CompRandFld/man/Irishcoords.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Irishwinds.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Kri.Rd |only
CompRandFld-1.0.3/CompRandFld/man/Likelihood.Rd | 9
CompRandFld-1.0.3/CompRandFld/man/MomEst.Rd | 7
CompRandFld-1.0.3/CompRandFld/man/NuisanceParam.Rd | 7
CompRandFld-1.0.3/CompRandFld/man/RFsim.Rd | 88
CompRandFld-1.0.3/CompRandFld/man/USarain.Rd |only
CompRandFld-1.0.3/CompRandFld/man/UScoord.Rd |only
CompRandFld-1.0.3/CompRandFld/man/WLeastSquare.Rd | 46
CompRandFld-1.0.3/CompRandFld/man/WlsInit.Rd | 29
CompRandFld-1.0.3/CompRandFld/src/CompositeLikelihood.c | 193 -
CompRandFld-1.0.3/CompRandFld/src/CorrelationFunction.c | 1218 +++++---
CompRandFld-1.0.3/CompRandFld/src/Godambe.c | 1520 +++++-----
CompRandFld-1.0.3/CompRandFld/src/Utility.c | 745 +++-
CompRandFld-1.0.3/CompRandFld/src/header.h | 154 -
CompRandFld-1.0.3/CompRandFld/src/weightedleastsquare.c | 415 +-
51 files changed, 3488 insertions(+), 2444 deletions(-)
Title: Graph Probability Distributions with User Supplied Parameters
and Stats.
Diff between visualize versions 3.0 dated 2013-02-15 and 4.1 dated 2013-05-22
Description: Graphs the pdf or pmf and highlights what area or
probability is present in user defined locations. Visualize is
able to provide lower tail, bounded, upper tail, and two tail
calculations. Supports strict and equal to inequalities. Also
provided on the graph is the mean and variance of the
distribution.
Author: James Balamuta
Maintainer: James Balamuta
DESCRIPTION | 10 ++---
MD5 | 50 ++++++++++++++---------------
R/visualize.continuous.R | 74 +++++++++++++++++++++++++++++++++-----------
R/visualize.discrete.R | 53 ++++++++++++++++++++++++++++++-
R/visualize.it.R | 6 +--
man/visualize-package.Rd | 17 +++++++---
man/visualize.beta.Rd | 2 -
man/visualize.binom.Rd | 5 --
man/visualize.cauchy.Rd | 2 -
man/visualize.chisq.Rd | 2 -
man/visualize.continuous.Rd | 2 -
man/visualize.discrete.Rd | 7 ++--
man/visualize.exp.Rd | 2 -
man/visualize.f.Rd | 2 -
man/visualize.gamma.Rd | 2 -
man/visualize.geom.Rd | 8 +---
man/visualize.hyper.Rd | 7 +---
man/visualize.it.Rd | 10 +++--
man/visualize.lnorm.Rd | 2 -
man/visualize.logis.Rd | 2 -
man/visualize.nbinom.Rd | 11 ++----
man/visualize.norm.Rd | 2 -
man/visualize.pois.Rd | 7 +---
man/visualize.t.Rd | 2 -
man/visualize.unif.Rd | 2 -
man/visualize.wilcox.Rd | 2 -
26 files changed, 188 insertions(+), 103 deletions(-)
Title: PopGen: A simple way to analyse and visualize population genetic
data
Diff between PopGenReport versions 0.96 dated 2012-11-28 and 1.01 dated 2013-05-22
Description: This package provides an easy way to analyse population
genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber,
DESCRIPTION | 12
MD5 | 42 +-
R/gd_kosman.r | 66 +--
R/popgenreport.r | 534 ++++++++++++++++---------------
R/read.genetable.r | 6
inst/swchunks/allele.dist.snw | 47 +-
inst/swchunks/counts.snw | 208 ++++++------
inst/swchunks/differ.stats.snw | 128 ++-----
inst/swchunks/fst.snw | 136 ++++----
inst/swchunks/gd.kosman.snw | 17 -
inst/swchunks/gd.smouse.snw | 20 -
inst/swchunks/header.snw | 10
inst/swchunks/hwe.snw | 87 ++---
inst/swchunks/load.data.snw | 4
inst/swchunks/locihz.snw | 34 --
inst/swchunks/map.snw | 109 +++---
inst/swchunks/required.snw | 7
inst/swchunks/subgroups.header.snw | 391 ++++++++---------------
inst/swchunks/subgroups.sectionout.snw | 557 ++++++++++++++++-----------------
man/PopGen-package.Rd | 6
man/popgenreport.Rd | 27 -
man/read.genetable.Rd | 7
22 files changed, 1167 insertions(+), 1288 deletions(-)
Title: Bayesian semi and nonparametric growth curve models that
additionally include multiple membership random effects.
Diff between growcurves versions 0.2.3.4 dated 2013-03-16 and 0.2.3.5 dated 2013-05-22
Description: Employs a non-parametric formulation for by-subject random
effect parameters to borrow strength over a constrained number
of repeated measurement waves in a fashion that permits
multiple effects per subject. One class of models employs a
Dirichlet process (DP) prior for the subject random effects and
includes an additional set of random effects that utilize a
different grouping factor and are mapped back to clients
through a multiple membership weight matrix; e.g. treatment(s)
exposure or dosage. A second class of models employs a
dependent DP (DDP) prior for the subject random effects that
directly incorporates the multiple membership pattern.
Author: Terrance Savitsky
Maintainer: "terrance savitsky"
DESCRIPTION | 8 ++--
MD5 | 32 +++++++++---------
NEWS | 12 +++++--
R/ddp_quantiles.R | 2 -
R/ddpeffectsplot.R | 2 -
R/ddpgrow.R | 21 +++++++-----
R/dpgrow.R | 17 +++++-----
R/dpgrowmm.R | 30 +++++++++++------
R/dpgrowmult.R | 20 +++++++----
R/help.R | 71 ++++++++++++++++++++++++++----------------
inst/tests/test-dpgrowmm-mv.R | 55 ++++++++++++++++++++++++++------
man/ddpgrow.Rd | 21 +++++++-----
man/dpgrow.Rd | 17 +++++-----
man/dpgrowmm.Rd | 24 ++++++++------
man/dpgrowmult.Rd | 20 +++++++----
man/growcurves-package.Rd | 71 ++++++++++++++++++++++++++----------------
src/mmCmiar.cpp | 11 ++++--
17 files changed, 274 insertions(+), 160 deletions(-)
Title: An interface package (beta) for the BIOM file format.
Diff between biom versions 0.3.8 dated 2013-04-29 and 0.3.9 dated 2013-05-22
Description: This is an R package for interfacing with the BIOM format.
Currently in beta form, this package includes basic tools for
reading biom-format files, accessing and subsetting data tables
from a biom object (which is more complex than a single table),
as well as limited support for writing a biom-object back to a
biom-format file. The design of this API is intended to match
the python API and other tools included with the biom-format
project, but with a decidedly "R flavor" that should be
familiar to R users. This includes S4 classes and methods, as
well as extensions of common core functions/methods.
Author: Paul J. McMurdie
Maintainer: Paul J. McMurdie
DESCRIPTION | 12 ++++++------
MD5 | 7 ++++---
R/BIOM-class.R | 32 ++++++++++++++++++--------------
R/allPackage.R | 2 +-
inst/NEWS |only
5 files changed, 29 insertions(+), 24 deletions(-)