Thu, 14 Aug 2014

Package RcmdrMisc updated to version 1.0-1 with previous version 1.0-0 dated 2014-08-05

Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre], Robert Muenchen [ctb], Dan Putler [ctb]
Maintainer: John Fox

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New package mirtCAT with initial version 0.1
Package: mirtCAT
Version: 0.1
Date: 2014-07-10
Type: Package
Title: Computerized Adaptive Testing with Multidimensional Item Response Theory
Authors@R: c( person("Phil", family="Chalmers", email = "rphilip.chalmers@gmail.com", role = c("aut", "cre", "cph")))
Description: Provides tools to generate an HTML interface for creating adaptive and non-adaptive educational and psychological tests using the shiny package. Suitable for applying unidimensional and multidimensional computerized adaptive tests using item response theory methodology and for creating simple questionnaires forms to collect response data directly in R.
Depends: R (>= 2.15), mirt (>= 1.5), shiny (>= 0.10.0)
Imports: methods
Suggests: testthat
ByteCompile: no
LazyLoad: yes
LazyData: yes
License: GPL (>= 3)
Repository: CRAN
Maintainer: Phil Chalmers
URL: https://github.com/philchalmers/mirtCAT
BugReports: https://github.com/philchalmers/mirtCAT/issues?state=open
Packaged: 2014-08-14 17:43:58 UTC; phil
Author: Phil Chalmers [aut, cre, cph]
NeedsCompilation: no
Date/Publication: 2014-08-14 22:21:49

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Package diseasemapping updated to version 0.7.7 with previous version 0.7.5 dated 2013-07-17

Title: Calculate observed and expected disease incidence counts from a case file and population data.
Description: Tools for calculating rates and Standardized Incidence Ratios from case and population data.
Author: Patrick Brown
Maintainer: Patrick Brown

Diff between diseasemapping versions 0.7.5 dated 2013-07-17 and 0.7.7 dated 2014-08-14

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Package sjPlot updated to version 1.4.3 with previous version 1.4.2 dated 2014-05-20

Title: sjPlot - data visualization for statistics in social science
Description: Collection of several plotting / table output functions for visualizing data and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Luedecke

Diff between sjPlot versions 1.4.2 dated 2014-05-20 and 1.4.3 dated 2014-08-14

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Package mirt updated to version 1.5 with previous version 1.4 dated 2014-06-22

Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using unidimensional and multidimensional latent trait models under the Item Response Theory paradigm. Exploratory and confirmatory models can be estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier analyses are available for modeling item testlets. Multiple group analysis and mixed effects designs also are available for detecting differential item functioning and modelling item and person covariates.
Author: Phil Chalmers [aut, cre, cph], Joshua Pritikin [ctb], Mateusz Zoltak [ctb]
Maintainer: Phil Chalmers

Diff between mirt versions 1.4 dated 2014-06-22 and 1.5 dated 2014-08-14

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Package hmmm updated to version 1.0-3 with previous version 1.0-2 dated 2014-01-08

Title: hierarchical multinomial marginal models
Description: Functions for specifying and fitting marginal models for contingency tables proposed by Bergsma and Rudas (2002) here called hierarchical multinomial marginal models (hmmm) and their extensions presented by Bartolucci et al. (2007); multinomial Poisson homogeneous (mph) models and homogeneous linear predictor (hlp) models for contingency tables proposed by Lang (2004) and (2005); hidden Markov models where the distribution of the observed variables is described by a marginal model. Inequality constraints on the parameters are allowed and can be tested.
Author: Colombi Roberto and Sabrina Giordano and Manuela Cazzaro, with contributions from Joseph Lang
Maintainer: Colombi Roberto

Diff between hmmm versions 1.0-2 dated 2014-01-08 and 1.0-3 dated 2014-08-14

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Package effects updated to version 3.0-1 with previous version 3.0-0 dated 2014-03-21

Title: Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models
Description: Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Michael Friendly [aut], Jangman Hong [aut], Robert Andersen [ctb], David Firth [ctb], Steve Taylor [ctb]
Maintainer: John Fox

