Planet R

November 27, 2014

CRANberries

New package NormPsy with initial version 1.0.2

Package: NormPsy
Type: Package
Title: Normalisation of psychometric tests
Version: 1.0.2
Date: 2014-05-28
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima
Description: This package provides functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). The package also provides functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores.
License: GPL
Depends: R (>= 2.9.0)
Imports: lcmm (>= 1.6.4)
Packaged: 2014-11-27 20:56:50 UTC; cecile
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-27 23:19:56

More information about NormPsy at CRAN

November 27, 2014 11:12 PM

New package EnsemblePCReg with initial version 0.6

Package: EnsemblePCReg
Type: Package
Title: Extensible Package for Principal-Component-Regression-based Integration of Base Learners
Version: 0.6
Date: 2014-11-25
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: This package extends the base classes and methods of EnsembleBase package for Principal-Components-Regression-based (PCR) integration of base learners. Default implementation uses cross-validation error to choose the optimal number of PC components for the final predictor. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in EnsembleBase package as well as this package.
License: GPL (>= 2)
Depends: EnsembleBase
Imports: parallel,methods
Packaged: 2014-11-26 22:37:10 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-28 00:21:18

More information about EnsemblePCReg at CRAN

November 27, 2014 11:12 PM

New package cmprskQR with initial version 0.9.0

Package: cmprskQR
Version: 0.9.0
Date: 2014-11-26
Title: Analysis of Competing Risks Using Quantile Regressions
Author: Stephan Dlugosz, based on code from Limin Peng and Ruosha Li
Maintainer: Stephan Dlugosz
Depends: R (>= 2.13.0)
Imports: survival, quantreg
Description: Estimation, testing and regression modeling of subdistribution functions in competing risks using quantile regressions, as described in Peng and Fine JP (2009), Competing risks quantile regression, JASA, 104:1440-1453
License: GPL (>= 2)
URL: http://www.r-project.org
NeedsCompilation: yes
Repository: CRAN
Packaged: 2014-11-27 15:09:46 UTC; sdl
Date/Publication: 2014-11-27 18:38:56

More information about cmprskQR at CRAN

November 27, 2014 05:12 PM

New package SSrat with initial version 1.0

Package: SSrat
Type: Package
Title: Two-dimensional sociometric status determination with rating scales
Version: 1.0
Date: 2014-09-09
Author: Hans Landsheer
Maintainer: Hans Landsheer
Description: SSRAT is a computer program for two-dimensional sociometric status determination with rating scales. For each person assessed, SSRAT computes probability distributions of the total scores for `sympathy' (S), `antipathy' (A), `social preference' (P) and `social impact' (I), and applies the criteria for sociometric status categorization.
License: GPL-2
Depends: plyr, sna
LazyData: yes
Packaged: 2014-11-27 14:18:47 UTC; lands101
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-27 16:04:43

More information about SSrat at CRAN

November 27, 2014 03:12 PM

Removed CRANberries

Package DetR (with last version 0.0.1) was removed from CRAN

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

2014-11-13 0.0.1

November 27, 2014 09:12 AM

CRANberries

New package orderedLasso with initial version 1.7

Package: orderedLasso
Title: Ordered Lasso and Time-lag Sparse Regression
Version: 1.7
Author: Jerome Friedman, Xiaotong Suo and Robert Tibshirani
Description: Ordered lasso and time-lag sparse regression. Ordered Lasso fits a linear model and imposes an order constraint on the coefficients. It writes the coefficients as positive and negative parts, and requires positive parts and negative parts are non-increasing and positive. Time-Lag Lasso generalizes the ordered Lasso to a general data matrix with multiple predictors. For more details, see Suo, X.,Tibshirani, R., (2014) 'An Ordered Lasso and Sparse Time-lagged Regression'.
Maintainer: Xiaotong Suo
Depends: R (>= 3.0.0), Matrix
Imports: Iso,quadprog,ggplot2,reshape2
License: GPL-2
Packaged: 2014-11-27 07:18:25 UTC; xiaotong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-27 08:32:37

More information about orderedLasso at CRAN

November 27, 2014 07:12 AM

New package cqrReg with initial version 1.0

Package: cqrReg
Type: Package
Title: Quantile, Composite Quantile Regression and Regularized Versions
Version: 1.0
Date: 2014-11-07
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
License: GPL (>= 2)
Depends: Matrix,Rmosek
Imports: Rcpp (>= 0.10.0)
LinkingTo: Rcpp,RcppArmadillo
Packaged: 2014-11-27 00:30:38 UTC; billy
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-27 07:39:36

