[R] CRAN (and crantastic) updates this week
Crantastic
cranatic at gmail.com
Sun Oct 26 23:40:05 CET 2014
CRAN (and crantastic) updates this week
New packages
------------
* BayesMixSurv (0.9)
Maintainer: Alireza S. Mahani
Author(s): Alireza S. Mahani, Mansour T.A. Sharabiani
License: GPL (>= 2)
http://crantastic.org/packages/BayesMixSurv
Bayesian Mixture Survival Models using Additive Mixture-of-Weibull
Hazards, with Lasso Shrinkage and Stratification
* cdcsis (1.0)
Maintainer: Canhong Wen
Author(s): Canhong Wen, Wenliang Pan, Mian Huang, and Xueqin Wang
License: GPL (>= 2)
http://crantastic.org/packages/cdcsis
Gives conditional distance correlation and performs the conditional
distance correlation sure independence screening procedure for
ultrahigh dimensional data. The conditional distance correlation is
a novel conditional dependence measurement of two random variables
given a third variable. The conditional distance correlation sure
independence screening is used for screening variables in ultrahigh
dimensional setting.
* choroplethrMaps (1.0)
Maintainer: Ari Lamstein
Author(s): Ari Lamstein <arilamstein at gmail.com>
License: BSD_3_clause + file LICENSE
http://crantastic.org/packages/choroplethrMaps
Contains 3 maps. 1) US States 2) US Counties 3) Countries of the
world.
* commentr (0.1)
Maintainer: Erik Bulow
Author(s): Erik Bulow
License: GPL-2
http://crantastic.org/packages/commentr
Functions to produce nicely formatted comments to use in R-scripts (or
Latex/HTML/markdown etc). A comment with formatting is printed to
the console and can then be copied to a script.
* DetMCD (0.0.1)
Maintainer: Vakili Kaveh
Author(s): Vakili Kaveh [aut, cre], Mia Hubert [ths]
License: GPL (>= 2)
http://crantastic.org/packages/DetMCD
DetMCD is a new algorithm for robust and deterministic estimation of
location and scatter. The benefits of robust and deterministic
estimation are explained in Hubert, M., Rousseeuw, P.J. and
Verdonck, T. (2012),"A deterministic algorithm for robust location
and scatter", Journal of Computational and Graphical Statistics,
Volume 21, Number 3, Pages 618--637.
* FDGcopulas (1.0)
Maintainer: Gildas Mazo
Author(s): Gildas Mazo, Stephane Girard
License: GPL (>= 3)
http://crantastic.org/packages/FDGcopulas
FDG copulas are a class of copulas featuring an interesting balance
between flexibility and tractability. This package provides tools to
construct, calculate the pairwise dependence coefficients of,
simulate from, and fit FDG copulas. The acronym FDG stands for
'one-Factor with Durante Generators', as an FDG copula is a
one-factor copula -- that is, the variables are independent given a
latent factor -- whose linking copulas belong to the Durante class
of bivariate copulas (also referred to as exchangeable
Marshall-Olkin or semilinear copulas).
* glmvsd (1.0)
Maintainer: Yi Yang
Author(s): Ying Nan <nanx0006 at gmail.com>, Yi Yang <yiyang at umn.edu>, Yuhong Yang
<yyang at stat.umn.edu>
License: GPL-2
http://crantastic.org/packages/glmvsd
Variable selection deviation measures and instability tests for
high-dimensional model selection methods such as LASSO, SCAD and
MCP, etc., to decide whether the sparse patterns identified by those
methods are reliable.
* highD2pop (1.0)
Maintainer: Karl Gregory
Author(s): Karl Gregory
License: GPL (>= 2)
http://crantastic.org/packages/highD2pop
Performs the generalized component test from Gregory et al (2015), as
well as the tests from Chen and Qin (2010), Srivastava and Kubokawa
(2013), and Cai, Liu, and Xia (2014) for equality of two population
mean vectors when the length of the vectors exceeds the sample size.
* indicoio (0.3)
Maintainer: Madison May
Author(s): Alexander Gedranovich <gedranovich at gmail.com>
License: MIT + file LICENSE
http://crantastic.org/packages/indicoio
R-based client for Machine Learning APIs at http://indico.io. Provides
wrappers for following APIs: Positive/Negative Sentiment Analysis,
Political Sentiment Analysis, Image Feature Extraction, Facial
Emotion Recognition, Facial Feature Extraction, Language Detection
* JMdesign (1.1)
Maintainer: Shannon Holloway
Author(s): Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and
Joseph G. Ibrahim
License: GPL-2
http://crantastic.org/packages/JMdesign
Performs power calculations for joint modeling of longitudinal and
survival data with k-th order trajectories when the
variance-covariance matrix, Sigma_theta, is unknown.
