Planet R

October 25, 2014

CRANberries

New package managelocalrepo with initial version 0.1.4

Package: managelocalrepo
Type: Package
Title: Manage a CRAN-style Local Repository
Version: 0.1.4
Date: 2014-10-25
Author: Imanuel Costigan
Maintainer: Imanuel Costigan
Description: This will allow easier management of a CRAN-style repository on local networks (i.e. not on CRAN). This might be necessary where hosted packages contain intellectual property owned by a corporation.
License: GPL-2
Depends: R (>= 3.0)
Imports: stringr (>= 0.6.2), assertthat (>= 0.1), tools (>= 3.0)
Packaged: 2014-10-25 03:44:33 UTC; imanuel
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:55

More information about managelocalrepo at CRAN

October 25, 2014 07:13 AM

New package HiDimDA with initial version 0.2-2

Package: HiDimDA
Type: Package
Title: High Dimensional Discriminant Analysis
Version: 0.2-2
Date: 2014-10-24
Author: Antonio Pedro Duarte Silva
Maintainer: Antonio Pedro Duarte Silva
Depends: R (>= 2.10.0)
Imports: splines
Suggests: MASS
LazyLoad: yes
LazyData: yes
Description: Performs linear discriminant analysis in high dimensional problems based on reliable covariance estimators for problems with (many) more variables than observations. Includes routines for classifier training, prediction, cross-validation and variable selection.
License: GPL (>= 3)
URL: http://www.r-project.org
Repository: CRAN
Packaged: 2014-10-24 13:48:10 UTC; apedro
NeedsCompilation: yes
Date/Publication: 2014-10-25 07:51:03

More information about HiDimDA at CRAN

October 25, 2014 07:13 AM

New package choroplethrMaps with initial version 1.0

Package: choroplethrMaps
Type: Package
Title: Contains maps used by the choroplethr package
Version: 1.0
Date: 2014-10-22
Author: Ari Lamstein
Maintainer: Ari Lamstein
Description: Contains 3 maps. 1) US States 2) US Counties 3) Countries of the world.
License: BSD_3_clause + file LICENSE
URL: https://github.com/trulia/choroplethrMaps/, https://groups.google.com/forum/#!forum/choroplethr
BugReports: https://github.com/trulia/choroplethrMaps/issues
Suggests: ggplot2
Packaged: 2014-10-25 02:51:32 UTC; arilamstein
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:52

More information about choroplethrMaps at CRAN

October 25, 2014 07:13 AM

New package BayesMixSurv with initial version 0.9

Package: BayesMixSurv
Type: Package
Title: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification
Version: 0.9
Date: 2014-10-24
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification
License: GPL (>= 2)
Depends: survival
Packaged: 2014-10-25 01:34:35 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-25 08:07:48

More information about BayesMixSurv at CRAN

October 25, 2014 07:13 AM

New package highD2pop with initial version 1.0

Package: highD2pop
Type: Package
Title: Two-Sample Tests for Equality of Means in High Dimension
Version: 1.0
Date: 2012-11-02
Author: Karl Gregory
Maintainer: Karl Gregory
Description: Performs the generalized component test from Gregory et al (2015), as well as the tests from Chen and Qin (2010), Srivastava and Kubokawa (2013), and Cai, Liu, and Xia (2014) for equality of two population mean vectors when the length of the vectors exceeds the sample size.
License: GPL (>= 2)
LazyLoad: true
LazyData: true
ZipData: no
Depends: fastclime
Packaged: 2014-10-24 14:25:33 UTC; karlgregory
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-25 01:28:48

More information about highD2pop at CRAN

October 25, 2014 01:13 AM

October 24, 2014

CRANberries

New package ruv with initial version 0.9.4

Package: ruv
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: The algorithms in this package attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. The algorithms included in this package are RUV-2, RUV-4, RUV-inv, and RUV-rinv, along with various supporting algorithms. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specifiy a set of negative control variables, as described in the references.
Version: 0.9.4
Date: 2014-10-24
Author: Johann Gagnon-Bartsch
Maintainer: Johann Gagnon-Bartsch
License: GPL
URL: http://www.stat.berkeley.edu/~johann/ruv
LazyLoad: yes
Packaged: 2014-10-24 09:52:13 UTC; johann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-24 13:55:18

