CRAN (and crantastic) updates this week
New packages
------------
* adwave (1.0)
Maintainer: Murray Cox
Author(s): Jean Sanderson
License: GPL (>= 2)
http://crantastic.org/packages/adwave
Implements wavelet-based approaches for describing population
admixture. Principal Components Analysis (PCA) is used to define the
population structure and produce a localized admixture signal for
each individual. Wavelet summaries of the PCA output describe
variation present in the data and can be related to population-level
demographic processes. For more details, see accompanying paper.
* bdscale (1.0)
Maintainer: Dave Mills
Author(s): Dave Mills <dave.a.mills at gmail.com>
License: GPL-2
http://crantastic.org/packages/bdscale
Provides a continuous date scale, omitting weekends and holidays
* BNSP (1.0.0)
Maintainer: Georgios Papageorgiou
Author(s): Georgios Papageorgiou
License: GPL (>= 2)
http://crantastic.org/packages/BNSP
Markov chain Monte Carlo algorithms for non- and semi-parametric
models
* CEC (0.9.1)
Maintainer: Konrad Kamieniecki
Author(s): Konrad Kamieniecki
License: GPL-3
http://crantastic.org/packages/CEC
Cross-Entropy Clustering (CEC) divides the data into Gaussian type
clusters. It performs the automatic reduction of unnecessary
clusters, while at the same time allows the simultaneous use of
various type Gaussian mixture models.
* ENiRG (0.1)
Maintainer: Fernando Garcia Canovas
Author(s): Fernando Canovas, Chiara Magliozzi, Jose Antonio Palazon-Ferrando,
Frederico Mestre, Mercedes Gonzalez-Wanguemert
License: GPL (>= 2)
http://crantastic.org/packages/ENiRG
The package allows to perform the Ecological Niche Factor Analysis,
calculate habitat suitability maps and classify the habitat in
suitability classes. Computations are executed in a throw-away GRASS
environment from R in order to be able to perform analysis with
large data sets.
* HiDimMaxStable (0.1)
Maintainer: Alexis Bienvenue
Author(s): Alexis Bienven??e [aut, cre], Christian Robert [aut]
License: GPL (>= 2)
http://crantastic.org/packages/HiDimMaxStable
Inference of high dimensional max-stable distributions, from the paper
"Likelihood based inference for high-dimensional extreme value
distributions", by A. Bienven??e and C. Robert, arXiv:1403.0065
[stat.AP].
* HierO (0.1)
Maintainer: Kari Tokola
Author(s): Kari Tokola
License: GPL-2
http://crantastic.org/packages/HierO
HierO is a graphical user interface (GUI) tool for calculating optimal
statistical power and sample size for hierarchical data structure.
HierO constructs a user defined sample size optimization problem to
GAMS (General Algebraic Modeling System)form and uses Rneos package
to send the problem to NEOS server for solving.
* ibelief (1.0)
Maintainer: Kuang Zhou
Author(s): Kuang Zhou <kzhoumath at 163.com>; Arnaud Martin
<arnaud.martin at univ-rennes1.fr>
License: GPL (>= 2)
http://crantastic.org/packages/ibelief
This package contains several basic functions to implement belief
functions.
* MareyMap (1.2)
Maintainer: Aurelie Siberchicot
Author(s): Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent
Gueguen
and Gabriel Marais
License: GPL (>= 2)
http://crantastic.org/packages/MareyMap
A package to graphically estimate local recombination rates across a
genome using marey maps.
* mfblock (1.0)
Maintainer: Marc Fortier
Author(s): Marc Fortier
License: GPL-3
http://crantastic.org/packages/mfblock
Implementation of the simulated method of moments (smm) of Oh and
Patton for copula-based multivariate models
* msBP (1.0)
Maintainer: Antonio Canale
Author(s): Antonio Canale
License: GPL-2
http://crantastic.org/packages/msBP
Performs Bayesian nonparametric multiscale density estimation and
multiscale testing of group differences with multiscale Bernstein
polynomials (msBP) mixtures as in Canale and Dunson (2014).
