Title: Phylogenetic analysis in R
Diff between phangorn versions 1.3-0 dated 2011-01-31 and 1.3-1 dated 2011-02-14
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
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phangorn-1.3-0/phangorn/data/jtt-dcmut.dat |only
phangorn-1.3-0/phangorn/data/lg.dat |only
phangorn-1.3-0/phangorn/data/wag.dat |only
phangorn-1.3-1/phangorn/ChangeLog | 24 +
phangorn-1.3-1/phangorn/DESCRIPTION | 10
phangorn-1.3-1/phangorn/NAMESPACE | 3
phangorn-1.3-1/phangorn/R/phylo.R | 269 ++++++++---------
phangorn-1.3-1/phangorn/Thanks | 6
phangorn-1.3-1/phangorn/data/Laurasiatherian.RData |binary
phangorn-1.3-1/phangorn/data/chloroplast.RData |binary
phangorn-1.3-1/phangorn/data/yeast.RData |binary
phangorn-1.3-1/phangorn/inst/CITATION | 12
phangorn-1.3-1/phangorn/inst/doc/Ancestral.pdf |binary
phangorn-1.3-1/phangorn/inst/doc/Trees.pdf |binary
phangorn-1.3-1/phangorn/inst/doc/phangorn-specials.pdf |binary
phangorn-1.3-1/phangorn/inst/doc/phangorn.bib | 6
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phangorn-1.3-1/phangorn/man/bootstrap.pml.Rd | 14
phangorn-1.3-1/phangorn/man/modelTest.Rd | 4
phangorn-1.3-1/phangorn/man/parsimony.Rd | 9
phangorn-1.3-1/phangorn/src/phangorn.c | 158 ++++++++-
22 files changed, 335 insertions(+), 180 deletions(-)
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Diff between nparLD versions 1.2 dated 2009-12-30 and 1.3 dated 2011-02-14
Description: The package "nparLD" is designed to perform nonparametric
analysis of longitudinal data in factorial experiments.
Longitudinal data are those which are collected from the same
subjects over time, and they frequently arise in biological
sciences. Nonparametric methods do not require assumptions on
distributions of parameters, and are applicable to a variety of
data types (continuous, discrete, purely ordinal, and
dichotomous). Such methods are also robust with respect to
outliers and for small sample sizes.
Author: Kimihiro Noguchi
Maintainer: Kimihiro Noguchi
DESCRIPTION | 8
R/f1.ld.f1.R | 1694 ++++++++++++++++++++++++++++----------------------------
R/f1.ld.f2.R | 1289 ++++++++++++++++++++++--------------------
R/f2.ld.f1.R | 1493 +++++++++++++++++++++++++------------------------
R/ld.ci.R | 64 +-
R/ld.f1.R | 708 +++++++++++------------
R/ld.f2.R | 858 ++++++++++++++--------------
man/edema.rd | 3
man/f1.ld.f1.rd | 13
man/f1.ld.f2.rd | 20
man/f2.ld.f1.rd | 16
man/ld.ci.rd | 61 +-
man/ld.f1.rd | 12
man/ld.f2.rd | 13
man/shoulder.rd | 3
15 files changed, 3263 insertions(+), 2992 deletions(-)
Title: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
Diff between mgcv versions 1.7-2 dated 2010-11-13 and 1.7-3 dated 2011-02-14
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs by REML or PQL. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
DESCRIPTION | 6
NAMESPACE | 5
R/bam.r | 32 +
R/gam.fit3.r | 9
R/gamm.r | 8
R/mgcv.r | 96 ++++-
R/plots.r | 8
R/smooth.r | 584 ++++++++++++++++++++++++++++++--
changeLog | 23 +
inst/CITATION | 35 -
man/bam.Rd | 6
man/gam.Rd | 25 -
man/gam.control.Rd | 7
man/gam.fit3.Rd | 7
man/gam.models.Rd | 12
man/gam.outer.Rd | 7
man/gam.selection.Rd | 6
man/gam.vcomp.Rd | 6
man/gam2objective.Rd | 4
man/gamm.Rd | 19 -
man/logLik.gam.Rd | 7
man/magic.Rd | 3
man/mgcv-package.Rd | 7
man/mgcv.Rd | 8
man/random.effects.Rd | 5
man/slanczos.Rd |only
man/smooth.construct.Rd | 2
man/smooth.construct.ds.smooth.spec.Rd |only
man/smooth.construct.sos.smooth.spec.Rd |only
man/smooth.terms.Rd | 10
src/init.c | 3
src/mat.c | 59 +++
src/matrix.c | 243 ++++++++++++-
src/matrix.h | 2
src/mgcv.c | 45 +-
src/mgcv.h | 9
src/misc.c | 40 ++
src/tprs.c | 87 +++-
src/tprs.h | 2
39 files changed, 1235 insertions(+), 202 deletions(-)
Title: Everyone's Statistical Software
Diff between Zelig versions 3.4-8 dated 2010-01-21 and 3.5 dated 2011-02-14
Description: Zelig is an easy-to-use program that can estimate, and
help interpret the results of, an enormous range of statistical
models. It literally is ``everyone's statistical software''
because Zelig's simple unified framework incorporates everyone
else's (R) code. We also hope it will become ``everyone's
statistical software'' for applications and teaching, and so
have designed Zelig so that anyone can easily use it or add
their programs to it. Zelig also comes with infrastructure
that facilitates the use of any existing method, such as by
allowing multiply imputed data for any model, and mimicking the
program Clarify (for Stata) that takes the raw output of
existing statistical procedures and translates them into
quantities of direct interest.
