Thu, 31 Jul 2014

Package timsac updated to version 1.3.3 with previous version 1.3.2 dated 2014-06-02

Title: TIMe Series Analysis and Control package
Description: Functions for statistical analysis, prediction and control of time series.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga

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Package plotKML updated to version 0.4-5 with previous version 0.4-4 dated 2014-05-04

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

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Package bayou updated to version 1.0.1 with previous version 1.0 dated 2014-07-18

Title: Bayesian fitting of Ornstein-Uhlenbeck models to phylogenies
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda

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Package yuima updated to version 1.0.24 with previous version 1.0.21 dated 2014-05-05

Title: The YUIMA Project package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus

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Package GNE updated to version 0.99-0 with previous version 0.98 dated 2014-06-11

Title: Computation of generalized Nash equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria. The following optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation.
Author: Christophe Dutang
Maintainer: Christophe Dutang

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Package wskm updated to version 1.4.11 with previous version 1.4.7 dated 2014-06-02

Title: Weighted k-means Clustering
Description: Entropy weighted k-means (ewkm) is a weighted subspace clustering algorithm that is well suited to very high dimensional data. Weights are calculated as the importance of a variable with regard to cluster membership. The two-level variable weighting clustering algorithm TW-k-means (twkm) introduces two types of weights, the weights on individual variables and the weights on variable groups, and they are calculated during the clustering process. The feature group weighted k-means (fgkm) extends this concept by grouping features and weighting the group in addition to weighting individual features.
Author: Graham Williams [aut], Joshua Z Huang [aut], Xiaojun Chen [aut], Qiang Wang [aut], Longfei Xiao [aut], He Zhao [cre]
Maintainer: He Zhao

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New package spnet with initial version 0.9.0.1
Package: spnet
Type: Package
Title: Plotting (social) networks on maps
Version: 0.9.0.1
Date: 2014-07-24
Author: Emmanuel Rousseaux, Marion Deville
Maintainer: Emmanuel Rousseaux
Description: The spnet package offers methods for dealing with spacial social networks. It allows to plot networks for which actors have a specific location on a map (participants in a political debate, cities, etc.). SpatialPolygons objects from the sp package are supported.
URL: http://emmanuel.rousseaux.me/r-package-spnet
License: GPL-3
Depends: methods, sp, shape
Repository: CRAN
Repository/R-Forge/Project: spnet
Repository/R-Forge/Revision: 21
Repository/R-Forge/DateTimeStamp: 2014-07-25 07:34:41
Date/Publication: 2014-07-31 07:20:23
Packaged: 2014-07-28 12:16:19 UTC; rforge
NeedsCompilation: no

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Package rgbif updated to version 0.7.0 with previous version 0.6.2 dated 2014-04-24

Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Vijay Barve [aut], Dan Mcglinn [aut]
Maintainer: Scott Chamberlain

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Package RefFreeEWAS updated to version 1.3 with previous version 1.2 dated 2014-03-05

Title: EWAS using reference-Free DNA methylation mixture deconvolution
Description: Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. This method is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman

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Package lsmeans updated to version 2.11 with previous version 2.10 dated 2014-06-24

Title: Least-Squares Means
Description: This package provides methods for obtaining least-squares means for various linear models. It can also compute contrasts or linear combinations of these least-squares means, comparisons of slopes, interaction plots, and compact letter displays.
Author: Russell V. Lenth
Maintainer: Russ Lenth

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Package glarma updated to version 1.2-0 with previous version 1.1-0 dated 2014-01-17

Title: Generalized Linear Autoregressive Moving Average Models
Description: This package provides functions for estimation, testing and diagnostic checking of generalized linear autoregressive moving average (GLARMA) models for discrete valued time series with regression variables. These are a class of observation driven non-linear non-Gaussian state space models. The state vector consists of a linear regression component plus an observation driven component consisting of an autoregressive-moving average (ARMA) filter of past predictive residuals. Currently three distributions (Poisson, negative binomial and binomial) can be used for the response series. Three options (Pearson, score-type and unscaled) for the residuals in the observation driven component are available. Estimation is via maximum likelihood (conditional on initializing values for the ARMA process) optimized using Fisher scoring or Newton Raphson iterative methods. Likelihood ratio and Wald tests for the observation driven component allow testing for serial dependence in generalized linear model settings. Graphical diagnostics including model fits, autocorrelation functions and probability integral transform residuals are included in the package. Several standard data sets are included in the package.
Author: William T.M. Dunsmuir , Cenanning Li , and David J. Scott
Maintainer: "William T.M. Dunsmuir"

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New package GeoDE with initial version 1.0
Package: GeoDE
Type: Package
Title: A geometrical Approach to Differential expression and gene-set enrichment
Version: 1.0
Date: 2014-06-06
Author: Neil R. Clark and Avi Ma'ayan
Maintainer: Neil Clark
Description: Given expression data this package calculate a multivariate geometrical characterization of the differential expression and can also perform gene-set enrichment.
License: GPL-2
Depends: R (>= 2.10), Matrix, MASS
Packaged: 2014-07-30 21:26:23 UTC; Neil Clark
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-31 07:17:53

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Package fslr updated to version 1.1 with previous version 1.0 dated 2014-06-13

Title: Wrapper functions for FSL (FMRIB Software Library) from Functional MRI. of the Brain (FMRIB)
Description: Wrapper functions that interface with FSL (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used neuroimaging software, using system commands. The goal is to be able to interface with FSL completely in R, where you pass R nifti objects and the function executes an FSL command and returns an R nifti object if desired.
Author: John Muschelli
Maintainer: John Muschelli

Diff between fslr versions 1.0 dated 2014-06-13 and 1.1 dated 2014-07-31

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Package aoristic updated to version 0.5 with previous version 0.4 dated 2014-03-20

