[R] CRAN (and crantastic) updates this week

Crantastic cranatic at gmail.com
Mon Sep 29 00:40:06 CEST 2014

CRAN (and crantastic) updates this week

New packages

* ADDT (1.0)
  Maintainer: Yili Hong
  Author(s): Yili Hong, Yimeng Xie, and Caleb King
  License: GPL-2

  Accelerated destructive degradation tests (ADDT) are often used to
  collect necessary data for assessing the long-term properties of
  polymeric materials. Based on the collected data, a thermal index
  (TI) is estimated. The TI can be useful for material rating and
  comparison. This package performs the least squares (LS) and maximum
  likelihood (ML) procedures for estimating TI for polymeric
  materials. The LS approach is a two-step approach that is currently
  used in industrial standards, while the ML procedure is widely used
  in the statistical literature. The ML approach allows one to do
  statistical inference such as quantifying uncertainties in
  estimation, hypothesis testing, and predictions. Two publicly
  available datasets are provided to allow users to experiment and
  practice with the functions.

* ASMap (0.3)
  Maintainer: Julian Taylor
  Author(s): Julian Taylor <julian.taylor at adelaide.edu.au>, David Butler
             <david.butler at daff.qld.gov.au>.
  License: GPL (>= 2)

  Functions for (A)ccurate and (S)peedy linkage map construction,
  manipulation and diagnosis of double haploid, backcross and and RIL
  R/qtl objects. This includes extremely fast linkage map clustering
  and optimal marker ordering using MSTmap (see Wu et al.,2008).

* causaleffect (1.0)
  Maintainer: Santtu Tikka
  Author(s): Santtu Tikka
  License: GPL-2

  An implementation of the complete identification algorithm constructed
  by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of
  joint interventional distributions in causal models, which contain
  unobserved variables and induce directed acyclic graphs.

* Compind (1.0)
  Maintainer: Francesco Vidoli
  Author(s): Francesco Vidoli, Elisa Fusco
  License: GPL-3

  Compind package contains several functions to enhance approaches to
  the Composite Indicators
  https://composite-indicators.jrc.ec.europa.eu/) methods, focusing,
  in particular, on the normalisation and weighting-aggregation steps.

* crayon (1.0.0)
  Maintainer: "Gabor Csardi"
  Author(s): "Gabor Csardi" [aut, cre]
  License: MIT + file LICENSE

  Crayon adds support for colored terminal output on terminals that
  support ANSI color and highlight codes. ANSI color support is
  automatically detected. Colors and highlighting can be combined and
  nested. New styles can also be created easily. This package was
  inspired by the chalk JavaScript project.

* deming (1.0-1)
  Maintainer: Terry Therneau
  Author(s): Terry Therneau
  License: LGPL (>= 2)

  Generalized Deming regression, Theil-Sen regression and
  Passing-Bablock regression functions.

* documair (0.6-0)
  Maintainer: Jean-Baptiste Denis
  Author(s): Jean-Baptiste Denis <Jean-Baptiste.Denis at jouy.inra.fr>, Regis Pouillot
             <RPouillot at yahoo.fr>, Kien Kieu <Kien.Kieu at jouy.inra.fr>
  License: GPL (>= 2.15)

  Production of R packages from tagged comments introduced within the
  code  and a minimum of additional documentation files.

* GenWin (0.1)
  Maintainer: Timothy M. Beissinger
  Author(s): Timothy M. Beissinger <beissinger at ucdavis.edu>
  License: MIT + file LICENSE

  Defines window or bin boundaries for the analysis of genomic data.
  Boundaries are based on the inflection points of a cubic smoothing
  spline fitted to the raw data. Along with defining boundaries, a
  technique to evaluate results obtained from unequally-sized windows
  is provided. Applications are particularly pertinent for, though not
  limited to, genome scans for selection based on variability between
  populations (e.g. using Wright's fixations index, Fst, which
  measures variability in subpopulations relative to the total

* ivprobit (1.0)
  Maintainer: Zaghdoudi Taha
  Author(s): Zaghdoudi Taha
  License: Artistic-2.0

  ivprobit fit an Instrumental variables probit model using the
  generalized least squares estimator

* kofnGA (1.0)
  Maintainer: Mark A. Wolters
  Author(s): Mark A. Wolters
  License: GPL-2

  Function kofnGA uses a genetic algorithm to choose a subset of a 
  fixed size k from the integers 1:n, such that a user-supplied
  objective function  is minimized at that subset.  The selection step
  is done by tournament selection  based on ranks, and elitism may be
  used to retain a portion of the best solutions  from one generation
  to the next.

