Sat, 31 Jan 2015

Package wgaim updated to version 1.4-5 with previous version 1.4-3 dated 2014-09-03

Title: Whole Genome Average Interval Mapping for QTL Detection using Mixed Models
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor , Simon Diffey , Ari Verbyla and Brian Cullis .
Maintainer: Julian Taylor

Diff between wgaim versions 1.4-3 dated 2014-09-03 and 1.4-5 dated 2015-01-31

 wgaim-1.4-3/wgaim/R/wgaim7.R          |only
 wgaim-1.4-5/wgaim/DESCRIPTION         |   12 ++++++------
 wgaim-1.4-5/wgaim/MD5                 |   20 ++++++++++----------
 wgaim-1.4-5/wgaim/NAMESPACE           |    1 +
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 wgaim-1.4-5/wgaim/data/genoRxK.RData  |binary
 wgaim-1.4-5/wgaim/data/genoSxT.RData  |binary
 wgaim-1.4-5/wgaim/inst/NEWS.Rd        |    9 +++++++--
 wgaim-1.4-5/wgaim/inst/doc/wgaim.pdf  |binary
 wgaim-1.4-5/wgaim/man/cross2int.Rd    |   14 ++++++--------
 wgaim-1.4-5/wgaim/man/wgaim.asreml.Rd |    3 +--
 12 files changed, 31 insertions(+), 28 deletions(-)

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New package netassoc with initial version 0.4.1
Package: netassoc
Type: Package
Title: Inference of Species Associations from Co-occurrence Data
Version: 0.4.1
Date: 2015-01-29
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder
Description: Infers species associations from local and regional-scale co-occurrence data (species x site matrices)
License: GPL-3
Depends: igraph
Packaged: 2015-01-30 22:38:14 UTC; benjaminblonder
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-31 08:31:33

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Package mixlm updated to version 1.0.8.1 with previous version 1.0.8 dated 2015-01-21

Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre], Solve Sb [ctb], R-Core [ctb]
Maintainer: Kristian Hovde Liland

Diff between mixlm versions 1.0.8 dated 2015-01-21 and 1.0.8.1 dated 2015-01-31

 mixlm-1.0.8.1/mixlm/DESCRIPTION              |    8 
 mixlm-1.0.8.1/mixlm/MD5                      |   24 
 mixlm-1.0.8.1/mixlm/NAMESPACE                |   42 
 mixlm-1.0.8.1/mixlm/R/borrowed.R             |  480 ++---
 mixlm-1.0.8.1/mixlm/R/glm.R                  |  270 +--
 mixlm-1.0.8.1/mixlm/R/lm.R                   |  877 +++++-----
 mixlm-1.0.8.1/mixlm/R/mixlm.R                |   41 
 mixlm-1.0.8.1/mixlm/R/statistics.R           | 2319 +++++++++++++--------------
 mixlm-1.0.8.1/mixlm/R/utilities.R            |  214 +-
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 15 files changed, 2168 insertions(+), 2143 deletions(-)

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Fri, 30 Jan 2015

Package stylo updated to version 0.5.9 with previous version 0.5.8-2 dated 2014-10-19

Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder

Diff between stylo versions 0.5.8-2 dated 2014-10-19 and 0.5.9 dated 2015-01-30

 DESCRIPTION                |    8 ++++----
 MD5                        |   30 +++++++++++++++---------------
 NEWS                       |    9 +++++++++
 R/assign.plot.colors.R     |    2 +-
 R/classify.R               |    3 +--
 R/define.plot.area.R       |    2 +-
 R/draw.polygons.R          |    2 +-
 R/gui.classify.R           |   16 ++++++++--------
 R/gui.oppose.R             |    3 +--
 R/gui.stylo.R              |   16 ++++++++--------
 R/load.corpus.and.parse.R  |   10 ++++++----
 R/make.samples.R           |    2 +-
 R/oppose.R                 |    3 +--
 R/rolling.classify.r       |    1 -
 R/stylo.R                  |    3 +--
 R/stylo.default.settings.R |    6 ++----
 16 files changed, 60 insertions(+), 56 deletions(-)

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New package kissmig with initial version 1.0-3
Package: kissmig
Type: Package
Title: a Keep It Simple Species Migration Model
Version: 1.0-3
Date: 2014-12-09
Depends: raster, R (>= 2.15.0)
Authors@R: c( person("Michael P.", "Nobis", role = c("cre", "aut"), email = "michael.nobis@wsl.ch"), person("Signe", "Normand", role = "ctb"))
Author: Michael P. Nobis [cre, aut], Signe Normand [ctb]
Maintainer: Michael P. Nobis
Description: Simulating species migration and range dynamics under stable or changing environmental conditions based on a simple, raster-based, stochastic migration model. Providing accessibility for considering species migration in niche-based species distribution models.
License: GPL (>= 3)
URL: http://purl.oclc.org/wsl/kissmig
Packaged: 2014-12-09 12:18:20 UTC; nobis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-30 22:40:57

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New package fitbitScraper with initial version 0.1.1
Package: fitbitScraper
Title: Scrapes Data From Fitbit.com
Version: 0.1.1
Author: Cory Nissen [aut, cre]
Maintainer: Cory Nissen
Description: Scrapes data from fitbit.com. This does not use the official API, but instead uses the API that the web dashboard uses to generate the graphs displayed on the dashboard after login at www.fitbit.com.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: true
Imports: httr, stringr, RJSONIO
URL: https://github.com/corynissen/fitbitScraper
Packaged: 2015-01-24 23:28:43 UTC; c
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-30 22:56:39

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Package GSIF updated to version 0.4-4 with previous version 0.4-3 dated 2014-12-09

Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [ctb], Gerard Heuvelink [ctb], Brendan Malone [ctb]
Maintainer: Tomislav Hengl

Diff between GSIF versions 0.4-3 dated 2014-12-09 and 0.4-4 dated 2015-01-30

 DESCRIPTION            |   22 ++--
 MD5                    |   57 +++++-----
 NAMESPACE              |   11 --
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 31 files changed, 764 insertions(+), 676 deletions(-)

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Package copBasic updated to version 1.7.1 with previous version 1.7.0 dated 2015-01-03

Title: General Copula Theory and Many Utility Functions
Description: Extensive functions for copula computations and related mathematical operations are given that are oriented around the oft cited and fundamental copula theory described by Nelsen (2006), Joe (2015), and other selected works. The lower, upper, product, and select other copulas are implemented. Individual copula functional support is intentionally limited to keep the package focused on an API to general copula theory. Expressions available for an arbitrary copula include the diagonal of a copula, the survival copula, the dual of a copula, co-copula, and numerical copula density. Level curves (sets) are available. Horizontal and vertical copula sections and derivatives of such sections also are supported. The numerical derivatives of a copula are provided as well as inverses; functions for copula simulation thus are supported. Composition of copulas is provided: (1) composition of a single copula using two composition parameters, (2) composition of two copulas using two composition parameters, (3) composition of two copulas using four composition parameters, and (4) random variates of composited copulas. Characteristics of copulas include Kendall Tau, Spearman Rho, Gini Gamma, Blomqvist Beta, and Schweizer-Wolff Sigma, tail dependency, and tail order. Logical evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing also are available. The Kullback-Leibler divergence and Vuong's Procedure to support inference are available. Quantile and median regression for V with respect to U and U with respect to V is available. Empirical copulas (EC) are supported. ECs are dependent on gridded data structures for which generation capability is provided. The derivatives of the EC grid are computable. Also, the inverses of the derivatives, which are the conditional QDFs of copula sections also are computable. Median and quantile regression of an EC also is supported along with support for EC simulation of V conditional on U.
Author: William Asquith
Maintainer: William Asquith