Author: Kosuke Imai
Maintainer: Kosuke Imai
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Title: Student Growth Percentile and Percentile Growth
Projection/Trajectory Functions
Diff between SGP versions 0.0-6.7 dated 2011-02-09 and 0.0-6.8 dated 2011-02-14
Description: Functions to calculate student growth percentiles and
percentile growth projections/trajectories for students using
large scale, longitudinal assessment data. Functions use
quantile regression to estimate the conditional density
associated with each student's achievement history. Percentile
growth projections/trajectories are calculated using the
coefficient matrices derived from the quantile regression
analyses and specify what percentile growth is required for
students to reach future achievement targets.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 10 +++++-----
R/studentGrowthPercentiles.R | 27 ++++++++++++++-------------
R/studentGrowthProjections.R | 4 ++--
data/sgpData_LONG.rda |only
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inst/CITATION | 4 ++--
inst/NEWS | 10 ++++++++--
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man/sgpData.Rd | 7 ++++---
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11 files changed, 50 insertions(+), 31 deletions(-)
Title: Automating Mplus Model Estimation and Interpretation
Diff between MplusAutomation versions 0.4 dated 2010-11-03 and 0.4-1 dated 2011-02-14
More information about MplusAutomation at CRAN
Description: The MplusAutomation package leverages the flexibility of
the R language to automate latent variable model estimation and
interpretation using Mplus, a powerful latent variable modeling
program developed by Muthen and Muthen (www.statmodel.com).
Specifically, MplusAutomation provides routines for creating
related groups of models, running batches of models, and
extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist
Maintainer: Michael Hallquist
DESCRIPTION | 8 ++--
NEWS | 9 +++++
R/extractParameters.R | 30 +++++++++---------
R/parseOutput.R | 68 +++++++++++++++++++++++++++++------------
R/utilityFunctions.R | 12 ++++---
inst/doc/Vignette.pdf |binary
man/MplusAutomation-package.Rd | 4 +-
7 files changed, 88 insertions(+), 43 deletions(-)
Permanent link
Title: Distribution function of quadratic forms in normal variables
Diff between CompQuadForm versions 1.1 dated 2010-10-01 and 1.2 dated 2011-02-14
Description: Computes the distribution function of quadratic forms in
normal variables using Imhof's method, Davies's algorithm,
Farebrother's algorithm or Liu et al.'s algorithm.
Author: P. Lafaye de Micheaux
Maintainer: P. Lafaye de Micheaux
DESCRIPTION | 8 +++----
R/davies.R | 4 +--
inst/HISTORY | 10 ++++++++
man/davies.Rd | 66 ++++++++++++++++++++++++++++++++++------------------------
4 files changed, 55 insertions(+), 33 deletions(-)
Title: Bayesian Two-Zone Model
Diff between B2Z versions 1.1 dated 2010-06-05 and 1.2 dated 2011-02-14
Description: This package fits the Bayesian two-Zone Models.
Author: Joao Vitor Dias Monteiro
Maintainer: Joao Vitor Dias Monteiro
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B2Z-1.2/B2Z/R/rwish.R | 4
B2Z-1.2/B2Z/R/summary.bclt.R | 60 +--
B2Z-1.2/B2Z/R/summary.imis.R | 78 ++--
B2Z-1.2/B2Z/R/summary.mcmc.R |only
B2Z-1.2/B2Z/R/summary.out.R | 2
B2Z-1.2/B2Z/R/summary.sir.R | 74 ++--
B2Z-1.2/B2Z/R/verifying_priorBeta.R | 5
B2Z-1.2/B2Z/R/verifying_priorG.R | 4
B2Z-1.2/B2Z/R/verifying_priorQ.R | 5
B2Z-1.2/B2Z/R/which.dist.R | 5
B2Z-1.2/B2Z/R/wrapper_computeCNCF.R |only
B2Z-1.2/B2Z/man/B2Z-package.Rd | 8
B2Z-1.2/B2Z/man/B2ZM.Rd | 198 +++-------
B2Z-1.2/B2Z/man/B2ZM_BCLT.Rd | 84 ++--
B2Z-1.2/B2Z/man/B2ZM_IMIS.Rd | 60 +--
B2Z-1.2/B2Z/man/B2ZM_MCMC.Rd |only
B2Z-1.2/B2Z/man/B2ZM_SIR.Rd | 62 +--
75 files changed, 1919 insertions(+), 2159 deletions(-)
Title: apsrtable model-output formatter for social science
Diff between apsrtable versions 0.8-1 dated 2010-03-19 and 0.8-3 dated 2011-02-14
Description: Formats latex tables from one or more model objects
side-by-side with standard errors below, not unlike tables
found in such journals as the American Political Science
Review.
