Title: Phylogenetic analysis in R
Diff between phangorn versions 1.0-2 dated 2010-05-16 and 1.1-0 dated 2010-08-28
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Author: Klaus Schliep
Maintainer: Klaus Schliep
phangorn-1.0-2/phangorn/inst/doc/Trees.R |only
phangorn-1.1-0/phangorn/ChangeLog | 35
phangorn-1.1-0/phangorn/DESCRIPTION | 10
phangorn-1.1-0/phangorn/NAMESPACE | 4
phangorn-1.1-0/phangorn/R/phylo.R | 1668 +++++++++++------
phangorn-1.1-0/phangorn/Thanks | 6
phangorn-1.1-0/phangorn/inst/doc/Rplots.pdf |only
phangorn-1.1-0/phangorn/inst/doc/Trees.Rnw | 14
phangorn-1.1-0/phangorn/inst/doc/Trees.pdf |binary
phangorn-1.1-0/phangorn/inst/doc/exdna.txt |only
phangorn-1.1-0/phangorn/inst/doc/phangorn-specials.Rnw |only
phangorn-1.1-0/phangorn/inst/doc/phangorn-specials.pdf |only
phangorn-1.1-0/phangorn/inst/doc/phangorn.bib | 407 ++--
phangorn-1.1-0/phangorn/man/dist.hamming.Rd | 2
phangorn-1.1-0/phangorn/man/getClans.Rd |only
phangorn-1.1-0/phangorn/man/modelTest.Rd | 3
phangorn-1.1-0/phangorn/man/parsimony.Rd | 13
phangorn-1.1-0/phangorn/man/phyDat.Rd | 13
phangorn-1.1-0/phangorn/man/pml.Rd | 15
phangorn-1.1-0/phangorn/man/pmlCluster.Rd | 2
phangorn-1.1-0/phangorn/man/pmlMix.Rd | 2
phangorn-1.1-0/phangorn/man/pmlPart.Rd | 4
phangorn-1.1-0/phangorn/src/init.c | 10
phangorn-1.1-0/phangorn/src/phangorn.c | 300 ---
phangorn-1.1-0/phangorn/src/phangorn.h | 11
25 files changed, 1461 insertions(+), 1058 deletions(-)
Title: Interface between GMT Map-Making Software and R
Diff between gmt versions 1.1-6 dated 2010-08-27 and 1.1-7 dated 2010-08-28
Description: Interface between the GMT map-making software and R,
enabling the user to manipulate geographic data within R and
call GMT commands to draw and annotate maps in postscript
format. The 'gmt' package is about interactive data analysis,
rapidly visualizing subsets and summaries of geographic data,
while performing statistical analysis in the R console.
Author: Arni Magnusson
Maintainer: Arni Magnusson
DESCRIPTION | 6 +++---
NEWS | 2 +-
R/psbar.R | 2 +-
R/psclose.R | 2 +-
R/r2gmt.R | 4 ++--
5 files changed, 8 insertions(+), 8 deletions(-)
Title: Spherical Trigonometry
Diff between geosphere versions 1.2-7 dated 2010-07-26 and 1.2-10 dated 2010-08-28
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans, Ed Williams, Chris Vennes
Maintainer: Robert J. Hijmans
ChangeLog |only
DESCRIPTION | 10 ++---
R/areaPolygon.R | 12 ++++++
R/distPoint2Line.R |only
R/distVincentyEllipsoid.R | 2 +
R/makePoly.R | 91 +++++++++++++++++++++++++++++++++++++++++-----
R/midPoint.R | 27 ++++++-------
R/onGreatCircle.R |only
R/pointsToMatrix.R | 25 +++++++++---
inst/doc/geosphere.Rnw | 27 +++++++++++--
inst/doc/geosphere.pdf |binary
man/daylength.Rd | 13 ++++--
man/distHaversine.Rd | 2 -
man/distPoint2line.Rd |only
man/geosphere-package.Rd | 6 +--
man/makepoly.Rd | 9 +++-
man/midPoint.Rd | 4 +-
man/onGreatCircle.Rd |only
18 files changed, 175 insertions(+), 53 deletions(-)
Title: Multivariate Adaptive Regression Spline Models
Diff between earth versions 2.4-0 dated 2009-11-09 and 2.4-1 dated 2010-08-28
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is copyrighted and thus not used in
the name of the package.)
Author: Stephen Milborrow derived from mda:mars by Trevor Hastie and
Rob Tibshirani.
