Fri, 11 Mar 2011

Package lfe updated to version 1.1-427 with previous version 1.0-418 dated 2011-03-10

Title: Linear Group Fixed Effects
Description: Estimates linear models with multiple group fixed effects
Author: Simen Gaure
Maintainer: Simen Gaure

Diff between lfe versions 1.0-418 dated 2011-03-10 and 1.1-427 dated 2011-03-11

 lfe-1.0-418/lfe/man/print.lm.fe.Rd      |only
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 lfe-1.1-427/lfe/NAMESPACE               |    6 +
 lfe-1.1-427/lfe/R/lfe.R                 |  105 +-------------------------------
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 lfe-1.1-427/lfe/exec/lfescript          |    2 
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 lfe-1.1-427/lfe/man/lfe-package.Rd      |   12 +--
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 lfe-1.1-427/lfe/tests/verify.R          |only
 lfe-1.1-427/lfe/tests/verify.Rout.save  |only
 15 files changed, 40 insertions(+), 133 deletions(-)

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Package TripleR updated to version 1.0.6 with previous version 1.0.5 dated 2011-02-10

Title: Social Relation Model (SRM) analyses for single or multiple round-robin groups
Description: Social Relation Model (SRM) analyses for single or multiple round-robin groups are performed. These analyses are either based on one manifest variable, one latent construct measured by two manifest variables, two manifest variables and their bivariate relations, or two latent constructs each measured by two manifest variables. Within-group t-tests for variance components and covariances are provided for single groups, between-groups t-tests for multiple groups. Preliminary handling for missing values is provided.
Author: S.C. Schmukle, F.D. Schönbrodt and M.D. Back
Maintainer: Felix Schönbrodt

Diff between TripleR versions 1.0.5 dated 2011-02-10 and 1.0.6 dated 2011-03-11

 DESCRIPTION          |   12 ++++++------
 NEWS                 |    7 +++++++
 inst/doc/TripleR.pdf |binary
 3 files changed, 13 insertions(+), 6 deletions(-)

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Package RandomFields updated to version 2.0.45 with previous version 2.0.44 dated 2011-03-02

Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging
Author: Martin Schlather
Maintainer: Martin Schlather

Diff between RandomFields versions 2.0.44 dated 2011-03-02 and 2.0.45 dated 2011-03-11

 DESCRIPTION           |    6 
 R/MLE.R               |  426 +++++++++++++++++++++++++++++---------------------
 R/convert.R           |    2 
 R/getNset.R           |   30 ---
 man/Covariance.Rd     |  134 ++++++++-------
 man/CovarianceFct.Rd  |    9 +
 man/changings.Rd      |    4 
 man/fitvario.Rd       |   49 ++++-
 man/parampositions.Rd |   48 +++++
 src/InternalCov.cc    |   83 +++++----
 src/MLE.cc            |   12 -
 src/RF.h              |    9 -
 src/RandomFields.h    |    3 
 src/initNerror.cc     |   67 +++----
 src/simu.cc           |    6 
 tests/RFtest.stupid.R |   16 +
 16 files changed, 537 insertions(+), 367 deletions(-)

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Package PowerTOST updated to version 0.8-4 with previous version 0.8-3 dated 2011-01-18

Title: Power and Sample size based on two one-sided t-tests (TOST) for bioequivalence studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval).
Author: Detlew Labes
Maintainer: D. Labes

Diff between PowerTOST versions 0.8-3 dated 2011-01-18 and 0.8-4 dated 2011-03-11

 DESCRIPTION              |    8 ++++----
 NEWS                     |    7 +++++++
 R/Fieller.R              |   14 +++++++++-----
 R/SampleSize.R           |   31 ++++++++++++++++++++++---------
 R/expSampleSize.R        |   10 ++++++----
 man/PowerTOST-package.Rd |    4 ++--
 man/exppower.TOST.Rd     |    2 +-
 man/expsampleN.TOST.Rd   |    6 +++++-
 man/power.RatioF.Rd      |   14 ++++++++++----
 man/power.TOST.Rd        |    2 +-
 man/sampleN.RatioF.Rd    |   18 ++++++++++++------
 man/sampleN.TOST.Rd      |    8 ++++++--
 12 files changed, 85 insertions(+), 39 deletions(-)

