[R] CRAN (and crantastic) updates this week

Mon Nov 3 00:40:05 CET 2014

CRAN (and crantastic) updates this week

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

* addreg (1.2)
  Maintainer: Mark Donoghoe
  Author(s): Mark Donoghoe <mark.donoghoe at mq.edu.au>
  License: GPL (>= 2)
  http://crantastic.org/packages/addreg

  Methods for fitting identity-link GLMs and GAMs to discrete data. The
  package uses EM-type algorithms with more stable convergence
  properties than standard methods.

* CateSelection (1.0)
  Maintainer: Yi Xu
  Author(s): Yi Xu and Jixiang Wu
  License: GPL (>= 2)
  http://crantastic.org/packages/CateSelection

  A multi-factor dimensionality reduction based forward selection method
  for genetic association mapping.

* DAMOCLES (1.0)
  Maintainer: Rampal S. Etienne
  Author(s): Rampal S. Etienne & Alex L. Pigot
  License: GPL-2
  http://crantastic.org/packages/DAMOCLES

  Simulates and computes (maximum) likelihood of a dynamical model of
  community assembly that takes into account the phylogenetic history

* exCon (0.1-0)
  Maintainer: Bryan A. Hanson
  Author(s): Bryan Hanson [aut, cre], Kristina Mulry [ctb]
  License: GPL-3
  http://crantastic.org/packages/exCon

  exCon is an interactive tool to explore topographic-like data sets. 
  Such data sets take the form of a matrix in which the rows and
  columns provide location/frequency information, and the matrix
  elements contain altitude/response information.  Such data is found
  in cartography, 2D spectroscopy and chemometrics.  exCon creates an
  interactive web page showing the contoured data set along with
  slices from the original matrix parallel to each dimension. The page
  is written in d3/javascript.

* genpathmox (0.1)
  Maintainer: "Giuseppe Lamberti"
  Author(s): "Giuseppe Lamberti" [aut, cre]
  License: GPL-3
  http://crantastic.org/packages/genpathmox

  genpathmox provides a very interesting solution for handling
  segmentation variables in complex statistical methodology. It
  contains en extended version of the PATHMOX algorithm in the context
  of partial least square path modeling (Sanchez, 2009) including the
  F-block test (to detect the responsible latent endogenous equations
  of the difference), the F-coefficient (to detect the path
  coefficients responsible of the difference) and the invariance test
  (to realize a comparison between the sub-models' latent variables).
  Furthermore, the package contains a generalized version of the
  PATHMOX algorithm to approach different methodologies: linear
  regression and least absolute regression models.

* hermite (1.0)
  Maintainer: David MoriÃ±a Soler
  Author(s): David MoriÃ±a (Centre for Research in Environmental Epidemiology,
             CREAL), Manuel Higueras (Universitat AutÃ²noma de
             Barcelona and Public Health England) and Pedro Puig
             (Universitat AutÃ²noma de Barcelona)
  License: GPL (>= 2)
  http://crantastic.org/packages/hermite

  Probability functions for the generalized Hermite distribution

* MfUSampler (0.9)
  Maintainer: Alireza S. Mahani
  Author(s): Alireza S. Mahani, Mansour T.A. Sharabiani
  License: GPL (>= 2)
  http://crantastic.org/packages/MfUSampler

  Convenience Functions for Multivariate MCMC Using Univariate Samplers,
  including Slice Sampler with Stepout and Shrinkage (Neal, 2003), and
  Adaptive Rejection Sampler (Gilks and Wild, 1992).

* myTAI (0.0.1)
  Maintainer: Hajk-Georg Drost
  Author(s): Hajk-Georg Drost
  License: GPL-3
  http://crantastic.org/packages/myTAI

  The present collection of functions can be used to perform
  phylotranscriptomics analyses to investigate phenomena within the
  field of Evolutionary Developmental Biology

* PrevMap (1.0)
  Maintainer: Emanuele Giorgi
  Author(s): Emanuele Giorgi, Peter J. Diggle
  License: GPL (>= 2)
  http://crantastic.org/packages/PrevMap

  The PrevMap package provides functions for both likelihood-based and
  Bayesian analysis of spatially referenced prevalence data. 'PrevMap'
  is also an extension of the 'geoR' package which should be installed
  first together with the 'maxLik', 'raster' and 'pdist' packages.

* qdm (0.1-0)
  Maintainer: Nora Umbach
  Author(s): Nora Umbach [aut, cre], Florian Wickelmaier [aut]
  License: GPL (>= 2)
  http://crantastic.org/packages/qdm

  This package provides different specifications of a Quadrilateral
  Dissimilarity Model which can be used to fit same-different
  judgments in order to get a predicted matrix that satisfies regular
  minimality [Colonius & Dzhafarov, 2006, Measurement and
  representations of sensations, Erlbaum]. From such a matrix,
  Fechnerian distances can be computed.

