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)
http://crantastic.org/packages/classyfire
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
http://crantastic.org/packages/cooptrees
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
http://crantastic.org/packages/coreTDT
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)
http://crantastic.org/packages/descomponer
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)
http://crantastic.org/packages/Frames2
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
http://crantastic.org/packages/GUILDS
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
http://crantastic.org/packages/iBATCGH
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)
http://crantastic.org/packages/ica
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
http://crantastic.org/packages/insuranceData
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
http://crantastic.org/packages/JAGUAR
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)
http://crantastic.org/packages/mpcv
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)
http://crantastic.org/packages/MSIseq
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
http://crantastic.org/packages/nabor
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
http://crantastic.org/packages/optrees
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
http://crantastic.org/packages/packrat
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)
http://crantastic.org/packages/pdR
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
http://crantastic.org/packages/pxweb
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
http://crantastic.org/packages/rappdirs
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
http://crantastic.org/packages/rcbalance
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
http://crantastic.org/packages/recosystem
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)
http://crantastic.org/packages/subrank
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
http://crantastic.org/packages/sweidnumbr
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)
http://crantastic.org/packages/Tampo
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
http://crantastic.org/packages/trotter
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
http://crantastic.org/packages/xgboost
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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