Title: Profile Dirichlet Process Mixtures
Diff between profdpm versions 3.0 dated 2011-07-23 and 3.1 dated 2012-09-07
Description: This package facilitates profile inference (inference at
the posterior mode) for a class of product partition models
(PPM). The Dirichlet process mixture is currently the only
available member of this class. These methods search for the
maximum posterior (MAP) estimate for the data partition in a
PPM.
Author: Matt Shotwell
Maintainer: Matt Shotwell
profdpm-3.0/profdpm/inst/doc/Makefile |only
profdpm-3.0/profdpm/inst/doc/jss.bst |only
profdpm-3.0/profdpm/inst/doc/jss.cls |only
profdpm-3.0/profdpm/inst/doc/jsslogo.jpg |only
profdpm-3.0/profdpm/inst/doc/profdpm-004.pdf |only
profdpm-3.0/profdpm/inst/doc/profdpm-007.pdf |only
profdpm-3.0/profdpm/inst/doc/profdpm-010.pdf |only
profdpm-3.0/profdpm/inst/doc/profdpm.aux |only
profdpm-3.0/profdpm/inst/doc/profdpm.bbl |only
profdpm-3.0/profdpm/inst/doc/profdpm.bib |only
profdpm-3.0/profdpm/inst/doc/profdpm.blg |only
profdpm-3.0/profdpm/inst/doc/profdpm.log |only
profdpm-3.0/profdpm/inst/doc/profdpm.out |only
profdpm-3.0/profdpm/inst/doc/profdpm.tex |only
profdpm-3.1/profdpm/DESCRIPTION | 8
profdpm-3.1/profdpm/MD5 |only
profdpm-3.1/profdpm/R/profBinary.R | 12 -
profdpm-3.1/profdpm/R/profLinear.R | 25 +-
profdpm-3.1/profdpm/TODO | 1
profdpm-3.1/profdpm/inst/doc/profdpm.Rnw | 247 +++++++++++++++------------
profdpm-3.1/profdpm/inst/doc/profdpm.pdf |binary
profdpm-3.1/profdpm/man/profBinary.Rd | 22 ++
profdpm-3.1/profdpm/man/profLinear.Rd | 3
profdpm-3.1/profdpm/man/profdpm.Rd | 4
profdpm-3.1/profdpm/src/methods.c | 6
profdpm-3.1/profdpm/src/pdpmlm.c | 24 ++
profdpm-3.1/profdpm/src/profBinary.c | 3
profdpm-3.1/profdpm/src/profLinear.c | 11 -
profdpm-3.1/profdpm/src/profdpm.h | 8
profdpm-3.1/profdpm/src/util.c | 2
profdpm-3.1/profdpm/vignettes |only
31 files changed, 237 insertions(+), 139 deletions(-)
Title: Efficiently Read Variant Call Format (VCF) into R
Diff between vcf2geno versions 1.3 dated 2012-08-29 and 1.4 dated 2012-09-07
Description: A handy package to read VCF file
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan
vcf2geno-1.3/vcf2geno/configure.in |only
vcf2geno-1.3/vcf2geno/src/InfoGrepper.h |only
vcf2geno-1.3/vcf2geno/src/Regex.cpp |only
vcf2geno-1.3/vcf2geno/src/Regex.h |only
vcf2geno-1.3/vcf2geno/src/bzlib_flymake.h |only
vcf2geno-1.3/vcf2geno/src/config.h |only
vcf2geno-1.4/vcf2geno/ChangeLog | 7
vcf2geno-1.4/vcf2geno/DESCRIPTION | 25
vcf2geno-1.4/vcf2geno/MD5 | 38
vcf2geno-1.4/vcf2geno/configure | 4765 +++++++++++++----------------
vcf2geno-1.4/vcf2geno/configure.ac | 70
vcf2geno-1.4/vcf2geno/src/IO.cpp | 4
vcf2geno-1.4/vcf2geno/src/IO.h | 12
vcf2geno-1.4/vcf2geno/src/Makevars.in | 17
vcf2geno-1.4/vcf2geno/src/PatternMatch.cpp |only
vcf2geno-1.4/vcf2geno/src/PatternMatch.h |only
vcf2geno-1.4/vcf2geno/src/RangeList.h | 2
