Planet R

October 21, 2014

CRANberries

New package DetMCD with initial version 0.0.1

Package: DetMCD
Type: Package
Title: DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter)
Version: 0.0.1
Date: 2013-01-13
Depends: matrixStats, pcaPP (>= 1.8-1), robustbase, MASS
Suggests: mvtnorm
LinkingTo: Rcpp, RcppEigen
Description: DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
License: GPL (>= 2)
LazyLoad: yes
Authors@R: c(person("Vakili", "Kaveh", role = c("aut", "cre"), email = "vakili.kaveh.email@gmail.com"), person("Mia", "Hubert", role = "ths", email = "mia.hubert@wis.kuleuven.be"))
Maintainer: Vakili Kaveh
Author: Vakili Kaveh [aut, cre], Mia Hubert [ths]
Packaged: 2014-10-21 16:15:15 UTC; kaveh
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 20:01:49

More information about DetMCD at CRAN

October 21, 2014 07:13 PM

New package scrm with initial version 1.3-1

Package: scrm
Type: Package
Title: Simulating the Evolution of Biological Sequences
Version: 1.3-1
Date: 2014-10-21
Authors@R: c( person('Paul', 'Staab', , 'develop@paulstaab.de', role=c('aut', 'cre', 'cph')), person('Zhu', 'Sha', role=c('aut', 'cph')), person('Dirk', 'Metzler', role='ths'), person('Gerton', 'Lunter', role=c('aut', 'cph', 'ths')) )
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution.
URL: https://github.com/scrm/scrm-r
License: GPL (>= 3)
Suggests: testthat (>= 0.9.0), knitr, ape
Imports: Rcpp (>= 0.11.2)
SystemRequirements: C++11
VignetteBuilder: knitr
LinkingTo: Rcpp
Packaged: 2014-10-21 11:42:11 UTC; paul
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 17:48:23

More information about scrm at CRAN

October 21, 2014 05:13 PM

New package rtkpp with initial version 0.8.2

Package: rtkpp
Type: Package
Title: STK++ integration to R using Rcpp.
Version: 0.8.2
Encoding: UTF-8
Date: 2014-02-08
Authors@R: c(person("Serge", "Iovleff", role=c("aut","cre"), email="serge.iovleff@stkpp.org"), person("Vincent", "Kubicki", role="ctb", email="Vincent.Kubicki@inria.fr"), person("Quentin", "Grimonprez", role="ctb", email="Quentin.Grimonprez@inria.fr"), person("Parmeet", "Bhatia", role="ctb", email="bhatia.parmeet@gmail.com"))
Copyright: Inria, and specifically inst/COPYRIGHTS for the STK++ library
Maintainer: Serge Iovleff
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later.
License: GPL (>= 2) | LGPL (>= 2) | file LICENSE
BugReports: https://www.stkpp.org
LazyLoad: yes
Depends: R (>= 3.0.2), Rcpp
LinkingTo: Rcpp
Imports: methods
URL: http://www.stkpp.org
NeedsCompilation: yes
SystemRequirements: GNU make
Collate: 'ClusterAlgo.R' 'ClusterInit.R' 'ClusterStrategy.R' 'IClusterModel.R' 'ClusterCategorical.R' 'ClusterDiagGaussian.R' 'ClusterGamma.R' 'ClusterModelNames.R' 'ClusterPlot.R' 'global.R' 'rtkpp.R' 'rtkppFlags.R' 'inlineCxxPlugin.R'
Packaged: 2014-10-21 12:37:40 UTC; iovleff
Author: Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb]
Repository: CRAN
Date/Publication: 2014-10-21 17:48:19

More information about rtkpp at CRAN

October 21, 2014 05:13 PM

New package cdcsis with initial version 1.0

Package: cdcsis
Type: Package
Title: Conditional Distance Correlation and Its Related Feature Screening Method
Version: 1.0
Date: 2014-09-01
Author: Canhong Wen, Wenliang Pan, Mian Huang, and Xueqin Wang
Depends: R(>= 3.0.1), stats
Imports: ks
Suggests: MASS, energy
Maintainer: Canhong Wen
Description: Gives conditional distance correlation and performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data. The conditional distance correlation is a novel conditional dependence measurement of two random variables given a third variable. The conditional distance correlation sure independence screening is used for screening variables in ultrahigh dimensional setting.
License: GPL (>= 2)
Packaged: 2014-10-21 14:47:45 UTC; wencanh
Repository: CRAN
Collate: 'cdcov.R' 'cdcor.R' 'cdcor.ada.R' 'bw.R' 'cdcsis.R'
NeedsCompilation: yes
Date/Publication: 2014-10-21 17:48:22

More information about cdcsis at CRAN

October 21, 2014 05:13 PM

Removed CRANberries

Package vcf2geno (with last version 2.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-01-23 2.3
2013-03-15 2.0
2013-03-05 1.9
2013-02-01 1.8
2013-01-20 1.7
2013-01-02 1.6
2012-10-25 1.5
2012-09-07 1.4
2012-08-29 1.3
2012-08-22 1.0