More information about cqrReg at CRAN

November 27, 2014 07:12 AM

November 26, 2014

CRANberries

New package rclinicaltrials with initial version 1.4

Package: rclinicaltrials
Type: Package
Title: Download Aggregate Trial Information and Results from ClinicalTrials.gov
Description: ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. Users can search for information about and results from those trials. This provides a set of functions to interact with the search and download features. Results are downloaded to temporary directories and returned as R objects.
Version: 1.4
Date: 2014-11-25
Author: Michael C Sachs
Maintainer: Michael C Sachs
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
Imports: httr, XML, plyr
Suggests: devtools, knitr, roxygen2, testthat, ggplot2
VignetteBuilder: knitr
LazyData: true
Packaged: 2014-11-26 16:03:28 UTC; sachsmc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:37:28

More information about rclinicaltrials at CRAN

November 26, 2014 05:13 PM

New package pointdensityP with initial version 0.1

Package: pointdensityP
Title: Point density for geospatial data
Version: 0.1
Author: "Paul Evangelista and Dave Beskow "
Maintainer: Paul Evangelista
Description: pointdensity returns a density count and the temporal average for every point in the original list. The dataframe returned includes four columns: lat, lon, count, and date_avg. The "lat" column is the original latitude data; the "lon" column is the original longitude data; the "count" is the density count of the number of points within a radius of radius*grid_size (the neighborhood); and the date_avg column includes the average date of each point in the neighborhood.
Depends: R (>= 3.1.1)
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-11-26 15:07:34 UTC; Paul.Evangelista
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:39:20

More information about pointdensityP at CRAN

November 26, 2014 05:13 PM

New package kpodclustr with initial version 1.0

Package: kpodclustr
Title: Method for Clustering Partially Observed Data
Version: 1.0
Authors@R: as.person(c( "Jocelyn T. Chi [aut, cre]", "Eric C. Chi [ctb]" ))
Description: The kpodclustr package implements the k-POD method for clustering partially observed data.
URL: http://jocelynchi.com/kpodclustr
Depends: R (>= 3.1.0), clues
License: MIT + file LICENSE
LazyData: true
Packaged: 2014-11-26 15:37:47 UTC; jocelyn
Author: Jocelyn T. Chi [aut, cre], Eric C. Chi [ctb]
Maintainer: Jocelyn T. Chi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:33:47

More information about kpodclustr at CRAN

November 26, 2014 05:13 PM

New package EstSimPDMP with initial version 1.2

Package: EstSimPDMP
Type: Package
Title: Estimation and Simulation for PDMPs
Version: 1.2
Date: 2014-11-25
Author: Romain Azais
Maintainer: Romain Azais
Description: This package deals with the estimation of the jump rate for piecewise-deterministic Markov processes (PDMPs), from only one observation of the process within a long time. The main functions provide an estimate of this function. The state space may be discrete or continuous. The associated paper has been published in Scandinavian Journal of Statistics and is given in references. Other functions provide a method to simulate random variables from their (conditional) hazard rate, and then to simulate PDMPs.
License: GPL (>= 2)
Packaged: 2014-11-26 14:50:50 UTC; azais
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:53:19

More information about EstSimPDMP at CRAN

November 26, 2014 05:12 PM

New package BayesianAnimalTracker with initial version 1.0

Package: BayesianAnimalTracker
Type: Package
Title: Bayesian Melding of GPS and DR Path for Animal Tracking
Version: 1.0
Date: 2014-11-07
Author: Yang (Seagle) Liu
Maintainer: Yang (Seagle) Liu
Suggests: TrackReconstruction
Description: Bayesian melding approach to combine the GPS observations and Dead-Reckoned path for an accurate animal's track, or equivalently, use the GPS observations to correct the Dead-Reckoned path. It can take the measurement errors in the GPS observations into account and provide uncertainty statement about the corrected path. The main calculation can be done by the BMAnimalTrack function.
License: GPL (>= 2)
Packaged: 2014-11-26 17:37:12 UTC; User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 18:57:31

More information about BayesianAnimalTracker at CRAN

November 26, 2014 05:12 PM

New package timeseriesdb with initial version 0.1

Package: timeseriesdb
Title: Store and Organize Time Series in a Database
Description: An R package to store and organize time series and their multi-lingual meta information in a database. The timeseriesdb package suggests a simple yet powerful database structure to store a large amount of time series in a relational PostgreSQL database. The package provides an interface to the R user to create, update and delete time series.
Version: 0.1
Authors@R: 'Matthias Bannert [aut, cre]'
Depends: R (>= 3.0.0)
Suggests: RPostgreSQL
Imports: DBI
License: GPL-2
LazyData: true
Maintainer: 'Matthias Bannert'
Packaged: 2014-11-26 14:02:06 UTC; mbannert
Author: 'Matthias Bannert' [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 15:40:25

