Fri, 02 May 2014

New package sharpshootR with initial version 0.6-1
Package: sharpshootR
Type: Package
Title: A collection of functions to support soil survey
Description: A collection of functions to support soil survey
Version: 0.6-1
Date: 2014-05-02
Author: USDA-NRCS Soil Survey Staff
Maintainer: Dylan Beaudette
License: GPL (>= 2)
Repository: CRAN
URL: http://aqp.r-forge.r-project.org/
Suggests: soilDB, MASS
Depends: R (>= 2.15.0), aqp, ape
Imports: igraph, cluster, lattice, latticeExtra, vegan, sp, reshape2, Hmisc, scales, circular, RColorBrewer, plyr
Packaged: 2014-05-02 20:38:53 UTC; dylan
NeedsCompilation: no
Date/Publication: 2014-05-03 00:41:15

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New package sglr with initial version 0.7
Package: sglr
Type: Package
Title: An R package for power and boundary calculations in pre-licensure vaccine trials using a sequential generalized likelihood ratio test
Version: 0.7
Date: 2012-12-07
Authors@R: c( person("Balasubramanian", "Narasimhan", email = "naras@stat.stanford.edu", role = c("aut", "cre")), person("Mei-Chiung", "Shih", email = "meichiun@stanford.edu", role = "aut"))
Author: Balasubramanian Narasimhan [aut, cre], Mei-Chiung Shih [aut]
Maintainer: Balasubramanian Narasimhan
Description: Functions for computing power and boundaries for pre-licensure vaccine trials using the Generalized Likelihood Ratio tests proposed by Shih, Lai, Heyse and Chen
Depends: R (>= 3.0), ggplot2, shiny
License: GPL (>= 2)
Packaged: 2014-05-02 22:44:34 UTC; naras
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-03 00:54:29

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Package OrdinalLogisticBiplot updated to version 0.3 with previous version 0.2 dated 2013-11-26

Title: Biplot representations of ordinal variables
Description: Analysis of a matrix of polytomous items using Ordinal Logistic Biplots (OLB) The OLB procedure extends the binary logistic biplot to ordinal (polytomous) data. The individuals are represented as points on a plane and the variables are represented as lines rather than vectors as in a classical or binary biplot, specifying the points for each of the categories of the variable. The set of prediction regions is established by stripes perpendicular to the line between the category points, in such a way that the prediction for each individual is given by its projection into the line of the variable.
Author: Julio Cesar Hernandez Sanchez, Jose Luis Vicente-Villardon
Maintainer: Julio Cesar Hernandez Sanchez

Diff between OrdinalLogisticBiplot versions 0.2 dated 2013-11-26 and 0.3 dated 2014-05-02

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 OrdinalLogisticBiplot-0.3/OrdinalLogisticBiplot/R/BiplotDensity.r                      |    3 
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 36 files changed, 547 insertions(+), 374 deletions(-)

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Package aqp updated to version 1.7 with previous version 1.6 dated 2013-12-17

Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette , Pierre Roudier
Maintainer: Dylan Beaudette

Diff between aqp versions 1.6 dated 2013-12-17 and 1.7 dated 2014-05-02

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New package optR with initial version 1.0.3
Package: optR
Type: Package
Title: Optimization Toolbox for solving linear systems
Version: 1.0.3
Date: 2014-04-08
Author: Prakash (PKS Prakash)
Maintainer: Prakash
Description: The optR function provides an option to solve the linear system using numeric and non-meric approach. The current packages supports Gauss Elimination, LU decomposition, Gauss-Sideil, and CGM methods to solve equations having relationships of Ax=b form. The pacakge can be used to build linear and non-linear models by defining them in linear system.
License: GPL (>= 2)
Packaged: 2014-05-01 22:09:51 UTC; prakash
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 21:48:50

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Package NPCD updated to version 1.0-6 with previous version 1.0-5 dated 2014-02-13

Title: Nonparametric Methods for Cognitive Diagnosis
Description: This package performs an array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.
Author: Yi Zheng [aut, cre], Chia-Yi Chiu [aut], Jeffrey A. Douglas [ctb]
Maintainer: Yi Zheng

