Sun, 19 Apr 2015

Package hitandrun updated to version 0.5-1 with previous version 0.5 dated 2015-01-06

Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly from Convex Shapes
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef

Diff between hitandrun versions 0.5 dated 2015-01-06 and 0.5-1 dated 2015-04-19

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Package SKAT updated to version 1.0.7 with previous version 1.0.1 dated 2014-11-04

Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel regression based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently computes SNP-set level p-values, while adjusting for covariates.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee

Diff between SKAT versions 1.0.1 dated 2014-11-04 and 1.0.7 dated 2015-04-19

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Package phonR updated to version 1.0-3 with previous version 1.0-1 dated 2015-03-05

Title: Tools for Phoneticians and Phonologists
Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Author: Daniel R. McCloy
Maintainer: Daniel R. McCloy

Diff between phonR versions 1.0-1 dated 2015-03-05 and 1.0-3 dated 2015-04-19

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Package mixtools updated to version 1.0.3 with previous version 1.0.2 dated 2014-05-14

Title: Tools for Analyzing Finite Mixture Models
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre], Tatiana Benaglia [aut], Didier Chauveau [aut], David Hunter [aut], Ryan Elmore [ctb], Thomas Hettmansperger [ctb], Hoben Thomas [ctb], Fengjuan Xuan [ctb]
Maintainer: Derek Young

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Package gemtc updated to version 0.6-2 with previous version 0.6-1 dated 2014-12-12

Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian framework. You need either BUGS or JAGS to use this package, preferably JAGS (through the rjags package). Includes methods to assess heterogeneity and inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef

Diff between gemtc versions 0.6-1 dated 2014-12-12 and 0.6-2 dated 2015-04-19

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Package degreenet updated to version 1.3-1 with previous version 1.3 dated 2015-04-06

Title: Models for Skewed Count Distributions Relevant to Networks
Description: Likelihood-based inference for skewed count distributions used in network modeling. "degreenet" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock
Maintainer: Mark S. Handcock

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Package candisc updated to version 0.6-7 with previous version 0.6-5 dated 2013-06-12

Title: Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
Description: Functions for computing and visualizing generalized canonical discriminant analyses and canonical correlation analysis for a multivariate linear model. Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA' design and is equivalent to canonical correlation analysis between a set of quantitative response variables and a set of dummy variables coded from the factor variable. The 'candisc' package generalizes this to higher-way 'MANOVA' designs for all factors in a multivariate linear model, computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D) visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre], John Fox [aut]
Maintainer: Michael Friendly

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Package BDgraph updated to version 2.18 with previous version 2.17 dated 2015-03-10

Title: Graph Estimation Based on Birth-Death MCMC Approach
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi

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Sat, 18 Apr 2015

Package vegdata updated to version 0.6.9 with previous version 0.6-7 dated 2014-11-01

Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (http://www.synbiosys.alterra.nl/turboveg/) and other sources (http://www.vegetweb.de). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", http://www.botanik.uni-greifswald.de/GermanSL.html).
Author: Florian Jansen
Maintainer: Florian Jansen

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Package heplots updated to version 1.0-15 with previous version 1.0-12 dated 2014-07-02

Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot functions for visualizing hypothesis tests in multivariate linear models. They represents sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions).
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly

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Package eHOF updated to version 1.5.8 with previous version 1.5.7 dated 2015-01-14

Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen

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Package TKF updated to version 0.0.8 with previous version 0.0.3 dated 2015-02-10

Title: Pairwise Distance Estimation with TKF91 and TKF92 Model
Description: Pairwise evolutionary distance estimation between protein sequences with the TKF91 and TKF92 model, which consider all the possible paths of transforming from one sequence to another.
Author: Ge Tan
Maintainer: Ge Tan

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Package SSN updated to version 1.1.5 with previous version 1.1.4 dated 2014-11-03

Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef

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More information about SSN at CRAN
Permanent link

Package SSDforR updated to version 1.4.9 with previous version 1.4.8 dated 2014-12-07

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach

Diff between SSDforR versions 1.4.8 dated 2014-12-07 and 1.4.9 dated 2015-04-18

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Permanent link

Package sprex updated to version 1.1 with previous version 1.0 dated 2015-02-24

Title: Calculate Species Richness and Extrapolation Metrics
Description: Calculate species richness functions for rarefaction and extrapolation.
Author: Eric Archer
Maintainer: Eric Archer

Diff between sprex versions 1.0 dated 2015-02-24 and 1.1 dated 2015-04-18

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More information about sprex at CRAN
Permanent link

Package sjmisc updated to version 1.0.1 with previous version 1.0.0 dated 2015-03-22

Title: Miscellaneous Data Management Tools
Description: Collection of several utility functions for reading or writing data, recoding and labelling variables and some frequently used statistical tests.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke

Diff between sjmisc versions 1.0.0 dated 2015-03-22 and 1.0.1 dated 2015-04-18

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Permanent link

Package MATA updated to version 0.3 with previous version 0.2 dated 2015-01-08

Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Description: Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals, which are constructed using single-model estimators and model weights.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek

Diff between MATA versions 0.2 dated 2015-01-08 and 0.3 dated 2015-04-18

 DESCRIPTION |   14 +++++++-------
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More information about MATA at CRAN
Permanent link