* MetFns (1.0)
  Maintainer: Kristina Veljkovic
  Author(s): Kristina Veljkovic
  License: GPL-2 | GPL-3

  Functions for selection of visual meteor data, calculations of
  Zenithal Hourly Rate (ZHR) and population index, graphics of ZHR and
  magnitude distribution

* mpath (0.1-15)
  Maintainer: Zhu Wang
  Author(s): Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian
             Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian
             Narasimhan, Gil Chu and Patrick Breheny
  License: GPL-2

  Algorithms for fitting model-based penalized coefficient paths.
  Currently the models include penalized Poisson, negative binomial,
  zero-inflated Poisson and zero-inflated negative binomial regression
  models. The penalties include least absolute shrinkage and selection
  operator (LASSO), smoothly clipped absolute deviation (SCAD) and
  minimax concave penalty (MCP), and each possibly combining with L_2

* NHMM (3.3)
  Maintainer: Tracy Holsclaw
  Author(s): Tracy Holsclaw
  License: GPL (>= 3)

  Bayesian NHMM modeling for multiple time series. The emission
  distribution can be mixtures of Gammas, Poissons, Normals and zero
  inflation is possible.

* ordinalgmifs (1.0.0)
  Maintainer: Kellie J. Archer
  Author(s): Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne,
             Amanda Gentry
  License: GPL (>= 2)

  This package provides a function for fitting cumulative link, adjacent
  category, forward and backward continuation ratio, and stereotype
  ordinal response models when the number of parameters exceeds the
  sample size, using the the generalized monotone incremental forward
  stagewise method.

* pingr (1.0.0)
  Maintainer: "Gabor Csardi"
  Author(s): "Gabor Csardi" [aut, cre]
  License: MIT + file LICENSE

  Check if a remote computer is up. It can either just call the system
  ping command, or check a specified TCP port.

* RJSDMX (1.1)
  Maintainer: Attilio Mattiocco
  Author(s): Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
  License: EUPL

  This package provides functions that can be used to retrieve  			 data
  and metadata from SDMX compliant data providers.

* SimplicialCubature (1.0)
  Maintainer: John P. Nolan
  Author(s): John P. Nolan, with parts based on code by Alan Genz
  License: GPL (>= 2)

  This package provides methods to integrate functions over
  m-dimensional simplices  in n-dimensional Euclidean space.  There
  are exact methods for polynomials and adaptive methods for
  integrating an arbitrary function.

* SPREDA (1.0)
  Maintainer: Yili Hong
  Author(s): Yili Hong, Yimeng Xie, and Zhibing Xu
  License: GPL-2

  The Statistical Package for REliability Data Analysis (SPREDA)
  implements recently-developed statistical methods for the analysis
  of reliability data. Modern technological developments, such as
  sensors and smart chips, allow us to dynamically track
  product/system usage as well as other environmental variables, such
  as temperature and humidity. We refer to these variables as dynamic
  covariates. The package contains functions for the analysis of
  time-to-event data with dynamic covariates and degradation data with
  dynamic covariates. The package also contains functions that can be
  used for analyzing time-to-event data with right censoring, and with
  left truncation and right censoring. Financial support from NSF and
  DuPont are acknowledged.

* virtualspecies (1.0)
  Maintainer: Boris Leroy
  Author(s): Boris Leroy with help from C. N. Meynard, C. Bellard & F. Courchamp
  License: GPL (>= 2.0)

  Provides a framework for generating virtual species distributions,  a
  procedure increasingly used in ecology to improve species
  distribution models. This package integrates the existing
  methodological approaches with the  objective of generating virtual
  species distributions with increased  ecological realism.

Updated packages

agrmt (1.35), alr4 (1.0.5), aplpack (1.3.0), BatchExperiments (1.3),
BatchJobs (1.4), BDgraph (2.12), BDgraph (2.11), betareg (3.0-5),
BrailleR (0.11), cape (1.3), copBasic (1.6.0), datacheck (1.0.4), DBI
(0.3.1), Delaporte (2.2-1), devtools (1.6), diseasemapping (1.0.1),
eHOF (1.5), exactci (1.3-0), fAssets (3011.82), flexmix (2.3-12),
flexsurv (0.5), forecast (5.6), GENLIB (1.0.1), GSE (3.1), Guerry
(1.6-1), hglm (2.0-9), hht (2.1.0), HiddenMarkov (1.8-1), IBrokers
(0.9-12), indicspecies (1.7.3), ivivc (0.2.1), lessR (3.1.1),
lmSupport (2.9.1), lsmeans (2.12), maps (2.3-9), MAT (2.0), mmand
(1.1.0), Morpho (2.1), mpath (0.1-15), mrds (2.1.10), oc (0.95),
oro.pet (0.2.3), polysat (1.3-3), proxy (0.4-13), pvsR (0.3),
qdapRegex (0.1.2), RandomFields (3.0.42), Rcmdr (2.1-2), RcppArmadillo
(0.4.450.1.0), readBrukerFlexData (1.8), rentrez (0.3), rentrez
(0.3.1), rpf (0.39), RSurvey (0.8-2), RVAideMemoire (0.9-40), secr
(2.9.0), SemiPar (1.0-4.1), snpEnrichment (1.5-0), testthat (0.9),
TreePar (3.1), trip (1.1-18), trustOptim (, VennDiagram
(1.6.9), wnominate (0.99)

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