October 21, 2014 03:13 PM

CRANberries

New package openssl with initial version 0.1

Package: openssl
Type: Package
Title: Bindings to OpenSSL
Version: 0.1
Date: 2014-10-20
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: This package interfaces to the OpenSSL libraries libssl and libcrypto. Currently it only implements bindings to the OpenSSL random number generator in order to generate crypto secure random bytes in R.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/openssl
BugReports: https://github.com/jeroenooms/openssl/issues
SystemRequirements: OpenSSL (libssl-dev or openssl-devel)
Packaged: 2014-10-20 19:30:34 UTC; jeroen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 08:27:55

More information about openssl at CRAN

October 21, 2014 07:13 AM

New package tclust with initial version 1.2-3

Package: tclust
Version: 1.2-3
Date: 2014-10-20
Title: Robust Trimmed Clustering
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov
Description: Robust Trimmed Clustering
Depends: R (>= 2.12.0), mvtnorm, sn, mclust, cluster
License: GPL-3
Repository: CRAN
NeedsCompilation: yes
Packaged: 2014-10-20 13:49:50 UTC; TodorovV
Date/Publication: 2014-10-21 02:02:38

More information about tclust at CRAN

October 21, 2014 01:13 AM

October 20, 2014

CRANberries

New package ore with initial version 1.0.0

Package: ore
Version: 1.0.0
Date: 2014-10-20
Title: An R Interface to the Oniguruma Regular Expression Library
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
Depends: R (>= 2.12.1)
Suggests: crayon, rex, testthat
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Encoding: UTF-8
License: BSD_3_clause + file LICENCE
URL: https://github.com/jonclayden/ore
Packaged: 2014-10-20 15:15:03 UTC; jon
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-20 19:18:10

More information about ore at CRAN

October 20, 2014 07:13 PM

New package JMdesign with initial version 1.0

Package: JMdesign
Type: Package
Title: Joint Modeling of Longitudinal and Survival Data - Power Calculation
Version: 1.0
Date: 2012-06-01
Author: Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim
Maintainer: Shannon T. Holloway
Description: Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix Sigma_theta is unknown.
License: GPL-2
Depends: methods
Packaged: 2014-10-20 15:06:06 UTC; sthollow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-20 19:18:02

More information about JMdesign at CRAN

October 20, 2014 07:13 PM

Modern Toolmaking

For faster R on a mac, use veclib

Update: The links to all my github gists on blogger are broken, and I can't figure out how to fix them.  If you know how to insert gitub gists on a dynamic blogger template, please let me known.

In the meantime, here are instructions with links to the code:
First of all, use homebrew to compile openblas.  It's easy!  Second of all, you can also use homebrew to install R! (But maybe stick with the CRAN version unless you really want to compile your own R binary)

To use openblas with R, follow these instructions:
https://gist.github.com/zachmayer/e591cf868b3a381a01d6#file-openblas-sh

To use veclib with R, follow these intructions:
https://gist.github.com/zachmayer/e591cf868b3a381a01d6#file-veclib-sh

OLD POST:

Inspired by this post, I decided to try using OpenBLAS for R on my mac.  However, it turns out there's a simpler option, using the vecLib BLAS library, which is provided by Apple as part of the accelerate framework.

If you are using R 2.15, follow these instructions to change your BLAS from the default to vecLib:


However, as noted in r-sig-mac, these instructions do not work for R 3.0.  You have to directly link to the accelerate framework's version of vecLib:


Finally, test your new blas using this script:


On my system (a retina macbook pro), the default BLAS takes 141 seconds and vecLib takes 43 seconds, which is a significant speedup.  If you plan to use vecLib, note the following warning from the R development team "Although fast, it is not under our control and may possibly deliver inaccurate results."

So far, I have not encountered any issues using vecLib, but it's only been a few hours :-).

UPDATE: you can also install OpenBLAS on a mac:

If you do this, make sure to change the directories to point to the correct location on your system  (e.g. change /users/zach/source to whatever directory you clone the git repo into).  On my system, the benchmark script takes ~41 seconds when using openBLAS, which is a small but significant speedup.

by Zachary Deane-Mayer (noreply@blogger.com) at October 20, 2014 10:24 AM

CRANberries

New package restlos with initial version 0.1-3

Package: restlos
Type: Package
Title: Robust Estimation of Location and Scatter
Version: 0.1-3
Date: 2014-10-13
Author: Steffen Liebscher and Thomas Kirschstein
Maintainer: Steffen Liebscher
Description: The restlos package provides algorithms for robust estimation of location and scatter based on minimum spanning trees (pMST), self-organizing maps (Flood Algorithm), and Delaunay triangulations (RDELA). The functions are also suitable for outlier detection.
Depends: som, rgl, geometry, igraph
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2014-10-20 07:58:57 UTC; Steffen
X-CRAN-Comment: Archived on 2014-10-03 as depends on nnclust which has been archived.
Date/Publication: 2014-10-20 10:30:59

More information about restlos at CRAN

October 20, 2014 09:13 AM

New package commentr with initial version 0.1

Package: commentr
Type: Package
Title: Print Nicely Formatted Comments for use in Script Files
Version: 0.1
License: GPL-2
Date: 2014-10-13
Author: Erik Bulow
Maintainer: Erik Bulow
Description: Functions to produce nicely formatted comments to use in R-scripts (or Latex/HTML/markdown etc). A comment with formatting is printed to the console and can then be copied to a script.
Imports: stringr
Suggests: testthat
BugReports: https://github.com/cancercentrum/commentr/issues
Packaged: 2014-10-20 07:46:08 UTC; erikbulow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-20 10:30:16

More information about commentr at CRAN

October 20, 2014 09:13 AM

October 19, 2014

Dirk Eddelbuettel

littler 0.2.1

max-heap image

A new maintenance release of littler is available now.

