Title: Heteroscedastic Discriminant Analysis
Description: Functions to perform dimensionality reduction for
classification if the covariance matrices of the classes are
unequal.
Author: Gero Szepannek
Maintainer: Gero Szepannek
Diff between hda versions 0.1-17 dated 2011-11-03 and 0.1-18 dated 2012-06-25
DESCRIPTION | 12 +++++++----- MD5 | 4 ++-- R/hda.r | 15 ++++++++++++++- 3 files changed, 23 insertions(+), 8 deletions(-)
Title: Fit and test metaregression models
Description: This package fits meta regression models and generates a
Author: Hilde M. Huizenga & Ingmar Visser
Maintainer: Ingmar Visser
Diff between metatest versions 1.0-2 dated 2011-10-06 and 1.0-3 dated 2012-06-25
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE |only NEWS | 5 +++++ R/metareg.R | 4 ++-- data/metadata.rda |binary 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Causal Inference of QTL Networks
Description: Functions to Simultaneously Infer Causal Graphs and
Genetic Architecture
Author: Elias Chaibub Neto
Maintainer: Brian S. Yandell
Diff between qtlnet versions 1.2.4 dated 2012-06-08 and 1.2.5 dated 2012-06-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/igraph.R | 6 +++--- inst/doc/qtlnet.pdf |binary 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Unmarked fits hierarchical models of animal abundance and
occurrence to data collected using survey methods such as point
counts, site occupancy sampling, distance sampling, removal
sampling, and double observer sampling. Parameters governing
the state and observation processes can be modeled as functions
of covariates.
Author: Ian Fiske, Richard Chandler, Andy Royle, Marc Kery
Maintainer: Richard Chandler
Diff between unmarked versions 0.9-7 dated 2012-03-29 and 0.9-8 dated 2012-06-25
unmarked-0.9-7/unmarked/inst/csv/crossbill.csv |only unmarked-0.9-7/unmarked/vignettes/spp-dist-predict.pdf |only unmarked-0.9-7/unmarked/vignettes/spp-dist-psi1.pdf |only unmarked-0.9-8/unmarked/DESCRIPTION | 8 unmarked-0.9-8/unmarked/MD5 | 75 +- unmarked-0.9-8/unmarked/R/distsamp.R | 111 ++- unmarked-0.9-8/unmarked/R/ranef.R | 13 unmarked-0.9-8/unmarked/R/unmarkedEstimate.R | 148 ++--- unmarked-0.9-8/unmarked/R/unmarkedFit.R | 206 ++++++- unmarked-0.9-8/unmarked/R/unmarkedFitList.R | 34 - unmarked-0.9-8/unmarked/R/unmarkedLinComb.R | 205 +++---- unmarked-0.9-8/unmarked/data/Switzerland.txt.gz |only unmarked-0.9-8/unmarked/data/crossbill.rda |only unmarked-0.9-8/unmarked/data/cruz.rda |only unmarked-0.9-8/unmarked/data/issj.rda |only unmarked-0.9-8/unmarked/inst/doc/cap-recap.pdf |binary unmarked-0.9-8/unmarked/inst/doc/colext.Rnw | 11 unmarked-0.9-8/unmarked/inst/doc/colext.pdf |binary unmarked-0.9-8/unmarked/inst/doc/distsamp.Rnw | 10 unmarked-0.9-8/unmarked/inst/doc/distsamp.pdf |binary unmarked-0.9-8/unmarked/inst/doc/spp-dist.Rnw | 447 ++++++++++------ unmarked-0.9-8/unmarked/inst/doc/spp-dist.pdf |binary unmarked-0.9-8/unmarked/inst/doc/unmarked.pdf |binary unmarked-0.9-8/unmarked/inst/unitTests/runTests.R | 5 unmarked-0.9-8/unmarked/inst/unitTests/runit.distsamp.r | 18 unmarked-0.9-8/unmarked/inst/unitTests/runit.predict.R | 65 ++ unmarked-0.9-8/unmarked/inst/unitTests/runit.ranef.R | 15 unmarked-0.9-8/unmarked/man/Switzerland.Rd |only unmarked-0.9-8/unmarked/man/colext.Rd | 2 unmarked-0.9-8/unmarked/man/crossbill.Rd |only unmarked-0.9-8/unmarked/man/cruz.Rd |only unmarked-0.9-8/unmarked/man/distsamp.Rd | 85 ++- unmarked-0.9-8/unmarked/man/gmultmix.Rd | 1 unmarked-0.9-8/unmarked/man/issj.Rd |only unmarked-0.9-8/unmarked/man/predict-methods.Rd | 11 unmarked-0.9-8/unmarked/man/unmarked-package.Rd | 57 +- unmarked-0.9-8/unmarked/src/Makevars.win | 8 unmarked-0.9-8/unmarked/src/detfuns.cpp |only unmarked-0.9-8/unmarked/src/detfuns.h |only unmarked-0.9-8/unmarked/src/nll_distsamp.cpp |only unmarked-0.9-8/unmarked/src/nll_distsamp.h |only unmarked-0.9-8/unmarked/vignettes/auto |only unmarked-0.9-8/unmarked/vignettes/colext.Rnw | 11 unmarked-0.9-8/unmarked/vignettes/distsamp.Rnw | 10 unmarked-0.9-8/unmarked/vignettes/spp-dist-psi2.pdf |only unmarked-0.9-8/unmarked/vignettes/spp-dist.Rnw | 447 ++++++++++------ unmarked-0.9-8/unmarked/vignettes/unmarked.bib | 22 47 files changed, 1330 insertions(+), 695 deletions(-)
Title: Signal processing
Description: A set of signal processing R functions originally written
for Matlab/Octave. Includes filter generation utilities,
filtering functions, resampling routines, and visualization of
filter models. It also includes interpolation functions.