Diff between copBasic versions 1.7.0 dated 2015-01-03 and 1.7.1 dated 2015-01-30

 ChangeLog     |    4 ++++
 DESCRIPTION   |    8 ++++----
 MD5           |    6 +++---
 inst/CITATION |   15 ++++++++-------
 4 files changed, 19 insertions(+), 14 deletions(-)

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New package EcoGenetics with initial version 1.0
Package: EcoGenetics
Type: Package
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Version: 1.0
Date: 2015-01-13
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser
Description: Analysis of phenotypic, genotypic, and environmental data with an object of class "ecogen", designed to make easy the integration of the available information from multiple sources. Extra functions are also included, such as conversion tools and processing methods for Landsat images.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 3.0), methods
Imports: adegenet, ggplot2, gstat, gstudio, hierfstat, party, raster, rgdal, rkt, sp, spdep, tcltk, vegan
Suggests: animation, ape, Geneland, seqinr
Collate: 'ZZZ.R' 'auxiliar.R' 'ecogen.definition.R' 'other.classes.R' 'coordinates.R' 'eco.2columns.R' 'eco.2geneland.R' 'eco.2genepop.R' 'eco.2gstudio.R' 'eco.2hierfstat.R' 'eco.NDVI.R' 'eco.NDVI.post.R' 'eco.R' 'eco.alfreq.R' 'eco.append.R' 'eco.association.R' 'eco.autocor.R' 'eco.boothet.R' 'eco.cbind.R' 'eco.char2num.R' 'eco.clear.R' 'eco.lmtree.R' 'eco.merge.R' 'eco.order.R' 'eco.pairtest.R' 'eco.post.geneland.R' 'eco.rarefact.R' 'eco.rbind.R' 'eco.remove.R' 'eco.rescale.R' 'eco.sortalleles.R' 'eco.subset.R' 'eco.theilsen.R' 'eco.variogram.R' 'environment.R' 'genotype.R' 'phenotype.R' 'structure.R' 'tab.R'
NeedsCompilation: no
Packaged: 2015-01-30 15:10:26 UTC; amadeus-PC
Repository: CRAN
Date/Publication: 2015-01-30 17:40:06

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Package shinyFiles updated to version 0.5.0 with previous version 0.4.0 dated 2014-09-23

Title: A server-side file system viewer for shiny
Description: Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location.
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen

Diff between shinyFiles versions 0.4.0 dated 2014-09-23 and 0.5.0 dated 2015-01-30

 DESCRIPTION              |   10 +++----
 MD5                      |   22 ++++++++--------
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 man/fileGetter.Rd        |    3 +-
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 man/parseFilePaths.Rd    |    3 +-
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 man/shinyFilesButton.Rd  |    3 +-
 man/shinyFilesExample.Rd |    3 +-
 12 files changed, 95 insertions(+), 38 deletions(-)

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New package ppmlasso with initial version 1.1
Package: ppmlasso
Type: Package
Title: Point Process Models with LASSO Penalties
Version: 1.1
Date: 2015-01-30
Author: Ian Renner
Maintainer: Ian Renner
Description: Toolkit for fitting point process models with sequences of LASSO penalties ("regularisation paths"). Regularisation paths of Poisson point process models or area-interaction models can be fitted with LASSO, adaptive LASSO or elastic net penalties. A number of criteria are available to judge the bias-variance tradeoff.
License: GPL-3
Depends: R (>= 3.0.0), spatstat (>= 1.40-0)
Imports: methods
Packaged: 2015-01-30 12:20:07 UTC; Gwen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-30 13:34:19

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Package mvoutlier updated to version 2.0.6 with previous version 2.0.5 dated 2014-06-23

Title: Multivariate outlier detection based on robust methods
Description: various methods for multivariate outlier detection.
Author: Peter Filzmoser and Moritz Gschwandtner
Maintainer: Peter Filzmoser

Diff between mvoutlier versions 2.0.5 dated 2014-06-23 and 2.0.6 dated 2015-01-30

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New package GOplot with initial version 1.0
Package: GOplot
Type: Package
Title: Visualization Of Functional Analysis Data
Version: 1.0
Date: 2015-01-27
Author: Wencke Walter, Fatima Sanchez-Cabo
Maintainer: Wencke Walter
Description: Implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot).
Depends: ggplot2, ggdendro, grid, gridExtra, RColorBrewer, R (>= 3.0.3)
License: GPL-2
Suggests: knitr
VignetteBuilder: knitr
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-01-30 08:12:02 UTC; wwalter
Repository: CRAN
Date/Publication: 2015-01-30 12:56:15

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Package npIntFactRep (with last version 1.0) was removed from CRAN

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

2015-01-21 1.0

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Package compLasso (with last version 0.0-1) was removed from CRAN

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

2015-01-21 0.0-1

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Package SmarterPoland updated to version 1.5 with previous version 1.2 dated 2013-03-18

Title: Tools for Accessing Various Datasets Developed by the Foundation SmarterPoland.pl
Description: Tools for accessing and processing datasets presented on the blog SmarterPoland.pl. Among all: functions for downloading data from eurostat database, coordinates from Google Maps and data from GUS (Central Statistical Office of Poland).
Author: Przemyslaw Biecek (Foundation SmarterPoland.pl)
Maintainer: Przemyslaw Biecek

Diff between SmarterPoland versions 1.2 dated 2013-03-18 and 1.5 dated 2015-01-30

 DESCRIPTION                  |   16 +++---
 MD5                          |   42 +++++++++++-------
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Package rockchalk updated to version 1.8.91 with previous version 1.8.86 dated 2014-08-13

Title: Regression Estimation and Presentation
Description: A collection of functions for ease of presentation and interpretation of regression analysis. These functions are used to produce the statistics lectures in http://pj.freefaculty.org/guides. There are functions to explore the effect (or lack thereof) from "mean centering," "residual centering", and standardization. The vignette "rockchalk" offers a fairly comprehensive overview. The vignette "Rstyle" has advice about coding in R. See the outreg function for a convenient way to generate regression models for reports. For nice, easy to use pictures, see plotSlopes, plotCurves, plotPlane. The package title "rockchalk" refers to our school motto, "Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson
Maintainer: Paul E. Johnson

Diff between rockchalk versions 1.8.86 dated 2014-08-13 and 1.8.91 dated 2015-01-30

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New package randomizr with initial version 0.2.0
Package: randomizr
Title: Easy to Use Tools for Common Forms of Random Assignment
Version: 0.2.0
Authors@R: person("Alexander", "Coppock", role = c("aut", "cre"), email = "ac3242@columbia.edu")
Description: Generates random assignments for common experimental designs: simple, complete, blocked, and clustered.
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
Packaged: 2015-01-29 21:46:41 UTC; Alex
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-30 08:53:39

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Package P2C2M updated to version 0.6 with previous version 0.5 dated 2014-10-24

Title: Posterior Predictive Checks of Coalescent Models
Description: P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST or *BEAST. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, the installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is required.
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl

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Package DiagrammeR updated to version 0.4 with previous version 0.1 dated 2015-01-09

Title: Create Diagrams and Flowcharts Using R
Description: With the DiagrammeR package, you can create diagrams and flowcharts using R. Markdown-like text is used to describe a diagram and, by doing this in R, we can also add some R code into the mix and integrate these diagrams in the R console, through R Markdown, and in shiny apps.
Author: knsv [aut, cph] (mermaid.js library in htmlwidgets/lib, http://github.com/knsv/mermaid/), Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib, http://github.com/cpettitt/dagre-d3), mdaines [aut, cph] (viz.js library in htmlwidgets/lib, http://github.com/mdaines/viz.js/), Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone

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Package dataRetrieval updated to version 2.1.1 with previous version 2.1.0 dated 2014-12-17

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from the National Water Information Services (NWIS) tools found here: http://waterservices.usgs.gov/ Both EPA and USGS water quality data are obtained from the Water Quality Portal found here: http://www.waterqualitydata.us/portal.jsp
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut]
Maintainer: Laura DeCicco