Title: aoristic analysis with spatial output (kml)
Description: 'Aoristic' is one of the past tenses in Greek and represents an uncertain occurrence time. Aoristic analysis suggested by Ratcliffe (2002) is a method to analyze events that do not have exact times of occurrence but have starting times and ending times. For example, a property crime database (e.g., burglary) typically has a starting time and ending time of the crime that could have occurred. Aoristic analysis allocates the probability of a crime incident occurring at every hour over a 24-hour period. The probability is aggregated over a study area to create an aoristic graph. Using crime incident data with lat/lon, DateTimeFrom, and DateTimeTo, functions in this package create a total of three (3) kml files and corresponding aoristic graphs: 1) density and contour; 2) grid count; and 3) shapefile boundary. (see also: https://sites.google.com/site/georgekick/software)
Author: George Kikuchi
Maintainer: George Kikuchi

Diff between aoristic versions 0.4 dated 2014-03-20 and 0.5 dated 2014-07-31

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Wed, 30 Jul 2014

Package glcm updated to version 0.3.2 with previous version 0.3.1 dated 2014-04-24

Title: Calculate textures from grey-level co-occurrence matrices (GLCMs) in R
Description: Enables calculation of image textures derived from grey-level co-occurrence matrices (GLCMs) in R. The texture calculation is coded in C++ to optimize computation time.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff

Diff between glcm versions 0.3.1 dated 2014-04-24 and 0.3.2 dated 2014-07-30

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Package ExceedanceTools updated to version 1.2.2 with previous version 1.2.0 dated 2014-07-08

Title: Confidence regions for exceedance sets and contour lines
Description: Tools for constructing confidence regions for exceedance regions and contour lines.
Author: Joshua French
Maintainer: Joshua French

Diff between ExceedanceTools versions 1.2.0 dated 2014-07-08 and 1.2.2 dated 2014-07-30

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New package DDIwR with initial version 0.1-0
Package: DDIwR
Version: 0.1-0
Date: 2014-07-30
Title: DDI related functions
Authors@R: c(person("Adrian", "Dusa", role = c("aut", "cre"), email = "dusa.adrian@unibuc.ro"))
Depends: R (>= 3.0.0)
Imports: XML, foreign
Description: This package provides useful functions for various DDI (Data Documentation Initiative) related outputs.
License: GPL (>= 2)
Packaged: 2014-07-30 18:13:41 UTC; dusadrian
Author: Adrian Dusa [aut, cre]
Maintainer: Adrian Dusa
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 22:02:08

More information about DDIwR at CRAN
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Package metafor updated to version 1.9-4 with previous version 1.9-3 dated 2014-05-05

Title: Meta-Analysis Package for R
Description: The metafor package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer

Diff between metafor versions 1.9-3 dated 2014-05-05 and 1.9-4 dated 2014-07-30

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New package tmap with initial version 0.6
Package: tmap
Maintainer: Martijn Tennekes
License: GPL-3
Title: Thematic Maps
Type: Package
LazyLoad: yes
Author: Martijn Tennekes
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, way to create all kinds of thematic maps, such as choropleths and bubble maps.
Version: 0.6
Date: 2014-06-30
Depends: R (>= 3.0)
Imports: rgeos, grid, gridBase, sp, rgdal, classInt, RColorBrewer, igraph, fields, vegan
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-07-30 15:47:53 UTC; vt
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 18:25:21

More information about tmap at CRAN
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Package miceadds updated to version 0.14-9 with previous version 0.13-7 dated 2014-06-27

Title: Some additional multiple imputation functions, especially for mice
Description: The package miceadds contains some auxiliary functions for multiple imputation which complements existing functionality in R. In addition to some utility functions, main features include plausible value imputation, multilevel imputation functions, imputation using partial least squares (PLS) for high dimensional predictors and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch

Diff between miceadds versions 0.13-7 dated 2014-06-27 and 0.14-9 dated 2014-07-30

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Package GetoptLong updated to version 0.0.5 with previous version 0.0.4 dated 2014-06-17

Title: Parse 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 0.0.4 dated 2014-06-17 and 0.0.5 dated 2014-07-30

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Package codep updated to version 0.4-1 with previous version 0.2-2 dated 2013-09-05

Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional feature.
Author: Guillaume Guenard and Pierre Legendre, with contributions from Bertrand Pages
Maintainer: Guillaume Guenard

Diff between codep versions 0.2-2 dated 2013-09-05 and 0.4-1 dated 2014-07-30

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Package arulesNBMiner updated to version 0.1-4 with previous version 0.1-2 dated 2012-03-19

Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Description: NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets presented in "Michael Hahsler. A model-based frequency constraint for mining associations from transaction data. Data Mining and Knowledge Discovery, 13(2):137-166, September 2006." In addition an extension for NB-precise rules is implemented.
Author: Michael Hahsler
Maintainer: Michael Hahsler

Diff between arulesNBMiner versions 0.1-2 dated 2012-03-19 and 0.1-4 dated 2014-07-30

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Package twostageTE updated to version 1.01 with previous version 1.0 dated 2013-05-24

Title: Two-Stage Threshold Estimation
Description: Implements a variety of nonparametric methods for computing one-stage and two-stage confidence intervals, as well as point estimates of threshold values.
Author: Shawn Mankad, George Michailidis, Moulinath Banerjee
Maintainer: Shawn Mankad

Diff between twostageTE versions 1.0 dated 2013-05-24 and 1.01 dated 2014-07-30

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Package Surrogate updated to version 0.1-2 with previous version 0.1-1 dated 2014-05-11

Title: Evaluation of surrogate endpoints in clinical trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst

Diff between Surrogate versions 0.1-1 dated 2014-05-11 and 0.1-2 dated 2014-07-30

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Package CRF updated to version 0.3-8 with previous version 0.3-7 dated 2014-05-06