More information about timeseriesdb at CRAN

November 26, 2014 03:12 PM

Removed CRANberries

Package icomp (with last version 0.1) was removed from CRAN

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

2008-07-07 0.1

November 26, 2014 11:12 AM

CRANberries

New package SphericalK with initial version 1.0

Package: SphericalK
Type: Package
Title: Spherical K-function
Version: 1.0
Date: 2014-11-25
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li
Description: Spherical K-function for point-pattern analysis on the sphere
License: GPL (>= 2)
Packaged: 2014-11-26 02:06:14 UTC; Leon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 08:06:54

More information about SphericalK at CRAN

November 26, 2014 07:13 AM

November 25, 2014

CRANberries

New package lucid with initial version 1.0

Package: lucid
Version: 1.0
Date: 2014-11-24
Title: Lucid Printing of Floating Point Numbers
Author: Kevin Wright
Maintainer: Kevin Wright
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
LazyData: yes
License: GPL-2
URL: https://github.com/kwstat/lucid
BugReports: https://github.com/kwstat/lucid/issues
VignetteBuilder: knitr
Imports: nlme
Suggests: knitr, lattice, lme4
Packaged: 2014-11-25 22:00:33 UTC; wrightkevi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:52:34

More information about lucid at CRAN

November 25, 2014 11:12 PM

New package GMDH with initial version 1.0

Package: GMDH
Type: Package
Title: Predicting and Forecasting Time Series via GMDH-Type Neural Network Algorithms
Version: 1.0
Date: 2014-11-25
Depends: MASS, stats
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to predict and forecast a univariate time series.
License: GPL (>= 2)
Packaged: 2014-11-25 19:14:40 UTC; osmndg
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:48:49

More information about GMDH at CRAN

November 25, 2014 11:12 PM

New package EnsembleCV with initial version 0.7

Package: EnsembleCV
Type: Package
Title: Extensible Package for Cross-Validation-Based Integration of Base Learners
Version: 0.7
Date: 2014-11-17
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani
Description: This package extends the base classes and methods of EnsembleBase package for cross-validation-based integration of base learners. Default implementation calculates average of repeated CV errors, and selects the base learner / configuration with minimum average error. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. The package can be extended, e.g. by adding variants of the current implementation.
License: GPL (>= 2)
Depends: EnsembleBase
Imports: parallel,methods
Packaged: 2014-11-25 21:39:34 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-26 00:59:47

More information about EnsembleCV at CRAN

November 25, 2014 11:12 PM

New package gridGraphics with initial version 0.1-1

Package: gridGraphics
Title: Redraw Base Graphics Using grid Graphics
Version: 0.1-1
Authors@R: person("Paul", "Murrell", role = c("cre", "aut"), email = "paul@stat.auckland.ac.nz")
Description: Functions to convert a page of plots drawn with the graphics package into identical output drawn with the grid package. The result looks like the original graphics-based plot, but consists of grid grobs and viewports that can then be manipulated with grid functions (e.g., edit grobs and revisit viewports).
Depends: grid, graphics
Suggests: KernSmooth
SystemRequirements: ImageMagick (for testing)
License: GPL (>= 2)
URL: https://github.com/pmur002/gridgraphics
Packaged: 2014-11-25 20:01:49 UTC; EC\pmur002
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 22:24:13

More information about gridGraphics at CRAN

November 25, 2014 09:12 PM

New package KODAMA with initial version 0.0.1

Package: KODAMA
Version: 0.0.1
Date: 2013-11-20
Author: Stefano Cacciatore, Claudio Luchinat, Leonardo Tenori
Maintainer: Stefano Cacciatore
Title: Knowledge discovery by accuracy maximization
Description: KODAMA (KnOwledge Discovery by Accuracy MAximization) is an unsupervised and semisupervised learning algorithm that performs feature extraction from noisy and high-dimensional data.
Depends: R (>= 2.10.0),e1071,plsgenomics,class
Suggests: rgl,
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2014-11-25 15:41:39 UTC; Stefano
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 18:05:43

More information about KODAMA at CRAN

November 25, 2014 05:12 PM

New package empiricalFDR.DESeq2 with initial version 1.0

Package: empiricalFDR.DESeq2
Type: Package
Title: Simulation-based False Discovery Rate in RNA-seq
Version: 1.0
Date: 2014-11-25
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz
Description: Auxiliary functions for the DESeq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate.
License: GPL-3
Depends: DESeq2,GenomicRanges
Packaged: 2014-11-25 15:48:11 UTC; c-monster
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 18:03:34

