Mon, 17 Sep 2012

New package MAMA with initial version 2.1.0
Package: MAMA
Version: 2.1.0
Date: 2012-9-16
Title: Meta-Analysis of MicroArry
Author: Ivana Ihnatova <184415@mail.muni.cz>.
Maintainer: Ivana Ihnatova <184415@mail.muni.cz>
Depends: R (>= 2.15.1), methods, genefilter, metaMA, tspair, xtable, multtest, RankProd, gtools, grid, GeneMeta
Suggests: gplots
Imports: MergeMaid, GeneMeta, tspair, xtable, methods, metaArray
Description: Implementation of methods for microarray meta-analysis.
License: GPL (>= 2)
Packaged: 2012-09-16 17:28:21 UTC; user
Repository: CRAN
Date/Publication: 2012-09-17 17:27:50

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Package spikeSlabGAM updated to version 1.1-2 with previous version 1.1-0 dated 2012-03-13

Title: Bayesian variable selection and model choice for generalized additive mixed models
Description: Bayesian variable selection, model choice, and regularized estimation for (spatial) generalized additive mixed regression models via SSVS with spike-and-slab priors.
Author: Fabian Scheipl
Maintainer: Fabian Scheipl

Diff between spikeSlabGAM versions 1.1-0 dated 2012-03-13 and 1.1-2 dated 2012-09-17

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 spikeSlabGAM-1.1-2/spikeSlabGAM/R/summary.R                       |    4 
 spikeSlabGAM-1.1-2/spikeSlabGAM/R/terms.R                         |    4 
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 31 files changed, 1345 insertions(+), 1422 deletions(-)

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Package fArma updated to version 2160.78 with previous version 2160.77 dated 2012-03-20

Title: ARMA Time Series Modelling
Description: Environment for teaching "Financial Engineering and Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi

Diff between fArma versions 2160.77 dated 2012-03-20 and 2160.78 dated 2012-09-17

 ChangeLog   |   58 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 DESCRIPTION |   12 ++++++------
 MD5         |    6 +++---
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 4 files changed, 70 insertions(+), 21 deletions(-)

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Package synchronicity updated to version 1.1.0 with previous version 1.0.13 dated 2011-08-19

Title: Boost mutex functionality for R.
Description: This package provides Boost mutex functionality in R.
Author: Michael J. Kane
Maintainer: Michael J. Kane

Diff between synchronicity versions 1.0.13 dated 2011-08-19 and 1.1.0 dated 2012-09-17

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 7 files changed, 72 insertions(+), 78 deletions(-)

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Package simctest updated to version 2.1 with previous version 1.99-2 dated 2012-03-19

Title: Safe implementation of Monte Carlo tests.
Description: Algorithms for the implementation and evaluation of Monte Carlo tests, as well as for their use in multiple testing procedures.
Author: Axel Gandy with contributions from Patrick Rubin-Delanchy and Georg Hahn
Maintainer: Axel Gandy

Diff between simctest versions 1.99-2 dated 2012-03-19 and 2.1 dated 2012-09-17

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New package rbundler with initial version 0.2
Package: rbundler
Maintainer: Yoni Ben-Meshulam
Author: Yoni Ben-Meshulam
Version: 0.2
License: GPL-3
Title: Rbundler manages an application's dependencies systematically and repeatedly.
Description: Specify your dependencies in your project's root directory, and be able to install and use dependencies in a repeatable fashion without requiring manual maintenance. Uses a combination of project-specific R library in PROJECT_ROOT/.Rbundle and a project-specific R_LIBS_USER, set in PROJECT_ROOT/.Renviron
Depends: R (>= 2.15.1), devtools (>= 0.7)
Suggests: testthat, roxygen2
Collate: 'rbundler-package.r' 'bundle.r'
Packaged: 2012-09-17 13:23:12 UTC; yoni
Repository: CRAN
Date/Publication: 2012-09-17 13:57:58

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New package Giza with initial version 1.0
Package: Giza
Type: Package
Title: Constructing panels of population pyramid plots based on lattice
Version: 1.0
Date: 2011-11-08
Author: Erich Striessnig
Maintainer: Erich Striessnig
Description: `Giza' offers a simple way of creating multiple pyramid plots in one graphics window, exploiting the power of the lattice package. It is a handy way of visualizing longitudinal grouped (i.e.: age- and education-structured) data.
Depends: R (>= 2.10.0), reshape, lattice
Imports: lattice
License: GPL-2
LazyLoad: yes
Packaged: 2012-09-17 11:28:23 UTC; admin
Repository: CRAN
Date/Publication: 2012-09-17 14:00:01

