[R] CRAN (and crantastic) updates this week
Crantastic
cranatic at gmail.com
Mon May 14 00:40:05 CEST 2012
CRAN (and crantastic) updates this week
New packages
------------
* AGD (0.30)
Maintainer: Stef van Buuren
Author(s): Stef van Buuren <stef.vanbuuren at tno.nl>
License: GPL-2 | GPL-3
http://crantastic.org/packages/AGD
Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23 2012,
Rotterdam.
* bigml (0.1-1)
Maintainer: Justin Donaldson
Author(s): Justin Donaldson [aut, cre]
License: LGPL-3
http://crantastic.org/packages/bigml
The bigml package contains bindings for the BigML API. The package
includes methods that provide straightforward access to basic API
functionality, as well as methods that accommodate idiomatic R
datatypes and concepts.
* BVS (4.12.0)
Maintainer: Melanie Quintana
Author(s): Melanie Quintana <maw27.wilson at gmail.com>
License: Unlimited
http://crantastic.org/packages/BVS
The functions in this package focus on analyzing case-control
association studies involving a group of genetic variants. In
particular, we are interested in modeling the outcome variable as a
function of a multivariate genetic profile using Bayesian model
uncertainty and variable selection techniques. The package
incorporates functions to analyze data sets involving common
variants as well as extensions to model rare variants via the
Bayesian Risk Index (BRI) as well as haplotypes. Finally, the
package also allows the incorporation of external biological
information to inform the marginal inclusion probabilities via the
iBMU.
* gsbDesign (0.95)
Maintainer: Unknown
Author(s): Florian Gerber, Thomas Gsponer
License: GPL-3
http://crantastic.org/packages/gsbDesign
Group Sequential Operating Characteristics for Clinical, Bayesian
two-arm Trials with known Sigma and Normal Endpoints.
* marqLevAlg (1.0)
Maintainer: Melanie Prague
Author(s): D. Commenges <Daniel.Commenges at isped.u-bordeaux2.fr>, M. Prague
<Melanie.Prague at isped.u-bordeaux2.fr> and Amadou Diakite
License: GPL (>= 2.0)
http://crantastic.org/packages/marqLevAlg
This algorithm provides a numerical solution to the problem of
minimizing a function. This is more efficient than the
Gauss-Newton-like algorithm when starting from points vey far from
the final minimum. A new convergence test is implemented (RDM) in
addition to the usual stopping criterion : stopping rule is when the
gradients are small enough in the parameters metric (GH-1G).
* p2distance (1.0.1)
Maintainer: A.J. Perez-Luque
Author(s): A.J. Perez-Luque; R. Moreno; R. Perez-Perez and F.J. Bonet
License: GPL
http://crantastic.org/packages/p2distance
The welfare's synthetic indicator provides an ideal tool for measuring
multi-dimensional concepts such as welfare, development, living
standards, etc. It enables information from the various indicators
to be aggregated into a single synthetic measure.
* pcaPA (1.0)
Maintainer: Carlos A. Arias
Author(s): Carlos A. Arias <carias at icfes.gov.co> and Víctor H. Cervantes
<vcervantes at icfes.gov.co>.
License: GPL (>= 2)
http://crantastic.org/packages/pcaPA
A set of functions to perform parallel analysis for principal
components analysis intended mainly for large data sets. It performs
a parallel analysis of continuous, ordered (including
dichotomous/binary as a special case) or mixed type of data
associated with a principal components analysis. Polychoric
correlations among ordered variables, Pearson correlations among
continuous variables and polyserial correlation between mixed type
variables (one ordered and one continuous) are used. Whenever the
use of polyserial or polychoric correlations yields a non positive
definite correlation matrix, the resulting matrix is transformed
into the nearest positive definite matrix. For details on the GSL
installation in windows please visit the following link:
http://wiki.rglab.org/index.php?title=Public:Installation_of_GSL_from
Windows_binary
* phia (0.0-2)
Maintainer: Helios De Rosario-Martinez
Author(s): Helios De Rosario-Martinez
License: GPL (>= 3)
http://crantastic.org/packages/phia
Analysis of terms in linear and generalized linear models, on the
basis of multiple comparisons of factor contrasts. Specially suited
for the analysis of interaction terms.
* plmDE (1.0)
Maintainer: Jonas
Author(s): Jonas Mueller
License: GPL (>= 2)
http://crantastic.org/packages/plmDE
A set of tools for identifying genes whose differential expression is
associated with measurements of other covariates on a continuous
scale. These methods rely on generalized additive partially linear
models which can be fitted efficiently using a B-spline basis
approximation. Still under development: methods for interfacing
with objects extending the eSet class and a function to pass linear
models in edgeR and DEseq format.