More information about empiricalFDR.DESeq2 at CRAN

November 25, 2014 05:12 PM

New package maboost with initial version 1.0-0

Package: maboost
Version: 1.0-0
Date: 2014-11-01
Title: Binary and Multiclass Boosting Algorithms
Author: Tofigh Naghibi
Depends: R(>= 2.10),rpart,C50
Description: Performs binary and multiclass boosting in maximum-margin, sparse, smooth and normal settings as described in "A Boosting Framework on Grounds of Online Learning" by T. Naghibi and B. Pfister, (2014). For further information regarding the algorithms, please refer to http://arxiv.org/abs/1409.7202
Maintainer: Tofigh Naghibi
License: GPL (>= 2)
Packaged: 2014-11-25 15:05:38 UTC; tofighn
Repository: CRAN
Date/Publication: 2014-11-25 17:03:41
Collate: 'maboost-package.r' 'maboost.R' 'maboost.default.R' 'maboost.formula.R' 'maboost.machine.bin.R' 'maboost.machine.multi.R' 'predict.maboost.R' 'print.maboost.R' 'projsplx.R' 'projsplx_k.R' 'summary.maboost.R' 'update.maboost.R' 'varplot.maboost.R'
NeedsCompilation: no

More information about maboost at CRAN

November 25, 2014 03:12 PM

Dirk Eddelbuettel

Rcpp now used by 300 CRAN packages

max-heap image

This morning, Rcpp reached another round milestone: 300 packages on CRAN now depend on it (as measured by Depends, Imports and LinkingTo declarations). The graph is on the left depicts the growth of Rcpp usage over time. There are 41 more on BioConductor (which is not included in the chart).

The first and less detailed part uses manually save entries, the second half of the data set was generated semi-automatically via a short script appending updates to a small file-based backend. A list of user package is kept on this page.

Also displayed in the graph is the relative proportion of CRAN packages using Rcpp. The four per-cent hurdle was cleared just before useR! 2014 where I showed a similar graph (as two distinct graphs) in my invited talk. We may well hit five per-cent before the end of the year.

300 is a pretty humbling and staggering number. Also interesting that we we cleared 200 only at the end of April, and 250 in early August.

So from everybody behind Rcpp, a heartfelt Thank You! to all the users and of course other contributors.

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

November 25, 2014 12:14 PM

Removed CRANberries

Package audited (with last version 1.9) was removed from CRAN

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

2014-09-20 1.9

November 25, 2014 11:13 AM

Package metrumrg (with last version 5.55) was removed from CRAN

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

2014-02-18 5.55
2013-11-26 5.54
2013-06-06 5.50
2013-05-23 5.49
2013-05-01 5.45
2013-04-24 5.44
2013-03-28 5.36
2013-03-21 5.34
2012-11-27 5.27
2012-11-24 5.26
2012-11-05 5.25
2012-10-25 5.24
2012-10-01 5.23
2012-05-05 5.17
2012-02-09 5.13
2011-11-11 5.5
2011-10-24 5.3
2011-09-20 5.2
2011-09-08 5.1

November 25, 2014 11:13 AM

CRANberries

New package IRTShiny with initial version 1.0

Package: IRTShiny
Type: Package
Title: Item Response Theory via Shiny
Version: 1.0
Date: 2014-11-24
Author: William Kyle Hamilton , Atsushi Mizumoto
Maintainer: William Kyle Hamilton
Description: Interactive shiny application for running Item Response Theory analysis.
License: GPL-3
Imports: shiny, shinyAce, beeswarm, CTT, ltm, parallel,
Suggests: psych
LazyData: true
Packaged: 2014-11-25 08:29:49 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 11:33:45

More information about IRTShiny at CRAN

November 25, 2014 11:12 AM

New package USAboundaries with initial version 0.1

Package: USAboundaries
Type: Package
Title: Historical boundaries of the United States of America, 1629-2000
Date: 2014
Version: 0.1
Authors@R: c(person("Lincoln", "Mullen", email = "lincoln@lincolnmullen.com", role = c("aut", "cre")), person("Dr. William M. Scholl Center for American History and Culture, The Newberry Library", role = c("cph")))
Description: This package provides spatial objects with the boundaries of states or counties in the United States of America from 1629 to 2000. It provides data from the Atlas of Historical County Boundaries.
License: CC BY-NC-SA 4.0
LazyData: true
LazyDataCompression: xz
URL: https://github.com/ropensci/USAboundaries
BugReports: https://github.com/ropensci/USAboundaries/issues
Depends: R (>= 3.1.1),
Imports: assertthat (>= 0.1), dplyr (>= 0.3.0.1), ggplot2 (>= 1.0.0), lubridate (>= 1.3.3), maptools (>= 0.8-30), rgeos (>= 0.3-8), sp (>= 1.0.15)
Suggests: knitr, mapproj, testthat (>= 0.9.1)
VignetteBuilder: knitr
Packaged: 2014-11-24 18:25:13 UTC; lmullen
Author: Lincoln Mullen [aut, cre], Dr. William M. Scholl Center for American History and Culture, The Newberry Library [cph]
Maintainer: Lincoln Mullen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:42:09

