[R] CRAN (and crantastic) updates this week

Mon May 14 00:40:05 CEST 2012

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 Víctor 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)

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