Fri, 19 Oct 2018

New package Rwhois with initial version 1.0.2
Package: Rwhois
Title: WHOIS Server Querying
Version: 1.0.2
Date: 2018-10-14
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Description: Queries data from WHOIS servers.
Imports: stringr, utils
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2018-10-16 01:02:30 UTC; lister
Repository: CRAN
Date/Publication: 2018-10-19 23:00:10 UTC

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Package rts updated to version 1.0-47 with previous version 1.0-45 dated 2018-03-18

Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>

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Package rgbif updated to version 1.1.0 with previous version 1.0.2 dated 2018-07-06

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'; <https://www.gbif.org/developer/summary>). '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, getting counts of occurrence records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Vijay Barve [ctb], Dan Mcglinn [ctb], Damiano Oldoni [ctb], Laurens Geffert [ctb], Karthik Ram [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package hisse updated to version 1.8.8 with previous version 1.8.7 dated 2018-10-18

Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
Author: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Daniel Caetano [aut]
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>

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Package conStruct updated to version 1.0.1 with previous version 1.0.0 dated 2018-09-18

Title: Models Spatially Continuous and Discrete Population Genetic Structure
Description: A method for modeling genetic data as a combination of discrete layers, within each of which relatedness may decay continuously with geographic distance. This package contains code for running analyses (which are implemented in the modeling language 'rstan') and visualizing and interpreting output. See the paper for more details on the model and its utility.
Author: Gideon Bradburd [aut, cre]
Maintainer: Gideon Bradburd <bradburd@msu.edu>

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Package ciTools updated to version 0.5.0 with previous version 0.3.0 dated 2017-12-24

Title: Confidence or Prediction Intervals, Quantiles, and Probabilities for Statistical Models
Description: Functions to append confidence intervals, prediction intervals, and other quantities of interest to data frames. All appended quantities are for the response variable, after conditioning on the model and covariates. This package has a data frame first syntax that allows for easy piping. Currently supported models include (log-) linear, (log-) linear mixed, generalized linear models, generalized linear mixed models, and accelerated failure time models.
Author: John Haman [cre, aut], Matthew Avery [aut], Institute for Defense Analyses [cph]
Maintainer: John Haman <jhaman@ida.org>

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New package changer with initial version 0.0.2
Package: changer
Type: Package
Title: Change R Package Name
Version: 0.0.2
Date: 2018-10-15
Description: Changing the name of an existing R package is annoying but common task especially in the early stages of package development. This package (mostly) automates this task.
License: GPL (>= 2)
Imports: available, devtools, git2r
Encoding: UTF-8
RoxygenNote: 6.1.0
Authors@R: person(given = "Jouni", family = "Helske", role = c("aut", "cre"), email = "jouni.helske@iki.fi", comment = c(ORCID = "0000-0001-7130-793X"))
URL: https://github.com/helske/changer
BugReports: https://github.com/helske/changer/issues
NeedsCompilation: no
Packaged: 2018-10-15 21:11:40 UTC; jouhe21
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Repository: CRAN
Date/Publication: 2018-10-19 23:00:07 UTC

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Package ballr updated to version 0.2.2 with previous version 0.2.1 dated 2018-07-16

Title: Access to Current and Historical Basketball Data
Description: Provides simple functions for accessing data/tables on <http://www.basketball-reference.com>.
Author: Ryan Elmore [cre, aut], Peter DeWitt [ctb]
Maintainer: Ryan Elmore <rtelmore@gmail.com>

Diff between ballr versions 0.2.1 dated 2018-07-16 and 0.2.2 dated 2018-10-19

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Package wikitaxa updated to version 0.3.0 with previous version 0.2.0 dated 2017-12-21

Title: Taxonomic Information from 'Wikipedia'
Description: 'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
Author: Scott Chamberlain [aut, cre], Ethan Welty [aut]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

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Package remotes updated to version 2.0.1 with previous version 2.0.0 dated 2018-10-11

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package is a lightweight replacement of the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gábor Csárdi [aut, cre], Hadley Wickham [aut], Winston Chang [aut], Jim Hester [aut], RStudio [cph], Martin Morgan [aut], Dan Tenenbaum [aut], Mango Solutions [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package HextractoR updated to version 1.3 with previous version 1.2 dated 2018-08-28

