Mon, 02 Mar 2015

Package RobPer updated to version 1.2.1 with previous version 1.2 dated 2014-10-03

Title: Robust Periodogram and Periodicity Detection Methods
Description: Calculates periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit. Artificial light curves can be generated using the function tsgen. For more details see Thieler, Fried and Rathjens (2013).
Author: Anita M. Thieler, Jonathan Rathjens and Roland Fried, with contributions from Brenton R. Clarke, Uwe Ligges, Matias Salibian-Barrera, Gert Willems and Victor Yohai
Maintainer: Jonathan Rathjens

Diff between RobPer versions 1.2 dated 2014-10-03 and 1.2.1 dated 2015-03-02

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Package lsr updated to version 0.5 with previous version 0.3.2 dated 2014-01-31

Title: Companion to "Learning Statistics with R"
Description: A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.5. [Lecture notes] School of Psychology, University of Adelaide, Adelaide, Australia. ISBN: 978-1-326-18972-3. URL: http://health.adelaide.edu.au/psychology/ccs/teaching/lsr/.
Author: Daniel Navarro
Maintainer: Daniel Navarro

Diff between lsr versions 0.3.2 dated 2014-01-31 and 0.5 dated 2015-03-02

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More information about lsr at CRAN
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Sun, 01 Mar 2015

Package MazamaSpatialUtils updated to version 0.2.2 with previous version 0.2.1 dated 2015-02-22

Title: Mazama Science Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized spatial polygons dataframes. Utility scripts use these datasets to return values such as country, state, timezone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre], Will Leahy [aut], Henry Nguyen [aut]
Maintainer: Jonathan Callahan

Diff between MazamaSpatialUtils versions 0.2.1 dated 2015-02-22 and 0.2.2 dated 2015-03-01

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Package HiClimR updated to version 1.1.6 with previous version 1.1.5 dated 2014-11-13

Title: Hierarchical Climate Regionalization
Description: A tool for hierarchical climate regionalization applicable to any correlation-based clustering. It adds several features and a new clustering method (called, regional linkage) to hierarchical clustering in R (`hclust` function in `stats` library): regridding, coarsening spatial resolution, geographic masking, data filtering by thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function, hybrid hierarchical clustering, and cluster validation.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr

Diff between HiClimR versions 1.1.5 dated 2014-11-13 and 1.1.6 dated 2015-03-01

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More information about HiClimR at CRAN
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Package ggthemes updated to version 2.1.2 with previous version 2.1.0 dated 2014-12-18

Title: Extra Themes, Scales and Geoms for `ggplot2`
Description: Some extra themes, geoms, and scales for `ggplot2`.
Author: Jeffrey B. Arnold [aut, cre], Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb], Baptise Auguie [ctb], Justin Talbot [ctb] (Some code from the labeling package)
Maintainer: Jeffrey B. Arnold

Diff between ggthemes versions 2.1.0 dated 2014-12-18 and 2.1.2 dated 2015-03-01

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More information about ggthemes at CRAN
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Package archivist updated to version 1.3 with previous version 1.2 dated 2014-11-29

Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.
Author: Przemyslaw Biecek [aut, cre], Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek

Diff between archivist versions 1.2 dated 2014-11-29 and 1.3 dated 2015-03-01

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More information about archivist at CRAN
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Package XLConnect updated to version 0.2-11 with previous version 0.2-10 dated 2015-01-25

Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons Codec), Stephen Colebourne [ctb, cph] (Joda-Time Java library)
Maintainer: Martin Studer

Diff between XLConnect versions 0.2-10 dated 2015-01-25 and 0.2-11 dated 2015-03-01

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Package BinNonNor updated to version 1.2 with previous version 1.1 dated 2015-02-01

Title: Data Generation with Binary and Continuous Non-Normal Components
Description: Generation of multiple binary and continuous non-normal variables simultaneously given the marginal characteristics and association structure based on the methodology proposed by Demirtas et al. (2012).
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan

Diff between BinNonNor versions 1.1 dated 2015-02-01 and 1.2 dated 2015-03-01

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Package isingLenzMC updated to version 0.2.3 with previous version 0.2.1 dated 2014-05-18

Title: Monte Carlo for Classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics. Model explains physics of spin glasses and magnetic materials, but used in many different context for example phase transitions and neural systems. This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions.
Author: Mehmet Suzen
Maintainer: Mehmet Suzen

Diff between isingLenzMC versions 0.2.1 dated 2014-05-18 and 0.2.3 dated 2015-03-01

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Package R.utils updated to version 2.0.0 with previous version 1.34.0 dated 2014-10-08

Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.utils versions 1.34.0 dated 2014-10-08 and 2.0.0 dated 2015-03-01

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Package PoisBinOrd updated to version 1.1 with previous version 1.0 dated 2015-02-03

Title: Data Generation with Poisson, Binary and Ordinal Components
Description: Generation of multiple count, binary and ordinal variables simultaneously given the marginal characteristics and association structure. Throughout the package, the word 'Poisson' is used to imply count data under the assumption of Poisson distribution.
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan

Diff between PoisBinOrd versions 1.0 dated 2015-02-03 and 1.1 dated 2015-03-01

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Package gendata updated to version 1.1 with previous version 1.0 dated 2014-05-08