vcf2geno-1.4/vcf2geno/src/TypeConversion.h | 34
vcf2geno-1.4/vcf2geno/src/VCFFilter.h | 2
vcf2geno-1.4/vcf2geno/src/bgzf.c | 8
vcf2geno-1.4/vcf2geno/src/bgzf.h | 10
vcf2geno-1.4/vcf2geno/src/config.h.in | 16
vcf2geno-1.4/vcf2geno/src/zconf.h | 2
vcf2geno-1.4/vcf2geno/src/zlib.h | 7
24 files changed, 2398 insertions(+), 2621 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-03-24 1.0.0
Title: R package for simulating biological sequence evolution
Diff between phylosim versions 0.17 dated 2012-03-01 and 0.19 dated 2012-09-07
Description: PhyloSim is an extensible object-oriented framework for
the Monte Carlo simulation of sequence evolution written in 100
percent R. It is built on the top of the R.oo and ape packages
and uses Gillespie's direct method to simulate substitutions,
insertions and deletions.
Author: Botond Sipos
Maintainer: Botond Sipos
DESCRIPTION | 10 +--
MD5 | 110 ++++++++++++++++++------------------
R/PhyloSim.R | 137 +++++----------------------------------------
inst/doc/PhyloSim.pdf |binary
man/Alphabet.Rd | 4 -
man/AminoAcidAlphabet.Rd | 4 -
man/AminoAcidSequence.Rd | 4 -
man/AminoAcidSubst.Rd | 6 -
man/AnyAlphabet.Rd | 4 -
man/BinaryAlphabet.Rd | 4 -
man/BinarySequence.Rd | 4 -
man/BinarySubst.Rd | 6 -
man/BrownianInsertor.Rd | 4 -
man/CodonAlphabet.Rd | 4 -
man/CodonSequence.Rd | 4 -
man/CodonUNREST.Rd | 6 -
man/ContinuousDeletor.Rd | 4 -
man/ContinuousInsertor.Rd | 4 -
man/DiscreteDeletor.Rd | 4 -
man/DiscreteInsertor.Rd | 4 -
man/Event.Rd | 2
man/F81.Rd | 6 -
man/F84.Rd | 6 -
man/FastFieldDeletor.Rd | 4 -
man/GTR.Rd | 6 -
man/GY94.Rd | 6 -
man/GeneralDeletor.Rd | 4 -
man/GeneralInDel.Rd | 4 -
man/GeneralInsertor.Rd | 4 -
man/GeneralSubstitution.Rd | 6 -
man/HKY.Rd | 6 -
man/JC69.Rd | 6 -
man/JTT.Rd | 6 -
man/JTT.dcmut.Rd | 6 -
man/K80.Rd | 6 -
man/K81.Rd | 6 -
man/LG.Rd | 6 -
man/MtZoa.Rd | 6 -
man/NucleotideAlphabet.Rd | 4 -
man/NucleotideSequence.Rd | 4 -
man/PAM.Rd | 6 -
man/PAM.dcmut.Rd | 6 -
man/PSRoot.Rd | 2
man/PhyloSim.Rd | 111 +-----------------------------------
man/Process.Rd | 4 -
man/QMatrix.Rd | 6 -
man/Sequence.Rd | 8 +-
man/Site.Rd | 4 -
man/T92.Rd | 10 +--
man/TN93.Rd | 10 +--
man/UNREST.Rd | 6 -
man/WAG.Rd | 6 -
man/cpREV.Rd | 6 -
man/mtArt.Rd | 6 -
man/mtMam.Rd | 6 -
man/mtREV24.Rd | 6 -
56 files changed, 217 insertions(+), 417 deletions(-)
Title: Generalized Nonlinear Models
Diff between gnm versions 1.0-3 dated 2012-07-20 and 1.0-4 dated 2012-09-07
Description: Functions to specify and fit generalized nonlinear models,
including models with multiplicative interaction terms such as
the UNIDIFF model from sociology and the AMMI model from crop
science, and many others. Over-parameterized representations
of models are used throughout; functions are provided for
inference on estimable parameter combinations, as well as
standard methods for diagnostics etc.
