Wed, 30 Jan 2013

Package stargazer updated to version 3.0.1 with previous version 3.0 dated 2013-01-26

Title: LaTeX code for well-formatted regression and summary statistics tables
Description: Produces LaTeX code for well-formatted tables that hold regression analysis results from several models side-by-side, as well as summary statistics.
Author: Marek Hlavac
Maintainer: Marek Hlavac

Diff between stargazer versions 3.0 dated 2013-01-26 and 3.0.1 dated 2013-01-30

 DESCRIPTION                  |    8 ++++----
 MD5                          |   20 ++++++++++----------
 R/stargazer-internal.R       |   17 +++++++++++------
 inst/CITATION                |   24 ++++++++++++------------
 inst/ChangeLog               |    8 +++++++-
 inst/doc/stargazer.Rtex      |    2 +-
 inst/doc/stargazer.pdf       |binary
 man/stargazer.Rd             |    2 +-
 man/stargazer_acknowledge.Rd |    2 ++
 man/stargazer_news.Rd        |    6 ++++++
 vignettes/stargazer.Rtex     |    2 +-
 11 files changed, 55 insertions(+), 36 deletions(-)

More information about stargazer at CRAN
Permanent link

Package randomGLM updated to version 1.02-1 with previous version 1.00-1 dated 2013-01-14

Title: Random General Linear Model Prediction
Description: The package implements a bagging predictor based on general linear models
Author: Lin Song, Peter Langfelder
Maintainer: Peter Langfelder

Diff between randomGLM versions 1.00-1 dated 2013-01-14 and 1.02-1 dated 2013-01-30

 Changelog        |   30 +++++++++++
 DESCRIPTION      |   10 +--
 MD5              |   10 +--
 NAMESPACE        |    1 
 R/randomGLM.R    |  138 ++++++++++++++++++++++++++++++++++++++++++-------------
 man/randomGLM.Rd |   51 ++++++++++++++++++--
 6 files changed, 193 insertions(+), 47 deletions(-)

More information about randomGLM at CRAN
Permanent link

New package mlearning with initial version 1.0-0
Package: mlearning
Type: Package
Title: Machine learning algorithms with unified interface and confusion matrices
Version: 1.0-0
Date: 2012-08-04
Author: Ph. Grosjean & K. Denis
Maintainer: Ph. Grosjean
Depends: R (>= 2.14.0)
Imports: stats, grDevices, class, nnet, MASS, e1071, randomForest, ipred
Suggests: mlbench, datasets, RColorBrewer
Description: This package provides a unified interface to various machine learning algorithms. Confusion matrices are provided too.
License: GPL (>= 2)
URL: http://www.sciviews.org/zooimage
Packaged: 2013-01-30 17:43:21 UTC; phgrosjean
Repository: CRAN
Date/Publication: 2013-01-30 22:31:50

More information about mlearning at CRAN
Permanent link

Package mixsmsn updated to version 1.0-5 with previous version 1.0-4 dated 2013-01-23

Title: Fitting finite mixture of scale mixture of skew-normal distributions .
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions.
Author: Marcos Prates , Victor Lachos and Celso Cabral
Maintainer: Marcos Prates

Diff between mixsmsn versions 1.0-4 dated 2013-01-23 and 1.0-5 dated 2013-01-30

 ChangeLog        |    4 ++++
 DESCRIPTION      |    6 +++---
 MD5              |   13 +++++++------
 NAMESPACE        |    1 +
 R/mix.dens.R     |   44 ++++++++++++++++++++++++++++++++++++++++++++
 man/mix.dens.Rd  |    2 +-
 man/mix.lines.Rd |only
 man/smsn.mix.Rd  |    7 +++++++
 8 files changed, 67 insertions(+), 10 deletions(-)

More information about mixsmsn at CRAN
Permanent link

Package games updated to version 1.1-0 with previous version 1.0-5 dated 2012-03-05

Title: Statistical Estimation of Game-Theoretic Models
Description: Provides estimation and analysis functions for strategic statistical models.
Author: Curtis S. Signorino and Brenton Kenkel
Maintainer: Brenton Kenkel

Diff between games versions 1.0-5 dated 2012-03-05 and 1.1-0 dated 2013-01-30

 DESCRIPTION         |   12 ++++-----
 MD5                 |   26 ++++++++++----------
 NEWS                |    9 +++++++
 R/games.r           |   28 +++++++++++++---------
 R/predProbs.r       |    2 -
 R/profile.r         |    5 ++-
 R/ultimatum.r       |   66 ++++++++++++++++++++++++++++++++++------------------
 man/egame12.Rd      |   18 +++++++-------
 man/egame122.Rd     |   18 +++++++-------
 man/egame123.Rd     |   28 +++++++++++-----------
 man/makeFormulas.Rd |   11 ++++----
 man/predProbs.Rd    |    4 +--
 man/predict.game.Rd |   22 +++++++++++++----
 man/ultimatum.Rd    |   38 ++++++++++++++++-------------
 14 files changed, 171 insertions(+), 116 deletions(-)

More information about games at CRAN
Permanent link

Package sem updated to version 3.1-1 with previous version 3.1-0 dated 2013-01-17

