New package shapeR with initial version 0.1-3
Package: shapeR
Type: Package
Title: Collection and Analysis of Otolith Shape Data
Version: 0.1-3
Date: 2015-04-02
Authors@R: c(person("Lisa Anne", "Libungan", role = c("aut", "cre"), email = "lisa.libungan@gmail.com"), person("Snaebjorn", "Palsson", role = c("aut", "ths"), email = "snaebj@hi.is"))
Maintainer: Lisa Anne Libungan
Depends: R (>= 3.0.2)
Imports: gplots, jpeg, pixmap, wavethresh, methods, vegan, MASS
Description: Studies otolith shape variation among fish populations. Otoliths are calcified structures found in the inner ear of teleost fish and their shape has been known to vary among several fish populations and stocks, making them very useful in taxonomy, species identification and to study geographic variations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.
License: GPL (>= 2)
URL: https://github.com/lisalibungan/shapeR, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102
LazyDataCompression: yes
Packaged: 2015-04-03 12:52:19 UTC; lal
Author: Lisa Anne Libungan [aut, cre], Snaebjorn Palsson [aut, ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 22:48:14

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Package GUTS updated to version 0.4.14 with previous version 0.4.12 dated 2015-04-02

Title: Fast Calculation of the Likelihood of a Stochastic Survival Model
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert and Sören Vogel
Maintainer: Sören Vogel

Diff between GUTS versions 0.4.12 dated 2015-04-02 and 0.4.14 dated 2015-04-03

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New package fpCompare with initial version 0.1.0
Package: fpCompare
Type: Package
Title: Reliable Comparison of Floating Point Numbers
URL: https://github.com/PredictiveEcology/fpCompare
Version: 0.1.0
Date: 2015-04-03
Authors@R: c( person("Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada", role="cph"), person(c("Alex", "M"), "Chubaty", email="achubaty@NRCan.gc.ca", role=c("aut", "cre")) )
Description: Comparisons of floating point numbers are problematic due to errors associated with the binary representation of decimal numbers. Despite being aware of these problems, people still use numerical methods that fail to account for these and other rounding errors (this pitfall is the first to be highlighted in Circle 1 of Burns (2012) [The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)). This package provides four new relational operators useful for performing floating point number comparisons with a set tolerance.
Depends: R (>= 3.1.2)
Suggests: knitr, testthat
License: GPL-3
VignetteBuilder: knitr
ByteCompile: yes
BugReports: https://github.com/PredictiveEcology/fpCompare/issues
Packaged: 2015-04-03 20:35:16 UTC; achubaty
Author: Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph], Alex M Chubaty [aut, cre]
Maintainer: Alex M Chubaty
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 23:11:17

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New package EcoSimR with initial version 0.1.0
Package: EcoSimR
Type: Package
Title: Null Model Analysis for Ecological Data
Version: 0.1.0
Date: 2015-04-02
BugReports: https://github.com/GotelliLab/EcoSimR/issues
Authors@R: c(person("Nick", "Gotelli", role = c("aut"), email = "ngotelli@uvm.edu"), person("Edmund", "Hart", role = c("aut","cre"), email = "edmund.m.hart@gmail.com"), person("Aaron", "Ellison", role = c("aut"), email = "aellison@fas.harvard.edu") )
LazyLoad: yes
LazyData: yes
Description: Given a site by species interaction matrix, users can make inferences about species interactions by performance hypothesis comparing test statistics against a null distribution. The current package provides algorithms and metrics for niche-overlap, body size ratios and species co-occurrence. Users can also integrate their own algorithms and metrics within these frameworks or completely novel null models. Detailed explanations about the underlying assumptions of null model analysis in ecology can be found at http://ecosimr.org.
License: MIT + file LICENSE
Depends: MASS
Suggests: testthat, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-04-03 17:57:52 UTC; edmundhart
Author: Nick Gotelli [aut], Edmund Hart [aut, cre], Aaron Ellison [aut]
Maintainer: Edmund Hart
Repository: CRAN
Date/Publication: 2015-04-03 22:09:00

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Package wq updated to version 0.4.3 with previous version 0.4-1 dated 2014-05-14

Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and exploration of data from environmental monitoring programs. The name "wq" stands for "water quality" and reflects the original focus on time series data for physical and chemical properties of water, as well as the plankton. Intended for programs that sample approximately monthly at discrete stations, a feature of many legacy data sets. Most of the functions should be useful for analysis of similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby

Diff between wq versions 0.4-1 dated 2014-05-14 and 0.4.3 dated 2015-04-03

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New package thsls with initial version 0.1
Package: thsls
Type: Package
Title: Three-Stage Least Squares Estimation for Systems of Simultaneous Equations
Version: 0.1
Date: 2015-04-03
Author: Zaghdoudi Taha
Maintainer: Zaghdoudi Taha
Description: Fit the Simultaneous Systems of Linear Equations using Three-stage Least Squares.
License: GPL-3
LazyData: TRUE
Imports: Formula
Packaged: 2015-04-03 14:49:32 UTC; Taha
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 20:04:55

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Package arm updated to version 1.8-03 with previous version 1.7-07 dated 2014-08-27

Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing 'lm', 'glm', 'svy.glm', 'merMod' and 'polr' outputs.
Author: Andrew Gelman [aut], Yu-Sung Su [aut, cre], Masanao Yajima [ctb], Jennifer Hill [ctb], Maria Grazia Pittau [ctb], Jouni Kerman [ctb], Tian Zheng [ctb], Vicent Dorie [ctb]
Maintainer: Yu-Sung Su

Diff between arm versions 1.7-07 dated 2014-08-27 and 1.8-03 dated 2015-04-03

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New package RKEAjars with initial version 5.0-1
Package: RKEAjars
Version: 5.0-1
Title: R/KEA Interface Jars
Authors@R: c(person("Kurt", "Hornik", role = c("aut", "cre"), email = "Kurt.Hornik@R-project.org"), person("Eibe", "Frank", role = c("ctb", "cph"), comment = "KEA Java library"), person("Olena", "Medelyan", role = c("ctb", "cph"), comment = "KEA Java library"), person("The Apache Software Foundation", role = c("ctb", "cph"), comment = "Apache Commons Logging and Apache Jena Java libraries"), person("International Business Machines Corporation and others", role = c("ctb", "cph"), comment = "International Components for Unicode for Java (ICU4J)"), person("Martin", "Porter", role = c("ctb", "cph"), comment = "Snowball base"), person("Richard", "Boulton", role = c("ctb", "cph"), comment = "Snowball Java library"), person("University of Waikato", role = c("ctb", "cph"), comment = "Weka Java library"))
Description: External jars required for package RKEA.
Imports: rJava (>= 0.6-3)
SystemRequirements: Java (>= 5.0)
License: GPL-2
Packaged: 2015-04-03 15:14:37 UTC; hornik
Author: Kurt Hornik [aut, cre], Eibe Frank [ctb, cph] (KEA Java library), Olena Medelyan [ctb, cph] (KEA Java library), The Apache Software Foundation [ctb, cph] (Apache Commons Logging and Apache Jena Java libraries), International Business Machines Corporation and others [ctb, cph] (International Components for Unicode for Java (ICU4J)), Martin Porter [ctb, cph] (Snowball base), Richard Boulton [ctb, cph] (Snowball Java library), University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-03 17:27:47

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Package RKEA updated to version 0.0-6 with previous version 0.0-5 dated 2015-02-20

Title: R/KEA Interface
Description: An R interface to KEA (Version 5.0). KEA (for Keyphrase Extraction Algorithm) allows for extracting keyphrases from text documents. It can be either used for free indexing or for indexing with a controlled vocabulary. For more information see .
Author: Ingo Feinerer [aut], Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik

Diff between RKEA versions 0.0-5 dated 2015-02-20 and 0.0-6 dated 2015-04-03

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Package TAM updated to version 1.6-0 with previous version 1.5-2 dated 2015-02-24

Title: Test Analysis Modules
Description: Includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Nominal Item Response, Structured Latent Class Analysis, Mixture Distribution IRT Models, Located Latent Class Models, Cognitive Diagnostic Models). Latent regression models and plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch

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Package V8 updated to version 0.6 with previous version 0.5 dated 2015-02-03

Title: Embedded JavaScript Engine
Description: An R interface to Google's open source, high performance JavaScript engine. V8 is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition. In addition, this package implements typed arrays as specified in ECMA 6 in order to support high-performance computing and libraries compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between V8 versions 0.5 dated 2015-02-03 and 0.6 dated 2015-04-03

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Package relSim updated to version 0.2-0 with previous version 0.1-47 dated 2012-07-24

Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran

Diff between relSim versions 0.1-47 dated 2012-07-24 and 0.2-0 dated 2015-04-03

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Package mnormt updated to version 1.5-2 with previous version 1.5-1 dated 2014-06-29

Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via a non-Monte Carlo method. Different routines are used for the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini

Diff between mnormt versions 1.5-1 dated 2014-06-29 and 1.5-2 dated 2015-04-03

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Package rbiouml (with last version 1.5) was removed from CRAN

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

2014-12-04 1.5
2013-09-13 1.4
2013-08-23 1.3

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Package EMDomics (with last version 0.99.1) was removed from CRAN

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

2015-02-19 0.99.1
2014-11-15 0.99.0

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New package hgm with initial version 1.11
Package: hgm
Type: Package
Depends: R (>= 2.6.0), deSolve
Title: Holonomic Gradient Method and Gradient Descent
Version: 1.11
Date: 2015-03-26
Author: Nobuki Takayama, Tamio Koyama, Tomonari Sei, Hiromasa Nakayama, Kenta Nishiyama
Maintainer: Nobuki Takayama
Description: The holonomic gradient method (HGM, hgm) gives a way to evaluate normalization constants of unnormalized probability distributions by utilizing holonomic systems of differential or difference equations. The holonomic gradient descent (HGD, hgd) gives a method to find maximal likelihood estimates by utilizing the HGM.
License: GPL-2
LazyLoad: yes
URL: http://www.openxm.org
Packaged: 2015-04-02 23:09:09 UTC; taka
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-03 07:48:02

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