CRAN (and crantastic) updates this week New packages ------------
* awsMethods (1.0-0) Maintainer: Joerg Polzehl Author(s): Joerg Polzehl <polz...@wias-berlin.de> License: GPL (>= 2) http://crantastic.org/packages/awsMethods The package defines method extract that in needed in several packages * BatchExperiments (1.0-486) Maintainer: Michel Lang Author(s): Bernd Bischl <bernd_bis...@gmx.net>, Michel Lang <michell...@gmail.com>, Olaf Mersmann <ol...@p-value.net> License: BSD http://crantastic.org/packages/BatchExperiments Extends the BatchJobs package to run statistical experiments on batch computing clusters. For further details see the project web page. * BatchJobs (1.0-485) Maintainer: Bernd Bischl Author(s): Bernd Bischl <bernd_bis...@gmx.net>, Michel Lang <michell...@gmail.com>, Olaf Mersmann <ol...@p-value.net> License: BSD http://crantastic.org/packages/BatchJobs Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page. * CpGassoc (1.1) Maintainer: R Barfield Author(s): Barfield, R., Conneely, K., Kilaru,V License: GPL (>= 2) http://crantastic.org/packages/CpGassoc CpGassoc is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. CpGassoc also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites. * dataframe (2.5) Maintainer: Tim Hesterberg Author(s): Tim Hesterberg License: GPL-2 http://crantastic.org/packages/dataframe This contains versions of standard data frame functions in R, modified to avoid making extra copies of inputs. This is faster, particularly for large data. * fgof (0.2-1) Maintainer: Jun Yan Author(s): Ivan Kojadinovic and Jun Yan License: GPL (>= 3) http://crantastic.org/packages/fgof Goodness-of-fit test with multiplier or parametric bootstrap. * ForeCA (0.0.1) Maintainer: Georg M. Goerg Author(s): Georg M. Goerg <g...@stat.cmu.edu> License: GPL (>= 2) http://crantastic.org/packages/ForeCA ForeCA is a new blind source separation (BSS) technique for temporally dependent signals. Contrary to PCA or ICA it explicitly searches for the best linear transformation that makes the obtained sources as ''forecastable'' as possible. The measure of forecastability Omega(x_t) is the entropy of the spectral density of the signal. * Luminescence (0.1.7) Maintainer: Sebastian Kreutzer Author(s): Sebastian Kreutzer [aut, cre], Christoph Schmidt [aut, ctb], Margret C. Fuchs [aut, ctb], Michael Dietze [aut, ctb], Manfred Fischer [aut, ctb], Markus Fuchs [ths] License: GPL-3 http://crantastic.org/packages/Luminescence Package provides a collection of various R functions for Luminescence Dating data analysis. * mada (0.4) Maintainer: Philipp Doebler Author(s): Philipp Doebler License: GPL-2 http://crantastic.org/packages/mada This package provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Boehning et al. is also available. Standard methods like summary, plot and so on are provided. * MetaPath (0.9) Maintainer: Kui Shen Author(s): Kui Shen and Geroge Tseng License: GPL (>= 2.0) http://crantastic.org/packages/MetaPath This R package was implemented to perform the Meta-analysis for Pathway Enrichment (MAPE) methods introduced by Shen and Tseng (2010). It includes functions to automatically perform MAPE_G (integrating multiple studies at gene level), MAPE_P (integrating multiple studies at pathway level) and MAPE_I (a hybrid method integrating MAEP_G and MAPE_P methods). In the simulation and real data analyses in the paper, MAPE_G and MAPE_P have complementary advantages and detection power depending on the data structure. In general, the integrative form of MAPE_I is recommended to use. In the case that MAPE_G (or MAPE_P) detects almost none pathway, the integrative MAPE_I does not improve performance and MAPE_P (or MAPE_G) should be used. Reference: Shen, Kui, and George C Tseng. Meta-analysis for pathway enrichment analysis when combining multiple microarray studies.Bioinformatics (Oxford, England) 26, no. 10 (April 2010): 1316-1323. doi:10.1093/bioinformatics/btq148. http://www.ncbi.nlm.nih.gov/pubmed/20410053. * NbClust (1.0) Maintainer: : Nadia Ghazzali Author(s): Malika Charrad <malika.charra...