Diff between NPCD versions 1.0-5 dated 2014-02-13 and 1.0-6 dated 2014-05-02

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 4 files changed, 131 insertions(+), 128 deletions(-)

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Package benchmark updated to version 0.3-6 with previous version 0.3-5 dated 2012-12-03

Title: Benchmark Experiments Toolbox
Description: The benchmark package provides a toolbox for setup, execution and analysis of benchmark experiments. Main focus is the analysis of data accumulating during the execution -- one primary objective is the statistical correct computation of the candidate algorithms' order.
Author: Manuel J. A. Eugster [aut, cre]
Maintainer: Manuel J. A. Eugster

Diff between benchmark versions 0.3-5 dated 2012-12-03 and 0.3-6 dated 2014-05-02

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Package BalancedSampling updated to version 1.4 with previous version 1.0 dated 2014-03-24

Title: Balanced and spatially balanced sampling
Description: This package includes methods that can select balanced and spatially balanced probability samples in multi-dimensional spaces with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of the included sampling methods. The local pivotal method and spatially correlated Poisson sampling (for spatially balanced sampling) are included. Also the cube method (for balanced sampling) and the local cube method (for doubly balanced sampling) are included.
Author: Anton Grafström
Maintainer: Anton Grafström

Diff between BalancedSampling versions 1.0 dated 2014-03-24 and 1.4 dated 2014-05-02

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Package TopKLists updated to version 1.0.1 with previous version 1.0.0 dated 2014-04-28

Title: Inference, aggregation and visualization for top-k ranked lists
Description: For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Author: Michael G. Schimek, Medical University of Graz, Graz, Austria; Eva Budinska, Masaryk University, Brno, Czech Republic; Jie Ding, Harvard University, Cambridge, Massachusetts, USA; Karl G. Kugler, Helmholtz Centre Munich, Neuherberg, Germany; Vendula Svendova, Medical University of Graz, Graz, Austria; Shili Lin, The Ohio State University, Columbus, Ohio, USA.
Maintainer: Michael G. Schimek

Diff between TopKLists versions 1.0.0 dated 2014-04-28 and 1.0.1 dated 2014-05-02

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New package irtProb with initial version 1.2
Package: irtProb
Version: 1.2
Date: 2014-05-01
Title: Utilities and Probability Distributions Related to Multidimensional Person Item Response Models
Author: Gilles Raiche
Maintainer: Gilles Raiche
Depends: R (>= 3.0.0), stats, lattice, moments, methods
Description: Multidimensional Person Item Response Theory probability distributions
License: GPL (>= 2)
Packaged: 2014-05-02 18:02:08 UTC; utilisateur
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 18:41:01

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New package HK80 with initial version 0.0.1
Package: HK80
Type: Package
Title: Conversion Tools for HK80 Geographical Coordinate System
Version: 0.0.1
Date: 2014-03-13
Author: Jinlong Zhang
Maintainer: Jinlong Zhang
Description: Conversion and Reverse Conversion between WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems. Algorithms follow Survey and Mapping Office Lands Department, Hong Kong Government (1995)
License: GPL-2
Packaged: 2014-03-20 01:15:59 UTC; jlzhang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 18:41:26

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Package compareGroups updated to version 2.0.4 with previous version 2.0.3 dated 2014-04-29

Title: Descriptive analysis by groups
Description: A package designed to read, interpret, summarise, display and analyse epidemiological data. Can be used to create data summaries for quality control, extensive reports for exploring data, including publication-ready univariate or bivariate tables in plain text HTML and LaTeX, and a figures to quickly visualise the distribution of your data. Depending on the nature of the variable, various statistics are calculated (mean, median, frequencies, incidences) and appropriate tests are performed (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...). The latest version includes functionality for summarising genetic data, and for performing low-level quality control of your database (see radiograph()) to help identify data-entry errors. This version has also been implemented in a web-interface to make this package accessible to non-R-users (see www.comparegroups.eu).
Author: Isaac Subirana, Joan Vila, Hctor Sanz, Gavin Lucas, Judith Peafiel and David Gimnez
Maintainer: Isaac Subirana

Diff between compareGroups versions 2.0.3 dated 2014-04-29 and 2.0.4 dated 2014-05-02