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Package GenABEL updated to version 1.7-2 with previous version 1.7-0 dated 2011-12-21

Title: genome-wide SNP association analysis
Description: a package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).
Author: GenABEL project developers
Maintainer: Yurii Aulchenko

Diff between GenABEL versions 1.7-0 dated 2011-12-21 and 1.7-2 dated 2012-09-17

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Package BioPhysConnectoR updated to version 1.6-8 with previous version 1.6-7 dated 2011-03-12

Title: BioPhysConnectoR
Description: Utilities and functions to investigate the relation between biomolecular structures, their interactions, and the evolutionary information revealed in sequence alignments of these molecules.
Author: Franziska Hoffgaard , with contributions from Philipp Weil and Kay Hamacher
Maintainer: Franziska Hoffgaard

Diff between BioPhysConnectoR versions 1.6-7 dated 2011-03-12 and 1.6-8 dated 2012-09-17

 DESCRIPTION  |    6 +++---
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 R/scpcp.r    |    2 +-
 man/scpcp.Rd |    2 ++
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 6 files changed, 15 insertions(+), 9 deletions(-)

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Package bigtabulate updated to version 1.1.0 with previous version 1.0.13 dated 2010-07-24

Title: table-, tapply-, and split-like functionality for matrix and big.matrix objects.
Description: This package extends the bigmemory package with table- and split-like support for big.matrix objects. The functions may also be used with regular R matrices for improving speed and memory-efficiency.
Author: Michael J. Kane and John W. Emerson
Maintainer: Michael J. Kane

Diff between bigtabulate versions 1.0.13 dated 2010-07-24 and 1.1.0 dated 2012-09-17

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New package bigmemory.sri with initial version 0.1.2
Package: bigmemory.sri
Type: Package
Title: A shared resource interface for Bigmemory Project packages
Version: 0.1.2
Date: 2012-09-15
Author: Michael J. Kane
Maintainer: Michael J. Kane
Contact: Michael J. Kane
Description: This package provides a shared resource interface for the bigmemory and synchronicity packages.
License: LGPL-3
OS_type: unix
Depends: methods
Enhances: bigmemory, synchronicity
Packaged: 2012-09-15 17:59:42 UTC; jay
Repository: CRAN
Date/Publication: 2012-09-17 14:57:19

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Package bigmemory updated to version 4.3.0 with previous version 4.2.11 dated 2011-07-26

Title: Manage massive matrices with shared memory and memory-mapped files
Description: Create, store, access, and manipulate massive matrices. Matrices are allocated to shared memory and may use memory-mapped files. Packages biganalytics, bigtabulate, synchronicity, and bigalgebra provide advanced functionality.
Author: Michael J. Kane and John W. Emerson
Maintainer: Michael J. Kane

Diff between bigmemory versions 4.2.11 dated 2011-07-26 and 4.3.0 dated 2012-09-17

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Package biganalytics updated to version 1.1.0 with previous version 1.0.14 dated 2010-06-25

Title: A library of utilities for big.matrix objects of package bigmemory.
Description: This package extends the bigmemory package with various analytics. Functions bigkmeans and binit may also be used with native R objects. For tapply-like functions, the bigtabulate package may also be helpful. For linear algebra support, see bigalgebra. For mutex (locking) support for advanced shared-memory usage, see synchronicity.
Author: John W. Emerson and Michael J. Kane
Maintainer: Michael J. Kane

Diff between biganalytics versions 1.0.14 dated 2010-06-25 and 1.1.0 dated 2012-09-17

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Package afex updated to version 0.3-42 with previous version 0.2-26 dated 2012-08-09