Title: Generate and Modify Synthetic Datasets
Description: Set of functions to create datasets using a correlation matrix.
Author: Francis Huang
Maintainer: Francis Huang

Diff between gendata versions 1.0 dated 2014-05-08 and 1.1 dated 2015-03-01

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Package drat updated to version 0.0.2 with previous version 0.0.1 dated 2015-02-05

Title: Drat R Archive Template
Description: Creation and Use of R Repositories via two helper functions to insert packages into a repository, and to add repository information to the current R session. Two primary types of repositories are support: gh-pages at GitHub, as well as local repositories on either the same machine or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between drat versions 0.0.1 dated 2015-02-05 and 0.0.2 dated 2015-03-01

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Package cqrReg updated to version 1.1 with previous version 1.0 dated 2014-11-27

Title: Quantile, Composite Quantile Regression and Regularized Versions
Description: Estimate quantile regression(QR) and composite quantile regression (cqr) and with adaptive lasso penalty using interior point (IP), majorize and minimize(MM), coordinate descent (CD), and alternating direction method of multipliers algorithms(ADMM).
Author: Jueyu Gao & Linglong Kong
Maintainer: Jueyu Gao

Diff between cqrReg versions 1.0 dated 2014-11-27 and 1.1 dated 2015-03-01

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Sat, 28 Feb 2015

Package timma updated to version 1.2.1 with previous version 1.2.0 dated 2015-01-11

Title: Target Inhibition Interaction using Maximization and Minimization Averaging
Description: Prediction and ranking of drug combinations based on their drug-target interaction profiles and single-drug sensitivities in a given cancer cell line or patient-derived sample.
Author: Liye He, Krister Wennerberg, Tero Aittokallio and Jing Tang
Maintainer: Jing Tang

Diff between timma versions 1.2.0 dated 2015-01-11 and 1.2.1 dated 2015-02-28

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Package rSPACE updated to version 1.1.0 with previous version 1.0.4 dated 2015-01-06

Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis

Diff between rSPACE versions 1.0.4 dated 2015-01-06 and 1.1.0 dated 2015-02-28

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Package hypervolume updated to version 1.2 with previous version 1.1.2 dated 2015-01-16

Title: High-Dimensional Kernel Density Estimation and Geometry Operations
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder

Diff between hypervolume versions 1.1.2 dated 2015-01-16 and 1.2 dated 2015-02-28

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Package fields updated to version 8.2-1 with previous version 7.1 dated 2014-05-16

Title: Tools for Spatial Data
Description: Fields is for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging and compact covariances for large data sets. The splines and Kriging methods are supporting by functions that can determine the smoothing parameter (nugget and sill variance) by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to function that also estimates the correlation scale (range). A major feature is that any covariance function implemented in R and following a simple fields format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details in addition to the manual pages. The commented source code can be viewed by expanding the source code .tar.gz file and looking in R subdirectory.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka

Diff between fields versions 7.1 dated 2014-05-16 and 8.2-1 dated 2015-02-28

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Package ExtremeBounds updated to version 0.1.5 with previous version 0.1.4.2 dated 2014-11-18

Title: Extreme Bounds Analysis (EBA)
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac
Maintainer: Marek Hlavac

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Fri, 27 Feb 2015

Package sidier updated to version 3.0.1 with previous version 3.0 dated 2014-11-18

Title: Substitution and Indel Distances to Infer Evolutionary Relationships
Description: Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares

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Package R.oo updated to version 1.19.0 with previous version 1.18.0 dated 2014-02-25

Title: R Object-Oriented Programming with or without References
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

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Package pwr updated to version 1.1-2 with previous version 1.1.1 dated 2009-10-26

Title: Basic Functions for Power Analysis
Description: Power analysis functions along the lines of Cohen (1988).
Author: Stephane Champely [aut], Claus Ekstrom [ctb], Peter Dalgaard [ctb], Jeffrey Gill [ctb], Helios De Rosario [cre]
Maintainer: Helios De Rosario

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Package MAMS updated to version 0.4 with previous version 0.3 dated 2014-05-07

Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki and Dominic Magirr
Maintainer: Thomas Jaki

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Package BDgraph updated to version 2.16 with previous version 2.15 dated 2015-01-23

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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Package openNLP updated to version 0.2-4 with previous version 0.2-3 dated 2014-04-19

Title: Apache OpenNLP Tools Interface
Description: An interface to the Apache OpenNLP tools (version 1.5.3). The Apache OpenNLP library is a machine learning based toolkit for the processing of natural language text written in Java. It supports the most common NLP tasks, such as tokenization, sentence segmentation, part-of-speech tagging, named entity extraction, chunking, parsing, and coreference resolution. See for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik

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Package MicSim updated to version 1.0.7 with previous version 1.0.6 dated 2014-07-02

Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn

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Package RObsDat updated to version 15.02 with previous version 14.12 dated 2014-12-29

Title: Data Mangement for Hydrology and Beyond Using the Observations Data Model
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser

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Package lcmm updated to version 1.7.2 with previous version 1.7.1 dated 2015-02-26

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima

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Package NormPsy updated to version 1.0.3 with previous version 1.0.2 dated 2014-11-27

Title: Normalisation of Psychometric Tests
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima

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Package FindIt updated to version 0.5 with previous version 0.4 dated 2015-02-07

Title: Finding Heterogeneous Treatment Effects
Description: The heterogeneous treatment effect estimation procedure proposed by Imai and Ratkovic (2013). The proposed method is applicable, for example, when selecting a small number of most (or least) efficacious treatments from a large number of alternative treatments as well as when identifying subsets of the population who benefit (or are harmed by) a treatment of interest. The method adapts the Support Vector Machine classifier by placing separate LASSO constraints over the pre-treatment parameters and causal heterogeneity parameters of interest. This allows for the qualitative distinction between causal and other parameters, thereby making the variable selection suitable for the exploration of causal heterogeneity. The package also contains the function, INT, which estimates the average marginal treatment effect, the average treatment combination effect, and the average marginal treatment interaction effect proposed by Egami and Imai (2015).
Author: Naoki Egami , Marc Ratkovic , Kosuke Imai ,
Maintainer: Naoki Egami

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Package CoxRidge updated to version 0.9.2 with previous version 0.9.1 dated 2013-06-26

Title: Cox Models with Dynamic Ridge Penalties
Description: A package for fitting Cox models with penalized ridge-type partial likelihood. The package includes functions for fitting simple Cox models with all covariates controlled by a ridge penalty. The weight of the penalty is optimised by using a REML type-algorithm. Models with time varying effects of the covariates can also be fitted. Some of the covariates may be allowed to be fixed and thus not controlled by the penalty. There are three different penalty functions, ridge, dynamic and weighted dynamic. Time varying effects can be fitted without the need of an expanded dataset.
Author: Aris Perperoglou
Maintainer: Aris Perperoglou

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Package userfriendlyscience updated to version 0.2-0 with previous version 0.1-2 dated 2014-04-22

Title: Quantitative Analysis Made Accessible
Description: Contains a number of functions that serve two goals: first, make R more accessible to people migrating from SPSS by adding a number of functions that behave roughly like their SPSS equivalents; and second, make a number of slightly more advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters

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Package spatstat updated to version 1.41-1 with previous version 1.40-0 dated 2014-12-31

Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley , Rolf Turner and Ege Rubak , with substantial contributions of code by Kasper Klitgaard Berthelsen; Abdollah Jalilian; Marie-Colette van Lieshout; Tuomas Rajala; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; M. Baddeley; C. Beale; M. Bell; R. Bernhardt; T. Bendtsen; A. Bevan; B. Biggerstaff; L. Bischof; R. Bivand; J.M. Blanco Moreno; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; R. Corria Ainslie; M. de la Cruz; P. Dalgaard; S. Das; P.J. Diggle; P. Donnelly; I. Dryden; S. Eglen; A. El-Gabbas; O. Flores; E.D. Ford; P. Forbes; S. Frank; J. Franklin; N. Funwi-Gabga; O. Garcia; A. Gault; M. Genton; S. Ghalandarayeshi; J. Gilbey; J. Goldstick; P. Grabarnik; C. Graf; U. Hahn; A. Hardegen; M.B. Hansen; M. Hazelton; J. Heikkinen; M. Hering; M. Herrmann; K. Hornik; P. Hunziker; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Khanmohammadi; P. Kovesi; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; G. Limitsios; A. Lister; B. Madin; J. Marcus; K. Marchikanti; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; L. De Middeleer; R.K. Milne; E. Miranda; J. Moller; E. Mudrak; G.M. Nair; N. Nava; L.S. Nielsen; F. Nunes; J.R. Nyengaard; J. Oehlschlaegel; T. Onkelinx; S. O'Riordan; E. Parilov; J. Picka; N. Picard; M. Porter; S. Protsiv; A. Raftery; S. Rakshit; P. Ramon; X. Raynaud, M. Reiter; I. Renner; T.O. Richardson; B.D. Ripley; E. Rosenbaum; B. Rowlingson; J. Rudokas; J. Rudge; C. Ryan; F. Safavimanesh; A. Sarkka; K. Schladitz; S. Schutte; B.T. Scott; G.C. Shen; V. Shcherbakov; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; T. Thorarinsdottir; B. Turlach; T. Tvedebrink; K. Ummer; M. Uppala; A. van Burgel; T. Verbeke; M. Vihtakari; A. Villers; F. Vinatier; S. Voss; H. Wang; H. Wendrock; J. Wild; C. Witthoft; S. Wong; M. Woringer; M.E. Zamboni and A. Zeileis.
Maintainer: Adrian Baddeley

Diff between spatstat versions 1.40-0 dated 2014-12-31 and 1.41-1 dated 2015-02-27

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More information about spatstat at CRAN
Permanent link

Package RcppEigen updated to version 0.3.2.4.0 with previous version 0.3.2.3.0 dated 2014-12-23

Title: Rcpp Integration for the Eigen Templated Linear Algebra Library
Description: R and Eigen integration using Rcpp. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on Lapack and level-3 BLAS. The RcppEigen package includes the header files from the Eigen C++ template library (currently version 3.2.3). Thus users do not need to install Eigen itself in order to use RcppEigen. Since version 3.1.1, Eigen is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. RcppEigen (the Rcpp bindings/bridge to Eigen) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel; the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel

Diff between RcppEigen versions 0.3.2.3.0 dated 2014-12-23 and 0.3.2.4.0 dated 2015-02-27