Author: Michael Malecki
Maintainer: Michael Malecki
apsrtable-0.8-1/apsrtable/guide.tex |only
apsrtable-0.8-3/apsrtable/DESCRIPTION | 6
apsrtable-0.8-3/apsrtable/R/apsrtable.R | 65 ++--
apsrtable-0.8-3/apsrtable/apsrtable-Ex.R |only
apsrtable-0.8-3/apsrtable/inst/doc/Makefile | 10
apsrtable-0.8-3/apsrtable/inst/doc/guide-real.pdf |only
apsrtable-0.8-3/apsrtable/inst/doc/guide.Rnw | 347 ---------------------
apsrtable-0.8-3/apsrtable/inst/doc/guide.Rnw.real |only
apsrtable-0.8-3/apsrtable/inst/doc/guide.pdf |binary
apsrtable-0.8-3/apsrtable/inst/doc/guide.tex | 357 ----------------------
apsrtable-0.8-3/apsrtable/inst/doc/tpm_v16_n2.pdf |only
apsrtable-0.8-3/apsrtable/man/apsrtable.Rd | 13
apsrtable-0.8-3/apsrtable/man/notefunctions.Rd | 44 +-
13 files changed, 86 insertions(+), 756 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.9.0 dated 2010-12-20 and 0.9.1 dated 2011-02-14
Description: The Rcpp package provides a C++ library which facilitates
the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Several examples are included, and 753 unit tests in 335 unit test
functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic and it is still available for code relying on this
interface. New development should use this package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois
ChangeLog | 129 +
DESCRIPTION | 10
NAMESPACE | 35
R/00_classes.R | 2
R/01_show.R | 2
R/02_completion.R | 2
R/03_prompt.R | 2
R/Module.R | 2
R/Rcpp.package.skeleton.R | 2
R/SHLIB.R | 2
R/bib.R | 2
R/exceptions.R | 2
R/inline.R | 36
R/populate.R | 2
R/tools.R | 2
R/unit.tests.R | 2
R/zzz.R | 6
inst/NEWS | 23
inst/THANKS | 3
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-FAQ/Rcpp-FAQ.Rnw | 122 +
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-modules/Rcpp-modules.Rnw | 457 ++---
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-quickref/Rcpp-quickref.Rnw | 126 -
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp.bib | 77
inst/doc/unitTests-results/Rcpp-unitTests.html | 10
inst/doc/unitTests-results/Rcpp-unitTests.txt | 57
inst/include/Rcpp.h | 2
inst/include/Rcpp/DataFrame.h | 83
inst/include/Rcpp/DataFrame_generated.h | 384 +---
inst/include/Rcpp/Date.h | 4
inst/include/Rcpp/DateVector.h | 2
inst/include/Rcpp/Date_forward.h | 2
inst/include/Rcpp/Datetime.h | 2
inst/include/Rcpp/DatetimeVector.h | 2
inst/include/Rcpp/Datetime_forward.h | 2
inst/include/Rcpp/Dimension.h | 2
inst/include/Rcpp/DottedPair.h | 5
inst/include/Rcpp/Environment.h | 2
inst/include/Rcpp/Evaluator.h | 2
inst/include/Rcpp/Extractor.h | 3
inst/include/Rcpp/Fast.h | 2
inst/include/Rcpp/Formula.h | 2
inst/include/Rcpp/Function.h | 6
inst/include/Rcpp/Generator.h | 2
inst/include/Rcpp/InternalFunction.h | 2
inst/include/Rcpp/Language.h | 2
inst/include/Rcpp/Module.h | 17
inst/include/Rcpp/Named.h | 2
inst/include/Rcpp/Pairlist.h | 2
inst/include/Rcpp/Promise.h | 2
inst/include/Rcpp/RObject.h | 30
inst/include/Rcpp/Reference.h | 2
inst/include/Rcpp/S4.h | 2
inst/include/Rcpp/StringTransformer.h | 2
inst/include/Rcpp/Symbol.h | 2
inst/include/Rcpp/Vector.h | 2
inst/include/Rcpp/WeakReference.h | 2
inst/include/Rcpp/XPtr.h | 10
inst/include/Rcpp/algo.h | 2
inst/include/Rcpp/as.h | 2
inst/include/Rcpp/barrier.h | 2
inst/include/Rcpp/cache.h | 2
inst/include/Rcpp/clone.h | 2
inst/include/Rcpp/complex.h | 2
