[R] CRAN (and crantastic) updates this week

Crantastic cranatic at gmail.com
Mon Sep 8 00:40:05 CEST 2014

CRAN (and crantastic) updates this week

New packages

* classyfire (0.1-0)
  Maintainer: Eleni Chatzimichali
  Author(s): Eleni Chatzimichali <ea.chatzimichali at gmail.com> and Conrad Bessant
             <c.bessant at qmul.ac.uk>
  License: GPL (>= 2)

  A collection of functions for the creation and application of highly
  optimised, robustly evaluated ensembles of support vector machines
  (SVMs). The package takes care of training individual SVM
  classifiers using a fast parallel heuristic algorithm, and combines
  individual classifiers into ensembles. Robust metrics of
  classification performance are offered by bootstrap resampling and
  permutation testing.

* cooptrees (1.0)
  Maintainer: Manuel Fontenla
  Author(s): Manuel Fontenla
  License: GPL-3

  Computes several cooperative games and allocation rules associated
  with minimum cost spanning tree problems and minimum cost
  arborescence problems.

* coreTDT (1.0)
  Maintainer: Yu Jiang
  Author(s): Yu Jiang, Andrew S Allen
  License: GPL-3

  Use to analysis case-parent trio sequencing studies. Test the compound
  heterozygous and recessive disease models

* descomponer (1.0)
  Maintainer: Francisco Parra
  Author(s): Francisco Parra  <parra_fj at cantabria.es>
  License: GPL (>= 2)

  Decompose a time series into seasonal, trend and irregular components
  using transformations to amplitude-frequency domain.

* Frames2 (0.0.3)
  Maintainer: David Molina
  Author(s): Antonio Arcos <arcos at ugr.es>, Maria del Mar Rueda <mrueda at ugr.es>,
             Maria Giovanna Ranalli <giovanna.ranalli at stat.unipg.it>
             and David Molina <dmolinam at ugr.es>
  License: GPL (>= 2)

  Point and interval estimation in dual frame surveys. In contrast to
  classic sampling theory, where only one sampling frame is
  considered, dual frame methodology assumes that there are two frames
  available for sampling and that, overall, they cover the entire
  target population. Then, two probability samples (one from each
  frame) are drawn and information collected is suitably combined to
  get estimators of the parameter of interest.

* GUILDS (1.2)
  Maintainer: Thijs Janzen
  Author(s): Thijs Janzen
  License: GPL-2

  The GUILDS package combines a range of sampling formulas for the
  unified neutral model of biogeography and biodiversity. Alongside
  the sampling formulas, it includes methods to perform maximum
  likelihood optimization of the sampling formulas, methods to
  generate data given the neutral model, and methods to estimate the
  expected species abundance distribution. Sampling formulas included
  in the GUILDS package are the Etienne Sampling Formula (Etienne
  2005), the guild sampling formula, where guilds are assumed to
  differ in dispersal ability (Janzen 2014), and  the guilds sampling
  formula conditioned on guild size (Janzen 2014).

* iBATCGH (1.0)
  Maintainer: Alberto Cassese
  Author(s): Alberto Cassese
  License: GPL-2

  Bayesian integrative models of gene expression and comparative genomic
  hybridization data. The package provides inference on copy number
  variations and their association with gene expression

* ica (1.0-0)
  Maintainer: Nathaniel E. Helwig
  Author(s): Nathaniel E. Helwig <helwig at umn.edu>
  License: GPL (>= 2)

  Independent Component Analysis (ICA) using various algorithms:
  FastICA, Information-Maximization (Infomax), and Joint Approximate
  Diagonalization of Eigenmatrices (JADE).

* insuranceData (1.0)
  Maintainer: Alicja Wolny--Dominiak
  Author(s): Alicja Wolny--Dominiak and Michal Trzesiok
  License: GPL-2

  Insurance datasets, which are often used in claims severity and claims
  frequency modelling. It helps testing new regression models in those
  problems, such as GLM, GLMM, HGLM, non-linear mixed models etc. Most
  of the data sets are applied in the project "Mixed models in
  ratemaking" supported by grant NN 111461540 from Polish National
  Science Center.

* JAGUAR (1.1)
  Maintainer: Chaitanya Acharya
  Author(s): Chaitanya R. Acharya and Andrew S. Allen
  License: GPL-2

  Implements a 2 degree-of-freedom score test that measures 1) the
  overall shift in the gene expression due to genotype, and 2)
  group-specific changes in gene expression due to genotype
  (interaction term) in a mixed-effects model framework.