Author: Heather Turner and David Firth
Maintainer: Heather Turner
gnm-1.0-3/gnm/R/quick.rowsum.R |only
gnm-1.0-4/gnm/DESCRIPTION | 8 ++++----
gnm-1.0-4/gnm/MD5 | 25 ++++++++++++-------------
gnm-1.0-4/gnm/R/glm.fit.e.R | 4 ++--
gnm-1.0-4/gnm/R/gnmFit.R | 33 ++++++++++++++++++---------------
gnm-1.0-4/gnm/R/gnmTools.R | 2 +-
gnm-1.0-4/gnm/inst/NEWS | 11 +++++++++++
gnm-1.0-4/gnm/inst/doc/gnmOverview.pdf |binary
gnm-1.0-4/gnm/man/MultHomog.Rd | 12 ++++++++++++
gnm-1.0-4/gnm/man/confint.gnm.Rd | 3 ++-
gnm-1.0-4/gnm/man/friend.Rd | 2 ++
gnm-1.0-4/gnm/man/summary.gnm.Rd | 27 ++++++++++++++++++---------
gnm-1.0-4/gnm/tests/RChomog.R | 8 ++++++--
gnm-1.0-4/gnm/tests/RChomog.Rout.save | 15 ++++++++++-----
14 files changed, 98 insertions(+), 52 deletions(-)
Title: Inference for Phase-type Distributions
Diff between PhaseType versions 0.1.1 dated 2012-08-23 and 0.1.2 dated 2012-09-07
Description: Functions to perform Bayesian inference on absorption time
data for Phase-type distributions. Plans to expand this to
include frequentist inference and simulation tools.
Author: Louis Aslett
Maintainer: Louis Aslett
DESCRIPTION | 6 +++---
MD5 | 6 +++---
NEWS | 5 +++++
R/plot.phtMCMC.R | 6 +++---
4 files changed, 14 insertions(+), 9 deletions(-)
Title: linear Likelihood-based Imprecise Regression
Diff between linLIR versions 1.0-1 dated 2012-06-26 and 1.0-2 dated 2012-09-07
Description: This package implements the methodology of
Likelihood-based Imprecise Regression (LIR) for the case of
linear regression with interval data.
Author: Andrea Wiencierz
Maintainer: Andrea Wiencierz
DESCRIPTION | 11 -
MD5 | 18 +-
R/linLIRfunctions.R | 345 +++++++++++++++++++++++++++++++++-------------------
data/pm10.RData |only
man/gen.lms.Rd | 4
man/idf.Rd | 10 +
man/kl.ku.Rd | 4
man/pm10.Rd |only
man/s.linlir.Rd | 4
man/toy.smps.Rd | 4
man/undom.Rd | 4
11 files changed, 263 insertions(+), 141 deletions(-)
Title: Detection of structure from multilocus genetic data.
Diff between Geneland versions 4.0.2 dated 2012-03-24 and 4.0.3 dated 2012-09-07
Description: Stochastic simulation and MCMC inference of structure from
genetic data.
