CRAN (and crantastic) updates this week
New packages
------------
* disclapmix (0.1)
Maintainer: Mikkel Meyer Andersen
Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen
License: GPL-2
http://crantastic.org/packages/disclapmix
disclapmix makes inference in a mixture of Discrete Laplace
distributions using the EM algorithm.
* EstSimPDMP (1.1)
Maintainer: Unknown
Author(s): Romain Azais
License: GPL (>= 2)
http://crantastic.org/packages/EstSimPDMP
This package deals with the estimation of the jump rate for
piecewise-deterministic Markov processes (PDMPs), from only one
observation of the process within a long time. The main functions
provide an estimate of this function. The state space may be
discrete or continuous. The associated paper is given in References.
Other functions provide a method to simulate random variables from
their (conditional) hazard rate, and then to simulate PDMPs.
* faoutlier (0.2.2)
Maintainer: Phil Chalmers
Author(s): Phil Chalmers <rphilip.chalmers at gmail.com>
License: GPL (>= 2)
http://crantastic.org/packages/faoutlier
Tools for detecting and summarize influential cases that can affect
exploratory and confirmatory factor analysis models as well as
structural equation models more generally.
* FastImputation (1.0)
Maintainer: Stephen R. Haptonstahl
Author(s): Stephen R. Haptonstahl
License: GPL (>= 2)
http://crantastic.org/packages/FastImputation
TrainFastImputation uses training data to describe a multivariate
normal distribution that the data approximates or can be transformed
into approximating and stores this information as an object of class
FastImputationPatterns. The FastImputation function uses this
FastImputationPatterns object to impute (make a good guess at)
missing data in a single line or a whole dataframe of data. This
approximates the process used by Amelia
(\url{http://gking.harvard.edu/amelia/}) but is much faster when
filling in values for a single line of data.
* hydroPSO (0.1-54-1)
Maintainer: Mauricio Zambrano-Bigiarini
Author(s): Mauricio Zambrano-Bigiarini [aut, cre] and Rodrigo Rojas [ctb]
License: GPL (>= 2)
http://crantastic.org/packages/hydroPSO
This package implements a state-of-the-art version of the Particle
Swarm Optimisation (PSO) algorithm, with a special focus on the
calibration of environmental models. hydroPSO is model-independent,
allowing the user to easily interface any model code with the
calibration engine (PSO). hydroPSO includes a series of controlling
options and PSO variants to fine-tune the performance of the
calibration engine. An advanced sensitivity analysis function
together with user-friendly plotting summaries facilitate the
interpretation and assessment of the calibration results. Bugs
reports/comments/questions are very welcomed.
* OOmisc (1.0)
Maintainer: Ozgur Asar
Author(s): Ozgur Asar, Ozlem Ilk
License: GPL (>= 2)
http://crantastic.org/packages/OOmisc
Includes miscellaneous functions.
* robustHD (0.1.0)
Maintainer: Andreas Alfons
Author(s): Andreas Alfons
License: GPL (>= 2)
http://crantastic.org/packages/robustHD
Robust methods for high-dimensional data, in particular linear model
selection techniques based on least angle regression and sparse
regression.
* sparseLTSEigen (0.1.0)
Maintainer: Andreas Alfons
Author(s): Andreas Alfons
License: GPL (>= 2)
http://crantastic.org/packages/sparseLTSEigen
Use RcppEigen to fit least trimmed squares regression models with an
L1 penalty in order to obtain sparse models.
* sROC (0.1-2)
Maintainer: Xiao-Feng Wang
Author(s): Xiao-Feng Wang
License: GPL (>= 3)
http://crantastic.org/packages/sROC
This package contains a collection of functions to perform
nonparametric estimation of receiver operating characteristic (ROC)
curves for continuous data.
* sybilDynFBA (0.0.1)
Maintainer: Abdelmoneim Amer Desouki
Author(s): Abdelmoneim Amer Desouki
License: GPL-3
http://crantastic.org/packages/sybilDynFBA
In this package the dynamic FBA technique proposed by Varma was
implemented.
* tfplot (2012.4-1)
Maintainer: Paul Gilbert and Erik Meijer
Author(s): Paul Gilbert <pgilbert.ttv9z at ncf.ca>
License: GPL-2
http://crantastic.org/packages/tfplot
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe package
which provides a programming kernel for time series. Extension to
tframe provided in tframePlus can also be used. See the Guide
vignette for examples.
* varbvs (1.0)
Maintainer: Peter Carbonetto
Author(s): Peter Carbonetto
License: GPL (>= 3)
http://crantastic.org/packages/varbvs
Implements the variational inference procedure for Bayesian variable
selection, as described in the "Scalable variational inference for
Bayesian variable selection in regression, and its accuracy in
genetic association studies" (Bayesian Analysis 7, March 2012, pages
73-108). This software has been used to implement Bayesian variable
selection for large problems with over a million variables and
thousands of samples.
* waffect (1.2)
Maintainer: G. Nuel
Author(s): Gregory Nuel and Vittorio Perduca
License: GPL (>= 3)
http://crantastic.org/packages/waffect
waffect (pronounced 'double-u affect' for 'weighted
affectation') is a
package to simulate phenotypic (case or control) datasets under a
disease model H1 such that the total number of cases is constant
across all the simulations (the constrain in the title). The package
also makes it possible to generate phenotypes in the case of more
than two classes, so that the number of phenotypes belonging to each
class is constant across all the simulations. waffect is used to
assess empirically the statistical power of Genome Wide Association
studies.
Updated packages
----------------
adaptivetau (1.0), adehabitat (1.8.10), adehabitatLT (0.3.5), aod
(1.3), asypow (2012.04-1), BayesDA (2012.04-1), bayesTFR (1.5-1),
Bergm (2.3), BoolNet (1.50), bqtl (1.0-27), cccrm (1.1), censReg
(0.5-10), cherry (0.2-6), coefplot (1.1.7), coloc (1.08), CompRandFld
(1.0.2), ConjointChecks (0.0.7), copula (0.99-1), crawl (1.3-4),
deseasonalize (1.03), digeR (1.3), DistributionUtils (0.5-1), effects
(2.1-1), elec.strat (0.1.1), ElemStatLearn (2012.04-0), EVER (1.2),
evtree (0.1-2), fanovaGraph (1.1), gbm (1.6-3.2),
GeneralizedHyperbolic (0.8-0), GGEBiplotGUI (1.0-1), ggmap (2.0),
growcurves (0.1.1), gWidgetsRGtk2 (0.0-81), hash (2.1.0.1),
HiddenMarkov (1.7-0), ISIPTA (0.1-7), lavaan (0.4-13), lcmm (1.5.1),
lifecontingencies (0.9.2), LIHNPSD (0.2.1), LMERConvenienceFunctions
(1.6.8.2), markdown (0.4), medAdherence (1.03), MKmisc (0.91),
modTempEff (1.5.1), mvnormtest (0.1-9), ncdf4 (1.6), ncdf4 (1.6.1),
negenes (1.0-1), oposSOM (0.1-4), pcaPP (1.9-46), phenology (3.29),
polySegratioMM (0.6-2), pomp (0.41-3), psgp (0.3-1), QCA (1.0-1), QCA3
(0.0-5), quantreg (4.79), Rcmdr (1.8-4), RcppArmadillo (0.3.0.1),
RcppArmadillo (0.3.0), RcppDE (0.1.1), RDieHarder (0.1.2), rEMM
(1.0-5), reweight (1.2.1), rockchalk (1.5.4), rrBLUP (3.7), rrcovNA
(0.4-03), RRF (1.2), RXMCDA (1.4.2), scriptests (1.0-9), sdcMicro
(3.1.1), SDMTools (1.1-11), seewave (1.6.3), sem (3.0-0), SGP
(0.9-0.0), SkewHyperbolic (0.3-1), SpatialTools (0.3.5), sphet
(1.1-12), splus2R (1.1-1), STAR (0.3-5), tmvtnorm (1.4-6), track
(1.0-15), VarianceGamma (0.3-1), VBmix (0.2.7), verification (1.32),
VGAM (0.8-7), vines (1.0.4), x12 (1.0-1)
This email provided as a service for the R community by
http://crantastic.org.