The main change are a few updates and extensions to the examples provided along with littler. Several of those continue to make use of the wonderful docopt package by Edwin de Jonge. Carl Boettiger and I are making good use of these littler examples, particularly to install directly from CRAN or GitHub, in our Rocker builds of R for Docker (about which we should have a bit more to blog soon too).

Full details for the littler release are provided as usual at the ChangeLog page.

The code is available via the GitHub repo, from tarballs off my littler page and the local directory here. A fresh package has gone to the incoming queue at Debian; Michael Rutter will probably have new Ubuntu binaries at CRAN in a few days too.

Comments and suggestions are welcome via the mailing list or issue tracker at the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

October 19, 2014 09:09 PM

CRANberries

New package multispatialCCM with initial version 1.0

Package: multispatialCCM
Title: Multispatial Convergent Cross Mapping
Version: 1.0
Date: 2014-10-18
Author: Adam Clark
Maintainer: Adam Clark
Depends: R (>= 3.0.2)
Description: The multispatial convergent cross mapping algorithm can be used as a test for causal associations between pairs of processes represented by time series. This is a combination of convergent cross mapping (CCM), described in Sugihara et al., 2012, Science, 338, 496-500, and dew-drop regression, described in Hsieh et al., 2008, American Naturalist, 171, 71–80. The algorithm allows CCM to be implemented on data that are not from a single long time series. Instead, data can come from many short time series, which are stitched together using bootstrapping.
License: GPL (>= 2)
Encoding: UTF-8
Packaged: 2014-10-18 23:48:53 UTC; atclark
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-19 01:55:59

More information about multispatialCCM at CRAN

October 19, 2014 01:13 AM

New package logconPH with initial version 1.0

Package: logconPH
Type: Package
Title: CoxPH Model with Log Concave Baseline Distribution
Version: 1.0
Date: 2014-08-19
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman
Description: 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.
License: GPL-2
Packaged: 2014-10-18 23:32:43 UTC; Cliff
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-19 01:49:27

More information about logconPH at CRAN

October 19, 2014 01:13 AM

October 18, 2014

CRANberries

New package landpred with initial version 1.0

Package: landpred
Type: Package
Title: Landmark Prediction of a Survival Outcome
Version: 1.0
Author: Layla Parast
Maintainer: Layla Parast
Description: 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.
License: GPL
Imports: survival
Packaged: 2014-10-17 22:28:12 UTC; parast
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-18 06:36:04

More information about landpred at CRAN

October 18, 2014 05:13 AM

October 17, 2014

CRANberries

New package RMKdiscrete with initial version 0.1

Package: RMKdiscrete
Version: 0.1
Date: 2014-10-17
Title: Sundry Discrete Probability Distributions
Author: Robert M. Kirkpatrick
Maintainer: Robert M. Kirkpatrick
Description: Sundry discrete probability distributions and helper functions.
Depends: stats, R (>= 2.15.0)
NeedsCompilation: yes
Repository: CRAN
License: GPL (>= 2)
Packaged: 2014-10-17 16:15:33 UTC; Rob
Date/Publication: 2014-10-17 20:23:16

More information about RMKdiscrete at CRAN

October 17, 2014 07:13 PM

New package highTtest with initial version 1.0

Package: highTtest
Type: Package
Title: Simultaneous Critical Values for t-Tests in Very High Dimensions
Version: 1.0
Date: 2014-10-14
Authors@R: c(person("Hongyuan", "Cao", role = c("aut"), email = "caohong@missouri.edu"), person("Michael", "Kosorok", role = c("aut"), email = "kosorok@unc.edu"), person("Shannon","Holloway", role=c("aut","cre"), email="sthollow@ncsu.edu"))
Description: 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.
License: GPL-2
Depends: methods, colorfulVennPlot
Packaged: 2014-10-17 16:31:13 UTC; sthollow
Author: Hongyuan Cao [aut], Michael Kosorok [aut], Shannon Holloway [aut, cre]
Maintainer: Shannon Holloway
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 19:54:38

More information about highTtest at CRAN

October 17, 2014 07:13 PM

New package sisVIVE with initial version 1.0

Package: sisVIVE
Type: Package
Title: Some Invalid Some Valid Instrumental Variables Estimator
Version: 1.0
Date: 2014-07-31
Author: Hyunseung Kang
Maintainer: Hyunseung Kang
Depends: lars
Suggests: MASS
Description: 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.
License: GPL-2
Packaged: 2014-10-17 14:29:30 UTC; khyuns
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:39:17

More information about sisVIVE at CRAN

October 17, 2014 05:13 PM

New package MRH with initial version 1.0

Package: MRH
Type: Package
Title: Multi-Resolution Estimation of the Hazard Rate
Version: 1.0
Date: 2013-10-28
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times.
License: GPL-2
Depends: survival, KMsurv
Suggests: R.rsp
VignetteBuilder: R.rsp
Imports: coda, HI
Packaged: 2014-10-17 15:44:27 UTC; Yolanda
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-17 17:52:12