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Package AICcmodavg updated to version 1.14 with previous version 1.13 dated 2011-01-11

Title: Model selection and multimodel inference based on (Q)AIC(c)
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). Tables are printed with delta AIC and Akaike weights. The package also includes functions to conduct model averaging (multimodel inference) for a given parameter of interest or predicted values. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with linear models ('lm' class), generalized linear models ('glm' class), linear models fit by generalized least squares ('gls' class), linear mixed models ('lme' class), generalized linear mixed models ('mer' class), multinomial and ordinal logistic regressions ('multinom' and 'polr' classes).
Author: Marc J. Mazerolle . Special thanks to T. Ergon for the original idea of storing candidate models in a list.
Maintainer: Marc J. Mazerolle

Diff between AICcmodavg versions 1.13 dated 2011-01-11 and 1.14 dated 2011-03-11

 DESCRIPTION               |    8 ++++----
 R/modavg.mer.R            |   11 ++++++++---
 inst/NEWS                 |   10 ++++++++--
 man/AICcmodavg-package.Rd |    4 ++--
 4 files changed, 22 insertions(+), 11 deletions(-)

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Package mvpart updated to version 1.4-0 with previous version 1.3-1 dated 2010-03-01

Title: Multivariate partitioning
Description: Multivariate regression trees
Author: rpart by Terry M Therneau and Beth Atkinson . R port of rpart by Brian Ripley . Some routines from vegan -- Jari Oksanen Extensions and adaptations of rpart to mvpart by Glenn De'ath .
Maintainer: Glenn De'ath

Diff between mvpart versions 1.3-1 dated 2010-03-01 and 1.4-0 dated 2011-03-11

 Changelog   |    1 +
 DESCRIPTION |    8 ++++----
 R/gdist.R   |    3 ++-
 3 files changed, 7 insertions(+), 5 deletions(-)

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New package mgpd with initial version 1.0
Package: mgpd
Type: Package
Title: Functions for multivariate generalized Pareto distribution (MGPD of Type II)
Version: 1.0
Date: 2011-03-10
Author: Pal Rakonczai
Maintainer: Pal Rakonczai
Depends: R (>= 2.10.1), evd
Description: Extends density functions to parametric multivariate generalized Pareto distributions (MGPD of Type II), and provides fitting functions which calculate maximum likelihood estimates for bivariate models (BGPD). There are seven "classical" parametric dependence models within BGPD available: logistic, negative logistic, bilogistic, negative bilogistic, Tajvidi's generalised symmetric logistic, Dirichlet and mixed. Beyond these, two novel asymmetric approaches giving absolutely continuous BGPD are implemented as psi-logistic and psi-negative logistic models.
License: GPL-2
LazyLoad: yes
Packaged: 2011-03-10 14:46:16 UTC; Pal
Repository: CRAN
Date/Publication: 2011-03-11 07:14:20

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Package eVenn updated to version 2.0.1 with previous version 2.0 dated 2011-03-08

Title: eVenn: A powerful tool to compare lists and draw Venn diagrams.
Description: Compute a matrix comparison of lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4). It is possible to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to compute the overlaps proportions of all the couples of lists.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard

Diff between eVenn versions 2.0 dated 2011-03-08 and 2.0.1 dated 2011-03-11

 DESCRIPTION          |    8 ++++----
 R/evenn.R            |   20 ++++++++------------
 man/eVenn-package.Rd |    5 +++--
 3 files changed, 15 insertions(+), 18 deletions(-)

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Package diffractometry updated to version 0.1-03 with previous version 0.1-02 dated 2010-03-07

