CRAN (and crantastic) updates this week
New packages
------------
* apcluster (1.0.1)
Ulrich Bodenhofer
http://crantastic.org/packages/apcluster
The apcluster package implements Frey's and Dueck's Affinity
Propagation clustering in R. The algorithms are analogous to the
Matlab code published by Frey and Dueck.
* BioPhysConnectoR (1.6-1)
Franziska Hoffgaard
http://crantastic.org/packages/BioPhysConnectoR
Utilities and functions to investigate the relation between
biomolecular structures, their interactions, and the evolutionary
information revealed in sequence alignments of these molecules.
* BradleyTerry2 (0.9-1)
Heather Turner
http://crantastic.org/packages/BradleyTerry2
Specify and fit the Bradley-Terry model and structured versions
* catnet (1.00.0)
Nikolay Balov
http://crantastic.org/packages/catnet
A package that handles discrete Bayesian network models and provides
inference using the frequentist approach
* CAVIAR (0.1-0)
Cyrille Rathgeber
http://crantastic.org/packages/CAVIAR
Allows processing, visualisation and analysis of data coming from
cambial activity and wood formation monitoring studies.
* CCMtools (1.0)
Mathieu Vrac
http://crantastic.org/packages/CCMtools
This package proposes a clustering method called "Correlation
Clustering Model" (CCM) based on mixture of canonical correlation
analysis (CCA). It also provides some tools for cluster analysis.
* clusterCons (0.4)
Dr. T. Ian Simpson
http://crantastic.org/packages/clusterCons
clusterCons is a package containing functions that generate robustness
measures for clusters and cluster membership based on generating
consensus matrices from bootstrapped clustering experiments in which
a random proportion of rows of the data set are used in each
individual clustering. This allows the user to prioritise clusters
and the members of clusters based on their consistency in this
regime. The functions allow the user to select several algorithms to
use in the re-sampling scheme and with any of the parameters that
the algorithm would normally take.
* dagR (1.0.1)
Lutz P Breitling
http://crantastic.org/packages/dagR
Functions to draw, manipulate and evaluate directed acyclic graphs.
* DatABEL (0.0-6)
Yurii Aulchenko
http://crantastic.org/packages/DatABEL
a package providing interface to C++ FILEVECTOR library facilitating
analysis of large (giga- to tera-bytes) matrices; matrix storage is
organized in a way that either columns or rows are quickly
accessible; primarily aimed to support genome-wide association
analyzes e.g. using GenABEL and ProbABEL
* DeducerPlugInExample (0.1)
Ian Fellows
http://crantastic.org/packages/DeducerPlugInExample
A example GUI plug-in package to serve as a template.
* DiceDesign (1.0)
D. Dupuy
http://crantastic.org/packages/DiceDesign
Space-Filling Designs and Uniformity Criteria.
* DiceEval (1.0)
D. Dupuy
http://crantastic.org/packages/DiceEval
Estimation, validation and prediction of metamodels (linear models,
additive models, MARS and PolyMARS)
* DiceKriging (1.0)
O. Roustant
http://crantastic.org/packages/DiceKriging
Estimation, validation and prediction of kriging models. Important
functions : km, print.km, plot.km, predict.km.
* DiceOptim (1.0)
D. Ginsbourger
http://crantastic.org/packages/DiceOptim
Expected Improvement. EGO algorithm. Parallelized versions of EGO:
Constant Liars.
* digitize (0.0.1-07)
Timothee Poisot
http://crantastic.org/packages/digitize
Allows to get the data from a graph by providing calibration points
* DistributionUtils (0.1-0)
David Scott
http://crantastic.org/packages/DistributionUtils
This package contains utilities which are of use in the packages I
have developed for dealing with distributions. Currently these
packages are GeneralizedHyperbolic, VarianceGamma, and
SkewHyperbolic. Additional packages are under development. Each of
these packages requires DistributionUtils. Functionality includes
sample skewness and kurtosis, log-histogram, moments by integration,
changing the pint about which a moment is calculated, functions for
testing distributions using inversion tests and the Massart
inequality.
* DoseFinding (0.1)
Bjoern Bornkamp
http://crantastic.org/packages/DoseFinding
The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (for example pharmaceutical Phase II
clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models, calculating optimal
designs and an implementation of the MCPMod methodology. Currently
only normally distributed homoscedastic endpoints are supported.
