Fri, 18 May 2012

Package rpartOrdinal updated to version 2.0.4 with previous version 2.0.3 dated 2011-10-14

Title: Ordinal classification tree functions
Description: This package contains functions that can be called in conjunction with rpart for deriving a classification tree when the response to be predicted is ordinal.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer

Diff between rpartOrdinal versions 2.0.3 dated 2011-10-14 and 2.0.4 dated 2012-05-18

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 rpartOrdinal-2.0.4/rpartOrdinal/inst/doc/rpartOrdinal.pdf |binary
 11 files changed, 474 insertions(+), 568 deletions(-)

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New package mcmcse with initial version 0.1
Package: mcmcse
Type: Package
Title: Monte Carlo standard errors for MCMC
Version: 0.1
Date: 2012-05-14
Author: James M. Flegal
Maintainer: James M. Flegal
Description: Tools for calculating Monte Carlo standard errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. This package considers standard errors for expectation and quantile estimators.
License: GPL
LazyLoad: yes
Packaged: 2012-05-18 16:17:25 UTC; jamesflegal
Repository: CRAN
Date/Publication: 2012-05-18 17:58:52

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New package HIest with initial version 1.0
Package: HIest
Type: Package
Title: Hybrid index estimation
Version: 1.0
Date: 2012-03-13
Author: Ben Fitzpatrick
Maintainer:
Description: Uses likelihood to estimate ancestry and heterozygosity. Evaluates simple hybrid classifications (parentals, F1, F2, backcrosses). Estimates genomic clines.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2012-05-18 18:34:55 UTC; benfitzpatrick
Repository: CRAN
Date/Publication: 2012-05-18 18:42:52

More information about HIest at CRAN
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New package simsem with initial version 0.2-0
Package: simsem
Type: Package
Title: SIMulated Structural Equation Modeling.
Version: 0.2-0
Date: 2012-05-17
Authors@R: c(person("Sunthud", "Pornprasertmanit", role = c("aut", "cre"), email = "psunthud@ku.edu"), person("Patrick", "Miller", role = c("aut", "cre"), email="patr1ckm@ku.edu"), person("Alexander", "Schoemann", role = c("aut", "cre"), email="schoemann@ku.edu") )
Author: Sunthud Pornprasertmanit , Patrick Miller , Alexander Schoemann
Maintainer: Sunthud Pornprasertmanit , Patrick Miller , Alexander Schoemann
Depends: R(>= 2.14), methods, lavaan, MASS
Suggests: parallel, Amelia, copula, quantreg, splines, foreign
Description: This package can be used to generate data using the structural equation modeling framework. This package is tailored to use those simulated data for various purposes, such as model fit evaluation, power analysis, or missing data handling and planning.
License: GPL (>= 2)
LazyLoad: yes
URL: https://github.com/simsem/simsem/wiki
Packaged: 2012-05-18 14:30:14 UTC; Sunthud
Repository: CRAN
Date/Publication: 2012-05-18 14:54:32

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New package semTools with initial version 0.1-0
Package: semTools
Type: Package
Title: Useful tools for structural equation modeling.
Version: 0.1-0
Date: 2012-05-17
Authors@R: c(person("Sunthud", "Pornprasertmanit", role = c("aut", "cre"), email = "psunthud@ku.edu"), person("Patrick", "Miller", role = c("aut", "cre"), email="patr1ckm@ku.edu"), person("Alexander", "Schoemann", role = c("aut", "cre"), email="schoemann@ku.edu"), person("Yves", "Rosseel", role = c("aut"), email="Yves.Rosseel@UGent.be") )
Author: Sunthud Pornprasertmanit , Patrick Miller , Alex Schoemann , Yves Rosseel
Maintainer: Sunthud Pornprasertmanit , Patrick Miller , Alex Schoemann
Depends: R(>= 2.14), MASS, lavaan, methods
Suggests: parallel, Amelia, mice
Description: This package provide useful tools for structural equation modeling analysis.
License: GPL (>= 2)
LazyLoad: yes
URL: https://github.com/simsem/semTools/wiki
Packaged: 2012-05-18 14:05:23 UTC; Sunthud
Repository: CRAN
Date/Publication: 2012-05-18 14:54:40

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Package meta updated to version 2.1-0 with previous version 2.0-4 dated 2012-05-03

Title: Meta-Analysis with R
Description: Fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot.
Author: Guido Schwarzer
Maintainer: Guido Schwarzer