Title: CRF - Conditional Random Fields
Description: This package implements modeling and computational tools for conditional random fields model (CRF) as well as other probabilistic undirected graphical models of discrete data with pairwise and unary potentials.
Author: Ling-Yun Wu [aut, cre]
Maintainer: Ling-Yun Wu

Diff between CRF versions 0.3-7 dated 2014-05-06 and 0.3-8 dated 2014-07-30

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Package btf updated to version 1.1 with previous version 1.0 dated 2014-07-15

Title: Estimates univariate function via Bayesian trend filtering
Description: Trend filtering uses the generalized lasso framework to fit an adaptive polynomial of degree k to estimate the function f_0 at each input x_i in the model: y_i = f_0(x_i) + epsilon_i, for i = 1, ..., n, and epsilon_i is sub-Gaussian with E(epsilon_i) = 0. Bayesian trend filtering adapts the genlasso framework to a fully Bayesian hierarchical model, estimating the penalty parameter lambda within a tractable Gibbs sampler.
Author: Edward A. Roualdes
Maintainer: Edward A. Roualdes

Diff between btf versions 1.0 dated 2014-07-15 and 1.1 dated 2014-07-30

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Package BLCOP updated to version 0.2.8 with previous version 0.2.7 dated 2014-01-07

Title: Black-Litterman and copula-opinion pooling frameworks
Description: An implementation of the Black-Litterman Model and Atilio Meucci's copula opinion pooling framework. This should be regarded as a beta release.
Author: Francisco Gochez
Maintainer: Mango Solutions

Diff between BLCOP versions 0.2.7 dated 2014-01-07 and 0.2.8 dated 2014-07-30

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Package mwa updated to version 0.3.2 with previous version 0.3.1 dated 2014-06-15

Title: MWA package for causal inference in spatiotemporal event data
Description: MWA grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte

Diff between mwa versions 0.3.1 dated 2014-06-15 and 0.3.2 dated 2014-07-30

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Package SSDforR updated to version 1.4.6 with previous version 1.4.5 dated 2014-06-20

Title: SSD for R to analyze single system data
Description: Package to visually and statistically analyze single system data
Author: Charles Auerbach,PHD Wendy Zeitlin Schudrich,PHD Wurzweiler School of Social Work
Maintainer: Charles Auerbach

Diff between SSDforR versions 1.4.5 dated 2014-06-20 and 1.4.6 dated 2014-07-30

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Package RbioRXN updated to version 1.3.1 with previous version 1.3 dated 2014-06-17

Title: RbioRXN - process Rhea, KEGG, MetaCyc, Unipathway biochemical reaction data
Description: RbioRXN is an R package that facilitates retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway. The package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
Author: Byoungnam Min, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min

Diff between RbioRXN versions 1.3 dated 2014-06-17 and 1.3.1 dated 2014-07-30

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New package extlasso with initial version 0.1
Package: extlasso
Type: Package
Title: Maximum penalized likelihood estimation with extended lasso penalty
Version: 0.1
Date: 2014-26-06
Author: B N Mandal and Jun Ma
Maintainer: B N Mandal
Depends: R (>= 3.1.1)
Description: The package estimates coefficients of extended LASSO penalized linear regression and generalized linear models. Currently lasso and elastic net penalized linear regression and generalized linear models are considered. The package currently utilizes an accurate approximation of L1 penalty and then a modified Jacobi algorithm to estimate the coefficients. There is provision for plotting of the solutions and predictions of coefficients at given values of lambda. The package also contains functions for cross validation to select a suitable lambda value given the data. The package also provides a function for estimation in fused lasso penalized linear regression.
License: GPL (>= 2)
Packaged: 2014-07-30 05:44:05 UTC; User
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 07:58:08

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Package Rdroolsjars (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:

2011-11-26 0.0.1

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Package Rdrools (with last version 0.0.2) was removed from CRAN

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

2011-11-29 0.0.2
2011-11-26 0.0.1

Permanent link
Package swirl updated to version 2.2.14 with previous version 2.2.9 dated 2014-05-30

Title: Learn R, in R.
Description: swirl turns the R console into an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.
Author: Nick Carchedi [aut, cre], Bill Bauer [aut], Gina Grdina [aut], Sean Kross [aut]
Maintainer: Nick Carchedi

Diff between swirl versions 2.2.9 dated 2014-05-30 and 2.2.14 dated 2014-07-30

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New package rareGE with initial version 0.1
Package: rareGE
Type: Package
Title: Testing Gene-Environment Interaction for Rare Genetic Variants
Version: 0.1
Date: 2014-07-28
Author: Han Chen
Maintainer: Han Chen
Description: Tests gene-environment interaction for rare genetic variants using Sequence Kernel Association Test (SKAT) type gene-based tests. Includes two tests for the interaction term only, and one joint test for genetic main effects and gene-environment interaction.
License: GPL-3
Imports: MASS, nlme, survey
URL: http://www.hsph.harvard.edu/han-chen/
Packaged: 2014-07-29 19:59:09 UTC; hanchen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-30 06:57:34

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Tue, 29 Jul 2014

Package stocc updated to version 1.23 with previous version 1.0-7 dated 2012-11-27

Title: Fit a spatial occupancy model via Gibbs sampling
Description: Fit a spatial-temporal occupancy models using a probit formulation instead of a traditional logit model.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson

Diff between stocc versions 1.0-7 dated 2012-11-27 and 1.23 dated 2014-07-29

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Package rpg updated to version 1.1 with previous version 1.0 dated 2014-07-24

Title: Easy interface to advanced PostgreSQL features
Description: Allows ad hoc queries and reading and writing data frames to and from a database.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt

Diff between rpg versions 1.0 dated 2014-07-24 and 1.1 dated 2014-07-29

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Package RODBCext updated to version 0.2.3 with previous version 0.2.2 dated 2014-07-07