Author: For Details on the authors of original functions (e.g. ported
from Octave) see the code and help files. Ported to R by Tom
Short
Maintainer: Uwe Ligges
Diff between signal versions 0.7-1 dated 2011-10-08 and 0.7-2 dated 2012-06-25
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ R/bilinear.R | 4 ++-- R/boxcar.R | 2 +- R/butter.R | 2 +- R/chebwin.R | 2 +- R/cheby1.R | 2 +- R/ellipke.R | 5 +++-- R/fftfilt.R | 4 ++-- R/filtfilt.R | 6 ++---- R/fir1.R | 4 ++-- R/impz.R | 4 ++-- R/interp.R | 2 +- R/interp1.R | 4 ++-- R/pchip.R | 2 +- R/poly.R | 2 +- R/resample.R | 4 ++-- R/sftrans.R | 16 ++++++++-------- tests/savedTests.Rdata |binary 19 files changed, 54 insertions(+), 55 deletions(-)
Title: Package for ttf2pt1 program
Description: This package contains the program ttf2pt1, for use with
the extrafont package. This product includes software developed
by the TTF2PT1 Project and its contributors.
Author: Winston Chang, Andrew Weeks, Frank M. Siegert, Mark Heath,
Thomas Henlick, Sergey Babkin, Turgut Uyar, Rihardas Hepas,
Szalay Tamas, Johan Vromans, Petr Titera, Lei Wang, Chen
Xiangyang, Zvezdan Petkovic, Rigel, I. Lee Hetherington
Maintainer: Winston Chang
Diff between Rttf2pt1 versions 1.0 dated 2012-06-11 and 1.1 dated 2012-06-25
DESCRIPTION | 40 ++++++++-------------------------------- MD5 | 13 +++++++------ NEWS |only R/Rttf2pt1.r | 5 +++++ README.md | 2 +- Rttf2pt1.sublime-workspace | 16 ++++++++-------- man/Rttf2pt1.Rd | 2 +- src/Makefile.win | 4 ++-- 8 files changed, 32 insertions(+), 50 deletions(-)
Title: QuasiSeq
Description: This package is used to apply the QL, QLShrink and
QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012)
to quasi-Poisson or quasi-negative binomial models for
identifying differentially expressed genes in RNA-seq data.
Author: Steve Lund
Maintainer: Steve Lund
Diff between QuasiSeq versions 1.0-1 dated 2012-04-15 and 1.0-2 dated 2012-06-25
DESCRIPTION | 12 ++++----- MD5 | 12 ++++----- NAMESPACE | 4 +-- R/QL.fit.R | 13 +++++----- R/QL.results.R | 67 ++++++++++++++++++++++++++++++++++++++---------------- man/QL.fit.Rd | 25 ++++++++------------ man/QL.results.Rd | 26 ++++++++++---------- 7 files changed, 92 insertions(+), 67 deletions(-)
Title: Clustering Graphics
Description: Orders panels in scatterplot matrices and parallel
coordinate displays by some merit index. Package contains
various indices of merit, ordering functions, and enhanced
versions of pairs and parcoord which color panels according to
their merit level.
Author: Catherine Hurley
Maintainer: Catherine Hurley
Diff between gclus versions 1.3 dated 2010-05-25 and 1.3.1 dated 2012-06-25
gclus-1.3.1/gclus/DESCRIPTION | 9 +++++---- gclus-1.3.1/gclus/MD5 |only gclus-1.3.1/gclus/NAMESPACE |only gclus-1.3.1/gclus/data/bank.RData |binary gclus-1.3.1/gclus/data/body.RData |binary gclus-1.3.1/gclus/data/ozone.RData |binary gclus-1.3.1/gclus/data/wine.RData |binary gclus-1.3/gclus/INDEX |only 8 files changed, 5 insertions(+), 4 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-25 0.1
Title: Quantile Regression
Description: Quantile regression and related methods.