Title: Analysis of Factorial Experiments
Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed-models. Functions ez.glm() and aov.car() allow convenient specification of pure-between, pure-within (i.e., repeated-measures), and mixed between-within (i.e., split-plot) ANOVAs and ANCOVAs with type 2 and type 3 sums of squares for data in the long format (i.e., one observation per row) wrapping car::Anova() (aggregating more then one observation per individual and cell of the design). Function nice.anova() produces publication ready ANOVA tables. Function mixed() fits a mixed model using lme4::lmer() and computes p-values for all effects in the model (using the Kenward-Rogers approximation of degrees of freedom). afex uses type 3 sums of squares as default (imitating commercial statistical software) and sets the default contrasts to contr.sum.
Author: Henrik Singmann
Maintainer: Henrik Singmann

Diff between afex versions 0.2-26 dated 2012-08-09 and 0.3-42 dated 2012-09-17

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Package DiceOptim updated to version 1.3.2 with previous version 1.3.1 dated 2012-06-04

Title: Kriging-based optimization for computer experiments
Description: Expected Improvement. EGO algorithm. Multipoints EI and parallelized versions of EGO: Constant Liars. Noisy Kriging-based Optimization criteria and algorithms, including AEI, AKG, EQI, and EI.plugin.
Author: D. Ginsbourger, V. Picheny, O. Roustant, with contributions by C. Chevalier and T. Wagner
Maintainer: D. Ginsbourger

Diff between DiceOptim versions 1.3.1 dated 2012-06-04 and 1.3.2 dated 2012-09-17

 DESCRIPTION             |   16 +-
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Package NSA updated to version 0.0.3 with previous version 0.0.2 dated 2011-11-09

Title: Post-normalization of total copy numbers
Description: Post-normalization of total copy-number estimates.
Author: Maria Ortiz-Estevez , Ander Aranburu , Angel Rubio
Maintainer: Maria Ortiz-Estevez

Diff between NSA versions 0.0.2 dated 2011-11-09 and 0.0.3 dated 2012-09-17

 DESCRIPTION                   |   14 +++--
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 R/fitNSA.R                    |   11 ++--
 R/fitNSAcnPs.R                |    9 +--
 R/sampleNByTotalAndFracB.R    |   15 ++----
 R/snpsNByTotalAndFracB.R      |   16 ++----
 man/NSA-package.Rd            |    6 +-
 man/Non-documented_objects.Rd |    1 
 13 files changed, 119 insertions(+), 131 deletions(-)

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New package JMbayes with initial version 0.1-1
Package: JMbayes
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a Bayesian Approach
Version: 0.1-1
Date: 2012-09-17
Authors@R: c(person("Dimitris", "Rizopoulos", role = c("aut", "cre"), email = "d.rizopoulos@erasmusmc.nl"))
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using JAGS, WinBUGS, or OpenBUGS.
Depends: R (>= 2.14.0), MASS, nlme, splines, survival, rjags, coda
Suggests: R2WinBUGS, R2OpenBUGS
SystemRequirements: JAGS (>= 3.2.0) (or WinBUGS (>= 1.4) or OpenBUGS (>= 3.2.2))
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
Packaged: 2012-09-17 06:29:31 UTC; 698791
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos
Repository: CRAN
Date/Publication: 2012-09-17 07:27:06

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New package DeducerSurvival with initial version 0.1-0
Package: DeducerSurvival
Type: Package
Title: Add Survival Dialogue to Deducer
Version: 0.1-0
Date: 2012-07-08
Author: Matthew Ockendon, Paul Cool
Maintainer: Matthew Ockendon
Description: Adds Kaplan-Meier Survival Analysis to the Deducer GUI
Depends: Deducer (>= 0.5-0)
License: GPL-2
Packaged: 2012-07-11 05:29:08 UTC; root
Repository: CRAN
Date/Publication: 2012-07-11 11:15:58

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New package DeducerPlugInScaling with initial version 0.1-0
Package: DeducerPlugInScaling
Version: 0.1-0
Date: 2012-03-09
Title: Reliability and factor analysis plugin
Author: Alberto Mirisola, Ian Fellows and Helios De Rosario-Martinez
Maintainer: Alberto Mirisola
Description: A Deducer plug-in for factor analysis, reliability analysis and discriminant analysis, using psych, GPArotation and mvnormtest packages.
License: GPL (>= 2)
Depends: Deducer, psych, GPArotation, mvnormtest, irr, klaR
LazyLoad: yes
Repository: CRAN
Packaged: 2012-03-16 22:49:33 UTC; ianfellows
Date/Publication: 2012-03-17 06:57:40

