Wed, 07 Dec 2016

Package transport updated to version 0.8-1 with previous version 0.7-3 dated 2016-02-24

Title: Optimal Transport in Various Forms
Description: Solve optimal transport problems. Compute Wasserstein metrics (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p metrics), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre], Björn Bähre [aut] (aha and power diagrams), Carsten Gottschlich [aut] (simplex und shortlist), Florian Heinemann [aut] (transport_track), Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>

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Package mregions updated to version 0.1.4 with previous version 0.1.0 dated 2016-08-03

Title: Marine Regions Data from 'Marineregions.org'
Description: Tools to get marine regions data from <http:// www.marineregions.org/>. Includes tools to get region metadata, as well as data in 'GeoJSON' format, as well as Shape files. Use cases include using data downstream to visualize 'geospatial' data by marine region, mapping variation among different regions, and more.
Author: Scott Chamberlain [aut, cre], Francois Michonneau [ctb], Pieter Provoost [ctb], Michael Sumner [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package ecm updated to version 0.3.0 with previous version 0.2.0 dated 2016-12-02

Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>

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Package subcopem2D updated to version 1.1 with previous version 1.0-0 dated 2016-04-25

Title: Bivariate Empirical Subcopula
Description: Calculate empirical subcopula and dependence measures from a given bivariate sample.
Author: Arturo Erdely
Maintainer: Arturo Erdely <arturo.erdely@comunidad.unam.mx>

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Package simstudy updated to version 0.1.2 with previous version 0.1.1 dated 2016-06-21

Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or better understand data generating processes. The user specifies a set of relationships between covariates, and generates data based on these specifications. The final data sets can represent data from randomized control trials, repeated measure (longitudinal) designs, and cluster randomized trials. Missingness can be generated using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre]
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>

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Package NonCompart updated to version 0.2.4 with previous version 0.2.3 dated 2016-11-27

Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>. Some features include: - Use CDISC SDTM PP domain terms. - Automatic slope selection with the same criterion of WinNonlin(R) - Support both 'linear-up linear-down' and 'linear-up log-down' method - Calculate partial(interval) AUC with 'linear' or 'log' interpolation method For more details on noncompartmental analysis, see the reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107) Acknowldegement: Author thanks for the careful review and valuable input of Dr. Jee Eun Lee.
Author: Kyun-Seop Bae
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package micromapST updated to version 1.1.1 with previous version 1.1.0 dated 2016-12-06

Title: Linked Micromap Plots for General U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create Linked Micromap plots for a collection of geographic areas. Linked Micromaps are visualizations of georeferenced data that link statistical graphics to an organized series of small maps or graphic images. The Help description contains examples of how to use the micromapST function. Contained in this package are border group datasets to support creating micromaps for the 50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas, the 62 counties of New York, the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas in China, the 218 administrative areas in the UK and Ireland (for testing only), the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa continent. A border group dataset contains the boundaries related to the data level areas, a second layer boundaries, a top or third layer boundary, a parameter list of run options, and a cross indexing table between area names, abbreviations, numeric identification and alias matching strings for the specific geographic area. By specifying a border group, the package create micromaps for any geographic region. The user can create and provide their own border group dataset for any area beyond the areas contained within the package. Copyrighted 2013, 2014, 2015 and 2016 by Carr, Pearson and Pickle.
Author: Jim Pearson <jpearson@statnetconsulting.com> and Dan Carr <dcarr@gmu.edu>, with contributions from Linda Pickle <linda@statnetconsulting.com>.
Maintainer: Jim Pearson <jpearson@statnetconsulting.com>

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Package fsia updated to version 1.1 with previous version 1.0 dated 2015-01-13

Title: Import and Analysis of OMR Data from FormScanner
Description: Import data of tests and questionnaires from FormScanner. FormScanner is an open source software that converts scanned images to data using optical mark recognition (OMR) and it can be downloaded from <http://sourceforge.net/projects/formscanner/>. The spreadsheet file created by FormScanner is imported in a convenient format to perform the analyses provided by the package. These analyses include the conversion of multiple responses to binary (correct/incorrect) data, the computation of the number of corrected responses for each subject or item, scoring using weights,the computation and the graphical representation of the frequencies of the responses to each item and the report of the responses of a few persons.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>

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Package etasFLP updated to version 1.3.1 with previous version 1.3.0 dated 2015-06-03

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 <marcello.chiodi@unipa.it>

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Package dataRetrieval updated to version 2.6.3 with previous version 2.5.13 dated 2016-09-27

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from National Water Information System (NWIS) tools. Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Robert Hirsch [aut], Laura DeCicco [aut, cre], David Lorenz [aut], Jordan Read [ctb], Lindsay Carr [ctb], David Watkins [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

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Package ChannelAttribution updated to version 1.10 with previous version 1.9 dated 2016-08-24

Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare, David Loris
Maintainer: Davide Altomare <davide.altomare@gmail.com>

Diff between ChannelAttribution versions 1.9 dated 2016-08-24 and 1.10 dated 2016-12-07

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Package seeclickfixr updated to version 1.1.0 with previous version 1.0.0 dated 2015-11-13

Title: Access Data from the SeeClickFix Web API
Description: Provides a wrapper to access data from the SeeClickFix web API for R. SeeClickFix is a central platform employed by many cities that allows citizens to request their city's services. This package creates several functions to work with all the built-in calls to the SeeClickFix API. Allows users to download service request data from numerous locations in easy-to-use dataframe format manipulable in standard R functions.
Author: Justin de Benedictis-Kessner [aut, cre], Christian Lemp [ctb]
Maintainer: Justin de Benedictis-Kessner <justindbk@gmail.com>