More information about MRH at CRAN

October 17, 2014 05:13 PM

New package mdscore with initial version 0.1-2

Package: mdscore
Type: Package
Title: Improved Score Tests for Generalized Linear Models
Version: 0.1-2
Date: 2014-10-15
Depends: R (>= 3.1.1), MASS
Suggests: Sleuth3
Authors@R: c(person("Antonio Hermes M.","da Silva-Junior", email = "hermes@ccet.ufrn.br", role = c("aut", "cre")), person("Damiao N.","da Silva", email = "damiao@ccet.ufrn.br", role = "aut"), person("Silvia L. P.", "Ferrari", email = "silviaferrari.usp@gmail.com", role = "ctb"))
Author: Antonio Hermes M. da Silva-Junior [aut, cre], Damiao N. da Silva [aut], Silvia L. P. Ferrari [ctb]
Maintainer: Antonio Hermes M. da Silva-Junior
Description: A set of functions to obtain modified score test for generalized linear models.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2014-10-17 12:28:47 UTC; mlfd58
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:50:40

More information about mdscore at CRAN

October 17, 2014 05:13 PM

New package likert with initial version 1.2

Package: likert
Type: Package
Title: Functions to analyze and visualize likert type items
Version: 1.2
Date: 2014-09-28
Author: Jason Bryer , Kimberly Speerschneider
Maintainer: Jason Bryer
URL: http://jason.bryer.org/likert, http://github.com/jbryer/likert
BugReports: https://github.com/jbryer/likert/issues
Description: Functions to analyze and visualize likert type items
License: GPL
LazyLoad: yes
VignetteBuilder: utils
Depends: R (>= 3.0),ggplot2,xtable
Imports: psych,reshape,gridExtra,grid,plyr
Suggests: devtools,shiny
Packaged: 2014-10-17 14:01:18 UTC; jbryer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:43:09

More information about likert at CRAN

October 17, 2014 05:13 PM

New package ecoval with initial version 1.0

Package: ecoval
Type: Package
Title: Procedures for Ecological Assessment of Surface Waters
Version: 1.0
Date: 2014-10-17
Author: Nele Schuwirth and Peter Reichert with contributions by Simone Langhans
Maintainer: Nele Schuwirth
Description: Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.
License: GPL (>= 2)
Depends: utility, rivernet
LazyData: true
Packaged: 2014-10-17 14:19:43 UTC; schuwine
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:36:36

More information about ecoval at CRAN

October 17, 2014 05:13 PM

New package CLME with initial version 1.0-1

Package: CLME
Title: Constrained Inference for Linear Mixed Effects Models.
Version: 1.0-1
Depends: R (>= 3.0.2)
Imports: MASS, quadprog, shiny, methods, Iso
Suggests: nnet
Date: 2014-09-09
Description: Implements constrained inference for linear mixed effects models using residual bootstrap methodology.
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema
BugReports: https://github.com/jelsema/CLME/issues
BuildVignettes: true
LazyLoad: yes
License: GPL-2 | GPL-3
Packaged: 2014-10-17 16:02:45 UTC; jelsemacm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 18:22:17

More information about CLME at CRAN

October 17, 2014 05:13 PM

Removed CRANberries

Package WebDevelopR (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-04-09 1.0

October 17, 2014 03:13 PM

CRANberries

New package pBrackets with initial version 1.0

Package: pBrackets
Version: 1.0
Date: 2014-10-17
Title: Plot Brackets
Author: Andreas Schulz
Maintainer: Andreas Schulz
Depends: R (>= 3.0.0)
Imports: grid
Description: Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets.
License: GPL (>= 2.0)
Packaged: 2014-10-17 09:30:23 UTC; scu9a
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 13:08:28

More information about pBrackets at CRAN

October 17, 2014 01:13 PM

New package segmag with initial version 1.2.2

Package: segmag
Type: Package
Version: 1.2.2
Date: 2014-10-06
Title: Determine Event Boundaries in Event Segmentation Experiments
Maintainer: Frank Papenmeier
Author: Frank Papenmeier [aut, cre], Konstantin Sering [ctb]
Authors@R: c(person("Frank","Papenmeier", role=c("aut","cre"), email="frank.papenmeier@uni-tuebingen.de"), person("Konstantin","Sering", role="ctb"))
Description: 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.
License: GPL (>= 3)
Suggests: testthat
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Packaged: 2014-10-06 15:55:49 UTC; fpapenmeier
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-17 10:30:45

More information about segmag at CRAN

October 17, 2014 09:13 AM

October 16, 2014

CRANberries

New package rivernet with initial version 1.0

Package: rivernet
Type: Package
Title: Read, Analyze and Plot River Networks
Version: 1.0
Date: 2014-10-16
Author: Peter Reichert
Maintainer: Peter Reichert
Description: 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.
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-16 07:39:29 UTC; reichert
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 23:51:16

More information about rivernet at CRAN

October 16, 2014 11:13 PM

New package enigma with initial version 0.1.0

Package: enigma
Title: R Client for the Enigma API
Description: 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.
Version: 0.1.0
Date: 2014-10-16
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"))
License: MIT + file LICENSE
LazyData: true
Imports: httr, jsonlite, plyr
Suggests: testthat
Packaged: 2014-10-16 21:25:40 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 00:42:42