* GeneralizedHyperbolic (0.2-0)
David Scott
http://crantastic.org/packages/GeneralizedHyperbolic
This package provides functions for the hyperbolic and related
distributions. Density, distribution and quantile functions and
random number generation are provided for the hyperbolic
distribution, the generalized hyperbolic distribution, the
generalized inverse Gaussian distribution and the skew-Laplace
distribution. Additional functionality is provided for the
hyperbolic distribution, including fitting of the hyperbolic to
data.
* hergm (1.1-1)
Michael Schweinberger
http://crantastic.org/packages/hergm
* hglm (1.0)
Lars Ronnegard
http://crantastic.org/packages/hglm
The hglm package is used to fit hierarchical generalized linear
models. It can be used for linear mixed models and generalized
linear mixed models with random effects for a variety of links and a
variety of distributions for both the outcomes and the random
effects. Fixed effects can also be fitted in the dispersion part of
the mean model.
* HGLMMM (0.1)
Marek Molas
http://crantastic.org/packages/HGLMMM
Hierarchical Generalized Linear Models
* isopam (0.9-6)
Sebastian Schmidtlein
http://crantastic.org/packages/isopam
Isopam clustering algorithm and utilities. Isopam optimizes clusters
and optionally cluster numbers in a brute force style and aims at an
optimum separation by a limited number of indicative descriptors
(typically species).
* MAd (0.2)
AC Del Re
http://crantastic.org/packages/MAd
This is an integrated meta-analysis package for conducting a research
synthesis with mean differences data. One of the unique features of
this package is in its integration of user-friendly functions to
complete most of the statistical steps involved in a meta-analysis
with mean differences. It uses recommended procedures as described
in The Handbook of Research Synthesis and Meta-Analysis (Cooper,
Hedges, & Valentine, 2009).
* mbmdr (2.0)
Victor Urrea
http://crantastic.org/packages/mbmdr
Model Based Multifactor Dimension Reduction proposed by Calle et al.
(2008) as a dimension reduction method for exploring gene-gene
interactions.
* minqa (1.1)
Katharine Mullen
http://crantastic.org/packages/minqa
Derivative-free optimization by quadratic approximation based on an
interface to Fortran implementations by M. J. D. Powell
* mixOmics (2.6)
Kim-Anh Le Cao
http://crantastic.org/packages/mixOmics
The package supplies two efficients methodologies: regularized CCA and
sparse PLS to unravel relationships between two heterogeneous data
sets of size (nxp) and (nxq) where the p and q variables are
measured on the same samples or individuals n. These data may come
from high throughput technologies, such as omics data (e.g.
transcriptomics, metabolomics or proteomics data) that require an
integrative or joint analysis. However, mixOmics can also be applied
to any other large data sets where p+q>>n. rCCA is a regularized
version of CCA to deal with the large number of variables. sPLS
allows variable selection in a one step procedure and two frameworks
are proposed: regression and canonical analysis. Numerous graphical
outputs are provided to help interpreting the results.
* MplusAutomation (0.2-3)
Michael Hallquist
http://crantastic.org/packages/MplusAutomation
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.
* mtsc (0.0.1)
Charlotte Maia
http://crantastic.org/packages/mtsc
Place-holder package (roughly speaking an empty package) for finding
clusters in multivariate timeseries. Full implementation pending.
* ncdf4 (1.0)
David Pierce
http://crantastic.org/packages/ncdf4
This package provides a high-level R interface to data files written
using Unidata's netCDF library (version 4 or earlier), which are
binary data files that are portable across platforms and include
metadata information in addition to the data sets. Using this
package, netCDF files (either version 4 or "classic" version 3) can
be opened and data sets read in easily. It is also easy to create
new netCDF dimensions, variables, and files, in either version 3 or
4 format, and manipulate existing netCDF files. This package
replaces the former ncdf package, which only worked with netcdf
version 3 files. For various reasons the names of the functions
have had to be changed from the names in the ncdf package. The old
ncdf package is still available at the URL given below, if you need
to have backward compatibility. It should be possible to have both
the ncdf and ncdf4 packages installed simultaneously without a
problem. However, the ncdf package does not provide an interface for
netcdf version 4 files.