More information about USAboundaries at CRAN

November 25, 2014 09:13 AM

New package musicNMR with initial version 0.0.2

Package: musicNMR
Version: 0.0.2
Date: 2013-11-21
Author: Stefano Cacciatore, Edoardo Saccenti, Mario Piccioli
Maintainer: Stefano Cacciatore
Title: Conversion of Nuclear Magnetic Resonance spectrum in audio file
Description: This package is a collection of function for converting and modifying mono dimensional nuclear magnetic resonance spectra.
Depends: R (>= 2.10.0), seewave
Suggests: plsgenomics
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2014-11-25 06:58:47 UTC; Stefano
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:50:06

More information about musicNMR at CRAN

November 25, 2014 09:13 AM

Removed CRANberries

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

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

2014-11-25 1.1

November 25, 2014 09:13 AM

CRANberries

New package cjoint with initial version 1.0.2

Package: cjoint
Version: 1.0.2
Date: 2014-10-18
Title: AMCE Estimator for Conjoint Experiments
Author: Anton Strezhnev, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev
Depends: R (>= 2.0.0), sandwich, lmtest, ggplot2
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
License: GPL (>= 2)
Packaged: 2014-11-25 07:53:08 UTC; anton
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:24:01

More information about cjoint at CRAN

November 25, 2014 09:12 AM

Journal of Statistical Software

BayesLCA: An R Package for Bayesian Latent Class Analysis

Vol. 61, Issue 13, Nov 2014

Abstract:

The BayesLCA package for R provides tools for performing latent class analysis within a Bayesian setting. Three methods for fitting the model are provided, incorporating an expectation-maximization algorithm, Gibbs sampling and a variational Bayes approximation. The article briefly outlines the methodology behind each of these techniques and discusses some of the technical difficulties associated with them. Methods to remedy these problems are also described. Visualization methods for each of these techniques are included, as well as criteria to aid model selection.

November 25, 2014 08:00 AM

coneproj: An R Package for the Primal or Dual Cone Projections with Routines for Constrained Regression

Vol. 61, Issue 12, Nov 2014

Abstract:

The coneproj package contains routines for cone projection and quadratic programming, plus applications in estimation and inference for constrained parametric regression and shape-restricted regression problems. A short routine check_irred is included to check the irreducibility of a matrix, whose rows are supposed to be a set of cone edges used by coneA or coneB. For the coneA and coneB functions, the vector to project is provided by the user, along with the cone specification and a weight vector. For coneA, a constraint matrix is specified to define the cone, and for coneB, the cone edges are provided. The coneA and coneB algorithms have been coded and compiled in C++, and are called by R. The qprog function transforms a quadratic programming problem into a cone projection problem and calls coneA. The constreg function does estimation and inference for parametric least-squares regression with constraints on the parameters (using coneA). A p value for the “one-sided" test is provided. The shapereg function uses coneB to provide a least-squares estimator for a regression function with several choices of constraints including isotonic and convex regression functions, as well as estimates of parametrically modeled covariate effects. Results from hypothesis tests for significance of the effects are also provided. This package is now available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=coneproj.

November 25, 2014 08:00 AM

CRANberries

New package mads with initial version 0.1.0

Package: mads
Depends: mrds
Suggests: testthat
Type: Package
Title: Multi-Analysis Distance Sampling.
Version: 0.1.0
Date: 2014-11-27
Author: Laura Marshall
Maintainer: Laura Marshall
Description: Performs distance sampling analyses on a number of species accounting for unidentified sightings, model uncertainty and covariate uncertainty.
License: GPL (>= 2)
Packaged: 2014-11-25 02:50:52 UTC; laura
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-25 09:01:38

More information about mads at CRAN

November 25, 2014 07:13 AM

New package iccbeta with initial version 1.0

Package: iccbeta
Type: Package
Title: Multilevel model intraclass correlation for slope heterogeneity
Version: 1.0
Date: 2014-11-21
Authors@R: c(person("Steven Andrew", "Culpepper", role = c("aut", "cph","cre"), email = "sculpepp@illinois.edu"),person("Herman", "Aguinis", role = c("aut", "cph"), email = "haguinis@indiana.edu"))
Maintainer: Steven Andrew Culpepper
Description: A function and vignettes for computing an intraclass correlation described in Aguinis & Culpepper (in press). iccbeta quantifies the share of variance in a dependent variable that is attributed to group heterogeneity in slopes.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.1)
LinkingTo: Rcpp (>= 0.11.1), RcppArmadillo
Depends: R (>= 3.0.2), lme4
Packaged: 2014-11-25 02:21:38 UTC; sculpepp
Author: Steven Andrew Culpepper [aut, cph, cre], Herman Aguinis [aut, cph]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-25 08:52:58