Author: Gilles Guillot, Filipe Santos, Arnaud Estoup
Maintainer: Gilles Guillot
Geneland-4.0.2/Geneland/R/PostProcessMultChain.R |only
Geneland-4.0.2/Geneland/man/PostProcessMultChain.Rd |only
Geneland-4.0.3/Geneland/ChangeLog | 20
Geneland-4.0.3/Geneland/DESCRIPTION | 8
Geneland-4.0.3/Geneland/MD5 | 28
Geneland-4.0.3/Geneland/R/Fstat.R | 14
Geneland-4.0.3/Geneland/R/HZ.R | 26
Geneland-4.0.3/Geneland/R/MCMC.R | 104 +-
Geneland-4.0.3/Geneland/R/PostProcessChain.R | 31
Geneland-4.0.3/Geneland/R/zzz.R | 2
Geneland-4.0.3/Geneland/src/hz.f | 63 -
Geneland-4.0.3/Geneland/src/main.f | 841 ++++++++------------
Geneland-4.0.3/Geneland/src/wrapper.c | 21
Geneland-4.0.3/Geneland/vignettes/Geneland-Doc.bbl | 34
Geneland-4.0.3/Geneland/vignettes/Geneland-Doc.pdf |binary
Geneland-4.0.3/Geneland/vignettes/Geneland-Doc.tex | 169 ++--
16 files changed, 738 insertions(+), 623 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Diff between psych versions 1.2.4 dated 2012-05-02 and 1.2.8 dated 2012-09-07
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Item Response Theory is done using factor analysis
of tetrachoric and polychoric correlations. Functions for
simulating particular item and test structures are included.
Several functions serve as a useful front end for structural
equation modeling. Graphical displays of path diagrams, factor
analysis and structural equation models are created using basic
graphics. Some of the functions are written to support a book
on psychometrics as well as publications in personality
research. For more information, see the
personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
psych-1.2.4/psych/R/super.matrix.R |only
psych-1.2.4/psych/rmssd.R |only
psych-1.2.8/psych/DESCRIPTION | 12
psych-1.2.8/psych/MD5 | 169 +++++-----
psych-1.2.8/psych/NAMESPACE | 15
psych-1.2.8/psych/R/ICLUST.R | 12
psych-1.2.8/psych/R/ICLUST.diagram.R | 2
psych-1.2.8/psych/R/ICLUST.sort.R | 11
psych-1.2.8/psych/R/biplot.psych.R | 5
psych-1.2.8/psych/R/cluster.fit.R | 2
psych-1.2.8/psych/R/cluster.plot.R | 6
psych-1.2.8/psych/R/cor.plot.R | 21 -
psych-1.2.8/psych/R/describe.by.R | 2
psych-1.2.8/psych/R/df2latex.R | 2
psych-1.2.8/psych/R/dia.cone.R | 4
psych-1.2.8/psych/R/error.bars.by.R | 4
psych-1.2.8/psych/R/errorCircles.r |only
psych-1.2.8/psych/R/fa.R | 7
psych-1.2.8/psych/R/factor.rotate.R | 2
psych-1.2.8/psych/R/factor.stats.R | 2
psych-1.2.8/psych/R/glb.algebraic.R | 3
psych-1.2.8/psych/R/headtail.R | 70 +++-
psych-1.2.8/psych/R/lowerUpper.R |only
psych-1.2.8/psych/R/misc.R | 13
psych-1.2.8/psych/R/model.fit.R | 4
psych-1.2.8/psych/R/omega.sem.R | 23 -
psych-1.2.8/psych/R/omegaSem.R | 5
psych-1.2.8/psych/R/paired.r.R | 7
psych-1.2.8/psych/R/pairs.panels.R | 2
psych-1.2.8/psych/R/plot.irt.R | 40 +-