* mvprpb (1.0.4)
Maintainer: Noboru Nomura
Author(s): Noboru Nomura
License: BSD_3_clause + file LICENSE
http://crantastic.org/packages/mvprpb
Computes orthant probabilities multivariate normal distribution.
* NB (0.9)
Maintainer: Tin-Yu Hui
Author(s): Tin-Yu Hui @ Imperial College London
License: GPL (>= 2)
http://crantastic.org/packages/NB
Estimate the effective population size of a closed population using
genetic data collected from two or more data points.
* PerFit (1.2)
Maintainer: Jorge N. Tendeiro
Author(s): Jorge N. Tendeiro
License: GPL (>= 2)
http://crantastic.org/packages/PerFit
PerFit contains several person fit indices that allow assessing
whether individual response patterns to tests or questionnaires are
(im)plausible given the other respondents in the sample or a
specified Item Response Theory model.
* PLordprob (1.0)
Maintainer: Euloge Clovis Kenne Pagui
Author(s): Euloge Clovis Kenne Pagui [aut,cre], Antonio Canale [aut], Alan
Genz
[ctb], Adelchi Azzalini [ctb]
License: GPL-2
http://crantastic.org/packages/PLordprob
Multivariate ordered probit model, i.e. the extension of the scalar
ordered probit model where the observed variables have dimension
greater than one. Estimation of the parameters is done via
maximization of the pairwise likelihood, a special case of the
composite likehood obtained as product of bivariate marginal
distributions. The package uses the Fortran 77 subroutine SADMVN by
Alan Genz, with minor adaptations made by Adelchi Azzalini in his
"mvnormt" package for evaluating the two-dimensional
Gaussian
integrals involved in the pairwise log-likelihood. Optimization of
the latter objective function is performed via quasi-Newton
box-constrained optimization algorithm, as implemented in nlminb.
* qicharts (0.1.0)
Maintainer: Jacob Anhoej
Author(s): Jacob Anhoej [aut, cre]
License: GPL-3
http://crantastic.org/packages/qicharts
Functions for making run charts and basic Shewhart control charts for
measure and count data. The main function, qic, creates run and
control charts and has a simple interface with a rich set of options
to control data analysis and plotting, including options for
automatic data aggregation by subgroups, easy analysis of
before-and-after data, exclusion of one or more data points from
analysis, and splitting charts into sequential time periods. Missing
values and empty subgroups are handled gracefully.
* RAdwords (0.1)
Maintainer: Johannes Burkhardt
Author(s): Johannes Burkhardt <johannes.burkhardt at gmail.com>,
Matthias Bannert
<matthias.bannert at gmail.com>
License: GPL (>= 2) | MIT + file LICENSE
http://crantastic.org/packages/RAdwords
The aim of RAdwords is loading Adwords data into R. Therefore the
package implements three main features. First, the package provides
an authentication process for R with the Adwords API via OAUTH2.
Second, the package offers an interface to apply the Adwords query
language in R and query the Adwords API with ad-hoc reports. Third,
the received data are transformed into suitable data formats for
further data processing and data analysis.
* RSQLServer (0.1.1)
Maintainer: Imanuel Costigan
Author(s): Imanuel Costigan [aut, cre], The jTDS Project [aut] (for MSSQL
Server
driver), Simon Urbanek [ctb], The Legion Of The Bouncy
Castle [cph, ctb]
License: GPL-2
http://crantastic.org/packages/RSQLServer
RSQLServer wraps the jTDS Project's JDBC 3.0 SQL Server driver and
extends the RJDBC classes and DBI methods. It defines a
SQLServerDriver, SQLServerConnection & SQLServerRsult S4 classes as
extensions of the RJDBC equivalent classes. Most of the DBI methods
will simply be calls to methods defined by RJDBC classes. However,
the dbConnect and some of the dbGetInfo methods are specific to SQL
Server. The jTDS drivers do extend to Sybase SQL Server, but
currently, only Microsoft SQL Server is supported by this package.