Author: Roger Koenker
Maintainer: Roger Koenker
Diff between quantreg versions 4.79 dated 2012-04-13 and 4.81 dated 2012-06-25
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- R/anova.R | 4 +- R/crq.R | 67 +++++++++++++++++++++++++++++++------------------ inst/Changelog | 17 +++++++++++- inst/doc/crq0.pdf |binary inst/doc/engelcoef.pdf |binary inst/doc/rq.pdf |binary man/anova.rq.Rd | 3 +- man/boot.crq.Rd | 3 +- man/crq.Rd | 15 +++++++--- 11 files changed, 88 insertions(+), 47 deletions(-)
Title: Parametric Frailty Models
Description: Parametric Frailty Models, fitted by maximum marginal
likelihood method. Possible baseline hazards: Weibull,
Exponential, Gompertz, logNormal and loglogistic Possible
Frailty distributions: Gamma, Inverse Gaussian and Positive
Stable
Author: Federico Rotolo
Maintainer: Federico Rotolo
Diff between parfm versions 2.00-3 dated 2012-06-04 and 2.02 dated 2012-06-25
DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 1 + R/anova.parfm.R |only R/parfm.R | 15 +++++++++++++-- R/plot.select.parfm.R | 9 --------- man/anova.parfm.Rd |only 7 files changed, 25 insertions(+), 20 deletions(-)
Title: ada: an R package for stochastic boosting
Description: Performs discrete, real, and gentle boost under both
exponential and logistic loss on a given data set. The package
ada provides a straightforward, well-documented, and broad
boosting routine for classification, ideally suited for small
to moderate-sized data sets. Please refer to the Url below for
more information.
Author: Mark Culp, Kjell Johnson, and George Michailidis
Maintainer: Mark Culp
Diff between ada versions 2.0-2 dated 2010-07-30 and 2.0-3 dated 2012-06-25
DESCRIPTION | 11 +++++------ MD5 |only R/ada.default.R | 9 +++++---- R/ada.formula.R | 2 +- R/predict.ada.R | 9 ++++++--- data/datalist |only data/soldat.rda |binary 7 files changed, 17 insertions(+), 14 deletions(-)
Title: Paired Data Analysis
Description: This package provides many datasets and a set of graphics
(based on ggplot2), statistics, effect sizes and hypothesis
tests for analysing paired data with S4 class.
Author: Stephane Champely
Maintainer: Stephane Champely
Diff between PairedData versions 0.9.9 dated 2012-06-13 and 1.0.0 dated 2012-06-25
DESCRIPTION | 6 - MD5 | 8 + R/global1.R | 199 ++++++++++++++++++++++++++++++++++++++++++ man/imam.var.test.Rd |only man/levene.var.test.Rd |only man/mcculloch.var.test.Rd |only man/sandvikolsson.var.test.Rd |only 7 files changed, 208 insertions(+), 5 deletions(-)
Title: Estimation for multivariate normal and Student-t data with
monotone missingness
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is
monotone. Through the use of parsimonious/shrinkage
regressions (plsr, pcr, lasso, ridge, etc.), where standard
regressions fail, the package can handle a nearly arbitrary
amount of missing data. The current version supports maximum
likelihood inference and a full Bayesian approach employing
scale-mixtures for Gibbs sampling. Monotone data augmentation
extends this Bayesian approach to arbitrary missingness
patterns. A fully functional standalone interface to the
Bayesian lasso (from Park & Casella), Normal-Gamma (from
Griffin & Brown), Horseshoe (from Carvalho, Polson, & Scott),
and ridge regression with model selection via Reversible Jump,
and student-t errors (from Geweke) is also provided
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
Diff between monomvn versions 1.9 dated 2012-06-21 and 1.9-1 dated 2012-06-25
ChangeLog | 6 ++++++ DESCRIPTION | 25 ++++++++++++------------- MD5 | 8 ++++---- man/blasso.Rd | 4 ++-- man/monomvn-package.Rd | 8 +++----- 5 files changed, 27 insertions(+), 24 deletions(-)
Title: Discrete Laplace Exponential Family
Description: Discrete Laplace exponential family for models such as a
generalized linear model
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen
Diff between disclap versions 1.0 dated 2012-04-01 and 1.1 dated 2012-06-25