Like it? Hate it? Please let us know: cranatic at gmail.com.
CRAN (and crantastic) updates this week
New packages
------------
* appell (0.0-3)
Maintainer: Daniel Sabanes Bove
Author(s): Daniel Sabanes Bove <daniel.sabanesbove at ifspm.uzh.ch> with
contributions by F. D. Colavecchia, R. C. Forrey, G.
Gasaneo, N. L. J. Michel, L. F. Shampine, M. V. Stoitsov
and H. A. Watts.
License: GPL (>= 3)
http://crantastic.org/packages/appell
This package wraps Fortran code by F. D. Colavecchia and G. Gasaneo
for computing the Appell's F1 hypergeometric function. Their program
uses Fortran code by L. F. Shampine and H. A. Watts. Moreover, the
hypergeometric function with complex arguments is computed with
Fortran code by N. L. J. Michel and M. V. Stoitsov or with Fortran
code by R. C. Forrey. See the function documentations for the
references and please cite them accordingly.
* bayesPop (0.2-2)
Maintainer: Hana Sevcikova
Author(s): Hana Sevcikova, Adrian Raftery
License: GPL (>= 2)
http://crantastic.org/packages/bayesPop
The package allows to generate population projections for all
countries of the world using several probabilistic components, such
as total fertility rate (TFR) and life expectancy.
* cec2005benchmark (1.0.0)
Maintainer: Yasser Gonz?lez-Fern?ndez
Author(s): Yasser Gonz?lez-Fern?ndez <ygonzalezfernandez at gmail.com>
and Marta
Soto <mrosa at icimaf.cu>
License: GPL (>= 3)
http://crantastic.org/packages/cec2005benchmark
This package is a wrapper for the C implementation of the 25 benchmark
functions for the CEC 2005 Special Session on Real-Parameter
Optimization. The original C code by Santosh Tiwari and related
documentation are available at http://www.ntu.edu.sg/home/EPNSugan/.
* compound.Cox (1.0)
Maintainer: Takeshi Emura, Graduate Institute of Statistics, National Central
University, Taiwan
Author(s): Takeshi Emura & Yi-Hau Chen
License: GPL-2
http://crantastic.org/packages/compound-Cox
Calculate regression coefficients and their standard errors under the
Cox proportional hazard model with the large number of covariates.
* dgmb (1.0)
Maintainer: Alba Martinez-Ruiz
Author(s): Alba Martinez-Ruiz <amartine at ucsc.cl> and Claudia
Martinez-Araneda
<cmartinez at ucsc.cl>
License: GPL (>= 2)
http://crantastic.org/packages/dgmb
Random data generation for PLS structural models.
* diffEq (1.0)
Maintainer: Karline Soetaert
Author(s): Karline Soetaert <karline.soetaert at nioz.nl>
License: GPL
http://crantastic.org/packages/diffEq
Functions and examples from the book Solving Differential Equations in
R by Karline Soetaert, Jeff R Cash and Francesca Mazzia. Springer,
2012.
* dkDNA (0.1.0)
Maintainer: Gota Morota
Author(s): Gota Morota and Masanori Koyama
License: GPL-2
http://crantastic.org/packages/dkDNA
Compute diffusion kernels on DNA polymorphisms, including SNP and
bi-allelic genotypes.
* frmqa (0.1-0)
Maintainer: Thanh T. Tran
Author(s): Thanh T. Tran
License: GPL (>= 2)
http://crantastic.org/packages/frmqa
R and C++ functions for financial risk management and quantative
analysis, using the generalized perbolic and its related
distributions.
* geospt (0.4-9)
Maintainer: Al? Santacruz
Author(s): Carlos Melo <cmelo at udistrital.edu.co>, Al? Santacruz,
Oscar Melo
<oomelom at unal.edu.co> and others
License: GPL (>= 2)
http://crantastic.org/packages/geospt
This package contains functions for: estimation of the variogram
through trimmed mean, radial basis functions (optimization,
prediction and cross-validation), summary statistics from
cross-validation, pocket plot, and design of optimal sampling
networks through sequential and simultaneous points methods
* JohnsonDistribution (0.24)
Maintainer: A.I. McLeod
Author(s): A.I. McLeod and Leanna King
License: GPL (>= 2)
http://crantastic.org/packages/JohnsonDistribution
Johnson curve distributions. Implementation of AS100 and AS99.
* labeledLoop (0.1)
Maintainer: Kohske Takahashi
Author(s): Kohske Takahashi
License: MIT
http://crantastic.org/packages/labeledLoop
Support labeled loop and escape from nested loop
* logitnorm (0.8.26)
Maintainer: Thomas Wutzler
Author(s): Thomas Wutzler
License: GPL-2
http://crantastic.org/packages/logitnorm
Density, distribution, quantile and random generation function for the
logitnormal distribution. Estimation of the mode and the first two
moments. Estimation of distribution parameters.
* LOST (1.0)
Maintainer: Jessica Arbour
Author(s): J. Arbour and C. Brown
License: GPL (>= 2)
http://crantastic.org/packages/LOST
LOST includes functions for simulating missing morphometric data
randomly, with taxonomic bias and with anatomical bias. This package
also includes functions for estimating missing morphometric data
based on regression.
* NHPoisson (1.0)
Maintainer: Ana C. Cebrian
Author(s): Ana C. Cebrian
License: GPL (>= 2)
http://crantastic.org/packages/NHPoisson
Tools for modelling, ML estimation, validation analysis and simulation
of non homogeneous Poisson processes in time.
* pacose (1.0)
Maintainer: Vincent Guillemot
Author(s): Vincent Guillemot, Andreas Bender
License: GPL
http://crantastic.org/packages/pacose
Implementation of iPACOSE, PACOSE and of various methods for the
estimation of covariance/precision matrices under the constraint
that some partial correlation coefficients are equal to zero.
* pcaL1 (1.0)
Maintainer: Paul Brooks
Author(s): Sapan Jot <sapan.madaan at gmail.com> and Paul Brooks
<jpbrooks at vcu.edu>.
The scripts configure and configure.ac and the file
INSTALL are based on those in R package clpAPI
<geliudie at uni-duesseldorf.de>.
License: GPL (>= 2)
http://crantastic.org/packages/pcaL1
This package contains three implementations of principal component
analysis methods using the L1 norm. The package depends on COIN-OR
Clp version >= 1.12.0. The methods implemented are PCA-L1 (Kwak
2008), L1-PCA (Ke and Kanade 2003, 2005), and L1-PCA* (Brooks, Dula,
and Boone 2012).
* sft (0.0-4)
Maintainer: Joe Houpt
Author(s): Joe Houpt <jhoupt at indiana.edu>, Leslie Blaha
<Leslie.Blaha at wpafb.af.mil>
License: GPL (>= 2)
http://crantastic.org/packages/sft
This package contains a series of tools for analyzing Systems
Factorial Technology data. This includes functions for plotting and
statistically testing capacity coefficient functions and survivor
interaction contrast functions.