* mpcv (1.0)
  Maintainer: Krzysztof Ciupke
  Author(s): Krzysztof Ciupke <krzysztof.ciupke at polsl.pl>
  License: GPL (>= 2.0)

  Multivariate process capability analysis using the multivariate
  process capability vector. Allows to analyze a multivariate process
  with both normally and non-normally distributed and also with
  dependent and independent quality characteristics.

* MSIseq (0.99.1)
  Maintainer: Mini Huang
  Author(s): Mini Huang
  License: GPL (>= 2)

  A decision tree classifier for detecting microsatellite instability
  (MSI) in somatic mutation data from whole exome sequencing. MSI is
  detected based on different mutation rates in all sites as well as
  in simple sequence repeats. This mechanism can also be applied to
  sequence data of targeted gene panels with shorter sequence length.

* nabor (0.4.3)
  Maintainer: Gregory Jefferis
  Author(s): Stephane Mangenat (for libnabo), Gregory Jefferis
  License: BSD_3_clause + file LICENSE

  An R wrapper for libnabo, an exact or approximate k nearest neighbour
  library which is optimised for low dimensional spaces (e.g. 3D).
  libnabo has speed and space advantages over the ANN library wrapped
  by package RANN. nabor includes a knn function that is designed as a
  drop-in replacement for RANN::nn2. In addition, objects which
  include the k-d tree search structure can be returned to speed up
  repeated queries of the same set of target points.

* optrees (1.0)
  Maintainer: Manuel Fontenla
  Author(s): Manuel Fontenla [aut, cre]
  License: GPL-3

  Finds optimal trees in weighted graphs. In particular, this package
  provides solving tools for minimum cost spanning tree problems,
  minimum cost arborescence problems, shortest path tree problems and
  minimum cut tree problem.

* packrat (0.4.1-1)
  Maintainer: Kevin Ushey
  Author(s): Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
  License: GPL-2

  Packrat is a tool for managing the R packages your project depends on
  in an isolated, portable, and reproducible way.

* pdR (1.1)
  Maintainer: Ho Tsung-wu
  Author(s): Ho Tsung-wu
  License: GPL (>= 2)

  threshold regression in panel data

* pxweb (0.4)
  Maintainer: Mans Magnusson
  Author(s): Mans Magnusson, Leo Lahti, Love Hansson
  License: BSD_2_clause + file LICENSE

  Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API
  is used by organizations such as Statistics Sweden and Statistics
  Finland to disseminate data. The R package can interact with all
  PX-Web/PC-Axis APIs to fetch information about the data hierarchy,
  extract metadata and extract and parse statistics to R data.frame
  format. PX-Web is a solution to disseminate PC-Axis data files in
  dynamic tables on the web. Since 2013 PX-Web contains an API to
  disseminate PC-Axis files. PX-Web/PC-Axis API information can be
  found at: http://www.scb.se/Grupp/OmSCB/API/API-description.pdf

* rappdirs (0.3)
  Maintainer: Hadley Wickham
  Author(s): Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar
             [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r,
             R/cache.r, R/data.r, R/log.r translated from appdirs),
             Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor
             Csardi [ctb], Gregory Jefferis [ctb]
  License: MIT + file LICENSE

  An easy way to determine which directories on the users computer you
  should use to save data, caches and logs. A port of Python's Appdirs
  (\url{https://github.com/ActiveState/appdirs}) to R.

* rcbalance (1.0)
  Maintainer: Samuel D. Pimentel
  Author(s): Samuel D. Pimentel
  License: MIT + file LICENSE

  Tools for large, sparse optimal matching of treated units 	and control
  units in observational studies.  Provisions are 	made for refined
  covariate balance constraints, which include 	fine and near-fine
  balance as special cases.  Matches are  	optimal in the sense that
  they are computed as solutions to 	network optimization problems
  rather than greedy algorithms.

* recosystem (0.2.1)
  Maintainer: Yixuan Qiu
  Author(s): Chih-Jen Lin, Yu-Chin Juan, Yong Zhuang, and Wei-Sheng Chin for the
             original C++ code, Yixuan Qiu for the R wrapper
  License: BSD_3_clause + file LICENSE

  This package is an R wrapper of the libmf library
  (http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender system
  using matrix factorization. It's typically used to approximate an
  incomplete matrix using the product of two matrices in a latent
  space. Other common names for this task include "collaborative
  filtering", "matrix completion", "matrix recovery", etc. This
  package mainly supports UNIX-like operating systems, with
  experimental support for Windows. See README for the links of
  precompiled packages.