* RealVAMS (0.3-1)
  Maintainer: Andrew Karl
  Author(s): Andrew Karl, Jennifer Broatch, and Jennifer Green
  License: GPL-2
  http://crantastic.org/packages/RealVAMS

  The RealVAMs package fits a multivariate value-added model (VAM) (see
  Broatch and Lohr 2012) with normally distributed test scores and a
  binary outcome indicator. This material is based upon work supported
  by the National Science Foundation under grants DRL-1336027 and
  DRL-1336265.

* rqPen (1.0)
  Maintainer: Ben Sherwood
  Author(s): Ben Sherwood
  License: MIT + file LICENSE
  http://crantastic.org/packages/rqPen

  Performs penalized quantile regression for LASSO, SCAD and MCP
  functions. Provides a function that automatically generates lambdas
  and evaluates different models with cross validation or BIC,
  including a large p version of BIC.

* safi (1.0)
  Maintainer: Jana Fruth
  Author(s): Jana Fruth, Malte Jastrow
  License: GPL (>= 2)
  http://crantastic.org/packages/safi

  Design and sensitivity analysis for computer experiments with
  scalar-valued output and functional input, e.g. over time or space.
  The aim is to explore the behavior of the sensitivity over the
  functional domain.

* settings (0.1.1)
  Maintainer: Mark van der Loo
  Author(s): Mark van der Loo
  License: GPL-3
  http://crantastic.org/packages/settings

  Provides option settings management that goes beyond R's default
  'options' function. With this package, users can define their own
  option settings manager holding option names and default values.
  Settings can then be retrieved, altered and reset to defaults with
  ease. For R programmers and package developers it offers cloning and
  merging functionality which allows for conveniently defining global
  and local options, possibly in a multilevel options hierarchy. See
  the package vignette for some examples concerning functions, S4
  classes, and reference classes.

* smac (1.0)
  Maintainer: Chong Zhang
  Author(s): Chong Zhang, Guo Xian Yau, Yufeng Liu
  License: GPL-2
  http://crantastic.org/packages/smac

  This package provides a solution path for L1-penalized angle-based
  classification. Three loss functions are implemented in smac,
  including the deviance loss in logistic regression, the exponential
  loss in boosting, and the proximal support vector machine loss.

* smacpod (1.0.0)
  Maintainer: Joshua French
  Author(s): Joshua French
  License: GPL (>= 2)
  http://crantastic.org/packages/smacpod

  Various statistical methods for analyzing case-control point data. The
  methods available closely follow those in chapter 6 of Applied
  Spatial Statistics for Public Health Data by Waller and Gotway
  (2004).

* webutils (0.2)
  Maintainer: Jeroen Ooms
  Author(s): Jeroen Ooms
  License: MIT + file LICENSE
  http://crantastic.org/packages/webutils

  Utility functions for developing web applications. Includes parsers
  for application/x-www-form-urlencoded as well as multipart/form-data
  and examples of using the parser with either httpuv or rhttpd.

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

astsa (1.3), BatchExperiments (1.4), BatchJobs (1.5), BBmisc (1.8),
bdscale (1.1), bio3d (2.1-3), CountsEPPM (2.0), DALY (1.4.0), deSolve
(1.11), eHOF (1.5.4), energy (1.6.2), FAOSTAT (1.9), fAssets
(3011.83), fBasics (3011.87), fPortfolio (3011.81), GLDEX (2.0.0.1),
hglm (2.0-11), hht (2.1.1), isdals (2.0-4), kaps (1.0.2),
knitcitations (1.0.4), ldr (1.3.3), logconPH (1.3), mapplots (1.5),
MortalitySmooth (2.3.3), nullabor (0.3.0), pander (0.5.0), pander
(0.5.1), pitchRx (1.6), PopGenReport (2.1), PrivateLR (1.2-21), qtl
(1.34-16), qtl (1.34-17), rangeMapper (0.2-8), Rcmdr (2.1-4),
RcppArmadillo (0.4.500.0), rex (0.1.2), rgl (0.95.1157), rjags (3-14),
RMTstat (0.3), rNOMADS (2.0.4), robustreg (0.1-7), ropensecretsapi
(1.0.1), RQDA (0.2-7), seqinr (3.0-9), seqMeta (1.5), sirt (1.0-3),
SKAT (1.0), sn (1.1-1), sqldf (0.4-9), statar (0.1.2), surveillance
(1.8-1), Taxonstand (1.5), texreg (1.34), timeDate (3011.99),
timeSeries (3011.98), TSclust (1.2.2), vcdExtra (0.6-3), vegdata
(0.6-7)

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