inst/include/Rcpp/config.h | 4
inst/include/Rcpp/exceptions.h | 2
inst/include/Rcpp/generated/DottedPair__ctors.h | 2
inst/include/Rcpp/generated/Function__operator.h | 44
inst/include/Rcpp/generated/InternalFunction__ctors.h | 2
inst/include/Rcpp/generated/Language__ctors.h | 2
inst/include/Rcpp/generated/Pairlist__ctors.h | 2
inst/include/Rcpp/generated/Vector__create.h | 2
inst/include/Rcpp/generated/grow__pairlist.h | 2
inst/include/Rcpp/grow.h | 16
inst/include/Rcpp/internal/ListInitialization.h | 2
inst/include/Rcpp/internal/Proxy_Iterator.h | 2
inst/include/Rcpp/internal/caster.h | 2
inst/include/Rcpp/internal/export.h | 2
inst/include/Rcpp/internal/posixt.h | 2
inst/include/Rcpp/internal/r_coerce.h | 2
inst/include/Rcpp/internal/r_vector.h | 2
inst/include/Rcpp/internal/wrap.h | 2
inst/include/Rcpp/internal/wrap_forward.h | 2
inst/include/Rcpp/lang.h |only
inst/include/Rcpp/macros/unroll.h | 2
inst/include/Rcpp/module/Module_Add_Property.h | 2
inst/include/Rcpp/module/Module_Field.h | 2
inst/include/Rcpp/module/Module_Property.h | 2
inst/include/Rcpp/module/Module_generated_Constructor.h | 2
inst/include/Rcpp/module/Module_generated_CppFunction.h | 2
inst/include/Rcpp/module/Module_generated_CppMethod.h | 2
inst/include/Rcpp/module/Module_generated_Pointer_CppMethod.h | 2
inst/include/Rcpp/module/Module_generated_Pointer_method.h | 2
inst/include/Rcpp/module/Module_generated_class_constructor.h | 2
inst/include/Rcpp/module/Module_generated_class_signature.h | 2
inst/include/Rcpp/module/Module_generated_ctor_signature.h | 2
inst/include/Rcpp/module/Module_generated_function.h | 2
inst/include/Rcpp/module/Module_generated_get_return_type.h | 2
inst/include/Rcpp/module/Module_generated_get_signature.h | 2
inst/include/Rcpp/module/Module_generated_method.h | 2
inst/include/Rcpp/preprocessor.h | 2
inst/include/Rcpp/preprocessor_generated.h | 2
inst/include/Rcpp/r_cast.h | 2
inst/include/Rcpp/routines.h | 2
inst/include/Rcpp/sprintf.h | 2
inst/include/Rcpp/stats/beta.h | 2
inst/include/Rcpp/stats/binom.h | 2
inst/include/Rcpp/stats/cauchy.h | 2
inst/include/Rcpp/stats/chisq.h | 2
inst/include/Rcpp/stats/dpq/dpq.h | 2
inst/include/Rcpp/stats/exp.h | 2
inst/include/Rcpp/stats/f.h | 2
inst/include/Rcpp/stats/gamma.h | 2
inst/include/Rcpp/stats/geom.h | 2
inst/include/Rcpp/stats/hyper.h | 2
inst/include/Rcpp/stats/lnorm.h | 2
inst/include/Rcpp/stats/logis.h | 2
inst/include/Rcpp/stats/nbeta.h | 2
inst/include/Rcpp/stats/nbinom.h | 2
inst/include/Rcpp/stats/nbinom_mu.h | 2
inst/include/Rcpp/stats/nchisq.h | 2
inst/include/Rcpp/stats/nf.h | 2
inst/include/Rcpp/stats/norm.h | 2
inst/include/Rcpp/stats/nt.h | 2
inst/include/Rcpp/stats/pois.h | 2
inst/include/Rcpp/stats/random/random.h | 2
inst/include/Rcpp/stats/random/rbeta.h | 2
inst/include/Rcpp/stats/random/rbinom.h | 2
inst/include/Rcpp/stats/random/rcauchy.h | 2
inst/include/Rcpp/stats/random/rchisq.h | 2
inst/include/Rcpp/stats/random/rexp.h | 2
inst/include/Rcpp/stats/random/rf.h | 2
inst/include/Rcpp/stats/random/rgamma.h | 2
inst/include/Rcpp/stats/random/rgeom.h | 2
inst/include/Rcpp/stats/random/rhyper.h | 2
inst/include/Rcpp/stats/random/rlnorm.h | 2
inst/include/Rcpp/stats/random/rlogis.h | 2
inst/include/Rcpp/stats/random/rnbinom.h | 2
inst/include/Rcpp/stats/random/rnbinom_mu.h | 2
inst/include/Rcpp/stats/random/rnchisq.h | 2