* polywog (0.1-0)
Maintainer: Brenton Kenkel
Author(s): Brenton Kenkel and Curtis S. Signorino
License: GPL (>= 2)
http://crantastic.org/packages/polywog
Routines for flexible functional form estimation via basis regression,
with model selection via the adaptive LASSO or SCAD to prevent
overfitting.
* qtutils (0.1-2)
Maintainer: Deepayan Sarkar
Author(s): Deepayan Sarkar
License: LGPL (>= 2)
http://crantastic.org/packages/qtutils
Miscellaneous Qt-based tools for R
* RCassandra (0.1-0)
Maintainer: Simon Urbanek
Author(s): Simon Urbanek <simon.urbanek at r-project.org>
License: GPL-2
http://crantastic.org/packages/RCassandra
This packages provides a direct interface (without the use of Java) to
the most basic functionality of Apache Cassanda such as login,
updates and queries.
* rolasized (1.0)
Maintainer: Christian Zang
Author(s): Christian Zang
License: MIT
http://crantastic.org/packages/rolasized
Ethan Schoonover's solarized colour scheme for R
(http://ethanschoonover.com/solarized)
* RTDAmeritrade (0.0.1)
Maintainer: Theodore Van Rooy
Author(s): Theodore Van Rooy
License: GPL (>= 2)
http://crantastic.org/packages/RTDAmeritrade
The package contains functions that can be used to interface with the
TDAmeritrade API.
* SightabilityModel (1.0)
Maintainer: John Fieberg
Author(s): John Fieberg
License: GPL-2
http://crantastic.org/packages/SightabilityModel
Uses logistic regression to model the probability of detection as a
function of covariates. This model is then used with observational
survey data to estimate population size, while accounting for
uncertain detection. See Steinhorst and Samuel (1989).
* SKAT (0.75)
Maintainer: Seunggeun (Shawn) Lee
Author(s): Seunggeun Lee, Larisa Miropolsky and Micheal Wu
License: GPL (>= 2)
http://crantastic.org/packages/SKAT
Kernel based SNP set test
* SunterSampling (1.0)
Maintainer: alessandro.barbiero
Author(s): Alessandro Barbiero, Giancarlo Manzi
License: GPL
http://crantastic.org/packages/SunterSampling
Functions for drawing samples according to Sunter's sampling design,
and for computing first and second order inclusion probabilities
* TCC (0.2)
Maintainer: Tomoaki Nishiyama
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
License: GPL-2
http://crantastic.org/packages/TCC
This package provides normalization method of tag count data by
TMM-bayseq-TMM pipeline. Expected application includes RNA-seq,
SAGE, ChIP-seq and a like.
Updated packages
----------------
Animal (1.04), BaSAR (1.3), BBmisc (1.1-125), beeswarm (0.1.5),
betareg (3.0-0), blockTools (0.5-4), caroline (0.7.2), catR (2.3),
cccd (1.02), ChoiceModelR (1.1), CityPlot (2.0), corpcor (1.6.3),
cvplogistic (2.0-0), cvTools (0.3.1), dafs (1.0-37), diveMove (1.3.4),
diversitree (0.9-3), DNAtools (0.1-6), fda.usc (0.9.7), ff (2.2-7),
flexmix (2.3-8), FlexParamCurve (1.4), frailtyHL (1.1), geometry
(0.3-2), ggplot2 (0.9.1), gMCP (0.7-9), hydroPSO (0.1-55), iCluster
(2.1.0), LaplacesDemon (12.05.07), lavaan (0.4-14), lmomco (1.6.1),
LPCM (0.44-6), mfr (1.04), mht (2.00), MigClim (1.2), minpack.lm
(1.1-6), minqa (1.2.1), mirt (0.2.4), mokken (2.7.2), msm (1.1.1),
mutoss (0.1-7), mutossGUI (0.1-7), nullabor (0.2), nutshellDE (1.0-2),
openair (0.6-0), orloca (4.0), pegas (0.4-2), processdata (0.8.1),
qgraph (1.0.4), RghcnV3 (2.8), rgl (0.92.880), rgr (1.1.6), RGtk2
(2.20.24), RISmed (2.0.1), RMAWGEN (1.2.5), robustbase (0.9-0),
robustfa (1.0-01), rtf (0.4-4), s20x (3.1-9), scales (0.2.1),
segmented (0.2-9.1), SemiParBIVProbit (3.2), shotGroups (0.2-1),
spatialsegregation (2.38), TDMR (0.3.0), timereg (1.6-5), tmle
(1.2.0-1), TSPostgreSQL (2012.5-1), vcdExtra (0.5-3)
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