CRAN (and crantastic) updates this week New packages ------------
* bio3d (2.1-1) Maintainer: Barry Grant Author(s): Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide License: GPL (>= 2) http://crantastic.org/packages/bio3d Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. * CLME (1.0-1) Maintainer: Casey M. Jelsema Author(s): Casey M. Jelsema License: GPL-2 | GPL-3 http://crantastic.org/packages/CLME Implements constrained inference for linear mixed effects models using residual bootstrap methodology. * CP (1.5) Maintainer: Andreas Kuehnapfel Author(s): Andreas Kuehnapfel License: GPL-3 http://crantastic.org/packages/CP Functions for calculating the conditional power for different models in survival time analysis within randomized clinical trials with two different treatments to be compared and survival as an endpoint. * dataRetrieval (1.4.0) Maintainer: Laura DeCicco Author(s): Robert Hirsch [aut], Laura DeCicco [aut, cre] License: Unlimited | file LICENSE http://crantastic.org/packages/dataRetrieval Collection of functions to help retrieve USGS data from either web services or user-provided data files. * ecoval (1.0) Maintainer: Nele Schuwirth Author(s): Nele Schuwirth <nele.schuwi...@eawag.ch> and Peter Reichert <peter.reich...@eawag.ch> with contributions by Simone Langhans License: GPL (>= 2) http://crantastic.org/packages/ecoval Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions. * enigma (0.1.0) Maintainer: Scott Chamberlain Author(s): Scott Chamberlain [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/enigma Enigma (https://enigma.io) holds many public datasets from governments, companies, universities, and organizations. Enigma provides an API for data, metadata, and statistics on each of the datasets. enigma is an R client to interact with the Enigma API, including getting the data and metadata for datasets in Enigma, as well as collecting statistics on datasets. In addition, you can download a gzipped csv file of a dataset if you want the whole dataset. An API key from Enigma is required to use enigma. * flam (1.0) Maintainer: Ashley Petersen Author(s): Ashley Petersen License: GPL (>= 2) http://crantastic.org/packages/flam Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391. * gets (0.1) Maintainer: Genaro Sucarrat Author(s): Genaro Sucarrat License: GPL-2 http://crantastic.org/packages/gets Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or a log-ARCH-X model of the log-variance. The three main functions of the package are arx, getsm and getsv. The first function estimates an AR-X model with log-ARCH-X errors. The second function undertakes GETS model selection of the mean specification of an arx object, whereas the third function undertakes GETS model selection of the log-variance specification of an arx object. * ggRandomForests (1.0.0) Maintainer: John Ehrlinger Author(s): John Ehrlinger <john.ehrlin...@gmail.com> License: GPL (>= 3) http://crantastic.org/packages/ggRandomForests The ggRandomForests package contains tools for creating and plotting data structures to visually understand random forest models. The functions are designed for use with the randomForestSRC package. This package is structured to extract intermediate data objects from the random forest. S3 Plot functions, which use the ggplot2 package, are included for each data object. * highTtest (1.0) Maintainer: Shannon Holloway Author(s): Hongyuan Cao [aut], Michael Kosorok [aut], Shannon Holloway [aut, cre] License: GPL-2 http://crantastic.org/packages/highTtest Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion. * landpred (1.0) Maintainer: Layla Parast Author(s): Layla Parast License: GPL http://crantastic.org/packages/landpred This package includes functions for landmark prediction of a survival outcome incorporating covariate and short-term event information. For more information about landmark prediction please see: Parast, Layla, Su-Chun Cheng, and Tianxi Cai. Incorporating short-term outcome information to predict long-term survival with discrete markers. Biometrical Journal 53.2 (2011): 294-307. * logbin (1.0) Maintainer: Mark Donoghoe Author(s): Mark Donoghoe <mark.donog...