Diff between effects versions 3.0-0 dated 2014-03-21 and 3.0-1 dated 2014-08-14

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Package OceanView updated to version 1.0.1 with previous version 1.0 dated 2014-04-14

Title: Visualisation of Oceanographic Data and Model Output.
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Author: Karline Soetaert
Maintainer: Karline Soetaert

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Package survey updated to version 3.30-2 with previous version 3.29-5 dated 2013-06-12

Title: analysis of complex survey samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley"

Diff between survey versions 3.29-5 dated 2013-06-12 and 3.30-2 dated 2014-08-14

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Package spatialTailDep updated to version 1.0.1 with previous version 1.0 dated 2014-04-02

Title: Estimation of spatial tail dependence models
Description: Provides functions implementing the pairwise M-estimator for parametric models for stable tail dependence functions described in "An M-estimator of spatial tail dependence" (Einmahl, J.H.J., Kiriliouk, A., Krajina, A. and Segers, J., 2014). See http://arxiv.org/abs/1403.1975.
Author: Anna Kiriliouk, Johan Segers
Maintainer: Anna Kiriliouk

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Package parcor updated to version 0.2-5 with previous version 0.2-4 dated 2013-08-20

Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso and Ridge regression based on cross-validation.
Author: Nicole Kraemer, Juliane Schaefer
Maintainer: Nicole Kraemer

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Package jaatha updated to version 2.5.1 with previous version 2.5 dated 2014-07-28

Title: A Fast Parameter Estimation Method for Evolutionary Biology
Description: Jaatha is a composite likelihood method for inferring evolutionary parameters using genetic data. Given a model of the evolutionary history of two biological populations as well as SNP data from multiple individuals from each population, it estimates model parameters like the time of separation of both species.
Author: Paul R. Staab, Lisha Mathew and Dirk Metzler
Maintainer: Paul R. Staab

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 jaatha-2.5.1/jaatha/src/parse_output.cpp                      |   35 +-
 jaatha-2.5/jaatha/inst/integrationTests/it.sim_prog_seqgen.R  |only
 jaatha-2.5/jaatha/inst/unitTests/runit.sim_program_msms.r     |only
 15 files changed, 285 insertions(+), 117 deletions(-)

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New package bamboo with initial version 0.9.5
Package: bamboo
Type: Package
Title: Protein Secondary Structure Prediction Using the Bamboo Method
Version: 0.9.5
Date: 2014-08-14
Author: David B. Dahl
Maintainer: David B. Dahl
URL: http://dahl.byu.edu/software/bamboo/
Imports: rJava, jvmr
SystemRequirements: Java (>= 1.6)
Description: Implementation of the methods described in the paper Li, Dahl, Vannucci, Joo, and Tsai (2014), Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction, PLOS ONE, revise and resubmit.
License: GPL-3
Packaged: 2014-08-14 06:37:44 UTC; dahl
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-08-14 10:21:35

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Package XLConnectJars updated to version 0.2-9 with previous version 0.2-8 dated 2014-08-06

Title: JAR dependencies for the XLConnect package
Description: Provides external JAR dependencies for the XLConnect package
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] (Apache POI, Apache XMLBeans)
Maintainer: Martin Studer

Diff between XLConnectJars versions 0.2-8 dated 2014-08-06 and 0.2-9 dated 2014-08-14

 XLConnectJars-0.2-8/XLConnectJars/inst/java/stax-api-1.0.1.jar |only
 XLConnectJars-0.2-9/XLConnectJars/DESCRIPTION                  |   23 ++++++----
 XLConnectJars-0.2-9/XLConnectJars/MD5                          |   11 ++--
 XLConnectJars-0.2-9/XLConnectJars/NEWS                         |    5 ++
 XLConnectJars-0.2-9/XLConnectJars/inst/COPYRIGHTS              |   14 ------
 XLConnectJars-0.2-9/XLConnectJars/java/README                  |   11 ++--
 XLConnectJars-0.2-9/XLConnectJars/man/XLConnectJars-package.Rd |    7 +--
 7 files changed, 35 insertions(+), 36 deletions(-)

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Package XLConnect updated to version 0.2-9 with previous version 0.2-8 dated 2014-08-06