Title: Parameterized queries extension for RODBC
Description: An extension for RODBC package adding support for parameterized queries
Author: Mateusz Zoltak [aut, cre], Brian Ripley [aut], Michael Lapsley [aut]
Maintainer: Mateusz Zoltak

Diff between RODBCext versions 0.2.2 dated 2014-07-07 and 0.2.3 dated 2014-07-29

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New package miniCRAN with initial version 0.0-16
Package: miniCRAN
Authors@R: c(person("Andrie", "de Vries", role=c("aut", "cre"), email="apdevries@gmail.com"))
License: GPL-2 | GPL-3
Title: Tools to create an internally consistent, mini version of CRAN with selected packages only.
LazyData: true
LazyLoad: true
Description: Tools to create a internally consistent, mini version of CRAN with selected packages only.
Version: 0.0-16
URL: https://github.com/andrie/miniCRAN
Date: 2014-07-29
Imports: tools, XML
Suggests: igraph, RCurl, testthat, knitr
VignetteBuilder: knitr
Packaged: 2014-07-29 16:43:31 UTC; Andrie
Author: Andrie de Vries [aut, cre]
Maintainer: Andrie de Vries
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-29 19:44:51

More information about miniCRAN at CRAN
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Package heatmapFit updated to version 2.0.1 with previous version 2.0 dated 2014-07-22

Title: Fit statistic for binary dependent variable models
Description: Generates a fit plot for diagnosing misspecification in models of binary dependent variables, and calculates the related heatmap fit statistic (Esarey and Pierce, 2012).
Author: Justin Esarey [aut, cre], Andrew Pierce [aut], Jericho Du [aut]
Maintainer: Justin Esarey

Diff between heatmapFit versions 2.0 dated 2014-07-22 and 2.0.1 dated 2014-07-29

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Package psychomix updated to version 1.1-1 with previous version 1.1-0 dated 2013-12-10

Title: Psychometric Mixture Models
Description: Psychometric mixture models based on flexmix infrastructure. At the moment Rasch mixture models with different parametrizations of the score distribution (saturated vs. mean/variance specification) and Bradley-Terry mixture models are implemented. Both mixture models can be estimated with or without concomitant variables. See vignette("raschmix", package = "psychomix") for details on the Rasch mixture models.
Author: Hannah Frick [aut, cre], Carolin Strobl [aut], Friedrich Leisch [aut], Achim Zeileis [aut]
Maintainer: Hannah Frick

Diff between psychomix versions 1.1-0 dated 2013-12-10 and 1.1-1 dated 2014-07-29

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Package netmeta updated to version 0.6-0 with previous version 0.5-0 dated 2014-06-24

Title: Network meta-analysis with R
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut], Guido Schwarzer [aut, cre], Ulrike Krahn [aut], Jochem König [aut]
Maintainer: Guido Schwarzer

Diff between netmeta versions 0.5-0 dated 2014-06-24 and 0.6-0 dated 2014-07-29

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Package rbamtools updated to version 2.9.14 with previous version 2.9.11 dated 2014-06-24

Title: Reading, manipulation and writing BAM (Binary alignment) files.
Description: This package provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers

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Package RCurl updated to version 1.95-4.3 with previous version 1.95-4.2 dated 2014-07-28

Title: General network (HTTP/FTP/...) client interface for R
Description: The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang

Diff between RCurl versions 1.95-4.2 dated 2014-07-28 and 1.95-4.3 dated 2014-07-29

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Package Familias updated to version 2.0 with previous version 1.2 dated 2013-04-17

Title: Probabilities for Pedigrees given DNA data
Description: This package represents an interface to the core Familias functions (www.familias.name), which are programmed in C++. The interface is completely changed from version 1.2 of this package, so programs dependent on the old functions should continue to use that version.
Author: Petter Mostad and Thore Egeland
Maintainer: Petter Mostad

Diff between Familias versions 1.2 dated 2013-04-17 and 2.0 dated 2014-07-29

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Package pheno2geno updated to version 1.2.1 with previous version 1.2.0 dated 2014-06-10

Title: Pheno2Geno - Generating genetic markers and maps from molecular phenotypes
Description: Pheno2Geno is an R package for the computational generation genetic markers and maps from molecular phenotypes
Author: Konrad Zych and Danny Arends
Maintainer: Konrad Zych

Diff between pheno2geno versions 1.2.0 dated 2014-06-10 and 1.2.1 dated 2014-07-29

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Package rorutadis updated to version 0.1.3 with previous version 0.1.1 dated 2014-04-11

Title: Robust Ordinal Regression UTADIS
Description: Implementation of Robust Ordinal Regression for value-based sorting with some extensions and additional tools. It is a novel Multiple-Criteria Decision Aiding (MCDA) framework.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek

Diff between rorutadis versions 0.1.1 dated 2014-04-11 and 0.1.3 dated 2014-07-29

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Package poppr updated to version 1.1.2 with previous version 1.1.1 dated 2014-07-27

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

Diff between poppr versions 1.1.1 dated 2014-07-27 and 1.1.2 dated 2014-07-29

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Package phreeqc updated to version 1.0-8877 with previous version 1.0-8847 dated 2014-07-16

Title: R interface to the phreeqc geochemical modeling program
Description: R interface to PHREEQC (Version 3). PHREEQC is a geochemical modeling program developed by the US Geological Survey that is designed to perform a wide variety of aqueous geochemical calculations, including speciation, batch-reaction, one-dimensional reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh, R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton

Diff between phreeqc versions 1.0-8847 dated 2014-07-16 and 1.0-8877 dated 2014-07-29

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More information about phreeqc at CRAN
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Package NeatMap updated to version 0.3.6.2 with previous version 0.3.6.1 dated 2013-11-01