Diff between seeclickfixr versions 1.0.0 dated 2015-11-13 and 1.1.0 dated 2016-12-07

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Package compareGroups updated to version 3.2.2 with previous version 3.2.1 dated 2016-05-13

Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well aspublication-ready univariate or bivariate tablesin several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figuresto quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics(mean, median, frequencies, incidences, etc.). Perform the appropriate tests(t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data(Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Hctor Sanz, Gavin Lucas, Judith Peafiel and David Gimnez
Maintainer: Isaac Subirana <isubirana@imim.es>

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Package tesseract updated to version 1.3 with previous version 1.2 dated 2016-11-13

Title: Open Source OCR Engine
Description: An OCR engine with unicode (UTF-8) support that can recognize over 100 languages out of the box.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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Package sf updated to version 0.2-7 with previous version 0.2-6 dated 2016-12-06

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre], Roger Bivand [ctb], Ian Cook [ctb], Tim Keitt [ctb], Michael Sumner [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package RcppAPT updated to version 0.0.3 with previous version 0.0.2 dated 2016-04-04

Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and Debian-derived Linux systems with a powerful system to resolve package dependencies. This package offers access directly from R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package madsim updated to version 1.2.1 with previous version 1.2 dated 2016-06-16

Title: A Flexible Microarray Data Simulation Model
Description: This function allows to generate two biological conditions synthetic microarray dataset which has similar behavior to those currently observed with common platforms. User provides a subset of parameters. Available default parameters settings can be modified.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>

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Package KernelKnn updated to version 1.0.3 with previous version 1.0.2 dated 2016-09-08

Title: Kernel k Nearest Neighbors
Description: Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of 'RcppArmadillo' to speed up the calculation of distances between observations.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package icesSAG updated to version 1.2-0 with previous version 1.0 dated 2016-08-09

Title: Stock Assessment Graphs Database Web Services
Description: R interface to access the web services of the ICES (International Council for the Exploration of the Sea) Stock Assessment Graphs database <http://ices.dk/marine-data/tools/Pages/stock-assessment-graphs.aspx>.
Author: Colin Millar [aut, cre], Scott Large [aut], Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>

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Package hunspell updated to version 2.3 with previous version 2.2 dated 2016-11-09

Title: High-Performance Stemmer, Tokenizer, and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for languages with rich morphology and complex word compounding or character encoding. The package can check and analyze individual words as well as search for incorrect words within a text, latex, html or xml document. Use the 'devtools' package to spell check R documentation with 'hunspell'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between hunspell versions 2.2 dated 2016-11-09 and 2.3 dated 2016-12-07

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Package aws.signature updated to version 0.2.6 with previous version 0.2.5 dated 2016-08-09

Title: Amazon Web Services Request Signatures
Description: Generates request signatures for Amazon Web Services (AWS) APIs.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package teigen updated to version 2.2.0 with previous version 2.1.1 dated 2016-09-11

Title: Model-Based Clustering and Classification with the Multivariate t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the expectation conditional-maximization algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Jaymeson R. Wickins, Nicholas M. Boers, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews <jeff.andrews@ubc.ca>

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Package survminer updated to version 0.2.3 with previous version 0.2.2 dated 2016-07-28

Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table. Other functions are also available for visual examinations of 'cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre], Marcin Kosinski [aut]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package spocc updated to version 0.6.0 with previous version 0.5.4 dated 2016-10-08

Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
Author: Scott Chamberlain [aut, cre], Karthik Ram [ctb], Ted Hart [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package regsem updated to version 0.4.5 with previous version 0.4.3 dated 2016-11-15

Title: Performs Regularization on Structural Equation Models
Description: Uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional SEM.
Author: Ross Jacobucci[aut,cre], Kevin J. Grimm [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>

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Package red updated to version 0.2.0 with previous version 0.1.2 dated 2016-10-12

Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <http://www.iucn.org> for more information) red list criteria.
Author: Pedro Cardoso
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>

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Package R2admb updated to version 0.7.15 with previous version 0.7.13 dated 2015-04-13

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 <bolker@mcmaster.ca>

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Package preseqR updated to version 3.0.0 with previous version 2.0.1.1 dated 2016-07-12

Title: Predicting the Number of Species in a Random Sample
Description: Estimating the number of species represented at least r times in a random sample.
Author: Chao Deng, Timothy Daley and Andrew D. Smith
Maintainer: Chao Deng <chaodeng@usc.edu>

Diff between preseqR versions 2.0.1.1 dated 2016-07-12 and 3.0.0 dated 2016-12-07

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Package originr updated to version 0.2.0 with previous version 0.1.0 dated 2016-05-06

Title: Fetch Species Origin Data from the Web
Description: Get species origin data (whether species is native/invasive) from the following sources on the web: Encyclopedia of Life (<http://eol.org>), Flora 'Europaea' (<http://rbg-web2.rbge.org.uk/FE/fe.html>), Global Invasive Species Database (<http://www.iucngisd.org/gisd>), the Native Species Resolver (<http://bien.nceas.ucsb.edu/bien/tools/nsr/nsr-ws/>), Integrated Taxonomic Information Service (<http://www.itis.gov/>), and Global Register of Introduced and Invasive Species (<http://www.griis.org/>).
Author: Scott Chamberlain [aut, cre], Ignasi Bartomeus [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package MultivariateRandomForest updated to version 1.1.2 with previous version 1.1.1 dated 2016-10-23