More information about enigma at CRAN

October 16, 2014 11:13 PM

New package statar with initial version 0.1

Package: statar
Title: Tools Inspired by Stata to Clean, Explore and Join Datasets
Version: 0.1
Authors@R: person("Matthieu","Gomez", email = "mattg@princeton.edu", role = c("aut", "cre"))
Description: 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.
License: GPL-2
URL: https://github.com/matthieugomez/statar
BugReports: https://github.com/matthieugomez/statar/issues
Depends: R (>= 3.1.0)
Imports: data.table, dplyr (>= 0.3), ggplot2, grid, Hmisc, lazyeval, lubridate, matrixStats, stringr, tidyr
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-10-16 15:26:12 UTC; Matthieu
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 22:56:33

More information about statar at CRAN

October 16, 2014 09:13 PM

New package RCMIP5 with initial version 1.0

Package: RCMIP5
Title: Tools for Manipulating and Summarizing CMIP5 Data
Description: 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.
Imports: abind (>= 1.4-0), plyr (>= 1.8.1), reshape2 (>= 1.4), foreach (>= 1.4.2), digest
Depends: R (>= 2.11.0)
Suggests: ggplot2 (>= 0.9.3), ncdf4 (>= 1.9), ncdf (>= 1.6), doParallel (>= 1.0.8), fields(>= 7.1), testthat (>= 0.9), knitr
Version: 1.0
Authors@R: c( person("Ben", "Bond-Lamberty", role = c("aut")), person("Kathe", "Todd-Brown", role = c("aut", "cre"), email = "ktoddbrown@gmail.com") )
License: MIT + file LICENSE
VignetteBuilder: knitr
Packaged: 2014-10-15 03:07:51 UTC; ben
Author: Ben Bond-Lamberty [aut], Kathe Todd-Brown [aut, cre]
Maintainer: Kathe Todd-Brown
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 14:03:50

More information about RCMIP5 at CRAN

October 16, 2014 01:13 PM

New package RcmdrPlugin.steepness with initial version 0.3-2

Package: RcmdrPlugin.steepness
Type: Package
Title: Steepness Rcmdr Plug-in
Version: 0.3-2
Date: 2014-29-09
Author: David Leiva & Han de Vries
Maintainer: David Leiva
Depends: Rcmdr (>= 2.1-2), tcltk, steepness
Description: This package provides a GUI for the steepness package, it is written as an Rcmdr plug-in.
License: GPL (>= 2)
Packaged: 2014-09-29 21:07:02 UTC; dleivaur
NeedsCompilation: no
X-CRAN-Comment: Archived on 2013-03-23 and again on 2014-05-30 as steepness was.
Repository: CRAN
Date/Publication: 2014-10-16 14:05:53

More information about RcmdrPlugin.steepness at CRAN

October 16, 2014 01:13 PM

New package logbin with initial version 1.0

Package: logbin
Title: Relative Risk Regression Using the Log Binomial Model
Description: 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.
Version: 1.0
Date: 2014-10-16
Author: Mark Donoghoe
Maintainer: Mark Donoghoe
Depends: R (>= 3.0.1)
Imports: splines, glm2
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-16 03:19:53 UTC; mdonoghoe
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 07:58:44

More information about logbin at CRAN

October 16, 2014 07:13 AM

Removed CRANberries

Package GOsummaries (with last version 1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-03-12 1.1
2013-04-04 1.0

October 16, 2014 07:13 AM

CRANberries

New package rfoaas with initial version 0.0.4

Package: rfoaas
Type: Package
Title: R Interface to FOAAS
Version: 0.0.4
Date: 2014-10-15
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Description: R access to the FOAAS (F... Off As A Service) web service
License: GPL (>= 2)
Packaged: 2014-10-15 10:55:44.845568 UTC; edd
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 01:17:17

More information about rfoaas at CRAN

October 16, 2014 01:13 AM

New package metaMix with initial version 0.1

Package: metaMix
Title: Bayesian Mixture Analysis for Metagenomic Community Profiling
Version: 0.1
Author: Sofia Morfopoulou
Maintainer: Sofia Morfopoulou
Depends: R (>= 3.0.1)
Imports: data.table (>= 1.9.2), Matrix, gtools, Rmpi, ggplot2
Suggests: knitr
VignetteBuilder: knitr
Description: 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.
License: GPL-3
LazyData: true
SystemRequirements: Open MPI (>=1.4.3)
Packaged: 2014-10-15 11:36:19 UTC; psofaki
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-16 01:26:14

More information about metaMix at CRAN

October 16, 2014 01:13 AM

October 15, 2014

CRANberries

New package windex with initial version 1.0

Package: windex
Type: Package
Title: windex: Analysing convergent evolution using the Wheatsheaf index
Version: 1.0
Date: 2014-09-05
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle
Description: Analysing convergent evolution using the Wheatsheaf index.
License: GPL-2
Depends: geiger (>= 2.0), ape, scatterplot3d, utils, R (>= 3.0.0)
Packaged: 2014-10-14 13:49:37 UTC; aminter
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 00:01:11

