Mon, 12 Jan 2015

Package seacarb updated to version 3.0.5 with previous version 3.0.4 dated 2015-01-05

Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph], Jean-Marie Epitalon [aut], Heloise Lavigne [aut], James Orr [ctb], Bernard Gentili [ctb], Andreas Hofmann [ctb], Aurélien Proye [ctb], Karline Soetaert [ctb], James Rae [ctb]
Maintainer: Jean-Pierre Gattuso

Diff between seacarb versions 3.0.4 dated 2015-01-05 and 3.0.5 dated 2015-01-12

 ChangeLog   |    7 +++++++
 DESCRIPTION |   10 +++++-----
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 R/carb.R    |    2 +-
 5 files changed, 49 insertions(+), 31 deletions(-)

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Package randomForestSRC updated to version 1.6.0 with previous version 1.5.5 dated 2014-08-26

Title: Random Forests for Survival, Regression and Classification (RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran , Udaya B. Kogalur
Maintainer: Udaya B. Kogalur

Diff between randomForestSRC versions 1.5.5 dated 2014-08-26 and 1.6.0 dated 2015-01-12

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Package nabor updated to version 0.4.4 with previous version 0.4.3 dated 2014-09-03

Title: Wraps libnabo, a fast K Nearest Neighbour library for low dimensions
Description: An R wrapper for libnabo, an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). libnabo has speed and space advantages over the ANN library wrapped by package RANN. nabor includes a knn function that is designed as a drop-in replacement for RANN::nn2. In addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.
Author: Stephane Mangenat (for libnabo), Gregory Jefferis
Maintainer: Gregory Jefferis

Diff between nabor versions 0.4.3 dated 2014-09-03 and 0.4.4 dated 2015-01-12

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New package mlxR with initial version 2.1.0
Package: mlxR
Type: Package
Version: 2.1.0
Title: Simulation of Longitudinal Data
Description: Simulation and visualization of complex models for longitudinal data. The models are encoded using the model coding language Mlxtran, automatically converted into C++ codes, compiled on the fly and linked to R using the Rcpp package. That allows one to implement very easily complex ODE-based models and complex statistical models, including mixed effects models, for continuous, count, categorical, and time-to-event data.
Authors@R: c( person( "Marc", "Lavielle", role = c("aut","cre"), email = "Marc.Lavielle@inria.fr" ), person( "Romain", "Francois", role = "aut", email = "romain@r-enthusiasts.com"), person( "Fazia", "Bellal", role = "ctb" ) )
URL: http://simulx.webpopix.org
BugReports: https://github.com/MarcLavielle/mlxR/issues
Depends: R (>= 3.0.3), ggplot2
Suggests: reshape2, gridExtra
Imports: XML, Rcpp (>= 0.11.3), tools
License: BSD_2_clause + file LICENSE
Copyright: Inria
Packaged: 2015-01-12 14:10:36 UTC; romain
Author: Marc Lavielle [aut, cre], Romain Francois [aut], Fazia Bellal [ctb]
Maintainer: Marc Lavielle
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-12 23:27:59

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New package hwwntest with initial version 1.3
Package: hwwntest
Type: Package
Title: Tests of White Noise using Wavelets
Version: 1.3
Date: 2014-05-14
Authors@R: c(person("Delyan", "Savchev", role=c("aut"),email="madbss@bristol.ac.uk"), person("Guy", "Nason", role=c("aut","cre"), email="g.p.nason@bristol.ac.uk"))
Description: Provides methods to test whether time series is consistent with white noise.
Depends: R(>= 3.0)
Imports: parallel, polynom, wavethresh
License: GPL-2
Packaged: 2015-01-12 15:54:43 UTC; magpn
Author: Delyan Savchev [aut], Guy Nason [aut, cre]
Maintainer: Guy Nason
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-13 00:18:30

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Package hpoPlot updated to version 2.0 with previous version 1.0 dated 2014-05-10

Title: Functions for Plotting HPO Terms
Description: Collection of functions for manipulating sets of HPO terms and plotting them with a various options
Author: Daniel Greene
Maintainer: Daniel Greene

Diff between hpoPlot versions 1.0 dated 2014-05-10 and 2.0 dated 2015-01-12

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Package sysfonts updated to version 0.4 with previous version 0.3 dated 2014-12-21