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Package roxygen2 updated to version 4.0.0 with previous version 3.1.0 dated 2014-01-29

Title: In-source documentation for R
Description: A Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE.
Author: Hadley Wickham [aut, cre], Peter Danenberg [aut], Manuel Eugster [aut]
Maintainer: Hadley Wickham

Diff between roxygen2 versions 3.1.0 dated 2014-01-29 and 4.0.0 dated 2014-05-02

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Package RcppSMC updated to version 0.1.4 with previous version 0.1.3 dated 2014-05-02

Title: Rcpp bindings for Sequential Monte Carlo
Description: This package provides R with access to the Sequential Monte Carlo Template Classes by Johansen (Journal of Statistical Software, 2009, v30, i6). At present, two additional examples have been added, and the first example from the JSS paper has been extended. Further integration and extensions are planned.
Author: Dirk Eddelbuettel and Adam M. Johansen
Maintainer: Dirk Eddelbuettel

Diff between RcppSMC versions 0.1.3 dated 2014-05-02 and 0.1.4 dated 2014-05-02

 ChangeLog              |    6 ++++++
 DESCRIPTION            |    8 ++++----
 MD5                    |    8 ++++----
 inst/NEWS.Rd           |    6 ++++++
 inst/include/sampler.h |    8 +++++---
 5 files changed, 25 insertions(+), 11 deletions(-)

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New package DiscML with initial version 1.0
Package: DiscML
Type: Package
Title: DiscML: An R package for estimating evolutionary rates of discrete characters using maximum likelihood
Version: 1.0
Date: 2014-04-28
Author: Tane Kim, Weilong Hao
Maintainer: Weilong Hao
Description: DiscML performs maximum likelihood estimation with the options to correct for unobservable data, to implement a Gamma-distribution for rate variation, and to estimate the prior root probabilities from the empirical data.
Depends: ape
Packaged: 2014-05-01 19:02:22 UTC; Tane
License: GPL (>= 2)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 16:07:31

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Package TAM updated to version 1.0-2.1 with previous version 1.0-2 dated 2014-04-02

Title: Test Analysis Modules
Description: The package includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, Generalized Partial Credit, Rating Scale, Multi Facets), fit statistics, standard error estimation, as well as plausible value imputation and weighted likelihood estimation of ability.
Author: Thomas Kiefer [aut, cre], Alexander Robitzsch [aut], Margaret Wu [aut]
Maintainer: Thomas Kiefer

Diff between TAM versions 1.0-2 dated 2014-04-02 and 1.0-2.1 dated 2014-05-02

 DESCRIPTION                 |    6 +++---
 MD5                         |    4 ++--
 src/tamwle_helper_ccode.cpp |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

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New package secrdesign with initial version 2.1.2
Package: secrdesign
Type: Package
Title: Tools for Designing Spatially Explicit Capture--Recapture Studies
Version: 2.1.2
Depends: R (>= 3.0.0), secr(>= 2.8.2)
Imports: parallel, abind
Date: 2014-05-02
Author: Murray Efford
Maintainer: Murray Efford
Description: Tools for designing spatially explicit capture--recapture studies of animal populations (primarily a simulation manager for package secr)
License: GPL (>= 2)
LazyData: yes
LazyDataCompression: xz
URL: http://www.otago.ac.nz/density
Packaged: 2014-05-02 08:30:21 UTC; Murray
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 11:59:41

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Package SpatialEpi updated to version 1.2 with previous version 1.1 dated 2013-01-05

Title: Performs various spatial epidemiological analyses
Description: Cluster Detection, Disease Mapping
Author: Cici Chen , Albert Y. Kim , Michelle Ross , Jon Wakefield , E. S. Venkatraman
Maintainer: Albert Y. Kim

Diff between SpatialEpi versions 1.1 dated 2013-01-05 and 1.2 dated 2014-05-02

 DESCRIPTION          |   20 +++++++++-----------
 MD5                  |   18 +++++++++++-------
 NAMESPACE            |   13 ++++++++++++-
 R/EBpostdens.R       |only
 R/EBpostthresh.R     |only
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 man/mapvariable.Rd   |    3 ++-
 man/plotmap.Rd       |    3 ++-
 12 files changed, 46 insertions(+), 27 deletions(-)