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Permanent link

Package climdex.pcic updated to version 1.1-5 with previous version 1.1-4 dated 2014-11-19

Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of extreme climate indices.
Author: David Bronaugh for the Pacific Climate Impacts Consortium
Maintainer: James Hiebert

Diff between climdex.pcic versions 1.1-4 dated 2014-11-19 and 1.1-5 dated 2015-01-30

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Permanent link

Package circlize updated to version 0.2.2 with previous version 0.2.1 dated 2015-01-08

Title: Circular Visualization in R
Description: This package implements circular visualization (http://circos.ca/) in R. Due to the natural born feature of R to draw statistical graphics, this package can provide a more general and flexible way to visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between circlize versions 0.2.1 dated 2015-01-08 and 0.2.2 dated 2015-01-30

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Package brewdata updated to version 0.4 with previous version 0.3 dated 2015-01-28

Title: Extracting Usable Data from the Grad Cafe Results Search
Description: Retrieves and parses graduate admissions survey data from the Grad Cafe website (http://thegradcafe.com).
Author: Nathan Welch
Maintainer: Nathan Welch

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Thu, 29 Jan 2015

New package StochKit2R with initial version 0.2
Package: StochKit2R
Type: Package
Title: Efficient Discrete Stochastic Simulation
Version: 0.2
Date: 2015-01-29
Author: Kevin R. Sanft
Maintainer: Kevin R. Sanft
Copyright: Kevin R. Sanft, Linda R. Petzold
Description: Efficient discrete stochastic simulation using the Gillespie algorithm (aka the Stochastic Simulation Algorithm or SSA) and adaptive tau-leaping. It provides an R interface to simulation algorithms and it provides functions for visualizing (plotting) simulation output.
License: GPL-3
Imports: Rcpp (>= 0.11.2), reshape, ggplot2, XML
LinkingTo: Rcpp, BH
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2015-01-29 17:24:12 UTC; kevinsanft
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-29 21:39:56

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Package portfolio updated to version 0.4-7 with previous version 0.4-6 dated 2013-07-09

Title: Analysing equity portfolios
Description: Classes for analysing and implementing equity portfolios.
Author: Jeff Enos and David Kane , with contributions from Daniel Gerlanc and Kyle Campbell
Maintainer: Daniel Gerlanc

Diff between portfolio versions 0.4-6 dated 2013-07-09 and 0.4-7 dated 2015-01-29

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New package devEMF with initial version 2.0
Package: devEMF
Type: Package
Title: EMF Graphics Output Device
Version: 2.0
Date: 2015-1-29
Author: Philip Johnson
Maintainer: Philip Johnson
Depends: R (>= 2.10.1)
SystemRequirements: Xft (only needed for platforms other than OSX and Windows)
Description: Output graphics to EMF (enhanced metafile).
License: GPL-3
Packaged: 2015-01-29 18:45:58 UTC; pjohnson
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-29 20:37:36

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Permanent link

Package AGSDest updated to version 2.2 with previous version 2.1 dated 2013-11-06

Title: Estimation in Adaptive Group Sequential Trials
Description: Calculation of repeated confidence intervals as well as confidence intervals based on the stage-wise ordering in group sequential designs and adaptive group sequential designs. For adaptive group sequential designs the confidence intervals are based on the conditional rejection probability principle. Currently the procedures do not support the use of futility boundaries or more than one adaptive interim analysis.
Author: Niklas Hack, Werner Brannath, Matthias Brueckner
Maintainer: Matthias Brueckner

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Package StatMatch updated to version 1.2.3 with previous version 1.2.2 dated 2014-06-19

Title: Statistical Matching
Description: Integration of two data sources referred to the same target population which share a number of common variables (aka data fusion). Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio

Diff between StatMatch versions 1.2.2 dated 2014-06-19 and 1.2.3 dated 2015-01-29

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 R/RANDwNND.hotdeck.r                              |    4 -
 R/mixed.mtc.R                                     |    2 
 R/rankNND_hotdeck.R                               |    2 
 build/vignette.rds                                |binary
 inst/doc/Statistical_Matching_with_StatMatch.R    |   56 +++++++++++-----------
 inst/doc/Statistical_Matching_with_StatMatch.Rnw  |   19 ++++---
 inst/doc/Statistical_Matching_with_StatMatch.pdf  |binary
 man/Fbwidths.by.x.Rd                              |   21 +++-----
 man/Frechet.bounds.cat.Rd                         |    6 +-
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 man/StatMatch-package.Rd                          |    2 
 man/mixed.mtc.Rd                                  |    1 
 vignettes/Statistical_Matching_with_StatMatch.Rnw |   19 ++++---
 20 files changed, 114 insertions(+), 119 deletions(-)

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New package elastic with initial version 0.3.0
Package: elastic
Title: General Purpose Interface to Elasticsearch
Description: Connect to Elasticsearch, a NoSQL database built on the Java Virtual Machine. Interacts with the Elasticsearch HTTP API (http://elasticsearch.org), including functions for setting connection details to Elasticsearch instances, loading bulk data, searching for documents with both HTTP query variables and JSON based body requests. In addition, elastic provides functions for interacting with APIs for indices, documents, nodes, clusters, an interface to the cat API, and more.
Version: 0.3.0
Date: 2015-01-29
License: MIT + file LICENSE
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com")
URL: https://github.com/sckott/elastic
BugReports: https://github.com/sckott/elastic/issues
VignetteBuilder: knitr
Imports: httr, jsonlite
Suggests: testthat, roxygen2, knitr
Packaged: 2015-01-29 15:54:32 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 18:08:01

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New package DVHmetrics with initial version 0.1
Package: DVHmetrics
Type: Package
Title: Analyze Dose-Volume Histograms and Check Constraints
Version: 0.1
Date: 2015-01-29
Authors@R: c(person("Daniel", "Wollschlaeger", role = c("aut", "cre"), email = "wollschlaeger@uni-mainz.de"), person("Heiko", "Karle", role="aut"), person("Heinz", "Schmidberger", role="ctb"))
Depends: R (>= 3.0.0)
Imports: ggplot2, reshape2, grid, shiny
Suggests: knitr
VignetteBuilder: knitr
LazyData: yes
Description: Functionality for analyzing dose-volume histograms (DVH) in radiation oncology: Read DVH text files, calculate DVH metrics, show DVH diagrams, check and visualize quality assurance constraints for the DVH. Includes web-based graphical user interface.
License: GPL (>= 2)
URL: https://github.com/dwoll/DVHmetrics/
NeedsCompilation: no
Packaged: 2015-01-29 15:17:47 UTC; dwollsch
Author: Daniel Wollschlaeger [aut, cre], Heiko Karle [aut], Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger
Repository: CRAN
Date/Publication: 2015-01-29 18:07:24

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New package cchs with initial version 0.1.0
Package: cchs
Type: Package
Title: Cox Model for Case-Cohort Data with Stratified Subcohort-Selection
Version: 0.1.0
Date: 2015-01-29
Author: E. Jones
Maintainer: E. Jones
Description: Contains a function, also called cchs, that calculates Estimator III of Borgan et al (2000), Exposure-stratified Case-cohort Designs. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
License: GPL-3
Depends: R (>= 2.15.0), survival (>= 2.36-12)
LazyData: yes
Packaged: 2015-01-29 15:12:28 UTC; anon
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 18:00:19

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Package biotools updated to version 2.0 with previous version 1.2 dated 2014-05-25

Title: Tools for Biometry and Applied Statistics in Agricultural Science
Description: Tools designed to perform and work with cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations.
Author: Anderson Rodrigo da Silva
Maintainer: Anderson Rodrigo da Silva