More information about windex at CRAN

October 15, 2014 11:13 PM

New package ggRandomForests with initial version 1.0.0

Package: ggRandomForests
Type: Package
Title: Creating and Plotting Data Objects for Understanding Random Forests
Version: 1.0.0
Date: 2014-10-15
Author: John Ehrlinger
Maintainer: John Ehrlinger
License: GPL (>= 3)
URL: https://github.com/ehrlinger/ggRandomForests
Description: 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.
Depends: R (>= 3.1.0), ggplot2, randomForestSRC, reshape2, survival, dplyr
Suggests: testthat
Packaged: 2014-10-15 18:13:42 UTC; ehrlinj
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:53:25

More information about ggRandomForests at CRAN

October 15, 2014 11:13 PM

New package cwhmisc with initial version 5.0

Package: cwhmisc
Version: 5.0
Date: 2014-10-15
Title: Miscellaneous Functions for math, plotting, printing, statistics, strings, and tools
Author: Christian W. Hoffmann
Maintainer: Christian W. Hoffmann
Depends: R (>= 2.0), lattice, grid
Description: Miscellaneous useful or interesting functions. Some parameters of functions may have changed, so beware!
License: GPL (>= 2)
Packaged: 2014-10-15 14:05:48 UTC; hoffmann
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:37:39

More information about cwhmisc at CRAN

October 15, 2014 11:13 PM

New package bio3d with initial version 2.1-1

Package: bio3d
Title: Biological Structure Analysis
Version: 2.1-1
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
VignetteBuilder: knitr
Imports: parallel, grid
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat
Depends: R (>= 3.0.0)
LazyData: yes
Description: 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.
Maintainer: Barry Grant
License: GPL (>= 2)
URL: http://thegrantlab.org/bio3d/, http://bitbucket.org/Grantlab/bio3d
Packaged: 2014-10-15 20:07:48 UTC; xinqyao
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 23:56:55

More information about bio3d at CRAN

October 15, 2014 11:13 PM

New package gets with initial version 0.1

Package: gets
Type: Package
Title: General-to-Specific (GETS) Model Selection
Version: 0.1
Depends: R (>= 2.4.1), zoo, lgarch
Date: 2014-10-14
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
Description: 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.
License: GPL-2
Packaged: 2014-10-15 09:28:20 UTC; admin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 13:16:36

More information about gets at CRAN

October 15, 2014 01:13 PM

New package vetools with initial version 1.3-28

Encoding: UTF-8
Package: vetools
Depends: R (>= 2.10), sp
Imports: stringr, tis, lubridate, maptools, plyr, xts, scales
Maintainer: Andrew Sajo-Castelli
License: GPL
Title: Tools for Venezuelan Environmental Data
LazyData: false
Type: Package
Authors@R: c(person("Andrew", "Sajo-Castelli", email="asajo@usb.ve", role = c("aut", "cre")), person("Desiree", "Villalta", role = "ctb"),person("Lelys", "Bravo", role = "ctb"))
Description: 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.
Version: 1.3-28
Revision: $Rev: 4 $
BugReports: https://github.com/talassio/vetools/issues
Packaged: 2014-10-15 05:41:42 UTC; cesma
Author: Andrew Sajo-Castelli [aut, cre], Desiree Villalta [ctb], Lelys Bravo [ctb]
NeedsCompilation: no
Repository: CRAN
Date: 2013-08-01 14:10:01
Date/Publication: 2014-10-15 08:47:53

More information about vetools at CRAN

October 15, 2014 07:13 AM

Statistical Modelling

Sensitivity analysis and calibration of population size estimates obtained with the zero-truncated Poisson regression model

Zero-truncated regression models for count data can be used to estimate the size of an elusive population. A frequently encountered problem is that the Poisson model underestimates the population size due to unobserved heterogeneity, while the negative binomial model is not identified. A sensitivity analysis using the negative binomial model with fixed dispersion parameter might provide inside in the robustness of the population size estimate against unobserved heterogeneity, but as yet there is no method to determine realistic values for the dispersion parameter. This article introduces an R-squared measure and the use of the Pearson dispersion statistic to alleviate this problem. As a spin-off, a method is proposed for calibration of population size estimates in monitoring studies where the number of covariates varies over the measurement occasions. The performance of these methods is evaluated in simulation studies, and is illustrated on a population of drunk drivers.

by Cruyff, M. J., Van der Heijden, P. G. at October 15, 2014 06:25 AM

Modelling and coherent forecasting of zero-inflated count time series

In this article, a new kind of stationary zero-inflated Pegram’s operator based integer-valued time series process of order p with Poisson marginal or ZIPPAR(p) process is constructed for modelling count time series consisting a large number of zeros compared to standard Poisson time series processes. Several properties like stationarity, ergodicity are examined. Estimates of the model parameters are studied using three methods of estimation, namely Yule–Walker, conditional least squares and maximum likelihood estimation. Also h-step ahead coherent forecasting distributions of the proposed process for p = 1, 2 are derived. Real data set is used to examine and illustrate the proposed process with some simulation studies.