* lmenssp (1.0)
Maintainer: Ozgur Asar
Author(s): Ozgur Asar, Peter J. Diggle
License: GPL (>= 2)
http://crantastic.org/packages/lmenssp
Fit, filter and smooth mixed models with non-stationary processes
* managelocalrepo (0.1.4)
Maintainer: Imanuel Costigan
Author(s): Imanuel Costigan <i.costigan at me.com>
License: GPL-2
http://crantastic.org/packages/managelocalrepo
This will allow easier management of a CRAN-style repository on local
networks (i.e. not on CRAN). This might be necessary where hosted
packages contain intellectual property owned by a corporation.
* matR (0.9)
Maintainer: Daniel Braithwaite
Author(s): Daniel Braithwaite [aut, cre], Kevin Keegan [aut], University of
Chicago [cph]
License: BSD_2_clause + file LICENSE
http://crantastic.org/packages/matR
An analysis platform for metagenomics combining specialized tools and
workflows, easy handling of the BIOM format, and transparent access
to MG-RAST resources. matR integrates easily with other R packages
and non-R software.
* openssl (0.1)
Maintainer: Jeroen Ooms
Author(s): Jeroen Ooms
License: MIT + file LICENSE
http://crantastic.org/packages/openssl
This package interfaces to the OpenSSL libraries libssl and libcrypto.
Currently it only implements bindings to the OpenSSL random number
generator in order to generate crypto secure random bytes in R.
* ore (1.0.1)
Maintainer: Jon Clayden
Author(s): Jon Clayden, based on Onigmo by K. Kosako and K. Takata
License: BSD_3_clause + file LICENCE
http://crantastic.org/packages/ore
Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers
first-class compiled regex objects, partial matching and
function-based substitutions, amongst other features.
* P2C2M (0.5)
Maintainer: Michael Gruenstaeudl
Author(s): Michael Gruenstaeudl, Noah Reid
License: GPL (>= 2)
http://crantastic.org/packages/P2C2M
P2C2M is an R package to conduct posterior predictive checks of
coalescent models using gene and species trees generated by BEAST
and *BEAST, respectively. The functionality of P2C2M can be extended
via two third-party R packages that are available from the author
websites only: genealogicalSorting
(http://www.genealogicalsorting.org) and phybase
(http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these
optional packages, installation of the Python libraries NumPy (>=
1.9.0) and DendroPy (= 3.12.0) is necessary.
* PANICr (0.0.0.2)
Maintainer: Steve Bronder
Author(s): Steve Bronder <sbronder at stevebronder.com>
License: GPL-3
http://crantastic.org/packages/PANICr
This package contains a methodology that makes use of the factor
structure of large dimensional panels to understand the nature of
nonstationarity inherent in data. This is referred to as PANIC -
Panel Analysis of Nonstationarity in Idiosyncratic and Common
Components. PANIC (2004) includes valid pooling methods that allow
panel tests to be constructed. PANIC (2004) can detect whether the
nonstationarity in a series is pervasive, or variable specific, or
both. PANIC (2010) includes two new tests on the idiosyncratic
component that estimates the pooled autoregressive coefficient and
sample moment, respectively. The PANIC model approximates the number
of factors based on Bai and Ng (2002)
* PHENIX (1.0)
Maintainer: A. J. Muñoz-Pajares
Author(s): R. Torices, A. J. Muñoz-Pajares
License: GPL (>= 2)
http://crantastic.org/packages/PHENIX
Provides functions to estimate the size-controlled phenotypic
integration index, a novel method by Torices & Méndez (2014) to
solve problems due to individual size when estimating integration
(namely, larger individuals have larger components, which will drive
a correlation between components only due to resource availability
that might overestimate the observed measures of integration). In
addition, the package also provides the classical estimation by
Wagner (1984) and a bootstrapping method to test the significance of
both integration indices.
* rsml (1.0)
Maintainer: Guillaume Lobet
Author(s): Guillaume Lobet
License: GPL-2
http://crantastic.org/packages/rsml
Read and analyse Root System Markup Language (RSML) files.
* rtkpp (0.8.3)
Maintainer: Serge Iovleff
Author(s): Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez
[ctb], Parmeet Bhatia [ctb]
License: GPL (>= 2) | LGPL (>= 2) | file LICENSE
http://crantastic.org/packages/rtkpp
STK++ (http://www.stkpp.org) is a collection of C++ classes for
statistics, clustering, linear algebra, arrays (with an Eigen-like
API), regression, dimension reduction, etc. The integration of the
library to R is using Rcpp. Some functionalities of the Clustering
project provided by the library are available in the R environment
as R functions. . The rtkpp package includes the header files from
the STK++ library (currently version 0.8.2). Thus users do not need
to install STK++ itself in order to use it. . STK++ is licensed
under the GNU LGPL version 2 or later. rtkpp (the stkpp integration
into R) is licensed under the GNU GPL version 2 or later.
