[R] CRAN (and crantastic) updates this week

[Crantastic]

CRAN (and crantastic) updates this week

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

* bisectr (0.0.2)
  Maintainer: Winston Chang
  Author(s): Winston Chang <winston at stdout.org>
  License: GPL-2
  http://crantastic.org/packages/bisectr

  Tools to find bad commits with git bisect

* CUMP (1.0)
  Maintainer: Xuan Liu
  Author(s): Xuan Liu <liuxuan at bu.edu> and Qiong Yang <qyang at bu.edu>
  License: GPL (>= 2)
  http://crantastic.org/packages/CUMP

  Combining Univariate Association Test Results of Multiple Phenotypes
  for Detecting Pleiotropy

* cumplyr (0.1-1)
  Maintainer: John Myles White
  Author(s): John Myles White
  License: MIT
  http://crantastic.org/packages/cumplyr

  Extends ddply to allow calculation of cumulative quantities.

* dma (1.1)
  Maintainer: Tyler H. McCormick
  Author(s): Tyler H. McCormick, Adrian Raftery, David Madigan
  License: GPL-2
  http://crantastic.org/packages/dma

  Dynamic model averaging for binary and continuous outcomes.

* fanc (0.18)
  Maintainer: Kei Hirose
  Author(s): Kei Hirose, Michio Yamamoto
  License: GPL (>= 2)
  http://crantastic.org/packages/fanc

  This package computes the penalized maximum likelihood estimates of
  factor loadings and unique variances for various tuning parameters. 
  The pathwise coordinate descent along with EM algorithm is used.

* fishmove (0.0-1)
  Maintainer: Johannes Radinger
  Author(s): Johannes Radinger
  License: GPL (>= 2)
  http://crantastic.org/packages/fishmove

  Functions to predict fish movement parameters based on multiple
  regression and plotting leptokurtic fish dispersal kernels

* googlePublicData (0.12.05)
  Maintainer: George Vega Yon
  Author(s): George Vega Yon
  License: GPL (>= 3)
  http://crantastic.org/packages/googlePublicData

  package provides a collection of functions to set up Google Public
  Data Explorer data visualization tool with your own data, building
  automaticaly the corresponding DSPL (XML) metadata file jointly with
  the CSV files. All zipped up and ready to be published at Public
  Data Explorer.

* gsmaRt (1.0)
  Maintainer: Stephan Artmann
  Author(s): Stephan Artmann, Mathias Fuchs
  License: GPL
  http://crantastic.org/packages/gsmaRt

  combined miRNA- and mRNA-testing

* HIest (1.0)
  Maintainer: Unknown
  Author(s): Ben Fitzpatrick
  License: GPL (>= 3)
  http://crantastic.org/packages/HIest

  Uses likelihood to estimate ancestry and heterozygosity. Evaluates
  simple hybrid classifications (parentals, F1, F2, backcrosses).
  Estimates genomic clines.

* igraphdata (0.1)
  Maintainer: Gabor Csardi
  Author(s): Gabor Csardi <csardi.gabor at gmail.com>
  License: GPL (>= 2) + file LICENSE
  http://crantastic.org/packages/igraphdata

  A small collection of various network data sets, to use with the
  igraph package. They also work with the igraph0 package.

* irtrees (0.1.0)
  Maintainer: Ivailo Partchev
  Author(s): Ivailo Partchev and Paul De Boeck
  License: GPL (>= 2)
  http://crantastic.org/packages/irtrees

  Helper functions and example data sets accompanying De Boeck, P. and
  Partchev, I. (2012) IRTrees: Tree-Based Item Response Models of the
  GLMM Family, Journal of Statistical Software - Code Snippets, 48(1),
  1-28.

* lava (1.0-5)
  Maintainer: Klaus. K. Holst
  Author(s): Klaus K. Holst
  License: GPL-3
  http://crantastic.org/packages/lava

  Estimation and simulation of latent variable models

* lava.tobit (0.4-6)
  Maintainer: Klaus. K. Holst
  Author(s): Klaus K. Holst
  License: GPL-3
  http://crantastic.org/packages/lava-tobit

  lava plugin allowing combinations of left and right censored and
  binary outcomes

* LeafAngle (1.1)
  Maintainer: Unknown
  Author(s): Remko Duursma
  License: GPL
  http://crantastic.org/packages/LeafAngle

  A leaf angle distribution is a special distribution that is defined
  between 0 and 90 degrees, and a number of distributions are used to
  characterize the leaf angle distribution in real plant canopies.
  This package includes methods to fit distributions to data,
  visualize the fit, and compare fits of nine different distributions.