* ordinal (2010.03-04)
Rune Haubo B Christensen
http://crantastic.org/packages/ordinal
This package implements likelihood based models for ordinal (ordered
categorical) data based on cumulative probabilities in the framework
of cumulative link models. This includes the important proportional
odds model but also allows for general regression structures for
location as well as scale of the latent distribution, i.e. additive
as well as multiplicative structures, structured thresholds
(cut-points), nominal effects and flexible link functions. Further,
a range of estimation procedures and a range of auxiliary functions
are implemented.
* oro.dicom (0.2.4)
Brandon Whitcher
http://crantastic.org/packages/oro-dicom
Data input/output functions for data that conform to the Digital
Imaging and Communications in Medicine (DICOM) standard, part of the
Rigorous Analytics bundle.
* oro.nifti (0.1.3)
Brandon Whitcher
http://crantastic.org/packages/oro-nifti
Data input/output functions for data that follow either Analyze or
NIfTI standards, part of the Rigorous Analytics bundle.
* r2lh (0.6)
Christophe M. Genolini
http://crantastic.org/packages/r2lh
generate univariate and bivariate analyses in LaTeX or HTML formats
* random.polychor.pa (1.0)
Fabio Presaghi
http://crantastic.org/packages/random-polychor-pa
The Function perform a parallel analysis using simulated polychoric
correlation matrices. The nth-percentile of the eigenvalues
distribution obtained from the randomly generated polychoric
correlation matrices is returned. A plot comparing the two types of
eigenvalues (real and simulated) will help determine the number of
real eigenvalues that outperform random data. The function is based
on the idea that if real data are non-normal and the polychoric
correlation matrix is needed to perform a Factor Analysis, then the
Parallel Analysis method used to choose a non-random number of
factors should also be based on randomly generated polychoric
correlation matrices and not on Pearson correlation matrices.
* RcmdrPlugin.MAd (0.2)
AC Del Re
http://crantastic.org/packages/RcmdrPlugin-MAd
This is an R-Commander plug-in for the MAd package (Meta-Analysis with
Mean Differences). This package enables the user to conduct a
meta-analysis in a menu-driven, graphical user interface environment
(e.g., SPSS), while having the full statistical capabilities of R
and the MAd package. The MAd package itself contains a variety of
useful functions for conducting a research synthesis with mean
differences data. One of the unique features of the MAd package is
in its integration of user-friendly functions to complete many of
the statistical steps involved in a meta-analysis with mean
differences. It uses recommended procedures as described in The
Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, &
Valentine, 2009).
* RcppArmadillo (0.1.0)
Dirk Eddelbuettel and Romain Francois
http://crantastic.org/packages/RcppArmadillo
R and Armadillo integration using Rcpp Armadillo is a C++ linear
algebra library aiming towards a good balance between speed and ease
of use. Integer, floating point and complex numbers are supported,
as well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries. . A delayed evaluation
approach is employed (during compile time) to combine several
operations into one and reduce (or eliminate) the need for
temporaries. This is accomplished through recursive templates and
template meta-programming. . This library is useful if C++ has been
decided as the language of choice (due to speed and/or integration
capabilities), rather than another language. . This Armadillo / C
integration provides a nice illustration of the capabilities of the
Rcpp package for seamless R and C++ integration/
* RcppExamples (0.1.0)
Dirk Eddelbuettel and Romain Francois
http://crantastic.org/packages/RcppExamples
Examples for Seamless R and C++ integration The Rcpp package contains
a C++ library that facilitates the integration of R and C++ in
various ways. This package provides examples.
* Rdsm (1.0.0)
Norm Matloff
http://crantastic.org/packages/Rdsm
Provides a threads-like programming environment for R, usable both on
a multicore machine and across a network of multiple machines. The
package gives the illusion of shared memory, again even across
multiple machines on a network.
* ris (1.0)
Stephanie Kovalchik
http://crantastic.org/packages/ris
Importing RIS-formatted file into a list of Bibtex-like references;
checking for duplications; converting references to citEntry objects
* Rsolnp (1.0-2)
Alexios Ghalanos
http://crantastic.org/packages/Rsolnp
General Non-linear Optimization Using Augmented Lagrange Multiplier
Method
* saws (0.9-3.1)
M.P. Fay
http://crantastic.org/packages/saws
Tests coefficients with sandwich estimator of variance and with small
samples. Regression types supported are gee, cox regression, and
conditional logistic regression.
