Package robust updated to version 0.4-16 with previous version 0.4-15 dated 2013-06-17

Title: Robust Library
Description: A package of robust methods.
Author: Jiahui Wang, Ruben Zamar , Alfio Marazzi , Victor Yohai , Matias Salibian-Barrera , Ricardo Maronna , Eric Zivot , David Rocke , Doug Martin, Martin Maechler , Kjell Konis .
Maintainer: Kjell Konis

Diff between robust versions 0.4-15 dated 2013-06-17 and 0.4-16 dated 2014-05-18

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Package R4CDISC updated to version 0.2 with previous version 0.1 dated 2014-01-05

Title: Read CDISC data files
Description: R4CDISC package includes functions for reading Dataset-XML and Define-XML files.
Author: Ippei Akiya
Maintainer: Ippei Akiya

Diff between R4CDISC versions 0.1 dated 2014-01-05 and 0.2 dated 2014-05-18

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Package isingLenzMC updated to version 0.2.1 with previous version 0.1.1 dated 2014-04-25

Title: Monte Carlo for classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics. Model explains physics of spin glasses and magnetic materials, but used in many different context for example phase transitions and neural systems. This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions.
Author: Mehmet Suzen
Maintainer: Mehmet Suzen

Diff between isingLenzMC versions 0.1.1 dated 2014-04-25 and 0.2.1 dated 2014-05-18

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 17 files changed, 79 insertions(+), 58 deletions(-)

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Package ineq updated to version 0.2-12 with previous version 0.2-11 dated 2013-10-12

Title: Measuring Inequality, Concentration, and Poverty
Description: Inequality, concentration, and poverty measures. Lorenz curves (empirical and theoretical).
Author: Achim Zeileis [aut, cre], Christian Kleiber [ctb]
Maintainer: Achim Zeileis

Diff between ineq versions 0.2-11 dated 2013-10-12 and 0.2-12 dated 2014-05-18

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New package Hankel with initial version 0.0-1
Package: Hankel
Version: 0.0-1
Date: 2014/03/08
Title: Univariate non-parametric two-sample test based on empirical Hankel transforms.
Author: Daniel Kolbe
Maintainer: Daniel Kolbe
Description: Provides an R routine for a Cramer-von Mises type two sample test which is based on empirical Hankel transforms of the non-negative sample variables. The test is non-parametric and not distribution free. The exact value of the test statistic for univariate data as well as the p-value and the critical value are computed.
License: GPL (>= 2)
Packaged: 2014-05-18 08:29:08 UTC; daniel
Repository: CRAN
NeedsCompilation: yes
Date/Publication: 2014-05-18 11:55:19

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Package simsalapar (with last version 1.0-2) was removed from CRAN

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

2014-03-06 1.0-2
2013-09-20 1.0-1
2013-09-17 1.0-0

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Package R.devices updated to version 2.9.2 with previous version 2.8.2 dated 2014-01-02

Title: Unified handling of graphics devices
Description: This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.devices versions 2.8.2 dated 2014-01-02 and 2.9.2 dated 2014-05-18

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New package MC2toPath with initial version 0.0.16
Package: MC2toPath
Type: Package
Title: Translates information from netcdf files with MC2 output into inter-PVT transitions.
Version: 0.0.16
Date: 2014-05-16
Author: Dave Conklin and Emilie Henderson
Maintainer: Dave Conklin
Imports: RNetCDF
Description: Post processes MC2 output, especially for use by Path or ST-Sim. MC2 (short for "MC1 version 2") is a dynamic global vegetation model (en.wikipedia.org/wiki/DGVM). Path (essa.com/tools/path) and ST-Sim (www.apexrms.com) are state-and-transition model (STM) engines. MC2 has a user website at sites.google.com/site/mc1dgvmusers. Since 2001, MC1 has been used to simulate changes in natural vegetation due to climate change at scales from regional to global. In 2012, MC1 was reimplemented in C++ to make it faster and to reduce storage requirements. This newer version is referred to as MC2, an abbreviation of "MC1 version 2". Beginning in 2011, output from MC1 and MC2 has been used to inform regional state-and-transition model simulations by the U.S. Forest Service and the Washington State Department of Natural Resources. Projects to date have involved study areas in central Oregon, the Olympic Peninsula, the Blue Mountains ecoregion, southwestern Oregon, and southeastern Oregon. In the first of this series of projects, the netCDF output files from MC2 were manually post-processed, mostly in Excel, to produce input .csv files for the STM engines. Beginning with the second project, R scripts were used to automate the post-processing work. These R scripts have been collected into the MC2toPath R-package.
Collate: AggregateFireFracs.R AggregateVegFracs.R ReportMeanVegChanges.R SaveFireAreaFracs.R SaveMatrix.R SaveRatios.R SaveSequence.R SaveVegFracs.R VTnames.R VegTypeChanges.R SaveVegChangeProbabilityMultipliers.R SaveFireProbabilityMultipliers.R
License: GPL-2
Packaged: 2014-05-18 06:11:40 UTC; ripley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-18 08:11:42