Title: Models Multivariate Cases Using Random Forests
Description: Models and predicts Multiple Features in single random forest considering the linear relation among the features.
Author: Raziur Rahman
Maintainer: Raziur Rahman <razeeebuet@gmail.com>

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Package gcKrig updated to version 1.0.1 with previous version 1.0.0 dated 2016-11-10

Title: Analyze and Interpolate Geostatistical Count Data using Gaussian Copula
Description: Provides a variety of functions to analyze and model geostatistical count data with Gaussian copulas, including 1) data simulation and visualization; 2) correlation structure assessment (here also known as the NORTA); 3) calculate multivariate normal rectangle probabilities; 4) likelihood inference and parallel prediction at unsampled locations.
Author: Zifei Han
Maintainer: Zifei Han <hanzifei1@gmail.com>

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Package DCM updated to version 0.1.1 with previous version 0.1.0 dated 2016-12-04

Title: Data Converter Module
Description: Data Converter Module (DCM) converts the dataset format from split into stack and to the reverse.
Author: Delphi Intelligence
Maintainer: Nery Sofia Huerta-Pacheco <nehuerta@uv.mx>

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Package clickR updated to version 0.1.12 with previous version 0.1.8 dated 2016-11-21

Title: Fix Data and Create Report Tables from Different Objects
Description: Fixes data errors in numerical, factor and date variables and performs report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

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Package cdcfluview updated to version 0.5.1 with previous version 0.4.0 dated 2015-08-09

Title: Retrieve U.S. Flu Season Data from the CDC FluView Portal
Description: The U.S. Centers for Disease Control (CDC) maintains a portal <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing state, regional and national influenza statistics as well as Mortality Surveillance Data. The Flash interface makes it difficult and time-consuming to select and retrieve influenza data. This package provides functions to access the data provided by the portal's underlying API.
Author: Bob Rudis (bob@rud.is)
Maintainer: Bob Rudis <bob@rud.is>

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Tue, 06 Dec 2016

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

Title: Microbial Pan-Genome Analysis
Description: A collection of functions for computations and visualizations of microbial pan-genomes.
Author: Lars Snipen and Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>

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Package micromapST updated to version 1.1.0 with previous version 1.0.5 dated 2015-01-21

Title: Linked Micromap Plots for General U. S. Geographic Areas
Description: Provides the users with the ability to quickly create Linked Micromap plots for a collection of geographic areas. Linked Micromaps are visualizations of georeferenced data that link statistical graphics to an organized series of small maps or graphic images. The Help description contains examples of how to use the micromapST function. Contained in this package are border group datasets to support creating micromaps for the 50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas, the 62 counties of New York, the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas in China, the 218 administrative areas in the UK and Ireland (for testing only), the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa continent. A border group dataset contains the boundaries related to the data level areas, a second layer boundaries, a top or third layer boundary, a parameter list of run options, and a cross indexing table between area names, abbreviations, numeric identification and alias matching strings for the specific geographic area. By specifying a border group, the package create micromaps for any geographic region. The user can create and provide their own border group dataset for any area beyond the areas contained within the package. Copyrighted 2013, 2014, 2015 and 2016 by Carr, Pearson and Pickle.
Author: Jim Pearson <jpearson@statnetconsulting.com> and Dan Carr <dcarr@gmu.edu>, with contributions from Linda Pickle <linda@statnetconsulting.com>.
Maintainer: Jim Pearson <jpearson@statnetconsulting.com>

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Package icesVocab updated to version 1.1-2 with previous version 1.1-0 dated 2016-12-06

Title: ICES Vocabularies Database Web Services
Description: R interface to access the RECO POX web services of the ICES (International Council for the Exploration of the Sea) Vocabularies database <http://vocab.ices.dk/services/POX.aspx>.
Author: Colin Millar [aut, cre], Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>

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Package btergm updated to version 1.8.1 with previous version 1.7.6 dated 2016-06-18

Title: Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb], Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>

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Package marked updated to version 1.1.13 with previous version 1.1.11 dated 2016-03-07

Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. Includes a CJS models that concurrently estimates and corrects for tag loss. Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty.
Author: Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson <devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Maintainer: Jeff Laake <jefflaake@gmail.com>

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Package deTestSet updated to version 1.1.3 with previous version 1.1.2 dated 2014-12-03

Title: Testset for Differential Equations
Description: Solvers and testset for stiff and nonstiff differential equations, and differential algebraic equations.
Author: Karline Soetaert [aut, cre], Jeff Cash [aut], Francesca Mazzia [aut], LAPACK authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

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Package clustrd updated to version 1.1.0 with previous version 1.0.9 dated 2016-11-10

Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous or categorical data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2016; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means.
Author: Alfonso Iodice D'Enza [aut], Angelos Markos [aut, cre], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>

Diff between clustrd versions 1.0.9 dated 2016-11-10 and 1.1.0 dated 2016-12-06

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Package SPEDInstabR updated to version 1.3 with previous version 1.2 dated 2016-11-04