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Package mads updated to version 0.1.2 with previous version 0.1.1 dated 2014-12-23

Title: Multi-Analysis Distance Sampling
Description: Performs distance sampling analyses on a number of species accounting for unidentified sightings, model uncertainty and covariate uncertainty.
Author: Laura Marshall
Maintainer: Laura Marshall

Diff between mads versions 0.1.1 dated 2014-12-23 and 0.1.2 dated 2015-02-27

 DESCRIPTION                 |    8 ++++----
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Permanent link

Package geostatsp updated to version 1.2.1 with previous version 1.1.9 dated 2015-01-23

Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation..
Author: Patrick Brown [aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown

Diff between geostatsp versions 1.1.9 dated 2015-01-23 and 1.2.1 dated 2015-02-27

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Package DSsim updated to version 1.0.3 with previous version 1.0.2 dated 2014-12-23

Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. It repeatedly generates instances of a user defined population within a given survey region, generates realisations of a survey design (currently these must be pre-generated using Distance software) and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This will allow users to select survey designs which will give them the best accuracy and precision given their expectations about population distribution. Any uncertainty in population distribution or population parameters can be included by running the different survey designs for a number of different population descriptions. An example simulation can be found in the help file for make.simulation.
Author: Laura Marshall
Maintainer: Laura Marshall

Diff between DSsim versions 1.0.2 dated 2014-12-23 and 1.0.3 dated 2015-02-27

 DESCRIPTION                    |    8 +-
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 NEWS                           |   71 +++++++++++-------
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More information about DSsim at CRAN
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Package bio3d updated to version 2.2-1 with previous version 2.1-3 dated 2014-10-27

Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant

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Thu, 26 Feb 2015

Package nortest updated to version 1.0-3 with previous version 1.0-2 dated 2012-05-30

Title: Tests for Normality
Description: Five omnibus tests for testing the composite hypothesis of normality.
Author: Juergen Gross [aut], Uwe Ligges [aut, cre]
Maintainer: Uwe Ligges

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Package gte updated to version 1.2-2 with previous version 1.2-1 dated 2014-01-06

Title: Generalized Turnbull's Estimator
Description: Generalized Turnbull's estimator proposed by Dehghan and Duchesne (2011).
Author: Mohammad Hossein Dehghan, Thierry Duchesne and Sophie Baillargeon
Maintainer: Thierry Duchesne

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Package amen updated to version 1.0 with previous version 0.999 dated 2014-03-01

Title: Additive and Multiplicative Effects Models for Networks and Relational Data
Description: Analysis of network and relational data using additive and multiplicative effects (AME) models. The basic model includes regression terms, the covariance structure of the social relations model (Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor models (Hoff(2009)). Four different link functions accommodate different relational data structures, including binary/network data (bin), normal relational data (nrm), ordinal relational data (ord) and data from fixed-rank nomination schemes (frn). Several of these link functions are discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this software was supported in part by NICHD grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff

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More information about amen at CRAN
Permanent link

Package RcppArmadillo updated to version 0.4.650.1.1 with previous version 0.4.600.4.0 dated 2015-01-25

Title: Rcpp Integration for the Armadillo Templated Linear Algebra Library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The RcppArmadillo package includes the header files from the templated Armadillo library. Thus users do not need to install Armadillo itself in order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.4.600.4.0 dated 2015-01-25 and 0.4.650.1.1 dated 2015-02-26

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Package PDQutils updated to version 0.1.1 with previous version 0.1.0 dated 2015-02-12

Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher Approximations
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the cumulative distribution, density, and quantile) of probability distributions via classical expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav

Diff between PDQutils versions 0.1.0 dated 2015-02-12 and 0.1.1 dated 2015-02-26

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Permanent link

Package CNVassoc updated to version 2.1 with previous version 2.0.1 dated 2013-09-19

Title: Association Analysis of CNV Data and Imputed SNPs
Description: The CNVassoc package carries out analysis of common Copy Number Variants (CNVs) and imputed Single Nucleotide Polymorphisms (SNPs) in population-based studies. It includes tools for estimating association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. Moreover, it is possible to perform epistasis studies with pairs of CNVs or imputed SNPs. It has been optimized in order to make feasible the analyses of Genome Wide Association studies (GWAs) with hundreds of thousands of genetic variants (CNVs / imputed SNPs). Also, it incorporates functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ...) have been created to facilitate the analysis.
Author: Juan R Gonzlez, Isaac Subirana
Maintainer: Isaac Subirana

Diff between CNVassoc versions 2.0.1 dated 2013-09-19 and 2.1 dated 2015-02-26

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Permanent link

Package RcmdrPlugin.ROC updated to version 1.0-18 with previous version 1.0-17 dated 2014-12-20

Title: Rcmdr Receiver Operator Characteristic Plug-In PACKAGE
Description: Rcmdr GUI extension plug-in for Receiver Operator Characteristic tools from pROC and ROCR packages. Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package ResourceSelection.
Author: Daniel-Corneliu Leucuta [aut, cre], Mihaela Hedesiu [ctb], Andrei Achimas [ctb], Oana Almasan [ctb]
Maintainer: Daniel-Corneliu Leucuta