Package Luminescence updated to version 0.4.3 with previous version 0.4.2 dated 2015-03-23

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

Diff between Luminescence versions 0.4.2 dated 2015-03-23 and 0.4.3 dated 2015-04-18

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More information about Luminescence at CRAN
Permanent link

Package KFAS updated to version 1.1.0 with previous version 1.0.4-1 dated 2014-06-06

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: Functions for Kalman filtering, smoothing, forecasting and simulation of multivariate exponential family state space models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske

Diff between KFAS versions 1.0.4-1 dated 2014-06-06 and 1.1.0 dated 2015-04-18

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More information about KFAS at CRAN
Permanent link

Package datacheck updated to version 1.2.2 with previous version 1.0.4 dated 2014-09-23

Title: Tools for Checking Data Consistency
Description: Functions to check variables against a set of data quality rules. A rule file can be accompanied by look-up tables. In addition, there are some convenience functions that may serve as an example for defining clearer 'data rules'. An HTML based user interface facilitates initial exploration of the functionality.
Author: "Simon, Reinhard (CIP)" , Jose Francisco Loff
Maintainer: "Simon, Reinhard (CIP)"

Diff between datacheck versions 1.0.4 dated 2014-09-23 and 1.2.2 dated 2015-04-18

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Package daff updated to version 0.1.4 with previous version 0.1.2 dated 2015-02-24

Title: Diff, Patch and Merge for Data.frames
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff. The V8 package is used to wrap the 'daff.js' JavaScript library which is included in the package.
Author: Paul Fitzpatrick [aut] (JavaScript original, http://paulfitz.github.io/daff/), Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge

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Package cna updated to version 1.0-3 with previous version 1.0-2 dated 2015-01-03

Title: A Package for Coincidence Analysis (CNA)
Description: Provides functions for performing Coincidence Analysis (CNA).
Author: Ambuehl, Mathias, Michael Baumgartner, Ruedi Epple, Alexis Kauffmann and Alrik Thiem
Maintainer: Alexis Kauffmann

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Package cheddar updated to version 0.1-629 with previous version 0.1-626 dated 2014-08-28

Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson

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Package bold updated to version 0.2.6 with previous version 0.2.0 dated 2014-08-20

Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by Bold Systems for genetic barcode data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain

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Fri, 17 Apr 2015

Package VLMC updated to version 1.4-1 with previous version 1.4-0 dated 2014-10-06

Title: Variable Length Markov Chains ('VLMC') Models
Description: Functions, Classes & Methods for estimation, prediction, and simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
Author: Martin Maechler
Maintainer: Martin Maechler

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Package TDMR updated to version 1.3 with previous version 1.2 dated 2014-08-30

Title: Tuned Data Mining in R
Description: Tuned Data Mining in R (TDMR) performs a complete tuning of a data mining task.
Author: Wolfgang Konen , Patrick Koch
Maintainer: Wolfgang Konen

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Thu, 16 Apr 2015

Package LindenmayeR updated to version 0.1.4 with previous version 0.1-0 dated 2014-08-12

Title: Functions to Explore L-Systems (Lindenmayer Systems)
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can be used to simulate biological forms and certain kinds of fractals. Briefly, in an L-system a series of symbols in a string are replaced iteratively according to rules to give a more complex string. Eventually, the symbols are translated into turtle graphics for plotting. Wikipedia has a very good introduction: en.wikipedia.org/wiki/L-system This package provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson

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Package crunch updated to version 1.1.0 with previous version 1.0.2 dated 2015-04-04

Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson

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Package poweRlaw updated to version 0.30.2 with previous version 0.30.1 dated 2015-03-13

Title: Analysis of Heavy Tailed Distributions
Description: An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie

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Package mi updated to version 1.0 with previous version 0.10-2 dated 2015-04-07

Title: Missing Data Imputation and Model Checking
Description: The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.
Author: Andrew Gelman [ctb], Jennifer Hill [ctb], Yu-Sung Su [aut], Masanao Yajima [ctb], Maria Pittau [ctb], Ben Goodrich [cre, aut], Yajuan Si [ctb], Jon Kropko [aut]
Maintainer: Ben Goodrich

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Package lsmeans updated to version 2.17 with previous version 2.16 dated 2015-03-14

Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth

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Package compendiumdb updated to version 1.0.0 with previous version 0.1.0 dated 2014-08-29

Title: Tools for Retrieval and Storage of Functional Genomics Data
Description: Package for the systematic retrieval and storage of functional genomics data via a MySQL database.
Author: Umesh K. Nandal and Perry D. Moerland
Maintainer: Umesh Nandal

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Package softclassval updated to version 1.0-20150416 with previous version 1.0-20130317 dated 2013-04-03

Title: Soft Classification Performance Measures
Description: An extension of sensitivity, specificity, positive and negative predictive value to continuous predicted and reference memberships in [0, 1].
Author: C. Beleites
Maintainer: C. Beleites

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Package RAdwords updated to version 0.1.4 with previous version 0.1.3 dated 2015-04-07