Maintainer: Stephen Milborrow
DESCRIPTION | 8
NEWS | 14 -
R/earth.R | 9
R/earth.cv.R | 20 -
R/earth.glm.R | 16 -
R/earthlib.R | 35 +-
R/evimp.R | 4
R/expand.arg.R | 4
R/format.earth.R | 2
R/model.matrix.earth.R | 15 -
R/plot.earth.R | 24 +
R/plotd.R | 83 +++---
R/plotmo.R | 8
R/predict.earth.R | 2
R/print.earth.R | 6
man/earth.Rd | 494 +++++++++++++++++++-----------------
man/evimp.Rd | 37 +-
man/format.earth.Rd | 8
man/mars.to.earth.Rd | 2
man/plot.earth.Rd | 29 +-
man/plotd.Rd | 26 +
man/plotmo.Rd | 13
man/predict.earth.Rd | 16 -
man/summary.earth.Rd | 14 -
man/update.earth.Rd | 10
src/tests/earth.times.bat | 2
src/tests/test.earth.big.Rout.save | 1
src/tests/test.earth.big.bat | 9
src/tests/test.earth.cv.R | 5
src/tests/test.earth.cv.Rout.save | 7
src/tests/test.earth.cv.bat | 9
src/tests/test.earth.full.Rout.save | 9
src/tests/test.earth.full.bat | 9
src/tests/test.earth.glm.Rout.save | 118 +++-----
src/tests/test.earth.glm.bat | 9
src/tests/test.earthc.mak | 2
src/tests/test.plotd.R | 5
src/tests/test.plotd.Rout.save | 10
src/tests/test.plotd.bat | 9
src/tests/test.plotmo.Rout.save | 9
src/tests/test.plotmo.bat | 9
41 files changed, 605 insertions(+), 516 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Diff between dclone versions 1.1-0 dated 2010-05-04 and 1.2-0 dated 2010-08-28
Description: Low level functions for implementing maximum likelihood
estimating procedures for complex models using data cloning and
Bayesian Markov chain Monte Carlo methods with support for
JAGS, WinBUGS and OpenBUGS, with support for parallel
computing.
Author: Peter Solymos
Maintainer: Peter Solymos
DESCRIPTION | 12 ++++++------
R/dc.parfit.R | 2 +-
R/dcdiag.default.R | 3 +++
R/extractdcdiag.default.R | 4 +++-
R/extractdctable.default.R | 5 ++++-
R/jags.parfit.R | 35 +++++------------------------------
R/plot.dctable.R | 4 ++--
R/print.custommodel.R | 5 +++--
R/snowWrapper.R | 4 +---
R/summary.mcmc.list.dc.R | 13 ++++++++-----
R/zzz.R | 3 +++
inst/CITATION |only
inst/ChangeLog | 11 +++++++++++
man/dctable.Rd | 2 +-
man/jags.parfit.Rd | 2 +-
man/snowWrapper.Rd | 12 +-----------
16 files changed, 53 insertions(+), 64 deletions(-)
More information about RcmdrPlugin.TextMining at CRAN
Permanent link
Title: Solver for Delay Differential Equations
Diff between PBSddesolve versions 1.08.9 dated 2010-04-29 and 1.08.11 dated 2010-08-28
Description: This package solves systems of delay differential
equations. by interfacing numerical routines written by Simon
N. Wood
Author: Alex Couture-Beil
Maintainer: Jon Schnute
DESCRIPTION | 8 ++++----
inst/doc/PBSddesolveIntro.pdf |binary
src/PBSddesolve.c | 1 +
3 files changed, 5 insertions(+), 4 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Diff between MIfuns versions 3.2.9 dated 2008-11-04 and 4.0.16 dated 2010-08-28
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of a
detailed analysis log.