inst/include/Rcpp/stats/random/rnorm.h | 2
inst/include/Rcpp/stats/random/rpois.h | 2
inst/include/Rcpp/stats/random/rsignrank.h | 2
inst/include/Rcpp/stats/random/rt.h | 2
inst/include/Rcpp/stats/random/runif.h | 2
inst/include/Rcpp/stats/random/rweibull.h | 2
inst/include/Rcpp/stats/random/rwilcox.h | 2
inst/include/Rcpp/stats/stats.h | 2
inst/include/Rcpp/stats/t.h | 2
inst/include/Rcpp/stats/unif.h | 2
inst/include/Rcpp/stats/weibull.h | 2
inst/include/Rcpp/sugar/Range.h | 2
inst/include/Rcpp/sugar/block/SugarBlock_1.h | 2
inst/include/Rcpp/sugar/block/SugarBlock_2.h | 2
inst/include/Rcpp/sugar/block/SugarBlock_3.h | 2
inst/include/Rcpp/sugar/block/SugarMath.h | 4
inst/include/Rcpp/sugar/block/Vectorized_Math.h |only
inst/include/Rcpp/sugar/block/block.h | 3
inst/include/Rcpp/sugar/functions/Lazy.h | 2
inst/include/Rcpp/sugar/functions/all.h | 2
inst/include/Rcpp/sugar/functions/any.h | 2
inst/include/Rcpp/sugar/functions/complex.h | 2
inst/include/Rcpp/sugar/functions/cumsum.h | 2
inst/include/Rcpp/sugar/functions/diff.h | 2
inst/include/Rcpp/sugar/functions/functions.h | 2
inst/include/Rcpp/sugar/functions/head.h | 2
inst/include/Rcpp/sugar/functions/ifelse.h | 2
inst/include/Rcpp/sugar/functions/is_na.h | 2
inst/include/Rcpp/sugar/functions/lapply.h | 2
inst/include/Rcpp/sugar/functions/math.h | 62
inst/include/Rcpp/sugar/functions/pmax.h | 2
inst/include/Rcpp/sugar/functions/pmin.h | 2
inst/include/Rcpp/sugar/functions/pow.h | 2
inst/include/Rcpp/sugar/functions/rep.h | 2
inst/include/Rcpp/sugar/functions/rep_each.h | 2
inst/include/Rcpp/sugar/functions/rep_len.h | 2
inst/include/Rcpp/sugar/functions/rev.h | 2
inst/include/Rcpp/sugar/functions/sapply.h | 2
inst/include/Rcpp/sugar/functions/seq_along.h | 2
inst/include/Rcpp/sugar/functions/sign.h | 2
inst/include/Rcpp/sugar/functions/sum.h | 35
inst/include/Rcpp/sugar/functions/tail.h | 2
inst/include/Rcpp/sugar/logical/SingleLogicalResult.h | 2
inst/include/Rcpp/sugar/logical/and.h | 2
inst/include/Rcpp/sugar/logical/can_have_na.h | 2
inst/include/Rcpp/sugar/logical/is.h | 2
inst/include/Rcpp/sugar/logical/logical.h | 2
inst/include/Rcpp/sugar/logical/not.h | 2
inst/include/Rcpp/sugar/logical/or.h | 2
inst/include/Rcpp/sugar/matrix/as_vector.h | 2
inst/include/Rcpp/sugar/matrix/col.h | 2
inst/include/Rcpp/sugar/matrix/diag.h | 2
inst/include/Rcpp/sugar/matrix/lower_tri.h | 2
inst/include/Rcpp/sugar/matrix/matrix_functions.h | 2
inst/include/Rcpp/sugar/matrix/outer.h | 2
inst/include/Rcpp/sugar/matrix/row.h | 2
inst/include/Rcpp/sugar/matrix/tools.h | 2
inst/include/Rcpp/sugar/matrix/upper_tri.h | 2
inst/include/Rcpp/sugar/nona/nona.h | 2
inst/include/Rcpp/sugar/operators/Comparator.h | 2
inst/include/Rcpp/sugar/operators/Comparator_With_One_Value.h | 2
inst/include/Rcpp/sugar/operators/divides.h | 308 ++-
inst/include/Rcpp/sugar/operators/logical_operators__Vector__Vector.h | 2
inst/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h | 2
inst/include/Rcpp/sugar/operators/minus.h | 240 ++
inst/include/Rcpp/sugar/operators/not.h | 2
inst/include/Rcpp/sugar/operators/operators.h | 2
inst/include/Rcpp/sugar/operators/plus.h | 207 ++
inst/include/Rcpp/sugar/operators/r_binary_op.h | 2
inst/include/Rcpp/sugar/operators/times.h | 194 ++
inst/include/Rcpp/sugar/operators/unary_minus.h | 2
inst/include/Rcpp/sugar/sugar.h | 2