Diff between RcmdrPlugin.ROC versions 1.0-17 dated 2014-12-20 and 1.0-18 dated 2015-02-26

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Package ore updated to version 1.1.0 with previous version 1.0.6 dated 2015-01-01

Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden

Diff between ore versions 1.0.6 dated 2015-01-01 and 1.1.0 dated 2015-02-26

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More information about ore at CRAN
Permanent link

Package nlstools updated to version 1.0-1 with previous version 1.0-0 dated 2014-06-25

Title: Tools for Nonlinear Regression Analysis
Description: Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.
Author: Florent Baty and Marie-Laure Delignette-Muller , with contributions from Sandrine Charles, Jean-Pierre Flandrois, and Christian Ritz
Maintainer: Florent Baty

Diff between nlstools versions 1.0-0 dated 2014-06-25 and 1.0-1 dated 2015-02-26

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Permanent link

Package HardyWeinberg updated to version 1.5.5 with previous version 1.5.4 dated 2014-08-11

Title: Graphical Tests for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman
Maintainer: Jan Graffelman

Diff between HardyWeinberg versions 1.5.4 dated 2014-08-11 and 1.5.5 dated 2015-02-26

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Package FuzzyNumbers updated to version 0.4-1 with previous version 0.3-5 dated 2014-10-01

Title: Tools to Deal with Fuzzy Numbers
Description: S4 classes and methods to deal with fuzzy numbers. With them you can compute any arithmetic operations (e.g. by using the Zadeh extension principle), perform approximation of arbitrary FNs by trapezoidal and piecewise linear FNs, prepare plots of FNs for publications, calculate possibility and necessity values for comparisons, etc.
Author: Marek Gagolewski [aut, cre], Jan Caha [ctb]
Maintainer: Marek Gagolewski

Diff between FuzzyNumbers versions 0.3-5 dated 2014-10-01 and 0.4-1 dated 2015-02-26

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Package forecast updated to version 5.9 with previous version 5.8 dated 2015-01-06

Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman with contributions from George Athanasopoulos, Slava Razbash, Drew Schmidt, Zhenyu Zhou, Yousaf Khan, Christoph Bergmeir, Earo Wang
Maintainer: Rob J Hyndman

Diff between forecast versions 5.8 dated 2015-01-06 and 5.9 dated 2015-02-26

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Package exact2x2 updated to version 1.4.1 with previous version 1.4.0 dated 2014-08-25

Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Description: Calculates Fisher's exact test, Blaker's exact test, or the exact McNemar's test with appropriate matching confidence intervals. Provides power and sample size calculations. Also gives melded confidence intervals for the binomial case.
Author: Michael P. Fay
Maintainer: Michael P. Fay

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Package RODBC updated to version 1.3-11 with previous version 1.3-10 dated 2013-11-25

Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre], Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley

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Package lcmm updated to version 1.7.1 with previous version 1.6.6 dated 2014-09-11

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima

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Package R2SWF updated to version 0.9 with previous version 0.8-2 dated 2014-12-19

Title: Convert R Graphics to Flash Animations
Description: Using the Ming library (http://www.libming.org/) to create Flash animations. Users can either use the SWF device swf() to generate SWF file directly through plotting functions like plot() and lines(), or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu

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Package polyCub updated to version 0.5-2 with previous version 0.5-1 dated 2014-10-24

Title: Cubature over Polygonal Domains
Description: The following methods for cubature (numerical integration) over polygonal domains are currently implemented: the two-dimensional midpoint rule as a simple wrapper around as.im.function() from package spatstat (Baddeley and Turner, 2005), the product Gauss cubature by Sommariva and Vianello (2007), an adaptive cubature for isotropic functions via line integrate() along the boundary (Meyer and Held, 2014), and quasi-exact methods specific to the integration of the bivariate Gaussian density over polygonal and circular domains (based on formulae from the Abramowitz and Stegun (1972) handbook). For cubature over simple hypercubes, the packages "cubature" and "R2Cuba" are more appropriate.
Author: Sebastian Meyer [aut, cre, trl], Leonhard Held [ths], Michael Hoehle [ths]
Maintainer: Sebastian Meyer

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Package multicool updated to version 0.1-5 with previous version 0.1-2 dated 2013-07-10

Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran

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Wed, 25 Feb 2015

Package PRROC updated to version 1.1 with previous version 1.0 dated 2014-12-16

Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau

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Package hergm updated to version 2.2-0 with previous version 2.1-1 dated 2015-01-11

Title: Hierarchical Exponential-Family Random Graph Models
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger [aut, cre], Mark S. Handcock [ctb], Pamela Luna [ctb]
Maintainer: Michael Schweinberger

Diff between hergm versions 2.1-1 dated 2015-01-11 and 2.2-0 dated 2015-02-25

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Package frailtypack updated to version 2.7.4 with previous version 2.7.2 dated 2014-10-16

Title: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction
Description: Frailtypack fits several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation. 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of joint modelling for recurrent events with terminal event for clustered data or not. Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have a gamma distribution, but you can switch to a log-normal in shared and joint models. Now, you can also consider time-varying covariates effects in Cox, shared and joint models. The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau

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Package diseasemapping updated to version 1.1.7 with previous version 1.1.5 dated 2015-01-15

Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown

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Package visreg updated to version 2.1-1 with previous version 2.1-0 dated 2014-11-27

Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

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Package survMisc updated to version 0.4.5 with previous version 0.4.4 dated 2015-01-06

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

Diff between survMisc versions 0.4.4 dated 2015-01-06 and 0.4.5 dated 2015-02-25

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Package multitaper updated to version 1.0-11 with previous version 1.0-10 dated 2015-02-18

Title: Multitaper Spectral Analysis Tools
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim , Wesley S. Burr
Maintainer: Karim Rahim

Diff between multitaper versions 1.0-10 dated 2015-02-18 and 1.0-11 dated 2015-02-25

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Package MuMIn updated to version 1.13.4 with previous version 1.12.1 dated 2014-12-17

Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria (AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń

Diff between MuMIn versions 1.12.1 dated 2014-12-17 and 1.13.4 dated 2015-02-25

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Package BoolNet updated to version 2.1.1 with previous version 2.1.0 dated 2015-02-23

Title: Construction, Simulation and Analysis of Boolean Networks
Description: Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb] (contributed PicoSAT code), Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler

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Package SDD updated to version 1.2 with previous version 1.1 dated 2014-02-27

Title: Serial Dependence Diagrams
Description: Allows for computing (and by default plotting) different types of serial dependence diagrams.
Author: Luca Bagnato, Lucio De Capitani, Angelo Mazza and Antonio Punzo
Maintainer: Angelo Mazza

Diff between SDD versions 1.1 dated 2014-02-27 and 1.2 dated 2015-02-25

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Package lgcp updated to version 1.3-9 with previous version 1.3-8 dated 2015-02-04

Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor

Diff between lgcp versions 1.3-8 dated 2015-02-04 and 1.3-9 dated 2015-02-25

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Package FGSG updated to version 1.0.2 with previous version 1.0 dated 2014-04-13

Title: Feature Grouping and Selection Over an Undirected Graph
Description: Implement algorithms for feature grouping and selection over an undirected graph, solves problems like graph fused lasso, graph OSCAR and so on.
Author: Xiaotong Shen, Yiwen Sun, Julie Langou
Maintainer: Yiwen Sun

Diff between FGSG versions 1.0 dated 2014-04-13 and 1.0.2 dated 2015-02-25

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Package soilDB updated to version 1.5-2 with previous version 1.5 dated 2015-02-20

Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette

Diff between soilDB versions 1.5 dated 2015-02-20 and 1.5-2 dated 2015-02-25

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Package sgt updated to version 1.1 with previous version 1.0 dated 2015-02-16

Title: Skewed Generalized T Distribution
Description: Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.
Author: Carter Davis
Maintainer: Carter Davis

Diff between sgt versions 1.0 dated 2015-02-16 and 1.1 dated 2015-02-25

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Package R.matlab updated to version 3.2.0 with previous version 3.1.1 dated 2014-10-10

Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files (via 'Rcompression'), sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson

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Package npmv updated to version 2.2 with previous version 2.1 dated 2013-12-04

Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis

Diff between npmv versions 2.1 dated 2013-12-04 and 2.2 dated 2015-02-25

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Package multiPIM updated to version 1.4-3 with previous version 1.4-1 dated 2014-04-14

Title: Variable Importance Analysis with Population Intervention Models
Description: Performs variable importance analysis using a causal inference approach. This is done by fitting Population Intervention Models. The default is to use a Targeted Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and Graphical Computation (G-COMP) estimators. Inference can be obtained from the influence curve (plug-in) or by bootstrapping.
Author: Stephan Ritter , Alan Hubbard , Nicholas Jewell
Maintainer: Stephan Ritter

Diff between multiPIM versions 1.4-1 dated 2014-04-14 and 1.4-3 dated 2015-02-25

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Package lessR updated to version 3.2 with previous version 3.1.1 dated 2014-09-23

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate descriptive statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function and color themes. The function Help provides a help system that suggests specific analyses and functions. Variable labels are available. A confirmatory factor analysis of multiple indicator measurement models is also available as is a pedagogical routines for data simulation such as for the Central Limit Theorem.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing

Diff between lessR versions 3.1.1 dated 2014-09-23 and 3.2 dated 2015-02-25

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Package iqLearn updated to version 1.3 with previous version 1.2 dated 2014-03-04

Title: Interactive Q-Learning
Description: Estimate an optimal dynamic treatment regime using Interactive Q-learning.
Author: Kristin A. Linn, Eric B. Laber, Leonard A. Stefanski
Maintainer: Kristin A. Linn

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Package dunn.test updated to version 1.2.3 with previous version 1.2.2 dated 2015-01-03

Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno

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Tue, 24 Feb 2015

Package tRakt updated to version 0.9.0 with previous version 0.7.4 dated 2015-02-23

Title: Pull Data from 'trakt.tv'
Description: A wrapper for the trakt.tv APIv2 which uses httr and jsonlite to send non-OAuth2 requests and receive tidied data.
Author: Lukas Burk [aut, cre]
Maintainer: Lukas Burk

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Package aroma.apd updated to version 0.6.0 with previous version 0.5.0 dated 2014-02-27

Title: A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
Description: DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

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Package speaq updated to version 1.2.1 with previous version 1.2.0 dated 2015-01-14