Title: Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept
Description: From output files obtained from the software 'ModestR', the relative contribution of factors to explain species distribution is depicted using several plots. A global geographic raster file for each environmental variable may be also obtained with the mean relative contribution, considering all species present in each raster cell, of the factor to explain species distribution. Finally, for each variable it is also possible to compare the frequencies of any variable obtained in the cells where the species is present with the frequencies of the same variable in the cells of the extent.
Author: Cstor Guisande Gonzlez
Maintainer: Cstor Guisande Gonzlez <castor@uvigo.es>

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Package sdcMicroGUI updated to version 1.4.0 with previous version 1.3.0 dated 2016-08-16

Title: Graphical User Interface for Package sdcMicro
Description: DEPRECATED: A new version of the graphical user interface is available directly in the package sdcMicro via function sdcApp(). A point and click graphical user interface based on top of the 'sdcMicro' package to create anonymized data set. The graphical user interface provides full reproducibility of any result via the script menu in the GUI.
Author: Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois Fonteneau
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>

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Package SafeQuant updated to version 2.3.1 with previous version 2.3 dated 2016-10-04

Title: A Toolbox for the Analysis of Proteomics Data
Description: Tools for the statistical analysis and visualization of (relative and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.
Author: Erik Ahrne
Maintainer: Erik Ahrne <erik.ahrne@unibas.ch>

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More information about SafeQuant at CRAN
Permanent link

Package rootSolve updated to version 1.7 with previous version 1.6.6 dated 2015-10-05

Title: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations
Description: Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE). Includes routines that: (1) generate gradient and jacobian matrices (full and banded), (2) find roots of non-linear equations by the 'Newton-Raphson' method, (3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the 'Newton-Raphson' method, or by dynamically running, (4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). Includes fortran code.
Author: Karline Soetaert [aut, cre], yale sparse matrix package authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

Diff between rootSolve versions 1.6.6 dated 2015-10-05 and 1.7 dated 2016-12-06

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More information about rootSolve at CRAN
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Package bvpSolve updated to version 1.3.3 with previous version 1.3.2 dated 2015-09-22

Title: Solvers for Boundary Value Problems of Differential Equations
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary differential equations ('ODE') and differential algebraic equations ('DAE'). The functions provide an interface to the FORTRAN functions 'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method.
Author: Karline Soetaert <karline.soetaert@nioz.nl>, Jeff Cash <j.cash@imperial.ac.uk>, Francesca Mazzia <mazzia@dm.uniba.it>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

Diff between bvpSolve versions 1.3.2 dated 2015-09-22 and 1.3.3 dated 2016-12-06

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Package sf updated to version 0.2-6 with previous version 0.2-5 dated 2016-11-24

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial data, in R.
Author: Edzer Pebesma [aut, cre], Roger Bivand [ctb], Ian Cook [ctb], Tim Keitt [ctb], Michael Sumner [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between sf versions 0.2-5 dated 2016-11-24 and 0.2-6 dated 2016-12-06

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Package R.rsp updated to version 0.40.0 with previous version 0.30.0 dated 2016-05-15

Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between R.rsp versions 0.30.0 dated 2016-05-15 and 0.40.0 dated 2016-12-06

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 R.rsp-0.40.0/R.rsp/R/rcat.R                                                           |    2 
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More information about R.rsp at CRAN
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Package rgbif updated to version 0.9.6 with previous version 0.9.5 dated 2016-10-06

Title: Interface to the Global 'Biodiversity' Information Facility 'API'
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, and getting counts of occurrence records.
Author: Scott Chamberlain [aut, cre], Vijay Barve [ctb], Dan Mcglinn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rgbif versions 0.9.5 dated 2016-10-06 and 0.9.6 dated 2016-12-06

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Package matrixpls updated to version 1.0.3 with previous version 1.0.2 dated 2016-12-05

Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling algorithm and related algorithms. The algorithm implementations aim for computational efficiency using matrix algebra and covariance data. The package is designed toward Monte Carlo simulations and includes functions to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>

Diff between matrixpls versions 1.0.2 dated 2016-12-05 and 1.0.3 dated 2016-12-06

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Package ManlyMix updated to version 0.1.7 with previous version 0.1.3 dated 2016-04-15

Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre], Volodymyr Melnykov [aut], Michael Hutt [ctb, cph] (NM optimization in c), Stephen Moshier [ctb, cph] (eigen calculations in c), Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>

Diff between ManlyMix versions 0.1.3 dated 2016-04-15 and 0.1.7 dated 2016-12-06

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Package Branching updated to version 0.9.4 with previous version 0.9.2 dated 2016-05-22

Title: Simulation and Estimation for Branching Processes
Description: Simulation and parameter estimation of multitype Bienayme - Galton - Watson processes.
Author: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Maintainer: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>

Diff between Branching versions 0.9.2 dated 2016-05-22 and 0.9.4 dated 2016-12-06

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Permanent link

Mon, 05 Dec 2016

Package colourpicker updated to version 0.3 with previous version 0.2 dated 2016-09-07

Title: A Colour Picker Tool for Shiny and for Selecting Colours in Plots
Description: A colour picker that can be used as an input in Shiny apps or 'Rmarkdown' documents. A Plot Colour Helper tool is available as an 'RStudio' addin, which helps you pick colours to use in your plots. A more generic Colour Picker 'RStudio' addin is also provided to let you select colours for use in your R code.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

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Package umx updated to version 1.4.9 with previous version 1.4.5 dated 2016-11-08