Title: Loading Google Adwords Data into R
Description: Aims at loading Google Adwords data into R. Adwords is an online advertising service that enables advertisers to display advertising copy to web users. Therefore the package implements three main features. First, the package provides an authentication process for R with the Google Adwords API via OAUTH2. Second, the package offers an interface to apply the Adwords query language in R and query the Adwords API with ad-hoc reports. Third, the received data are transformed into suitable data formats for further data processing and data analysis.
Author: Johannes Burkhardt , Matthias Bannert
Maintainer: Johannes Burkhardt

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Package letsR updated to version 2.1 with previous version 2.0 dated 2015-02-09

Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on species' distributions and environmental variables as well as species' description and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela

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Package iterpc updated to version 0.2.7 with previous version 0.2.6 dated 2014-11-14

Title: Efficient Iterator for Permutations and Combinations
Description: It helps in 1) generating permutations and combinations with or without replacement; 2) with distinct items or non-distinct items (multiset); 3) calculating number of combinations or permutations in various situations. All generated sequences are in lexicographical order (AKA, dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai

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Package etasFLP updated to version 1.2.1 with previous version 1.2.0 dated 2014-12-22

Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present, together with some diagnostic tools. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class 'etasclass').
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

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Package BAT updated to version 1.3.0 with previous version 1.2.1 dated 2015-03-05

Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso

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Package vcdExtra updated to version 0.6-8 with previous version 0.6-5 dated 2015-01-02

Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly

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Package smoother updated to version 1.1 with previous version 1.0.0.0 dated 2014-09-16

Title: Functions Relating to the Smoothing of Numerical Data
Description: A collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton

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Package networksis updated to version 2.1-3 with previous version 2.1-2 dated 2013-05-01

Title: Simulate Bipartite Graphs with Fixed Marginals Through Sequential Importance Sampling
Description: Tools to simulate bipartite networks/graphs with the degrees of the nodes fixed and specified. 'networksis' is part of the 'statnet' suite of packages for network analysis.
Author: Ryan Admiraal and Mark S. Handcock
Maintainer: Ryan Admiraal

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Package copCAR updated to version 1.0-1 with previous version 1.0 dated 2014-09-07

Title: Fitting the copCAR Regression Model for Discrete Areal Data
Description: Provides tools for fitting the copCAR regression model for discrete areal data. Three types of estimation are supported: continuous extension, composite marginal likelihood, and distributional transform.
Author: Emily Goren and John Hughes
Maintainer: John Hughes

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Package BiodiversityR updated to version 2.5-2 with previous version 2.5-1 dated 2014-11-23

Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt

Diff between BiodiversityR versions 2.5-1 dated 2014-11-23 and 2.5-2 dated 2015-04-16

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Wed, 15 Apr 2015

Package rmaf updated to version 3.0.1 with previous version 3.0 dated 2015-04-13

Title: Refined Moving Average Filter
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu

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Package rjags updated to version 3-15 with previous version 3-14 dated 2014-10-27

Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb]
Maintainer: Martyn Plummer

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Package rainbow updated to version 3.3 with previous version 3.2 dated 2013-08-28

Title: Rainbow Plots, Bagplots and Boxplots for Functional Data
Description: Functions and data sets for functional data display and outlier detection.
Author: Han Lin Shang and Rob J Hyndman
Maintainer: Han Lin Shang

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Package lctools updated to version 0.2-2 with previous version 0.2 dated 2015-04-05

Title: Local Correlation, Spatial Inequalities and Other Tools
Description: The main purpose of lctools is to assist researchers and educators to use user friendly tools for calculating key spatial statistics. These include: Local Pearson and Geographically Weighted Pearson Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I) and other Spatial Analysis tools (Geographically Weighted Statistics, Inferential Statistics). This package also contains functions for statistical inference for each statistic calculated.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou

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Package knockoff updated to version 0.2.1 with previous version 0.2 dated 2015-02-05

Title: Knockoff Filter for Controlling the False Discovery Rate
Description: The knockoff filter is a procedure for controlling the false discovery rate (FDR) when performing variable selection. For more information, see the website below and the accompanying paper.
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson

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Package domino updated to version 0.2-6 with previous version 0.2-5 dated 2015-04-14

Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite.
Author: Jacek Glodek
Maintainer: Nick Elprin

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Package CoClust updated to version 0.3-1 with previous version 0.3-0 dated 2014-07-07

Title: Copula Based Cluster Analysis
Description: Copula Based Cluster Analysis.
Author: Francesca Marta Lilja Di Lascio, Simone Giannerini
Maintainer: Simone Giannerini

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Package roxygen2 updated to version 4.1.1 with previous version 4.1.0 dated 2014-12-13

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

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Package cold updated to version 1.0-4 with previous version 1.0-3 dated 2013-10-05

Title: Count Longitudinal Data
Description: Performs regression analysis for longitudinal count data using a self-decomposable probability distribution, a random intercept term is also allowed. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed.
Author: M. Helena Gonalves and M. Salom Cabral, apart from a set of Fortran-77 subroutines written by R. Piessens and E. de Doncker, belonging to the suite "Quadpack".
Maintainer: M. Helena Gonalves

Diff between cold versions 1.0-3 dated 2013-10-05 and 1.0-4 dated 2015-04-15

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Package tolerance updated to version 1.1.0 with previous version 1.0.0 dated 2014-09-03