Diff between biotools versions 1.2 dated 2014-05-25 and 2.0 dated 2015-01-29

 DESCRIPTION             |   14 +++++++-------
 MD5                     |   23 +++++++++++++----------
 NAMESPACE               |    2 ++
 NEWS                    |   26 ++++++++++++++++++++------
 R/D2.disc.R             |   34 ++++++++++++++++++++++++++++++++++
 R/boxM.R                |    5 +++--
 R/cov2pcov.R            |only
 R/samplesize.R          |    2 +-
 R/tocher.R              |   10 ++++++++--
 man/biotools-package.Rd |   10 +++++-----
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 man/samplesize.Rd       |    4 ++--
 man/tocher.Rd           |    1 +
 14 files changed, 96 insertions(+), 35 deletions(-)

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Package GetoptLong updated to version 0.0.9 with previous version 0.0.8 dated 2014-11-05

Title: Parsing Command-line Arguments and Variable Interpolation
Description: Parsing command-line arguments by Perl module Getopt::Long. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GetoptLong versions 0.0.8 dated 2014-11-05 and 0.0.9 dated 2015-01-29

 DESCRIPTION                          |   10 ++++----
 MD5                                  |   24 +++++++++----------
 NEWS                                 |    5 ++++
 build/vignette.rds                   |binary
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 inst/doc/GetoptLong.pdf              |binary
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 inst/doc/variable_interpolation.pdf  |binary
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 vignettes/variable_interpolation.Rnw |    4 +--
 13 files changed, 85 insertions(+), 38 deletions(-)

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Package cluster updated to version 2.0.0 with previous version 1.15.3 dated 2014-09-04

Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster Analysis Methods. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990)
Author: Martin Maechler [aut, cre], Peter Rousseeuw [aut] (Fortran original), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)), Matthias Studer [ctb], Pierre Roudier [ctb]
Maintainer: Martin Maechler

Diff between cluster versions 1.15.3 dated 2014-09-04 and 2.0.0 dated 2015-01-29

 cluster-1.15.3/cluster/man/pltree.twins.Rd                     |only
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 cluster-2.0.0/cluster/R/diana.q                                |   11 
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 cluster-2.0.0/cluster/R/pam.q                                  |   95 ++-
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 cluster-2.0.0/cluster/inst/po/fr/LC_MESSAGES/R-cluster.mo      |binary
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 cluster-2.0.0/cluster/man/agnes.Rd                             |    4 
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 cluster-2.0.0/cluster/man/pltree.Rd                            |   61 +-
 cluster-2.0.0/cluster/man/pluton.Rd                            |    6 
 cluster-2.0.0/cluster/po/R-cluster.pot                         |    7 
 cluster-2.0.0/cluster/po/R-de.po                               |   16 
 cluster-2.0.0/cluster/po/R-fr.po                               |    5 
 cluster-2.0.0/cluster/po/R-pl.po                               |    5 
 cluster-2.0.0/cluster/po/cluster.pot                           |   14 
 cluster-2.0.0/cluster/src/clara.c                              |    6 
 cluster-2.0.0/cluster/src/cluster.h                            |   22 
 cluster-2.0.0/cluster/src/dysta.f                              |    4 
 cluster-2.0.0/cluster/src/fanny.c                              |   20 
 cluster-2.0.0/cluster/src/init.c                               |   13 
 cluster-2.0.0/cluster/src/pam.c                                |  293 ++++++++--
 cluster-2.0.0/cluster/src/twins.c                              |  127 +---
 cluster-2.0.0/cluster/tests/agnes-ex.R                         |   12 
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 cluster-2.0.0/cluster/tests/clara-ex.R                         |   23 
 cluster-2.0.0/cluster/tests/clara.Rout.save                    |   11 
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 44 files changed, 790 insertions(+), 451 deletions(-)

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New package ppiPre with initial version 1.6
Package: ppiPre
Type: Package
Title: Predict protein-protein interactions based on functional and topological similarities.
Version: 1.6
Date: 2015-01-25
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun, with contributions from Guangchuang Yu.
Maintainer: Yue Deng
Description: This package provides functions for computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
License: GPL-2
LazyLoad: yes
Depends: R (>= 3.0.0)
Imports: AnnotationDbi, igraph, e1071, GOSemSim, GO.db
Enhances: KEGG.db, org.Hs.eg.db, org.Sc.sgd.db, org.Ag.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Xl.eg.db
NeedsCompilation: no
Packaged: 2015-01-29 10:13:00 UTC; Administrator
X-CRAN-Comment: Earlier versions were removed as source code had been copied uncredited.
Repository: CRAN
Date/Publication: 2015-01-29 11:45:23

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New package mousetrack with initial version 1.0.0
Package: mousetrack
Type: Package
Title: Mouse-Tracking Measures from Trajectory Data
Version: 1.0.0
Date: 2015-01-29
Author: Moreno I. Coco and Nicholas D. Duran with contributions of Rick Dale, Denis O'Hora and Michael J. Spivey.
Maintainer: Moreno I. Coco
Description: Extract from two-dimensional x-y coordinates of an arm-reaching trajectory, several dependent measures such as area under the curve, latency to start the movement, x-flips, etc.; which characterize the action-dynamics of the response. Mainly developed to analyze data coming from mouse-tracking experiments.
License: GPL (>= 2)
Depends: R (>= 3.0.0), pracma
Collate: 'angdiffvec.R' 'areaunder.R' 'getmouseDV.R' 'interpltraj.R' 'makerun.R' 'maxdev.R' 'pathoffset.R' 'sampen.R' 'sampenc.R' 'sampense.R' 'trim0.R' 'trim1.R' 'velaj.R' 'xflip.R'
Packaged: 2015-01-29 10:21:39 UTC; root
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 11:43:37

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New package roughrf with initial version 1.0
Package: roughrf
Type: Package
Title: Roughened Random Forests for Binary Classification
Version: 1.0
Date: 2015-01-28
Author: Kuangnan Xiong
Maintainer: Kuangnan Xiong
Depends: R (>= 2.5.0), randomForest, mice, nnet
Suggests: MASS, caTools
Description: A set of functions to support Xiong K, 'Roughened Random Forests for Binary Classification' (2014). The functions include RRFA, RRFB, RRFC1-RRFC7, RRFD and RRFE. RRFB and RRFC6 are usually recommended. RRFB is much faster than RRFC6.
License: GPL (>= 2)
URL: http://pqdtopen.proquest.com/pqdtopen/doc/1554346548.html?FMT=ABS
Packaged: 2015-01-29 06:58:24 UTC; LAPTOP15
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 11:08:31

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Package Luminescence updated to version 0.4.1 with previous version 0.4.0 dated 2014-12-18

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

Diff between Luminescence versions 0.4.0 dated 2014-12-18 and 0.4.1 dated 2015-01-29

 DESCRIPTION                      |   17 
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 NAMESPACE                        |    1 
 NEWS                             |  124 ++++++
 R/RLum.Analysis-class.R          |   64 ++-
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 R/RisoeBINfileData-class.R       |   24 -
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 R/analyse_SAR.CWOSL.R            |  136 ++++---
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 36 files changed, 1601 insertions(+), 718 deletions(-)

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Package teigen updated to version 2.0.8 with previous version 2.0.7 dated 2014-08-19

Title: Model-Based Clustering and Classification with the Multivariate t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews

Diff between teigen versions 2.0.7 dated 2014-08-19 and 2.0.8 dated 2015-01-29

 ChangeLog              |   10 +++++++---
 DESCRIPTION            |   12 ++++++------
 MD5                    |   20 ++++++++++----------
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 11 files changed, 38 insertions(+), 29 deletions(-)