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Package rcppbugs updated to version 0.1.4.1 with previous version 0.1.4 dated 2013-08-28

Title: R binding for cppbugs
Description: R binding for cppbugs
Author: Whit Armstrong
Maintainer: Whit Armstrong

Diff between rcppbugs versions 0.1.4 dated 2013-08-28 and 0.1.4.1 dated 2014-05-02

 DESCRIPTION                       |   11 +++++------
 MD5                               |   10 +++++-----
 NAMESPACE                         |    2 ++
 src/Makevars                      |    2 +-
 src/Makevars.win                  |    4 ++--
 src/cppbugs/cppbugs/mcmc.math.hpp |    2 +-
 6 files changed, 16 insertions(+), 15 deletions(-)

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Package texreg updated to version 1.32 with previous version 1.31 dated 2014-02-13

Title: Conversion of R regression output to LaTeX or HTML tables.
Description: texreg converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented.
Author: Philip Leifeld
Maintainer: Philip Leifeld

Diff between texreg versions 1.31 dated 2014-02-13 and 1.32 dated 2014-05-02

 DESCRIPTION            |   14 +-
 MD5                    |   28 ++---
 NAMESPACE              |    3 
 R/extract.R            |  264 ++++++++++++++++++++++++++++++++++++++++++++++---
 R/internal.R           |   72 +++++++++++++
 R/texreg.R             |   27 +++--
 build/vignette.rds     |binary
 inst/doc/v55i08.R      |   46 ++++----
 inst/doc/v55i08.Rnw    |   13 +-
 inst/doc/v55i08.pdf    |binary
 man/extract-methods.Rd |   15 ++
 man/extract.Rd         |   23 +++-
 man/texreg.Rd          |    9 -
 vignettes/v55i08.Rnw   |   13 +-
 vignettes/v55i08.bib   |   12 +-
 15 files changed, 448 insertions(+), 91 deletions(-)

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New package stosim with initial version 0.0.11
Package: stosim
Type: Package
Title: Stochastic Simulator for Reliability Modeling of Repairable Systems
Version: 0.0.11
Date: 2014-5-1
Author: Jacob T. Ormerod
Maintainer: Jacob T. Ormerod
Description: A toolkit for Reliability Availability and Maintainability (RAM) modeling of industrial process systems.
License: GPL (>= 2)
LazyLoad: yes
Imports: Rcpp (>= 0.11.1)
Depends: tcltk2
LinkingTo: Rcpp
Repository: CRAN
Repository/R-Forge/Project: stosim
Repository/R-Forge/Revision: 26
Repository/R-Forge/DateTimeStamp: 2014-05-02 00:55:36
Date/Publication: 2014-05-02 07:13:28
Packaged: 2014-05-02 02:35:10 UTC; rforge
NeedsCompilation: yes

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Package sqlutils updated to version 1.1.2 with previous version 1.1.1 dated 2013-12-07

Title: Utilities for working with SQL files.
Description: This package provides utilities for working with a library of SQL files.
Author: Jason Bryer
Maintainer: Jason Bryer

Diff between sqlutils versions 1.1.1 dated 2013-12-07 and 1.1.2 dated 2014-05-02

 DESCRIPTION                         |   11 ++----
 MD5                                 |   64 ++++++++++++++++++------------------
 NAMESPACE                           |    5 ++
 NEWS                                |    9 +++--
 R/cacheQuery.r                      |    4 +-
 R/sqldoc.r                          |   19 +++++++++-
 R/sqlexec.R                         |    4 --
 R/sqlutils-package.r                |    3 +
 build/vignette.rds                  |binary
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 man/getQueries.Rd                   |    6 +--
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 man/is.null.string.Rd               |   10 ++---
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 man/parse.element.Rd                |   14 +++----
 man/parse.introduction.Rd           |   12 +++---
 man/print.Rd                        |    9 ++---
 man/recodeColumns.Rd                |   12 +++---
 man/sqlFile.Rd                      |    9 ++---
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 man/sqldoc.Rd                       |   12 +++---
 man/sqlexec.PostgreSQLConnection.Rd |   15 +++-----
 man/sqlexec.RMySQL.Rd               |   14 +++----
 man/sqlexec.RODBC.Rd                |   14 +++----
 man/sqlexec.Rd                      |   14 +++----
 man/sqlexec.SQLiteConnection.Rd     |   14 +++----
 man/sqlutils-package.Rd             |    5 +-
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 33 files changed, 222 insertions(+), 210 deletions(-)

