CRAN (and crantastic) updates this week New packages ------------
* AGD (0.30) Maintainer: Stef van Buuren Author(s): Stef van Buuren <stef.vanbuu...@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.wil...@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.commen...@isped.u-bordeaux2.fr>, M. Prague <melanie.pra...@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 <car...@icfes.gov.co> and VĂctor H. Cervantes <vcervan...@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.urba...@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) This email provided as a service for the R community by http://crantastic.org. 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