Title: Structural Equation Models
Description: This package contains functions for fitting general linear structural equation models (with observed and unobserved variables) using the RAM approach, and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre], Zhenghua Nie [aut], Jarrett Byrnes [aut], Michael Culbertson [ctb], Saikat DebRoy [ctb], Michael Friendly [ctb], Richard H. Jones [ctb], Adam Kramer [ctb], Georges Monette [ctb], R-Core [ctb]
Maintainer: John Fox

Diff between sem versions 3.1-0 dated 2013-01-17 and 3.1-1 dated 2013-01-30

 DESCRIPTION     |   12 ++++++------
 MD5             |   13 +++++++------
 NEWS            |    6 ++++++
 R/csem.R        |   19 ++++++++++++++++++-
 R/startvalues.R |    4 ++--
 src/csem.cpp    |   27 ++++++++++++++++++++++++++-
 src/uncmin.c    |   13 ++++++++-----
 src/utils.h     |only
 8 files changed, 73 insertions(+), 21 deletions(-)

More information about sem at CRAN
Permanent link

Package TESS updated to version 1.1.0 with previous version 1.0.0 dated 2012-10-10

Title: Fast simulation of reconstructed phylogenetic trees under time-dependent birth-death processes
Description: TESS is a package for simulation of reconstructed phylogenetic trees under global, time-dependent birth-death processes. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Author: Sebastian Hoehna
Maintainer: Sebastian Hoehna

Diff between TESS versions 1.0.0 dated 2012-10-10 and 1.1.0 dated 2013-01-30

 TESS-1.0.0/TESS/R/tess.integrate.R                  |only
 TESS-1.1.0/TESS/DESCRIPTION                         |   10 
 TESS-1.1.0/TESS/MD5                                 |   39 +
 TESS-1.1.0/TESS/NAMESPACE                           |    4 
 TESS-1.1.0/TESS/NEWS                                |only
 TESS-1.1.0/TESS/R/globalBiDe.equations.R            |  459 +++++++------------
 TESS-1.1.0/TESS/R/globalBiDe.likelihood.R           |  153 ++++--
 TESS-1.1.0/TESS/R/sim.globalBiDe.age.R              |  318 +++++--------
 TESS-1.1.0/TESS/R/sim.globalBiDe.taxa.R             |  300 ++++--------
 TESS-1.1.0/TESS/R/sim.globalBiDe.taxa.age.R         |  466 +++++---------------
 TESS-1.1.0/TESS/R/tess.PathSampling.R               |only
 TESS-1.1.0/TESS/R/tess.PosteriorPrediction.R        |only
 TESS-1.1.0/TESS/R/tess.PosteriorPredictiveTest.R    |only
 TESS-1.1.0/TESS/R/tess.SteppingStoneSampling.R      |only
 TESS-1.1.0/TESS/R/tess.mcmc.R                       |only
 TESS-1.1.0/TESS/R/tess.utilities.R                  |  237 +++++++---
 TESS-1.1.0/TESS/data                                |only
 TESS-1.1.0/TESS/man/TESS-package.Rd                 |    4 
 TESS-1.1.0/TESS/man/cettiidae.Rd                    |only
 TESS-1.1.0/TESS/man/globalBiDe.likelihood.Rd        |   24 -
 TESS-1.1.0/TESS/man/sim.globalBiDe.age.Rd           |   19 
 TESS-1.1.0/TESS/man/sim.globalBiDe.taxa.Rd          |   18 
 TESS-1.1.0/TESS/man/sim.globalBiDe.taxa.age.Rd      |   17 
 TESS-1.1.0/TESS/man/tess.PosteriorPrediction.Rd     |only
 TESS-1.1.0/TESS/man/tess.PosteriorPredictiveTest.Rd |only
 TESS-1.1.0/TESS/man/tess.mcmc.Rd                    |only
 TESS-1.1.0/TESS/man/tess.steppingStoneSampling.Rd   |only
 27 files changed, 869 insertions(+), 1199 deletions(-)

More information about TESS at CRAN
Permanent link

Package OUwie updated to version 1.32 with previous version 1.31 dated 2012-11-26

Title: Analysis of evolutionary rates in an OU framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu , Brian O'Meara
Maintainer: Jeremy M. Beaulieu

Diff between OUwie versions 1.31 dated 2012-11-26 and 1.32 dated 2013-01-30

 DESCRIPTION          |    8 +-
 MD5                  |   16 ++---
 R/OUwie.R            |  151 ++++++++++++++++++++++++++++++++++++++-------------
 R/OUwie.contour.R    |    2 
 R/OUwie.fixed.R      |   29 ++++++---
 man/OUwie.Rd         |    9 +--
 man/OUwie.contour.Rd |   11 ++-
 man/OUwie.fixed.Rd   |    9 ++-
 man/OUwie.sim.Rd     |    3 -
 9 files changed, 169 insertions(+), 69 deletions(-)