Title: Baseline identification and peak decomposition for x-ray diffractograms
Description: Residual-based baseline identification and peak decomposition for x-ray diffractograms as introduced in Davies/Gather/Mergel/Meise/Mildenberger (2008).
Author: P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger. Additional Code by T. Bernholt and T. Hofmeister
Maintainer: T. Mildenberger

Diff between diffractometry versions 0.1-02 dated 2010-03-07 and 0.1-03 dated 2011-03-11

 DESCRIPTION        |   10 +++++-----
 R/baselinefit.r    |    8 ++++++--
 src/Cbaselinefit.c |   22 +++++++++++-----------
 3 files changed, 22 insertions(+), 18 deletions(-)

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Package RcppArmadillo updated to version 0.2.16 with previous version 0.2.15 dated 2011-03-04

Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library (currently version 1.1.8). Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. Armadillo is licensed under the GNU LGPL version 3 or later, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licenses under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates

Diff between RcppArmadillo versions 0.2.15 dated 2011-03-04 and 0.2.16 dated 2011-03-11

 ChangeLog                                               |    6 
 DESCRIPTION                                             |   10 
 inst/NEWS                                               |   11 
 inst/doc/RcppArmadillo-unitTests.pdf                    |binary
 inst/doc/unitTests-results/RcppArmadillo-unitTests.html |    6 
 inst/doc/unitTests-results/RcppArmadillo-unitTests.txt  |   38 -
 inst/include/armadillo                                  |    2 
 inst/include/armadillo_bits/Cube_meat.hpp               |   10 
 inst/include/armadillo_bits/Mat_meat.hpp                |   30 -
 inst/include/armadillo_bits/arma_ostream_meat.hpp       |  119 ++---
 inst/include/armadillo_bits/arma_ostream_proto.hpp      |    8 
 inst/include/armadillo_bits/arma_version.hpp            |    6 
 inst/include/armadillo_bits/arrayops_meat.hpp           |   39 +
 inst/include/armadillo_bits/arrayops_proto.hpp          |    5 
 inst/include/armadillo_bits/auxlib_meat.hpp             |   10 
 inst/include/armadillo_bits/constants.hpp               |  322 +++++++++++---
 inst/include/armadillo_bits/diskio_meat.hpp             |   46 +-
 inst/include/armadillo_bits/eglue_core_meat.hpp         |  345 +++-------------
 inst/include/armadillo_bits/eop_aux.hpp                 |   16 
 inst/include/armadillo_bits/eop_core_meat.hpp           |  105 +---
 inst/include/armadillo_bits/eop_core_proto.hpp          |    6 
 inst/include/armadillo_bits/fn_elem.hpp                 |   58 ++
 inst/include/armadillo_bits/fn_misc.hpp                 |   53 ++
 inst/include/armadillo_bits/fn_norm.hpp                 |   14 
 inst/include/armadillo_bits/format_wrap.hpp             |   12 
 inst/include/armadillo_bits/op_max_meat.hpp             |   43 -
 inst/include/armadillo_bits/op_mean_meat.hpp            |   38 -
 inst/include/armadillo_bits/op_min_meat.hpp             |   46 +-
 inst/include/armadillo_bits/op_var_meat.hpp             |   27 -
 inst/include/armadillo_bits/restrictors.hpp             |    9 
 inst/include/armadillo_bits/traits.hpp                  |   20 
 31 files changed, 782 insertions(+), 678 deletions(-)

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Package QTLRel updated to version 0.2 with previous version 0.1 dated 2010-12-24

Title: Tools for mapping of quantitative traits of genetically related individuals and calculating identity coefficients from a pedigree
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variances, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients for pedigrees, especially suitable for pedigrees that consist of a large number of generations.
Author: Riyan Cheng
Maintainer: Riyan Cheng

Diff between QTLRel versions 0.1 dated 2010-12-24 and 0.2 dated 2011-03-11

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 QTLRel-0.2/QTLRel/R/estVC.R         |   55 +-
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 35 files changed, 222 insertions(+), 1030 deletions(-)

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