Diff between meta versions 2.0-4 dated 2012-05-03 and 2.1-0 dated 2012-05-18

 DESCRIPTION            |    8 ++++----
 MD5                    |   28 ++++++++++++++--------------
 NEWS                   |   34 ++++++++++++++++++++++++++++++++++
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 R/print.summary.meta.R |    3 ++-
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 15 files changed, 133 insertions(+), 48 deletions(-)

More information about meta at CRAN
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New package gsmaRt with initial version 1.0
Package: gsmaRt
Type: Package
Title: Gene Set Microarray Testing
Version: 1.0
Date: 2011-05-06
Author: Stephan Artmann, Mathias Fuchs
Maintainer: Stephan Artmann
Depends: GEOquery,R2HTML,qvalue,rgl,scatterplot3d,xtable,limma
Description: combined miRNA- and mRNA-testing
License: GPL
LazyLoad: yes
Packaged: 2012-05-18 11:48:48 UTC; stephan
Repository: CRAN
Date/Publication: 2012-05-18 14:56:42

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Package muma updated to version 1.1 with previous version 1.0 dated 2012-04-24

Title: Metabolomic Univariate and Multivariate Analysis
Description: Preprocessing of metabolomic data (normalization and scalings); Principal Component Analysis with help tool for choosing best-separating principal components and automatic outlier testing; automatic univariate analysis for parametric and non-parametric data, with report generation (volcano and box plots); partial least sqaure discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); Ratio Analysis NMR SpectroscopY (RANSY).
Author: Edoardo Gaude, Francesca Chignola, Dimitrios Spiliotopoulos, Silvia Mari, Andrea Spitaleri and Michela Ghitti
Maintainer: Edoardo gaude

Diff between muma versions 1.0 dated 2012-04-24 and 1.1 dated 2012-05-18

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New package MultiOrd with initial version 1.0
Package: MultiOrd
Type: Package
Title: Generation of multivariate ordinal variates.
Version: 1.0
Date: 2012-05-17
Author: Anup Amatya and Hakan Demirtas
Maintainer: Anup Amatya
Depends: mvtnorm, corpcor, Matrix, psych
Description: A method for multivariate ordinal data generation given marginal distributions and correlation based on the methodology proposed by Demirtas (2006).
License: GPL-2
LazyLoad: yes
Packaged: 2012-05-17 21:38:15 UTC; aamatya
Repository: CRAN
Date/Publication: 2012-05-18 13:36:54

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Package FrF2 updated to version 1.4-1 with previous version 1.4 dated 2012-03-17

Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional Factorial designs. Furthermore, analysis tools for Fractional Factorial designs with 2-level factors are offered (main effects and interaction plots for all factors simultaneously, cube plot for looking at the simultaneous effects of three factors, full or half normal plot, alias structure in a more readable format than with the built-in function alias). The package is still under development. While much of the intended functionality is already available, some changes and improvements are still to be expected. Suggestions are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping

Diff between FrF2 versions 1.4 dated 2012-03-17 and 1.4-1 dated 2012-05-18

 DESCRIPTION |   17 ++++++++---------
 MD5         |    4 ++--
 inst/NEWS   |    3 +++
 3 files changed, 13 insertions(+), 11 deletions(-)

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Package fanc updated to version 0.18 with previous version 0.17 dated 2012-05-17

Title: Penalized likelihood factor analysis via non-concave penalty
Description: This package computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used.
Author: Kei Hirose, Michio Yamamoto
Maintainer: Kei Hirose

Diff between fanc versions 0.17 dated 2012-05-17 and 0.18 dated 2012-05-18

 DESCRIPTION    |    8 ++++----
 MD5            |    6 +++---
 R/print.fanc.R |   27 +++++++++++++++++++--------
 man/fanc.Rd    |    4 ++--
 4 files changed, 28 insertions(+), 17 deletions(-)

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Package RcmdrPlugin.KMggplot2 updated to version 0.1-0 with previous version 0.0-4 dated 2012-03-01

Title: Rcmdr Plug-In for Kaplan-Meier Plot and Other Plots by Using the ggplot2 Package
Description: This package is an R Commander plug-in for Kaplan-Meier plot and other plots by using the ggplot2 package.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou.