by Maiti, R., Biswas, A., Guha, A., Ong, S. H. at October 15, 2014 06:25 AM

A model for overdispersed hierarchical ordinal data

Non-Gaussian outcomes are frequently modelled using members of the exponential family. In particular, the Bernoulli model for binary data and the Poisson model for count data are well-known. Two reasons for extending this family are (1) the occurrence of overdispersion, implying that the variability in the data is not adequately described by the models, and (2) the incorporation of hierarchical structure in the data. These issues are routinely addressed separately, the first one through overdispersion models, the second one, for example, by means of random effects within the generalized linear mixed models framework. Molenberghs et al. (2007, 2010) introduced a so-called ‘combined model’ that simultaneously addresses both. In these and subsequent papers, a lot of attention was given to binary outcomes, counts, and time-to-event responses. While common in practice, ordinal data have not been studied from this angle. In this article, a model for ordinal repeated measures, subject to overdispersion, is formulated. It can be fitted without difficulty using standard statistical software. The model is exemplified using data from an epidemiological study in diabetic patients and using data from a clinical trial in psychiatric patients.

by Ivanova, A., Molenberghs, G., Verbeke, G. at October 15, 2014 06:25 AM

Quasi-periodic spatiotemporal models of brain activation in single-trial MEG experiments

Magneto-encephalography (MEG) is an imaging technique which measures neuronal activity in the brain. Even when a subject is in a resting state, MEG data show characteristic spatial and temporal patterns, resulting from electrical current at specific locations in the brain. The key pattern of interest is a ‘dipole’, consisting of two adjacent regions of high and low activation which oscillate over time in an out-of-phase manner. Standard approaches are based on averages over large numbers of trials in order to reduce noise. In contrast, this article addresses the issue of dipole modelling for single trial data, as this is of interest in application areas. There is also clear evidence that the frequency of this oscillation in single trials generally changes over time and so exhibits quasi-periodic rather than periodic behaviour. A framework for the modelling of dipoles is proposed through estimation of a spatiotemporal smooth function constructed as a parametric function of space and a smooth function of time. Quasi-periodic behaviour is expressed in phase functions which are allowed to evolve smoothly over time. The model is fitted in two stages. First, the spatial location of the dipole is identified and the smooth signals characterizing the amplitude functions for each separate pole are estimated. Second, the phase and frequency of the amplitude signals are estimated as smooth functions. The model is applied to data from a real MEG experiment focusing on motor and visual brain processes. In contrast to existing standard approaches, the model allows the variability across trials and subjects to be identified. The nature of this variability is informative about the resting state of the brain.

by Ventrucci, M., Bowman, A. W., Miller, C., Gross, J. at October 15, 2014 06:25 AM

A zero-inflated overdispersed hierarchical Poisson model

Count data are most commonly modeled using the Poisson model, or by one of its many extensions. Such extensions are needed for a variety of reasons: (1) a hierarchical structure in the data, e.g., due to clustering, the collection of repeated measurements of the outcome, etc.; (2) the occurrence of overdispersion (or underdispersion), meaning that the variability encountered in the data is not equal to the mean, as prescribed by the Poisson distribution; and (3) the occurrence of extra zeros beyond what a Poisson model allows. The first issue is often accommodated through the inclusion of random subject-specific effects. Though not always, one conventionally assumes such random effects to be normally distributed. Overdispersion is often dealt with through a model developed for this purpose, such as, for example, the negative-binomial model for count data. This can be conceived through a random Poisson parameter. Excess zeros are regularly accounted for using so-called zero-inflated models, which combine either a Poisson or negative-binomial model with an atom at zero. The novelty of this article is that it combines all these features. The work builds upon the modelling framework defined by Molenberghs et al. (2010) in which clustering and overdispersion are accommodated for through two separate sets of random effects in a generalized linear model.

by Kassahun, W., Neyens, T., Faes, C., Molenberghs, G., Verbeke, G. at October 15, 2014 06:25 AM

Erratum

Harvey Goldstein, Daphne Kounali, and Anthony Robinson (2008), "Modelling measurement errors and category misclassifications in multilevel models," Statistical Modelling, 8(3), 243–261. DOI: 10.1177/1471082X0800800302

October 15, 2014 06:25 AM

CRANberries

New package nsgp with initial version 1.0.5

Package: nsgp
Title: Non-Stationary Gaussian Process Regression
Version: 1.0.5
Date: 2014-10-14
Author: Markus Heinonen
Maintainer: Markus Heinonen
Depends: R (>= 3.0.0)
Imports: MASS
Description: 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.
License: GPL-2
URL: http://amis-group.fr/software/nsgp
Packaged: 2014-10-14 14:29:42 UTC; markusheinonen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 06:54:09

More information about nsgp at CRAN

October 15, 2014 05:13 AM

New package spark with initial version 1.0.0

Package: spark
Title: Sparklines in the R Terminal
Version: 1.0.0
Authors@R: "Gabor Csardi [aut, cre]"
Description: Sparklines in the terminal. Essentially an R implementation of the original shell project: http://zachholman.com/spark/
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/gaborcsardi/spark
BugReports: https://github.com/gaborcsardi/pretty/spark
Imports: magrittr
Suggests: crayon, testthat
Packaged: 2014-10-14 13:44:34 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-15 02:45:14