Title: Non-clustered heatmap alternatives
Description: NeatMap is a package to create heatmap like plots in 2 and 3 dimensions, without the need for cluster analysis. Like the heatmap, the plots created by NeatMap display both a dimensionally reduced representation of the data as well as the data itself. They are intended to be used in conjunction with dimensional reduction techniques such as PCA.
Author: Satwik Rajaram and Yoshi Oono
Maintainer: Satwik Rajaram

Diff between NeatMap versions 0.3.6.1 dated 2013-11-01 and 0.3.6.2 dated 2014-07-29

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Package meta updated to version 3.7-1 with previous version 3.7-0 dated 2014-07-11

Title: Meta-Analysis with R
Description: User-friendly general package providing standard methods for meta-analysis: - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from RevMan 5; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer

Diff between meta versions 3.7-0 dated 2014-07-11 and 3.7-1 dated 2014-07-29

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More information about meta at CRAN
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Package lctools updated to version 0.1-3 with previous version 0.1-2 dated 2014-04-26

Title: Local Correlation, Spatial Inequalities and other tools
Description: Local Correlation Coefficients (Local Pearson and Geographically Weighted Pearson), Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics)
Author: Stamatis Kalogirou
Maintainer: Stamatis Kalogirou

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Package hasseDiagram updated to version 0.1.1 with previous version 0.1 dated 2014-04-12

Title: Drawing Hasse diagram
Description: Drawing Hasse diagram - visualization of transitive reduction of a finite partially ordered set.
Author: Krzysztof Ciomek
Maintainer: Krzysztof Ciomek

Diff between hasseDiagram versions 0.1 dated 2014-04-12 and 0.1.1 dated 2014-07-29

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Package EpiModel updated to version 1.0.1 with previous version 1.0 dated 2014-06-09

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with tools available for expansion to model complex epidemic processes.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Li Wang [ctb]
Maintainer: Samuel Jenness

Diff between EpiModel versions 1.0 dated 2014-06-09 and 1.0.1 dated 2014-07-29

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Mon, 28 Jul 2014

Package RMendeley (with last version 0.1-2) was removed from CRAN

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

2012-08-06 0.1-2
2012-01-18 0.1-1

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Package TreeSim updated to version 2.0 with previous version 1.9.1 dated 2013-12-10

Title: Simulating trees under the birth-death model
Description: The package simulates phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and number of tips (sim.bd.taxa.age). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa). The function sim.bd.age (and sim.rateshift.taxa without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot, LTT.plot.gen and LTT.average.root. TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim). (ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa. The function sim.genespeciestree simulates coalescent gene trees within birth-death species trees, and sim.genetree simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreeSim versions 1.9.1 dated 2013-12-10 and 2.0 dated 2014-07-28

 DESCRIPTION                 |   14 -
 MD5                         |   58 ++--
 NAMESPACE                   |    5 
 R/getx.R                    |   18 +
 R/reconstructed.age.R       |    3 
 R/sim.bd.age.help.R         |    2 
 R/sim.bd.taxa.R             |    8 
 R/sim.bd.taxa.age.help.R    |    1 
 R/sim.bdsky.stt.R           |  579 ++++++++++++++++++++++++++++++--------------
 R/sim.bdtypes.stt.taxa.R    |    5 
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 R/sim.rateshift.taxa.R      |    8 
 R/sim2.bd.R                 |    1 
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 33 files changed, 668 insertions(+), 358 deletions(-)

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Package TreePar updated to version 3.0 with previous version 2.5 dated 2013-06-09

Title: Estimating birth and death rates based on phylogenies
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. Both (1) and (2) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree).
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreePar versions 2.5 dated 2013-06-09 and 3.0 dated 2014-07-28

 TreePar-2.5/TreePar/R/BDSSsky.R                   |only
 TreePar-2.5/TreePar/R/LikComp2.R                  |only
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 TreePar-3.0/TreePar/man/bdsky.stt.optim.Rd        |   20 +++--
 TreePar-3.0/TreePar/man/get.groups.Rd             |   15 ++--
 56 files changed, 227 insertions(+), 172 deletions(-)

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Package RCurl updated to version 1.95-4.2 with previous version 1.95-4.1 dated 2013-03-06

Title: General network (HTTP/FTP/...) client interface for R
Description: The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang

Diff between RCurl versions 1.95-4.1 dated 2013-03-06 and 1.95-4.2 dated 2014-07-28

 DESCRIPTION                 |    6 
 MD5                         |   10 
 configure                   | 7467 ++++++++++++++++----------------------------
 configure.in                |    4 
 data/mimeTypeExtensions.rda |binary
 src/CURLOptTable.h          |    2 
 6 files changed, 2761 insertions(+), 4728 deletions(-)

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Package gmp updated to version 0.5-12 with previous version 0.5-11 dated 2013-12-04

Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme , Sylvain Jasson , Martin Maechler
Maintainer: Antoine Lucas

Diff between gmp versions 0.5-11 dated 2013-12-04 and 0.5-12 dated 2014-07-28

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 gmp-0.5-12/gmp/ChangeLog                |    4 +
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 gmp-0.5-12/gmp/R/biginteger.R           |   12 ++---
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 gmp-0.5-12/gmp/tests/arith-ex.R         |   11 ++++
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 gmp-0.5-12/gmp/tests/gmp-test.Rout.save |   73 ++++++++++++++++----------------
 12 files changed, 108 insertions(+), 76 deletions(-)

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Package lmPerm (with last version 1.1-2) was removed from CRAN

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

2010-08-16 1.1-2
2010-02-12 1.1-0
2010-01-27 1.0-1
2010-01-26 1.0-0

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Package rocplus (with last version 1.0-0) was removed from CRAN

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2011-03-14 1.0-0

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Package longclust (with last version 1.1) was removed from CRAN

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

2012-05-29 1.0
2012-05-29 1.1

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Package mvtBinaryEP (with last version 1.0.1) was removed from CRAN

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2011-01-25 1.0.1
2009-02-18 1.0