More information about ruv at CRAN

October 24, 2014 01:13 PM

New package PANICr with initial version 0.0.0.2

Package: PANICr
Title: PANIC Tests of Nonstationarity
Description: This package contains a methodology that makes use of the factor structure of large dimensional panels to understand the nature of nonstationarity inherent in data. This is referred to as PANIC - Panel Analysis of Nonstationarity in Idiosyncratic and Common Components. PANIC (2004) includes valid pooling methods that allow panel tests to be constructed. PANIC (2004) can detect whether the nonstationarity in a series is pervasive, or variable specific, or both. PANIC (2010) includes two new tests on the idiosyncratic component that estimates the pooled autoregressive coefficient and sample moment, respectively. The PANIC model approximates the number of factors based on Bai and Ng (2002)
Depends: R(>= 2.10.0)
Version: 0.0.0.2
License: GPL-3
LazyData: no
Author: Steve Bronder
Maintainer: Steve Bronder
URL: stevebronder.com
Suggests: knitr
VignetteBuilder: knitr
Imports: MCMCpack
Packaged: 2014-10-24 06:46:57 UTC; brond_000
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-24 10:55:46

More information about PANICr at CRAN

October 24, 2014 11:13 AM

Removed CRANberries

Package bio3d (with last version 2.1-2) was removed from CRAN

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

2014-10-21 2.1-2
2014-10-15 2.1-1

October 24, 2014 09:13 AM

CRANberries

New package PHENIX with initial version 1.0

Package: PHENIX
Type: Package
Title: Phenotypic Integration Index
Version: 1.0
Date: 2014-10-15
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
Imports: ppcor
Encoding: UTF-8
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might overestimate the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) and a bootstrapping method to test the significance of both integration indices.
License: GPL (>= 2)
Packaged: 2014-10-23 20:33:24 UTC; ajesusmp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-24 07:51:38

More information about PHENIX at CRAN

October 24, 2014 07:13 AM

New package P2C2M with initial version 0.5

Package: P2C2M
Type: Package
Title: Posterior Predictive Checks of Coalescent Models
Version: 0.5
Date: 2014-10-23
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl
Depends: R (>= 3.0.0)
Imports: ape (>= 3.1-4), apTreeshape (>= 1.4-5), ggplot2 (>= 1.0.0), rPython (>= 0.0-5), stringr (>= 0.6.2)
Suggests: genealogicalSorting (>= 0.92), phybase (>= 1.3.1), Rmpi (>= 0.6-5), xtermStyle (>= 2.2-4)
Description: P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST and *BEAST, respectively. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is necessary.
License: GPL (>= 2)
OS_type: unix
NeedsCompilation: yes (automatic)
SystemRequirements: Python (= 2.7)
Packaged: 2014-10-23 06:55:27 UTC; michael
Repository: CRAN
Date/Publication: 2014-10-24 07:51:37

More information about P2C2M at CRAN

October 24, 2014 07:13 AM

Removed CRANberries

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

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

2013-10-15 1.0

October 24, 2014 07:13 AM

Journal of Statistical Software

Implementing Reproducible Research

Vol. 61, Book Review 2, Oct 2014

Implementing Reproducible Research
Victoria Stodden, Friedrich Leisch, Roger D. Peng
CRC Press, 2014
ISBN: 978-1-4665-6159-5

October 24, 2014 07:00 AM

XML and Web Technologies for Data Sciences with R

Vol. 61, Book Review 1, Oct 2014

XML and Web Technologies for Data Sciences with R
Deborah Nolan and Duncan Temple Lang
Springer-Verlag, 2014
ISBN: 978-1-4614-7899-7

October 24, 2014 07:00 AM

Bergm: Bayesian Exponential Random Graphs in R

Vol. 61, Issue 2, Oct 2014

Abstract:

In this paper we describe the main features of the Bergm package for the open-source R software which provides a comprehensive framework for Bayesian analysis of exponential random graph models: tools for parameter estimation, model selection and goodness-of- fit diagnostics. We illustrate the capabilities of this package describing the algorithms through a tutorial analysis of three network datasets.