Title: Excel Connector for R
Description: Manipulate Excel files from R
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons Codec, XML Commons External Components XML APIs), Stephen Colebourne [ctb, cph] (Joda-Time Java library), Metastuff, Ltd. [ctb, cph] (dom4j)
Maintainer: Martin Studer

Diff between XLConnect versions 0.2-8 dated 2014-08-06 and 0.2-9 dated 2014-08-14

 DESCRIPTION                     |   29 ++++++++++++++++++++++-------
 MD5                             |   20 ++++++++++----------
 NEWS                            |    5 +++++
 README.md                       |    4 ++--
 inst/COPYRIGHTS                 |   23 ++---------------------
 inst/doc/XLConnect.Rnw          |   11 ++---------
 inst/doc/XLConnect.pdf          |binary
 inst/doc/XLConnectImpatient.pdf |binary
 java/README                     |   25 ++++++++++++-------------
 man/XLConnect-package.Rd        |    8 ++++----
 vignettes/XLConnect.Rnw         |   11 ++---------
 11 files changed, 61 insertions(+), 75 deletions(-)

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New package trimTrees with initial version 1.2
Package: trimTrees
Type: Package
Title: Trimmed opinion pools of trees in a random forest
Version: 1.2
Date: 2014-08-1
Depends: R (>= 2.5.0),stats,randomForest,mlbench
Author: Yael Grushka-Cockayne, Victor Richmond R. Jose, Kenneth C. Lichtendahl Jr. and Huanghui Zeng, based on the source code from the randomForest package by Andy Liaw and Matthew Wiener and on the original Fortran code by Leo Breiman and Adele Cutler.
Maintainer: Yael Grushka-Cockayne
Description: Creates point and probability forecasts from the trees in a random forest using a trimmed opinion pool.
Suggests: MASS
License: GPL (>= 2)
Packaged: 2014-08-13 21:48:25 UTC; lichtendahlc
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-08-14 07:11:17

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Package fastGHQuad updated to version 0.2 with previous version 0.1-1 dated 2011-12-05

Title: Fast Rcpp implementation of Gauss-Hermite quadrature
Description: Fast, numerically-stable Gauss-Hermite quadrature
Author: Alexander W Blocker
Maintainer: Alexander W Blocker

Diff between fastGHQuad versions 0.1-1 dated 2011-12-05 and 0.2 dated 2014-08-14

 fastGHQuad-0.1-1/fastGHQuad/.gitignore              |only
 fastGHQuad-0.2/fastGHQuad/DESCRIPTION               |   13 
 fastGHQuad-0.2/fastGHQuad/LICENSE                   |only
 fastGHQuad-0.2/fastGHQuad/MD5                       |   32 
 fastGHQuad-0.2/fastGHQuad/NAMESPACE                 |   10 
 fastGHQuad-0.2/fastGHQuad/R/integrate.R             |  120 +++
 fastGHQuad-0.2/fastGHQuad/R/lib.R                   |   78 ++
 fastGHQuad-0.2/fastGHQuad/R/zzz.R                   |only
 fastGHQuad-0.2/fastGHQuad/man/aghQuad.Rd            |   85 +-
 fastGHQuad-0.2/fastGHQuad/man/evalHermitePoly.Rd    |   34 
 fastGHQuad-0.2/fastGHQuad/man/fastGHQuad-package.Rd |   62 -
 fastGHQuad-0.2/fastGHQuad/man/findPolyRoots.Rd      |   37 -
 fastGHQuad-0.2/fastGHQuad/man/gaussHermiteData.Rd   |   59 -
 fastGHQuad-0.2/fastGHQuad/man/ghQuad.Rd             |   74 --
 fastGHQuad-0.2/fastGHQuad/man/hermitePolyCoef.Rd    |   32 
 fastGHQuad-0.2/fastGHQuad/src/Makevars              |   30 
 fastGHQuad-0.2/fastGHQuad/src/Makevars.win          |    7 
 fastGHQuad-0.2/fastGHQuad/src/lib.cpp               |  724 +++++++++-----------
 fastGHQuad-0.2/fastGHQuad/src/lib.h                 |   38 -
 19 files changed, 770 insertions(+), 665 deletions(-)

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