psych-1.2.8/psych/R/plot.psych.R | 4
psych-1.2.8/psych/R/principal.R | 2
psych-1.2.8/psych/R/print.psych.R | 33 +
psych-1.2.8/psych/R/print.psych.fa.R | 17 -
psych-1.2.8/psych/R/print.psych.iclust.R | 2
psych-1.2.8/psych/R/schmid.R | 16
psych-1.2.8/psych/R/score.irt.poly.R | 82 ++++
psych-1.2.8/psych/R/score.items.R | 3
psych-1.2.8/psych/R/score.multiple.choice.R | 7
psych-1.2.8/psych/R/sim.multilevel.R |only
psych-1.2.8/psych/R/sim.structural.R | 113 +++++-
psych-1.2.8/psych/R/stats.by.r |only
psych-1.2.8/psych/R/statsBy.boot.R |only
psych-1.2.8/psych/R/statsBy.r |only
psych-1.2.8/psych/R/superMatrix.R |only
psych-1.2.8/psych/R/toDotty.R | 5
psych-1.2.8/psych/data/iqitems.rda |binary
psych-1.2.8/psych/data/withinBetween.rda |only
psych-1.2.8/psych/inst/CITATION | 6
psych-1.2.8/psych/inst/NEWS.Rd | 92 ++++-
psych-1.2.8/psych/inst/doc/overview.Rnw | 415 +++++++++++++++++++++----
psych-1.2.8/psych/inst/doc/overview.pdf |binary
psych-1.2.8/psych/inst/doc/psych_for_sem.Rnw | 20 -
psych-1.2.8/psych/inst/doc/psych_for_sem.pdf |binary
psych-1.2.8/psych/man/00.psych-package.Rd | 4
psych-1.2.8/psych/man/ICLUST.Rd | 7
psych-1.2.8/psych/man/Promax.Rd | 17 -
psych-1.2.8/psych/man/biplot.psych.Rd | 2
psych-1.2.8/psych/man/cluster.plot.Rd | 5
psych-1.2.8/psych/man/cor.plot.Rd | 10
psych-1.2.8/psych/man/cor.wt.Rd |only
psych-1.2.8/psych/man/cor2dist.Rd | 8
psych-1.2.8/psych/man/describe.by.Rd | 24 -
psych-1.2.8/psych/man/diagram.Rd | 2
psych-1.2.8/psych/man/error.circles.Rd |only
psych-1.2.8/psych/man/error.crosses.Rd | 8
psych-1.2.8/psych/man/fa.Rd | 41 +-
psych-1.2.8/psych/man/factor.rotate.Rd | 2
psych-1.2.8/psych/man/headtail.Rd | 11
psych-1.2.8/psych/man/iclust.diagram.Rd | 15
psych-1.2.8/psych/man/interp.median.Rd | 2
psych-1.2.8/psych/man/iqitems.Rd | 58 ++-
psych-1.2.8/psych/man/irt.fa.Rd | 5
psych-1.2.8/psych/man/irt.responses.Rd |only
psych-1.2.8/psych/man/logistic.Rd | 2
psych-1.2.8/psych/man/lowerUpper.Rd |only
psych-1.2.8/psych/man/mat.sort.Rd | 2
psych-1.2.8/psych/man/misc.Rd | 2
psych-1.2.8/psych/man/msq.Rd | 4
psych-1.2.8/psych/man/paired.r.Rd | 3
psych-1.2.8/psych/man/plot.psych.Rd | 6
psych-1.2.8/psych/man/r.test.Rd | 10
psych-1.2.8/psych/man/reverse.code.Rd | 3
psych-1.2.8/psych/man/score.irt.Rd | 8
psych-1.2.8/psych/man/score.items.Rd | 5
psych-1.2.8/psych/man/score.multiple.choice.Rd | 2
psych-1.2.8/psych/man/set.cor.Rd | 2
psych-1.2.8/psych/man/sim.Rd | 13
psych-1.2.8/psych/man/sim.multilevel.Rd |only
psych-1.2.8/psych/man/statsBy.Rd |only
psych-1.2.8/psych/man/super.matrix.Rd | 23 -
psych-1.2.8/psych/man/withinBetween.Rd |only
psych-1.2.8/psych/vignettes/overview.Rnw | 415 +++++++++++++++++++++----
psych-1.2.8/psych/vignettes/psych_for_sem.Rnw | 20 -
94 files changed, 1512 insertions(+), 491 deletions(-)