Title: Integrated Tool for Hairping Extraction of RNA Sequences
Description: Simple and integrated tool that automatically extracts and folds all hairpin sequences from raw genome-wide data. It predicts the secondary structure of several overlapped segments, with longer length than the mean length of sequences of interest for the species under processing, ensuring that no one is lost nor inappropriately cut.
Author: Cristian Yones
Maintainer: Cristian Yones <cyones@sinc.unl.edu.ar>

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Package vcr updated to version 0.2.0 with previous version 0.1.0 dated 2018-05-14

Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

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Package tigger updated to version 0.3.1 with previous version 0.3.0 dated 2018-10-03

Title: Infers Novel Immunoglobulin Alleles from Sequencing Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>.
Author: Daniel Gadala-Maria [aut], Susanna Marquez [aut], Moriah Cohen [aut], Gur Yaari [aut], Jason Vander Heiden [ctb, cre], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>

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Package fulltext updated to version 1.1.0 with previous version 1.0.1 dated 2018-02-07

Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text 'scholarly' data, including 'Biomed Central', Public Library of Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ', 'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality included for searching for articles, downloading full or partial text, downloading supplementary materials, converting to various data formats.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Will Pearse [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rjags updated to version 4-8 with previous version 4-7 dated 2018-10-09

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

Diff between rjags versions 4-7 dated 2018-10-09 and 4-8 dated 2018-10-19

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 src/init.c  |    4 ++--
 src/jags.cc |    2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

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Package MGLM updated to version 0.2.0 with previous version 0.1.0 dated 2018-01-21

Title: Multivariate Response Generalized Linear Models
Description: Provides functions that (1) fit multivariate discrete distributions, (2) generate random numbers from multivariate discrete distributions, and (3) run regression and penalized regression on the multivariate categorical response data. Implemented models include: multinomial logit model, Dirichlet multinomial model, generalized Dirichlet multinomial model, and negative multinomial model. Making the best of the minorization-maximization (MM) algorithm and Newton-Raphson method, we derive and implement stable and efficient algorithms to find the maximum likelihood estimates. On a multi-core machine, multi-threading is supported.
Author: Yiwen Zhang <zhangyiwen1015@gmail.com> and Hua Zhou <huazhou@ucla.edu>
Maintainer: Juhyun Kim <juhkim111@ucla.edu>

Diff between MGLM versions 0.1.0 dated 2018-01-21 and 0.2.0 dated 2018-10-19

 DESCRIPTION        |    8 ++++----
 MD5                |   10 +++++-----
 R/MGLMreg.R        |    1 +
 R/aaclasses.R      |   10 ++++++----
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New package radtools with initial version 1.0.0
Package: radtools
Title: Utilities for Smooth Navigation of Medical Image Data
Version: 1.0.0
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@ucdenver.edu>
Authors@R: person("Pamela", "Russell", email = "pamela.russell@ucdenver.edu", role = c("aut", "cre"))
Description: A collection of utilities for navigating medical image data. The DICOM and NIfTI formats are supported. Functions provide simple interfaces to the data and metadata contained in these formats. A particular emphasis on metadata allows simple conversion of image metadata to familiar R data structures such as lists and data frames. Where possible, generic functions can silently process either DICOM or NIfTI data. Additionally, image data can be extracted and viewed.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: oro.dicom, dplyr, Hmisc, oro.nifti, magrittr, methods
RoxygenNote: 6.1.0
Suggests: testthat, covr, knitr, rmarkdown, rvest, hashmap, stringr, xml2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-15 22:39:13 UTC; Pamela
Repository: CRAN
Date/Publication: 2018-10-19 16:10:03 UTC