More information about iccbeta at CRAN

November 25, 2014 07:13 AM

New package GCPM with initial version 1.1

Package: GCPM
Type: Package
Title: Generalized Credit Portfolio Model
Version: 1.1
Date: 2014-11-24
Author: Kevin Jakob
Maintainer: Kevin Jakob
Description: The package helps to analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.
License: GPL-2
Imports: Rcpp (>= 0.11.2), methods, RcppProgress(>= 0.1)
LinkingTo: Rcpp, RcppProgress
Packaged: 2014-11-24 18:46:01 UTC; Kevin_Jakob
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-11-25 08:40:13

More information about GCPM at CRAN

November 25, 2014 07:12 AM

Dirk Eddelbuettel

YATORP -- Yet Another Tutorial on R Packaging

What the world needs right now is yet another tutorial on R packages and their creation. Luckily, this last Friday and Saturday, I had the opportunity to present in a workshop organized by Frank DiTraglia at Penn's shiny new Warren Center, and held at Wharton.

Given the Warren Center's focus, the workshop centered around Big Data and Open Science with R. Yihui Xie and myself alternated on delivering four units on an Introduction to R, Writing R packages, Dynamic Documents with R, and HPC with Rcpp and RcppArmadillo.

So I had to come up with a plan for teaching creating R packages -- and decided to do it from the very bottom up, clearly introducing the underlying R CMD ... commands and only then switching to taking advantage of an environment such as the RStudio IDE.

The resulting slides are now available on my presentations page. The code examples are in a repo subdirectory on GitHub as well. While both were designed to support the parallel live instruction offered in the workshop, I would be interested in feedback (preferably via email) about how useful the slides are by themselves.

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

November 25, 2014 02:42 AM

November 24, 2014

Removed CRANberries

Package dse2 (with last version 2011.11-2) was removed from CRAN

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

2011-11-28 2011.11-2
2011-11-03 2011.11-1
2009-10-13 2009.10-1

November 24, 2014 11:12 PM

Package dse1 (with last version 2011.11-2) was removed from CRAN

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

2011-11-28 2011.11-2
2011-11-03 2011.11-1
2009-10-13 2009.10-1

November 24, 2014 11:12 PM

CRANberries

New package EGRET with initial version 2.0.1

Package: EGRET
Type: Package
Title: Exploration and Graphics for RivEr Trends (EGRET)
Version: 2.0.1
Date: 2014-11-24
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: EGRET includes statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm Weighted Regressions on Time, Discharge, and Season (WRTDS).
License: CC0
Depends: R (>= 3.0)
Imports: dataRetrieval, survival, fields, stats, lubridate, methods
Suggests: xtable, knitr, extrafont
LazyLoad: yes
LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
URL: http://pubs.usgs.gov/tm/04/a10/, https://github.com/USGS-R/EGRET/wiki
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
Packaged: 2014-11-24 15:17:25 UTC; ldecicco
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-24 18:31:16

More information about EGRET at CRAN

November 24, 2014 05:12 PM

New package choiceDes with initial version 0.9-1

Package: choiceDes
Type: Package
Title: Design Functions for Choice Studies
Version: 0.9-1
Date: 2014-11-24
Authors@R: person("Jack", "Horne", role=c("aut", "cre"), email="jack@jackhorne.net")
Maintainer: Jack Horne
Description: This package consists of functions to design DCMs and other types of choice studies (including MaxDiff and other tradeoffs)
License: GPL (>= 2)
Depends: R (>= 2.15.2), AlgDesign
Packaged: 2014-11-24 16:12:17 UTC; Jack
Author: Jack Horne [aut, cre]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-24 18:38:56

More information about choiceDes at CRAN

November 24, 2014 05:12 PM

Bioconductor Project Working Papers

Removed CRANberries

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

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

2009-11-17 1.1
2009-08-05 1.0

November 24, 2014 01:13 PM

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

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

2011-08-06 1.0

November 24, 2014 01:13 PM

Package SesIndexCreatoR (with last version 1.0-2) was removed from CRAN

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

2013-05-27 1.0-2

November 24, 2014 01:13 PM

Package visualizationTools (with last version 0.2.05) was removed from CRAN

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

2012-08-01 0.2.05
2011-10-19 0.2.04
2011-08-23 0.2.03
2011-07-23 0.2.02
2011-05-23 0.2.01
2011-04-24 0.2
2011-02-28 0.1