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Package ldDesign (with last version 2.0-1) was removed from CRAN

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2012-03-26 2.0-1
2011-11-18 2.0-0
2010-04-15 1.2-0
2007-04-11 1.1-0

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Package cosinor updated to version 1.1 with previous version 1.0 dated 2014-07-25

Title: Tools for estimating and predicting the cosinor model
Description: cosinor is a set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients.
Author: Michael Sachs
Maintainer: Michael Sachs

Diff between cosinor versions 1.0 dated 2014-07-25 and 1.1 dated 2014-07-28

 DESCRIPTION                     |   19 +++++++++--------
 MD5                             |   27 +++++++++++++++----------
 NAMESPACE                       |    4 +++
 NEWS                            |    7 ++++++
 R/cosinor.lm.R                  |   20 +++++++++++++++---
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 16 files changed, 119 insertions(+), 37 deletions(-)

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Package cramer (with last version 0.8-1) was removed from CRAN

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

2006-06-19 0.8-1

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Package ant (with last version 0.0-10) was removed from CRAN

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2009-10-28 0.0-10
2009-09-18 0.0-8
2009-09-08 0.0-6
2009-09-07 0.0-5

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Package ipw (with last version 1.0-10) was removed from CRAN

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2011-09-11 1.0-10
2011-04-04 1.0-9
2010-09-30 1.0-8
2010-09-09 1.0-7
2010-08-20 1.0-6
2010-03-25 1.0-5
2010-03-08 1.0-4
2010-03-05 1.0-3
2010-02-14 1.0-2
2010-02-08 1.0-1
2010-02-04 1.0

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Package biOpsGUI (with last version 0.1.2) was removed from CRAN

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

2008-02-11 0.1.2
2007-12-07 0.1.1

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Package biOps (with last version 0.2.2) was removed from CRAN

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

2013-03-29 0.2.2
2010-05-07 0.2.1.1
2008-02-11 0.2.1
2007-11-22 0.2
2007-08-14 0.1-1

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Package jmec (with last version 1.0-4) was removed from CRAN

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

2012-06-21 1.0-4
2012-06-02 1.0-3

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Package RelativeRisk (with last version 1.1-1) was removed from CRAN

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2009-10-20 1.1-1
2009-09-30 1.0-1

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Package FRBData (with last version 0.3) was removed from CRAN

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2011-10-27 0.3
2011-04-24 0.2
2011-04-23 0.1

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Package BayesQTLBIC (with last version 1.0-2) was removed from CRAN

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2011-10-17 1.0-2
2010-05-18 1.0-1
2009-10-30 1.0-0

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

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2009-02-11 1.0

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Package sda updated to version 1.3.4 with previous version 1.3.3 dated 2014-04-18

Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: This package provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with variable selection. The classifier is trained using James-Stein-type shrinkage estimators and predictor variables are ranked using correlation-adjusted t-scores (CAT scores). Variable selection error is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer

Diff between sda versions 1.3.3 dated 2014-04-18 and 1.3.4 dated 2014-07-28

 DESCRIPTION         |   12 ++++++------
 MD5                 |    6 +++---
 NEWS                |    6 ++++++
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 4 files changed, 27 insertions(+), 17 deletions(-)

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New package rYoutheria with initial version 1.0.0
Package: rYoutheria
Type: Package
Title: Access to the YouTheria mammal trait database
Description: A programmatic interface to web-services of Youtheria. Youtheria is an online database of mammalian trait data.
Version: 1.0.0
Date: 2014-07-24
Author: Tom August
Maintainer: Tom August
VignetteBuilder: knitr
URL: https://github.com/biologicalrecordscentre/rYoutheria
BugReports: https://github.com/biologicalrecordscentre/rYoutheria/issues
Depends: R (>= 3.0.0)
Imports: plyr, RJSONIO, reshape2, RCurl
Suggests: knitr, testthat, roxygen2
License: MIT + file LICENSE
Packaged: 2014-07-28 14:04:59 UTC; tomaug
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-28 17:46:15

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Package Rtsne updated to version 0.8 with previous version 0.6 dated 2014-06-23

Title: T-distributed Stochastic Neighbor Embedding using Barnes-Hut implementation
Description: An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten
Author: Jesse Krijthe
Maintainer: Jesse Krijthe

Diff between Rtsne versions 0.6 dated 2014-06-23 and 0.8 dated 2014-07-28

 DESCRIPTION         |    6 +++---
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Package RJSONIO updated to version 1.3-0 with previous version 1.2-0.2 dated 2014-04-29

Title: Serialize R objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang

Diff between RJSONIO versions 1.2-0.2 dated 2014-04-29 and 1.3-0 dated 2014-07-28

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 31 files changed, 100 insertions(+), 64 deletions(-)

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Package ltbayes updated to version 0.3 with previous version 0.2 dated 2014-05-15

Title: Simulation-Based Bayesian Inference for Latent Traits of Item Response Models
Description: Functions for simulating realizations from the posterior distribution of a latent trait of an item response model. Distributions are conditional on one or a subset of response patterns (e.g., sum scores). Functions for computing likelihoods, Fisher and observed information, posterior modes, and profile likelihood confidence intervals are also included. These functions are designed to be easily amenable to user-specified models.
Author: Timothy R. Johnson
Maintainer: Timothy R. Johnson

Diff between ltbayes versions 0.2 dated 2014-05-15 and 0.3 dated 2014-07-28

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Package jaatha updated to version 2.5 with previous version 2.4 dated 2014-06-03

Title: A Fast Parameter Estimation Method for Evolutionary Biology
Description: Jaatha is a composite likelihood method for inferring evolutionary parameters using genetic data. Given a model of the evolutionary history of two biological populations as well as SNP data from multiple individuals from each population, it estimates model parameters like the time of separation of both species.
Author: Paul R. Staab, Lisha Mathew and Dirk Metzler
Maintainer: Paul R. Staab