Title: Functions for Calculating Tolerance Intervals
Description: Statistical tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence. This package provides functions for estimating tolerance limits for various distributions. Plotting is also available for tolerance limits of continuous random variables.
Author: Derek S. Young [aut, cre]
Maintainer: Derek S. Young

Diff between tolerance versions 1.0.0 dated 2014-09-03 and 1.1.0 dated 2015-04-15

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Package survMisc updated to version 0.4.6 with previous version 0.4.5 dated 2015-02-25

Title: Miscellaneous Functions for Survival Data
Description: A collection of functions for analysis of survival data. These extend the methods available in the package survival.
Author: Chris Dardis
Maintainer: Chris Dardis

Diff between survMisc versions 0.4.5 dated 2015-02-25 and 0.4.6 dated 2015-04-15

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Package sse updated to version 0.5-4 with previous version 0.5-1 dated 2014-05-19

Title: Sample Size Estimation
Description: Provides functions to evaluate user-defined power functions for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding information to a Sweave report.
Author: Thomas Fabbro
Maintainer: Thomas Fabbro

Diff between sse versions 0.5-1 dated 2014-05-19 and 0.5-4 dated 2015-04-15

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Package highlight updated to version 0.4.5 with previous version 0.4.4 dated 2013-12-16

Title: Syntax Highlighter
Description: Syntax highlighter for R code based on the results of the R parser. Rendering in HTML and latex markup. Custom Sweave driver performing syntax highlighting of R code chunks.
Author: Romain Francois [aut, cre], Andre Simon [ctb]
Maintainer: Romain Francois

Diff between highlight versions 0.4.4 dated 2013-12-16 and 0.4.5 dated 2015-04-15

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Package chillR updated to version 0.55 with previous version 0.54 dated 2013-05-16

Title: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat. 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records.
Author: Eike Luedeling
Maintainer: Eike Luedeling

Diff between chillR versions 0.54 dated 2013-05-16 and 0.55 dated 2015-04-15

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Tue, 14 Apr 2015

Package runjags updated to version 2.0.1-4 with previous version 2.0.1-2 dated 2015-04-12

Title: Interface Utilities, Model Templates, Parallel Computing Methods and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.
Author: Matthew Denwood [aut, cre], Martyn Plummer [cph] (Copyright holder of the code in /src/distributions/jags, src/distributions/DPar1.*, configure.ac, and original copyright holder of some modified code where indicated)
Maintainer: Matthew Denwood

Diff between runjags versions 2.0.1-2 dated 2015-04-12 and 2.0.1-4 dated 2015-04-14

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Package bild updated to version 1.1-5 with previous version 1.1-3 dated 2013-02-18

Title: BInary Longitudinal Data
Description: Performs logistic regression for binary longitudinal data, allowing for serial dependence among observations from a given individual and a random intercept term. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed, with some restrictions.
Author: M. Helena Gonalves, M. Salom Cabral and Adelchi Azzalini, apart from a set of Fortran-77 subroutines written by R. Piessens and E. de Doncker, belonging to the suite "Quadpack".
Maintainer: M. Helena Gonalves

Diff between bild versions 1.1-3 dated 2013-02-18 and 1.1-5 dated 2015-04-14

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Package openair updated to version 1.5 with previous version 1.1-5 dated 2015-02-09

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

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More information about openair at CRAN
Permanent link

Package InvariantCausalPrediction updated to version 0.3-1 with previous version 0.3 dated 2015-04-13

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen

Diff between InvariantCausalPrediction versions 0.3 dated 2015-04-13 and 0.3-1 dated 2015-04-14

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Package flexsurv updated to version 0.6 with previous version 0.5 dated 2014-09-22

Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson
Maintainer: Christopher Jackson

Diff between flexsurv versions 0.5 dated 2014-09-22 and 0.6 dated 2015-04-14

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More information about flexsurv at CRAN
Permanent link

Package CRTSize updated to version 1.0 with previous version 0.4 dated 2015-02-02

Title: Sample Size Estimation Functions for Cluster Randomized Trials
Description: Sample size estimation in cluster (group) randomized trials. Contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
Author: Michael A Rotondi
Maintainer: Michael A Rotondi

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Permanent link

Package Rvcg updated to version 0.11 with previous version 0.10.1 dated 2014-12-22

Title: Manipulations of Triangular Meshes Based on the VCGLIB API
Description: Operations on triangular meshes based on VCGLIB. This package integrates nicely with the R-package "rgl" to render the meshes processed by Rvcg. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it), like metro and MeshLab. The vcglib source is pulled from trunk (svn://svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options determined by the configure script as well as to work with the header files included by RcppEigen.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager