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New package divo with initial version 0.1
Package: divo
Version: 0.1
Type: Package
Date: 2015-01-28
Title: Tools for Analysis of Diversity and Similarity in Biological Systems
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak
Depends: R (>= 3.1.0), RcppCNPy, cluster
SystemRequirements: Python (>=2.76), NumPy
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
License: GPL (>= 2)
Packaged: 2015-01-29 03:22:30 UTC; Maciej
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-29 07:24:08

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Wed, 28 Jan 2015

Package packrat updated to version 0.4.3 with previous version 0.4.2-1 dated 2014-12-16

Title: A Dependency Management System for Projects and their R Package Dependencies
Description: A tool for managing the R packages your project depends on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey

Diff between packrat versions 0.4.2-1 dated 2014-12-16 and 0.4.3 dated 2015-01-28

 DESCRIPTION                    |    8 +--
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New package partialAR with initial version 1.0.3
Package: partialAR
Type: Package
Title: Partial Autoregression
Version: 1.0.3
Date: 2015-01-12
Author: Matthew Clegg
Maintainer: Matthew Clegg
Description: Fits time series models which consist of a sum of a permanent and a transient component.
License: GPL-2 | GPL-3
Imports: Rcpp (>= 0.11.2), zoo, parallel, ggplot2, grid, MASS, tseries, data.table, FKF, urca, plot3D
Suggests: egcm, TTR
LinkingTo: Rcpp
Packaged: 2015-01-28 22:43:42 UTC; matthewclegg
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-29 00:25:11

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Package metaMA updated to version 3.1.2 with previous version 3.1.1 dated 2015-01-26

Title: Meta-analysis for MicroArrays
Description: Combines either p-values or modified effect sizes from different studies to find differentially expressed genes
Author: Guillemette Marot
Maintainer: Guillemette Marot

Diff between metaMA versions 3.1.1 dated 2015-01-26 and 3.1.2 dated 2015-01-28

 DESCRIPTION           |   10 +-
 MD5                   |   14 +--
 inst/NEWS             |    4 
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 inst/doc/metaMA.pdf   |binary
 man/metaMA-package.Rd |    4 
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 8 files changed, 198 insertions(+), 196 deletions(-)

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Package marmap updated to version 0.9.2 with previous version 0.9.1 dated 2014-12-16

Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante

Diff between marmap versions 0.9.1 dated 2014-12-16 and 0.9.2 dated 2015-01-28

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Package GlobalOptions updated to version 0.0.6 with previous version 0.0.5 dated 2014-12-24

Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GlobalOptions versions 0.0.5 dated 2014-12-24 and 0.0.6 dated 2015-01-28

 GlobalOptions-0.0.5/GlobalOptions/inst/tests/package1         |only
 GlobalOptions-0.0.5/GlobalOptions/inst/tests/package2         |only
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 GlobalOptions-0.0.6/GlobalOptions/vignettes/GlobalOptions.Rnw |   28 
 14 files changed, 170 insertions(+), 388 deletions(-)

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New package compareC with initial version 1.3.1
Package: compareC
Type: Package
Title: Compare Two Correlated C Indices with Right-censored Survival Outcome
Version: 1.3.1
Date: 2014-12-18
Author: Le Kang, Weijie Chen
Maintainer: Le Kang
Description: Proposed by Harrell, the C index or concordance C, is considered an overall measure of discrimination in survival analysis between a survival outcome that is possibly right censored and a predictive-score variable, which can represent a measured biomarker or a composite-score output from an algorithm that combines multiple biomarkers. This package aims to statistically compare two C indices with right-censored survival outcome, which commonly arise from a paired design and thus resulting two correlated C indices.
License: GPL (>= 2.0)
Packaged: 2015-01-28 20:34:48 UTC; lkang
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-28 23:45:51

More information about compareC at CRAN
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Package visualFields updated to version 0.4.2 with previous version 0.4 dated 2014-03-03

Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch
Maintainer: Ivan Marin-Franch

Diff between visualFields versions 0.4 dated 2014-03-03 and 0.4.2 dated 2015-01-28

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Package SMNCensReg updated to version 3.0 with previous version 2.4 dated 2014-07-17

Title: Fitting Univariate Censored Regression Model Under the Family of Scale Mixture of Normal Distributions
Description: Fit univariate right, left or interval censored regression model under the scale mixture of normal distributions
Author: Aldo M. Garay , Monique Bettio Massuia and Victor Lachos
Maintainer: Aldo M. Garay

Diff between SMNCensReg versions 2.4 dated 2014-07-17 and 3.0 dated 2015-01-28

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Package plotKML updated to version 0.5-0 with previous version 0.4-8 dated 2014-12-09

Title: Visualization of Spatial and Spatio-temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl

Diff between plotKML versions 0.4-8 dated 2014-12-09 and 0.5-0 dated 2015-01-28

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Package MarkowitzR updated to version 0.1502 with previous version 0.1402 dated 2014-02-12

Title: Statistical Significance of the Markowitz Portfolio
Description: a collection of tools for analyzing significance of Markowitz portfolios.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav

Diff between MarkowitzR versions 0.1402 dated 2014-02-12 and 0.1502 dated 2015-01-28

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Package LaF updated to version 0.6.2 with previous version 0.6.1 dated 2014-04-21

Title: Fast access to large ASCII files
Description: Methods for fast access to large ASCII files. Currently the following file formats are supported: comma separated format (csv) and fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. Methods are provided to access and process files blockwise. Furthermore, an opened file can be accessed as one would an ordinary data.frame. The LaF vignette gives an overview of the functionality provided.
Author: Jan van der Laan
Maintainer: Jan van der Laan

Diff between LaF versions 0.6.1 dated 2014-04-21 and 0.6.2 dated 2015-01-28

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More information about LaF at CRAN
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Package KFKSDS updated to version 1.6 with previous version 1.5 dated 2014-07-27

Title: Kalman Filter, Smoother and Disturbance Smoother
Description: Naive implementation of the Kalman filter, smoother and disturbance smoother for state space models.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between KFKSDS versions 1.5 dated 2014-07-27 and 1.6 dated 2015-01-28

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Package CpGassoc updated to version 2.50 with previous version 2.11 dated 2014-01-10

Title: Association Between Methylation and a Phenotype of Interest
Description: Is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. Also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.
Author: Barfield, R., Conneely, K., Kilaru,V
Maintainer: R Barfield

Diff between CpGassoc versions 2.11 dated 2014-01-10 and 2.50 dated 2015-01-28

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More information about CpGassoc at CRAN
Permanent link

Package stochvol updated to version 1.0.0 with previous version 0.9-1 dated 2014-12-27

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner

Diff between stochvol versions 0.9-1 dated 2014-12-27 and 1.0.0 dated 2015-01-28

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More information about stochvol at CRAN
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Package kedd updated to version 1.0.2 with previous version 1.0.1 dated 2014-08-18

Title: Kernel Estimator and Bandwidth Selection for Density and its Derivatives
Description: Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
Author: Arsalane Chouaib Guidoum
Maintainer: Arsalane Chouaib Guidoum

Diff between kedd versions 1.0.1 dated 2014-08-18 and 1.0.2 dated 2015-01-28

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Package VineCopula updated to version 1.4 with previous version 1.3 dated 2014-04-22

Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package CDVine are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler
Maintainer: Tobias Erhardt

Diff between VineCopula versions 1.3 dated 2014-04-22 and 1.4 dated 2015-01-28

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More information about VineCopula at CRAN
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Package RInside updated to version 0.2.12 with previous version 0.2.11 dated 2014-02-12

Title: C++ Classes to Embed R in C++ Applications
Description: C++ classes to embed R in C++ applications The RInside packages makes it easier to have 'R inside' your C++ application by providing a C++ wrapper class providing the R interpreter. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the eight subdirectories of the examples/ directory of the installed package: standard, mpi (for parallel computing) qt (showing how to embed RInside inside a Qt GUI application), wt (showing how to build a 'web-application' using the Wt toolkit), armadillo (for RInside use with RcppArmadillo) and eigen (for RInside use with RcppEigen). The example use GNUmakefile(s) with GNU extensions, so a GNU make is required (and will use the GNUmakefile automatically). Doxygen-generated documentation of the C++ classes is available at the RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel

Diff between RInside versions 0.2.11 dated 2014-02-12 and 0.2.12 dated 2015-01-28

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More information about RInside at CRAN
Permanent link

New package rglobi with initial version 0.2.4
Package: rglobi
Type: Package
Title: R interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI). GloBI provides access to spatial-temporal species interaction records from source all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. In addition, it supports Cypher, a graph query language, to allow for executing custom queries on the GloBI aggregate species interaction dataset.
Version: 0.2.4
Date: 2015-01-27
Authors@R: c(person("Jorrit", "Poelen", role = c("aut", "cre"), email = "jhpoelen@xs4all.nl"), person("Stephen", "Gosnell", role = "aut", email = "stephen.gosnell@baruch.cuny.edu"), person("Sergey", "Slyusarev", role = "aut", email = "cph.lmy@gmail.com"))
URL: https://github.com/ropensci/rglobi
BugReports: https://github.com/ropensci/rglobi/issues
VignetteBuilder: knitr
Depends: R (>= 3.0.1)
License: MIT + file LICENSE
Imports: rjson (>= 0.2.13), RCurl
Suggests: testthat, knitr
Packaged: 2015-01-28 07:47:36 UTC; jorrit
Author: Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-28 11:31:24

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Package MVN updated to version 3.8 with previous version 3.7 dated 2014-11-16

Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz

Diff between MVN versions 3.7 dated 2014-11-16 and 3.8 dated 2015-01-28

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 16 files changed, 982 insertions(+), 528 deletions(-)

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New package flower with initial version 1.0
Package: flower
Type: Package
Title: Tools for characterizing flowering traits
Version: 1.0
Date: 2015-01-23
Author: Xie WANG
Maintainer: Xie WANG
Description: Flowering is an important life history trait of flowering plants. It has been mainly analyzed with respect to flowering onset and duration of flowering. This tools provide some functions to compute the temporal distribution of an flowering individual related to other population members. fCV() measures the temporal variation in flowering. RIind() measures the rank order of flowering for individual plants within a population. SI(), SI2(), SI3(), and SI4() calculate flowering synchrony with different methods.
License: GPL (>= 1.0)
Packaged: 2015-01-28 01:47:26 UTC; Wangxie
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-28 12:18:13

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Package HTSDiff (with last version 1.0.5) was removed from CRAN

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

2014-10-29 1.0.5
2014-07-28 1.0.2
2013-12-10 1.0.1
2013-09-25 1.0.0

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Package SLHD updated to version 2.1-1 with previous version 1.2-1 dated 2013-05-14

Title: Maximin-Distance (Sliced) Latin Hypercube Designs
Description: Generate the optimal Latin Hypercube Designs (LHDs) for computer experiments with quantitative factors and the optimal Sliced Latin Hypercube Designs (SLHDs) for computer experiments with both quantitative and qualitative factors. Details of the algorithm can be found in Ba, S., Brenneman, W. A. and Myers, W. R. (2015), "Optimal Sliced Latin Hypercube Designs," Technometrics. Important function in this package is "maximinSLHD".
Author: Shan Ba
Maintainer: Shan Ba

Diff between SLHD versions 1.2-1 dated 2013-05-14 and 2.1-1 dated 2015-01-28

 DESCRIPTION         |   16 ++-----
 MD5                 |   12 ++---
 NAMESPACE           |    2 
 R/maximinSLHD.R     |   19 +++-----
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 7 files changed, 85 insertions(+), 108 deletions(-)

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Package rvalues updated to version 0.3 with previous version 0.2 dated 2014-07-24

Title: R-values for Ranking in High-Dimensional Settings
Description: A collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
Author: Nicholas Henderson and Michael Newton
Maintainer: Nicholas Henderson

Diff between rvalues versions 0.2 dated 2014-07-24 and 0.3 dated 2015-01-28

 DESCRIPTION        |   14 +++++-----
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New package rLTP with initial version 0.1
Package: rLTP
Title: R interface to LTP-Cloud service
Description: R interface to LTP-Cloud service for Natural Language Processing in Chinese. For more details please visit http://www.ltp-cloud.com/. Visit https://github.com/hetong007/rLTP for up-to-date version.
Version: 0.1
Author: Tong He
Maintainer: Tong He
BugReports: https://github.com/hetong007/rLTP/issues
Depends: R (>= 3.0.2),RCurl
License: LGPL
LazyData: true
Packaged: 2015-01-27 23:27:21 UTC; hetongh
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-28 07:43:17

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Package RandomFields updated to version 3.0.60 with previous version 3.0.59 dated 2015-01-27

Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather

Diff between RandomFields versions 3.0.59 dated 2015-01-27 and 3.0.60 dated 2015-01-28

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 38 files changed, 506 insertions(+), 458 deletions(-)

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New package protoclust with initial version 1.4
Package: protoclust
Type: Package
Title: Hierarchical Clustering with Prototypes
Version: 1.4
Date: 2015-01-26
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien
Description: Performs minimax linkage hierarchical clustering. Every cluster has an associated prototype element that represents that cluster as described in Bien, J., and Tibshirani, R. (2011), "Hierarchical Clustering with Prototypes via Minimax Linkage," accepted for publication in The Journal of the American Statistical Association, DOI: 10.1198/jasa.2011.tm10183.
License: GPL-2
LazyLoad: yes
Packaged: 2015-01-27 20:50:17 UTC; jbien
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-01-28 07:58:35

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Package numbers updated to version 0.5-2 with previous version 0.4-5 dated 2014-01-08

Title: Number-theoretic Functions
Description: Provides some number-theoretic functions for R.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers

Diff between numbers versions 0.4-5 dated 2014-01-08 and 0.5-2 dated 2015-01-28

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Package NeuralNetTools updated to version 1.0.1 with previous version 1.0.0 dated 2014-12-16

Title: Visualization and Analysis Tools for Neural Networks
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck

Diff between NeuralNetTools versions 1.0.0 dated 2014-12-16 and 1.0.1 dated 2015-01-28

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 14 files changed, 105 insertions(+), 93 deletions(-)

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Package fanplot updated to version 3.4.0 with previous version 3.3 dated 2014-08-01

Title: Visualisation of Sequential Probability Distributions Using Fan Charts
Description: Visualise sequential distributions using a range of plotting styles. Sequential distribution data can be input as either simulations or values corresponding to percentiles over time. Plots are added to existing graphic devices using the fan function. Users can choose from four different styles, including fan chart type plots, where a set of coloured polygon, with shadings corresponding to the percentile values are layered to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel"

Diff between fanplot versions 3.3 dated 2014-08-01 and 3.4.0 dated 2015-01-28

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New package decode with initial version 1.0
Package: decode
Title: Differential Co-expression and Differential Expression Analysis
Version: 1.0
Authors@R: person("Thomas", "Lui", , "tlui27@yahoo.com", role = c("aut", "cre"))
Description: Given a set of gene expression data and functional gene set data, the program will return a table summary of the selected gene sets with high differential co-expression and high differential expression (HDC-HDE).
Depends: R (>= 3.1.2)
License: GPL-3
LazyData: false
Packaged: 2015-01-27 22:36:15 UTC; T
Author: Thomas Lui [aut, cre]
Maintainer: Thomas Lui
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-28 07:41:03

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New package brewdata with initial version 0.3
Package: brewdata
Type: Package
Title: Extracting Usable Data from the Grad Cafe Results Search
Version: 0.3
Date: 2015-01-27
Author: Nathan Welch
Maintainer: Nathan Welch
Description: Retrieves and parses graduate admissions survey data from the Grad Cafe website (http://thegradcafe.com).
License: GPL (>= 2)
Depends: RCurl, XML, stringdist, tools
Suggests: rgl, scatterplot3d
LazyData: TRUE
Packaged: 2015-01-28 02:50:13 UTC; Nathan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-28 07:39:54