@ulaval.ca> and Nadia Ghazzali <nadia.ghazz...@mat.ulaval.ca> and Veronique Boiteau <veronique.boitea...@ulaval.ca> and Azam Niknafs <azam.niknaf...@ulaval.ca> License: GPL-2 http://crantastic.org/packages/NbClust This package provides most of the popular indices for cluster validation ready to use for the outputs produced by functions coming from the same package. It also proposes to user the best clustering scheme from the different results obtained by varying all combinations of number of clusters, distance measures, and clustering methods. * OptimalCutpoints (1.0) Maintainer: Monica Lopez Raton Author(s): Monica Lopez-Raton, Maria Xose Rodriguez-Alvarez License: GPL http://crantastic.org/packages/OptimalCutpoints This package enables users to compute one or more optimal cutpoints for diagnostic tests or continuous markers. Various approaches for selecting optimal cutoffs have been implemented, including methods based on cost-benefit analysis and diagnostic test accuracy measures (Sensitivity/Specificity, Predictive Values and Diagnostic Likelihood Ratios). Numerical and graphical output for all methods is easily obtained. * Taxonstand (1.0) Maintainer: Luis Cayuela Author(s): Luis Cayuela License: GPL (>= 2) http://crantastic.org/packages/Taxonstand Automated standardization of taxonomic names and removal of orthograhpic errors in plant species names using the The Plant List (TPL) website (www.theplantlist.org) * WeightedPortTest (1.0) Maintainer: Thomas J. Fisher Author(s): Thomas J. Fisher and Colin M. Gallagher License: GPL (>= 3) http://crantastic.org/packages/WeightedPortTest This packages contains the Weighted Portmanteau Tests as described in "New Weighted Portmanteau Statistics for Time Series Goodness-of-Fit Testing' accepted for publication by the Journal of the American Statistical Association. Updated packages ---------------- actuar (1.1-4), aws (1.8-0), BinNor (2.0), caTools (1.13), CDVine (1.1-7), changepoint (0.7), ChemoSpec (1.51-0), cosso (2.0-2), CpGassoc (1.1), doRNG (1.3), doRNG (1.4.1), dti (1.0-3), dynsurv (0.1-8), EcoHydRology (0.4.1), EffectStars (1.1), fastICA (1.1-16), foreign (0.8-50), ftsa (3.2), G1DBN (3.1), gdistance (1.1-3), gmm (1.4-0), gnm (1.0-2), hash (2.2.3), HH (2.3-15), igraph0 (0.5.5-1), inlinedocs (1.9.1), iterLap (1.1-2), kaps (0.9-3), ks (1.8.8), Maeswrap (1.4.11), MatrixEQTL (1.6.1), maxent (1.3.2), mgcv (1.7-17), ModelMap (2.3.1), multcompView (0.1-5), muma (1.2), NBPSeq (0.1.6), nlme (3.1-104), oce (0.8-8), oce (0.8-9), okmesonet (0.1.3), OpenCL (0.1-3), osDesign (1.6), osmar (1.1-4), pdc (0.3), qgraph (1.0.5), qtl (1.24-9), qtutils (0.1-3), RcppArmadillo (0.3.2.0), rcppbugs (0.1.0), RForcecom (0.2), Rjms (0.0.3), Rmpfr (0.4-8), ror (0.8), Rsolnp (1.12), rtape (2.1), rugarch (1.0-9), SamplingStrata (0.9-3), spacetime (0.7-0), SPARQL (1.9), SparseGrid (0.8.1), SpatialTools (0.4.1), survey (3.28-1), synbreed (0.9-3) New reviews ----------- * xlsx, by fiutzi http://crantastic.org/reviews/149 This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: crana...@gmail.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.