Diff between Rvcg versions 0.10.1 dated 2014-12-22 and 0.11 dated 2015-04-14

 Rvcg-0.10.1/Rvcg/src/vcglib/vcg/space/index/index2D                                                 |only
 Rvcg-0.10.1/Rvcg/src/vcglib/wrap/miq                                                                |only
 Rvcg-0.11/Rvcg/DESCRIPTION                                                                          |    8 
 Rvcg-0.11/Rvcg/MD5                                                                                  |  342 
 Rvcg-0.11/Rvcg/NAMESPACE                                                                            |    2 
 Rvcg-0.11/Rvcg/R/Rvcg-package.R                                                                     |    4 
 Rvcg-0.11/Rvcg/R/vcgClost.r                                                                         |    1 
 Rvcg-0.11/Rvcg/R/vcgKDtree.r                                                                        |   11 
 Rvcg-0.11/Rvcg/inst/NEWS.Rd                                                                         |   18 
 Rvcg-0.11/Rvcg/man/Rvcg-package.Rd                                                                  |    7 
 Rvcg-0.11/Rvcg/man/dummyhead.Rd                                                                     |    3 
 Rvcg-0.11/Rvcg/man/humface.Rd                                                                       |    3 
 Rvcg-0.11/Rvcg/man/meshintegrity.Rd                                                                 |    3 
 Rvcg-0.11/Rvcg/man/setRays.Rd                                                                       |    3 
 Rvcg-0.11/Rvcg/man/vcgBary.Rd                                                                       |    3 
 Rvcg-0.11/Rvcg/man/vcgBorder.Rd                                                                     |    3 
 Rvcg-0.11/Rvcg/man/vcgClean.Rd                                                                      |    3 
 Rvcg-0.11/Rvcg/man/vcgClost.Rd                                                                      |    4 
 Rvcg-0.11/Rvcg/man/vcgClostKD.Rd                                                                    |    3 
 Rvcg-0.11/Rvcg/man/vcgCurve.Rd                                                                      |    3 
 Rvcg-0.11/Rvcg/man/vcgGetEdge.Rd                                                                    |    3 
 Rvcg-0.11/Rvcg/man/vcgImport.Rd                                                                     |    3 
 Rvcg-0.11/Rvcg/man/vcgIsolated.Rd                                                                   |    3 
 Rvcg-0.11/Rvcg/man/vcgIsosurface.Rd                                                                 |    3 
 Rvcg-0.11/Rvcg/man/vcgKDtree.Rd                                                                     |    3 
 Rvcg-0.11/Rvcg/man/vcgMeshres.Rd                                                                    |    3 
 Rvcg-0.11/Rvcg/man/vcgNonBorderEdge.Rd                                                              |    3 
 Rvcg-0.11/Rvcg/man/vcgPlyRead.Rd                                                                    |    3 
 Rvcg-0.11/Rvcg/man/vcgPlyWrite.Rd                                                                   |    3 
 Rvcg-0.11/Rvcg/man/vcgQEdecim.Rd                                                                    |    3 
 Rvcg-0.11/Rvcg/man/vcgRaySearch.Rd                                                                  |    3 
 Rvcg-0.11/Rvcg/man/vcgSample.Rd                                                                     |    3 
 Rvcg-0.11/Rvcg/man/vcgSmooth.Rd                                                                     |    3 
 Rvcg-0.11/Rvcg/man/vcgStlWrite.Rd                                                                   |    3 
 Rvcg-0.11/Rvcg/man/vcgUniformRemesh.Rd                                                              |    3 
 Rvcg-0.11/Rvcg/man/vcgUpdateNormals.Rd                                                              |    3 
 Rvcg-0.11/Rvcg/man/vcgVFadj.Rd                                                                      |    3 
 Rvcg-0.11/Rvcg/src/Rclean.cpp                                                                       |    8 
 Rvcg-0.11/Rvcg/src/Rkdtree.cpp                                                                      |   37 
 Rvcg-0.11/Rvcg/src/Runiform_resample.cpp                                                            |    2 
 Rvcg-0.11/Rvcg/src/RvcgKD.h                                                                         |   11 
 Rvcg-0.11/Rvcg/src/Volume.h                                                                         |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/autoalign_4pcs.h                                   |   33 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/clean.h                                            | 2039 ++---
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/closest.h                                          |   64 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/clustering.h                                       |   34 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/advancing_front.h                           |   47 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/ball_pivoting.h                             |  286 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/marching_cubes.h                            |   10 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/mc_trivial_walker.h                         |  101 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/platonic.h                                  |  221 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/create/resampler.h                                 | 1127 +--
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/geodesic.h                                         |   20 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/harmonic.h                                         |  490 -
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/hole.h                                             |    8 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/inside.h                                           |   43 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/point_sampling.h                                   |  265 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/pointcloud_normal.h                                |   49 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/polygon_support.h                                  |   80 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/refine.h                                           |    1 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/smooth.h                                           |  147 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/stat.h                                             |    6 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/symmetry.h                                         |   49 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/color.h                                     |  115 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/curvature.h                                 |   36 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/flag.h                                      |   80 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/normal.h                                    |   41 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/quality.h                                   |   20 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/update/selection.h                                 |    3 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_processing.h                               |  113 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/algorithms/voronoi_volume_sampling.h                          |  244 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/allocate.h                                                    | 2475 +++---
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/append.h                                                      |   66 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/base.h                                                        |   82 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/complex.h                                                     |    1 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/exception.h                                                   |   17 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/complex/used_types.h                                                  |    1 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/container/simple_temporary_data.h                                     |   20 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/math/camera.h                                                         |   19 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/math/gen_normal.h                                                     |  103 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/math/matrix33.h                                                       |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/math/matrix44.h                                                       |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/math/quadric5.h                                                       | 1059 +-
 Rvcg-0.11/Rvcg/src/vcglib/vcg/math/shot.h                                                           |  130 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/edge/component.h                                              |  154 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/edge/pos.h                                                    |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/base.h                                                   |  306 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/component.h                                              |   50 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/component_ocf.h                                          |   83 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/component_polygon.h                                      |  123 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/pos.h                                                    |  677 -
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/face/topology.h                                               |    4 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/tetrahedron/pos.h                                             |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/vertex/component.h                                            |  151 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/simplex/vertex/component_ocf.h                                        |  350 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/box2.h                                                          |    6 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/color4.h                                                        |  147 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/colorspace.h                                                    | 3664 +++++-----
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/deprecated_point3.h                                             |    7 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/base2d.h                                                  |only
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/grid_util.h                                               |   20 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/octree.h                                                  |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/perfect_spatial_hashing.h                                 | 3062 ++++----
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/index/space_iterators.h                                         |    2 
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 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/intersection2.h                                                 |   52 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/intersection3.h                                                 |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/polygon3.h                                                      |only
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/ray2.h                                                          |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/rect_packer.h                                                   |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/segment2.h                                                      |   25 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/tetra3.h                                                        |    2 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/texcoord2.h                                                     |   75 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/triangle2.h                                                     |  183 
 Rvcg-0.11/Rvcg/src/vcglib/vcg/space/triangle3.h                                                     |  171 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/gl_field.h                                                        |   92 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/glu_tessellator_cap.h                                             |    7 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/math.h                                                            |   33 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/pick.h                                                            |  124 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gl/trimesh.h                                                         |  320 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/glw/program.h                                                        | 1062 +-
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/coordinateframe.cpp                                              |   46 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/coordinateframe.h                                                |    4 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/rubberband.cpp                                                   |    4 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/trackmode.cpp                                                    |  354 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/trackmode.h                                                      |    2 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/trackutils.h                                                     |  200 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/gui/view.h                                                           |   49 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/igl                                                                  |only
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_dxf.h                                              |    5 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_field.h                                            |   83 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_idtf.h                                             |    4 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_obj.h                                              |   19 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_off.h                                              |  272 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_ply.h                                              | 1214 +--
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_stl.h                                              |  156 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/export_u3d.h                                              |  423 -
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_asc.h                                              |    4 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_ctm.h                                              |    3 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_field.h                                            |    1 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_gts.h                                              |    2 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_nvm.h                                              |   89 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_obj.h                                              |   58 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_off.h                                              |   19 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_out.h                                              |  102 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_ply.h                                              | 1842 ++---
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/import_ptx.h                                              |  782 +-
 Rvcg-0.11/Rvcg/src/vcglib/wrap/io_trimesh/precision.h                                               |only
 Rvcg-0.11/Rvcg/src/vcglib/wrap/qt/gl_label.h                                                        |   14 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/system/qgetopt.cpp                                                   |   15 
 Rvcg-0.11/Rvcg/src/vcglib/wrap/system/qgetopt.h                                                     |    7 
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More information about Rvcg at CRAN
Permanent link