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New package ald with initial version 1.0
Package: ald
Type: Package
Title: The Asymmetric Laplace Distribution
Version: 1.0
Date: 2015-01-27
Author: Christian E. Galarza and Victor H. Lachos
Maintainer: Christian E. Galarza
Description: It provides the density, distribution function, quantile function, random number generator, likelihood function, moments and Maximum Likelihood estimators for a given sample, all this for the three parameter Asymmetric Laplace Distribution defined in Koenker and Machado (1999) useful for quantile regression.
License: GPL (>= 2)
Packaged: 2015-01-28 02:26:49 UTC; ra143711
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-28 07:39:03

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Tue, 27 Jan 2015

Package plotROC updated to version 1.3 with previous version 1.2 dated 2014-11-13

Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.
Author: Michael C Sachs
Maintainer: Michael C Sachs

Diff between plotROC versions 1.2 dated 2014-11-13 and 1.3 dated 2015-01-27

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Package tufterhandout updated to version 1.2.1 with previous version 1.2 dated 2014-11-12

Title: Tufte-style html document format for rmarkdown
Description: Custom template and output formats for use with rmarkdown. Produce Edward Tufte-style handouts in html formats with full support for rmarkdown features
Author: Michael C Sachs
Maintainer: Michael C Sachs

Diff between tufterhandout versions 1.2 dated 2014-11-12 and 1.2.1 dated 2015-01-27

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Package tsoutliers updated to version 0.6 with previous version 0.5 dated 2015-01-25

Title: Detection of Outliers in Time Series
Description: Detection of outliers in time series following the Chen and Liu (1993) procedure. Innovative outliers, additive outliers, level shifts, temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between tsoutliers versions 0.5 dated 2015-01-25 and 0.6 dated 2015-01-27

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Package rplexos updated to version 0.12 with previous version 0.11 dated 2014-12-16

Title: Read and Analyze PLEXOS Solutions from R
Description: Efficiently read and analyze PLEXOS solutions by converting them into SQLite databases that can be easily queried. It supports collation of solutions that may have been divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.11 dated 2014-12-16 and 0.12 dated 2015-01-27

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Package MCMC.qpcr updated to version 1.1.5 with previous version 1.1.3 dated 2014-04-13

Title: Bayesian analysis of qRT-PCR data
Description: This package implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. Tutorial: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/mcmc.qpcr.tutorial.pdf
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz

Diff between MCMC.qpcr versions 1.1.3 dated 2014-04-13 and 1.1.5 dated 2015-01-27

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Package Ecfun updated to version 0.1-4 with previous version 0.1-3 dated 2014-11-27

Title: Functions for Ecdat
Description: Functions to update datasets in Ecdat and to create, manipulate, plot and analyze those and similar datasets.
Author: Spencer Graves
Maintainer: Spencer Graves

Diff between Ecfun versions 0.1-3 dated 2014-11-27 and 0.1-4 dated 2015-01-27

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Package CLME updated to version 2.0-2 with previous version 2.0-1 dated 2014-12-05

Title: Constrained Inference for Linear Mixed Effects Models
Description: Constrained inference for linear mixed effects models using residual bootstrap methodology
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema

Diff between CLME versions 2.0-1 dated 2014-12-05 and 2.0-2 dated 2015-01-27

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Package unmarked updated to version 0.10-6 with previous version 0.10-5 dated 2015-01-23

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler
Maintainer: Richard Chandler

Diff between unmarked versions 0.10-5 dated 2015-01-23 and 0.10-6 dated 2015-01-27

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Package MaxPro updated to version 3.1-2 with previous version 3.1-1 dated 2015-01-27

Title: Maximum Projection Designs
Description: Generate a maximum projection (MaxPro) design, a MaxPro Latin hypercube design or improve an initial design based on the MaxPro criterion. Details of the MaxPro criterion can be found in: Joseph, V. R., Gul, E., and Ba, S. (2015) "Maximum Projection Designs for Computer Experiments", Biometrika.
Author: Shan Ba and V. Roshan Joseph
Maintainer: Shan Ba

Diff between MaxPro versions 3.1-1 dated 2015-01-27 and 3.1-2 dated 2015-01-27

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Package TraMineRextras updated to version 0.2.3 with previous version 0.2.2 dated 2013-10-29

Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of TraMineR.
Author: Gilbert Ritschard [aut, cre, ths, cph], Matthias Studer [aut], Reto Buergin [aut], Alexis Gabadinho [ctb], Nicolas Muller [ctb], Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard

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Package TraMineR updated to version 1.8-9 with previous version 1.8-8 dated 2014-01-14

Title: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
Description: This is a toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph], Nicolas Muller [aut], Reto Buergin [aut], Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard

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Package sequenza updated to version 2.1.1 with previous version 2.1.0 dated 2014-10-08

Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero

Diff between sequenza versions 2.1.0 dated 2014-10-08 and 2.1.1 dated 2015-01-27

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Package SCVA updated to version 1.1.1 with previous version 1.1 dated 2014-09-02

Title: Single-Case Visual Analysis
Description: A package to make graphical representations of single case data and to transform graphical displays back to raw data. The package also includes tools for visually analyzing single-case data, by displaying central location, variability and trend.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels

Diff between SCVA versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27

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Package SCRT updated to version 1.1.1 with previous version 1.1 dated 2014-09-02

Title: Single-Case Randomization Tests
Description: A package for designing single-case phase, alternation and multiple-baseline experiments, as well as for conducting randomization tests on data gathered by means of such designs.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels

Diff between SCRT versions 1.1 dated 2014-09-02 and 1.1.1 dated 2015-01-27

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Package SCMA updated to version 1.1.1 with previous version 1.1 dated 2014-01-13

Title: Single-Case Meta-Analysis
Description: An R package for single-case meta-analysis.
Author: Isis Bulte
Maintainer: Bart Michiels

Diff between SCMA versions 1.1 dated 2014-01-13 and 1.1.1 dated 2015-01-27

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Package RcmdrPlugin.SCDA updated to version 1.1 with previous version 1.0 dated 2014-03-19

Title: Rcmdr Plugin for Designing and Analyzing Single-case Experiments
Description: Provides a GUI for the SCVA, SCRT and SCMA packages. The package is written as an Rcmdr plugin.
Author: Isis Bulte and Patrick Onghena
Maintainer: Bart Michiels

Diff between RcmdrPlugin.SCDA versions 1.0 dated 2014-03-19 and 1.1 dated 2015-01-27

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Package qrLMM updated to version 1.1 with previous version 1.0-9 dated 2015-01-08

Title: Quantile Regression for Linear Mixed-Effects Models
Description: Quantile regression (QR) for Linear Mixed-Effects Models via the asymmetric Laplace distribution (ALD). It uses the Stochastic Approximation of the EM (SAEM) algorithm for deriving exact maximum likelihood estimates and full inference results for the fixed-effects and variance components. It also provides graphical summaries for assessing the algorithm convergence and fitting results.
Author: Christian E. Galarza and Victor H. Lachos
Maintainer: Christian E. Galarza

Diff between qrLMM versions 1.0-9 dated 2015-01-08 and 1.1 dated 2015-01-27

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Package openair updated to version 1.1-3 with previous version 1.1-0 dated 2015-01-05

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw

Diff between openair versions 1.1-0 dated 2015-01-05 and 1.1-3 dated 2015-01-27

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Package msarc updated to version 1.4.5 with previous version 1.4.3 dated 2014-12-04