* stpp (0.1)
Maintainer: Edith Gabriel
Author(s): Edith Gabriel
License: GPL-3
http://crantastic.org/packages/stpp
A package for analysing, simulating and displaying space-time point
patterns
* TestSurvRec (1.01)
Maintainer: Carlos Martinez
Author(s): Dr. Carlos Martinez
License: GPL-2
http://crantastic.org/packages/TestSurvRec
These tests are weighted tests type logrank
* VarEff (1.0)
Maintainer: Natacha Nikolic
Author(s): Natacha Nikolic and Claude Chevalet
License: GPL (>= 2)
http://crantastic.org/packages/VarEff
Functions for estimate the changes of effective population size with
coalescent approach.
* vec2dtransf (1.0)
Maintainer: German Carrillo
Author(s): German Carrillo
License: GPL (>= 2)
http://crantastic.org/packages/vec2dtransf
A package for applying affine and similarity transformations on vector
spatial data (sp objects). Transformations can be defined from
control points or directly from parameters. If redundant control
points are provided Least Squares is applied allowing to obtain
residuals and RMSE.
Updated packages
----------------
abn (0.7), afmtools (0.1.7), ANN (0.1.4), bayesDem (1.5-1), bayesLife
(0.3-3), bclust (1.3), bcp (3.0.1), blighty (3.1-4), bootRes (1.2.1),
cccd (1.01), clpAPI (1.2.1), comparison (0.4-0), crs (0.15-15),
dcemriS4 (0.47), ddepn (2.1), deldir (0.0-18), diptest (0.75-3),
disclapmix (0.2), dlmap (1.12), dlnm (1.6.1), dlnm (1.6.2), doMC
(1.2.5), doParallel (1.0.1), doRNG (1.2.6), doSNOW (1.0.6), flux
(0.2-1), fOptions (2160.81), foreach (1.4.0), gdsfmt (0.9.8),
GeneCycle (1.1.2), geometry (0.3-0), GGally (0.3.2), glpkAPI (1.2.3),
gmodels (2.15.2), GWAF (2.0), GWAtoolbox (2.0.2), HAC (0.2-0), hash
(2.1.0.2), hdlm (1.1.1), iterators (1.0.6), kaps (0.9-2), lcmm
(1.5.2), LeLogicielR (1.2), lgcp (0.9-4), limSolve (1.5.3), lmomco
(1.5.1), MCMCpack (1.2-3), MDM (1.1), mediation (4.0.1), meta (2.0-2),
monomvn (1.8-10), MPTinR (0.8.10), mritc (0.4-0), msSurv (1.1-0),
mvoutlier (1.9.7), nlsmsn (0.0-3), oblique.tree (1.1), oro.nifti
(0.3.3), OUwie (1.18), pracma (1.0.5), qgraph (1.0.3), qualityTools
(1.52), RcppArmadillo (0.3.0.2), ReadImages (0.1.3.2), rgrs (0.2-17),
RHRV (2.6), robfilter (3.1), RVAideMemoire (0.9-9), RXKCD (1.7-2),
saws (0.9-5.3), segmented (0.2-9.0), SPACECAP (1.0.5), spatstat
(1.26-1), sprint (1.0.1), sybil (1.0.2), tempdisagg (0.13), tgp
(2.4-7), timereg (1.6-3), tis (1.22), topicmodels (0.1-5), trio
(1.4.26), xlsxjars (0.4.0), xpose4 (4.3.5), xpose4classic (4.3.5),
xpose4data (4.3.5), xpose4generic (4.3.5), xpose4specific (4.3.5), zic
(0.7.0)
This email provided as a service for the R community by
http://crantastic.org.
Like it? Hate it? Please let us know: cranatic at gmail.com.
CRAN (and crantastic) updates this week
New packages
------------
* anoint (1.0)
Maintainer: S. A. Kovalchik
Author(s): Ravi Varadhan <rvaradhan at jhmi.edu> and Stephanie Kovalchik
License: GPL (>= 2)
http://crantastic.org/packages/anoint
Tools for assessing multiple treatment-covariate interactions with
data from a parallel-group randomized controlled clinical trial
* BINCO (0.1-1)
Maintainer: Shuang Li
Author(s): Shuang Li <shuangli at fhcrc.org>,Li Hsu <lih at
fhcrc.org>, Jie Peng
<jiepeng at ucdavis.edu>, Pei Wang <pwang at
fhcrc.org>,
License: GPL (>= 2)
http://crantastic.org/packages/BINCO
Network construction based on inference on edge selection frequencies
generated from bootstrap resamples
* binomlogit (1.0)
Maintainer: Agnes Fussl
Author(s): Agnes Fussl
License: GPL-3
http://crantastic.org/packages/binomlogit
The R package contains different MCMC schemes to estimate the
regression coefficients of a binomial (or binary) logit model within
a Bayesian framework: a data-augmented independence MH-sampler, an
auxiliary mixture sampler and a hybrid auxiliary mixture (HAM)
sampler. All sampling procedures are based on algorithms using data
augmentation, where the regression coefficients are estimated by
rewriting the logit model as a latent variable model called
difference random utility model (dRUM).
* biwavelet (0.1)
Maintainer: Tarik C. Gouhier
Author(s): Tarik C. Gouhier, Aslak Grinsted
License: GPL (>= 2)
http://crantastic.org/packages/biwavelet
This is a port of the WTC MATLAB package written by Aslak Grinsted and
the wavelet program written by Christopher Torrence and Gibert P.
Compo. This package can be used to perform univariate and bivariate
(cross-wavelet, wavelet coherence) wavelet analyses.
* CePa (0.1)
Maintainer: Zuguang Gu
Author(s): Zuguang Gu
License: GPL (>= 2)
http://crantastic.org/packages/CePa
Use pathway topology information to assign weight to pathway nodes.
* fracprolif (1.0.2)
Maintainer: Shawn Garbett
Author(s): Shawn Garbett, Darren Tyson
License: GPL-2
http://crantastic.org/packages/fracprolif
Functions for fitting data to a quiescent growth model, i.e. a growth
process that involves members of the population who stop dividing or
propagating.
* GUniFrac (1.0)
Maintainer: Jun Chen
Author(s): Jun Chen
License: GPL-2
http://crantastic.org/packages/GUniFrac
Generalized UniFrac distance for comparing microbial communities.
Permutational multivariate analysis of variance using multiple
distance matrices.
* MAMS (0.1)
Maintainer: Thomas Jaki
Author(s): Thomas Jaki <jaki.thomas at gmail.com> and Dominic Magirr
<d.magirr at lancaster.ac.uk>
License: GPL-2
http://crantastic.org/packages/MAMS
Designing multi-arm multi-stage studies with normal endpoints and
known variance
* mmand (0.1.0)
Maintainer: Jon Clayden
Author(s): Jon Clayden
License: GPL-2
http://crantastic.org/packages/mmand
This package provides tools for performing mathematical morphology
operations, such as erosion and dilation, on data of arbitrary
dimensionality. It can also be used for smoothing and other image
processing-style operations.
* muma (1.0)
Maintainer: Edoardo Gaude
Author(s): Edoardo Gaude, Dimitrios Spiliotopoulos, Silvia Mari, Andrea
Spitaleri
and Michela Ghitti
License: GPL-2
http://crantastic.org/packages/muma
Preprocessing of metabolomic data (normalization and scalings);
Principal Component Analysis with help tool for choosing
best-separating principal components and automatic outlier testing;
automatic univariate analysis for parametric and non-parametric
data, with report generation (volcano and box plots); partial least
sqaure discriminant analysis (PLS-DA); orthogonal partial least
square discriminant analysis (OPLS-DA); Statistical Total
Correlation Spectroscopy (STOCSY); Ratio Analysis NMR SpectroscopY
(RANSY).