* subrank (0.8.5)
  Maintainer: Jerome Collet
  Author(s): Jerome Collet
  License: GPL (>= 3)

  essentially a discussion tool about estimation of copula using ranks
  and subsampling.

* sweidnumbr (0.1.1)
  Maintainer: Mans Magnusson
  Author(s): Mans Magnusson
  License: BSD_2_clause + file LICENSE

  Structural handling of identity numbers used in the Swedish
  administration such as personal identity numbers ('personnummer')
  and organizational identity numbers ('organisationsnummer').

* Tampo (1.0)
  Maintainer: Matthias Vignon
  Author(s): Matthias Vignon
  License: GPL (>= 2)

  Facilitates analyzing microchemical profiles (both mono- and
  multielemental composition) from fish otoliths (stones from the
  inner ear) using a recursive partitioning approach that can
  accommodate some form of user-specified constraints. It also allows
  extracting environmental histories from otolith based on typical
  elemental sequences generated using methods such as LA-ICPMS.
  Microchemical analysis is widely used in fisheries management and
  fisheries biology to identify stocks and characterize fish movements
  but the provided functions may be considered from the more general
  perspective of the chronological clustering of multivariate time
  series using piecewise constant regressions.

* trotter (0.5)
  Maintainer: Richard Ambler
  Author(s): Richard Ambler
  License: GPL-3

  Class definitions and constructors for pseudo-vectors containing all
  permutations and combinations of objects taken from a vector.

* xgboost (0.3-2)
  Maintainer: Tong He
  Author(s): Tianqi Chen <tianqi.tchen at gmail.com>, Tong He <hetong007 at gmail.com>
  License: Apache License (== 2.0) | file LICENSE

  This package is a R wrapper of xgboost, which is short for eXtreme
  Gradient Boosting. It is an efficient and scalable implementation of
  gradient boosting framework. The package includes efficient linear
  model solver and tree learning algorithms. The package can
  automatically do parallel computation with OpenMP, and it can be
  more than 10 times faster than existing gradient boosting packages
  such as gbm. It supports various objective functions, including
  regression, classification and ranking. The package is made to be
  extensible, so that users are also allowed to define their own
  objectives easily.

Updated packages

agricolae (1.2-1), asbio (1.1-1), BCA (0.9-3), chebpol (1.3-1367),
circlize (0.1.1), cluster (1.15.3), copula (0.999-11),
CopulaRegression (0.1-5), Cprob (1.2.3), DBI (0.3.0), DNAtools
(0.1-21), ds (3.0), e1071 (1.6-4), Ecdat (0.2-7), fMultivar (3011.78),
GGIR (1.0-6), GPfit (0.2-1), GUILDS (1.1), haplo.stats (1.6.11), heavy
(0.2-35), helloJavaWorld (0.0-9), httr (0.5), idr (1.2), jaatha (2.6),
kmi (0.5.1), lmSupport (2.09), logcondens (2.1.2), mht (3.0.11), mixAK
(3.8), mixOmics (5.0-3), MPV (1.35), MRCV (0.3-3), nabor (0.4.3),
NbClust (2.0.2), NCmisc (1.1.3), NCmisc (1.1.2), nor1mix (1.2-0),
OpasnetUtils (1.1.0), OrdFacReg (1.0.5), packrat (0.4.1-1), parcor
(0.2-6), pec (2.3.7), plsdof (0.2-7), powerGWASinteraction (1.1.0), PP
(0.5.3), ppls (1.6-1), prodlim (1.4.5), pyramid (1.4), R.devices
(2.11.0), R2HTML (2.3.0), RankAggreg (0.5), raster (2.3-0), Rcmdr
(2.1-1), RcmdrPlugin.BCA (0.9-8), RcmdrPlugin.temis (0.7.2),
RcmdrPlugin.temis (0.7.1), readbitmap (0.1-4), REBayes (0.50), rebmix
(2.6.2), REPPlab (0.9), Rmpfr (0.5-6), rNOMADS (2.0.2), roxygen2
(4.0.2), rpf (0.38), sanon (1.4), SCRT (1.1), SCVA (1.1), SDaA
(0.1-3), selectMeta (1.0.7), sgr (1.2), StAMPP (1.3), structSSI (1.1),
stylo (0.5.8), synbreed (0.10-1), tolerance (1.0.0), traitr (0.14),
upclass (2.0), UsingR (2.0-2), wgaim (1.4-3), wordnet (0.1-10)

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