Title: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments
Description: The output of an affinity-purification mass spectrometry experiment is typically a list of proteins that were observed in the experiment, identified by UniProt identifiers (http://www.uniprot.org/). This package takes as input a list of UniProt identifiers, and the associated Mascot scores from the experiment (which indicate the likelihood that the protein has been correctly identified), clusters them by gene ontology category (http://geneontology.org/), then draws diagrams showing the results in hierarchical clusters by category, with lines for individual proteins representing the associated Mascot score. The results are in general not publication-ready, but will rather require editing via a graphics editor that can interpret SVG (scalable vector graphics) format. As an alternative representation, the package will also generate tag clouds based on the Mascot scores.
Author: Gord Brown, Hisham Mohammed
Maintainer: Gord Brown

Diff between msarc versions 1.4.3 dated 2014-12-04 and 1.4.5 dated 2015-01-27

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Package lawstat updated to version 2.5 with previous version 2.4.1 dated 2013-12-16

Title: Tools for Biostatistics, Public Policy, and Law
Description: Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness, measures of relative variability etc, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as Robust QQ plot; a robust trend tests for variances etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.
Author: (in alphabetical order) Joseph L. Gastwirth ; Yulia R. Gel ; W. L. Wallace Hui ; Weiwen Miao ; Kimihiro Noguchi
Maintainer: Vyacheslav Lyubchich

Diff between lawstat versions 2.4.1 dated 2013-12-16 and 2.5 dated 2015-01-27

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Package HMR updated to version 0.4.1 with previous version 0.3.2 dated 2014-12-12

Title: Flux Estimation with Static Chamber Data
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger R. Pedersen
Maintainer: Asger R. Pedersen

Diff between HMR versions 0.3.2 dated 2014-12-12 and 0.4.1 dated 2015-01-27

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New package funtimes with initial version 1.0
Package: funtimes
Type: Package
Title: Functions for Time Series Analysis
Version: 1.0
Date: 2015-01-26
Author: Vyacheslav Lyubchich ; Yulia R. Gel ; Xingyu Wang
Maintainer: Vyacheslav Lyubchich
Depends: Jmisc, R (>= 3.0.0)
License: GPL (>= 2)
Description: Includes non-parametric estimators and tests for time series analysis. The functions allow to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
NeedsCompilation: no
Packaged: 2015-01-27 04:21:18 UTC; slava
Repository: CRAN
Date/Publication: 2015-01-27 16:55:52

More information about funtimes at CRAN
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Package decompr updated to version 2.0 with previous version 1.3.2 dated 2014-12-10

Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Description: Two Global Value Chains decompositions are implemented. Firstly, the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross exports into 16 value added components. Secondly, the Leontief decomposition (default) derives the value added origin of exports by country and industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre], Fei Wang [aut], Victor Kummritz [aut]
Maintainer: Bastiaan Quast

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Package PHENIX updated to version 1.1 with previous version 1.0 dated 2014-10-24

Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), a bootstrapping method to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares

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New package Kernelheaping with initial version 0.2
Package: Kernelheaping
Type: Package
Title: Kernel Density Estimation for Heaped Data
Version: 0.2
Date: 2015-01-19
Depends: R (>= 2.15.0), plyr, evmix, MASS
Author: Marcus Gross
Maintainer: Marcus Gross
Description: In self-reported data the user often encounters heaped data, i.e. data which are rounded to a different degree of coarseness. While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Additionally varying rounding probabilities (with the true value) and asymmetric rounding is estimable as well.
License: GPL-2
Packaged: 2015-01-27 09:10:46 UTC; marcusgross
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-27 12:10:10

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Package FeedbackTS updated to version 1.3.1 with previous version 1.3 dated 2015-01-05

Title: Analysis of Feedback in Time Series
Description: Analysis of fragmented time directionality to investigate feedback in time series. Tools provided by the package allow the analysis of feedback for a single time series and the analysis of feedback for a set of time series collected across a spatial domain.
Author: Samuel Soubeyrand, Cindy E. Morris, E. Keith Bigg
Maintainer: Samuel Soubeyrand

Diff between FeedbackTS versions 1.3 dated 2015-01-05 and 1.3.1 dated 2015-01-27

 DESCRIPTION                     |    8 ++++----
 MD5                             |   14 +++++++-------
 NAMESPACE                       |    6 ++++--
 man/FeedbackTS-package.Rd       |    6 +++---
 man/KDD-class.Rd                |   27 +++++++++++++++------------
 man/KDD.yearly.average-class.Rd |   11 ++++++-----
 man/KT.output-class.Rd          |   22 ++++++++++++++--------
 man/feedback.test.Rd            |    5 ++---
 8 files changed, 55 insertions(+), 44 deletions(-)

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Package raster updated to version 2.3-24 with previous version 2.3-12 dated 2014-10-18

Title: Geographic data analysis and modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut], Jacob van Etten [ctb], Matteo Mattiuzzi [ctb], Michael Sumner [ctb], Jonathan A. Greenberg [ctb], Oscar Perpinan Lamigueiro [ctb], Andrew Bevan [ctb], Etienne B. Racine [ctb], Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans

Diff between raster versions 2.3-12 dated 2014-10-18 and 2.3-24 dated 2015-01-27

 ChangeLog                |   11 +
 DESCRIPTION              |   14 +-
 MD5                      |  121 ++++++++---------
 R/AAAClasses.R           |    1 
 R/aggregate_sp.R         |    2 
 R/buffer.R               |    2 
 R/canProcessInMemory.R   |    4 
 R/clump.R                |    2 
 R/connection.R           |    6 
 R/coverPolygons.R        |    2 
 R/cropSpatial.R          |    4 
 R/erase.R                |    2 
 R/extractPoints.R        |   25 ---
 R/extractPoints_sp.R     |only
 R/extractPolygons.R      |   16 +-
 R/factor.R               |    7 -
 R/freq.R                 |   12 -
 R/gdal.R                 |    2 
 R/getData.R              |    4 
 R/gridDistance.R         |    2 
 R/hillShade.R            |    2 
 R/imageplot.R            |   30 ----
 R/indexReplace.R         |    2 
 R/indexReplaceBrick.R    |    6 
 R/intersect.R            |   12 -
 R/intersect_sp.R         |  101 +++++++++++++-
 R/isLonLat.R             |   10 +
 R/kml_multiple.R         |    6 
 R/mean.R                 |  101 ++------------
 R/multiCore.R            |    2 
 R/netCDFtoRasterCD.R     |    4 
 R/netCDFutil.R           |    4 
 R/netCDFwriteCD.R        |   99 +++++++-------
 R/nsidcICE.R             |  114 ++++++++--------
 R/overlay.R              |    2 
 R/plotCT.R               |    2 
 R/plotRGB.R              |    2 
 R/progressBar.R          |    2 
 R/rasterFromFile.R       |    2 
 R/rasterFromRasterFile.R |    2 
 R/rasterToPolygons.R     |    2 
 R/rowMinMax.R            |    5 
 R/sampleStratified.R     |    5 
 R/select.R               |    4 
 R/symdif.R               |    2 
 R/tmpFile.R              |    4 
 R/trim.R                 |   10 -
 R/union_sp.R             |    4 
 R/writeRaster.R          |    2 
 R/zApply.R               |    2 
 build/vignette.rds       |binary
 inst/doc/Raster.pdf      |binary
 inst/doc/functions.pdf   |binary
 inst/doc/rasterfile.pdf  |binary
 man/Raster-classes.Rd    |    1 
 man/extract.Rd           |   25 ++-
 man/getData.Rd           |   17 ++
 man/interpolate.Rd       |    5 
 man/intersect.Rd         |   10 -
 man/raster.Rd            |  326 ++++++++++++++++++++++++-----------------------
 src/dist_util.c          |    2 
 src/edge.c               |    2 
 62 files changed, 594 insertions(+), 578 deletions(-)

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