More information about spark at CRAN

October 15, 2014 01:13 AM

October 14, 2014

Bioconductor Project Working Papers

CRANberries

New package rex with initial version 0.1.0

Package: rex
Type: Package
Title: Simpler Regular Expressions
Version: 0.1.0
Date: 2013-01-16
Author: Kevin Ushey, Jim Hester
Maintainer: Jim Hester
Description: A simpler, human-readable interface for the construction of regular expressions.
Imports: magrittr, lazyeval
License: MIT + file LICENSE
Suggests: testthat, knitr, dplyr, ggplot2
VignetteBuilder: knitr
Collate: 'aaa.R' 'utils.R' 'escape.R' 'capture.R' 'character_class.R' 'counts.R' 'lookarounds.R' 'match.R' 'or.R' 'rex-mode.R' 'rex.R' 'shortcuts.R' 'wildcards.R' 'zzz.R'
Packaged: 2014-10-13 20:22:57 UTC; james.hester
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-14 05:27:22

More information about rex at CRAN

October 14, 2014 05:13 AM

Removed CRANberries

Package oposSOM (with last version 0.2-3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-08-13 0.2-3
2012-10-17 0.2-2
2012-06-27 0.2-1
2012-04-12 0.1-4
2011-07-27 0.1-3
2011-06-17 0.1-1

October 14, 2014 05:13 AM

October 13, 2014

CRANberries

New package flam with initial version 1.0

Package: flam
Type: Package
Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Version: 1.0
Date: 2014-10-13
Author: Ashley Petersen
Maintainer: Ashley Petersen
Imports: MASS
Description: 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.
License: GPL (>= 2)
Packaged: 2014-10-13 17:51:08 UTC; ajpete
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-13 21:53:48

More information about flam at CRAN

October 13, 2014 09:13 PM

New package dataRetrieval with initial version 1.4.0

Package: dataRetrieval
Type: Package
Title: Retrieval functions for hydrologic data
Version: 1.4.0
Date: 2014-10-13
Authors@R: c( person("Robert", "Hirsch", role = c("aut"), email = "rhirsch@usgs.gov"), person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov"))
Description: Collection of functions to help retrieve USGS data from either web services or user-provided data files.
License: Unlimited | file LICENSE
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright
Depends: R (>= 3.0)
Imports: zoo, XML, RCurl, reshape2, lubridate
Suggests: xtable, EGRET, knitr, testthat
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
Additional_repositories: http://usgs-r.github.com
Packaged: 2014-10-13 15:59:48 UTC; ldecicco
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 21:59:18

More information about dataRetrieval at CRAN

October 13, 2014 09:13 PM

New package prettyunits with initial version 1.0.0

Package: prettyunits
Title: Pretty, Human Readable Formatting of Quantities
Version: 1.0.0
Authors@R: "Gabor Csardi [aut, cre]"
Description: 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.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/gaborcsardi/prettyunits
BugReports: https://github.com/gaborcsardi/prettyunits/issues
Imports: magrittr, assertthat
Suggests: testthat
Packaged: 2014-10-13 13:22:50 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 17:32:18

More information about prettyunits at CRAN

October 13, 2014 05:13 PM

New package CP with initial version 1.5

Package: CP
Type: Package
Title: Conditional Power Calculations
Version: 1.5
Date: 2014-10-13
Author: Andreas Kuehnapfel
Maintainer: Andreas Kuehnapfel
Depends: R(>= 3.0.1)
Imports: survival
Description: 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.
License: GPL-3
URL: https://www.imise.uni-leipzig.de
LazyLoad: yes
LazyData: yes
Packaged: 2014-10-13 07:35:22 UTC; akuehnapfel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 13:35:27

More information about CP at CRAN

October 13, 2014 01:13 PM

New package QualInt with initial version 1.0.0

Package: QualInt
Title: Test for Qualitative Interactions
Version: 1.0.0
Author: Lixi Yu, Eun-Young Suh, Guohua (James) Pan
Maintainer: Lixi Yu
Description: 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.
Depends: survival, ggplot2
License: GPL-2
LazyLoad: yes
Packaged: 2014-10-13 06:18:25 UTC; Lixi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-13 09:58:21

More information about QualInt at CRAN

October 13, 2014 09:13 AM

Dirk Eddelbuettel

Seinfeld streak at GitHub

Early last year, I referred to a Seinfeld Streak in a blog post referring to almost two months of updates to the Rcpp Gallery. This is sometimes called Jerry Seinfeld's secret to productivity: Just keep at it. Don't break the streak.

I now have different streak:

github activity october 2013 to october 2014

Now we'll see how far this one will go.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

October 13, 2014 12:23 AM

October 12, 2014

CRANberries

New package RNetLogo with initial version 1.0-1

Package: RNetLogo
Version: 1.0-1
Date: 2014-10-12
Title: Provides an Interface to the Agent-Based Modelling Platform NetLogo
Author: Jan C. Thiele
Maintainer: Jan C. Thiele
Description: Interface to use and access Wilensky's NetLogo (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the NetLogo Mathematica Link http://ccl.northwestern.edu/netlogo/docs/mathematica.html
Depends: R (>= 2.12.1), rJava (>= 0.6-3), igraph
Suggests: parallel
SystemRequirements: Java (>= 6.0), NetLogo (>= 5.0)
License: GPL-2
LazyLoad: yes
URL: http://rnetlogo.r-forge.r-project.org/
Packaged: 2014-10-12 13:24:12 UTC; jthiele
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-12 18:56:10

More information about RNetLogo at CRAN

October 12, 2014 05:13 PM