Title: Structural Equation Modelling in R with 'OpenMx'
Description: Create, run, and report structural equation and twin models quickly. If you're just starting out, try typing '?umx'.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>

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Package phytools updated to version 0.5-64 with previous version 0.5-38 dated 2016-06-24

Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis. This functionality is concentrated in the phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian and ML ancestral state estimation; visual simulation of trait evolution; fitting models of trait evolution with multiple Brownian rates and correlations; visualizing discrete and continuous character evolution using colors or projections into trait space; identifying the location of a change in the rate of character evolution on the tree; fast Brownian motion simulation and simulation under several other models of continuous trait evolution; fitting a model of correlated binary trait evolution; locating the position of a fossil or an recently extinct lineage on a tree using continuous character data with ML; plotting lineage accumulation through time, including across multiple trees (such as a Bayesian posterior sample); conducting an analysis called stochastic character mapping, in which character histories for a discrete trait are sampled from their posterior probability distribution under a model; conducting a multiple (i.e., partial) Mantel test; fitting a phylogenetic regression model with error in predictor and response variables; conducting a phylogenetic principal components analysis, a phylogenetic regression, a reduced major axis regression, a phylogenetic canonical correlation analysis, and a phylogenetic ANOVA; projecting a tree onto a geographic map; simulating discrete character histories on the tree; fitting a model in which a discrete character evolves under the threshold model; visualization of cospeciation; a simple statistical test for cospeciation between two trees. In addition to this phylogenetic comparative method functionality, the package also contains functions for a wide range of other purposes in phylogenetic biology. For instance, functionality in this package includes (but is not restricted to): adding taxa to a tree (including randomly, everywhere, or automatically to genera); generating all bi- and multi-furcating trees for a set of taxa; reducing a phylogeny to its backbone tree; dropping tips or adding tips to special types of phylogenetic trees; exporting a tree as an XML file; converting a tree with a mapped character to a tree with singleton nodes and one character state per edge; estimating a phylogeny using the least squares method; simulating birth-death trees under a range of conditions; rerooting trees; computing a consensus tree under multiple methods, including via minimization of the distance to other trees in the set; a wide range of visualizations of trees; and a variety of other manipulations and analyses that phylogenetic biologists may find useful for their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>

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Package paco updated to version 0.3.1 with previous version 0.3.0 dated 2016-10-03

Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot <tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>, Fernando Cagua <fernando@cagua.co>
Maintainer: Matthew Hutchinson <matthewhutchinson15@gmail.com>

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Package nucim updated to version 1.0.0 with previous version 0.5.3 dated 2016-10-15

Title: Nucleome Imaging Toolbox
Description: Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.
Author: Volker Schmid [aut, cre]
Maintainer: Volker Schmid <stats@volkerschmid.de>

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Package mctest updated to version 1.1 with previous version 1.0 dated 2016-06-29

Title: Multicollinearity Diagnostic Measures
Description: Package computes popular and widely used multicollinearity diagnostic measures. Package also indicates which regressors may be the reason of collinearity among regressors.
Author: Muhammad Imdadullah and Dr. Muhammad Aslam
Maintainer: Muhammad Imdadullah <mimdadasad@gmail.com>

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Package matrixpls updated to version 1.0.2 with previous version 1.0.1 dated 2016-06-18

Title: Matrix-Based Partial Least Squares Estimation
Description: Partial Least Squares Path Modeling algorithm and related algorithms. The algorithm implementations aim for computational efficiency using matrix algebra and covariance data. The package is designed toward Monte Carlo simulations and includes functions to perform simple Monte Carlo simulations.
Author: Mikko Rönkkö [aut, cre]
Maintainer: Mikko Rönkkö <mikko.ronkko@aalto.fi>

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Package ggparallel updated to version 0.2.0 with previous version 0.1.2 dated 2015-08-21

Title: Variations of Parallel Coordinate Plots for Categorical Data
Description: Create hammock plots, parallel sets, and common angle plots with 'ggplot2'.
Author: Heike Hofmann [aut, cre], Marie Vendettuoli [aut]
Maintainer: Heike Hofmann <hofmann@mail.iastate.edu>

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Package GetHFData updated to version 1.2.2 with previous version 1.2.1 dated 2016-11-07

Title: Download and Aggregate High Frequency Trading Data from Bovespa
Description: Downloads and aggregates high frequency trading data for Brazilian instruments directly from Bovespa ftp site <ftp://ftp.bmf.com.br/MarketData/>.
Author: Marcelo Perlin [aut, cre], Henrique Ramos [ctb]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between GetHFData versions 1.2.1 dated 2016-11-07 and 1.2.2 dated 2016-12-05

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Package geeM updated to version 0.10.0 with previous version 0.9.0 dated 2016-06-17

Title: Solve Generalized Estimating Equations
Description: GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The "M" in the name "geeM" is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.
Author: Lee McDaniel [aut, cre], Nick Henderson [aut], Melanie Prague [ctb] (Suggested code to fix weighting)
Maintainer: Lee McDaniel <lmcda4@lsuhsc.edu>

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Package BatchGetSymbols updated to version 1.1 with previous version 1.0 dated 2016-11-06

Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo or Google Finance.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package mlt.docreg updated to version 0.1-4 with previous version 0.1-3 dated 2016-12-01

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package IHSEP updated to version 0.1 with previous version 0.0 dated 2016-08-18