* TreeRank (1.0-0)
Nicolas Baskiotis
http://crantastic.org/packages/TreeRank
Implementation of the TreeRank methodology for building tree-based
ranking rules for bipartite ranking through ROC curve optimization.
* TreeSim (1.0)
Tanja Stadler
http://crantastic.org/packages/TreeSim
The package simulates phylogenetic trees under a constant-rate
birth-death process, conditioned on having a fixed number of final
tips, or a fixed age, or a fixed age and number of tips. When
conditioning on the number of final tips, the method allows for
shifts in rates and mass extinction events during the birth-death
process. TreeSim further samples appropriately trees with n final
tips from a set of trees generated by the common sampling algorithm
stopping when a fixed number m>>n of leaves is first reached. This
latter method is appropriate for m-tip trees generated under a big
class of models (details in the bd.gsa.taxa man page).
* tsne (0.1-1)
Unknown
http://crantastic.org/packages/tsne
A "pure R" implementation of the t-SNE algorithm.
* ttime (1.0)
Radhakrishnan Nagarajan
http://crantastic.org/packages/ttime
Translate neurodevelopmental event timing across species. Predict
unknown event timings and investigate phylogenetic proximity by
hiearchical clustering of the known and predicted event timings.
* UScensus2000blkgrp (0.03)
Zack W. Almquist
http://crantastic.org/packages/UScensus2000blkgrp
US Census 2000 Block Group shapefiles and additional demographic data
from the SF1 100 percent files. This data set contains polygon files
in lat/lon coordinates and the corresponding demographic data for a
number of different variables.
* vcdExtra (0.4-1)
Michael Friendly
http://crantastic.org/packages/vcdExtra
Provides additional data sets, methods and documentation to complement
the vcd package for Visualizing Categorical Data.
* VizCompX (0.1)
Neil Diamond
http://crantastic.org/packages/VizCompX
Nimrod generates a Latin Hypercube Design using the emulator package.
Based on this design, any function can be evaluated on the design
points. A generalisation of the Nimrod/O test case is included. A
Gaussian model can be fit to the data using the mlegp package. The
resulting surface can be viewed using a wireframe plot with choice
of viewing and conditioning variables and levels.
* vmv (1.0)
Waqas Ahmed Malik
http://crantastic.org/packages/vmv
Visualization of Missing Values
* wq (0.2-2)
Alan Jassby
http://crantastic.org/packages/wq
Functions to assist in the processing and exploration of data from
monitoring programs for aquatic ecosystems. The focus is 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.
Updated packages
----------------
actuar (1.1-0), agricolae (1.0-9), AlgDesign (1.1-2), analogue
(0.6-23), animation (1.1-0), aroma.affymetrix (1.5.0), aroma.core
(1.5.0), arulesSequences (0.1-9), backtest (0.3-1), bayesclust (3.0),
bcp (2.1.3), betareg (2.2-0), bio.infer (1.2-8), bipartite (1.07),
BoolNet (1.4), BradleyTerry (0.8-8), CADStat (2.2-2), caGUI (0.1-4),
caret (4.33), chemometrics (0.8), cocorresp (0.1-9), compHclust