Title: Tools for Nuclear Magnetic Resonance Spectrum Alignment and Quantitative Analysis
Description: We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Related publication is available at http://www.biomedcentral.com/1471-2105/12/405/.
Author: Trung Nghia Vu, Kris Laukens and Dirk Valkenborg
Maintainer: Trung Nghia Vu

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Package rfUtilities updated to version 1.0-1 with previous version 1.0 dated 2014-11-21

Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance correction, significance test, cross validation and partial dependency plots.
Author: Jeffrey S. Evans [cre, aut], Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans

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Package rglobi updated to version 0.2.5 with previous version 0.2.4 dated 2015-01-28

Title: R interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI). GloBI provides access to spatial-temporal species interaction records from source all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. In addition, it supports Cypher, a graph query language, to allow for executing custom queries on the GloBI aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen

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Package rasterVis updated to version 0.35 with previous version 0.32 dated 2014-10-25

Title: Visualization Methods for Raster Data
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut], Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro

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Package phenability updated to version 2.0 with previous version 1.0 dated 2014-04-23

Title: Nonparametric Stability Analysis
Description: An alternative to carrying out phenotypic adaptability and stability analyses, taking into account nonparametric statistics. Can be used as a robust approach, less sensitive to departures from common genotypic, environmental, and GxE effects data assumptions (e.g., normal distribution of errors).
Author: Leonardo Castelo Branco
Maintainer: Leonardo C. Branco

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Package likelihood updated to version 1.7 with previous version 1.6 dated 2014-06-27

Title: Methods for Maximum Likelihood Estimation
Description: Tools for maximum likelihood estimation of parameters of scientific models.
Author: Lora Murphy
Maintainer: Lora Murphy

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Package FFD updated to version 1.0-6 with previous version 1.0-2 dated 2013-04-22

Title: Freedom from Disease
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka

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Package clinfun updated to version 1.0.9 with previous version 1.0.6 dated 2014-07-22

Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan

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Package AER updated to version 1.2-3 with previous version 1.2-2 dated 2014-01-28

Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Author: Christian Kleiber [aut], Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis

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Package SvyNom updated to version 1.1 with previous version 1.0 dated 2012-12-07

Title: Nomograms for Right-Censored Outcomes from Survey Designs
Description: Builds, evaluates and validates a nomogram with survey data and right-censored outcomes.
Author: Mithat Gonen, Marinela Capanu
Maintainer: Mithat Gonen

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Package HistDAWass updated to version 0.1.1 with previous version 0.1 dated 2015-02-18

Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new approach to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e., data described by univariate histograms. The methods and the basic statistics for histogram-valued data are mainly based on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric between quantile functions. The package contains unsupervised classification techniques, least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino

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Package CombinS updated to version 1.1 with previous version 1.0 dated 2013-12-12

Title: Construction Methods of some Series of PBIB Designs
Description: The Combinatory Method (s) to Construct a series of PBIB designs and we give their associated U-type design.
Author: Mohamed Laib, Imane Rezgui, Zebida Gheribi-Aoulmi and Herve Monod
Maintainer: Mohamed Laib

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Package autopls updated to version 1.3 with previous version 1.2-7 dated 2013-08-13

Title: Partial Least Squares Regression with Backward Selection of Predictors
Description: Some convenience functions for pls regression, including backward variable selection and validation procedures, image based predictions and plotting.
Author: Sebastian Schmidtlein, with contributions from C. Oldenburg and H. Feilhauer and with a code snipped borrowed from Bjorn-Helge Mevik
Maintainer: Sebastian Schmidtlein

Diff between autopls versions 1.2-7 dated 2013-08-13 and 1.3 dated 2015-02-24

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Package daff updated to version 0.1.2 with previous version 0.1.1 dated 2015-02-23

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. Daff uses the V8 package to wrap the 'daff.js' javascript library which is included in the package. Daff exposes a subset of 'daff.js' functionality, tailored for usage within R.
Author: Paul Fitzpatrick [aut] (javascript original, http://paulfitz.github.io/daff/), Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge

Diff between daff versions 0.1.1 dated 2015-02-23 and 0.1.2 dated 2015-02-24

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Package cds updated to version 1.0.1 with previous version 1.0 dated 2015-02-16

Title: Constrained Dual Scaling for Detecting Response Styles
Description: This is an implementation of constrained dual scaling for detecting response styles in categorical data, including utility functions. The procedure involves adding additional columns to the data matrix representing the boundaries between the rating categories. The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are sought which provide optimal scores for the rating categories. These optimal scores are constrained to follow monotone quadratic splines. Clusters are introduced within which the response styles can vary. The type of response style present in a cluster can be diagnosed from the optimal scores for said cluster, and this can be used to construct an imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees

Diff between cds versions 1.0 dated 2015-02-16 and 1.0.1 dated 2015-02-24

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Package TAM updated to version 1.5-2 with previous version 1.4-1 dated 2015-01-16

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

Diff between TAM versions 1.4-1 dated 2015-01-16 and 1.5-2 dated 2015-02-24

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Package survival updated to version 2.38-1 with previous version 2.37-7 dated 2014-01-22

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau

Diff between survival versions 2.37-7 dated 2014-01-22 and 2.38-1 dated 2015-02-24

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More information about survival at CRAN
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Package mwa updated to version 0.4.1 with previous version 0.4 dated 2014-12-17