Title: Inhomogeneous Self-Exciting Process
Description: Simulate an inhomogeneous self-exciting process (IHSEP), or Hawkes process, with a given (possibly time-varying) baseline intensity and an excitation function. Calculate the likelihood of an IHSEP with given baseline intensity and excitation functions for an (increasing) sequence of event times. Calculate the point process residuals (integral transforms of the original event times). Calculate the mean intensity process.
Author: Feng Chen <feng.chen@unsw.edu.au>
Maintainer: Feng Chen <feng.chen@unsw.edu.au>

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Package ggpubr updated to version 0.1.1 with previous version 0.1.0 dated 2016-07-20

Title: 'ggplot2' Based Publication Ready Plots
Description: 'ggplot2' is an excellent and flexible package for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package condSURV updated to version 2.0.0 with previous version 1.0.0 dated 2016-10-29

Title: Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data
Description: Method to implement some newly developed methods for the estimation of the conditional survival function.
Author: Luis Meira-Machado and Marta Sestelo
Maintainer: Marta Sestelo <sestelo@uvigo.es>

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Package Ckmeans.1d.dp updated to version 3.4.6-5 with previous version 3.4.6-4 dated 2016-10-22

Title: Optimal and Fast Univariate k-Means Clustering
Description: A dynamic programming algorithm for optimal univariate k-means clustering. Minimizing the sum of squares of within-cluster distances, the algorithm guarantees optimality and reproducibility. Its advantage over heuristic clustering algorithms in efficiency and accuracy is increasingly pronounced as the number of clusters k increases. With optional weights, the algorithm can also analyze 1-D signals for segmentation and peak calling. An auxiliary function can generate adaptive histograms to make patterns in data stand out. For univariate data analysis, the package provides a powerful alternative to heuristic clustering algorithms.
Author: Joe Song [aut, cre], Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

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Package vdmR updated to version 0.2.3 with previous version 0.2.2 dated 2016-02-27

Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding interactive functions to 'ggplot2' graphics. Brushing and linking between the multiple plots is one of the main feature of this package. Currently scatter plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>

Diff between vdmR versions 0.2.2 dated 2016-02-27 and 0.2.3 dated 2016-12-05

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Package summarytools updated to version 0.6.5 with previous version 0.6 dated 2016-11-21

Title: Dataframe Summaries, Frequency Tables and Descriptive Stats with Various Output Formats
Description: Built around three key functions: 1) freq() generates frequency tables reporting counts and proportions (including cumulative) for factors and other discrete data; 2) descr() gives all common central tendency statistics and measures of dispersion for numerical data; 3) dfSummary() gives as much information as possible on a dataframe's columns in a legible table. freq() and descr() support weights, and all three functions support 'Hmisc' or 'pander' labels. A variety of output formats are available (plain text, 'rmarkdown' and HTML). An additional misc function, what.is(), displays all common properties of an object (its class, type, mode, attributes, etc.) and extends the base is() function, checking the object against most is.() functions.
Author: Dominic Comtois
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>

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Package sudokuAlt updated to version 0.1-9 with previous version 0.1-7 dated 2016-07-04

Title: Tools for Making and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games. This package is an alternative to the earlier sudoku-solver package, 'sudoku'. The present package uses a slightly different algorithm, has a simpler coding and presents a few more sugar tools, such as plot and print methods. Solved sudoku games are of some interest in Experimental Design as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>

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Package popprxl updated to version 0.1.3 with previous version 0.1.2 dated 2016-05-25

Title: Read GenAlEx Files Directly from Excel
Description: GenAlEx is a popular Excel macro for genetic analysis and the 'poppr' R package allows import of GenAlEx formatted CSV data for genetic data analysis in R. This package allows for the import of GenAlEx formatted Excel files, serving as a small 'poppr' add on for those who have trouble or simply do not want to export their data into CSV format.
Author: Zhian N. Kamvar [cre, aut], Niklaus J. Grünwald [ths]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

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Package phylocurve updated to version 2.0.7 with previous version 2.0.6 dated 2016-06-15

Title: Phylogenetic Comparative Methods for High-Dimensional Traits
Description: Tools for studying the evolution of high-dimensional traits (morphometric, function-valued, etc.) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>

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Package pavo updated to version 1.0.0 with previous version 0.5-6 dated 2016-10-20

Title: Perceptual Analysis, Visualization and Organization of Spectral Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color from spectral data.
Author: Rafael Maia [aut, cre], Chad Eliason [aut], Pierre-Paul Bitton [aut], Thomas White [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>

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Package labstats updated to version 1.0.1 with previous version 1.0 dated 2016-01-14

Title: Data Sets for the Book "Experimental Design for Laboratory Biologists"
Description: Contains data sets to accompany the book: Lazic SE (2016). "Experimental Design for Laboratory Biologists: Maximising Information and Improving Reproducibility". Cambridge University Press.
Author: Stanley E. Lazic
Maintainer: Stanley E. Lazic <stan.lazic@cantab.net>

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Package gld updated to version 2.4.1 with previous version 2.4 dated 2016-09-18