Package drc updated to version 2.5-12 with previous version 2.5-11 dated 2015-04-13

Title: Analysis of Dose-Response Curves
Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Author: Christian Ritz , Jens C. Strebig
Maintainer: Christian Ritz

Diff between drc versions 2.5-11 dated 2015-04-13 and 2.5-12 dated 2015-04-14

 DESCRIPTION     |    8 -
 MD5             |    8 -
 R/plot.drc.R    |  271 ++++++++++++++++++++++++++++++--------------------------
 man/ED.drc.Rd   |    3 
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More information about drc at CRAN
Permanent link

Package ade4 updated to version 1.7-2 with previous version 1.6-2 dated 2013-11-20

Title: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray , Anne-Béatrice Dufour , and Jean Thioulouse , with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot

Diff between ade4 versions 1.6-2 dated 2013-11-20 and 1.7-2 dated 2015-04-14

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 man/between.Rd             |   30 +
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More information about ade4 at CRAN
Permanent link

Package TSdist updated to version 2.2 with previous version 2.1 dated 2015-03-31

Title: Distance Measures for Time Series Data
Description: A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series.
Author: Usue Mori, Alexander Mendiburu, J.A. Lozano
Maintainer: Usue Mori

Diff between TSdist versions 2.1 dated 2015-03-31 and 2.2 dated 2015-04-14

 DESCRIPTION             |    8 ++++----
 MD5                     |    6 +++---
 man/TSdist-package.Rd   |    5 ++---
 man/lb.keoghDistance.Rd |    2 +-
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More information about TSdist at CRAN
Permanent link

Package RcppParallel updated to version 4.3.8 with previous version 4.3.6 dated 2015-03-10

Title: Parallel Programming Tools for Rcpp
Description: High level functions for doing parallel programming with Rcpp. For example, the parallelFor() function can be used to convert the work of a standard serial "for" loop into a parallel one and the parallelReduce() function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre], Romain Francois [aut, cph], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/), RStudio [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]
Maintainer: JJ Allaire

Diff between RcppParallel versions 4.3.6 dated 2015-03-10 and 4.3.8 dated 2015-04-14

