Wed, 14 Nov 2012

Package visreg updated to version 1.1-1 with previous version 1.1-0 dated 2012-09-28

Title: Visualization of regression models
Description: Provides convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

Diff between visreg versions 1.1-0 dated 2012-09-28 and 1.1-1 dated 2012-11-14

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Package msap updated to version 1.1.0 with previous version 1.0.2 dated 2012-10-04

Title: Statistical analysis for Methylation-sensitive Amplification Polymorphism data
Description: Statistical Analyses of Methylation-sensitive Amplification Polymorphism (MSAP) assays.
Author: Andres Perez-Figueroa
Maintainer: Andres Perez-Figueroa

Diff between msap versions 1.0.2 dated 2012-10-04 and 1.1.0 dated 2012-11-14

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Package mmm2 updated to version 1.1 with previous version 1.0 dated 2012-05-05

Title: Multivariate marginal models with shared regression parameters
Description: Fits multivariate marginal models with shared regression parameters for discrete and continuous responses
Author: Ozgur Asar, Ozlem Ilk
Maintainer: Ozgur Asar

Diff between mmm2 versions 1.0 dated 2012-05-05 and 1.1 dated 2012-11-14

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Package BBmisc updated to version 1.1-164 with previous version 1.1-132 dated 2012-07-04

Title: Miscellaneous helper functions for B. Bischl.
Description: Miscellaneous helper functions for and from B. Bischl and some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl , Michel Lang , Olaf Mersmann
Maintainer: Bernd Bischl

Diff between BBmisc versions 1.1-132 dated 2012-07-04 and 1.1-164 dated 2012-11-14

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Package wfe updated to version 1.1 with previous version 1.0 dated 2012-07-18

Title: Weighted Linear Fixed Effects Regression Models for Causal Inference
Description: This R package provides a computationally efficient way of fitting weighted linear fixed effects estimators for causal inference with various weighting schemes. Imai and Kim (2012) show that weighted linear fixed effects estimators can be used to estimate the average treatment effects under different identification strategies. This includes stratified randomized experiments, matching and stratification for observational studies, first differencing, and difference-in-differences. The package also provides various robust standard errors and a specification test for standard linear fixed effects estimators.
Author: In Song Kim , Kosuke Imai
Maintainer: In Song Kim

Diff between wfe versions 1.0 dated 2012-07-18 and 1.1 dated 2012-11-14

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Package biomod2 updated to version 1.3.5 with previous version 1.3.1 dated 2012-11-09

Title: Ensemble platform for species distribution modeling
Description: Functions for species distribution modeling, calibration and evaluation, ensemble of models.
Author: Wilfried Thuiller, Damien Georges and Robin Engler
Maintainer: Damien Georges

Diff between biomod2 versions 1.3.1 dated 2012-11-09 and 1.3.5 dated 2012-11-14

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New package tmle with initial version 1.2.0-2
Package: tmle
Type: Package
Title: Targeted Maximum Likelihood Estimation
Version: 1.2.0-2
Date: 2012-11-11
Author: Susan Gruber, in collaboration with Mark van der Laan
Maintainer: Susan Gruber
Copyright: Copyright 2012. The Regents of the University of California (Regents). All Rights Reserved.
Depends: SuperLearner
Description: tmle implements targeted maximum likelihood estimation, first described in van der Laan and Rubin, 2006 (Targeted Maximum Likelihood Learning, The International Journal of biostatistics, 2(1), 2006. This version adds the tmleMSM function to the package, for estimating the parameters of a marginal structural model (MSM) for a binary point treatment effect. The tmle function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. Effect estimation stratified by a binary mediating variable is also available. The population mean is calculated when there is missingness, and no variation in the treatment assignment. An ID argument can be used to identify repeated measures. Default settings call SuperLearner to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
License: BSD
URL: http://cran.r-project.org/package=tmle
Packaged: 2012-11-14 13:51:30 UTC; Susan
X-CRAN-Comment: Older versions were removed as it became clear that the license stated did not cover the package.
Repository: CRAN
Date/Publication: 2012-11-14 14:11:37

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Package lsr updated to version 0.2 with previous version 0.1.1 dated 2012-01-23

Title: Companion package to "Learning Statistics with R"
Description: Functions that I have found useful for teaching purposes.
Author: Daniel Navarro
Maintainer: Daniel Navarro