(1.0-1), conf.design (1.01), corpcor (1.5.6), countrycode (0.4),
cshapes (0.2-3), Deducer (0.2-3), DEoptim (2.0-4), DescribeDisplay
(0.2.2), deSolve (1.7), DiagnosisMed (0.2.3), diffractometry (0.1-02),
DoE.base (0.9-17), dplR (1.2.9), dti (0.9-0), dynGraph (0.99100403),
e1071 (1.5-23), eha (1.2-18), epitools (0.5-5), estout (1.0.1-1),
extracat (1.0-1), extremevalues (2.0), far (0.6-3), farmR (1.1), FD
(1.0-7), flashClust (1.00), flexmix (2.2-5), fmri (1.4-0), forensim
(1.1-4), FrF2 (1.1), ftsa (1.5), fxregime (1.0-0), GAMens (1.1.1),
gcExplorer (0.9-3), GEOmap (1.5-4), GeoXp (1.4.2), GeoXp (1.4.3),
ggplot2 (0.8.7), gmt (1.1-4), gRapHD (0.1.6), gRbase (1.3.4), gsDesign
(2.2-11), gstat (0.9-69), gWidgetsRGtk2 (0.0-62), gWidgetstcltk
(0.0-31), helloJavaWorld (0.0-7), hergm (1.1-1), HiddenMarkov (1.3-1),
hyperdirichlet (1.4-2), ibr (1.2.1), ic.infer (1.1-3), Imap (1.32),
integrativeME (1.2), integrOmics (2.55), interval (0.9-9.6), ipw
(1.0-4), kml (1.1.1), ks (1.6.11), latticeExtra (0.6-9), lda (1.2),
lokern (1.0-9), longitudinalData (0.6.3), MAc (1.0.5), MAc (1.0.6),
MAd (0.2), mboost (2.0-3), mc2d (0.1-7), mclust (3.4.3), MCMCglmm
(2.03), mhsmm (0.3.2), mixAK (0.8), MKmisc (0.6.1), monomvn (1.8-1),
MplusAutomation (0.2-2), MplusAutomation (0.2-3), multcomp (1.1-6),
mvpart (1.3-1), ncvreg (2.0), neuralnet (1.3), nlstools (0.0-10), noia
(0.94), nor1mix (1.1-2), party (0.9-9993), pcaPP (1.8), penalized
(0.9-30), pgirmess (1.4.4), phyclust (0.1-5), picante (1.0-1), plotrix
(2.8-3), plsdof (0.2-0), pmg (0.9-42), portfolio (0.4-5), portfolioSim
(0.2-6), prefmod (0.8-19), PropCIs (0.1-5), PwrGSD (1.16), pyramid
(1.2), qpcR (1.2-6), QRMlib (1.4.5), qvcalc (0.8-5), R.filesets
(0.8.0), R2HTML (2.0.0), R2jags (0.02-02), randomSurvivalForest
(3.6.2), rattle (2.5.24), rbenchmark (0.3), RcmdrPlugin.MAc (1.0.6),
RcmdrPlugin.MAc (1.0.5), Rcpp (0.7.8), Rcpp (0.7.9), relations
(0.5-7), reporttools (1.0.5), REQS (0.8-6), RFLPtools (1.1), RFOC
(1.0-9), RGtk2DfEdit (0.5.4), rimage (0.5-8.1), rms (2.2-0), RQDA
(0.1-9), Rsolnp (1.0-2), rsprng (1.0), RSQLite (0.8-4), RTOMO (1.0-7),
runjags (0.9.6-3), s20x (3.1-7), sandwich (2.2-6), sbgcop (0.975),
sdef (1.5), seacarb (2.3.2), season (0.2-4), seqinr (2.0-8), sfsmisc
(1.0-11), SGP (0.0-5), signal (0.6-1), simecol (0.6-10), simPopulation
(0.1.1), SkewHyperbolic (0.2-0), sm (2.2-4), snowfall (1.83), sp
(0.9-61), spatstat (1.18-0), spBayes (0.1-6), spdep (0.4-59), stab
(0.0.7), statmod (1.4.3), stoichcalc (1.1-1), strucchange (1.4-0),
survey (3.21), SweaveListingUtils (0.4.3), tau (0.0-7), TeachingDemos
(2.6), TeachingSampling (1.4.9), textcat (0.0-2), TGUITeaching
(0.9.6), TGUITeaching (0.9.5), tm (0.5-3), tm.plugin.mail (0.0-2),
tmvtnorm (1.0-2), tnet (2.5), topicmodels (0.0-4), topmodel (0.7.2),
tradeCosts (0.3-1), trio (1.0.14), tsDyn (0.7-22), tseriesChaos
(0.1-10), ttrTests (1.5), unmarked (0.8-3), UScensus2000 (0.07),
UScensus2000add (0.04), UScensus2000cdp (0.03), UScensus2000tract
(0.03), VarianceGamma (0.3-0), vars (1.4-7), vegan (1.17-2),
WMBrukerParser (1.2)
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