Title: Loading System Fonts into R
Description: This package uses FreeType to load system fonts and Google Fonts (https://www.google.com/fonts) into R. It is supposed to support other packages like R2SWF and showtext.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu

Diff between sysfonts versions 0.3 dated 2014-12-21 and 0.4 dated 2015-01-12

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Package stabs updated to version 0.5-1 with previous version 0.5-0 dated 2014-12-09

Title: Stability Selection with Error Control
Description: Resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting
Author: Benjamin Hofner [aut, cre], Torsten Hothorn [aut]
Maintainer: Benjamin Hofner

Diff between stabs versions 0.5-0 dated 2014-12-09 and 0.5-1 dated 2015-01-12

 ChangeLog     |   37 ++++++++++++++++++++++++++++++++--
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Package Geneland updated to version 4.0.5 with previous version 4.0.4 dated 2014-03-24

Title: Detection of structure from multilocus genetic data.
Description: Stochastic simulation and MCMC inference of structure from genetic data.
Author: Gilles Guillot, Filipe Santos, Arnaud Estoup
Maintainer: Gilles Guillot

Diff between Geneland versions 4.0.4 dated 2014-03-24 and 4.0.5 dated 2015-01-12

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Package gamboostLSS updated to version 1.1-3 with previous version 1.1-2 dated 2014-06-26

Title: Boosting Methods for GAMLSS
Description: Boosting models for fitting generalized additive models for location, shape and scale (GAMLSS) to potentially high dimensional data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner

Diff between gamboostLSS versions 1.1-2 dated 2014-06-26 and 1.1-3 dated 2015-01-12

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Package emdbook updated to version 1.3.7 with previous version 1.3.6 dated 2014-11-25

Title: Ecological models and data (book support)
Description: Auxiliary functions and data sets for _Ecological Models and Data_, a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0)
Author: Ben Bolker
Maintainer: Ben Bolker

Diff between emdbook versions 1.3.6 dated 2014-11-25 and 1.3.7 dated 2015-01-12

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Package earth updated to version 4.2.0 with previous version 4.1.0 dated 2014-12-17

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow

Diff between earth versions 4.1.0 dated 2014-12-17 and 4.2.0 dated 2015-01-12

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New package DEEPR with initial version 0.1
Package: DEEPR
Version: 0.1
Date: 2015-01-08
Title: Dirichlet-multinomial Evolutionary Event Profile Randomization (DEEPR) test
Author: Mark T Merilo
Maintainer: Mark T Merilo
Description: Tests for, and describe differences in event count profiles in groups of reconstructed cophylogenies
Depends: R (>= 3.0), dirmult
License: GPL (>= 2)
Packaged: 2015-01-12 20:25:16 UTC; Mark
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-12 23:03:29

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Package CNOGpro updated to version 1.1 with previous version 1.0 dated 2014-07-09

Title: Copy Numbers of Genes in prokaryotes
Description: Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.
Author: Ola Brynildsrud, Lars-Gustav Snipen
Maintainer: Ola Brynildsrud

Diff between CNOGpro versions 1.0 dated 2014-07-09 and 1.1 dated 2015-01-12

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Package afex updated to version 0.13-145 with previous version 0.12-135 dated 2014-11-03

Title: Analysis of Factorial Experiments
Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. ez.glm(), aov.car(), and aov4() allow convenient specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating multiple observations per individual and cell of the design. mixed() fits a mixed model using lme4::lmer() and computes p-values for all effects using either Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software). compare.2.vectors() compares two vectors using a variety of tests (t, Wilcoxon, and permutation).
Author: Henrik Singmann [aut, cre], Ben Bolker [aut], Jake Westfall [aut], Søren Højsgaard [ctb], John Fox [ctb], Michael A. Lawrence [ctb], Ulf Mertens [ctb]
Maintainer: Henrik Singmann

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Package RcppGSL updated to version 0.2.3 with previous version 0.2.2 dated 2014-05-31

Title: Rcpp Integration for GNU GSL Vectors and Matrices
Description: Rcpp integration for GNU GSL vectors and matrices The GNU Scientific Library (GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines such as special functions, permutations, combinations, fast fourier transforms, eigensystems, random numbers, quadrature, random distributions, quasi-random sequences, Monte Carlo integration, N-tuples, differential equations, simulated annealing, numerical differentiation, interpolation, series acceleration, Chebyshev approximations, root-finding, discrete Hankel transforms physical constants, basis splines and wavelets. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses Rcpp to connect to another third-party library. The autoconf script, inline plugin and example package can all be used as a stanza to write a similar package against another library.
Author: Romain Francois and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

