Mon, 02 Mar 2015

Package BayesSummaryStatLM updated to version 1.0-1 with previous version 1.0 dated 2015-02-25

Title: MCMC Sampling of Bayesian Linear Models via Summary Statistics
Description: Methods for generating Markov Chain Monte Carlo (MCMC) posterior samples of Bayesian linear regression model parameters that require only summary statistics of data as input. Summary statistics are useful for systems with very limited amounts of physical memory. The package provides two functions: one function that computes summary statistics of data and one function that carries out the MCMC posterior sampling for Bayesian linear regression models where summary statistics are used as input. The function read.regress.data.ff utilizes the R package 'ff' to handle data sets that are too large to fit into a user's physical memory, by reading in data in chunks.
Author: Evgeny Savel'ev, Alexey Miroshnikov, Erin Conlon
Maintainer: Evgeny Savel'ev

Diff between BayesSummaryStatLM versions 1.0 dated 2015-02-25 and 1.0-1 dated 2015-03-02

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Package shinythemes updated to version 1.0.1 with previous version 1.0 dated 2015-01-20

Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes from http://bootswatch.com/, which are packaged for use with Shiny applications.
Author: Winston Chang [aut, cre], RStudio [cph], Thomas Park [ctb, cph] (Bootswatch themes), Lukasz Dziedzic [ctb, cph] (Lato font), Nathan Willis [ctb, cph] (News Cycle font), Google Corporation [ctb, cph] (Open Sans font), Matt McInerney [ctb, cph] (Raleway font), Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font), Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang

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Package NbClust updated to version 2.0.4 with previous version 2.0.3 dated 2014-10-15

Title: Determining the Best Number of Clusters in a Data Set
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad

Diff between NbClust versions 2.0.3 dated 2014-10-15 and 2.0.4 dated 2015-03-02

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Package mediation updated to version 4.4.4 with previous version 4.4.3 dated 2014-11-23

Title: Causal Mediation Analysis
Description: We implement parametric and non parametric mediation analysis. This package performs the methods and suggestions in Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley , Teppei Yamamoto , Kentaro Hirose , Luke Keele , Kosuke Imai
Maintainer: Teppei Yamamoto

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Package lfe updated to version 2.1-1620 with previous version 2.0-1570 dated 2015-02-10

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure

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Package JAGUAR updated to version 2.0 with previous version 1.1 dated 2014-09-07

Title: Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map eQTL
Description: Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.
Author: Chaitanya R. Acharya and Andrew S. Allen
Maintainer: Chaitanya Acharya

Diff between JAGUAR versions 1.1 dated 2014-09-07 and 2.0 dated 2015-03-02

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New package hornpa with initial version 1.0
Package: hornpa
Type: Package
Title: Horn's (1965) Test to Determine the Number of Components/Factors
Version: 1.0
Date: 2015-03-01
Author: Francis Huang
Maintainer: Francis Huang
Description: A stand-alone function that generates a user specified number of random datasets and computes eigenvalues using the random datasets (i.e., implements Horn's [1965, Psychometrika] parallel analysis). Users then compare the resulting eigenvalues (the mean or the specified percentile) from the random datasets (i.e., eigenvalues resulting from noise) to the eigenvalues generated with the user's data. Can be used for both principal components analysis (PCA) and common/exploratory factor analysis (EFA). The output table shows how large eigenvalues can be as a result of merely using randomly generated datasets. If the user's own dataset has actual eigenvalues greater than the corresponding eigenvalues, that lends support to retain that factor/component. In other words, if the i(th) eigenvalue from the actual data was larger than the percentile of the (i)th eigenvalue generated using randomly generated data, empirical support is provided to retain that factor/component. Horn, J. (1965). A rationale and test for the number of factors in factor analysis. Psychometrika, 32, 179-185.
License: GPL-3
Packaged: 2015-03-02 14:29:58 UTC; huangf
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-03 01:01:34

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Package capm updated to version 0.6.0 with previous version 0.5 dated 2014-05-27

Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population management.
Author: Oswaldo Santos [aut, cre], Marcos Amaku [ctb], Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos

Diff between capm versions 0.5 dated 2014-05-27 and 0.6.0 dated 2015-03-02

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Package strum updated to version 0.6 with previous version 0.5.1 dated 2015-02-02

Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: Implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre], Yeunjoo Song [aut], Stephen Cahn [ctb]
Maintainer: Nathan Morris

Diff between strum versions 0.5.1 dated 2015-02-02 and 0.6 dated 2015-03-02

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New package ggenealogy with initial version 0.1.0
Package: ggenealogy
Version: 0.1.0
Title: Visualization Tools for Genealogical Data
Description: Methods for searching through genealogical data and displaying the results. Plotting algorithms assist with data exploration and publication-quality image generation. Uses the Grammar of Graphics.
Author: Lindsay Rutter, Susan Vanderplas, Di Cook
Maintainer: Lindsay Rutter
License: GPL
Depends: R (>= 3.0.2)
Imports: ggplot2 (>= 1.0.0), igraph (>= 0.7.1), plyr (>= 1.8.1), reshape2 (>= 1.4)
VignetteBuilder: knitr
Suggests: stringr (>= 0.6.2), knitr, roxygen2 (>= 3.0.0)
Packaged: 2015-03-02 14:49:09 UTC; lindz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-02 18:45:03

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New package bootnet with initial version 0.1
Package: bootnet
Type: Package
Title: Bootstrap Methods for Various Network Estimation Routines
Version: 0.1
Date: 2015-03-02
Author: Sacha Epskamp
Maintainer: Sacha Epskamp
Depends: ggplot2
Imports: IsingFit, qgraph, dplyr, gtools, corpcor
Suggests: psych
Description: Bootstrap standard errors on various network estimation routines, such as EBICglasso from the qgraph package and IsingFit from the IsingFit package.
License: GPL-2
NeedsCompilation: no
Packaged: 2015-03-02 16:22:12 UTC; sacha
Repository: CRAN
Date/Publication: 2015-03-02 19:02:25

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Package jwutil (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:

2015-01-06 1.0.2

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Package msSurv updated to version 1.2-1 with previous version 1.1-2 dated 2012-09-18

Title: Nonparametric Estimation for Multistate Models
Description: Nonparametric estimation for right censored, left truncated time to event data in multistate models.
Author: Nicole Ferguson , Somnath Datta , Guy Brock
Maintainer: Guy Brock

Diff between msSurv versions 1.1-2 dated 2012-09-18 and 1.2-1 dated 2015-03-02

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Package IsingSampler updated to version 0.2 with previous version 0.1.1 dated 2014-01-09

Title: Sampling Methods and Distribution Functions for the Ising Model
Description: Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp

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Package bayescount updated to version 0.9.99-4 with previous version 0.9.9-2 dated 2014-06-22

Title: Power Calculations and Bayesian Analysis of Count Distributions and FECRT Data using MCMC
Description: A set of functions to allow analysis of count data (such as faecal egg count data) using Bayesian MCMC methods. Returns information on the possible values for mean count, coefficient of variation and zero inflation (true prevalence) present in the data. A complete faecal egg count reduction test (FECRT) model is implemented, which returns inference on the true efficacy of the drug from the pre- and post-treatment data provided, using non-parametric bootstrapping as well as using Bayesian MCMC. Functions to perform power analyses for faecal egg counts (including FECRT) are also provided.
Author: Matthew Denwood
Maintainer: Matthew Denwood

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Package ppiPre updated to version 1.7 with previous version 1.6 dated 2015-01-29

Title: Predict Protein-Protein Interactions Based on Functional and Topological Similarities
Description: Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Maintainer: Yue Deng

Diff between ppiPre versions 1.6 dated 2015-01-29 and 1.7 dated 2015-03-02

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Package RobPer updated to version 1.2.1 with previous version 1.2 dated 2014-10-03