* okmesonet (0.1.1)
Maintainer: Brady Allred
Author(s): Brady Allred, Torre Hovick, Samuel Fuhlendorf
License: GPL (>= 2)
http://crantastic.org/packages/okmesonet
okmesonet retrieves and summarizes Oklahoma (USA) Mesonet
climatological data provided by the Oklahoma Climatological Survey.
Measurements are recorded every five minutes at approximately 120
stations throughout Oklahoma and are available in near real-time.
* QRM (0.4-7)
Maintainer: Bernhard Pfaff
Author(s): Bernhard Pfaff
License: GPL (>= 2)
http://crantastic.org/packages/QRM
This package is designed to accompany the book Quantitative Risk
Management: Concepts, Techniques and Tools by Alexander J. McNeil,
Rudiger Frey and Paul Embrechts.
* rcppbugs (0.0.8)
Maintainer: Whit Armstrong
Author(s): Whit Armstrong <armstrong.whit at gmail.com>
License: GPL-3
http://crantastic.org/packages/rcppbugs
R binding for cppbugs
* RfmriVC (1.0)
Maintainer: Stefanie Kalus
Author(s): Ludwig Bothmann, Stefanie Kalus
License: GPL-2
http://crantastic.org/packages/RfmriVC
A varying coefficient on the stimulus effect is introduced into the
voxelwise fMRI regression model. By this the effects of the
canonical hemodynamic response function are allowed to vary with
another variable, like for example time or a vigilance parameter.
* risaac (0.1)
Maintainer: David L Gibbs
Author(s): David L Gibbs
License: GPL-3
http://crantastic.org/packages/risaac
Uses the ISAAC algorithm:
http://burtleburtle.net/bob/rand/isaacafa.html
* rknn (1.0)
Maintainer: Shengqiao Li
Author(s): Shengqiao Li <shli at stat.wvu.edu>
License: GPL (>= 2)
http://crantastic.org/packages/rknn
Random KNN Classification and Regression
* superdiag (1.1)
Maintainer: Tsung-han Tsai
Author(s): Tsung-han Tsai <t.tsai at wustl.edu>, Jeff Gill <jgill at
wustl.edu> and
Jonathan Rapkin <rapkin at wustl.edu>
License: GPL
http://crantastic.org/packages/superdiag
A Comprehensive Test Suite for Markov Chain Nonconvergence.
* weightedKmeans (1.2.0)
Maintainer: Graham Williams
Author(s): Graham Williams, Joshua Z Huang, Xiaojun Chen, Qiang Wang, Longfei
Xiao
License: GPL (>= 3)
http://crantastic.org/packages/weightedKmeans
Entropy weighted kmeans (ewkm) is a weighted subspace clustering
algorithm that is well suited to very high dimensional data. Weights
are calculated as the importance of a variable with regard to
cluster membership. The feature group weighted kmenas (fgkm) extends
this concept by grouping features and weighting the group in
addition to weihgting individual features.
Updated packages
----------------
ade4 (1.5-0), ahaz (1.12), ape (3.0-3), arules (1.0-8), BMA (3.15.1),
bsml (1.5-1), cec2005benchmark (1.0.1), CHCN (1.4), cloudRmpi (1.1),
cloudRmpiJars (1.1), CONORData (1.0.1), constrainedKriging (0.1.7),
coxme (2.2-2), cplexAPI (1.2.2), CrypticIBDcheck (0.2-3), deldir
(0.0-19), demography (1.12), dplR (1.5.4), dynaTree (1.2-6), earth
(3.2-3), ENmisc (1.2-4), ffbase (0.4), ffbase (0.4-1), fmsb (0.3.4),
fracprolif (1.0.2), frmqa (0.1-1), gamlss (4.1-5), gcdnet (1.0.1),
GenSA (1.0.3), geospt (0.5-0), GLDEX (1.0.4.4), glmmLasso (1.0.2),
glmnet (1.7.4), gvcm.cat (1.3), HMP (1.1), ivbma (1.02), libamtrack
(0.5.3), locfit (1.5-8), MASS (7.3-18), MetaQC (0.1.10-1), mgcv
(1.7-14), MPCI (1.0.4), multitable (1.4), multitaper (1.0-0), NetComp
(1.4), noia (0.96), nortest (1.0-1), partsm (1.1), party (1.0-2),
pbkrtest (0.3-1), pcaL1 (1.1), pcalg (1.1-5), pdc (0.2), QCA (1.0-3),
QCAGUI (1.8-4), qualityTools (1.53), rattle (2.6.18), rcom (2.2-5),
rcom (2.2-4), rcppbugs (0.0.8), rebmix (2.4.0), rfPermute (1.1),
RghcnV3 (2.7), RnavGraph (0.1.3), robust (0.3-19), rpartScore (1.0-0),
rreval (1.1), rscproxy (2.0-1), rtape (2.0), rworldmap (0.1310), smatr
(3.2.6), snow (0.3-9), SNPRelate (0.9.5), spBayes (0.2-4), spider
(1.1-3), sprint (1.0.2), survival (2.36-13), survival (2.36-14),
textcat (0.1-1), trio (1.5.0), WGCNA (1.20)
This email provided as a service for the R community by
http://crantastic.org.
Like it? Hate it? Please let us know: cranatic at gmail.com.
CRAN (and crantastic) updates this week
New packages
------------
* condmixt (1.0)
Maintainer: Julie Carreau
Author(s): Julie Carreau
License: GPL-2
http://crantastic.org/packages/condmixt
Conditional density estimation with mixtures for heavy-tailed
distributions
* crrstep (2012-5.3)
Maintainer: Ravi Varadhan
Author(s): Ravi Varadhan & Deborah Kuk
License: GPL (>= 2)
http://crantastic.org/packages/crrstep
Performs forward and backwards stepwise regression for the
Proportional subdistribution hazards model in competing risks (Fine
& Gray 1999). Procedure uses AIC, BIC and BICcr as selection
criteria. BICcr has a penalty of k = log(n*), where n* is the number
of primary events.
* discreteMTP (0.1-2)
Maintainer: Shay Yaacoby
Author(s): Ruth Heller [aut], Hadas Gur [aut], Shay Yaacoby [aut, cre]
License: GPL (>= 2)
http://crantastic.org/packages/discreteMTP
Multiple testing procedures for discrete test statistics, that use the
known discrete null distribution of the p-values for simultaneous
inference.
* gglasso (1.0)
Maintainer: Yi Yang
Author(s): Yi Yang <yiyang at umn.edu>, Hui Zou <hzou at
stat.umn.edu>
License: GPL-2
http://crantastic.org/packages/gglasso
This package implements a unified algorithm,
blockwise-majorization-decent (BMD), for efficiently computing the
solution paths of the group-lasso penalized least squares, logistic
regression, Huberized SVM and squared SVM.
* ISBF (0.1)
Maintainer: Pierre Alquier
Author(s): Pierre Alquier
License: GPL
http://crantastic.org/packages/ISBF
Selection of features for sparse regression estimation (like the
LASSO). Selection of blocks of features when the regression
parameter is sparse and constant by blocks (like the Fused-LASSO).
Application to cgh arrays. TEST VERSION, USE AT YOUR OWN RISK!
* mmm2 (1.0)
Maintainer: Ozgur Asar
Author(s): Ozgur Asar, Ozlem Ilk
License: GPL (>= 2)
http://crantastic.org/packages/mmm2
Fits multivariate marginal models with shared regression parameters
for discrete and continuous responses
* Momocs (0.1-01)
Maintainer: Vincent Bonhomme
Author(s): Vincent Bonhomme, Sandrine Picq, Julien Claude
License: GPL (>= 2)
http://crantastic.org/packages/Momocs
Momocs is intended to ease and popularize shape analysis of outlines
(especially using elliptical Fourier analysis). It mostly hinges on
the functions developped in Morphometrics with R (Claude, 2008).