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Package vegan updated to version 2.2-1 with previous version 2.2-0 dated 2014-11-17

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen

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Package treeclim updated to version 1.0.9 with previous version 1.0.7 dated 2014-08-08

Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions, seasonal correlations and evaluation of reconstruction skills for use in dendroclimatology and dendroecology
Author: Christian Zang [aut, cre, cph, trl], Franco Biondi [ctb, cph]
Maintainer: Christian Zang

Diff between treeclim versions 1.0.7 dated 2014-08-08 and 1.0.9 dated 2015-01-12

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Package simMSM updated to version 1.1.2 with previous version 1.0.1 dated 2014-03-28

Title: Simulation of Event Histories for Multi-state Models
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen

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Package penMSM updated to version 0.99 with previous version 0.97 dated 2014-07-02

Title: Estimating Regularized Multi-state Models Using L1 Penalties
Description: Structured fusion Lasso penalized estimation of multi-state models with the penalty applied to absolute effects and absolute effect differences (i.e., effects on transition-type specific hazard rates).
Author: Holger Reulen
Maintainer: Holger Reulen

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Package V8 updated to version 0.4 with previous version 0.3 dated 2014-12-21

Title: Embedded JavaScript Engine
Description: V8 is Google's open source, high performance JavaScript engine. It is written in C++ and implements ECMAScript as specified in ECMA-262, 5th edition.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

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Package soundecology updated to version 1.2 with previous version 1.1.1 dated 2014-04-14

Title: Soundscape ecology
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera

Diff between soundecology versions 1.1.1 dated 2014-04-14 and 1.2 dated 2015-01-12

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New package readGenalex with initial version 0.4.1
Package: readGenalex
Type: Package
Title: Read and Manipulate GenAlEx-format Genotype Files
Version: 0.4.1
Date: 2015-01-12
Author: Douglas G. Scofield
Maintainer: "Douglas G. Scofield"
Description: A collection of R functions to read genotype data file in GenAlEx format, as exported from Excel as a delimited text file, into an annotated data.frame, and manipulate it in that form. Several functions are provided for accessing and printing this data. GenAlEx and its documentation are available at http://biology-assets.anu.edu.au/GenAlEx.
URL: https://github.com/douglasgscofield/readGenalex
License: LGPL-3 | file LICENSE
Packaged: 2015-01-12 00:51:07 UTC; douglasgscofield
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-12 10:33:07

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New package HomoPolymer with initial version 1.0
Package: HomoPolymer
Type: Package
Title: Theoretical Model to Simulate Radical Polymerization
Version: 1.0
Date: 2014-12-23
Author: Gianmarco Polotti
Maintainer: Gianmarco Polotti
Description: A theoretical model to simulate radical polymerization. Material, energy and population balances are integrated for batch, semi batch and continuous process in a ideally mixed reactor. Limitations: single monomer (i.e.homo polymer), one phase (organic, aqueous). Datasets with chemical-physical data for the most common monomers is included. Some background in polymer science is suggested for its use. Graphical interface for a quick and friendly use is available.
Depends: R (>= 3.0.0), RGtk2, MenuCollection
Imports: deSolve
LazyData: true
LazyLoad: true
License: GPL-2
Packaged: 2015-01-11 19:21:42 UTC; PolGia0
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-12 10:27:23

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Package dfmta updated to version 1.1-0 with previous version 1.0-3 dated 2014-11-20

Title: Phase I/II Adaptive Dose-Finding Design For MTA
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization".
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere

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 dfmta-1.1-0/dfmta/src/dfmta.cpp                                                   |  533 ++++------
 dfmta-1.1-0/dfmta/tools                                                           |only
 24 files changed, 553 insertions(+), 517 deletions(-)

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Package robumeta updated to version 1.5 with previous version 1.4 dated 2014-12-09

Title: Robust Variance Meta-regression
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher

Diff between robumeta versions 1.4 dated 2014-12-09 and 1.5 dated 2015-01-12

 DESCRIPTION  |    6 +++---
 MD5          |    4 ++--
 R/robumeta.R |   37 ++++++++++++++++++++++++++-----------
 3 files changed, 31 insertions(+), 16 deletions(-)

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