October 24, 2014 07:00 AM

evtree: Evolutionary Learning of Globally Optimal Classification and Regression Trees in R

Vol. 61, Issue 1, Oct 2014

Abstract:

Commonly used classification and regression tree methods like the CART algorithm are recursive partitioning methods that build the model in a forward stepwise search. Although this approach is known to be an efficient heuristic, the results of recursive tree methods are only locally optimal, as splits are chosen to maximize homogeneity at the next step only. An alternative way to search over the parameter space of trees is to use global optimization methods like evolutionary algorithms. This paper describes the evtree package, which implements an evolutionary algorithm for learning globally optimal classification and regression trees in R. Computationally intensive tasks are fully computed in C++ while the partykit package is leveraged for representing the resulting trees in R, providing unified infrastructure for summaries, visualizations, and predictions. evtree is compared to the open-source CART implementation rpart, conditional inference trees (ctree), and the open-source C4.5 implementation J48. A benchmark study of predictive accuracy and complexity is carried out in which evtree achieved at least similar and most of the time better results compared to rpart, ctree, and J48. Furthermore, the usefulness of evtree in practice is illustrated in a textbook customer classification task.

October 24, 2014 07:00 AM

October 23, 2014

CRANberries

New package rsml with initial version 1.0

Package: rsml
Type: Package
Title: Root System Markup Language (RSML) file processing
Version: 1.0
Date: 2014-07-22
Author: Guillaume Lobet
Maintainer: Guillaume Lobet
Description: Read and analyse Root System Markup Language (RSML) files.
License: GPL-2
Imports: XML,rgl
Packaged: 2014-10-23 14:10:40 UTC; guillaumelobet
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-23 17:25:08

More information about rsml at CRAN

October 23, 2014 05:13 PM

Dirk Eddelbuettel

<h2 id="introducing-rocker-docker-for-r">Introducing Rocker: Docker for R</h2>

You only know two things about Docker. First, it uses Linux
containers. Second, the Internet won't shut up about it.

-- attributed to Solomon Hykes, Docker CEO

So what is Docker?

Docker is a relatively new open source application and service, which is seeing interest across a number of areas. It uses recent Linux kernel features (containers, namespaces) to shield processes. While its use (superficially) resembles that of virtual machines, it is much more lightweight as it operates at the level of a single process (rather than an emulation of an entire OS layer). This also allows it to start almost instantly, require very little resources and hence permits an order of magnitude more deployments per host than a virtual machine.

Docker offers a standard interface to creation, distribution and deployment. The shipping container analogy is apt: just how shipping containers (via their standard size and "interface") allow global trade to prosper, Docker is aiming for nothing less for deployment. A Dockerfile provides a concise, extensible, and executable description of the computational environment. Docker software then builds a Docker image from the Dockerfile. Docker images are analogous to virtual machine images, but smaller and built in discrete, extensible and reuseable layers. Images can be distributed and run on any machine that has Docker software installed---including Windows, OS X and of course Linux. Running instances are called Docker containers. A single machine can run hundreds of such containers, including multiple containers running the same image.

There are many good tutorials and introductory materials on Docker on the web. The official online tutorial is a good place to start; this post can not go into more detail in order to remain short and introductory.

So what is Rocker?

rocker logo

At its core, Rocker is a project for running R using Docker containers. We provide a collection of Dockerfiles and pre-built Docker images that can be used and extended for many purposes.

Rocker is the the name of our GitHub repository contained with the Rocker-Org GitHub organization.

Rocker is also the name the account under which the automated builds at Docker provide containers ready for download.