Title: Estimation and Use of the Generalised (Tukey) Lambda Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form. This package provides random numbers, quantiles, probabilities, densities and density quantiles for four different parameterisations of the distribution. It provides the density function, distribution function, and Quantile-Quantile plots. It implements a variety of estimation methods for the distribution, including diagnostic plots. Estimation methods include the starship (all 4 parameterisations) and a number of methods for only the FKML parameterisation. These include maximum likelihood, maximum product of spacings, Titterington's method, Moments, L-Moments, Trimmed L-Moments and Distributional Least Absolutes.
Author: Robert King <Robert.King@newcastle.edu.au>, Benjamin Dean <Benjamin.Dean@uon.edu.au>, Sigbert Klinke
Maintainer: Robert King <Robert.King@newcastle.edu.au>

Diff between gld versions 2.4 dated 2016-09-18 and 2.4.1 dated 2016-12-05

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Package FinePop updated to version 1.2.0 with previous version 1.1.1 dated 2016-10-17

Title: Fine-Scale Population Analysis
Description: Statistical tool set for population genetics. The package provides empirical Bayes estimator of Fst, Nei's Gst, Nei & Chesser's Gst, and Weir & Cockerham's theta adapted for pairwise comparison. It also provides interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
Author: Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
Maintainer: Reiichiro Nakamichi <nakamichi@affrc.go.jp>

Diff between FinePop versions 1.1.1 dated 2016-10-17 and 1.2.0 dated 2016-12-05

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Package FAwR updated to version 1.1.1 with previous version 1.1.0 dated 2015-03-24

Title: Functions and Datasets for "Forest Analytics with R"
Description: Provides functions and datasets from the book "Forest Analytics with R".
Author: Andrew Robinson and Jeff Hamann
Maintainer: Andrew Robinson <apro@unimelb.edu.au>

Diff between FAwR versions 1.1.0 dated 2015-03-24 and 1.1.1 dated 2016-12-05

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Package ezec updated to version 1.0.1 with previous version 1.0.0 dated 2016-06-13

Title: Easy Interface to Effective Concentration Calculations
Description: Because fungicide resistance is an important phenotypic trait for fungi and oomycetes, it is necessary to have a standardized method of statistically analyzing the Effective Concentration (EC) values. This package is designed for those who are not terribly familiar with R to be able to analyze and plot an entire set of isolates using the 'drc' package.
Author: Zhian N. Kamvar [cre, aut], Niklaus J. Grunwald [ths, ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

Diff between ezec versions 1.0.0 dated 2016-06-13 and 1.0.1 dated 2016-12-05

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Package cplm updated to version 0.7-5 with previous version 0.7-4 dated 2015-08-21

Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models.
Author: Yanwei (Wayne) Zhang
Maintainer: Yanwei (Wayne) Zhang <actuary_zhang@hotmail.com>

Diff between cplm versions 0.7-4 dated 2015-08-21 and 0.7-5 dated 2016-12-05

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Package bunchr updated to version 1.1.1 with previous version 1.1.0 dated 2016-12-02

Title: Analyze Bunching in a Kink or Notch Setting
Description: View and analyze data where bunching is expected. Estimate counter- factual distributions. For earnings data, estimate the compensated elasticity of earnings w.r.t. the net-of-tax rate.
Author: Itai Trilnick [aut, cre]
Maintainer: Itai Trilnick <itai.trilnick@berkeley.edu>

Diff between bunchr versions 1.1.0 dated 2016-12-02 and 1.1.1 dated 2016-12-05

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Package binomSamSize updated to version 0.1-4 with previous version 0.1-3 dated 2013-12-10

Title: Confidence Intervals and Sample Size Determination for a Binomial Proportion under Simple Random Sampling and Pooled Sampling
Description: A suite of functions to compute confidence intervals and necessary sample sizes for the parameter p of the Bernoulli B(p) distribution under simple random sampling or under pooled sampling. Such computations are e.g. of interest when investigating the incidence or prevalence in populations. The package contains functions to compute coverage probabilities and coverage coefficients of the provided confidence intervals procedures. Sample size calculations are based on expected length.
Author: Michael Hhle [aut, cre], Wei Liu [ctb]
Maintainer: Michael Hhle <hoehle@math.su.se>

Diff between binomSamSize versions 0.1-3 dated 2013-12-10 and 0.1-4 dated 2016-12-05

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Sun, 04 Dec 2016

Package rly updated to version 1.1.0 with previous version 1.0.3 dated 2016-11-26

Title: Lex and Yacc
Description: R implementation of the common parsing tools lex and yacc.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>

Diff between rly versions 1.0.3 dated 2016-11-26 and 1.1.0 dated 2016-12-04

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Package CensSpatial updated to version 1.2 with previous version 1.1 dated 2016-10-17

Title: Censored Spatial Models
Description: Fits linear regression models for censored spatial data. Provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. Also offers graphical tools for assessing the fitted model.
Author: Alejandro Ordonez, Christian E. Galarza, Victor H. Lachos
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>

Diff between CensSpatial versions 1.1 dated 2016-10-17 and 1.2 dated 2016-12-04

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Package cmaesr updated to version 1.0.3 with previous version 1.0.2 dated 2016-08-04

Title: Covariance Matrix Adaptation Evolution Strategy
Description: Pure R implementation of the Covariance Matrix Adaptation - Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>

Diff between cmaesr versions 1.0.2 dated 2016-08-04 and 1.0.3 dated 2016-12-04

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Package secr updated to version 2.10.4 with previous version 2.10.3 dated 2016-05-13

Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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Package phuassess updated to version 1.1 with previous version 1.0 dated 2016-10-22