More information about OUwie at CRAN
Permanent link

New package nephro with initial version 1.0
Package: nephro
Type: Package
Title: Biostatistics utilities for nephrology
Version: 1.0
Date: 2013-01-30
Author: Cristian Pattaro
Maintainer: Cristian Pattaro
Description: Set of functions to estimate the Glomerular Filtration Rate (GFR) using different biomarkers and other phenotypes of interest for nephrology.
License: GPL (>= 3)
Packaged: 2013-01-30 10:54:35 UTC; cpattaro
Repository: CRAN
Date/Publication: 2013-01-30 16:13:19

More information about nephro at CRAN
Permanent link

Package YieldCurve updated to version 4.1 with previous version 4.0 dated 2012-12-04

Title: Modelling and estimation of the yield curve
Description: Modelling the yield curve with some parametric models. The models implemented are: Nelson-Siegel, Diebold-Li and Svensson. The package also includes the data of the term structure of interest rate of Federal Reserve Bank and European Central Bank.
Author: Sergio Salvino Guirreri
Maintainer: Sergio Salvino Guirreri

Diff between YieldCurve versions 4.0 dated 2012-12-04 and 4.1 dated 2013-01-30

 DESCRIPTION               |   12 ++++-----
 MD5                       |   28 ++++++++++-----------
 R/NSrates.R               |   13 ++++-----
 R/Srates.R                |    6 ++--
 R/Svensson.R              |    4 +--
 R/beta.R                  |   12 ++++-----
 data/ECBYieldCurve.rda    |binary
 data/FedYieldCurve.rda    |binary
 man/ECBYieldCurve.Rd      |   60 +++++++++++-----------------------------------
 man/FedYieldCurve.Rd      |   30 ++++++++++++++++-------
 man/NSrates.Rd            |    4 +--
 man/Nelson.Siegel.Rd      |    4 +--
 man/Srates.Rd             |    7 +++--
 man/Svensson.Rd           |    2 -
 man/YieldCurve-package.Rd |    8 +++---
 15 files changed, 87 insertions(+), 103 deletions(-)

More information about YieldCurve at CRAN
Permanent link

Package spcosa updated to version 0.3-3 with previous version 0.3-2 dated 2012-12-05

Title: Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata
Description: Spatial coverage sampling and random sampling from compact geographical strata created by k-means.
Author: Dennis Walvoort [aut, cre, cph], Dick Brus [aut, cph], Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort

Diff between spcosa versions 0.3-2 dated 2012-12-05 and 0.3-3 dated 2013-01-30

 DESCRIPTION            |   13 +++++++------
 MD5                    |   13 +++++++------
 R/onAttach.R           |only
 R/onLoad.R             |    3 ---
 build/spcosa.pdf       |binary
 inst/NEWS.Rd           |    8 ++++++++
 inst/doc/spcosa.pdf    |binary
 tests/unitTesting.html |    6 +++---
 8 files changed, 25 insertions(+), 18 deletions(-)

More information about spcosa at CRAN
Permanent link

Package SpatialExtremes updated to version 1.9-1 with previous version 1.9-0 dated 2012-11-06

Title: Modelling Spatial Extremes
Description: This package proposes several approaches for spatial extremes modelling.
Author: Mathieu Ribatet, Richard Singleton, R Core team
Maintainer: Mathieu Ribatet

Diff between SpatialExtremes versions 1.9-0 dated 2012-11-06 and 1.9-1 dated 2013-01-30

 SpatialExtremes-1.9-0/SpatialExtremes/R/zzz.R                           |only
 SpatialExtremes-1.9-1/SpatialExtremes/Copyright                         |only
 SpatialExtremes-1.9-1/SpatialExtremes/DESCRIPTION                       |   15 +++------
 SpatialExtremes-1.9-1/SpatialExtremes/MD5                               |   16 +++++-----
 SpatialExtremes-1.9-1/SpatialExtremes/R/simmaxstab.R                    |    2 -
 SpatialExtremes-1.9-1/SpatialExtremes/data/rainfall.RData               |binary
 SpatialExtremes-1.9-1/SpatialExtremes/data/swissalt.RData               |binary
 SpatialExtremes-1.9-1/SpatialExtremes/inst/doc/SpatialExtremesGuide.pdf |binary
 SpatialExtremes-1.9-1/SpatialExtremes/src/fft.c                         |only
 SpatialExtremes-1.9-1/SpatialExtremes/src/gpdproc.c                     |only
 SpatialExtremes-1.9-1/SpatialExtremes/src/header.h                      |   12 ++++++-
 11 files changed, 27 insertions(+), 18 deletions(-)

More information about SpatialExtremes at CRAN
Permanent link

Package PReMiuM updated to version 3.0.13 with previous version 3.0.11 dated 2013-01-29

Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Dirichlet process Bayesian clustering, also known as profile regression.
Author: David I. Hastie , Silvia Liverani and Sylvia Richardson , with a contribution by Lamiae Azizi
Maintainer: Silvia Liverani

Diff between PReMiuM versions 3.0.11 dated 2013-01-29 and 3.0.13 dated 2013-01-30

 PReMiuM-3.0.11/PReMiuM/src/lib/include/boost  |only
 PReMiuM-3.0.13/PReMiuM/DESCRIPTION            |   15 
 PReMiuM-3.0.13/PReMiuM/MD5                    | 1370 --------------------------
 PReMiuM-3.0.13/PReMiuM/man/PReMiuM-package.Rd |    2 
 PReMiuM-3.0.13/PReMiuM/src/Makevars           |   25 
 PReMiuM-3.0.13/PReMiuM/src/Makevars.win       |    2 
 6 files changed, 15 insertions(+), 1399 deletions(-)