@mq.edu.au> License: GPL (>= 2) http://crantastic.org/packages/logbin Methods for fitting log-link GLMs and GAMs for binomial data. The package uses EM-type algorithms with more stable convergence properties than standard methods. * logconPH (1.0) Maintainer: Clifford Anderson-Bergman Author(s): Clifford Anderson-Bergman License: GPL-2 http://crantastic.org/packages/logconPH Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector. * mdscore (0.1-2) Maintainer: Antonio Hermes M. da Silva-Junior Author(s): Antonio Hermes M. da Silva-Junior [aut, cre], Damiao N. da Silva [aut], Silvia L. P. Ferrari [ctb] License: GPL (>= 2) http://crantastic.org/packages/mdscore A set of functions to obtain modified score test for generalized linear models. * metaMix (0.1) Maintainer: Sofia Morfopoulou Author(s): Sofia Morfopoulou <sofia.morfopoulou...@ucl.ac.uk> License: GPL-3 http://crantastic.org/packages/metaMix metaMix resolves complex metagenomic mixtures by analysing deep sequencing data, using a Mixture Model based approach. The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture. * MRH (1.0) Maintainer: Yolanda Hagar Author(s): Yolanda Hagar, Yuanting Chen, Vanja Dukic License: GPL-2 http://crantastic.org/packages/MRH Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times. * nsgp (1.0.5) Maintainer: Markus Heinonen Author(s): Markus Heinonen License: GPL-2 http://crantastic.org/packages/nsgp A Gaussian process regression using a Gaussian kernel for both one-sample and two-sample cases. Includes non-stationary Gaussian kernel (exponential decay function) and several likelihood ratio tests for differential testing along target points. * pBrackets (1.0) Maintainer: ADES Author(s): Andreas Schulz License: GPL (>= 2.0) http://crantastic.org/packages/pBrackets Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets. * prettyunits (1.0.0) Maintainer: "Gabor Csardi" Author(s): "Gabor Csardi" [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/prettyunits Pretty, human readable formatting of quantities. Time intervals: 1337000 -> 15d 11h 23m 20s. Vague time intervals: 2674000 -> about a month ago. Bytes: 1337 -> 1.34 kB. * QualInt (1.0.0) Maintainer: Lixi Yu Author(s): Lixi Yu, Eun-Young Suh, Guohua (James) Pan License: GPL-2 http://crantastic.org/packages/QualInt Used for testing for qualitative interactions between treatment effects and patient subgroups. Here the term treatment effect means a comparison result of two treatments within each patient subgroup. Models included in this package are Gaussian, binomial and Cox models. Methods included here are interval based graphical approach and Gail Simon LRT. * RCMIP5 (1.0) Maintainer: Kathe Todd-Brown Author(s): Ben Bond-Lamberty [aut], Kathe Todd-Brown [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/RCMIP5 Working with CMIP5 data can be tricky, forcing scientists to write custom scripts and programs. The `RCMIP5` package aims to ease this process, providing a standard, robust, and high-performance set of scripts to (i) explore what data have been downloaded, (ii) identify missing data, (iii) average (or apply other mathematical operations) across experimental ensembles, (iv) produce both temporal and spatial statistical summaries, (v) regrid data, and (vi) produce easy-to-work-with graphical and data summaries. * rex (0.1.0) Maintainer: Jim Hester Author(s): Kevin Ushey, Jim Hester License: MIT + file LICENSE http://crantastic.org/packages/rex A simpler, human-readable interface for the construction of regular expressions. * rfoaas (0.0.4) Maintainer: Dirk Eddelbuettel Author(s): Dirk Eddelbuettel <e...