Diff between jaatha versions 2.4 dated 2014-06-03 and 2.5 dated 2014-07-28

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Permanent link

Package httr updated to version 0.4 with previous version 0.3 dated 2014-03-19

Title: Tools for working with URLs and HTTP
Description: Provides useful tools for working with HTTP. The API is based around http verbs (GET(), POST(), etc) with pluggable components to control the request (authenticate(), add_headers() and so on).
Author: Hadley Wickham
Maintainer: Hadley Wickham

Diff between httr versions 0.3 dated 2014-03-19 and 0.4 dated 2014-07-28

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Package HTSDiff updated to version 1.0.2 with previous version 1.0.1 dated 2013-12-10

Title: Differential analysis of RNA-seq data with Poisson mixture models
Description: This package implements a Poisson mixture model to identify differentially expressed genes from RNA-seq data.
Author: Andrea Rau, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

Diff between HTSDiff versions 1.0.1 dated 2013-12-10 and 1.0.2 dated 2014-07-28

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Package HTSCluster updated to version 2.0.3 with previous version 2.0.1 dated 2013-12-10

Title: Clustering high throughput sequencing (HTS) data
Description: This package implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the ICL criterion is used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

Diff between HTSCluster versions 2.0.1 dated 2013-12-10 and 2.0.3 dated 2014-07-28

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Package HDPenReg updated to version 0.89.8 with previous version 0.89.7 dated 2014-07-17

Title: High-Dimensional Penalized Regression.
Description: This package contains algorithms for lasso and fused-lasso problems. It contains an implementation of the lars algorithm [1], for the lasso and fusion penalization and EM-based algorithms for (logistic) lasso and fused-lasso.
Author: Quentin Grimonprez [aut, cre], Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez

Diff between HDPenReg versions 0.89.7 dated 2014-07-17 and 0.89.8 dated 2014-07-28

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Package GeneNet updated to version 1.2.10 with previous version 1.2.9 dated 2014-04-15

Title: Modeling and Inferring Gene Networks
Description: GeneNet is a package for analyzing gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between GeneNet versions 1.2.9 dated 2014-04-15 and 1.2.10 dated 2014-07-28

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Permanent link

Package cplexAPI updated to version 1.2.11 with previous version 1.2.9 dated 2013-05-23

Title: R Interface to C API of IBM ILOG CPLEX
Description: R Interface to C API of IBM ILOG CPLEX, depends on IBM ILOG CPLEX (>= 12.1)
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

Diff between cplexAPI versions 1.2.9 dated 2013-05-23 and 1.2.11 dated 2014-07-28

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More information about cplexAPI at CRAN
Permanent link

Package care updated to version 1.1.5 with previous version 1.1.4 dated 2014-04-18

Title: High-Dimensional Regression and CAR Score Variable Selection
Description: The "care" package implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between care versions 1.1.4 dated 2014-04-18 and 1.1.5 dated 2014-07-28

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More information about care at CRAN
Permanent link

Package peptider updated to version 0.1.5 with previous version 0.1.4 dated 2014-05-19

Title: Evaluation of diversity in nucleotide libraries
Description: Functions for evaluating diversity in peptide libraries, including NNN, NNB, NNK/S, and trimer schemes. This includes expected coverage, relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare

Diff between peptider versions 0.1.4 dated 2014-05-19 and 0.1.5 dated 2014-07-28

 DESCRIPTION                 |   10 
 MD5                         |   53 +-
 NAMESPACE                   |   37 -
 R/peptider.r                | 1095 +++++++++++++++++++++++---------------------
 R/tabulate.r                |  392 ++++++---------
 README.md                   |    8 
 man/BLOSUM80.Rd             |   30 -
 man/codons.Rd               |   50 +-
 man/coverage.Rd             |   58 +-
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 man/makowski.Rd             |   54 +-
 man/ppeptide.Rd             |   50 +-
 man/scheme.Rd               |   46 -
 man/schemes.Rd              |   56 +-
 29 files changed, 1308 insertions(+), 1277 deletions(-)

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Package discreteRV updated to version 1.1.2 with previous version 1.1 dated 2014-04-01

Title: Functions to create and manipulate discrete random variables
Description: discreteRV implements a set of functions that allow computations involving discrete random variables. It uses a syntax which is familiar to that which is used in mathematical statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare

Diff between discreteRV versions 1.1 dated 2014-04-01 and 1.1.2 dated 2014-07-28

 DESCRIPTION                  |    6 +--
 MD5                          |   58 +++++++++++++++++-----------------
 NAMESPACE                    |    6 +++
 R/discreteRV-Probabilities.r |   72 ++++++++++++++++++++++++++++---------------
 man/Conditional.Rd           |    5 +-
 man/E.Rd                     |    3 +
 man/KURT.Rd                  |    3 +
 man/P.Rd                     |    3 +
 man/Prop.Rd                  |    7 +---
 man/SD.Rd                    |    3 +
 man/SKEW.Rd                  |    3 +
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 man/SofIID.Rd                |   10 ++---
 man/V.Rd                     |    3 +
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 man/grapes-AND-grapes.Rd     |    5 +-
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 man/props.Rd                 |    7 +---
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 31 files changed, 190 insertions(+), 175 deletions(-)

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Package drfit updated to version 0.6.3 with previous version 0.6.1 dated 2014-03-20

Title: Dose-response data evaluation
Description: drfit provides basic and easy-to-use functions for fitting dose-response curves to dose-response data, calculating some (eco)toxicological parameters and plotting the results. Functions that are fitted are the cumulative density function of the lognormal distribution (probit fit), of the logistic distribution (logit fit), of the weibull distribution (weibull fit) and a linear-logistic model ("linlogit" fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving dose-response data retrieved from a database accessed via RODBC are included. As an alternative to the original fitting methods, the algorithms from the drc package can be used.
Author: Johannes Ranke [aut, cre]
Maintainer: Johannes Ranke