* makeProject (1.0)
  Maintainer: Noah Silverman
  Author(s): Noah Silverman
  License: GPL-3
  http://crantastic.org/packages/makeProject

  This package creates an empty framework of files and directories for
  the "Load, Clean, Func, Do" structure described by Josh Reich.

* mcmcse (0.1)
  Maintainer: James M. Flegal
  Author(s): James M. Flegal <jflegal at ucr.edu>
  License: GPL
  http://crantastic.org/packages/mcmcse

  Tools for calculating Monte Carlo standard errors (MCSE) in Markov
  chain Monte Carlo (MCMC) settings.  This package considers standard
  errors for expectation and quantile estimators.

* MetaDE (1.0)
  Maintainer: Jia Li
  Author(s): Jia Li and Xingbin Wang
  License: GPL-2
  http://crantastic.org/packages/MetaDE

  A collection of functions for conducting genomic meta-analysis in R.

* mets (0.1-8)
  Maintainer: Klaus. K. Holst
  Author(s): Klaus K. Holst and Thomas Scheike
  License: GPL (>= 2)
  http://crantastic.org/packages/mets

  Implementation of various statistical models for multivariate event
  history data. Including multivariate cumulative incidence models,
  and bivariate random effects probit models (Liability models)

* MultiOrd (1.0)
  Maintainer: Anup Amatya
  Author(s): Anup Amatya and Hakan Demirtas
  License: GPL-2
  http://crantastic.org/packages/MultiOrd

  A method for multivariate ordinal data generation given marginal
  distributions and correlation based on the methodology proposed by
  Demirtas (2006).

* PEIP (1.2)
  Maintainer: Jonathan M. Lees
  Author(s): Jonathan M. Lees
  License: GPL
  http://crantastic.org/packages/PEIP

  Several Functions for Aster Book on Inverse Theory. These functiuons
  are translations of MATLAB code developed by the authors to
  illustrate the concepts of Inverse theory as applied to geophysics.

* pgnorm (1.1)
  Maintainer: Unknown
  Author(s): Steve Kalke
  License: GPL (>= 2)
  http://crantastic.org/packages/pgnorm

  Evaluation of the pdf and the cdf of the univariate p-generalized
  normal distribution. Sampling from the p-generalized normal
  distribution using either the p-generalized polar method, the
  p-generalized rejecting polar method, the Monty Python method, the
  Ziggurat method or the method of Nardon and Pianca. The package also
  includes routines for the simulation of the bivariate, p-generalized
  uniform distribution on the p-generalized unit circle and the
  simulation of the corresponding angular distribution.

* RcmdrPlugin.SCDA (0.0)
  Maintainer: Isis Bulte
  Author(s): Isis Bulte and Patrick Onghena
  License: GPL (>= 2)
  http://crantastic.org/packages/RcmdrPlugin-SCDA

  This package provides a GUI for the SCVA, SCRT and SCMA packages. It
  is written as an Rcmdr plugin.

* ri (0.9)
  Maintainer: Cyrus Samii
  Author(s): Peter M. Aronow <peter.aronow at yale.edu> and Cyrus Samii
             <cds2083 at nyu.edu>
  License: GPL (>= 2)
  http://crantastic.org/packages/ri

  This package provides a set of tools for conducting exact or
  approximate randomization-based inference for experiments of
  arbitrary design. The primary functionality of the package is in the
  generation, manipulation and use of permutation matrices implied by
  given experimental designs. Among other features, the package
  facilitates estimation of average treatment effects, constant
  effects variance estimation, randomization inference for
  significance testing against sharp null hypotheses and visualization
  of data and results.

* semTools (0.1-0)
  Maintainer: Sunthud Pornprasertmanit
  Author(s): Sunthud Pornprasertmanit <psunthud at ku.edu>, Patrick Miller
             <patr1ckm at ku.edu>, Alex Schoemann <schoemann at ku.edu>,
             Yves Rosseel <Yves.Rosseel at UGent.be>
  License: GPL (>= 2)
  http://crantastic.org/packages/semTools

  This package provide useful tools for structural equation modeling
  analysis.

* simsem (0.2-0)
  Maintainer: Sunthud Pornprasertmanit
  Author(s): Sunthud Pornprasertmanit <psunthud at ku.edu>, Patrick Miller
             <patr1ckm at ku.edu>, Alexander Schoemann <schoemann at ku.edu>
  License: GPL (>= 2)
  http://crantastic.org/packages/simsem

  This package can be used to generate data using the structural
  equation modeling framework. This package is tailored to use those
  simulated data for various purposes, such as model fit evaluation,
  power analysis, or missing data handling and planning.