* ruv (0.9.4)
Maintainer: Johann Gagnon-Bartsch
Author(s): Johann Gagnon-Bartsch <johann at stat.berkeley.edu>
License: GPL
http://crantastic.org/packages/ruv
The algorithms in this package attempt to adjust for systematic errors
of unknown origin in high-dimensional data. The algorithms were
originally developed for use with genomic data, especially
microarray data, but may be useful with other types of
high-dimensional data as well. The algorithms included in this
package are RUV-2, RUV-4, RUV-inv, and RUV-rinv, along with various
supporting algorithms. These algorithms were proposed by
Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and
Speed (2013). The algorithms require the user to specifiy a set of
negative control variables, as described in the references.
* saeSim (0.6.0)
Maintainer: Sebastian Warnholz
Author(s): Sebastian Warnholz <Sebastian.Warnholz at fu-berlin.de>
License: GPL-3 | file LICENSE
http://crantastic.org/packages/saeSim
Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data
generation over drawing samples to model fitting - in one object.
This enables easy modification and combination of different
scenarios. You can store your results in a folder or start the
simulation in parallel.
* scrm (1.3-2)
Maintainer: Paul Staab
Author(s): Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [ths],
Gerton Lunter [aut, cph, ths]
License: GPL (>= 3)
http://crantastic.org/packages/scrm
A coalescent simulator that allows the rapid simulation of biological
sequences under neutral models of evolution.
* sigloc (0.0.4)
Maintainer: Sergey S. Berg
Author(s): Sergey S. Berg
License: GPL (>= 2)
http://crantastic.org/packages/sigloc
A collection of tools for estimating the location of a transmitter
signal from radio telemetry studies using the maximum likelihood
estimation (MLE) approach described in Lenth (1981).
* TDboost (1.0)
Maintainer: Yi Yang
Author(s): Yi Yang <yiyang at umn.edu>, Wei Qian <weiqian at stat.umn.edu>, Hui Zou
<hzou at stat.umn.edu>
License: GPL-3
http://crantastic.org/packages/TDboost
A fully nonparametric Tweedie model using the gradient boosting. It is
capable of fitting a flexible nonlinear model and capturing
interactions among predictors.
* traj (1.0)
Maintainer: Dan Vatnik
Author(s): Marie-Pierre Sylvestre, Dan Vatnik
License: GPL-2
http://crantastic.org/packages/traj
Implements the three step procedure proposed by Leffondree et al.
(2004) to identify clusters of individual longitudinal trajectories.
The procedure involves (1) calculating 24 measures describing the
features of the trajectories; (2) using factor analysis to select a
subset of the 24 measures and (3) using cluster analysis to identify
clusters of trajectories, and classify each individual trajectory in
one of the clusters.
Updated packages
----------------
AutoSEARCH (1.3), BayesFactor (0.9.9), bio3d (2.1-2), CAMAN (0.72),
confidence (1.1-0), DBKGrad (1.6), equate (2.0-3), extracat (1.7-1),
FSelector (0.20), GGIR (1.1-3), HiDimDA (0.2-2), highr (0.4), httpuv
(1.3.2), imputeYn (1.2), jackknifeKME (1.1), JADE (1.9-92), JMdesign
(1.1), logconPH (1.2), logconPH (1.1), MAINT.Data (0.3), MESS (0.3-2),
MPTinR (1.6.3), MRH (1.1), nhlscrapr (1.8), npmlreg (0.46-1), ore
(1.0.1), pcaPP (1.9-60), PKfit (1.2.4), polyCub (0.5-1), prevalence
(0.3.0), rasterVis (0.32), redcapAPI (1.0.1), restlos (0.1-3), rex
(0.1.1), RnavGraph (0.1.7), Rook (1.1-1), rpf (0.40), RSQLite (1.0.0),
rtkpp (0.8.3), SamplingStrata (1.0-3), scrm (1.3-2), sgof (2.1.1),
sparr (0.3-6), spatstat (1.39-1), spatstat (1.39-0), speedglm
(0.2-1.0), STARSEQ (1.2.1), stepp (3.0-11), synbreed (0.10-3), tclust
(1.2-3), timeordered (0.9.7), TwoStepCLogit (1.2.3), VIM (4.1.0), WRS2
(0.2-0)
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