DESCRIPTION | 14 +++++++------- MD5 | 14 ++++++++------ NAMESPACE | 2 +- R/ddisclap.R | 12 ++++++------ R/pdisclap.R |only R/rdisclap.R |only man/DiscreteLaplace.Rd | 13 +++++++++---- man/ddisclap.Rd | 30 +++++++++++++++++++----------- man/disclap-package.Rd | 21 +++++++-------------- 9 files changed, 57 insertions(+), 49 deletions(-)
Title: Plot publication-grade gene and genome maps
Description: genoPlotR draws gene or genome maps and comparisons
between these, in a publication-grade manner. Starting from
simple, common files, it will draw postscript or pdf files that
can be sent as such to journals
Author: Lionel Guy
Maintainer: Lionel Guy
Diff between genoPlotR versions 0.7 dated 2011-05-03 and 0.8 dated 2012-06-25
DESCRIPTION | 14 +++++++------- MD5 |only NEWS | 19 +++++++++++++++++++ R/comparison.R | 19 +++++++++++++++++++ R/genoPlotR.R | 48 +++++++++++++++++++++++++++++++++--------------- R/grobs.R | 12 ++++++------ R/minimize_comps.R | 1 + R/phylog_grob.R | 17 ++++++++++++++++- R/read_dna_seg.R | 5 +++-- data/barto.RData |binary data/chrY_subseg.RData |binary data/mauve_bbone.RData |binary data/three_genes.RData |binary inst/doc/genoPlotR.pdf |binary man/plot_gene_map.Rd | 4 ++++ man/read_functions.Rd | 5 ++++- 16 files changed, 112 insertions(+), 32 deletions(-)
Title: World Development Indicators (World Bank)
Description: Search, extract and format data from the World Bank's
World Development Indicators
Author: Vincent Arel-Bundock
Maintainer: Vincent Arel-Bundock
Diff between WDI versions 2.0 dated 2012-06-19 and 2.1 dated 2012-06-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 8 +++++++- R/WDI.R | 35 ++++++++++++++++++++++++----------- 4 files changed, 37 insertions(+), 18 deletions(-)
Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++
library which facilitate 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 more than 770 unit tests in over 349
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 the
older interface. New development should always use this Rcpp
package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel
Diff between Rcpp versions 0.9.11 dated 2012-06-22 and 0.9.12 dated 2012-06-25
Rcpp-0.9.11/Rcpp/inst/unitTests/testRcppClass/src/Num.o |only Rcpp-0.9.11/Rcpp/inst/unitTests/testRcppClass/src/rcpp_hello_world.o |only Rcpp-0.9.11/Rcpp/inst/unitTests/testRcppClass/src/rcpp_module.o |only Rcpp-0.9.11/Rcpp/inst/unitTests/testRcppClass/src/stdVector.o |only Rcpp-0.9.11/Rcpp/inst/unitTests/testRcppClass/src/testRcppClass.so |only Rcpp-0.9.12/Rcpp/ChangeLog | 27 ++- Rcpp-0.9.12/Rcpp/DESCRIPTION | 11 - Rcpp-0.9.12/Rcpp/MD5 | 53 ++---- Rcpp-0.9.12/Rcpp/cleanup | 2 Rcpp-0.9.12/Rcpp/inst/NEWS | 12 + Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary Rcpp-0.9.12/Rcpp/inst/doc/unitTests-results/Rcpp-unitTests.html | 6 Rcpp-0.9.12/Rcpp/inst/doc/unitTests-results/Rcpp-unitTests.txt | 46 ++--- Rcpp-0.9.12/Rcpp/inst/doc/unitTests/Rcpp-unitTests.R | 3 Rcpp-0.9.12/Rcpp/inst/include/Rcpp/Environment.h | 2 Rcpp-0.9.12/Rcpp/inst/include/Rcpp/config.h | 2 Rcpp-0.9.12/Rcpp/inst/unitTests/runTests.R | 39 +++- Rcpp-0.9.12/Rcpp/inst/unitTests/runit.Module.R | 6 Rcpp-0.9.12/Rcpp/inst/unitTests/runit.Module.client.package.R | 3 Rcpp-0.9.12/Rcpp/inst/unitTests/runit.XPTr.R | 84 +++++----- Rcpp-0.9.12/Rcpp/inst/unitTests/runit.client.package.R | 6 Rcpp-0.9.12/Rcpp/inst/unitTests/runit.macros.R | 10 - Rcpp-0.9.12/Rcpp/src/Environment.cpp | 2 30 files changed, 186 insertions(+), 128 deletions(-)
Title: mapReduce - flexible mapReduce algorithm for parallel
computation
Description: mapReduce is an algorithm provides a simple framework for
parallel computations. This implementation provides (a) a pure
R implementation (b) a syntax following the mapReduce paper and
(c) flexible and parallelizable back end.
Author: Christopher Brown
Maintainer: Christopher Brown
Diff between mapReduce versions 1.2.5 dated 2012-06-14 and 1.2.6 dated 2012-06-25
ChangeLog | 3 +++ DESCRIPTION | 10 +++++----- LICENSE | 3 +-- MD5 | 8 ++++---- man/mapReduce-package.Rd | 4 ++-- 5 files changed, 15 insertions(+), 13 deletions(-)