* saps (1.0.0)
Maintainer: Daniel Schmolze
Author(s): Daniel Schmolze [aut, cre], Andrew Beck [aut], Benjamin Haibe-Kains
[aut]
License: MIT + file LICENSE
http://crantastic.org/packages/saps
Functions implementing the Significance Analysis of Prognostic
Signatures method (SAPS). SAPS provides a robust method for
identifying biologically significant gene sets associated with
patient survival. Three basic statistics are computed. First,
patients are clustered into two survival groups based on
differential expression of a candidate gene set. P_pure is
calculated as the probability of no survival difference between the
two groups. Next, the same procedure is applied to randomly
generated gene sets, and P_random is calculated as the proportion
achieving a P_pure as significant as the candidate gene set.
Finally, a pre-ranked Gene Set Enrichment Analysis (GSEA) is
performed by ranking all genes by concordance index, and P_enrich is
computed to indicate the degree to which the candidate gene set is
enriched for genes with univariate prognostic significance. A
SAPS_score is calculated to summarize the three statistics, and
optionally a Q-value is computed to estimate the significance of the
SAPS_score by calculating SAPS_scores for random gene sets.
* snipEM (1.0)
Maintainer: Alessio Farcomeni
Author(s): Alessio Farcomeni, Andy Leung
License: GPL (>= 2)
http://crantastic.org/packages/snipEM
Snipping methods
* sptm (14.10-8)
Maintainer: Youyi Fong
Author(s): Youyi Fong <yfong at fhcrc.org>, Krisztian Sebestyen
<ksebestyen at gmail.com>
License: GPL (>= 2)
http://crantastic.org/packages/sptm
Semiparametric transformation model, calibration weights
* TEEReg (1.0)
Maintainer: Wei Jiang
Author(s): Wei Jiang and Matthew S. Mayo
License: GPL (>= 2)
http://crantastic.org/packages/TEEReg
For fitting multiple linear regressions, the ordinary least squares
approach is sensitive to outliers and/or violations of model
assumptions. The trimmed elemental estimators are more robust to
such situations. This package contains functions for computing the
trimmed elemental estimates, as well as for creating the
bias-corrected and accelerated bootstrap confidence intervals in the
context of trimmed elemental regressions.
* vegan3d (0.65-0)
Maintainer: Jari Oksanen
Author(s): Jari Oksanen [aut, cre], Roeland Kindt [aut], Gavin L. Simpson
[aut]
License: GPL-2
http://crantastic.org/packages/vegan3d
Static and dynamic 3D plots to be used with ordination results and in
diversity analysis, especially with the vegan package
Updated packages
----------------
Benchmarking (0.24), cclust (0.6-19), checkpoint (0.3.3), devtools
(1.6.1), diseasemapping (1.1.0), frailtypack (2.7.1), fscaret
(0.8.6.3), G2Sd (2.1.2), geospt (1.0-0), GISTools (0.7-4),
GlobalOptions (0.0.2), grofit (1.1.1-1), lfe (1.7-1404), lfe
(1.7-1401), minqa (1.2.4), mirt (1.6.1), mnormpow (0.1.1), MonetDB.R
(0.9.5), moult (1.4), mpcv (1.1), MplusAutomation (0.6-3), mpt
(0.5-0), MTurkR (0.5.51), nlme (3.1-118), ParamHelpers (1.4), phangorn
(1.99-9), pingr (1.1.0), PivotalR (0.1.17.8), PowerTOST (1.2-02),
protr (0.4-1), pvclust (1.3-0), qcc (2.6), quantmod (0.4-2), R.matlab
(3.1.1), R.utils (1.34.0), rcdk (3.3.1), Rcmdr (2.1-3), Rdsm (2.1.1),
repra (0.4.2), RMark (2.1.9), robustreg (0.1-5), sft (2.0-7),
stringdist (0.8.1), subselect (0.12-4), VecStatGraphs3D (1.6), VLMC
(1.4-0), YourCast (1.6.2), ZIM (1.0.2)
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