[R] CRAN (and crantastic) updates this week

Mon May 28 00:40:05 CEST 2012

CRAN (and crantastic) updates this week

New packages
------------

* awsMethods (1.0-0)
  Maintainer: Joerg Polzehl
  Author(s): Joerg Polzehl <polzehl at wias-berlin.de>
  License: GPL (>= 2)
  http://crantastic.org/packages/awsMethods

  The package defines method extract that in needed in several packages

* BatchExperiments (1.0-486)
  Maintainer: Michel Lang
  Author(s): Bernd Bischl <bernd_bischl at gmx.net>, Michel Lang
             <michellang at gmail.com>, Olaf Mersmann <olafm at p-value.net>
  License: BSD
  http://crantastic.org/packages/BatchExperiments

  Extends the BatchJobs package to run statistical experiments on batch
  computing clusters. For further details see the project web page.

* BatchJobs (1.0-485)
  Maintainer: Bernd Bischl
  Author(s): Bernd Bischl <bernd_bischl at gmx.net>, Michel Lang
             <michellang at gmail.com>, Olaf Mersmann <olafm at p-value.net>
  License: BSD
  http://crantastic.org/packages/BatchJobs

  Provides Map, Reduce and Filter variants to generate jobs on batch
  computing systems like PBS/Torque, LSF and Sun Grid Engine.
  Multicore and SSH systems are also supported. For further details
  see the project web page.

* CpGassoc (1.1)
  Maintainer: R Barfield
  Author(s): Barfield, R., Conneely, K., Kilaru,V
  License: GPL (>= 2)
  http://crantastic.org/packages/CpGassoc

  CpGassoc is designed to test for association between methylation at
  CpG sites across the genome and a phenotype of interest, adjusting
  for any relevant covariates. The package can perform standard
  analyses of large datasets very quickly with no need to impute the
  data. It can also handle mixed effects models with chip or batch
  entering the model as a random intercept.  CpGassoc also includes
  tools to apply quality control filters, perform permutation tests,
  and create QQ plots, manhattan plots, and scatterplots for
  individual CpG sites.

* dataframe (2.5)
  Maintainer: Tim Hesterberg
  Author(s): Tim Hesterberg
  License: GPL-2
  http://crantastic.org/packages/dataframe

  This contains versions of standard data frame functions in R, modified
  to avoid making extra copies of inputs.  This is faster,
  particularly for large data.

* fgof (0.2-1)
  Maintainer: Jun Yan
  Author(s): Ivan Kojadinovic and Jun Yan
  License: GPL (>= 3)
  http://crantastic.org/packages/fgof

  Goodness-of-fit test with multiplier or parametric bootstrap.

* ForeCA (0.0.1)
  Maintainer: Georg M. Goerg
  Author(s): Georg M. Goerg <gmg at stat.cmu.edu>
  License: GPL (>= 2)
  http://crantastic.org/packages/ForeCA

  ForeCA is a new blind source separation (BSS) technique for temporally
  dependent signals. Contrary to PCA or ICA it explicitly searches for
  the best linear transformation that makes the obtained sources as
  ''forecastable'' as possible. The measure of forecastability
  Omega(x_t) is the entropy of the spectral density of the signal.

* Luminescence (0.1.7)
  Maintainer: Sebastian Kreutzer
  Author(s): Sebastian Kreutzer [aut, cre], Christoph Schmidt [aut, ctb], Margret
             C. Fuchs [aut, ctb], Michael Dietze [aut, ctb], Manfred
             Fischer [aut, ctb], Markus Fuchs [ths]
  License: GPL-3
  http://crantastic.org/packages/Luminescence

  Package provides a collection of various R functions for Luminescence
  Dating data analysis.

* mada (0.4)
  Maintainer: Philipp Doebler
  Author(s): Philipp Doebler
  License: GPL-2
  http://crantastic.org/packages/mada

  This package provides functions for diagnostic meta-analysis. Next to
  basic analysis and visualization the bivariate Model of Reitsma et
  al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001)
  can be fitted. A new approach based to diagnostic meta-analysis of
  Boehning et al. is also available. Standard methods like summary,
  plot and so on are provided.