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Package MissMech updated to version 1.0.2 with previous version 1.0.1 dated 2014-01-20

Title: Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random
Description: To test whether the missing data mechanism, in a set of incompletely observed data, is one of missing completely at random (MCAR). For detailed description see Jamshidian, M. Jalal, S., and Jansen, C. (2014). "MissMech: An R Package for Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random (MCAR)," Journal of Statistical Software, 56(6), 1-31. URL http://www.jstatsoft.org/v56/i06/.
Author: Mortaza Jamshidian, Siavash Jalal, and Camden Jansen
Maintainer: Mortaza Jamshidian

Diff between MissMech versions 1.0.1 dated 2014-01-20 and 1.0.2 dated 2015-04-14

 MissMech-1.0.1/MissMech/R/AndersonDarling.r      |only
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 7 files changed, 25 insertions(+), 17 deletions(-)

More information about MissMech at CRAN
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Package lucid updated to version 1.2 with previous version 1.1 dated 2015-02-10

Title: Lucid Printing of Floating Point Numbers
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright
Maintainer: Kevin Wright

Diff between lucid versions 1.1 dated 2015-02-10 and 1.2 dated 2015-04-14

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Package gamlr updated to version 1.13-1 with previous version 1.13 dated 2015-04-01

Title: Gamma Lasso Regression
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2015), One-Step Estimator Paths for Concave Regularization, http://arxiv.org/abs/1308.5623.
Author: Matt Taddy
Maintainer: Matt Taddy

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Package EGRET updated to version 2.2.0 with previous version 2.1.1 dated 2015-02-17

Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco

Diff between EGRET versions 2.1.1 dated 2015-02-17 and 2.2.0 dated 2015-04-14

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Package dummy updated to version 0.1.2 with previous version 0.1.0 dated 2014-11-07

Title: Automatic Creation of Dummies with Support for Predictive Modeling
Description: Efficiently create dummies of all factors and character vectors in a data frame. Support is included for learning the categories on one data set (e.g., a training set) and deploying them on another (e.g., a test set).
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings

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Package domino updated to version 0.2-5 with previous version 0.2-1 dated 2014-09-09

Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite.
Author: Jacek Glodek
Maintainer: Nick Elprin

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Package descr updated to version 1.1 with previous version 1.0.4 dated 2014-11-04

Title: Descriptive Statistics
Description: Weighted frequency and contingency tables of categorical variables and of the comparison of the mean value of a numerical variable by the levels of a factor, and methods to produce xtable objects of the tables and to plot them. There are also functions to facilitate the character encoding conversion of objects, to quickly convert fixed width files into csv ones, and to export a data.frame to a text file with the necessary R and SPSS codes to reread the data.
Author: Jakson Aquino. Includes R source code and/or documentation written by Dirk Enzmann, Marc Schwartz, Nitin Jain, and Stefan Kraft
Maintainer: Jakson Aquino

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Mon, 13 Apr 2015

Package evaluate updated to version 0.6 with previous version 0.5.5 dated 2014-04-29

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [cre, ctb], Barret Schloerke [ctb]
Maintainer: Yihui Xie

Diff between evaluate versions 0.5.5 dated 2014-04-29 and 0.6 dated 2015-04-13

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Package spartan updated to version 2.2.1 with previous version 2.2 dated 2015-03-23

Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden

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Package settings updated to version 0.2.1 with previous version 0.1.1 dated 2014-10-28

Title: Software Option Settings Manager for R
Description: Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names and default values. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes. There are convenience functions to reset par() and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo

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Package rstackdeque updated to version 1.1.1 with previous version 1.1 dated 2014-12-04

Title: Persistent Fast Amortized Stack and Queue Data Structures
Description: Provides fast, persistent (side-effect-free) stack, queue and deque (double-ended-queue) data structures. While deques include a superset of functionality provided by queues, in these implementations queues are more efficient in some specialized situations. See the documentation for rstack, rdeque, and rpqueue for details.
Author: Shawn T. O'Neil
Maintainer: Shawn T. O'Neil

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Package rmaf updated to version 3.0 with previous version 2.0 dated 2014-03-10

Title: Refined Moving Average Filter
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu

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Package retrosheet updated to version 1.0.2 with previous version 1.0.1 dated 2015-04-09

Title: Import Professional Baseball Data from 'Retrosheet'
Description: A collection of tools to import and structure the (currently) single-season event, game-log, roster, and schedule data available from http://www.retrosheet.org. In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse. This package does the parsing on those files, returning the requested data in the most practical R structure to use for sabermetric or other analyses.
Author: Richard Scriven [aut, cre]
Maintainer: Richard Scriven

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Package NbClust updated to version 3.0 with previous version 2.0.4 dated 2015-03-02

Title: Determining the Best Number of Clusters in a Data Set
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad

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Package HiLMM updated to version 1.1 with previous version 1.0 dated 2014-04-15

Title: Estimation of Heritability in Linear Mixed Models
Description: Estimation of heritability with confidence intervals in linear mixed models.
Author: Anna Bonnet
Maintainer: Anna Bonnet

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Package InvariantCausalPrediction updated to version 0.3 with previous version 0.1-4 dated 2014-12-12