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Package spocc updated to version 0.1.2 with previous version 0.1.0 dated 2014-03-05

Title: R interface to many species occurrence data sources
Description: A programmatic interface to many species occurrence data sources, including GBIF, USGS's BISON, iNaturalist, Berkeley Ecoinformatics Engine eBird, AntWeb, and more as they sources become easily available.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Ted Hart [aut]
Maintainer: Scott Chamberlain

Diff between spocc versions 0.1.0 dated 2014-03-05 and 0.1.2 dated 2014-05-02

 DESCRIPTION                     |   20 +++--
 MD5                             |   97 ++++++++++++++----------
 NAMESPACE                       |    6 +
 NEWS                            |   18 ++++
 R/clean_spocc.r                 |only
 R/fixnames.r                    |   13 +++
 R/mapgist.r                     |    2 
 R/mapleaflet.r                  |    6 -
 R/methods.r                     |   26 +++---
 R/occ.r                         |   20 +++--
 R/occ_to_sp.r                   |   10 +-
 R/util_github.r                 |    4 -
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 R/zzz.r                         |    6 -
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 man/basemaps.Rd                 |    1 
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 man/get_colors.Rd               |    8 +-
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 man/mapggplot.Rd                |    8 +-
 man/mapgist.Rd                  |   50 +++++-------
 man/mapleaflet.Rd               |   80 +++++++++-----------
 man/occ.Rd                      |  158 ++++++++++++++++++----------------------
 man/occ2df.Rd                   |    7 +
 man/occ2sp.Rd                   |   17 ++--
 man/occ_options.Rd              |   21 ++---
 man/occ_to_sp.Rd                |   21 +----
 man/occdat.Rd                   |   11 +-
 man/palettes.Rd                 |    1 
 man/spocc_blanktheme.Rd         |    1 
 man/spocc_capwords.Rd           |   10 +-
 man/spocc_colClasses.Rd         |    7 +
 man/spocc_commas_to_periods.Rd  |    3 
 man/spocc_create_gist.Rd        |   10 +-
 man/spocc_gbifxmlToDataFrame.Rd |    8 +-
 man/spocc_get_credentials.Rd    |    1 
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 man/spocc_parseresults.Rd       |    7 +
 man/spocc_rcharts_togeojson.Rd  |    7 +
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 48 files changed, 453 insertions(+), 431 deletions(-)

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New package SpecsVerification with initial version 0.1-1
Package: SpecsVerification
Version: 0.1-1
Date: 2014-04-30
Title: Forecast verification routines for the SPECS FP7 project
Authors@R: c(person("Stefan", "Siegert", role = c("aut", "cre"), email = "s.siegert@exeter.ac.uk"))
Maintainer: Stefan Siegert
Depends:
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Suggests:
License: GPL (>= 2)
Packaged: 2014-05-01 12:59:17 UTC; stefan
Author: Stefan Siegert [aut, cre]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-05-02 07:32:42

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Package RcppSMC updated to version 0.1.3 with previous version 0.1.2 dated 2014-02-06

Title: Rcpp bindings for Sequential Monte Carlo
Description: This package provides R with access to the Sequential Monte Carlo Template Classes by Johansen (Journal of Statistical Software, 2009, v30, i6). At present, two additional examples have been added, and the first example from the JSS paper has been extended. Further integration and extensions are planned.
Author: Dirk Eddelbuettel and Adam M. Johansen
Maintainer: Dirk Eddelbuettel

Diff between RcppSMC versions 0.1.2 dated 2014-02-06 and 0.1.3 dated 2014-05-02

 ChangeLog         |   13 ++++++++++++-
 DESCRIPTION       |    8 ++++----
 MD5               |   10 +++++-----
 cleanup           |    2 +-
 inst/NEWS.Rd      |    7 +++++++
 src/pflineart.cpp |    7 ++++++-
 6 files changed, 35 insertions(+), 12 deletions(-)