Diff between RcmdrPlugin.KMggplot2 versions 0.0-4 dated 2012-03-01 and 0.1-0 dated 2012-05-18

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 180 files changed, 1079 insertions(+), 935 deletions(-)

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New package LeafAngle with initial version 1.1
Package: LeafAngle
Type: Package
Title: Fits, plots, and summarizes leaf angle distributions.
Version: 1.1
Date: 2012-05-18
Author: Remko Duursma
Maintainer:
Description: A leaf angle distribution is a special distribution that is defined between 0 and 90 degrees, and a number of distributions are used to characterize the leaf angle distribution in real plant canopies. This package includes methods to fit distributions to data, visualize the fit, and compare fits of nine different distributions.
License: GPL
LazyLoad: yes
Packaged: 2012-05-18 08:24:25 UTC; 30022860
Repository: CRAN
Date/Publication: 2012-05-18 08:46:20

More information about LeafAngle at CRAN
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Package dbstats updated to version 1.0.2 with previous version 1.0.1 dated 2011-06-30

Title: Distance-based statistics (dbstats)
Description: This package contains functions for distance-based prediction methods. These are methods for prediction where predictor information is coded as a matrix of distances between individuals. Distances can either be directly input as an interdistances matrix, a squared interdistances matrix, an inner-products matrix or computed from observed explanatory variables.
Author: Boj, Eva , Caballe, Adria , Delicado, Pedro and Fortiana, Josep .
Maintainer: Fortiana, Josep

Diff between dbstats versions 1.0.1 dated 2011-06-30 and 1.0.2 dated 2012-05-18

 DESCRIPTION                 |   11 +-
 MD5                         |only
 NAMESPACE                   |   30 ++++++-
 R/Gcalc.r                   |    3 
 R/controls_ldblm.r          |   20 -----
 R/dbglm.r                   |  152 +++++++++++++++++++-------------------
 R/dblm.r                    |  100 ++++++++++++-------------
 R/dbplsr.r                  |   98 ++++++++++++------------
 R/ldbglm.r                  |  174 +++++++++++++++++++++++---------------------
 R/ldblm.r                   |  170 +++++++++++++++++++++---------------------
 R/plot.dblm.r               |    2 
 R/pred.train.sample.dbglm.r |    2 
 R/pred.train.sample.r       |    2 
 R/predict.dbplsr.r          |    2 
 R/predict.ldbglm.r          |    2 
 R/predict.ldblm.r           |    2 
 R/print.summary.dblm.r      |   16 ++++
 R/print.summary.dbplsr.r    |   23 +++++
 R/print.summary.ldblm.r     |   17 ++++
 R/summary.dblm.r            |   16 +++-
 R/summary.dbplsr.r          |   17 ++++
 R/summary.ldblm.r           |   28 ++++++-
 man/dbglm.Rd                |   16 +---
 man/dblm.Rd                 |   14 +--
 man/dbplsr.Rd               |   13 +--
 man/dbstats-package.Rd      |    6 -
 man/ldbglm.Rd               |   23 ++---
 man/ldblm.Rd                |   29 +++----
 man/plot.dbplsr.rd          |    4 -
 man/plot.ldblm.rd           |    5 -
 man/predict.dbglm.rd        |    2 
 man/predict.dblm.rd         |    4 -
 man/predict.dbplsr.rd       |    2 
 man/predict.ldbglm.rd       |    8 +-
 man/predict.ldblm.rd        |    6 -
 man/summary.dbglm.rd        |    7 +
 man/summary.dblm.rd         |   17 ++++
 man/summary.dbplsr.rd       |    8 +-
 man/summary.ldblm.rd        |    9 ++
 39 files changed, 596 insertions(+), 464 deletions(-)

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Package multitaper updated to version 1.0-1 with previous version 1.0-0 dated 2012-04-24

Title: Multitaper Spectral Analysis
Description: Generates Discrete Prolate Spheroidal Sequences, provides functions and utilities for multitaper spectral analysis and related problems.
Author: Karim Rahim , Wesley Burr
Maintainer: Karim Rahim

Diff between multitaper versions 1.0-0 dated 2012-04-24 and 1.0-1 dated 2012-05-18

 multitaper-1.0-0/multitaper/data/.RData    |only
 multitaper-1.0-0/multitaper/data/.Rhistory |only
 multitaper-1.0-1/multitaper/DESCRIPTION    |   10 +++++-----
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 multitaper-1.0-1/multitaper/R/multitaper.R |    8 ++++++--
 multitaper-1.0-1/multitaper/R/plots.R      |    2 +-
 6 files changed, 15 insertions(+), 11 deletions(-)