More information about PReMiuM at CRAN
Permanent link

New package KappaGUI with initial version 1.1
Package: KappaGUI
Type: Package
Title: GUI for Cohen's and Fleiss' Kappa
Version: 1.1
Date: 2013-01-30
Author: Frederic Santos
Maintainer: Frederic Santos
Depends: R (>= 2.4.1), tcltk, irr
Description: Offers a complete and interactive GUI to work out Cohen's and Fleiss' Kappa.
License: GPL (>= 2)
Packaged: 2013-01-30 10:04:01 UTC; fsantos
Repository: CRAN
Date/Publication: 2013-01-30 15:16:37

More information about KappaGUI at CRAN
Permanent link

Package difR updated to version 4.4 with previous version 4.3 dated 2012-06-13

Title: Collection of methods to detect dichotomous differential item functioning (DIF) in psychometrics
Description: The difR package contains several traditional methods to detect DIF in dichotomously scored items. Both uniform and non-uniform DIF effects can be detected, with methods relying upon item response models or not. Some methods deal with more than one focal group.
Author: David Magis (U Liege), Sebastien Beland (UQAM) and Gilles Raiche (UQAM)
Maintainer: David Magis

Diff between difR versions 4.3 dated 2012-06-13 and 4.4 dated 2013-01-30

 difR-4.3/difR/inst/doc           |only
 difR-4.4/difR/DESCRIPTION        |    8 ++++----
 difR-4.4/difR/MD5                |    9 ++++-----
 difR-4.4/difR/NEWS               |   17 +++++++++++++++++
 difR-4.4/difR/R/mantelHaenszel.R |    1 +
 difR-4.4/difR/inst/CITATION      |    4 ++--
 6 files changed, 28 insertions(+), 11 deletions(-)

More information about difR at CRAN
Permanent link

Package candisc updated to version 0.6-1 with previous version 0.6-0 dated 2013-01-23

Title: Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
Description: This package includes functions for computing and visualizing generalized canonical discriminant analyses and canonical correlation analysis for a multivariate linear model. Traditional canonical discriminant analysis is restricted to a one-way MANOVA design and is equivalent to canonical correlation analysis between a set of quantitative response variables and a set of dummy variables coded from the factor variable. The candisc package generalizes this to multi-way MANOVA designs for all factors in a multivariate linear model, computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D) visualizations of terms in an mlm via the plot.candisc and heplot.candisc methods.
Author: Michael Friendly and John Fox
Maintainer: Michael Friendly

Diff between candisc versions 0.6-0 dated 2013-01-23 and 0.6-1 dated 2013-01-30

 DESCRIPTION            |   35 +++++------
 MD5                    |   28 +++++---
 NAMESPACE              |    8 ++
 NEWS                   |   14 ++++
 R/cancor.R             |   87 ++++++++++++++++++++++-----
 R/heplot.cancor.R      |    2 
 R/heplot3d.cancor.R    |only
 R/plot.cancor.R        |only
 R/plot.candisc.R       |    2 
 R/redundancy.R         |only
 R/vectors.R            |   13 +++-
 R/vectors3d.R          |only
 man/cancor.Rd          |  154 ++++++++++++++++++++++++++++++++++++++++++-------
 man/candisc-package.Rd |   21 +++++-
 man/heplot.cancor.Rd   |   66 ++++++++++++++++-----
 man/plot.cancor.Rd     |only
 man/redundancy.Rd      |only
 man/vectors.Rd         |   51 +++++++++-------
 18 files changed, 371 insertions(+), 110 deletions(-)

More information about candisc at CRAN
Permanent link

Package taxize updated to version 0.0.3 with previous version 0.0.2 dated 2012-12-07

Title: Taxonomic information from around the web.
Description: Taxonomic information from around the web.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Carl Boettiger [aut], Ignasi Bartomeus [aut]
Maintainer: Scott Chamberlain