* simSummary (0.1.0)
  Maintainer: Gregor Gorjanc
  Author(s): Gregor Gorjanc
  License: GPL (>= 2)
  http://crantastic.org/packages/simSummary

  simSummary is a small utility package which eases the process of
  summarizing simulation results. Simulations often produce
  intermediate results - some focal statistics that need to be
  summarized over several scenarios and many replications. This step
  is in principle easy, but tedious. The package simSummary fills this
  niche by providing a generic way of summarizing the focal statistics
  of simulations. The useR must provide properly structured input,
  holding focal statistics, and then the summary step can be performed
  with one line of code, calling the simSummary function.

* spartan (1.0)
  Maintainer: Kieran Alden
  Author(s): Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique
             Veiga-Fernandes, Mark Coles
  License: GPL-2
  http://crantastic.org/packages/spartan

  Computer simulations are becoming a popular technique to use in
  attempts to further our understanding of complex systems. This
  package provides code for four techniques described in available
  literature which aid the analysis of simulation results, at both
  single and multiple timepoints in the simulation run. The first
  technique addresses aleatory uncertainty in the system caused
  through inherent stochasticity, and determines the number of
  replicate runs necessary to generate a representative result. The
  second examines how robust asimulation is to parameter perturbation,
  through the use of a one-at-a-time parameter analysis technique.
  Thirdly, a latin hypercube based sensitivity analysis technique is
  included which can elucidate non-linear effects between parameters
  and indicate implications of epistemic uncertainty with reference to
  the system being modelled. Finally, a further sensitivity analysis
  technique, the extended Fourier Amplitude Sampling Test (eFAST) has
  been included to partition the variance in simulation results
  between input parameters, to determine the parameters which have a
  significant effect on simulation behaviour.

* SPSL (0.1-5)
  Maintainer: Pavel V. Moskalev
  Author(s): Pavel V. Moskalev <moskalefff at gmail.com>
  License: GPL-3
  http://crantastic.org/packages/SPSL

  SPSL package provides functionality for labeling of percolation
  cluster on 2D & 3D square lattice with various lattice size,
  relative fraction of accessible sites (occupation probability), iso-
  & anisotropy, von Neumann & Moore d-neighborhood

* tm.plugin.factiva (1.0)
  Maintainer: Milan Bouchet-Valat
  Author(s): Milan Bouchet-Valat <nalimilan at club.fr>
  License: GPL (>= 2)
  http://crantastic.org/packages/tm-plugin-factiva

  This package provides a tm Source to create corpora from articles
  exported from the Dow Jones Factiva content provider as XML files.


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

adaptMCMC (1.0.3), bayesclust (3.1), bayesm (2.2-5), biwavelet (0.11),
blm (2012.2.1), boss (1.1), BradleyTerry2 (1.0-0), CDVine (1.1-6),
cloudRmpi (1.2), coxme (2.2-3), cvTools (0.3.2), dbstats (1.0.2),
dcmle (0.2-1), DescribeDisplay (0.2.3), doBy (4.5-3), extracat
(1.5-0), fanc (0.18), fanovaGraph (1.2), fastICA (1.1-15), fda
(2.2.8), FrF2 (1.4-1), gdsfmt (0.9.9), gmp (0.5-2), HAC (0.2-2),
heplots (0.9-12), HTMLUtils (0.1.5), ImageMetrics (0.5), IPMpack
(1.1), IsotopeR (0.4.2), lifecontingencies (0.9.3), M3 (0.3), maps
(2.2-6), MatrixEQTL (1.6.0), mefa4 (0.2-7), meta (2.1-0),
MissingDataGUI (0.1-3), msgps (1.3), multitaper (1.0-1), muma (1.1),
OrgMassSpecR (0.3-12), pcaPP (1.9-47), phenology (3.31), planar
(1.2.1), plotrix (3.4-1), pomp (0.42-4), prefmod (0.8-31), primer
(1.0), psychomix (1.0-0), psychotools (0.1-3), QUIC (1.0), QUIC (1.1),
RcmdrPlugin.KMggplot2 (0.1-0), RcmdrPlugin.survival (1.0-1), RcppSMC
(0.1.1), relsurv (2.0-2), rfishbase (0.0-9), Rmpfr (0.4-7),
robCompositions (1.6.0), robustbase (0.9-1), rpartOrdinal (2.0.4),
RProtoBuf (0.2.4), rrBLUP (3.8), rredis (1.6.6), RSEIS (3.0-6),
sampSurf (0.6-4), SDMTools (1.1-12), secr (2.3.2), SemiParBIVProbit
(3.2-1), semPLS (1.0-8), spatstat (1.27-0), tclust (1.1-02), timsac
(1.2.7), tm.plugin.mail (0.0-5), WMTregions (3.2.5)



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