Current Rocker Status

Core Rocker Containers

The Rocker project develops the following containers in the core Rocker repository

  • r-base provides a base R container to build from
  • r-devel provides the basic R container, as well as a complete R-devel build based on current SVN sources of R
  • rstudio provides the base R container as well an RStudio Server instance

We have settled on these three core images after earlier work in repositories such as docker-debian-r and docker-ubuntu-r.

Rocker Use Case Containers

Within the Rocker-org organization on GitHub, we are also working on

  • Hadleyverse which extends the rstudio container with a number of Hadley packages
  • rOpenSci which extends hadleyverse with a number of rOpenSci packages
  • r-devel-san provides an R-devel build for "Sanitizer" run-time diagnostics via a properly instrumented version of R-devel via a recent compiler build
  • rocker-versioned aims to provided containers with 'versioned' previous R releases and matching packages

Other repositories will probably be added as new needs and opportunities are identified.

Deprecation

The Rocker effort supersedes and replaces earlier work by Dirk (in the docker-debian-r and docker-ubuntu-r GitHub repositories) and Carl. Please use the Rocker GitHub repo and Rocker Containers from Docker.com going forward.

Next Steps

We intend to follow-up with more posts detailing usage of both the source Dockerfiles and binary containers on different platforms.

Rocker containers are fully functional. We invite you to take them for a spin. Bug reports, comments, and suggestions are welcome; we suggest you use the GitHub issue tracker.

Acknowledgments

We are very appreciative of all comments received by early adopters and testers. We also would like to thank RStudio for allowing us the redistribution of their RStudio Server binary.

Published concurrently at rOpenSci blog and Dirk's blog.

Authors

Dirk Eddelbuettel and Carl Boettiger

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 23, 2014 04:39 PM

CRANberries

New package matR with initial version 0.9

Package: matR
Type: Package
Title: Metagenomics Analysis Tools for R
Authors@R: c (person ("Daniel", "Braithwaite", role = c ("aut", "cre"), email = "contact.dtb@gmail.com"), person ("Kevin", "Keegan", role = "aut", email = "keegan@mcs.anl.gov"), person (c ("University", "of"), "Chicago", role = "cph"))
Version: 0.9
Depends: R (>= 2.10), MGRASTer, BIOM.utils, graphics, stats, utils
Imports:
Suggests: RJSONIO, qvalue, ecodist, gplots, scatterplot3d
URL: https://github.com/MG-RAST/matR/
Date: 2014-10-22
Description: An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. matR integrates easily with other R packages and non-R software.
License: BSD_2_clause + file LICENSE
Copyright: University of Chicago
LazyData: yes
Collate: utils.R biom-ext.R client.R graphics.R analysis-support.R analysis-misc.R distx.R rowstats.R transform.R boxplot.R princomp.R image.R init.R
Packaged: 2014-10-23 07:39:09 UTC; dan
Author: Daniel Braithwaite [aut, cre], Kevin Keegan [aut], University of Chicago [cph]
Maintainer: Daniel Braithwaite
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-23 11:50:13

More information about matR at CRAN

October 23, 2014 11:13 AM

October 22, 2014

CRANberries

New package sigloc with initial version 0.0.4

Package: sigloc
Version: 0.0.4
Date: 2013-04-23
Title: Signal Location Estimation
Author: Sergey S. Berg
Maintainer: Sergey S. Berg
Depends: R (>= 2.15.3), nleqslv, ellipse
Description: A collection of tools for estimating the location of a transmitter signal from radio telemetry studies using the maximum likelihood estimation (MLE) approach described in Lenth (1981).
License: GPL (>= 2)
URL: http://www.r-project.org
Packaged: 2014-10-22 20:22:57 UTC; Serge
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 23:14:50

More information about sigloc at CRAN

October 22, 2014 11:13 PM

New package TDboost with initial version 1.0

Package: TDboost
Title: A Boosted Nonparametric Tweedie Model
Version: 1.0
Date: 2013-10-11
Author: Yi Yang , Wei Qian , Hui Zou
Maintainer: Yi Yang
Depends: R (>= 2.12.0), lattice
Description: A fully nonparametric Tweedie model using the gradient boosting. It is capable of fitting a flexible nonlinear model and capturing interactions among predictors.
LazyData: yes
License: GPL-3
Packaged: 2014-10-22 16:33:11 UTC; emeryyi
NeedsCompilation: yes
Date/Publication: 2014-10-22 20:48:02
Repository: CRAN