Diff between taxize versions 0.0.2 dated 2012-12-07 and 0.0.3 dated 2013-01-30

 taxize-0.0.2/taxize/man/itis.Rd                                |only
 taxize-0.0.3/taxize/CONTRIBUTING.md                            |only
 taxize-0.0.3/taxize/DESCRIPTION                                |   38 
 taxize-0.0.3/taxize/MD5                                        |  169 -
 taxize-0.0.3/taxize/NAMESPACE                                  |   61 
 taxize-0.0.3/taxize/NEWS                                       |   25 
 taxize-0.0.3/taxize/R/classification.R                         |   18 
 taxize-0.0.3/taxize/R/col_children.R                           |only
 taxize-0.0.3/taxize/R/col_classification.R                     |only
 taxize-0.0.3/taxize/R/col_downstream.R                         |only
 taxize-0.0.3/taxize/R/eol_dataobjects.R                        |only
 taxize-0.0.3/taxize/R/get_genes.R                              |only
 taxize-0.0.3/taxize/R/get_genes_avail.R                        |   10 
 taxize-0.0.3/taxize/R/get_seqs.R                               |   18 
 taxize-0.0.3/taxize/R/get_tsn.R                                |   50 
 taxize-0.0.3/taxize/R/get_uid.R                                |   47 
 taxize-0.0.3/taxize/R/gisd_isinvasive.R                        |only
 taxize-0.0.3/taxize/R/itis.R                                   | 1472 +++++++++-
 taxize-0.0.3/taxize/R/itis_acceptname.R                        |    1 
 taxize-0.0.3/taxize/R/itis_downstream.R                        |    2 
 taxize-0.0.3/taxize/R/itis_name.R                              |    8 
 taxize-0.0.3/taxize/R/itis_phymat_format.R                     |   38 
 taxize-0.0.3/taxize/R/itis_taxrank.R                           |    8 
 taxize-0.0.3/taxize/R/iucn_summary.R                           |   10 
 taxize-0.0.3/taxize/R/phylomatic_tree.R                        |  111 
 taxize-0.0.3/taxize/R/tax_name.R                               |only
 taxize-0.0.3/taxize/R/taxize-package.R                         |   20 
 taxize-0.0.3/taxize/R/tnrs.R                                   |only
 taxize-0.0.3/taxize/R/tnrs_sources.r                           |only
 taxize-0.0.3/taxize/R/tpl_search.r                             |   10 
 taxize-0.0.3/taxize/R/ubio_namebank.R                          |    8 
 taxize-0.0.3/taxize/R/zzz.R                                    |    1 
 taxize-0.0.3/taxize/README.md                                  |   94 
 taxize-0.0.3/taxize/inst                                       |only
 taxize-0.0.3/taxize/man/col_children.Rd                        |only
 taxize-0.0.3/taxize/man/col_classification.Rd                  |only
 taxize-0.0.3/taxize/man/col_downstream.Rd                      |only
 taxize-0.0.3/taxize/man/eol_dataobjects.Rd                     |only
 taxize-0.0.3/taxize/man/get_genes.Rd                           |only
 taxize-0.0.3/taxize/man/get_seqs.Rd                            |    3 
 taxize-0.0.3/taxize/man/get_tsn.Rd                             |   15 
 taxize-0.0.3/taxize/man/get_uid.Rd                             |    7 
 taxize-0.0.3/taxize/man/getacceptednamesfromtsn.Rd             |only
 taxize-0.0.3/taxize/man/getanymatchcount.Rd                    |only
 taxize-0.0.3/taxize/man/getcommentdetailfromtsn.Rd             |only
 taxize-0.0.3/taxize/man/getcommonnamesfromtsn.Rd               |only
 taxize-0.0.3/taxize/man/getcoremetadatafromtsn.Rd              |only
 taxize-0.0.3/taxize/man/getcoveragefromtsn.Rd                  |only
 taxize-0.0.3/taxize/man/getcredibilityratingfromtsn.Rd         |only
 taxize-0.0.3/taxize/man/getcredibilityratings.Rd               |only
 taxize-0.0.3/taxize/man/getcurrencyfromtsn.Rd                  |only
 taxize-0.0.3/taxize/man/getdatedatafromtsn.Rd                  |only
 taxize-0.0.3/taxize/man/getdescription.Rd                      |only
 taxize-0.0.3/taxize/man/getexpertsfromtsn.Rd                   |only
 taxize-0.0.3/taxize/man/getfullhierarchyfromtsn.Rd             |only
 taxize-0.0.3/taxize/man/getfullrecordfromlsid.Rd               |only
 taxize-0.0.3/taxize/man/getfullrecordfromtsn.Rd                |only
 taxize-0.0.3/taxize/man/getgeographicdivisionsfromtsn.Rd       |only
 taxize-0.0.3/taxize/man/getgeographicvalues.Rd                 |only
 taxize-0.0.3/taxize/man/getglobalspeciescompletenessfromtsn.Rd |only
 taxize-0.0.3/taxize/man/gethierarchydownfromtsn.Rd             |only
 taxize-0.0.3/taxize/man/gethierarchyupfromtsn.Rd               |only
 taxize-0.0.3/taxize/man/getitistermsfromcommonname.Rd          |only
 taxize-0.0.3/taxize/man/getitistermsfromscientificname.Rd      |only
 taxize-0.0.3/taxize/man/getjurisdictionaloriginfromtsn.Rd      |only
 taxize-0.0.3/taxize/man/getjurisdictionoriginvalues.Rd         |only
 taxize-0.0.3/taxize/man/getjurisdictionvalues.Rd               |only
 taxize-0.0.3/taxize/man/getkey.Rd                              |    1 
 taxize-0.0.3/taxize/man/getkingdomnamefromtsn.Rd               |only
 taxize-0.0.3/taxize/man/getkingdomnames.Rd                     |only
 taxize-0.0.3/taxize/man/getlastchangedate.Rd                   |only
 taxize-0.0.3/taxize/man/getlsidfromtsn.Rd                      |only
 taxize-0.0.3/taxize/man/getothersourcesfromtsn.Rd              |only
 taxize-0.0.3/taxize/man/getparenttsnfromtsn.Rd                 |only
 taxize-0.0.3/taxize/man/getpublicationsfromtsn.Rd              |only
 taxize-0.0.3/taxize/man/getranknames.Rd                        |only
 taxize-0.0.3/taxize/man/getrecordfromlsid.Rd                   |only
 taxize-0.0.3/taxize/man/getreviewyearfromtsn.Rd                |only
 taxize-0.0.3/taxize/man/getscientificnamefromtsn.Rd            |only
 taxize-0.0.3/taxize/man/getsynonymnamesfromtsn.Rd              |only
 taxize-0.0.3/taxize/man/gettaxonauthorshipfromtsn.Rd           |only
 taxize-0.0.3/taxize/man/gettaxonomicranknamefromtsn.Rd         |only
 taxize-0.0.3/taxize/man/gettaxonomicusagefromtsn.Rd            |only
 taxize-0.0.3/taxize/man/gettsnbyvernacularlanguage.Rd          |only
 taxize-0.0.3/taxize/man/gettsnfromlsid.Rd                      |only
 taxize-0.0.3/taxize/man/getunacceptabilityreasonfromtsn.Rd     |only
 taxize-0.0.3/taxize/man/getvernacularlanguages.Rd              |only
 taxize-0.0.3/taxize/man/gisd_isinvasive.Rd                     |only
 taxize-0.0.3/taxize/man/itis_phymat_format.Rd                  |   14 
 taxize-0.0.3/taxize/man/itis_taxrank.Rd                        |    2 
 taxize-0.0.3/taxize/man/iucn_summary.Rd                        |    2 
 taxize-0.0.3/taxize/man/phylomatic_tree.Rd                     |   58 
 taxize-0.0.3/taxize/man/searchbycommonname.Rd                  |only
 taxize-0.0.3/taxize/man/searchbycommonnamebeginswith.Rd        |only
 taxize-0.0.3/taxize/man/searchbycommonnameendswith.Rd          |only
 taxize-0.0.3/taxize/man/searchbyscientificname.Rd              |only
 taxize-0.0.3/taxize/man/searchforanymatch.Rd                   |only
 taxize-0.0.3/taxize/man/searchforanymatchpaged.Rd              |only
 taxize-0.0.3/taxize/man/tax_name.Rd                            |only
 taxize-0.0.3/taxize/man/taxize-package.Rd                      |   30 
 taxize-0.0.3/taxize/man/tnrs.Rd                                |only
 taxize-0.0.3/taxize/man/tnrs_sources.Rd                        |only
 taxize-0.0.3/taxize/man/tpl_search.Rd                          |   10 
 taxize-0.0.3/taxize/man/ubio_namebank.Rd                       |   10 
 taxize-0.0.3/taxize/tests                                      |only
 105 files changed, 2032 insertions(+), 339 deletions(-)