Title: Robust Periodogram and Periodicity Detection Methods
Description: Calculates periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit. Artificial light curves can be generated using the function tsgen. For more details see Thieler, Fried and Rathjens (2013).
Author: Anita M. Thieler, Jonathan Rathjens and Roland Fried, with contributions from Brenton R. Clarke, Uwe Ligges, Matias Salibian-Barrera, Gert Willems and Victor Yohai
Maintainer: Jonathan Rathjens

Diff between RobPer versions 1.2 dated 2014-10-03 and 1.2.1 dated 2015-03-02

 RobPer-1.2.1/RobPer/DESCRIPTION                   |   13 ++---
 RobPer-1.2.1/RobPer/MD5                           |   24 ++++------
 RobPer-1.2.1/RobPer/build/vignette.rds            |binary
 RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.Rnw  |   51 ++++++++++------------
 RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.pdf  |binary
 RobPer-1.2.1/RobPer/man/RobPer-package.rd         |    8 +--
 RobPer-1.2.1/RobPer/vignettes/RobPer_Art.bib      |    4 -
 RobPer-1.2.1/RobPer/vignettes/RobPer_Vignette.Rnw |   51 ++++++++++------------
 RobPer-1.2.1/RobPer/vignettes/chart/IRWLS.tex     |    2 
 RobPer-1.2.1/RobPer/vignettes/chart/RobPer.tex    |    2 
 RobPer-1.2.1/RobPer/vignettes/chart/boxenecht.tex |    2 
 RobPer-1.2.1/RobPer/vignettes/chart/singleFun.tex |    2 
 RobPer-1.2/RobPer/inst/CITATION                   |only
 RobPer-1.2/RobPer/vignettes/chart/boxenzahlen.tex |only
 14 files changed, 77 insertions(+), 82 deletions(-)

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New package stmCorrViz with initial version 1.1
Package: stmCorrViz
Type: Package
Title: A Tool for Structural Topic Model Visualizations
Version: 1.1
Date: 2015-02-14
Imports: jsonlite, stm
Authors@R: c(person("Antonio", "Coppola", role = c("aut", "cre", "cph"), email = "acoppola@college.harvard.edu"), person("Margaret", "Roberts", role = c("ctb", "cph")), person("Brandon", "Stewart", role = c("aut", "cph")), person("Dustin", "Tingley", role = c("ctb", "ths", "cph")))
Author: Antonio Coppola [aut, cre, cph], Margaret Roberts [ctb, cph], Brandon Stewart [aut, cph], Dustin Tingley [ctb, ths, cph]
Maintainer: Antonio Coppola
Description: Generates an interactive visualization of topic correlations/hierarchy in a Structural Topic Model (STM) of Roberts, Stewart, and Tingley. The package performs a hierarchical clustering of topics which are then exported to a JSON object and visualized using D3.
License: GPL (>= 2)
Packaged: 2015-03-01 23:15:59 UTC; antonio12
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-02 08:03:14

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Package lsr updated to version 0.5 with previous version 0.3.2 dated 2014-01-31

Title: Companion to "Learning Statistics with R"
Description: A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.5. [Lecture notes] School of Psychology, University of Adelaide, Adelaide, Australia. ISBN: 978-1-326-18972-3. URL: http://health.adelaide.edu.au/psychology/ccs/teaching/lsr/.
Author: Daniel Navarro
Maintainer: Daniel Navarro

Diff between lsr versions 0.3.2 dated 2014-01-31 and 0.5 dated 2015-03-02

 DESCRIPTION        |   13 +++++++------
 MD5                |   14 +++++++-------
 NEWS               |    6 ++++++
 R/correlate.R      |   20 ++++++++++++++++++--
 R/maxFreq.R        |    6 ++++--
 R/modeOf.R         |    8 +++++---
 inst/CITATION      |   13 +++++++------
 man/lsr-package.Rd |   16 +++++++++-------
 8 files changed, 63 insertions(+), 33 deletions(-)

More information about lsr at CRAN
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