Author: Metrum Institute (http://metruminstitute.org): Bill Knebel,
Leonid Gibianski, Tim Bergsma
Maintainer: Tim Bergsma
MIfuns-3.2.9/MIfuns/R/AUC.R |only
MIfuns-3.2.9/MIfuns/R/CWRES.R |only
MIfuns-3.2.9/MIfuns/R/CheckPositiveMatrix.R |only
MIfuns-3.2.9/MIfuns/R/CheckPositiveVector.R |only
MIfuns-3.2.9/MIfuns/R/CheckWS.R |only
MIfuns-3.2.9/MIfuns/R/ComputePredictiveCheck.R |only
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MIfuns-3.2.9/MIfuns/R/Omega.MtoV.R |only
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MIfuns-4.0.16/MIfuns/DESCRIPTION | 25
MIfuns-4.0.16/MIfuns/R/CLNR.R | 14
MIfuns-4.0.16/MIfuns/R/NONR.R | 127 ++-
MIfuns-4.0.16/MIfuns/R/PLOTR.R | 430 +++++++++----
MIfuns-4.0.16/MIfuns/R/Tmax.R | 24
MIfuns-4.0.16/MIfuns/R/accept.R | 28
MIfuns-4.0.16/MIfuns/R/as.comment.R |only
MIfuns-4.0.16/MIfuns/R/as.data.frame.block.R |only
MIfuns-4.0.16/MIfuns/R/as.filename.R | 14
MIfuns-4.0.16/MIfuns/R/as.flag.R |only
MIfuns-4.0.16/MIfuns/R/as.keyed.R |only
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MIfuns-4.0.16/MIfuns/R/bin.R | 9
MIfuns-4.0.16/MIfuns/R/bracket.R |only
MIfuns-4.0.16/MIfuns/R/check.subjects.R |only
MIfuns-4.0.16/MIfuns/R/compute.cwres.R | 65 +
MIfuns-4.0.16/MIfuns/R/constant.R | 14
MIfuns-4.0.16/MIfuns/R/contains.R |only
MIfuns-4.0.16/MIfuns/R/covariatePlots.R |only
MIfuns-4.0.16/MIfuns/R/css.R | 27
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MIfuns-4.0.16/MIfuns/R/hash.R | 10
MIfuns-4.0.16/MIfuns/R/ibw.R | 19
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MIfuns-4.0.16/MIfuns/R/locf.R | 6
MIfuns-4.0.16/MIfuns/R/lookup.R |only
MIfuns-4.0.16/MIfuns/R/metaSub.character.R | 49 +
MIfuns-4.0.16/MIfuns/R/miTemporal.R | 86 +-
MIfuns-4.0.16/MIfuns/R/nest.R |only
MIfuns-4.0.16/MIfuns/R/ops.keyed.R |only
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MIfuns-4.0.16/MIfuns/R/prev.R | 12
MIfuns-4.0.16/MIfuns/R/read.cwres.data.R | 2
MIfuns-4.0.16/MIfuns/R/resample.data.frame.R | 57 +
MIfuns-4.0.16/MIfuns/R/rig.R |only
MIfuns-4.0.16/MIfuns/R/rlog.R | 162 ++--
MIfuns-4.0.16/MIfuns/R/runCommand.R |only
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MIfuns-4.0.16/MIfuns/man/CLNR.Rd | 30
MIfuns-4.0.16/MIfuns/man/MIfuns-package.Rd | 89 --
MIfuns-4.0.16/MIfuns/man/NONR.Rd | 396 +++++++----
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MIfuns-4.0.16/MIfuns/man/helpMatrix.Rd |only
MIfuns-4.0.16/MIfuns/man/helpModel.Rd |only
MIfuns-4.0.16/MIfuns/man/helpPharmacometric.Rd |only
MIfuns-4.0.16/MIfuns/man/helpPrepare.Rd |only
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MIfuns-4.0.16/MIfuns/man/helpReport.Rd |only
MIfuns-4.0.16/MIfuns/man/helpSimulate.Rd |only
MIfuns-4.0.16/MIfuns/man/helpStrategic.Rd |only
MIfuns-4.0.16/MIfuns/man/helpVector.Rd |only
MIfuns-4.0.16/MIfuns/man/helpVisualize.Rd |only
MIfuns-4.0.16/MIfuns/man/ibw.Rd |only
MIfuns-4.0.16/MIfuns/man/is.square.matrix.Rd |only
MIfuns-4.0.16/MIfuns/man/latest.Rd |only
MIfuns-4.0.16/MIfuns/man/locf.Rd |only
MIfuns-4.0.16/MIfuns/man/lookup.Rd |only
MIfuns-4.0.16/MIfuns/man/metaSub.character.Rd | 126 ++-
MIfuns-4.0.16/MIfuns/man/miTemporal.Rd | 234 ++++---
MIfuns-4.0.16/MIfuns/man/naInContext.Rd | 26
MIfuns-4.0.16/MIfuns/man/nest.Rd |only
MIfuns-4.0.16/MIfuns/man/nix.Rd |only
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MIfuns-4.0.16/MIfuns/man/ops.Rd |only
MIfuns-4.0.16/MIfuns/man/ord.matrix.Rd |only
MIfuns-4.0.16/MIfuns/man/packageCheck.Rd | 36 -
MIfuns-4.0.16/MIfuns/man/panel.densitystrip.Rd |only
MIfuns-4.0.16/MIfuns/man/panel.hist.Rd |only
MIfuns-4.0.16/MIfuns/man/panel.stratify.Rd |only
MIfuns-4.0.16/MIfuns/man/params.Rd |only