More information about taxize at CRAN
Permanent link

Package rdryad updated to version 0.1.1 with previous version 0.1 dated 2012-02-23

Title: Dryad API interface.
Description: Interface to the API for Dryad
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain

Diff between rdryad versions 0.1 dated 2012-02-23 and 0.1.1 dated 2013-01-30

 rdryad-0.1.1/rdryad/DESCRIPTION                   |   20 ++--
 rdryad-0.1.1/rdryad/MD5                           |   51 ++++------
 rdryad-0.1.1/rdryad/NAMESPACE                     |    8 -
 rdryad-0.1.1/rdryad/NEWS                          |    8 +
 rdryad-0.1.1/rdryad/R/download_dryadmetadata.r    |   18 +--
 rdryad-0.1.1/rdryad/R/download_url.r              |   33 +++---
 rdryad-0.1.1/rdryad/R/dr_identify.r               |only
 rdryad-0.1.1/rdryad/R/dr_listidentifiers.r        |only
 rdryad-0.1.1/rdryad/R/dr_listmetadataformats.r    |only
 rdryad-0.1.1/rdryad/R/dr_listsets.r               |only
 rdryad-0.1.1/rdryad/R/dryad_getfile.r             |   70 ++++++--------
 rdryad-0.1.1/rdryad/R/getalldryad_metadata.r      |   20 +---
 rdryad-0.1.1/rdryad/R/search_dryad.r              |  110 +++++++++++-----------
 rdryad-0.1.1/rdryad/R/totimp.r                    |   31 +++---
 rdryad-0.1.1/rdryad/R/totimp_dryad.r              |   52 ++++------
 rdryad-0.1.1/rdryad/README.md                     |    7 +
 rdryad-0.1.1/rdryad/man/download_dryadmetadata.Rd |    2 
 rdryad-0.1.1/rdryad/man/download_url.Rd           |    4 
 rdryad-0.1.1/rdryad/man/dr_identify.Rd            |only
 rdryad-0.1.1/rdryad/man/dr_listidentifiers.Rd     |only
 rdryad-0.1.1/rdryad/man/dr_listmetadataformats.Rd |only
 rdryad-0.1.1/rdryad/man/dr_listsets.Rd            |only
 rdryad-0.1.1/rdryad/man/dryad_getfile.Rd          |    3 
 rdryad-0.1.1/rdryad/man/getalldryad_metadata.Rd   |    2 
 rdryad-0.1.1/rdryad/man/search_dryad.Rd           |   14 +-
 rdryad-0.1/rdryad/.gitignore                      |only
 rdryad-0.1/rdryad/R/identify.r                    |only
 rdryad-0.1/rdryad/R/listidentifiers.r             |only
 rdryad-0.1/rdryad/R/listmetadataformats.r         |only
 rdryad-0.1/rdryad/demos                           |only
 rdryad-0.1/rdryad/man/identify.Rd                 |only
 rdryad-0.1/rdryad/man/listidentifiers.Rd          |only
 rdryad-0.1/rdryad/man/listmetadataformats.Rd      |only
 rdryad-0.1/rdryad/other                           |only
 34 files changed, 225 insertions(+), 228 deletions(-)