From outline extraction of images and elliptical Fourier calculation
to multivariate analysis and the visualization of transformations
within the morphological space, Momocs provides a complete and
convenient toolkit to specialists within every field that are, or
may be, interested in morphological comparisons of outlines.
* mpoly (0.0.1)
Maintainer: David Kahle
Author(s): David Kahle <david.kahle at gmail.com>
License: MIT
http://crantastic.org/packages/mpoly
mpoly allows for the symbolic manipulation of multivariate polynomials
in a general and consistent way designed especially for sparse and
super sparse polynomials. It also allows for basic differential
calculus with multivariate polynomials and Grobner basis
calculations from computational algebraic geometry.
* R.devices (2.1.1)
Maintainer: Henrik Bengtsson
Author(s): Henrik Bengtsson
License: LGPL (>= 2.1)
http://crantastic.org/packages/R-devices
This package provides utility methods that enhance the existing
graphical device functions already available in R for the purpose of
simplify the creation of figure files of various image formats and
much more.
* RcmdrPlugin.EBM (1.0-1)
Maintainer: Daniel Leucuta
Author(s): Daniel-Corneliu Leucuta <danny.ldc at gmail.com>
License: GPL (>= 2)
http://crantastic.org/packages/RcmdrPlugin-EBM
This package provides an Rcmdr plug-in for Evidence Based Medicine
medical indicators calculations (Sensitivity, specificity, absolute
risk reduction, relative risk, ...).
* RSeed (0.1.31)
Maintainer: Claus Jonathan Fritzemeier
Author(s): Claus Jonathan Fritzemeier
License: GNU General Public License
http://crantastic.org/packages/RSeed
an implementation of the analysis about seed components from
borenstein 2008
* SemiParSampleSel (0.1)
Maintainer: Giampiero Marra
Author(s): Giampiero Marra <giampiero at stats.ucl.ac.uk> and Rosalba
Radice
<rosalba.radice at lshtm.ac.uk>
License: GPL (>= 2)
http://crantastic.org/packages/SemiParSampleSel
Routine for fitting continuous response sample selection models with
semiparametric predictors, including linear and nonlinear effects.
* stellaR (0.2-0)
Maintainer: Matteo Dell'Omodarme
Author(s): Matteo Dell'Omodarme [aut, cre], Giada Valle [aut]
License: GPL (>= 2)
http://crantastic.org/packages/stellaR
A package to manage and display stellar tracks and isochrones from
Pisa low-mass database. Includes tools for isochrones construction
and tracks interpolation.
Updated packages
----------------
arm (1.5-04), bayesDem (1.6-0), bayesLife (0.4-0), betapart (1.1-2),
birch (1.2-3), birch (1.2-2), bootRes (1.2.2), CDNmoney (2012.4-1),
cosso (2.0-1), crs (0.15-16), csound (0.1-1), dclone (1.7-2), dcmle
(0.2-0), detect (0.2-2), dse (2012.4-1), emplik (0.9-8-2), EvalEst
(2012.4-1), forecast (3.21), fpp (0.4), geometry (0.3-1), GGEBiplotGUI
(1.0-2), ggmap (2.1), HAC (0.2-1), harvestr (0.3), hydroGOF (0.3-3),
hydroTSM (0.3-4), kappalab (0.4-6), KernSmoothIRT (3.0), lassoshooting
(0.1.5-1), LEAPFrOG (1.0.4), meta (2.0-4), metrumrg (5.17), mgcv
(1.7-16), MigClim (1.1), minPtest (1.2), mirt (0.2.3), mmand (0.1.1),
Modalclust (0.3), Momocs (0.1-01), mpmcorrelogram (0.1-2), MSeasy
(5.3), MSeasyTkGUI (5.3), MultiPhen (0.5), MVPARTwrap (0.1-9),
okmesonet (0.1.2), OUwie (1.21), pathClass (0.9.3), phytools (0.1-8),
playitbyr (0.2-0), playitbyr (0.2-1), plm (1.2-10), plotmo (1.3-2),
pomp (0.42-1), PropCIs (0.1-8), psych (1.2.4), raster (1.9-92),
RcppArmadillo (0.3.0.3), rgdal (0.7-11), rgdal (0.7-10), rgeos
(0.2-6), Rlabkey (2.1.118), RMark (2.1.1), rscproxy (2.0-5), Rz
(0.4-0), sculpt3d (0.3-1), sp (0.9-99), spam (0.29-1), spam (0.29-0),
spatialkernel (0.4-13), spatialkernel (0.4-14), StateTrace (1.0-4),
stellaR (0.2-0), survSNP (0.21-4), tabplot (0.11-2), tabplotGTK
(0.5-2), tcltk2 (1.2-3), tensor (1.5), tframe (2012.4-2), tframePlus
(2012.4-2), TSdbi (2012.4-1), tsfa (2012.4-1), TSfame (2012.4-1),
TSgetSymbol (2012.4-1), TShistQuote (2012.4-1), TSMySQL (2012.4-1),
tsne (0.1-2), TSpadi (2012.4-1), TSSQLite (2012.4-1), TSxls
(2012.4-1), TSzip (2012.4-1), varcompci (1.0.1)
New reviews
-----------
* qAnalyst, by atomicules
http://crantastic.org/reviews/148
This email provided as a service for the R community by
http://crantastic.org.
Like it? Hate it? Please let us know: cranatic at gmail.com.
CRAN (and crantastic) updates this week
New packages
------------
* AGD (0.30)
Maintainer: Stef van Buuren
Author(s): Stef van Buuren <stef.vanbuuren at tno.nl>
License: GPL-2 | GPL-3
http://crantastic.org/packages/AGD
Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23 2012,
Rotterdam.
* bigml (0.1-1)
Maintainer: Justin Donaldson
Author(s): Justin Donaldson [aut, cre]
License: LGPL-3
http://crantastic.org/packages/bigml
The bigml package contains bindings for the BigML API. The package
includes methods that provide straightforward access to basic API
functionality, as well as methods that accommodate idiomatic R
datatypes and concepts.
* BVS (4.12.0)
Maintainer: Melanie Quintana
Author(s): Melanie Quintana <maw27.wilson at gmail.com>
License: Unlimited
http://crantastic.org/packages/BVS
The functions in this package focus on analyzing case-control
association studies involving a group of genetic variants. In
particular, we are interested in modeling the outcome variable as a
function of a multivariate genetic profile using Bayesian model
uncertainty and variable selection techniques. The package
incorporates functions to analyze data sets involving common
variants as well as extensions to model rare variants via the
Bayesian Risk Index (BRI) as well as haplotypes. Finally, the
package also allows the incorporation of external biological
information to inform the marginal inclusion probabilities via the
iBMU.
* gsbDesign (0.95)
Maintainer: Unknown
Author(s): Florian Gerber, Thomas Gsponer
License: GPL-3
http://crantastic.org/packages/gsbDesign
Group Sequential Operating Characteristics for Clinical, Bayesian
two-arm Trials with known Sigma and Normal Endpoints.
* marqLevAlg (1.0)
Maintainer: Melanie Prague
Author(s): D. Commenges <Daniel.Commenges at isped.u-bordeaux2.fr>, M.
Prague
<Melanie.Prague at isped.u-bordeaux2.fr> and Amadou Diakite
License: GPL (>= 2.0)
http://crantastic.org/packages/marqLevAlg
This algorithm provides a numerical solution to the problem of
minimizing a function. This is more efficient than the
Gauss-Newton-like algorithm when starting from points vey far from
the final minimum. A new convergence test is implemented (RDM) in
addition to the usual stopping criterion : stopping rule is when the
gradients are small enough in the parameters metric (GH-1G).