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New package lbfgsb3c with initial version 2018-2.13
Package: lbfgsb3c
Type: Package
Title: Limited Memory BFGS Minimizer with Bounds on Parameters with optim() 'C' Interface
Version: 2018-2.13
Authors@R: c(person(given = c("Matthew", "L"), family = "Fidler", role = c("aut", "cre"), email = "matthew.fidler@gmail.com"), person(given = c("John", "C"), family = "Nash", role = c("aut"), email = "nashjc@uottawa.ca"), person(given = "Ciyou", family = "Zhu", role = "aut"), person(given = "Richard", family = "Byrd", role = "aut"), person(given = "Jorge", family = "Nocedal", role = "aut"), person(given = c("Jose", "Luis"), family = "Morales", role = "aut"))
Maintainer: Matthew L Fidler <matthew.fidler@gmail.com>
Description: Interfacing to Nocedal et al. L-BFGS-B.3.0 (2011 <doi:10.1145/2049662.2049669>) limited memory BFGS minimizer with bounds on parameters. This is a fork of 'lbfgsb3'. This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same function types and optimization as the optim() function (see writing 'R' extensions and source for details). Ths package also adds more stopping criterion as well as allows adjusting more tolerances.
License: GPL-2
Depends: R (>= 3.0.2)
Imports: Rcpp (>= 0.12.3), numDeriv, methods
LinkingTo: Rcpp (>= 0.12.3), RcppArmadillo
NeedsCompilation: yes
RoxygenNote: 6.1.0
Suggests: testthat
Packaged: 2018-10-15 23:19:11 UTC; FIDLEMA3
Author: Matthew L Fidler [aut, cre], John C Nash [aut], Ciyou Zhu [aut], Richard Byrd [aut], Jorge Nocedal [aut], Jose Luis Morales [aut]
Repository: CRAN
Date/Publication: 2018-10-19 16:20:03 UTC

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Package bamboo updated to version 0.9.23 with previous version 0.9.22 dated 2018-06-29

Title: Protein Secondary Structure Prediction Using the Bamboo Method
Description: Implementation of the Bamboo methods described in Li, Dahl, Vannucci, Joo, and Tsai (2014) <DOI:10.1371/journal.pone.0109832>.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between bamboo versions 0.9.22 dated 2018-06-29 and 0.9.23 dated 2018-10-19

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 12 files changed, 35 insertions(+), 24 deletions(-)

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New package stratEst with initial version 0.1.0
Package: stratEst
Type: Package
Title: Strategy Estimation
Version: 0.1.0
Author: Fabian Dvorak
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Date: 2018-10-15
Description: Implements variants of the strategy frequency estimation method by Dal Bo & Frechette (2011) <doi:10.1257/aer.101.1.411>, including its adaptation to behavioral memory-one Markov strategies by Breitmoser (2015) <doi:10.1257/aer.20130675>, and the extension in the spirit of latent-class regression by Dvorak & Fehrler (2018) <doi:10.2139/ssrn.2986445>.
Copyright: See the file COPYRIGHTS for copyright, authorship and license details
License: GPL-3
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp (>= 0.12.18)
RoxygenNote: 6.0.1
Suggests: testthat
Depends: R (>= 2.10)
URL: http://github.com/fdvorak/stratEst
BugReports: http://github.com/fdvorak/stratEst/issues
NeedsCompilation: yes
Packaged: 2018-10-15 08:02:04 UTC; anon
Repository: CRAN
Date/Publication: 2018-10-19 15:10:03 UTC

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Package RMixpanel updated to version 0.7-0 with previous version 0.6-3 dated 2018-01-10

Title: API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention, funnel and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner [aut, cre, cph], ProSiebenSat.1 Digital GmbH [cph], BCG Digital Ventures GmbH [cph]
Maintainer: Meinhard Ploner <meinhard.ploner@gmail.com>

Diff between RMixpanel versions 0.6-3 dated 2018-01-10 and 0.7-0 dated 2018-10-19

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 MD5                                 |   16 ++++++++--------
 R/mixpanelGetData.R                 |    5 +++--
 R/mixpanelGetEvents.R               |    3 ++-
 R/mixpanelGetEventsForProfiles.R    |    3 ++-
 build/partial.rdb                   |binary
 man/mixpanelGetData.Rd              |    3 ++-
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 9 files changed, 28 insertions(+), 20 deletions(-)

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New package RSE with initial version 1.2
Package: RSE
Type: Package
Title: Number of Newly Discovered Rare Species Estimation
Version: 1.2
Date: 2018-10-15
Author: Youhua Chen,Tsung-Jen Shen
Maintainer: Youhua Chen <haydi@126.com>
Description: A Bayesian-weighted estimator and two unweighted estimators are developed to estimate the number of newly found rare species in additional ecological samples. Among these methods, the Bayesian-weighted estimator and an unweighted (Chao-derived) estimator are of high accuracy and recommended for practical applications. Technical details of the proposed estimators have been well described in the following paper: Shen TJ, Chen YH (2018) A Bayesian weighted approach to predicting the number of newly discovered rare species. Conservation Biology, In press.
License: GPL-3
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-15 14:47:37 UTC; Adminstrator
Repository: CRAN
Date/Publication: 2018-10-19 15:30:07 UTC

