CRAN (and crantastic) updates this week New packages ------------
* anim.plots (0.1) Maintainer: David Hugh-Jones Author(s): David Hugh-Jones <davidhughjo...@gmail.com> License: GPL-2 http://crantastic.org/packages/anim-plots Simple animated versions of basic R plots, using the 'animation' package. Includes animated versions of plot, barplot, persp, contour, filled.contour, hist, curve, points, lines, text, symbols, segments, and arrows. * aoos (0.0.1) Maintainer: Sebastian Warnholz Author(s): Sebastian Warnholz License: GPL-3 | file LICENSE http://crantastic.org/packages/aoos Another implementation of object-orientation in R. Private and public methods are part of the class-definition. Allows to write a lot of small methods as part of the class definition without cluttering the object. * CpGFilter (1.0) Maintainer: Jun Chen Author(s): Jun Chen License: GPL-2 http://crantastic.org/packages/CpGFilter Filter CpGs based on Intra-class Correlation Coefficients (ICCs) when replicates are available. ICCs are calculated by fitting linear mixed effects models to all samples including the un-replicated samples. Including the large number of un-replicated samples improves ICC estimates dramatically. The method accommodates any replicate design. * dfcomb (1.0-1) Maintainer: Marie-Karelle Riviere Author(s): Marie-Karelle Riviere and Jacques-Henri Jourdan License: GPL-3 http://crantastic.org/packages/dfcomb Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent. * dfmta (1.0-1) Maintainer: Marie-Karelle Riviere Author(s): Marie-Karelle Riviere and Jacques-Henri Jourdan License: GPL-3 http://crantastic.org/packages/dfmta Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization", Statistics in Medicine, 2014. * dummy (0.1.0) Maintainer: Michel Ballings Author(s): Michel Ballings and Dirk Van den Poel License: GPL (>= 2) http://crantastic.org/packages/dummy Efficiently create dummies of all factors and character vectors in a data frame. Support is included for learning the categories on one data set (e.g., a training set) and deploying them on another (e.g., a test set). * FAMILY (0.1.18) Maintainer: Asad Haris Author(s): Asad Haris License: GPL (>= 2) http://crantastic.org/packages/FAMILY Fits penalized linear and logistic regression models with pairwise interaction terms. * geesmv (1.0) Maintainer: Zheng Li Author(s): Ming Wang <mw...@phs.psu.edu> License: GPL (>= 3) http://crantastic.org/packages/geesmv Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance. * geocodeHERE (0.1) Maintainer: Cory Nissen Author(s): "Cory Nissen <corynis...@gmail.com> [aut, cre]" License: MIT + file LICENSE http://crantastic.org/packages/geocodeHERE Wrapper for Nokia's HERE geocoding API. See http://here.com/ for more information on HERE and https://developer.here.com/geocoder for more information on the HERE geocoding API. * ggswissmaps (0.0.2) Maintainer: Sandro Petrillo Burri Author(s): Sandro Petrillo Burri <gibo....@gmail.com> License: GPL-2 http://crantastic.org/packages/ggswissmaps Offers various swiss maps as ggplot2 objects and gives the possibility to add layers of data on the maps. Data are publicly available from the swiss federal statistical office. * hcp (0.1) Maintainer: Yulei Wang Author(s): Stephen J.Ganocy, Jiayang Sun, and Yulei Wang License: GPL-2 | GPL-3 http://crantastic.org/packages/hcp Estimation of parameters in 3-segment (i.e. 2 change-point) regression models with heteroscedastic variances is provided based on both likelihood and hybrid Bayesian approaches, with and without continuity constraints at the change points. * heritability (1.0) Maintainer: Willem Kruijer Author(s): Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke. License: GPL-3 http://crantastic.org/packages/heritability implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana. * ionflows (1.0) Maintainer: Michael Bockmayr Author(s): Michael Bockmayr and Jan Budczies License: GPL-3 http://crantastic.org/packages/ionflows Two methods for calculation of the number of required flows for semiconductor sequencing: 1. Using a simulation, the number of flows can be calculated for a concrete list of amplicons. 