More information about TDboost at CRAN

October 22, 2014 07:13 PM

New package glmvsd with initial version 1.0

Package: glmvsd
Type: Package
Title: Variable Selection Deviation (VSD) Measures and Instability Tests for High-dimensional Generalized Linear Models
Version: 1.0
Date: 2014-09-19
Author: Ying Nan , Yi Yang , Yuhong Yang
Maintainer: Yi Yang
Depends: stats, glmnet, ncvreg, MASS
Description: Variable selection deviation measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
License: GPL-2
URL: https://github.com/emeryyi/glmvsd
Packaged: 2014-10-22 16:08:33 UTC; emeryyi
Date/Publication: 2014-10-22 20:49:00
NeedsCompilation: no
Repository: CRAN

More information about glmvsd at CRAN

October 22, 2014 07:13 PM

Bioconductor Project Working Papers

ENHANCED PRECISION IN THE ANALYSIS OF RANDOMIZED TRIALS WITH ORDINAL OUTCOMES

We present a general method for estimating the effect of a treatment on an ordinal outcome in randomized trials. The method is robust in that it does not rely on the proportional odds assumption. Our estimator leverages information in prognostic baseline variables, and has all of the following properties: (i) it is consistent; (ii) it is locally efficient; (iii) it is guaranteed to match or improve the precision of the standard, unadjusted estimator. To the best of our knowledge, this is the first estimator of the causal relation between a treatment and an ordinal outcome to satisfy these properties. We demonstrate the estimator in simulations based on resampling from a completed randomized clinical trial of a new treatment for stroke; we show potential gains of up to 39\% in relative efficiency compared to the unadjusted estimator. The proposed estimator could be a useful tool for analyzing randomized trials with ordinal outcomes, since existing methods either rely on model assumptions that are untenable in many practical applications, or lack the efficiency properties of the proposed estimator. We provide R code implementing the estimator.

by Iván Díaz et al. at October 22, 2014 05:36 PM

CRANberries

New package traj with initial version 1.0

Package: traj
Title: Trajectory Analysis
Description: Implements the three step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Version: 1.0
Date: 2014-07-10
Author: Marie-Pierre Sylvestre, Dan Vatnik
Maintainer: Dan Vatnik
License: GPL-2
LazyData: true
Depends: R (>= 3.0.3)
Imports: cluster, psych, pastecs, NbClust, graphics, grDevices, stats, utils, GPArotation
Packaged: 2014-10-22 15:47:16 UTC; Dan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 18:20:51

More information about traj at CRAN

October 22, 2014 05:13 PM

New package saeSim with initial version 0.6.0

Package: saeSim
Type: Package
Title: Simulation Tools for Small Area Estimation
Date: 2014-10-22
Version: 0.6.0
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz
URL: https://wahani.github.io/saeSim
BugReports: https://github.com/wahani/saeSim/issues
Depends: R(>= 3.1), methods
Imports: dplyr(>= 0.2), ggplot2, MASS, spdep, parallel
Suggests: testthat, knitr
Description: Tools for the simulation of data in the context of small area estimation. Combine all steps of your simulation - from data generation over drawing samples to model fitting - in one object. This enables easy modification and combination of different scenarios. You can store your results in a folder or start the simulation in parallel.
License: GPL-3 | file LICENSE
VignetteBuilder: knitr
Packaged: 2014-10-22 12:28:59 UTC; swarnholz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 16:04:46