MIfuns-4.0.16/MIfuns/man/partab.Rd |only
MIfuns-4.0.16/MIfuns/man/plot.nm.Rd |only
MIfuns-4.0.16/MIfuns/man/plotFileName.Rd |only
MIfuns-4.0.16/MIfuns/man/posmat.Rd |only
MIfuns-4.0.16/MIfuns/man/prev.Rd |only
MIfuns-4.0.16/MIfuns/man/purge.dir.Rd |only
MIfuns-4.0.16/MIfuns/man/purge.files.Rd |only
MIfuns-4.0.16/MIfuns/man/qsub.Rd |only
MIfuns-4.0.16/MIfuns/man/reapply.Rd |only
MIfuns-4.0.16/MIfuns/man/resample.data.frame.Rd | 67 +-
MIfuns-4.0.16/MIfuns/man/rinvchisq.Rd | 19
MIfuns-4.0.16/MIfuns/man/riwish.Rd | 26
MIfuns-4.0.16/MIfuns/man/rlog.Rd | 74 +-
MIfuns-4.0.16/MIfuns/man/runCommand.Rd |only
MIfuns-4.0.16/MIfuns/man/runNonmem.Rd |only
MIfuns-4.0.16/MIfuns/man/runlog.Rd |only
MIfuns-4.0.16/MIfuns/man/safe.call.Rd |only
MIfuns-4.0.16/MIfuns/man/setCwres.Rd |only
MIfuns-4.0.16/MIfuns/man/shuffle.Rd |only
MIfuns-4.0.16/MIfuns/man/simblock.Rd |only
MIfuns-4.0.16/MIfuns/man/simpar.Rd |only
MIfuns-4.0.16/MIfuns/man/snap.Rd |only
MIfuns-4.0.16/MIfuns/man/sqrtm.Rd | 17
MIfuns-4.0.16/MIfuns/man/stableMerge.Rd | 29
MIfuns-4.0.16/MIfuns/man/star.Rd |only
MIfuns-4.0.16/MIfuns/man/strain.Rd |only
MIfuns-4.0.16/MIfuns/man/summary.nm.Rd |only
MIfuns-4.0.16/MIfuns/man/synthesis.Rd |only
MIfuns-4.0.16/MIfuns/man/text2decimal.Rd |only
MIfuns-4.0.16/MIfuns/man/variants.Rd |only
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MIfuns-4.0.16/MIfuns/man/xyplot.ext.Rd |only
277 files changed, 1705 insertions(+), 1073 deletions(-)
Title: Subset AR Model Fitting
Diff between FitAR versions 1.80 dated 2010-08-16 and 1.85 dated 2010-08-28
Description: Comprehensive model building function for identification,
estimation and diagnostic checking for AR and subset AR models.
Two types of subset AR models are supported. One family of
subset AR models, denoted by ARp, is formed by taking subet of
the original AR coefficients and in the other, denoted by ARz,
subsets of the partial autocorrelations are used. The main
advantage of the ARz model is its applicability to very large
order models.
Author: A.I. McLeod and Ying Zhang
Maintainer: A.I. McLeod
DESCRIPTION | 12 +++++-----
NAMESPACE | 5 ++++
NEWS |only
R/BICqLL.R |only
R/GetFitARpLS.R | 4 +--
R/GetFitARpMLE.R | 37 +++++++++++++++++----------------
R/GetLeapsAR.R | 56 +++++++++++++++++++++++++++++++++++++++++++++-----
R/to.binary.R |only
man/BICqLL.Rd |only
man/BoxCox.Arima.Rd | 9 ++++----
man/BoxCox.FitAR.Rd | 5 ----
man/BoxCox.Rd | 11 ++++++++-
man/BoxCox.numeric.Rd | 3 ++
man/BoxCox.ts.Rd | 2 +
man/FitAR-package.Rd | 6 +++--
man/FitAR.Rd | 21 ++++++++++++++++++
man/GetLeapsAR.Rd | 51 +++++++++++++++++++++++++++++++++++++--------
man/bxcx.Rd | 3 +-
18 files changed, 174 insertions(+), 51 deletions(-)
Title: Provides a GUI to several statistical methods useful for causal
assessment.
Diff between CADStat versions 2.2-5 dated 2010-04-08 and 2.2-6 dated 2010-08-28
Description: Using JGR, provides a GUI to several statistical methods -
scatterplot, boxplot, linear regression, generalized linear
regression, quantile, regression, conditional probability
calculations, and regression trees.
Author: Lester Yuan, Tom Stockton, Doug Bronson, Pasha Minallah, and
Mark Fitzgerald
Maintainer: Lester Yuan
CADStat-2.2-5/CADStat/data/envdata.or.txt |only
CADStat-2.2-5/CADStat/data/eptpctfn.txt |only
CADStat-2.2-5/CADStat/data/refids.or.txt |only
CADStat-2.2-6/CADStat/DESCRIPTION | 8 ++++----
CADStat-2.2-6/CADStat/data/envdata.OR.txt |only
CADStat-2.2-6/CADStat/data/refids.OR.txt |only
CADStat-2.2-6/CADStat/man/envdata.OR.Rd |only
CADStat-2.2-6/CADStat/man/refids.OR.Rd |only
8 files changed, 4 insertions(+), 4 deletions(-)