November 24, 2014 01:13 PM

Package MMST (with last version 0.6-1.1) was removed from CRAN

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

2011-02-11 0.6-1.1
2010-07-05 0.6-1

November 24, 2014 01:13 PM

Package mrdrc (with last version 1.0-6) was removed from CRAN

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

2011-04-13 1.0-6
2010-06-10 1.0-5
2010-05-30 1.0-4
2010-05-04 1.0-3
2009-02-17 1.0-2
2008-05-06 1.0-0

November 24, 2014 11:13 AM

CRANberries

New package wux with initial version 1.2-2

Package: wux
Type: Package
Title: Wegener Center Climate Uncertainty Explorer
Version: 1.2-2
Date: 2014-10-20
Author: Thomas Mendlik, Georg Heinrich, Andreas Gobiet and Armin Leuprecht
Maintainer: Thomas Mendlik
Depends: sp, ncdf, reshape, abind, fields
Imports: rgdal, rgeos, class, stringr, Hmisc, gdata, corpcor
Suggests: lattice
Description: Analysis of climate model output uncertainties for specified geographical regions.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2014-11-24 08:28:33 UTC; tommaschku
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-24 10:36:38

More information about wux at CRAN

November 24, 2014 09:12 AM

November 23, 2014

CRANberries

New package RCryptsy with initial version 0.2

Package: RCryptsy
Type: Package
Title: Access to Cryptsy Crypto-Currency Exchange Public Information API via R
Version: 0.2
Date: 2014-11-19
Author: William Kyle Hamilton
Maintainer: William Kyle Hamilton
Description: Basic Public API for the Crypto-Currency exchange Cryptsy
Depends: R (>= 3.0.3), RJSONIO, RCurl
License: GPL-3
URL: https://github.com/kylehamilton/RCryptsy
BugReports: https://github.com/kylehamilton/RCryptsy/issues
Packaged: 2014-11-22 13:33:36 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-23 23:41:18

More information about RCryptsy at CRAN

November 23, 2014 11:12 PM

New package NHMSAR with initial version 1.0

Package: NHMSAR
Type: Package
Title: Non-Homogeneous Markov Switching Autoregressive Models: Fitting, Simulating, Validating.
Version: 1.0
Date: 2014-08-11
Author: Valerie Monbet
Maintainer: Valerie Monbet
Description: Calibration, simulation, validation of (non-)homogeneous Markov switching autoregressive models with Gaussian or von Mises innovations.
License: GPL
Depends: R (>= 2.10), ucminf
Packaged: 2014-11-23 12:24:14 UTC; monbet
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-23 23:32:31

More information about NHMSAR at CRAN

November 23, 2014 11:12 PM

Removed CRANberries

Package ppiPre (with last version 1.5) was removed from CRAN

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

2013-07-28 1.5
2013-07-04 1.4
2012-03-21 1.3
2011-10-19 1.2

November 23, 2014 07:12 PM

CRANberries

New package jiebaR with initial version 0.2

Package: jiebaR
Type: Package
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Version: 0.2
Date: 2014-11-23
Author: Qin Wenfeng, and the authors of CppJieba for the included version of CppJieba
Maintainer: Qin Wenfeng
License: MIT + file LICENSE
Depends: R (>= 3.1)
Imports: Rcpp,methods
LinkingTo: Rcpp
Suggests: testthat, knitr
URL: https://github.com/qinwf/jiebaR/
BugReports: https://github.com/qinwf/jiebaR/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2014-11-23 10:36:47 UTC; outwen
Repository: CRAN
Date/Publication: 2014-11-23 12:47:46

More information about jiebaR at CRAN

November 23, 2014 11:12 AM

New package matchingMarkets with initial version 0.1-2

Package: matchingMarkets
Version: 0.1-2
Depends: R (>= 2.15.2)
Imports: Rcpp (>= 0.11.2), lpSolve (>= 5.6.6), partitions
LinkingTo: Rcpp, RcppArmadillo
Date: 2014-08-14
Title: An R package for the analysis of stable matchings
Author: Thilo Klein
Maintainer: Thilo Klein
Description: This package implements a structural estimator to correct for the sample selection bias from observed outcomes in matching markets. It also contains R code for matching algorithms such as the deferred-acceptance algorithm for college admissions, the top-trading-cycles algorithm for house allocation and a partitioning linear program for the roommates problem.
URL: https://github.com/thiloklein/matchingMarkets
License: GPL (>= 2) | file LICENSE
Repository: CRAN
Repository/R-Forge/Project: matchingmarkets
Repository/R-Forge/Revision: 16
Repository/R-Forge/DateTimeStamp: 2014-11-22 23:10:11
Date/Publication: 2014-11-23 09:35:22
Packaged: 2014-11-22 23:25:30 UTC; rforge
NeedsCompilation: yes