* p2distance (1.0.1)
Maintainer: A.J. Perez-Luque
Author(s): A.J. Perez-Luque; R. Moreno; R. Perez-Perez and F.J. Bonet
License: GPL
http://crantastic.org/packages/p2distance
The welfare's synthetic indicator provides an ideal tool for measuring
multi-dimensional concepts such as welfare, development, living
standards, etc. It enables information from the various indicators
to be aggregated into a single synthetic measure.
* pcaPA (1.0)
Maintainer: Carlos A. Arias
Author(s): Carlos A. Arias <carias at icfes.gov.co> and V?ctor H.
Cervantes
<vcervantes at icfes.gov.co>.
License: GPL (>= 2)
http://crantastic.org/packages/pcaPA
A set of functions to perform parallel analysis for principal
components analysis intended mainly for large data sets. It performs
a parallel analysis of continuous, ordered (including
dichotomous/binary as a special case) or mixed type of data
associated with a principal components analysis. Polychoric
correlations among ordered variables, Pearson correlations among
continuous variables and polyserial correlation between mixed type
variables (one ordered and one continuous) are used. Whenever the
use of polyserial or polychoric correlations yields a non positive
definite correlation matrix, the resulting matrix is transformed
into the nearest positive definite matrix. For details on the GSL
installation in windows please visit the following link:
http://wiki.rglab.org/index.php?title=Public:Installation_of_GSL_from
Windows_binary
* phia (0.0-2)
Maintainer: Helios De Rosario-Martinez
Author(s): Helios De Rosario-Martinez
License: GPL (>= 3)
http://crantastic.org/packages/phia
Analysis of terms in linear and generalized linear models, on the
basis of multiple comparisons of factor contrasts. Specially suited
for the analysis of interaction terms.
* plmDE (1.0)
Maintainer: Jonas
Author(s): Jonas Mueller
License: GPL (>= 2)
http://crantastic.org/packages/plmDE
A set of tools for identifying genes whose differential expression is
associated with measurements of other covariates on a continuous
scale. These methods rely on generalized additive partially linear
models which can be fitted efficiently using a B-spline basis
approximation. Still under development: methods for interfacing
with objects extending the eSet class and a function to pass linear
models in edgeR and DEseq format.
* polywog (0.1-0)
Maintainer: Brenton Kenkel
Author(s): Brenton Kenkel and Curtis S. Signorino
License: GPL (>= 2)
http://crantastic.org/packages/polywog
Routines for flexible functional form estimation via basis regression,
with model selection via the adaptive LASSO or SCAD to prevent
overfitting.
* qtutils (0.1-2)
Maintainer: Deepayan Sarkar
Author(s): Deepayan Sarkar
License: LGPL (>= 2)
http://crantastic.org/packages/qtutils
Miscellaneous Qt-based tools for R
* RCassandra (0.1-0)
Maintainer: Simon Urbanek
Author(s): Simon Urbanek <simon.urbanek at r-project.org>
License: GPL-2
http://crantastic.org/packages/RCassandra
This packages provides a direct interface (without the use of Java) to
the most basic functionality of Apache Cassanda such as login,
updates and queries.
* rolasized (1.0)
Maintainer: Christian Zang
Author(s): Christian Zang
License: MIT
http://crantastic.org/packages/rolasized
Ethan Schoonover's solarized colour scheme for R
(http://ethanschoonover.com/solarized)
* RTDAmeritrade (0.0.1)
Maintainer: Theodore Van Rooy
Author(s): Theodore Van Rooy
License: GPL (>= 2)
http://crantastic.org/packages/RTDAmeritrade
The package contains functions that can be used to interface with the
TDAmeritrade API.
* SightabilityModel (1.0)
Maintainer: John Fieberg
Author(s): John Fieberg
License: GPL-2
http://crantastic.org/packages/SightabilityModel
Uses logistic regression to model the probability of detection as a
function of covariates. This model is then used with observational
survey data to estimate population size, while accounting for
uncertain detection. See Steinhorst and Samuel (1989).
* SKAT (0.75)
Maintainer: Seunggeun (Shawn) Lee
Author(s): Seunggeun Lee, Larisa Miropolsky and Micheal Wu
License: GPL (>= 2)
http://crantastic.org/packages/SKAT
Kernel based SNP set test
* SunterSampling (1.0)
Maintainer: alessandro.barbiero
Author(s): Alessandro Barbiero, Giancarlo Manzi
License: GPL
http://crantastic.org/packages/SunterSampling
Functions for drawing samples according to Sunter's sampling design,
and for computing first and second order inclusion probabilities
* TCC (0.2)
Maintainer: Tomoaki Nishiyama
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
License: GPL-2
http://crantastic.org/packages/TCC
This package provides normalization method of tag count data by
TMM-bayseq-TMM pipeline. Expected application includes RNA-seq,
SAGE, ChIP-seq and a like.
Updated packages
----------------
Animal (1.04), BaSAR (1.3), BBmisc (1.1-125), beeswarm (0.1.5),
betareg (3.0-0), blockTools (0.5-4), caroline (0.7.2), catR (2.3),
cccd (1.02), ChoiceModelR (1.1), CityPlot (2.0), corpcor (1.6.3),
cvplogistic (2.0-0), cvTools (0.3.1), dafs (1.0-37), diveMove (1.3.4),
diversitree (0.9-3), DNAtools (0.1-6), fda.usc (0.9.7), ff (2.2-7),
flexmix (2.3-8), FlexParamCurve (1.4), frailtyHL (1.1), geometry
(0.3-2), ggplot2 (0.9.1), gMCP (0.7-9), hydroPSO (0.1-55), iCluster
(2.1.0), LaplacesDemon (12.05.07), lavaan (0.4-14), lmomco (1.6.1),
LPCM (0.44-6), mfr (1.04), mht (2.00), MigClim (1.2), minpack.lm
(1.1-6), minqa (1.2.1), mirt (0.2.4), mokken (2.7.2), msm (1.1.1),
mutoss (0.1-7), mutossGUI (0.1-7), nullabor (0.2), nutshellDE (1.0-2),
openair (0.6-0), orloca (4.0), pegas (0.4-2), processdata (0.8.1),
qgraph (1.0.4), RghcnV3 (2.8), rgl (0.92.880), rgr (1.1.6), RGtk2
(2.20.24), RISmed (2.0.1), RMAWGEN (1.2.5), robustbase (0.9-0),
robustfa (1.0-01), rtf (0.4-4), s20x (3.1-9), scales (0.2.1),
segmented (0.2-9.1), SemiParBIVProbit (3.2), shotGroups (0.2-1),
spatialsegregation (2.38), TDMR (0.3.0), timereg (1.6-5), tmle
(1.2.0-1), TSPostgreSQL (2012.5-1), vcdExtra (0.5-3)
This email provided as a service for the R community by
http://crantastic.org.
Like it? Hate it? Please let us know: cranatic at gmail.com.
CRAN (and crantastic) updates this week
New packages
------------
* anametrix (0.1)
Maintainer: Roman Jugai
Author(s): Roman Jugai
License: LGPL
http://crantastic.org/packages/anametrix
Connects to Anametrix API and extracts data into R data structure
* assertive (0.1-4)
Maintainer: Richard Cotton
Author(s): Richard Cotton [aut, cre]
License: Unlimited
http://crantastic.org/packages/assertive
assertive contains lots of is_* functions to check the state of your
variables, and assert_* functions to throw errors if they aren't in
the right form.