More information about saeSim at CRAN

October 22, 2014 05:13 PM

Bioconductor Project Working Papers

Nonparametric Adjustment for Measurement Error in Time to Event Data

Measurement error in time to event data used as a predictor will lead to inaccurate predictions. This arises in the context of self-reported family history, a time to event predictor often measured with error, used in Mendelian risk prediction models. Using a validation data set, we propose a method to adjust for this type of measurement error. We estimate the measurement error process using a nonparametric smoothed Kaplan-Meier estimator, and use Monte Carlo integration to implement the adjustment. We apply our method to simulated data in the context of both Mendelian risk prediction models and multivariate survival prediction models, as well as illustrate our method using a data application for Mendelian risk prediction models. Results from simulations are evaluated using measures of mean squared error of prediction (MSEP), area under the response operating characteristics curve (ROC-AUC), and the ratio of observed to expected number of events. These results show that our adjusted method mitigates the effects of measurement error mainly by improving calibration and by improving total accuracy. In some scenarios discrimination is also improved.

by Danielle Braun et al. at October 22, 2014 04:37 PM

Extending Mendelian Risk Prediction Models to Handle Misreported Family History

Mendelian risk prediction models calculate the probability of a proband being a mutation carrier based on family history and known mutation prevalence and penetrance. Family history in this setting, is self-reported and is often reported with error. Various studies in the literature have evaluated misreporting of family history. Using a validation data set which includes both error-prone self-reported family history and error-free validated family history, we propose a method to adjust for misreporting of family history. We estimate the measurement error process in a validation data set (from University of California at Irvine (UCI)) using nonparametric smoothed Kaplan-Meier estimators, and use Monte Carlo integration to implement the adjustment. In this paper, we extend BRCAPRO, a Mendelian risk prediction model for breast and ovarian cancers, to adjust for misreporting in family history. We apply the extended model to data from the Cancer Genetics Network (CGN).

by Danielle Braun et al. at October 22, 2014 04:37 PM

CRANberries

New package lmenssp with initial version 1.0

Package: lmenssp
Type: Package
Title: Linear Mixed Effects Models with Non-stationary Stochastic Processes
Version: 1.0
Date: 2014-10-21
Author: Ozgur Asar, Peter J. Diggle
Maintainer: Ozgur Asar
Depends: MASS, nlme
Description: Fit, filter and smooth mixed models with non-stationary processes
License: GPL (>= 2)
Packaged: 2014-10-22 08:38:04 UTC; asar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 13:13:04

More information about lmenssp at CRAN

October 22, 2014 01:13 PM

New package FDGcopulas with initial version 1.0

Package: FDGcopulas
Type: Package
Title: Multivariate Dependence with FDG Copulas
Version: 1.0
Date: 2014-09-19
Author: Gildas Mazo, Stephane Girard
Maintainer: Gildas Mazo
Description: FDG copulas are a class of copulas featuring an interesting balance between flexibility and tractability. This package provides tools to construct, calculate the pairwise dependence coefficients of, simulate from, and fit FDG copulas. The acronym FDG stands for 'one-Factor with Durante Generators', as an FDG copula is a one-factor copula -- that is, the variables are independent given a latent factor -- whose linking copulas belong to the Durante class of bivariate copulas (also referred to as exchangeable Marshall-Olkin or semilinear copulas).
License: GPL (>= 3)
Depends: Rcpp (>= 0.10.6), methods
LinkingTo: Rcpp
Imports: numDeriv, randtoolbox
Packaged: 2014-10-22 07:24:07 UTC; mazo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-22 09:33:34

More information about FDGcopulas at CRAN

October 22, 2014 09:13 AM

New package indicoio with initial version 0.3

Package: indicoio
Title: A simple R Wrapper for the indico set of APIs - http://indico.io
Version: 0.3
Author: Alexander Gedranovich
Maintainer: Madison May
Description: R-based client for Machine Learning APIs at http://indico.io. Provides wrappers for following APIs: Positive/Negative Sentiment Analysis, Political Sentiment Analysis, Image Feature Extraction, Facial Emotion Recognition, Facial Feature Extraction, Language Detection
Depends: R (>= 3.0.2), httr, rjson, stringr, png
License: MIT + file LICENSE
LazyData: true
Suggests: testthat, jpeg
Packaged: 2014-10-22 00:37:34 UTC; mmay
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 08:58:17

More information about indicoio at CRAN

October 22, 2014 07:13 AM

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