More information about matchingMarkets at CRAN

November 23, 2014 09:12 AM

New package broom with initial version 0.3.4

Package: broom
Type: Package
Title: Convert Statistical Analysis Objects Into Tidy Data Frames
Version: 0.3.4
Date: 2014-09-11
Authors@R: as.person(c( "David Robinson [aut, cre]", "Matthieu Gomez [ctb]", "Boris Demeshev [ctb]", "Hadley Wickham [ctb]" ))
Maintainer: David Robinson
Description: Convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like dplyr, tidyr and ggplot2. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.
Imports: plyr, dplyr, tidyr, psych
Suggests: knitr, survival, glmnet, lfe, Lahman, MASS, sp, maps, maptools, multcomp, testthat, lme4, zoo, ggplot2
URL: http://github.com/dgrtwo/broom
BugReports: http://github.com/dgrtwo/broom/issues
VignetteBuilder: knitr
License: MIT + file LICENSE
Packaged: 2014-11-23 06:37:25 UTC; dgrtwo
Author: David Robinson [aut, cre], Matthieu Gomez [ctb], Boris Demeshev [ctb], Hadley Wickham [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-23 09:23:10

More information about broom at CRAN

November 23, 2014 09:12 AM

November 22, 2014

CRANberries

New package MAVIS with initial version 0.2

Package: MAVIS
Type: Package
Title: Meta Analysis via Shiny
Version: 0.2
Date: 2014-11-21
Author: William Kyle Hamilton , Atsushi Mizumoto
Maintainer: William Kyle Hamilton
Description: Interactive shiny application for running a meta-analysis, provides support for both random effects and fixed effects models.
License: GPL-3
Imports: shiny, shinyAce, metafor, MAd, MAc, quantreg, ggplot2
LazyData: true
Packaged: 2014-11-22 13:29:53 UTC; Kyle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 19:06:45

More information about MAVIS at CRAN

November 22, 2014 07:12 PM

Removed CRANberries

Package EGRET (with last version 2.0.0) was removed from CRAN

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

2014-11-20 2.0.0

November 22, 2014 05:12 PM

CRANberries

New package MATA with initial version 0.1

Package: MATA
Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Version: 0.1
Authors@R: person('Daniel', 'Turek', email='dturek@maths.otago.ac.nz', role=c('aut','cre'))
Description: Provides a function for calculating the Model-Averaged Tail Area Wald (MATA-Wald) confidence interval, which is generated from single-model estimators and AIC model weights
Depends: R (>= 3.1.1)
License: GPL-2
LazyData: true
Packaged: 2014-11-22 01:27:25 UTC; dturek
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 08:23:28

More information about MATA at CRAN

November 22, 2014 07:12 AM

New package EnsembleBase with initial version 0.7

Package: EnsembleBase
Type: Package
Title: Extensible Package for Parallel, Batch Training of Base Learners for Ensemble Modeling
Version: 0.7
Date: 2014-11-17
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, and K-Nearest Neighbors. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
License: GPL (>= 2)
Depends: kknn,methods
Imports: gbm,nnet,e1071,randomForest,doParallel,foreach
Packaged: 2014-11-22 01:26:03 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 08:23:23

More information about EnsembleBase at CRAN

November 22, 2014 07:12 AM

New package sisus with initial version 3.9-13

Package: sisus
Version: 3.9-13
Date: 2014-08-26
Title: SISUS: Stable Isotope Sourcing using Sampling
Authors@R: person(given = c("Erik", "Barry"), family = "Erhardt", email = "erike@stat.unm.edu", role = c("aut", "cre"))
Author: Erik Barry Erhardt [aut, cre]
Maintainer: Erik Barry Erhardt
Description: SISUS for source partitioning using stable isotopes. SISUS reads in a specific Excel-like workbook and performs an IsoSource-type analysis by returning a sample of feasible solutions to p in the non-over constrained linear systems, b=Ap. Edit \file{sisus_*_template.xls} and input data values and run parameters. Run \code{\link{sisus.run}(filename)}. See output in current working directory.
Depends: R (>= 3.0.0)
Imports: MASS, RColorBrewer, coda, gdata, gtools, moments, polyapost, rcdd, stats
Suggests:
License: GPL (>= 2)
LazyLoad: yes
URL: http://StatAcumen.com/sisus
Packaged: 2014-11-21 04:19:50 UTC; erik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-22 02:13:02

More information about sisus at CRAN

November 22, 2014 01:13 AM