* crblocks (0.5-0)
Maintainer: David Allingham
Author(s): David Allingham, D.J. Best
License: GPL (>= 2)
http://crantastic.org/packages/crblocks
Implements a statistical test for comparing bar plots or histograms of
categorical data derived from a randomized block repeated measures
layout.
* deltaPlotR (1.0)
Maintainer: David Magis
Author(s): David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France)
License: GPL (>= 2)
http://crantastic.org/packages/deltaPlotR
The deltaPlot package proposes an implementation of Angoff's elta Plot
method to detect dichotomous DIF. Several detection thresholds are
included, either from multivariate normality asumption, random
simulation, or by prior determination. Item purification is
supported.
* disp2D (1.0)
Maintainer: Guillermo Ayala
Author(s): Guillermo Ayala
License: GPL-2
http://crantastic.org/packages/disp2D
An implementation of two exact algorithms for testing the Hausdorff
and simplex dispersion orderings
* foodweb (1-0)
Maintainer: Giselle Perdomo
Author(s): Giselle Perdomo
License: GPL (>= 2)
http://crantastic.org/packages/foodweb
Calculates twelve commonly-used, basic measures of food web network
structure from binary, predator-prey matrices: species richness,
connectance, total number of links, link density, number of trophic
positions, predator:prey ratio, and fraction of carnivores,
herbivores, top species and intermediate species. Employs food web
language in the code and output, translates between a couple of
common food web formats, can handle food webs consisting of multiple
levels, and can automate the analysis for a large number of webs.
The program produces 3-dimensional graphs of high quality that can
be customized by the user.
* genomicper (1.3)
Maintainer: Claudia Cabrera
Author(s): Claudia P.Cabrera-Cardenas,Pau Navarro,Chris S.Haley
License: GPL-2
http://crantastic.org/packages/genomicper
Circular genomic permutation approach uses GWAS results to establish
the significance of pathway/gene-set associations whilst accounting
for genomic structure. All SNPs in the GWAS are placed in a
'circular genome' according to their location. Then the complete set
of SNP association p-values are permuted by rotation with respect to
the SNPs' genomic locations
* hiPOD (1.0)
Maintainer: Wei E. Liang
Author(s): Wei E. Liang
License: GPL-3
http://crantastic.org/packages/hiPOD
Based on hierarchical modeling, this package provides a few practical
functions to find and present the optimal designs for a pooled NGS
design.
* intpoint (1.0)
Maintainer: Alejandro Quintela del Rio
Author(s): Alejandro Quintela del Rio
License: GPL-2
http://crantastic.org/packages/intpoint
Solves linear programming problems by the interior point method, and
plots the graphical solution of a linear programming problem of two
dimensions.
* jmec (1.0-3)
Maintainer: Willem M. van der Wal
Author(s): Willem M. van der Wal <w.m.vd.wal at umcutrecht.nl>
License: GPL (>= 2)
http://crantastic.org/packages/jmec
Fit joint model for event and censoring, with cluster-level frailties,
according to Huang & Wolfe (2002).
* knnGarden (1.0)
Maintainer: Boxian Wei
Author(s): Boxian Wei & Fan Yang & Xinmiao Wang & Yanni Ge
License: GPL (>= 2)
http://crantastic.org/packages/knnGarden
Muti-distance based k-Nearest Neighbors Classification with K
Threshold Value Check and Same K_i Problem Dealing, Missing
Observations Filling
* longclust (1.1)
Maintainer: K. Raju Jampani
Author(s): P. D. McNicholas, K. Raju Jampani and Sanjeena Subedi
License: GPL-2
http://crantastic.org/packages/longclust
Clustering or classification of longitudinal data based on a mixture
of multivariate t or Gaussian distributions with a
Cholesky-decomposed covariance structure.
* OIdata (1.0)
Maintainer: Andrew P Bray
Author(s): Andrew P Bray and David M Diez
License: GPL-2 | GPL-3
http://crantastic.org/packages/OIdata
A collection of data sets from several sources that may be useful for
teaching, practice, or other purposes. Functions have also been
included to assist in the retrieval of table data from websites or
in visualizing sample data.
* ParamHelpers (1.0-55)
Maintainer: Bernd Bischl
Author(s): Bernd Bischl <bernd_bischl at gmx.net>, Patrick Koch
<patrick.koch at fh-koeln.de>
License: BSD
http://crantastic.org/packages/ParamHelpers
A small package containing useful functions for parameter descriptions
and operations in black-optimization, tuning and machine learning.
* pkgmaker (0.5.1)
Maintainer: Renaud Gaujoux
Author(s): Renaud Gaujoux
License: GPL (>= 2)
http://crantastic.org/packages/pkgmaker
This package provides some low-level utilities to use for package
development. It currently provides managers for multiple package
specific options and registries, vignette, unit test and bibtex
related utilities. It serves as a base package for packages like
NMF, RcppOctave, doRNG, and as an incubator package for other
general purposes utilities, that will eventually be packaged
separately. It is still under heavy development and changes in the
interface(s) are more than likely to happen.
* qtlhot (0.5.2)
Maintainer: Brian S. Yandell
Author(s): Elias Chaibub Neto <echaibub at hotmail.com> and Brian S
Yandell
<byandell at wisc.edu>
License: GPL (>= 2)
http://crantastic.org/packages/qtlhot
Functions to Determine significance of co-mapping trait hotspots
* visreg (1.0-0)
Maintainer: Patrick Breheny
Author(s): Patrick Breheny, Woodrow Burchett
License: GPL-2
http://crantastic.org/packages/visreg
Provides convenient interface for constructing plots to visualize the
fit of regression models arising from a wide variety of models in R
(lm, glm, coxph, rlm, gam, locfit, etc.)