2. An exact combinatorial model is evaluated to calculate the number of flows for a random ensemble of sequences. * LinCal (1.0) Maintainer: Derick L. Rivers Author(s): Derick L. Rivers <river...@vcu.edu> and Edward L. Boone License: GPL-2 http://crantastic.org/packages/LinCal Estimate and confidence/credible intervals for an unknown regressor x0 given an observed y0. * lpme (1.0.0) Maintainer: Haiming Zhou Author(s): Haiming Zhou <zh...@email.sc.edu> and Xianzheng Huang <hu...@stat.sc.edu> License: GPL (>= 2) http://crantastic.org/packages/lpme Two local polynomial estimators for solving the errors-in-variables problem: one is in Delaigle, Fan, and Carroll (2009), and one is in Huang and Zhou (2014+). The SIMEX bandwidth selection method is also provided for both estimators. * MGL (1.1) Maintainer: Safiye Celik Author(s): Safiye Celik License: GPL (>= 2) http://crantastic.org/packages/MGL An aggressive dimensionality reduction and network estimation technique for a high-dimensional Gaussian graphical model (GGM). Please refer to: Efficient Dimensionality Reduction for High-Dimensional Network Estimation, Safiye Celik, Benjamin A. Logsdon, Su-In Lee, Proceedings of The 31st International Conference on Machine Learning, 2014, p. 1953--1961. * OptionPricing (0.1) Maintainer: Wolfgang Hormann Author(s): Kemal Dingec, Wolfgang Hormann License: GPL-2 | GPL-3 http://crantastic.org/packages/OptionPricing Efficient Monte Carlo Algorithms for the price and the sensitivities of Asian and European Options under Geometric Brownian Motion. * PANDA (0.9.9) Maintainer: Hua Li Author(s): Hua Li and Pan Tong License: Artistic-2.0 http://crantastic.org/packages/PANDA PANDA (Preferential Attachment based common Neighbor Distribution derived Associations) is designed to perform the following tasks in PPI networks: (1) identify significantly functionally associated protein pairs, (2) predict GO terms and KEGG pathways for proteins, (3) make a cluster of proteins based on the significant protein pairs, (4) identify subclusters whose members are enriched in KEGG pathways. For other types of biological networks, (1) and (3) can still be performed. * pez (0.9-0) Maintainer: William D. Pearse Author(s): William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares, Caroline Tucker, Steve C. Walker, Matthew R. Helmus License: GPL-3 http://crantastic.org/packages/pez Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('shape', 'evenness', 'dispersion', and 'dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm'). * PLSbiplot1 (0.1) Maintainer: Opeoluwa F. Oyedele Author(s): Opeoluwa F. Oyedele [aut, cre], Sugnet Gardner-Lubbe [aut] License: GPL-2 http://crantastic.org/packages/PLSbiplot1 Principal Component Analysis (PCA) biplots, Covariance monoplots and biplots, Partial Least Squares (PLS) biplots, Partial Least Squares for Generalized Linear Model (PLS-GLM) biplots, Sparse Partial Least Squares (SPLS) biplots and Sparse Partial Least Squares for Generalized Linear Model (SPLS-GLM) biplots. * poplite (0.99.5) Maintainer: Daniel Bottomly Author(s): Daniel Bottomly License: GPL-3 http://crantastic.org/packages/poplite Provides objects and accompanying methods which facilitates populating and querying SQLite databases. * prc (2014.11-4) Maintainer: Youyi Fong Author(s): Youyi Fong License: GPL (>= 2) http://crantastic.org/packages/prc Estimation, prediction and testing for analyzing serial dilution assay data using paired response curve. * ScoreGGUM (1.0) Maintainer: David R. King Author(s): David R. King and James S. Roberts License: GPL (>= 2) http://crantastic.org/packages/ScoreGGUM Estimate GGUM Person Parameters Using Pre-Calibrated Item Parameters and Binary or Graded Disagree-Agree Responses * sdcTarget (0.9-11) Maintainer: Emmanuel Lazaridis Author(s): Emmanuel Lazaridis [aut, cre] License: CC BY-NC 4.0 http://crantastic.org/packages/sdcTarget Classes and methods to calculate and evaluate target matrices for statistical disclosure control. * snht (1.0) Maintainer: Josh Browning Author(s): Josh Browning License: GPL-3 http://crantastic.org/packages/snht Robust and non-robust SNHT tests for changepoint detection. * spareserver (1.0.0) Maintainer: "Gabor Csardi" Author(s): "Gabor Csardi" [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/spareserver Client size load balancing. Decide which server to connect to, based on previous response times, and configuration. * sudokuAlt (0.1-2) Maintainer: Bill Venables Author(s): Bill Venables <bill.venab...