@debian.org> License: GPL (>= 2) http://crantastic.org/packages/rfoaas R access to the FOAAS (F... Off As A Service) web service * rivernet (1.0) Maintainer: Peter Reichert Author(s): Peter Reichert License: GPL (>= 2) http://crantastic.org/packages/rivernet Functions for reading, analysing and plotting river networks. For this package, river networks consist of sections and nodes with associated attributes, e.g. to characterise their morphological, chemical and biological state. The package provides functions to read this data from text files, to analyse the network structure and network paths and regions consisting of sections and nodes that fulfill prescribed criteria, and to plot the river network and associated properties. * RMKdiscrete (0.1) Maintainer: Robert M. Kirkpatrick Author(s): Robert M. Kirkpatrick <rkirkpatri...@vcu.edu> License: GPL (>= 2) http://crantastic.org/packages/RMKdiscrete Sundry discrete probability distributions and helper functions. * segmag (1.2.2) Maintainer: Frank Papenmeier Author(s): Frank Papenmeier [aut, cre], Konstantin Sering [ctb] License: GPL (>= 3) http://crantastic.org/packages/segmag This package contains functions that help to determine event boundaries in event segmentation experiments by bootstrapping a critical segmentation magnitude under the null hypothesis that all key presses were randomly distributed across the experiment. Segmentation magnitude is defined as the sum of Gaussians centered at the times of the segmentation key presses performed by the participants. Within a participant, the maximum of the overlaid Gaussians is used to prevent an excessive influence of a single participant on the overall outcome (e.g. if a participant is pressing the key multiple times in succession). Further functions are included, such as plotting the results. * sisVIVE (1.0) Maintainer: Hyunseung Kang Author(s): Hyunseung Kang <khy...@wharton.upenn.edu> License: GPL-2 http://crantastic.org/packages/sisVIVE Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome. The paper, Instrumental Variables Estimation with Some Invalid Instruments and its Application to Mendelian Randomization by Hyunseung Kang, Anru Zhang, T. Tony Cai, and Dylan S. Small (on arXiv) has more details on this procedure. * spark (1.0.0) Maintainer: "Gabor Csardi" Author(s): "Gabor Csardi" [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/spark Sparklines in the terminal. Essentially an R implementation of the original shell project: http://zachholman.com/spark/ * statar (0.1) Maintainer: Matthieu Gomez Author(s): Matthieu Gomez [aut, cre] License: GPL-2 http://crantastic.org/packages/statar statar includes a set of functions for vectors: mode, tag, bin and winsorize. statar includes a set of functions for data.tables: summarize (in tables or graphs), panel data operations (lag, fill in gaps, fill in missing values) and SQL-type joins. * vetools (1.3-28) Maintainer: Andrew Sajo-Castelli Author(s): Andrew Sajo-Castelli [aut, cre], Desiree Villalta [ctb], Lelys Bravo [ctb] License: GPL http://crantastic.org/packages/vetools Integrated data management library that offers a variety of tools concerning the loading and manipulation of environmental data available from different Venezuelan governmental sources. Facilities are provided to plot temporal and spatial data as well as understand the health of a collection of meteorological data. * windex (1.0) Maintainer: Kevin Arbuckle Author(s): Kevin Arbuckle and Amanda Minter License: GPL-2 http://crantastic.org/packages/windex Analysing convergent evolution using the Wheatsheaf index. Updated packages ---------------- AICcmodavg (2.0-1), AlgDesign (1.1-7.3), ASMap (0.3-2), BcDiag (1.0.5), circlize (0.1.2), clustvarsel (2.1), crayon (1.1.0), cwhmisc (5.0), datamart (0.5.2), dice (1.2), eegkit (1.0-1), epinet (2.0.8), evtree (1.0-0), frailtypack (2.7.2), GA (2.2), gsg (2.0), kselection (0.1.1), matrixStats (0.10.3), mclogit (0.3-1), memisc (0.96-10), msBP (1.0-1), MVN (3.5), NbClust (2.0.3), NPCirc (2.0.1), overlap (0.2.4), pdc (1.0), PtProcess (3.3-7), R.devices (2.12.0), randomLCA (1.0-0), raster (2.3-12), raster (2.3-10), rcdk (3.3.2), RcmdrPlugin.steepness (0.3-2), rNOMADS (2.0.3), SCGLR (2.0.1), SemiParBIVProbit (3.2-12), SMR (2.0), spgrass6 (0.8-6), spgwr (0.6-25), sptm (14.10-11), StMoSim (3.0), stochvol (0.9-0), strvalidator (1.3.1), tis (1.27), utility (1.3) This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? 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