[R] CRAN (and crantastic) updates this week

Crantastic cranatic at gmail.com
Mon Apr 16 00:40:05 CEST 2012

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

  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)

  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)

  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)

  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)

  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)

  Includes miscellaneous functions.

* robustHD (0.1.0)
  Maintainer: Andreas Alfons
  Author(s): Andreas Alfons
  License: GPL (>= 2)

  Robust methods for high-dimensional data, in particular linear model
  selection techniques based on least angle regression and sparse

* sparseLTSEigen (0.1.0)
  Maintainer: Andreas Alfons
  Author(s): Andreas Alfons
  License: GPL (>= 2)

  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)

  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

  In this package the dynamic FBA technique proposed by Varma was

* tfplot (2012.4-1)
  Maintainer: Paul Gilbert and Erik Meijer
  Author(s): Paul Gilbert <pgilbert.ttv9z at ncf.ca>
  License: GPL-2

  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)

  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)

  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

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 (,
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
(, 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 (,
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)

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