More information about rdryad at CRAN
Permanent link

Package RcppArmadillo updated to version 0.3.6.2 with previous version 0.3.6.1 dated 2012-12-17

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 3.6.1). 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 licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.3.6.1 dated 2012-12-17 and 0.3.6.2 dated 2013-01-30

 ChangeLog                                               |   11 -
 DESCRIPTION                                             |    8 
 MD5                                                     |   47 ++--
 inst/NEWS.Rd                                            |   12 +
 inst/doc/RcppArmadillo-intro.pdf                        |binary
 inst/doc/RcppArmadillo-unitTests.pdf                    |binary
 inst/doc/unitTests-results/RcppArmadillo-unitTests.html |   18 -
 inst/doc/unitTests-results/RcppArmadillo-unitTests.txt  |   30 +-
 inst/examples/kalman                                    |only
 inst/include/armadillo                                  |    1 
 inst/include/armadillo_bits/arma_version.hpp            |    2 
 inst/include/armadillo_bits/compiler_setup.hpp          |   25 ++
 inst/include/armadillo_bits/config.hpp                  |    9 
 inst/include/armadillo_bits/diskio_meat.hpp             |  120 ++++++++++-
 inst/include/armadillo_bits/fn_det.hpp                  |   65 +++++-
 inst/include/armadillo_bits/hdf5_misc.hpp               |   84 ++++++-
 inst/include/armadillo_bits/promote_type.hpp            |  173 +++++++++-------
 inst/include/armadillo_bits/restrictors.hpp             |   56 +++--
 inst/include/armadillo_bits/traits.hpp                  |   81 ++++++-
 inst/include/armadillo_bits/typedef.hpp                 |   90 ++++----
 20 files changed, 612 insertions(+), 220 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link

Package qgraph updated to version 1.2.1 with previous version 1.2 dated 2013-01-24

Title: Network representations of relationships in data
Description: The qgraph package can be used to visualize data as networks.
Author: Sacha Epskamp, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp

Diff between qgraph versions 1.2 dated 2013-01-24 and 1.2.1 dated 2013-01-30

 DESCRIPTION                              |   12 
 MD5                                      |   96 
 NAMESPACE                                |   64 
 NEWS                                     |  490 +--
 R/Cent2EdgeNode.R                        |  124 
 R/DrawArrow.R                            |   62 
 R/Fade.R                                 |   40 
 R/SelfLoop.R                             |  160 -
 R/XKCD.R                                 |   20 
 R/addTrans.R                             |   40 
 R/centrality.R                           |  244 -
 R/getArgs.R                              |   22 
 R/igraphConversion.R                     |  106 
 R/isColor.R                              |   10 
 R/layout.R                               |  102 
 R/mapusr2in.R                            |  131 
 R/mixCols.R                              |   22 
 R/qgraph.R                               | 4550 +++++++++++++++----------------
 R/qgraph.lavaan.R                        | 1179 ++++----
 R/qgraph.panel.R                         |  116 
 R/qgraphGUI.R                            |  466 +--
 R/qgraph_cfa.R                           |  220 -
 R/qgraph_growth.R                        |  330 +-
 R/qgraph_loadings.R                      |  622 ++--
 R/qgraph_sem.R                           | 1049 +++----
 R/qgraph_semModel.R                      |  579 +--
 R/qgraph_svg.R                           |  358 +-
 README                                   |    8 
 man/as.igraph.Rd                         |   56 
 man/big5.Rd                              |   46 
 man/big5groups.Rd                        |   50 
 man/centrality.Rd                        |  124 
 man/plot.qgraph.Rd                       |   50 
 man/print.qgraph.Rd                      |   58 
 man/qgraph-package.Rd                    |   70 
 man/qgraph.Rd                            |  791 ++---
 man/qgraph.animate.Rd                    |  308 +-
 man/qgraph.cfa.Rd                        |  206 -
 man/qgraph.gui.Rd                        |  104 
 man/qgraph.lavaan.Rd                     |  278 -
 man/qgraph.layout.fruchtermanreingold.Rd |  202 -
 man/qgraph.panel.Rd                      |   96 
 man/qgraph.semModel.Rd                   |  208 -
 man/qgraph_efa.Rd                        |  106 
 man/qgraph_loadings.Rd                   |  122 
 man/qgraph_pca.Rd                        |  104 
 man/qgraph_sem.Rd                        |  286 -
 man/qgraph_svg.Rd                        |  138 
 man/summary.qgraph.Rd                    |   58 
 49 files changed, 7336 insertions(+), 7347 deletions(-)