inst/include/Rcpp/sugar/sugar_forward.h | 2
inst/include/Rcpp/sugar/undoRmath.h | 2
inst/include/Rcpp/traits/Exporter.h | 10
inst/include/Rcpp/traits/expands_to_logical.h | 2
inst/include/Rcpp/traits/get_na.h | 2
inst/include/Rcpp/traits/has_iterator.h | 2
inst/include/Rcpp/traits/has_na.h | 2
inst/include/Rcpp/traits/if_.h | 2
inst/include/Rcpp/traits/init_type.h | 2
inst/include/Rcpp/traits/integral_constant.h | 2
inst/include/Rcpp/traits/is_const.h | 2
inst/include/Rcpp/traits/is_convertible.h | 2
inst/include/Rcpp/traits/is_na.h | 2
inst/include/Rcpp/traits/is_reference.h | 2
inst/include/Rcpp/traits/is_sugar_expression.h | 2
inst/include/Rcpp/traits/is_trivial.h | 2
inst/include/Rcpp/traits/matrix_interface.h | 2
inst/include/Rcpp/traits/named_object.h | 2
inst/include/Rcpp/traits/r_sexptype_traits.h | 2
inst/include/Rcpp/traits/r_type_traits.h | 2
inst/include/Rcpp/traits/remove_const.h | 2
inst/include/Rcpp/traits/remove_const_and_reference.h | 2
inst/include/Rcpp/traits/remove_reference.h | 2
inst/include/Rcpp/traits/result_of.h | 2
inst/include/Rcpp/traits/same_type.h | 2
inst/include/Rcpp/traits/storage_type.h | 2
inst/include/Rcpp/traits/wrap_type_traits.h | 2
inst/include/Rcpp/vector/00_forward_Vector.h | 2
inst/include/Rcpp/vector/00_forward_eval_methods.h | 2
inst/include/Rcpp/vector/00_forward_proxy.h | 2
inst/include/Rcpp/vector/LazyVector.h | 2
inst/include/Rcpp/vector/Matrix.h | 2
inst/include/Rcpp/vector/MatrixBase.h | 2
inst/include/Rcpp/vector/MatrixColumn.h | 2
inst/include/Rcpp/vector/MatrixRow.h | 2
inst/include/Rcpp/vector/RangeIndexer.h | 2
inst/include/Rcpp/vector/SubMatrix.h | 2
inst/include/Rcpp/vector/Vector.h | 487 ++++-
inst/include/Rcpp/vector/VectorBase.h | 2
inst/include/Rcpp/vector/converter.h | 2
inst/include/Rcpp/vector/eval_methods.h | 30
inst/include/Rcpp/vector/instantiation.h | 2
inst/include/Rcpp/vector/proxy.h | 2
inst/include/Rcpp/vector/string_proxy.h | 8
inst/include/Rcpp/vector/swap.h | 2
inst/include/Rcpp/vector/traits.h | 2
inst/include/RcppCommon.h | 10
inst/include/doxygen/Examples.h | 2
inst/unitTests/runit.DataFrame.R | 7
inst/unitTests/runit.Module.R | 3
inst/unitTests/runit.Vector.R | 52
inst/unitTests/runit.sugar.R | 842 +++++-----
inst/unitTests/runit.support.R |only
src/Date.cpp | 2
src/DateVector.cpp | 2
src/Datetime.cpp | 2
src/DatetimeVector.cpp | 2
src/Dimension.cpp | 2
src/DottedPair.cpp | 2
src/Environment.cpp | 151 -
src/Evaluator.cpp | 30
src/Formula.cpp | 2
src/Function.cpp | 9
src/Language.cpp | 8
src/Makevars | 10
src/Module.cpp | 4
src/Pairlist.cpp | 2
src/Promise.cpp | 2
src/RObject.cpp | 75
src/RcppCommon.cpp | 2
src/Rcpp_init.c | 7
src/Reference.cpp | 49
src/S4.cpp | 24
src/Symbol.cpp | 69
src/WeakReference.cpp | 4
src/barrier.cpp | 2
src/cache.cpp | 36
src/coerce.cpp | 2
src/complex.cpp | 2
src/debugging.cpp | 10
src/exceptions.cpp | 18
src/posixt.cpp | 2
src/r_cast.cpp | 2
302 files changed, 3218 insertions(+), 1953 deletions(-)
Title: Graphical user interface for data mining in R
Diff between rattle versions 2.6.2 dated 2011-02-02 and 2.6.3 dated 2011-02-14
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab.
Thus they are available to the user as a script file or as an
aide for the user to learn R or to copy-and-paste directly into
R itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.