Diff between drfit versions 0.6.1 dated 2014-03-20 and 0.6.3 dated 2014-07-28

 drfit-0.6.1/drfit/ChangeLog                  |only
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 drfit-0.6.3/drfit/data/XY.rda                |binary
 drfit-0.6.3/drfit/inst/doc/drfit-Rnews.pdf   |binary
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 drfit-0.6.3/drfit/tests/IM1xIPC81.Rout.save  |    9 +--
 drfit-0.6.3/drfit/tests/IM1xVibrio.Rout.save |    9 +--
 drfit-0.6.3/drfit/tests/XY.Rout.save         |   11 ++--
 drfit-0.6.3/drfit/tests/antifoul.Rout.save   |   11 ++--
 drfit-0.6.3/drfit/tests/pyrithione.R         |    2 
 drfit-0.6.3/drfit/tests/pyrithione.Rout.save |   67 ++++++++++++---------------
 12 files changed, 68 insertions(+), 74 deletions(-)

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

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

2014-07-16 1.0

Permanent link
Package Gmisc updated to version 0.6.7 with previous version 0.6.4 dated 2014-06-16

Title: Collection of functions for plotting relations, generating tables, and more.
Description: This is a collection of functions for tables, plots, and more. For tables you'll find the convenient htmlTable() that I use for advanced markdown table layout. A major focus has been to have it compatible with LibreOffice and MS Word - you can now copy-paste most tables directly into your document from the viewer. The main plots in the package are the transitionPlot() and forestplot2(), see the examples for demo. Apart from those it is worth mentioning the getDescriptionStatsBy() and its associated function that help you generate a descriptive table (i.e. the Table 1 in most journals), the pvalueFormatter() that formats p-values, and mergeLists() that provides a complex recursive list merge.
Author: Max Gordon
Maintainer: Max Gordon

Diff between Gmisc versions 0.6.4 dated 2014-06-16 and 0.6.7 dated 2014-07-28

 Gmisc-0.6.4/Gmisc/man/Gmisc.Rd                                  |only
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 Gmisc-0.6.7/Gmisc/R/forestplot2.R                               |  345 ++--
 Gmisc-0.6.7/Gmisc/R/forestplot2_helpers.R                       |  762 +++++-----
 Gmisc-0.6.7/Gmisc/R/getDescriptionStatsBy.R                     |  189 +-
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 Gmisc-0.6.7/Gmisc/R/getTicks.R                                  |   37 
 Gmisc-0.6.7/Gmisc/R/grid_helpers.R                              |   15 
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 Gmisc-0.6.7/Gmisc/man/prFpPrintXaxis.Rd                         |    5 
 Gmisc-0.6.7/Gmisc/man/prFpValidateLabelList.Rd                  |    5 
 Gmisc-0.6.7/Gmisc/man/prFpXrange.Rd                             |    5 
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 Gmisc-0.6.7/Gmisc/man/prTpGetBoxPropClr.Rd                      |    5 
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More information about Gmisc at CRAN
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Package cvxclustr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-26

Title: Splitting methods for convex clustering
Description: Alternating Minimization Algorithm (AMA) and Alternating Direction Method of Multipliers (ADMM) splitting methods for convex clustering.
Author: Eric C. Chi, Kenneth Lange
Maintainer: Eric C. Chi

Diff between cvxclustr versions 1.1.0 dated 2014-07-26 and 1.1.1 dated 2014-07-28

 DESCRIPTION      |    8 ++++----
 MD5              |    6 ++++--
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 5 files changed, 14 insertions(+), 6 deletions(-)

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Sun, 27 Jul 2014

Package stsm updated to version 1.4 with previous version 1.3 dated 2014-05-30

Title: Structural Time Series Models
Description: This package provides algorithms to fit structural time series models by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between stsm versions 1.3 dated 2014-05-30 and 1.4 dated 2014-07-27

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 stsm-1.4/stsm/R/maxlik-td-scoring.R                    |  140 ++++--------
 stsm-1.4/stsm/R/mcloglik-fd.R                          |    8 
 stsm-1.4/stsm/R/methods-stsmFit.R                      |   65 ++++-
 stsm-1.4/stsm/R/methods-vcov-confint.R                 |   21 +
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 stsm-1.4/stsm/R/mloglik-td.R                           |  125 +++++++----
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Package migest updated to version 1.6 with previous version 1.5 dated 2014-03-27

Title: Useful R code for the Estimation of Migration
Description: The migest package contains a collection of R functions that are useful to estimate migration when there is missing data. Included is the ffs routine to estimate migration flows from stock data, as well as various other functions to indirectly estimate flows where marginal totals are known. Functions are illustrated with dummy data.
Author: Guy J. Abel
Maintainer: Guy J. Abel

Diff between migest versions 1.5 dated 2014-03-27 and 1.6 dated 2014-07-27

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Package GrapheR updated to version 1.9-84 with previous version 1.9-83 dated 2014-06-28

Title: A multi-platform GUI for drawing customizable graphs in R
Description: GrapheR is a multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Herv
Maintainer: Maxime Herv

Diff between GrapheR versions 1.9-83 dated 2014-06-28 and 1.9-84 dated 2014-07-27

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Package DatABEL updated to version 0.9-4.1 with previous version 0.9-4 dated 2013-03-12

Title: file-based access to large matrices stored on HDD in binary format
Description: a package providing an interface to the C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar
Maintainer: Yurii Aulchenko

Diff between DatABEL versions 0.9-4 dated 2013-03-12 and 0.9-4.1 dated 2014-07-27

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Package poppr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-24

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

Diff between poppr versions 1.1.0 dated 2014-07-24 and 1.1.1 dated 2014-07-27

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