Diff between lsr versions 0.1.1 dated 2012-01-23 and 0.2 dated 2012-11-14

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New package sExtinct with initial version 1.0
Package: sExtinct
Type: Package
Title: Calculates the historic date of extinction given a series of sighting events
Version: 1.0
Date: 2012-10-24
Author: Christopher Clements
Maintainer: Christopher Clements
Description: This package combines several sighting based estimators of historical extinction, allowing them to be run simultaneously or individually. Code for this package was contributed by Ben Collen, Gene Hunt and Tracy Rout. Additional code was taken from McPherson & Myers (2009).
License: GPL-2
Depends: graphics, grDevices, stats, utils, lattice
Packaged: 2012-11-10 19:12:19 UTC; chrisclements
Repository: CRAN
Date/Publication: 2012-11-14 10:32:12

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Package SemiParBIVProbit updated to version 3.2-4 with previous version 3.2-3 dated 2012-10-04

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate probit models with semiparametric predictors (including linear, nonlinear and nonparametric random effects) in the presence of correlated error equations, endogeneity or sample selection.
Author: Giampiero Marra and Rosalba Radice with contributions from Georgios Papageorgiou
Maintainer: Giampiero Marra

Diff between SemiParBIVProbit versions 3.2-3 dated 2012-10-04 and 3.2-4 dated 2012-11-14

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Package ipred updated to version 0.9-1 with previous version 0.9-0 dated 2012-10-22

Title: Improved Predictors
Description: Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.
Author: Andrea Peters and Torsten Hothorn
Maintainer: Torsten Hothorn

Diff between ipred versions 0.9-0 dated 2012-10-22 and 0.9-1 dated 2012-11-14

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Package linLIR updated to version 1.1 with previous version 1.0-2 dated 2012-09-07

Title: linear Likelihood-based Imprecise Regression
Description: This package implements the methodology of Likelihood-based Imprecise Regression (LIR) for the case of linear regression with interval data.
Author: Andrea Wiencierz
Maintainer: Andrea Wiencierz

Diff between linLIR versions 1.0-2 dated 2012-09-07 and 1.1 dated 2012-11-14

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Package tseries updated to version 0.10-30 with previous version 0.10-29 dated 2012-07-07

Title: Time series analysis and computational finance
Description: Package for time series analysis and computational finance
Author: Compiled by Adrian Trapletti
Maintainer: Kurt Hornik

Diff between tseries versions 0.10-29 dated 2012-07-07 and 0.10-30 dated 2012-11-14

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Package chron updated to version 2.3-43 with previous version 2.3-42 dated 2011-08-21

Title: Chronological objects which can handle dates and times
Description: Chronological objects which can handle dates and times
Author: David James [aut] (S original), Kurt Hornik [aut, trl, cre], Gabor Grothendieck [ctb]
Maintainer: Kurt Hornik

Diff between chron versions 2.3-42 dated 2011-08-21 and 2.3-43 dated 2012-11-14

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Package bindata updated to version 0.9-19 with previous version 0.9-18 dated 2011-09-18

Title: Generation of Artificial Binary Data
Description: Generation of correlated artificial binary data.
Author: Friedrich Leisch and Andreas Weingessel and Kurt Hornik
Maintainer: Friedrich Leisch

Diff between bindata versions 0.9-18 dated 2011-09-18 and 0.9-19 dated 2012-11-14

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Package visualFields updated to version 0.2-8 with previous version 0.2-4 dated 2012-09-18

Title: Statistical methods for visual fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch , Paul H Artes
Maintainer: Ivan Marin-Franch

Diff between visualFields versions 0.2-4 dated 2012-09-18 and 0.2-8 dated 2012-11-14