* MetaPath (0.9)
  Maintainer: Kui Shen
  Author(s): Kui Shen and Geroge Tseng
  License: GPL (>= 2.0)
  http://crantastic.org/packages/MetaPath

  This R package was implemented to perform the Meta-analysis for
  Pathway Enrichment (MAPE) methods introduced by Shen and Tseng
  (2010). It includes functions to automatically perform MAPE_G
  (integrating multiple studies at gene level), MAPE_P (integrating
  multiple studies at pathway level) and MAPE_I (a hybrid method
  integrating MAEP_G and MAPE_P methods). In the simulation and real
  data analyses in the paper, MAPE_G and MAPE_P have complementary
  advantages and detection power depending on the data structure. In
  general, the integrative form of MAPE_I is recommended to use. In
  the case that MAPE_G (or MAPE_P) detects almost none pathway, the
  integrative MAPE_I does not improve performance and MAPE_P (or
  MAPE_G) should be used. Reference: Shen, Kui, and George C Tseng.
  Meta-analysis for pathway enrichment analysis when combining
  multiple microarray studies.Bioinformatics (Oxford, England) 26, no.
  10 (April 2010): 1316-1323. doi:10.1093/bioinformatics/btq148.
  http://www.ncbi.nlm.nih.gov/pubmed/20410053.

* NbClust (1.0)
  Maintainer: : Nadia Ghazzali
  Author(s): Malika Charrad <malika.charrad.1 at ulaval.ca> and Nadia Ghazzali
             <nadia.ghazzali at mat.ulaval.ca> and Veronique Boiteau
             <veronique.boiteau.1 at ulaval.ca> and Azam Niknafs
             <azam.niknafs.1 at ulaval.ca>
  License: GPL-2
  http://crantastic.org/packages/NbClust

  This package provides most of the popular indices for cluster
  validation ready to use for the outputs produced by functions coming
  from the same package. It also proposes to user the best clustering
  scheme from the different results obtained by varying all
  combinations of number of clusters, distance measures, and
  clustering methods.

* OptimalCutpoints (1.0)
  Maintainer: Monica Lopez Raton
  Author(s): Monica Lopez-Raton, Maria Xose Rodriguez-Alvarez
  License: GPL
  http://crantastic.org/packages/OptimalCutpoints

  This package enables users to compute one or more optimal cutpoints
  for diagnostic tests or continuous markers. Various approaches for
  selecting optimal cutoffs have been implemented, including methods
  based on cost-benefit analysis and diagnostic test accuracy measures
  (Sensitivity/Specificity, Predictive Values and Diagnostic
  Likelihood Ratios). Numerical and graphical output for all methods
  is easily obtained.

* Taxonstand (1.0)
  Maintainer: Luis Cayuela
  Author(s): Luis Cayuela
  License: GPL (>= 2)
  http://crantastic.org/packages/Taxonstand

  Automated standardization of taxonomic names and removal of
  orthograhpic errors in plant species names using the The Plant List
  (TPL) website (www.theplantlist.org)

* WeightedPortTest (1.0)
  Maintainer: Thomas J. Fisher
  Author(s): Thomas J. Fisher and Colin M. Gallagher
  License: GPL (>= 3)
  http://crantastic.org/packages/WeightedPortTest

  This packages contains the Weighted Portmanteau Tests as described in
  "New Weighted Portmanteau Statistics for Time Series Goodness-of-Fit
  Testing' accepted for publication by the Journal of the American
  Statistical Association.

Updated packages
----------------

actuar (1.1-4), aws (1.8-0), BinNor (2.0), caTools (1.13), CDVine
(1.1-7), changepoint (0.7), ChemoSpec (1.51-0), cosso (2.0-2),
CpGassoc (1.1), doRNG (1.3), doRNG (1.4.1), dti (1.0-3), dynsurv
(0.1-8), EcoHydRology (0.4.1), EffectStars (1.1), fastICA (1.1-16),
foreign (0.8-50), ftsa (3.2), G1DBN (3.1), gdistance (1.1-3), gmm
(1.4-0), gnm (1.0-2), hash (2.2.3), HH (2.3-15), igraph0 (0.5.5-1),
inlinedocs (1.9.1), iterLap (1.1-2), kaps (0.9-3), ks (1.8.8),
Maeswrap (1.4.11), MatrixEQTL (1.6.1), maxent (1.3.2), mgcv (1.7-17),
ModelMap (2.3.1), multcompView (0.1-5), muma (1.2), NBPSeq (0.1.6),
nlme (3.1-104), oce (0.8-8), oce (0.8-9), okmesonet (0.1.3), OpenCL
(0.1-3), osDesign (1.6), osmar (1.1-4), pdc (0.3), qgraph (1.0.5), qtl
(1.24-9), qtutils (0.1-3), RcppArmadillo (0.3.2.0), rcppbugs (0.1.0),
RForcecom (0.2), Rjms (0.0.3), Rmpfr (0.4-8), ror (0.8), Rsolnp
(1.12), rtape (2.1), rugarch (1.0-9), SamplingStrata (0.9-3),
spacetime (0.7-0), SPARQL (1.9), SparseGrid (0.8.1), SpatialTools
(0.4.1), survey (3.28-1), synbreed (0.9-3)

New reviews
-----------

* xlsx, by fiutzi
  http://crantastic.org/reviews/149

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