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New package makeProject with initial version 1.0
Package: makeProject
Type: Package
Title: Creates an empty package framework for the LCFD format
Version: 1.0
Date: 2012-05-17
Author: Noah Silverman
Maintainer: Noah Silverman
Description: This package creates an empty framework of files and directories for the "Load, Clean, Func, Do" structure described by Josh Reich.
License: GPL-3
Packaged: 2012-05-18 06:42:44 UTC; noah
Repository: CRAN
Date/Publication: 2012-05-18 07:15:00

More information about makeProject at CRAN
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Package HTMLUtils updated to version 0.1.5 with previous version 0.1.4 dated 2010-08-10

Title: Facilitates automated HTML report creation
Description: Facilitates automated HTML report creation, in particular framed HTML pages and dynamically sortable tables.
Author: "Markus Loecher, Berlin School of Economics and Law (BSEL)"
Maintainer: "Markus Loecher, Berlin School of Economics and Law (BSEL)"

Diff between HTMLUtils versions 0.1.4 dated 2010-08-10 and 0.1.5 dated 2012-05-18

 HTMLUtils-0.1.4/HTMLUtils/R/CairoWorks.R           |only
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 HTMLUtils-0.1.5/HTMLUtils/R/BasicHTML.R            |  240 +++++++++++-------
 HTMLUtils-0.1.5/HTMLUtils/R/FramedHTML.R           |  277 +++++++++++++-------
 HTMLUtils-0.1.5/HTMLUtils/R/HTMLhref.R             |   13 
 HTMLUtils-0.1.5/HTMLUtils/R/HTMLsortedTable.R      |  126 +++++----
 HTMLUtils-0.1.5/HTMLUtils/R/InstallJSC.R           |   36 +-
 HTMLUtils-0.1.5/HTMLUtils/R/MyReportBegin.R        |   22 -
 HTMLUtils-0.1.5/HTMLUtils/R/MyReportEnd.R          |   14 -
 HTMLUtils-0.1.5/HTMLUtils/R/makePathName.R         |   39 +-
 HTMLUtils-0.1.5/HTMLUtils/R/myHTMLInitFile.R       |  278 +++++++++++----------
 HTMLUtils-0.1.5/HTMLUtils/man/BasicHTML.Rd         |  156 +++++------
 HTMLUtils-0.1.5/HTMLUtils/man/FramedHTML.Rd        |  186 +++++++-------
 HTMLUtils-0.1.5/HTMLUtils/man/HTMLUtils-package.Rd |   54 +---
 HTMLUtils-0.1.5/HTMLUtils/man/HTMLhref.Rd          |   44 +--
 HTMLUtils-0.1.5/HTMLUtils/man/HTMLsortedTable.Rd   |   52 +--
 HTMLUtils-0.1.5/HTMLUtils/man/InstallJSC.Rd        |   38 +-
 HTMLUtils-0.1.5/HTMLUtils/man/MyReportBegin.Rd     |   43 +--
 HTMLUtils-0.1.5/HTMLUtils/man/MyReportEnd.Rd       |   38 +-
 HTMLUtils-0.1.5/HTMLUtils/man/makePathName.Rd      |   42 +--
 HTMLUtils-0.1.5/HTMLUtils/man/myHTMLInitFile.Rd    |   79 +++--
 26 files changed, 977 insertions(+), 816 deletions(-)

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Package gdsfmt updated to version 0.9.9 with previous version 0.9.8 dated 2012-04-16

Title: CoreArray Genomic Data Structure (GDS) R Interface
Description: CoreArray project is to develop portable and scalable storage technologies for bioinformatics data, allowing parallel computing at the multicore and cluster levels.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng

Diff between gdsfmt versions 0.9.8 dated 2012-04-16 and 0.9.9 dated 2012-05-18

 DESCRIPTION                |   16 -
 MD5                        |   27 -
 R/GDS.all.r                |  710 +++++++++++++++++++++++++++++++++++++++++++--
 man/add.gdsn.Rd            |   19 +
 man/apply.gdsn.Rd          |   19 -
 man/applylt.gdsn.Rd        |only
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 man/clusterApplylt.gdsn.Rd |only
 man/gdsfmt-package.Rd      |    4 
 man/objdesp.gdsn.Rd        |    8 
 src/dBase.cpp              |    8 
 src/dBase.h                |    8 
 src/dPlatform.cpp          |    3 
 src/dSeq.h                 |    2 
 src/dType.h                |    6 
 src/gdsfmt.cpp             |   90 ++---
 16 files changed, 809 insertions(+), 111 deletions(-)

More information about gdsfmt at CRAN
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