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New package soilwater with initial version 1.0
Package: soilwater
Maintainer: Emanuele Cordano
License: GPL (>= 2)
Title: soilwatercurve: Implements paramatric formulas for soil water retention or conductivity curve
Type: Package
Author: Emanuele Cordano
Description: It contains implementations of parametric formulas for soil water retention or conductivity curve. At the moment, only Van Genuchten (for soil water retention curve) and Mualem (for hydraulic conductivity) were implemented. See reference \url{http://en.wikipedia.org/wiki/Water_retention_curve}. Any contributions or suggestions are warmly welcomed
Suggests: raster
Version: 1.0
In views: Environmetrics
Repository: CRAN
Date: 2012-11-13
URL: http://cri.gmpf.eu/Research/Sustainable-Agro-Ecosystems-and-Bioresources/Dynamics-in-the-agro-ecosystems,http://meteogis.fmach.it/wiki/index.php/Ecor,http://en.wikipedia.org/wiki/Water_retention_curve
Collate: 'hydraulic_diffusivity.R' 'soilwater-package.R' 'volume.R'
Packaged: 2012-11-14 07:27:26 UTC; ecor
Date/Publication: 2012-11-14 07:58:54

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Package sensitivity updated to version 1.6 with previous version 1.5 dated 2012-09-09

Title: Sensitivity Analysis
Description: A collection of functions for factor screening and global sensitivity analysis of model output.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon
Maintainer: Bertrand Iooss

Diff between sensitivity versions 1.5 dated 2012-09-09 and 1.6 dated 2012-11-14

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Package Rcpp updated to version 0.10.0 with previous version 0.9.15 dated 2012-10-14

Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++ library which facilitate the integration of R and C++. R data types (SEXP) are matched to C++ objects in a class hierarchy. All R types are supported (vectors, functions, environment, etc ...) and each type is mapped to a dedicated class. For example, numeric vectors are represented as instances of the Rcpp::NumericVector class, environments are represented as instances of Rcpp::Environment, functions are represented as Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good entry point to Rcpp. Conversion from C++ to R and back is driven by the templates Rcpp::wrap and Rcpp::as which are highly flexible and extensible, as documented in the "Rcpp-extending" vignette. Rcpp also provides Rcpp modules, a framework that allows exposing C++ functions and classes to the R level. The "Rcpp-modules" vignette details the current set of features of Rcpp-modules. Rcpp includes a concept called Rcpp sugar that brings many R functions into C++. Sugar takes advantage of lazy evaluation and expression templates to achieve great performance while exposing a syntax that is much nicer to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette gives an overview of the feature. Several examples are included, and over 860 unit tests in over 380 unit test functions provide additional usage examples. An earlier version of Rcpp, containing what we now call the 'classic Rcpp API' was written during 2005 and 2006 by Dominick Samperi. This code has been factored out of Rcpp into the package RcppClassic, and it is still available for code relying on the older interface. New development should always use this Rcpp package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel

Diff between Rcpp versions 0.9.15 dated 2012-10-14 and 0.10.0 dated 2012-11-14

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 inst/include/Rcpp/vector/Vector.h                             |   16 
 inst/include/Rcpp/vector/proxy.h                              |   14 
 inst/include/Rcpp/vector/traits.h                             |   29 
 inst/include/RcppCommon.h                                     |   14 
 inst/unitTests/runTests.R                                     |    2 
 inst/unitTests/runit.DataFrame.R                              |   11 
 inst/unitTests/runit.Date.R                                   |   10 
 inst/unitTests/runit.Function.R                               |    2 
 inst/unitTests/runit.Matrix.R                                 |  169 
 inst/unitTests/runit.RObject.R                                |   12 
 inst/unitTests/runit.S4.R                                     |   95 
 inst/unitTests/runit.Vector.R                                 |    6 
 inst/unitTests/runit.as.R                                     |   29 
 inst/unitTests/runit.misc.R                                   |   95 
 inst/unitTests/runit.rmath.R                                  |only
 inst/unitTests/runit.stats.R                                  |    9 
 inst/unitTests/runit.sugar.R                                  |    6 
 inst/unitTests/runit.sugarOps.R                               |    8 
 inst/unitTests/runit.wrap.R                                   |   11 
 man/CppClass-class.Rd                                         |    2 
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 src/Attributes.cpp                                            |only
 src/AttributesParser.cpp                                      |only
 src/AttributesParser.h                                        |only
 src/Date.cpp                                                  |    2 
 src/Language.cpp                                              |    8 
 src/Module.cpp                                                |   67 
 src/Rostream.cpp                                              |    6 
 src/Rstreambuf.cpp                                            |   19 
 src/barrier.cpp                                               |    3 
 src/exceptions.cpp                                            |    1 
 tests/doRUnit.R                                               |   14 
 106 files changed, 5426 insertions(+), 4420 deletions(-)