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New package pollstR with initial version 1.0-0
Package: pollstR
Title: R client for the Huffpost Pollster API
Description: An R interface to the Huffington Post Pollster API, which provides a programmatic interface to political polls.
Version: 1.0-0
Date: 2014-5-1
Authors@R: c(person("Jeffrey B.", "Arnold", email = "jeffrey.arnold@gmail.com", role = c("aut", "cre")), person("Thomas J.", "Leeper", role = c("aut"), email = "thosjleeper@gmail.com"))
Depends: R (>= 3.1.0)
Imports: httr, plyr, jsonlite
Suggests: knitr, dplyr, ggplot2, testthat
URL: https://github.com/rOpenGov/pollstR
BugReports: https://github.com/rOpenGov/pollstR/issues
VignetteBuilder: knitr
License: GPL-2
LazyLoad: yes
LazyData: true
Packaged: 2014-05-01 17:49:33 UTC; jrnold
Author: Jeffrey B. Arnold [aut, cre], Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-02 07:13:22

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New package phreeqc with initial version 1.0.0
Package: phreeqc
Version: 1.0.0
Title: R interface to the phreeqc geochemical modeling program
License: Unlimited
NeedsCompilation: yes
Depends: R (>= 2.10)
Author: David Parkhurst and C.A.J. Appelo
URL: http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc
Description: R interface to the PHREEQC program. PHREEQC is a geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of low-temperature aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations involving reversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and irreversible reactions, which include specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters, within specified compositional uncertainty limits.
Maintainer: Scott Charlton
LazyData: yes
Packaged: 2014-05-02 04:49:19 UTC; charlton
Repository: CRAN
Date/Publication: 2014-05-02 07:36:41

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Package NominalLogisticBiplot updated to version 0.2 with previous version 0.1 dated 2013-09-17

Title: Biplot representations of categorical data
Description: Analysis of a matrix of polytomous items using Nominal Logistic Biplots (NLB) according to Hernandez-Sanchez and Vicente-Villardon (2013). The NLB procedure extends the binary logistic biplot to nominal (polytomous) data. The individuals are represented as points on a plane and the variables are represented as convex prediction regions rather than vectors as in a classical or binary biplot. Using the methods from Computational Geometry, the set of prediction regions is converted to a set of points in such a way that the prediction for each individual is established by its closest "category point". Then interpretation is based on distances rather than on projections. In this package we implement the geometry of such a representation and construct computational algorithms for the estimation of parameters and the calculation of prediction regions.
Author: Julio Cesar Hernandez Sanchez, Jose Luis Vicente-Villardon
Maintainer: Julio Cesar Hernandez Sanchez

Diff between NominalLogisticBiplot versions 0.1 dated 2013-09-17 and 0.2 dated 2014-05-02

 DESCRIPTION                            |    8 -
 MD5                                    |   71 ++++++-----
 NAMESPACE                              |    3 
 R/Generators.R                         |   46 ++-----
 R/Nominal2Binary.R                     |    2 
 R/NominalDistances.R                   |    4 
 R/NominalLogBiplotEM.R                 |   77 ++++++++----
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 R/NominalMatrix2Binary.R               |    1 
 R/PCoA.R                               |    2 
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 man/summary.nominal.logistic.biplot.Rd |   12 +
 40 files changed, 558 insertions(+), 345 deletions(-)

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Package GeneFeST updated to version 1.0.1 with previous version 1.0.0 dated 2014-03-24

Title: Bayesian calculation of gene-specific FST from genomic SNP data
Description: GeneFeST is a genome scan method to detect outlier loci (genes) which are under balancing or directional selection.
Author: Bastian Pfeifer
Maintainer: Bastian Pfeifer

Diff between GeneFeST versions 1.0.0 dated 2014-03-24 and 1.0.1 dated 2014-05-02

 DESCRIPTION                |    6 +++---
 MD5                        |   14 +++++++-------
 R/slim.R                   |    9 +++++++--
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 inst/doc/Input_format.Rnw  |    2 +-
 inst/doc/Input_format.pdf  |binary
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 vignettes/Input_format.Rnw |    2 +-
 8 files changed, 40 insertions(+), 50 deletions(-)

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