More information about qgraph at CRAN
Permanent link

Package optparse updated to version 1.0.1 with previous version 1.0.0 dated 2012-11-21

Title: Command line option parser.
Description: A command line parser inspired by Python's 'optparse' library to be used with Rscript to write "#!" shebang scripts that accept short and long flag/options.
Author: Trevor L Davis. Some documentation and examples ported from Allen Day's getopt package. Some documentation from the optparse Python module by the Python Software Foundation. Contributions from Steve Lianoglou and Jim Nikelski.
Maintainer: Trevor L Davis

Diff between optparse versions 1.0.0 dated 2012-11-21 and 1.0.1 dated 2013-01-30

 DESCRIPTION           |   17 +++++++----------
 MD5                   |    4 ++--
 inst/doc/optparse.pdf |binary
 3 files changed, 9 insertions(+), 12 deletions(-)

More information about optparse at CRAN
Permanent link

Package MissingDataGUI updated to version 0.1-4 with previous version 0.1-3 dated 2012-05-17

Title: A GUI for Missing Data Exploration
Description: This package provides numeric and graphical summaries for the missing values from both discrete and continuous variables. A variety of imputation methods are applied, including univariate imputations like fixed or random values, multiple imputations based on other packages, and imputations conditioned on a categorical variable.
Author: Xiaoyue Cheng, Dianne Cook, Heike Hofmann
Maintainer: Xiaoyue Cheng

Diff between MissingDataGUI versions 0.1-3 dated 2012-05-17 and 0.1-4 dated 2013-01-30

 DESCRIPTION               |    8 ++--
 MD5                       |    7 ++-
 NEWS                      |only
 R/WatchMissingValues.r    |   89 +++++++++++++++++++++++++++++++++++-----------
 inst/doc/introduction.pdf |binary
 5 files changed, 76 insertions(+), 28 deletions(-)

More information about MissingDataGUI at CRAN
Permanent link

Package expoTree updated to version 0.8.1 with previous version 0.8 dated 2013-01-25

Title: Calculate density dependent likelihood of a phylogenetic tree
Description: Calculates the density dependent likelihood of a phylogenetic tree. It takes branching and sampling times as an argument and integrates the likelihood function over the whole tree.
Author: Gabriel E Leventhal, partly adapted from MATLAB code by Awad H. Al-Mohy and using the routines DLNAC1 and DLARPC by Sheung Hun Cheng, and DLAPST from ScaLAPACK.
Maintainer: Gabriel E Leventhal

Diff between expoTree versions 0.8 dated 2013-01-25 and 0.8.1 dated 2013-01-30

 ChangeLog              |only
 DESCRIPTION            |    8 ++++----
 MD5                    |   11 ++++++-----
 src/expmv.c            |    4 ++--
 src/expoTree.c         |   10 +++++-----
 src/expomv.c           |   10 +++++-----
 src/simulate_trees.cpp |    4 ++--
 7 files changed, 24 insertions(+), 23 deletions(-)

More information about expoTree at CRAN
Permanent link

Package ergm.userterms updated to version 3.0-2 with previous version 3.0-1 dated 2012-03-08

Title: User-specified terms for the statnet suite of packages
Description: A template package to demonstrate the use of user-specified statistics for use in "ergm" models as part of the "statnet" suite of packages.
Author: Mark S. Handcock , David R. Hunter , Carter T. Butts , Steven M. Goodreau , Pavel N. Krivitsky Martina Morris
Maintainer: David R. Hunter

Diff between ergm.userterms versions 3.0-1 dated 2012-03-08 and 3.0-2 dated 2013-01-30

 DESCRIPTION                   |   10 ++---
 MD5                           |    7 ++-
 inst/CITATION                 |   83 ++++++++++--------------------------------
 man/ergm.userterms-package.Rd |    9 ++--
 man/mindegree-term.Rd         |only
 5 files changed, 35 insertions(+), 74 deletions(-)

More information about ergm.userterms at CRAN
Permanent link

Package hexbin updated to version 1.26.1 with previous version 1.26.0 dated 2011-04-26

Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler
Maintainer: ORPHANED

Diff between hexbin versions 1.26.0 dated 2011-04-26 and 1.26.1 dated 2013-01-30

 DESCRIPTION                  |   13 ++++++----
 MD5                          |only
 R/hdiffplot.R                |   16 ++++++-------
 R/hexViewport.R              |    4 +--
 R/hexbinplot.R               |   36 +++++++++++++++---------------
 R/hexpanel.R                 |   51 ++++++++++++++++++++++---------------------
 inst/doc/hexagon_binning.pdf |binary
 man/NHANES.Rd                |    8 ------
 man/hexList.Rd               |    4 ---
 man/hexVP.abline.Rd          |    3 --
 man/hexViewport.Rd           |    3 --
 man/panel.hexgrid.Rd         |    4 ---
 man/panel.hexloess.Rd        |   12 ++++------
 tests/hdiffplot.Rout.save    |   44 ++++++++++++++++++-------------------
 14 files changed, 90 insertions(+), 108 deletions(-)

More information about hexbin at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.