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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