Author: Graham Williams
Maintainer: Graham Williams
DESCRIPTION | 8 ++++----
R/explore.R | 26 +++++++++++++++-----------
R/hclust.R | 4 ++--
R/rattle.R | 8 ++++----
R/zzz.R | 4 ++--
data/weatherAUS.RData |binary
inst/ChangeLog | 14 ++++++++++++++
inst/arff/weather.arff | 2 +-
inst/doc/rattle.pdf |binary
inst/po/de/LC_MESSAGES/R-rattle.mo |binary
inst/po/es/LC_MESSAGES/R-rattle.mo |binary
inst/po/fr/LC_MESSAGES/R-rattle.mo |binary
inst/po/ja/LC_MESSAGES/R-rattle.mo |binary
13 files changed, 42 insertions(+), 24 deletions(-)
Title: qgraph
Diff between qgraph versions 0.4.4 dated 2011-01-25 and 0.4.5 dated 2011-02-14
Description: The qgraph package can be used to visualize psychometric
data by using networks. (see URL).
Author: Sacha Epskamp, Angelique O. J. Cramer, Lourens J. Waldorp,
Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp
DESCRIPTION | 8 ++++----
NEWS | 9 ++++++++-
R/layout.R | 21 ++++++++-------------
R/qgraph.R | 23 +++++++++++++++++++----
R/qgraph_loadings.R | 16 +++++++++++++---
data |only
man/big5.Rd |only
man/big5groups.Rd |only
man/qgraph.Rd | 6 +++++-
9 files changed, 57 insertions(+), 26 deletions(-)
Title: Graphic Extensions for Categorical Data
Diff between extracat versions 1.0-1 dated 2010-03-02 and 1.1-0 dated 2011-02-14
Description: graphic extensions for categorical data
Author: Alexander Pilhoefer
Maintainer: Alexander Pilhoefer
extracat-1.0-1/extracat/R/irmb1.R |only
extracat-1.1-0/extracat/DESCRIPTION | 12
extracat-1.1-0/extracat/NAMESPACE | 8
extracat-1.1-0/extracat/R/cpcp2.R | 61 +--
extracat-1.1-0/extracat/R/irmb2.R |only
extracat-1.1-0/extracat/R/newrmb2.R | 520 +++++++++++++++++++++-----------
extracat-1.1-0/extracat/R/subtable.R | 187 +++++++----
extracat-1.1-0/extracat/man/cpcp.Rd | 194 +++++------
extracat-1.1-0/extracat/man/irmb.Rd | 70 ++--
extracat-1.1-0/extracat/man/rmb.Rd | 116 ++++---
extracat-1.1-0/extracat/man/subtable.Rd | 125 +++----
11 files changed, 778 insertions(+), 515 deletions(-)
Title: Generalized Dynamic Linear Modeler
Diff between dlmodeler versions 1.0-0 dated 2011-01-04 and 1.1-0 dated 2011-02-14
Description: dlmodeler is a set of user-friendly functions to simplify
the state-space modelling, fitting, analysis and forecasting of
Generalized Dynamic Linear Models (DLMs). It includes functions
to name and extract individual components of a DLM, build
classical seasonal time-series models (monthly, quarterly,
yearly, etc. with calendar adjustments) and provides a unified
interface compatible with other state-space packages including:
dlm, FKF and KFAS.
Author: Cyrille Szymanski
Maintainer: Cyrille Szymanski
dlmodeler-1.0-0/dlmodeler/R/dlmodeler-src.R |only
dlmodeler-1.1-0/dlmodeler/ChangeLog | 67 ++-
dlmodeler-1.1-0/dlmodeler/DESCRIPTION | 20
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-FKF.R |only
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-KFAS.R |only
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-core.R |only
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-dlm.R |only
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-fit.R |only
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-models-advanced.R |only
dlmodeler-1.1-0/dlmodeler/R/dlmodeler-models-basic.R |only
dlmodeler-1.1-0/dlmodeler/man/AIC.dlmodeler.fit.Rd | 22 -
dlmodeler-1.1-0/dlmodeler/man/dlmodeler-internal.Rd | 3
dlmodeler-1.1-0/dlmodeler/man/dlmodeler-package.Rd | 238 +++++-----
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.add.Rd | 9
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.bind.Rd | 9
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.Rd | 24 -
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.arima.Rd | 20
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.dseasonal.Rd | 20
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.polynomial.Rd | 20
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.regression.Rd | 18
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.structural.Rd | 18
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.build.tseasonal.Rd | 18
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.check.Rd | 33 -
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.extract.Rd | 10
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.filter.smooth.Rd | 7
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.fit.Rd | 61 +-
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.forecast.Rd | 13
dlmodeler-1.1-0/dlmodeler/man/dlmodeler.yeardays.Rd |only
dlmodeler-1.1-0/dlmodeler/man/print.dlmodeler.Rd | 6
dlmodeler-1.1-0/dlmodeler/tests/tests.R | 260 ++++++++++--
30 files changed, 540 insertions(+), 356 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.4-01 dated 2011-02-05 and 1.4-02.01 dated 2011-02-14
Description: R functions for processing lm, glm, mer and polr outputs.