@gmail.com> License: GPL (>= 2) http://crantastic.org/packages/sudokuAlt Tools for making, retrieving, displaying and solving sudoku games. This package is an alternative to the earlier sudoku-solver package, 'sudoku'. The present package uses a slightly different algorithm, has a simpler coding and presents a few more sugar tools, such as plot and print methods. * TRSbook (1.0.1) Maintainer: P. Lafaye de Micheaux Author(s): Lafaye de Micheaux Pierre, Drouilhet Remy, Liquet Benoit License: GPL (>= 2) http://crantastic.org/packages/TRSbook Functions and datasets for the reader of the book "The R Software: Fundamentals of Programming and Statistical Analysis". * Watersheds (1.0) Maintainer: J. A. Torres Author(s): J.A. Torres License: GPL (>= 2) http://crantastic.org/packages/Watersheds Methods for watersheds aggregation and spatial drainage network analysis. * WhiteStripe (1.0) Maintainer: John Muschelli Author(s): Taki Shinohara, John Muschelli License: GPL-2 http://crantastic.org/packages/WhiteStripe Whitestripe normalization from Shinohara et. al does For intensity-based normalization of T1 and T2 images, where normal appearing white matter performs well, but requires segmentation. This method performs white matter mean and standard deviation estimates on data that has been rigidly-registered to the MNI template and uses histogram-based methods. * wikipediatrend (0.2.0) Maintainer: Peter Meissner Author(s): Peter Meissner [aut, cre], R Core team [ctb] (wp_date derived from base package as.Date) License: GPL (>= 2) http://crantastic.org/packages/wikipediatrend Public attention is an interesting field of study. The internet not only allows to access information in no time on virtually any subject but via page access statistics gathered by website authors the subject of attention as well can be studied. For the omnipresent Wikipedia those access statistics are made available via stats.grok.se a server providing the information as file dumps as well as as web API. This package provides an easy to use, consistent and traffic minimizing approach to make those data accessible within R. * xtal (1.0) Maintainer: Qingan Sun Author(s): Qingan Sun, Xiaojun Li License: GPL-2 | GPL-3 http://crantastic.org/packages/xtal Tool set for crystallographer to design and analyze crystallization experiments of ribosome from Mycobacterium tuberculosis Updated packages ---------------- afex (0.12-135), aRxiv (0.5.5), bayesTFR (4.0-9), BayesTree (0.3-1.2), BB (2014.10-1), biwavelet (0.17.5), biwavelet (0.17.4), BNSP (1.0.1), BTYD (2.4), circlize (0.1.3), cvAUC (1.0.1), descr (1.0.4), dfcomb (1.0-1), dfmta (1.0-1), dglm (1.8), dglm (1.8.1), diagram (1.6.3), dma (1.2-2), elliptic (1.3-5), extraTrees (1.0.4), feature (1.2.11), FME (1.3.2), gdimap (0.1-8), geometry (0.3-5), geomorph (2.1.2), GGIR (1.1-4), hypergeo (1.2-9), limSolve (1.5.5.1), lpSolveAPI (5.5.2.0-12), marelac (2.1.4), marmap (0.9), MAT (2.2), MGL (1.1), msgl (2.0.125.1), NMOF (0.34-0), openssl (0.2), ordinalgmifs (1.0.2), pca3d (0.3), pracma (1.7.7), prim (1.0.15), pvar (2.0), Quandl (2.4.0), readBrukerFlexData (1.8.1), Rfit (0.21), rgbif (0.7.7), RJSDMX (1.2), rminer (1.4), RobustAFT (1.3), rootSolve (1.6.5.1), RPPanalyzer (1.4), rugarch (1.3-4), shape (1.4.2), SKAT (1.0.1), snpEnrichment (1.6.0), sqldf (0.4-10), SSN (1.1.4), tagcloud (0.5), tagcloud (0.4), tm.plugin.webmining (1.2.2), TreePar (3.2), trip (1.1-19), TRSbook (1.0.1), usl (1.4.0), vcrpart (0.2-2), VGAM (0.9-5), VGAMdata (0.9-5), WARN (1.1), weightedScores (0.9.1) This email provided as a service for the R community by http://crantastic.org. 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