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New package cladoRcpp with initial version 0.14.4
Package: cladoRcpp
Type: Package
Title: C++ implementations of phylogenetic cladogenesis calculations
Version: 0.14.4
Date: 2014-05-17
Authors@R: c(person("Nicholas J.", "Matzke", email = "matzke@berkeley.edu", role = c("aut", "cre", "cph")))
Maintainer: Nicholas J. Matzke
Depends:
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp
Description: This package implements in C++/Rcpp various cladogenesis-related calculations that are slow in pure R. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.
URL: http://phylo.wikidot.com/biogeobears
License: GPL (>= 2)
LazyLoad: yes
ByteCompile: true
Packaged: 2014-05-17 23:55:24 UTC; matzke
Author: Nicholas J. Matzke [aut, cre, cph]
NeedsCompilation: yes
X-CRAN-Comment: Archived on 2014-05-16 as C++ errors were not corrected.
Repository: CRAN
Date/Publication: 2014-05-18 07:22:40

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New package BioGeoBEARS with initial version 0.2.1
Package: BioGeoBEARS
Type: Package
Title: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
Version: 0.2.1
Date: 2013-07-27
Authors@R: c(person("Nicholas J.", "Matzke", email = "matzke@berkeley.edu", role = c("aut", "cre", "cph")))
Maintainer: Nicholas J. Matzke
Depends: rexpokit, cladoRcpp, ape, phylobase, methods
Imports: optimx, FD, parallel, xtable, plotrix, gdata
Description: BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution. It reproduces the model available in LAGRANGE (Ree and Smith 2008), as well as making available numerous additional models. For example, LAGRANGE as typically run has two free parameters, d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and e (extinction rate, really the rate of local range loss along a phylogenetic branch). LAGRANGE also has a fixed cladogenic model which gives equal probability to a number of allowed range inheritance events, e.g.: (1) vicariance, (2) a new species starts in a subset of the ancestral range, (3) the ancestral range is copied to both species; in all cases, at least one species must have a starting range of size 1. LAGRANGE assigns equal probability to each of these events, and zero probability to other events. BioGeoBEARS adds an additional cladogenic event: founder-event speciation (the new species jumps to a range outside of the ancestral range), and also allows the relative weighting of the different sorts of events to be made into free parameters, allowing optimization and standard model choice procedures to pick the best model. The relative probability of different descendent range sizes is also parameterized and thus can also be specified or estimated. The flexibility available in BioGeoBEARS also enables the natural incorporation of (1) imperfect detection of geographic ranges in the tips, and (2) inclusion of fossil geographic range data, when the fossils are tips on the phylogeny. Bayesian analysis has been implemented through use of the "LaplacesDemon" package, however this package is now maintained off of CRAN, so its usage is not formally included in BioGeoBEARS at the current time. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="BioGeoBEARS") to get the citation information.
URL: http://phylo.wikidot.com/biogeobears
License: GPL (>= 2)
LazyLoad: yes
ByteCompile: true
Packaged: 2014-01-02 14:02:17 UTC; ripley
Author: Nicholas J. Matzke [aut, cre, cph]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-01-02 15:15:11

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