[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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