Title: Causal Inference in Spatiotemporal Event Data
Description: Matched Wake Analysis (mwa) grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte

Diff between mwa versions 0.4 dated 2014-12-17 and 0.4.1 dated 2015-02-24

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Package dpcR updated to version 0.1.3.3 with previous version 0.1.3.2 dated 2014-12-24

Title: Digital PCR Analysis
Description: Analysis, visualisation and simulation of digital PCR experiments.
Author: Michal Burdukiewicz [cre, aut], Stefan Roediger [aut]
Maintainer: Michal Burdukiewicz

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 man/test_counts.Rd       |    3 +
 man/test_counts_gui.Rd   |    3 +
 man/test_panel.Rd        |    3 +
 man/test_peaks.Rd        |    3 +
 man/test_ratio.Rd        |    3 +
 41 files changed, 124 insertions(+), 82 deletions(-)

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Package spatialEco updated to version 0.1-1 with previous version 0.1-0 dated 2015-02-02

Title: Spatial Analysis and Modeling
Description: Utilities to support spatial data manipulation, query, sampling and modeling. Functions include models for species population density, download utilities for climate and global deforestation spatial products, spatial smoothing, multivariate separability, point process model for creating pseudo-absences and subsampling, polygon and point-distance landscape metrics, auto-logistic model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre], Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans

Diff between spatialEco versions 0.1-0 dated 2015-02-02 and 0.1-1 dated 2015-02-24

 DESCRIPTION                |    8 +-
 MD5                        |   81 +++++++++++++----------
 NAMESPACE                  |    3 
 R/breeding.density.R       |    6 -
 R/correlogram.R            |    4 -
 R/csi.R                    |only
 R/download.daymet.R        |    6 -
 R/download.prism.R         |    4 -
 R/idw.smoothing.R          |    6 -
 R/land.metrics.R           |    2 
 R/local.min.max.R          |only
 R/logistic.regression.R    |   58 ++++++++++-------
 R/moments.R                |    6 -
 R/nni.R                    |   14 ++--
 R/o.ring.R                 |    6 -
 R/optimal.k.R              |    2 
 R/outliers.R               |only
 R/parea.sample.R           |    2 
 R/point.in.poly.R          |   13 +--
 R/pp.subsample.R           |    2 
 R/pseudo.absence.R         |    6 -
 R/separability.R           |    8 +-
 R/stratified.random.R      |    4 -
 R/trend.line.R             |    2 
 inst/NEWS                  |only
 man/breeding.density.Rd    |  130 +++++++++++++++++++-------------------
 man/correlogram.Rd         |    4 -
 man/csi.Rd                 |only
 man/download.daymet.Rd     |    6 -
 man/download.prism.Rd      |    4 -
 man/idw.smoothing.Rd       |   90 +++++++++++++-------------
 man/land.metrics.Rd        |  118 +++++++++++++++++-----------------
 man/local.min.max.Rd       |only
 man/logistic.regression.Rd |   36 ++++++----
 man/moments.Rd             |    6 -
 man/nni.Rd                 |   88 +++++++++++++-------------
 man/o.ring.Rd              |   78 +++++++++++------------
 man/optimal.k.Rd           |  100 ++++++++++++++---------------
 man/outliers.Rd            |only
 man/parea.sample.Rd        |  108 +++++++++++++++----------------
 man/pp.subsample.Rd        |    2 
 man/pseudo.absence.Rd      |    6 -
 man/separability.Rd        |  152 ++++++++++++++++++++++-----------------------
 man/stratified.random.Rd   |  150 ++++++++++++++++++++++----------------------
 man/trend.line.Rd          |   86 ++++++++++++-------------
 45 files changed, 717 insertions(+), 690 deletions(-)

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Package RMySQL updated to version 0.10.2 with previous version 0.10.1 dated 2015-01-15

Title: Database Interface and MySQL Driver for R
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre], David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms

Diff between RMySQL versions 0.10.1 dated 2015-01-15 and 0.10.2 dated 2015-02-24

 DESCRIPTION      |    6 +++---
 MD5              |    8 ++++----
 configure        |   10 ++++++++++
 src/Makevars.win |    4 ++--
 tools/winlibs.R  |    4 ++--
 5 files changed, 21 insertions(+), 11 deletions(-)

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Package js updated to version 0.2 with previous version 0.1 dated 2015-02-15

Title: Tools for Working with JavaScript in R
Description: A set of utility functions for working with JavaScript in R. Currently includes functions to compile, validate, reformat, optimize and analyze JavaScript code.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between js versions 0.1 dated 2015-02-15 and 0.2 dated 2015-02-24

 DESCRIPTION           |   12 ++--
 MD5                   |   17 ++++--
 NAMESPACE             |    1 
 NEWS                  |only
 R/coffee.R            |only
 inst/doc/intro.R      |   13 +++++
 inst/doc/intro.Rmd    |   35 +++++++++++--
 inst/doc/intro.html   |  126 ++++++++++++++++++++++++++++++++++++++++++++++----
 inst/example          |only
 inst/js/coffee.min.js |only
 man/coffee_compile.Rd |only
 vignettes/intro.Rmd   |   35 +++++++++++--
 12 files changed, 208 insertions(+), 31 deletions(-)

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