Title: Proportional Habitat Use Assessment
Description: Assessment of habitat selection by means of the permutation-based combination of sign tests (Fattorini et al., 2014 <DOI:10.1007/s10651-013-0250-7>). To exemplify the application of this procedure, habitat selection is assessed for a population of European Brown Hares settled in central Italy.
Author: Caterina Pisani [aut, cre] Lorenzo Fattorini [aut] Francesco Riga [aut] Marco Zaccaroni [aut]
Maintainer: Caterina Pisani <caterina.pisani@unisi.it>

Diff between phuassess versions 1.0 dated 2016-10-22 and 1.1 dated 2016-12-04

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Package peakRAM updated to version 1.0.1 with previous version 1.0.0 dated 2016-07-29

Title: Monitor the Total and Peak RAM Used by an Expression or Function
Description: When working with big datasets, RAM conservation is critically important. However, it is not always enough to just monitor the size of the objects created. So-called "copy-on-modify" behavior, characteristic of R, means that some expressions or functions may require an unexpectedly large amount of RAM overhead. For example, replacing a single value in a matrix duplicates that matrix in the backend, making this task require twice as much RAM as that used by the matrix itself. This package makes it easy to monitor the total and peak RAM used so that developers can quickly identify and eliminate RAM hungry code.
Author: Thomas Quinn [aut, cre]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>

Diff between peakRAM versions 1.0.0 dated 2016-07-29 and 1.0.1 dated 2016-12-04

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Package mstate updated to version 0.2.10 with previous version 0.2.9 dated 2016-02-28

Title: Data Preparation, Estimation and Prediction in Multi-State Models
Description: Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.
Author: Hein Putter, Liesbeth de Wreede, Marta Fiocco, with contributions by Ronald Geskus
Maintainer: Hein Putter <H.Putter@lumc.nl>

Diff between mstate versions 0.2.9 dated 2016-02-28 and 0.2.10 dated 2016-12-04

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Package lazyData updated to version 1.1.0 with previous version 1.0.3 dated 2014-01-29

Title: A LazyData Facility
Description: Supplies a LazyData facility for packages which have data sets but do not provide LazyData: true. A single function is is included, requireData, which is a drop-in replacement for base::require, but carrying the additional functionality. By default, it suppresses package startup messages as well. See argument 'reallyQuitely'.
Author: Bill Venables
Maintainer: Bill Venables <bill.venables@gmail.com>

Diff between lazyData versions 1.0.3 dated 2014-01-29 and 1.1.0 dated 2016-12-04

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Package asymmetry updated to version 1.1.3 with previous version 1.1.2 dated 2016-11-11

Title: Visualizing Asymmetric Data
Description: Models and methods for the visualization for asymmetric data. A matrix is asymmetric if the number of rows equals the number of columns, and these rows and columns refer to the same set of objects. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. The slide-vector model, a heat map, and the decomposition of asymmetry are provided for the analysis of these tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>

Diff between asymmetry versions 1.1.2 dated 2016-11-11 and 1.1.3 dated 2016-12-04

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Package phangorn updated to version 2.1.1 with previous version 2.0.4 dated 2016-06-21

Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre], Emmanuel Paradis [aut], Leonardo de Oliveira Martins [aut], Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>

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Sat, 03 Dec 2016

Package BAT updated to version 1.5.5 with previous version 1.5.4 dated 2016-09-15

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 <pedro.cardoso@helsinki.fi>

Diff between BAT versions 1.5.4 dated 2016-09-15 and 1.5.5 dated 2016-12-03

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Package Rfast updated to version 1.7.1 with previous version 1.7 dated 2016-12-01

Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), Mahalanobis distance are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis and John Burkardt
Maintainer: Manos Papadakis <papadakm95@gmail.com>

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Package pdp updated to version 0.2.0 with previous version 0.1.0 dated 2016-10-06

Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e., marginal effect) plots from various types machine learning models in R.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>

Diff between pdp versions 0.1.0 dated 2016-10-06 and 0.2.0 dated 2016-12-03

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Package pdftools updated to version 1.0 with previous version 0.5 dated 2016-08-28

Title: Text Extraction and Rendering of PDF Documents
Description: Utilities based on libpoppler for extracting text, fonts, attachments and metadata from a pdf file. Also implements rendering of PDF to bitmaps on supported platforms.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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Package oXim updated to version 1.1.0 with previous version 1.0.1 dated 2016-08-17

Title: Oxycline Index from Matrix Echograms
Description: Tools for oxycline depth calculation from echogram matrices.
Author: Wencheng Lau-Medrano [aut, cre], Ricardo Oliveros-Ramos [ctb]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>

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Package lmerTest updated to version 2.0-33 with previous version 2.0-32 dated 2016-06-22

Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented in 'lme4' package are provided. The tests comprise types I - III F tests for fixed effects, LR tests for random effects. The package also provides the calculation of population means for fixed factors with confidence intervals and corresponding plots. Finally the backward elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut], Per Bruun Brockhoff [aut, ths, cre], Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>

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Package jagsUI updated to version 1.4.4 with previous version 1.4.2 dated 2016-02-22

Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Description: A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
Author: Ken Kellner <contact@kenkellner.com>
Maintainer: Ken Kellner <contact@kenkellner.com>

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Package DBItest updated to version 1.4 with previous version 1.3 dated 2016-07-07

Title: Testing 'DBI' Back Ends
Description: A helper that tests 'DBI' back ends for conformity to the interface.
Author: Kirill Müller [aut, cre], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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