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New package DeducerSpatial with initial version 0.5
Package: DeducerSpatial
Maintainer: Ian Fellows
License: GPL-2
Title: Deducer for spatial data analysis
Author: Ian Fellows and Alex Rickett with contributions from Neal Fultz.
Description: A Deducer plug-in for spatial data analysis. Includes The ability to plot and explore open street map and Bing satellite images.
SystemRequirements: Java (>= 1.5), JRI
Version: 0.5
URL: http://www.deducer.org/pmwiki/pmwiki.php?n=Main.DeducerSpatial http://www.fellstat.com http://research.cens.ucla.edu/
Date: 2012-02-21
Depends: JavaGD (>= 0.6-0), Deducer (>= 0.7-4), sp, maptools, OpenStreetMap, scales, rgdal
Imports: UScensus2010, Hmisc
Collate: 'DeducerSpatial-package.R' 'plot-util.R' 'census.R' 'zzz.R'
Packaged: 2012-09-16 22:33:49 UTC; ianfellows
Repository: CRAN
Date/Publication: 2012-09-17 08:08:47

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New package DeducerPlugInExample with initial version 0.2-0
Package: DeducerPlugInExample
Version: 0.2-0
Date: 2012-03-16
Title: Deducer Plug-in Example
Author: Ian Fellows
Maintainer: Ian Fellows
Description: A example GUI plug-in package to serve as a template.
Depends: Deducer (>= 0.5-0)
License: GPL-2
URL: http://www.deducer.org/pmwiki/index.php?n=Main.Development
Packaged: 2012-03-16 22:59:47 UTC; ianfellows
Repository: CRAN
Date/Publication: 2012-03-17 06:57:38

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Package bipartite updated to version 1.18 with previous version 1.17 dated 2011-08-10

Title: Visualising bipartite networks and calculating some (ecological) indices.
Description: Bipartite provides functions to visualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focusses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.
Author: Carsten F. Dormann and Bernd Gruber, with additional code from Mariano Devoto, Jochen Fruend, Jose Iriondo, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones.
Maintainer: Carsten F. Dormann

Diff between bipartite versions 1.17 dated 2011-08-10 and 1.18 dated 2012-09-17

 DESCRIPTION                      |   10 
 MD5                              |  121 +-
 NAMESPACE                        |only
 R/ND.r                           |   12 
 R/compart.R                      |   87 +-
 R/computeModules.R               |  186 +++-
 R/czvalues.R                     |only
 R/extinction.R                   |   21 
 R/fd.R                           |only
 R/networklevel.R                 |   17 
 R/plotweb.R                      |  108 +-
 R/prepareWebForPlottingModules.R |    8 
 R/robustness.r                   |   11 
 R/second.extinct.R               |  101 +-
 R/visweb.R                       |  372 ++++-----
 R/web2edges.R                    |  100 +-
 R/zzz.R                          |   15 
 inst/doc/Dormann2008Rnews.pdf    |binary
 man/ND.rd                        |   17 
 man/PAC.rd                       |   11 
 man/PDI.Rd                       |    2 
 man/as.one.mode.Rd               |    2 
 man/barrett1987.Rd               |    2 
 man/bezerra2009.Rd               |    3 
 man/bipartite-package.Rd         |  218 +----
 man/compart.Rd                   |   15 
 man/computeModules.Rd            |    8 
 man/czvalues.Rd                  |only
 man/degreedistr.Rd               |    2 
 man/dfun.Rd                      |    2 
 man/extinction.Rd                |   16 
 man/fd.Rd                        |only
 man/listModuleInformation.Rd     |    6 
 man/memmott1999.Rd               |    3 
 man/moduleWeb-class.Rd           |    7 
 man/nested.Rd                    |   21 
 man/nestedness.Rd                |   12 
 man/networklevel.Rd              |  148 +--
 man/nodespec.Rd                  |    2 
 man/null.distr.Rd                |    4 
 man/null.t.test.Rd               |    2 
 man/nullmodel.rd                 |   60 -
 man/plotModuleWeb.Rd             |    6 
 man/plotPAC.Rd                   |    2 
 man/plotweb.Rd                   |    2 
 man/plotweb2.rd                  |    9 
 man/printoutModuleInformation.Rd |    8 
 man/robustness.rd                |    4 
 man/second.extinct.Rd            |   16 
 man/shuffle.web.Rd               |    2 
 man/slope.bipartite.Rd           |    4 
 man/sortweb.Rd                   |    6 
 man/specieslevel.Rd              |    4 
 man/swap.web.Rd                  |    2 
 man/togetherness.Rd              |    4 
 man/vaznull.rd                   |    2 
 man/vazquez.example.rd           |  112 +-
 man/visweb.Rd                    |   20 
 src/bmn5.cc                      |  132 +--
 src/dendro.h                     | 1580 ++++++++++++++++-----------------------
 src/graph.h                      |  329 ++++----
 src/identifyModules.cc           |  715 ++++++++++-------
 src/rbtree.h                     |   27 
 src/splittree.h                  |   38 
 64 files changed, 2365 insertions(+), 2391 deletions(-)