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen

Diff between InvariantCausalPrediction versions 0.1-4 dated 2014-12-12 and 0.3 dated 2015-04-13

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Package GMCM updated to version 1.2 with previous version 1.1.1 dated 2014-10-06

Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau

Diff between GMCM versions 1.1.1 dated 2014-10-06 and 1.2 dated 2015-04-13

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More information about GMCM at CRAN
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Package cancerTiming updated to version 3.0.0 with previous version 2.0.0 dated 2014-05-07

Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: This is a package with functions for timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom

Diff between cancerTiming versions 2.0.0 dated 2014-05-07 and 3.0.0 dated 2015-04-13

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Package ASMap updated to version 0.4 with previous version 0.3-3 dated 2015-02-02

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor , David Butler .
Maintainer: Julian Taylor

Diff between ASMap versions 0.3-3 dated 2015-02-02 and 0.4 dated 2015-04-13

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Package ramify updated to version 0.2.0 with previous version 0.1.0 dated 2015-03-23

Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers for the base matrix function that allows matrices to be created from character strings and lists (the former is especially useful for creating block matrices), (ii) better default printing of large matrices, and (iii) a number of convenience functions for users more familiar with other scientific languages like Julia, Matlab/Octave, or Python.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell

Diff between ramify versions 0.1.0 dated 2015-03-23 and 0.2.0 dated 2015-04-13

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Package metacom updated to version 1.4.3 with previous version 1.4.2 dated 2014-12-11

Title: Analysis of the "Elements of Metacommunity Structure"
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas

Diff between metacom versions 1.4.2 dated 2014-12-11 and 1.4.3 dated 2015-04-13

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More information about metacom at CRAN
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Package drc updated to version 2.5-11 with previous version 2.3-96 dated 2013-11-29

Title: Analysis of Dose-Response Curves
Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Author: Christian Ritz , Jens C. Strebig
Maintainer: Christian Ritz

Diff between drc versions 2.3-96 dated 2013-11-29 and 2.5-11 dated 2015-04-13

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More information about drc at CRAN
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Package subselect updated to version 0.12-5 with previous version 0.12-4 dated 2014-10-08

Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima

Diff between subselect versions 0.12-4 dated 2014-10-08 and 0.12-5 dated 2015-04-13

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Package lfe updated to version 2.2-1699 with previous version 2.1-1640 dated 2015-03-11

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure

Diff between lfe versions 2.1-1640 dated 2015-03-11 and 2.2-1699 dated 2015-04-13

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Package geeM updated to version 0.7.3 with previous version 0.7.2 dated 2014-12-03

Title: Fit Generalized Estimating Equations
Description: Allows generalized estimating equation fits with user-specified link and variance functions.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel

Diff between geeM versions 0.7.2 dated 2014-12-03 and 0.7.3 dated 2015-04-13

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Package R2admb updated to version 0.7.13 with previous version 0.7.10 dated 2013-09-22

Title: 'ADMB' to R Interface Functions
Description: A series of functions to call AD Model Builder (i.e., compile and run models) from within R, read the results back into R as 'admb' objects, and provide standard accessors (i.e. coef(), vcov(), etc.)
Author: Ben Bolker, Hans Skaug, Jeff Laake
Maintainer: Ben Bolker

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Package inline updated to version 0.3.14 with previous version 0.3.13 dated 2013-08-08

Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel, Romain Francois, Karline Soetaert
Maintainer: Dirk Eddelbuettel

Diff between inline versions 0.3.13 dated 2013-08-08 and 0.3.14 dated 2015-04-13

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Package fCertificates updated to version 0.5-4 with previous version 0.5-3 dated 2014-03-02

Title: Basics of Certificates and Structured Products Valuation
Description: Collection of pricing by duplication methods for popular structured products ("Zertifikate").
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm

Diff between fCertificates versions 0.5-3 dated 2014-03-02 and 0.5-4 dated 2015-04-13

 DESCRIPTION                |   14 +++++++-------
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Package apc updated to version 1.1 with previous version 1.0 dated 2014-08-30

Title: Age-Period-Cohort Analysis
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen

Diff between apc versions 1.0 dated 2014-08-30 and 1.1 dated 2015-04-13

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Sun, 12 Apr 2015

Package PtProcess updated to version 3.3-9 with previous version 3.3-7 dated 2014-10-16

Title: Time Dependent Point Process Modelling
Description: Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte

Diff between PtProcess versions 3.3-7 dated 2014-10-16 and 3.3-9 dated 2015-04-12

 DESCRIPTION       |   11 +++++------
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Package HiddenMarkov updated to version 1.8-3 with previous version 1.8-1 dated 2014-09-25

Title: Hidden Markov Models
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte

Diff between HiddenMarkov versions 1.8-1 dated 2014-09-25 and 1.8-3 dated 2015-04-12

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Package resample updated to version 0.4 with previous version 0.2 dated 2014-03-12

Title: Resampling Functions
Description: Bootstrap, permutation tests, and other resampling functions, featuring easy-to-use syntax.
Author: Tim Hesterberg
Maintainer: Tim Hesterberg

Diff between resample versions 0.2 dated 2014-03-12 and 0.4 dated 2015-04-12

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 41 files changed, 1111 insertions(+), 489 deletions(-)

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