Author: Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 4 ++++
DESCRIPTION | 8 ++++----
R/bayesglm.R | 25 ++++++++++++++++++-------
R/load.first.R | 2 +-
4 files changed, 27 insertions(+), 12 deletions(-)
Title: Laplace's Demon: Software for Bayesian Inference
Diff between LaplacesDemon versions 11.02.07 dated 2011-02-07 and 11.02.14 dated 2011-02-14
Description: Laplace's Demon is MCMC-based software for Bayesian
inference, written entirely in R.
Author: Byron Hall
Maintainer: Byron Hall
LaplacesDemon-11.02.07/LaplacesDemon/R/IVO.R |only
LaplacesDemon-11.02.07/LaplacesDemon/man/IVO.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/bernoulli.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/demonsnacks.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/dirichlet.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/invgamma.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/invwishart.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/laplace.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/mvn.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/mvt.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/truncated.Rd |only
LaplacesDemon-11.02.07/LaplacesDemon/man/wishart.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/CHANGELOG | 8
LaplacesDemon-11.02.14/LaplacesDemon/DESCRIPTION | 8
LaplacesDemon-11.02.14/LaplacesDemon/NAMESPACE | 14
LaplacesDemon-11.02.14/LaplacesDemon/R/BayesFactor.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/CenterScale.R | 14
LaplacesDemon-11.02.14/LaplacesDemon/R/LaplaceApproximation.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/LaplacesDemon.R | 13
LaplacesDemon-11.02.14/LaplacesDemon/R/Mode.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/caterpillar.plot.R | 81
LaplacesDemon-11.02.14/LaplacesDemon/R/joint.density.plot.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/logit.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/plot.demonoid.R | 46
LaplacesDemon-11.02.14/LaplacesDemon/R/plot.demonoid.ppc.R | 10
LaplacesDemon-11.02.14/LaplacesDemon/R/plot.laplace.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/plot.laplace.ppc.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/predict.demonoid.R | 17
LaplacesDemon-11.02.14/LaplacesDemon/R/predict.laplace.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/print.demonoid.R | 6
LaplacesDemon-11.02.14/LaplacesDemon/R/print.laplace.R |only
LaplacesDemon-11.02.14/LaplacesDemon/R/summary.demonoid.ppc.R | 22
LaplacesDemon-11.02.14/LaplacesDemon/R/summary.laplace.ppc.R |only
LaplacesDemon-11.02.14/LaplacesDemon/inst/CITATION | 2
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/BayesianInference.Stex | 71
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/BayesianInference.pdf |binary
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/Examples.Stex | 39
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/Examples.pdf | 1354 +++++-----
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/LaplacesDemon.Stex | 167 -
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/LaplacesDemon.pdf |binary
LaplacesDemon-11.02.14/LaplacesDemon/inst/doc/References.bib | 59
LaplacesDemon-11.02.14/LaplacesDemon/man/BayesFactor.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/CenterScale.Rd | 4
LaplacesDemon-11.02.14/LaplacesDemon/man/LaplaceApproximation.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/LaplacesDemon.Rd | 35
LaplacesDemon-11.02.14/LaplacesDemon/man/Mode.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/caterpillar.plot.Rd | 20
LaplacesDemon-11.02.14/LaplacesDemon/man/data.demonsnacks.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Bernoulli.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Dirichlet.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Inverse.Gamma.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Inverse.Wishart.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Laplace.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Multivariate.Normal.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Multivariate.t.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Truncated.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/dist.Wishart.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/joint.density.plot.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/logit.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/plot.demonoid.ppc.Rd | 6
LaplacesDemon-11.02.14/LaplacesDemon/man/plot.laplace.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/plot.laplace.ppc.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/predict.demonoid.Rd | 9
LaplacesDemon-11.02.14/LaplacesDemon/man/predict.laplace.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/print.laplace.Rd |only
LaplacesDemon-11.02.14/LaplacesDemon/man/summary.demonoid.ppc.Rd | 40
LaplacesDemon-11.02.14/LaplacesDemon/man/summary.laplace.ppc.Rd |only
67 files changed, 1192 insertions(+), 853 deletions(-)
Title: Joint Modelling of Longitudinal and Survival Data
Diff between JM versions 0.8-1 dated 2011-01-27 and 0.8-2 dated 2011-02-14
Description: Shared parameter models for the joint modelling of
longitudinal and time-to-event data.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos
DESCRIPTION | 8 ++++----
R/ModelMats.R | 12 +++++++-----
R/jointModel.R | 4 ++--
R/rocJM.R | 35 +++++++++++++++++++++--------------
R/survfitJM.R | 6 ++----
inst/NEWS | 7 +++++++
man/JM.Rd | 10 +++++-----
man/dynC.Rd | 2 +-
man/jointModel.Rd | 8 ++++----
man/plot-rocJM.Rd | 2 +-
man/plot-survfitJM.Rd | 4 ++--
man/rocJM.Rd | 6 +++---
man/survfitJM.Rd | 4 ++--
13 files changed, 61 insertions(+), 47 deletions(-)