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Package ltm updated to version 0.9-9 with previous version 0.9-8 dated 2012-08-17

Title: Latent Trait Models under IRT
Description: Analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos

Diff between ltm versions 0.9-8 dated 2012-08-17 and 0.9-9 dated 2012-09-17

 DESCRIPTION        |   10 +++++-----
 MD5                |    7 ++++---
 R/globals.R        |only
 inst/NEWS          |    9 +++++++++
 man/ltm-package.Rd |    4 ++--
 5 files changed, 20 insertions(+), 10 deletions(-)

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Package JM updated to version 1.0-1 with previous version 1.0-0 dated 2012-07-03

Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos

Diff between JM versions 1.0-0 dated 2012-07-03 and 1.0-1 dated 2012-09-17

 DESCRIPTION           |   10 +++++-----
 MD5                   |   13 +++++++------
 R/globals.R           |only
 R/log.posterior.b.R   |    2 +-
 R/plot.jointModel.R   |    2 ++
 R/xtable.jointModel.R |    2 ++
 inst/NEWS             |   10 ++++++++++
 man/JM.Rd             |    8 ++++----
 8 files changed, 31 insertions(+), 16 deletions(-)

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New package glmperm with initial version 1.0-4
Package: glmperm
Type: Package
Title: Inference in Generalized Linear Models
Version: 1.0-4
Date: 2012-09-14
Author: Wiebke Werft and Douglas M. Potter
Maintainer: Wiebke Werft
Description: A permutation test is used for inference in generalized linear models (glm). The procedure is useful when parameter estimates in ordinary glm fail to converge or are unreliable due to small sample size.
License: GPL-3
Suggests: coin, MASS
Packaged: 2012-09-17 06:35:28 UTC; werft
X-CRAN-Comment: This package has been archived: it had check ERRORs since R-2.15.0 (at least) and was not fixed for weeks even after reminders
Repository: CRAN
Date/Publication: 2012-09-17 06:52:44

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Package actuar updated to version 1.1-5 with previous version 1.1-4 dated 2012-05-26

Title: Actuarial functions
Description: Additional actuarial science functionality, mostly in the fields of loss distributions, risk theory (including ruin theory), simulation of compound hierarchical models and credibility theory. The package also features 17 new probability laws commonly used in insurance, most notably heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet

Diff between actuar versions 1.1-4 dated 2012-05-26 and 1.1-5 dated 2012-09-17

 DESCRIPTION              |    8 -
 MD5                      |   28 ++--
 NAMESPACE                |    1 
 R/coverage.R             |  290 ++++++++++++++++++++++++++++++++---------------
 R/ogive.R                |   31 +++--
 inst/NEWS.Rd             |   18 ++
 inst/doc/actuar.pdf      |binary
 inst/doc/coverage.Rnw    |   50 +++-----
 inst/doc/coverage.pdf    |binary
 inst/doc/credibility.pdf |binary
 inst/doc/lossdist.pdf    |binary
 inst/doc/risk.pdf        |binary
 inst/doc/simulation.pdf  |binary
 man/coverage.Rd          |    4 
 vignettes/coverage.Rnw   |   50 +++-----
 15 files changed, 303 insertions(+), 177 deletions(-)

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Package FAiR (with last version 0.4-8) was removed from CRAN

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

2012-02-27 0.4-8
2011-02-25 0.4-7
2010-09-29 0.4-6
2009-11-03 0.4-5
2009-01-12 0.4-4
2008-10-06 0.4-2
2008-07-11 0.4-0
2008-02-01 0.2-0

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