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Package mada updated to version 0.5.0 with previous version 0.4.1 dated 2012-06-02

Title: Meta-Analysis of Diagnostic Accuracy (mada)
Description: This package provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Boehning et al. is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler

Diff between mada versions 0.4.1 dated 2012-06-02 and 0.5.0 dated 2012-11-14

 DESCRIPTION          |   13 -
 MD5                  |   38 ++--
 NAMESPACE            |    6 
 R/AUC.R              |only
 R/ROCellipse.R       |  128 ++++++-------
 R/phm.R              |  474 +++++++++++++++++++++++++--------------------------
 R/reitsma.R          |  422 ++++++++++++++++++++++++++-------------------
 R/sroc.R             |   83 ++++----
 data/AuditC.rda      |binary
 data/Dementia.rda    |binary
 data/IAQ.rda         |binary
 data/SAQ.rda         |binary
 data/smoking.rda     |only
 inst/doc/mada.Rnw    |   58 +++++-
 inst/doc/mada.bib    |    8 
 inst/doc/mada.pdf    |binary
 man/AUC.Rd           |only
 man/mada-data.Rd     |    9 
 man/phm-class.Rd     |  161 +++++++++--------
 man/reitsma-class.Rd |    5 
 man/reitsma.Rd       |   48 +++--
 man/talpha.Rd        |only
 22 files changed, 811 insertions(+), 642 deletions(-)

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Package GEVcdn updated to version 1.1.2 with previous version 1.1.1 dated 2012-07-30

Title: GEV conditional density estimation network
Description: A flexible nonlinear modelling framework for nonstationary generalized extreme value analysis in hydroclimatology
Author: Alex J. Cannon
Maintainer: Alex J. Cannon

Diff between GEVcdn versions 1.1.1 dated 2012-07-30 and 1.1.2 dated 2012-11-14

 DESCRIPTION              |    6 
 MD5                      |   40 ++--
 R/gevcdn.bag.R           |  206 ++++++++++++-------------
 R/gevcdn.bootstrap.R     |  140 ++++++++---------
 R/gevcdn.cost.R          |   76 ++++-----
 R/gevcdn.evaluate.R      |   62 +++----
 R/gevcdn.fit.R           |  186 +++++++++++-----------
 R/gevcdn.identity.R      |   12 -
 R/gevcdn.initialize.R    |   22 +-
 R/gevcdn.logistic.R      |   12 -
 R/gevcdn.reshape.R       |   32 +--
 man/GEVcdn-package.Rd    |  110 ++++++-------
 man/gevcdn.bag.Rd        |  365 ++++++++++++++++++++++----------------------
 man/gevcdn.bootstrap.Rd  |  305 ++++++++++++++++++-------------------
 man/gevcdn.cost.Rd       |  126 +++++++--------
 man/gevcdn.evaluate.Rd   |  108 ++++++-------
 man/gevcdn.fit.Rd        |  382 +++++++++++++++++++++++------------------------
 man/gevcdn.identity.Rd   |   42 ++---
 man/gevcdn.initialize.Rd |   54 +++---
 man/gevcdn.logistic.Rd   |   42 ++---
 man/gevcdn.reshape.Rd    |   54 +++---
 21 files changed, 1191 insertions(+), 1191 deletions(-)

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Package JOP updated to version 3.2 with previous version 3.1 dated 2012-11-12

Title: Joint Optimization Plot
Description: JOP is a tool for simultaneous optimization of multiple responses and visualization of the results. The visualization is done by the joint optimization plot introduced by Kuhnt and Erdbruegge (2004).
Author: Sonja Kuhnt and Nikolaus Rudak
Maintainer: Nikolaus Rudak

Diff between JOP versions 3.1 dated 2012-11-12 and 3.2 dated 2012-11-14

 DESCRIPTION     |    8 ++++----
 MD5             |    8 ++++----
 man/JOP.Rd      |   10 +++++-----
 man/locate.rd   |   10 +++++-----
 man/plot.JOP.rd |   10 +++++-----
 5 files changed, 23 insertions(+), 23 deletions(-)

More information about JOP at CRAN
Permanent link

Package tmle (with last version 1.2.0-1) was removed from CRAN

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

2012-05-11 1.2.0-1
2012-04-03 1.2
2011-09-29 1.1.1
2011-02-04 1.1

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