Updated packages
----------------
adehabitatHR (0.4.2), adehabitatHS (0.3.5), adehabitatLT (0.3.6),
adehabitatMA (0.3.4), aqfig (0.3), ARTIVA (1.1), BAS (1.0),
BatchExperiments (1.0-528), BatchJobs (1.0-527), bfp (0.0-25), censReg
(0.5-12), cloudRmpi (1.2.1), copula (0.99-2), DAAG (1.13), Devore6
(0.6-0), DiceKriging (1.3.3), dmt (0.8.10), ebdbNet (1.2.2), epiR
(0.9-43), ergm (3.0-3), ExomeCNV (1.3), fanc (1.1), fanc (1.0), ftsa
(3.3), GGally (0.3.3), gmm (1.4-1), googleVis (0.2.16), gss (2.0-10),
GWAtoolbox (2.1.2), howmany (0.3-1), iRegression (1.1), isdals
(1.0-6), ismev (1.38), IsotopeR (0.4.3), kulife (0.1-11), laeken
(0.3.3), lgcp (0.9-4-2), linkcomm (1.0-5), LMERConvenienceFunctions
(1.6.8.3), lmtest (0.9-30), longclust (1.1), longpower (1.0-2), lqmm
(1.01), mada (0.4.1), MAMS (0.2), markdown (0.5), MARSS (2.9), mhurdle
(0.1-2), micEcon (0.6-10), mitools (2.2), mixOmics (4.0-2), Mobilize
(2.11-1), msir (1.1), ncf (1.1-4), nortest (1.0-2), Ohmage (2.11-1),
pencopula (0.3.2), plus (1.0), quantregForest (0.2-3), Rcapture
(1.3-1), relaxo (0.1-2), rEMM (1.0-6), rfPermute (1.2), rgr (1.1.7),
Rook (1.0-5), rpart (3.1-53), Rssa (0.9.2), scuba (1.5-0), spacom
(0.9-4), spsurvey (2.4), stabledist (0.6-4), strucchange (1.4-7),
support.CEs (0.2-2), SYNCSA (1.2.1), systemfit (1.1-12), TDMR (0.3.1),
WriteXLS (2.1.1)
New reviews
-----------
* gtools, by jenifferhomes
http://crantastic.org/reviews/164
* RSiteSearch, by jenifferhomes
http://crantastic.org/reviews/163
* LogicForest, by jenifferhomes
http://crantastic.org/reviews/162
* TradeStrategyAnalyzer, by jenifferhomes
http://crantastic.org/reviews/161
* DCluster, by jenifferhomes
http://crantastic.org/reviews/160
* ICSNP, by jenifferhomes
http://crantastic.org/reviews/159
* JavaGD, by jenifferhomes
http://crantastic.org/reviews/158
* quantmod, by jenifferhomes
http://crantastic.org/reviews/157
* Defaults, by jenifferhomes
http://crantastic.org/reviews/156
* wordnet, by jenifferhomes
http://crantastic.org/reviews/155
* ggmap, by fiutzi
http://crantastic.org/reviews/154
* boot, by jenifferhomes
http://crantastic.org/reviews/153
* ccgarch, by jenifferhomes
http://crantastic.org/reviews/152
* data.table, by jenifferhomes
http://crantastic.org/reviews/151
* GEVcdn, by jenifferhomes
http://crantastic.org/reviews/150
This email provided as a service for the R community by
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CRAN (and crantastic) updates this week
New packages
------------
* complex.surv.dat.sim (1.0)
Maintainer: David Mori?a
Author(s): David Mori?a, Centre Tecnol?gic de Nutrici? i Salut and Albert
Navarro, Universitat Aut?noma de Barcelona
License: GPL (>= 2)
http://crantastic.org/packages/complex-surv-dat-sim
Simulation of complex survival data
* EpiEstim (1.0-0)
Maintainer: Anne Cori
Author(s): Anne Cori <a.cori at imperial.ac.uk>
License: GPL (>= 2)
http://crantastic.org/packages/EpiEstim
This package provides tools to quantify transmissibility throughout an
epidemic from the analysis of time series of incidence.
* JMLSD (1.0)
Maintainer: Emil A. Cornea
Author(s): Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and
Joseph G. Ibrahim
License: GPL-2
http://crantastic.org/packages/JMLSD
The package contains a R-function to perform power calculation for
joint modeling of longitudinal and survival data, with k-th order
trajectories, when the variance-covariance matrix Sigma_theta is
unknown.
* mpMap (1.14)
Maintainer: Emma Huang
Author(s): Emma Huang
License: GPL-2
http://crantastic.org/packages/mpMap
Tools for constructing linkage maps, reconstructing haplotypes,
estimating linkage disequilibrium and QTL mapping in multi-parent
RIL designs (e.g. MAGIC)
* phcfM (1.0)
Maintainer: Ghislain Vieilledent
Author(s): Ghislain Vieilledent <ghislain.vieilledent at cirad.fr>
License: GPL (>= 2)
http://crantastic.org/packages/phcfM
A package for modelling anthropogenic deforestation
* qtlnet (1.2.4)
Maintainer: Brian S. Yandell
Author(s): Elias Chaibub Neto <echaibub at hotmail.com> and Brian S.
yandell
<yandell at stat.wisc.edu>
License: GPL (>= 2)
http://crantastic.org/packages/qtlnet
Functions to Simultaneously Infer Causal Graphs and Genetic
Architecture
* R330 (1.0)
Maintainer: Alan Lee
Author(s): Alan Lee, Blair Robertson
License: GPL-2
http://crantastic.org/packages/R330
This is a collection of useful functions and data for Stats 330
* RIFS (0.1-5)
Maintainer: Pavel V. Moskalev
Author(s): Pavel V. Moskalev, Alexey G. Bukhovets and Tatyana Ya. Biruchinskay
License: GPL-3
http://crantastic.org/packages/RIFS
RIFS package provides functionality for generating & plotting
prefractals in R^n with various protofractal sets and partition
coefficient for iterative segments
* rriskDistributions (1.7)
Maintainer: Federal Institute for Risk Assessment, Matthias Greiner
Author(s): Natalia Belgorodski (STAT-UP Statistical Consulting, Germany),
Matthias Greiner (Federal Institute for Risk Assessment,
Germany), Kristin Tolksdorf (Federal Institute for Risk
Assessment, Germany), Katharina Schueller (STAT-UP
Statistical Consulting, Germany)
License: GPL (>= 3)
http://crantastic.org/packages/rriskDistributions
Collection of functions for fitting distributions to given data or by
known quantiles. Two main functions fit.perc() and fit.cont()
provide users a GUI that allows to choose a most appropriate
distribution without any knowledge of the R syntax.
* spclust (1.0)
Maintainer: Emma Huang
Author(s): Emma Huang
License: GPL-2
http://crantastic.org/packages/spclust
Selection of subsets of experimental crosses in order to maximize
genetic diversity
* SteinerNet (1.0)
Maintainer: Afshin Sadeghi
Author(s): Afshin Sadeghi, Holger Froehlich
License: GPL-3
http://crantastic.org/packages/SteinerNet
A set of graph functions writen in R to perform steiner tree network
data analysis on biological pathway data
* Voss (0.1-4)
Maintainer: Pavel V. Moskalev
Author(s): Pavel V. Moskalev
License: GPL-3
http://crantastic.org/packages/Voss
Voss package provides functionality for generating realizations of a
fractal Brownian function on uniform 1D & 2D grid with classic and
generic versions of the Voss algorithm (random sequential additions)
Updated packages
----------------
AICcmodavg (1.25), anametrix (0.2), arm (1.5-05), bayesDem (1.7-0),
bayesPop (2.0-2), betategarch (1.2), Biograph (2.0.1), bios2mds
(1.2.2), CHCN (1.5), countrycode (0.7), crs (0.15-17), cvplogistic
(2.1-0), deducorrect (1.2-0), DiceOptim (1.3.1), DiceView (1.2-1),
directlabels (2.6), DSL (0.1-2), editrules (2.5-0), faoutlier (0.2.3),
fda.usc (0.9.8), ffbase (0.5), fGarch (2110.80.1), forecast (3.22),
forensim (3.1), gdata (2.10.0), gdata (2.10.5), gplots (2.11.0), gRim
(0.1-9), gWidgetstcltk (0.0-51), gWidgetsWWW (0.0-23), harvestr (0.4),
HMPTrees (1.1), iDEMO (0.2-01), IPMpack (1.2), joineR (1.0-2),
LaplacesDemon (12.06.04), lazyWeave (2.1.4), leiv (2.0-5), markdown
(0.5.1), mc2d (0.1-13), minPtest (1.3), mirt (0.2.5), modelcf (2.1.1),
ModelMap (2.3.2), movMF (0.0-1), MultiPhen (0.6), pacose (1.1),
partykit (0.1-4), pdfCluster (1.0-0), phyclust (0.1-12), pracma
(1.1.0), qvcalc (0.8-8), R2Cuba (1.0-7), rainbow (2.9), relsurv
(2.0-3), rgenoud (5.7-8), RghcnV3 (2.9), RHive (0.0-6), Rmosek
(1.2.3), robustbase (0.9-2), rrlda (1.1), RXKCD (1.7-3), Rz (0.5-0),
Sim.DiffProc (2.5), skmeans (0.2-2), sparkTable (0.9.4), SpatialVx
(0.1-2), SPSL (0.1-6), standGL (1.1), stpp (0.3), timeordered (0.9.1),
TraMineR (1.8-2), TSodbc (2012.5-1), VennDiagram (1.2.1), x12 (1.0-2)
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