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Package poliscidata updated to version 2.2.3 with previous version 2.2.2 dated 2018-09-10

Title: Datasets and Functions Featured in Pollock and Edwards, An R Companion to Essentials of Political Analysis, Second Edition
Description: Bundles the datasets and functions used in the textbook by Philip Pollock and Barry Edwards, An R Companion to Essentials of Political Analysis, Second Edition.
Author: Barry Edwards and Philip Pollock
Maintainer: Barry Edwards <barry.edwards@ucf.edu>

Diff between poliscidata versions 2.2.2 dated 2018-09-10 and 2.2.3 dated 2018-10-19

 DESCRIPTION              |    6 +++---
 MD5                      |   10 ++++++----
 NEWS.md                  |    8 ++++++++
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 7 files changed, 55 insertions(+), 17 deletions(-)

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Package pmatch updated to version 0.1.4 with previous version 0.1.3 dated 2018-03-22

Title: Pattern Matching
Description: Implements type constructions and pattern matching. Using this package, you can specify a type of object and write functions that matches against the structure of objects of such types to program data structure transformations more succinctly.
Author: Thomas Mailund [aut, cre]
Maintainer: Thomas Mailund <mailund@birc.au.dk>

Diff between pmatch versions 0.1.3 dated 2018-03-22 and 0.1.4 dated 2018-10-19

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New package khroma with initial version 1.0.0
Package: khroma
Title: Colour Schemes for Archaeological Data Visualization
Version: 1.0.0
Authors@R: person("Nicolas", "Frerebeau", email = "nicolas.frerebeau@cea.fr", role = c("aut", "cre"), comment = c(ORCID = "https://orcid.org/0000-0001-5759-4944"))
Description: Colour schemes for archaeological data visualization. Provides Paul Tol's colour schemes and several thematic palettes (geologic timescale, etc.) with scales for 'ggplot2'.
URL: http://github.com/nfrerebeau/khroma
BugReports: http://github.com/nfrerebeau/khroma/issues
Depends: R (>= 3.4)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: ggplot2 (>= 3.0.0), scales
Imports: grDevices
Collate: 'colour.R' 'utilities.R' 'ggplot2.R'
NeedsCompilation: no
Packaged: 2018-10-15 10:43:26 UTC; nicolas
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>)
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@cea.fr>
Repository: CRAN
Date/Publication: 2018-10-19 15:20:06 UTC

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New package JMI with initial version 0.1.0
Package: JMI
Type: Package
Title: Jackknife Mutual Information
Version: 0.1.0
Author: Zeng Xianli <a0123862@u.nus.edu>, Hang Weiqiang <e0010758@u.nus.edu>
Maintainer: Zeng Xianli <a0123862@u.nus.edu>
Description: Computes the Jackknife Mutual Information (JMI) between two random vectors and provides the p-value for dependence tests. See Zeng, X., Xia, Y. and Tong, H. (2018) <doi:10.1073/pnas.1715593115>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: Rcpp
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-10-15 08:00:58 UTC; weiqianghang
Repository: CRAN
Date/Publication: 2018-10-19 15:10:12 UTC

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New package arena2r with initial version 1.0.0
Package: arena2r
Type: Package
Title: Plots, Summary Statistics and Tools for Arena Simulation Users
Version: 1.0.0
Author: Pedro Nascimento de Lima [aut, cre]
Maintainer: Pedro Nascimento de Lima <pedrolima.n@gmail.com>
Authors@R: person("Pedro Nascimento de", "Lima", email = "pedrolima.n@gmail.com", role = c("aut", "cre"))
Description: Reads Arena <https://www.arenasimulation.com/> CSV output files and generates nice tables and plots. The package contains a Shiny App that can be used to interactively visualize Arena's results.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: stats, utils, rlang, tidyr, magrittr, dplyr, purrr, shiny, shinydashboard, shinyBS, shinyjs, ggplot2
Depends: R (>= 2.10)
Suggests: testthat, covr, knitr, rmarkdown
RoxygenNote: 6.1.0
URL: https://github.com/pedroliman/arena2r
BugReports: https://github.com/pedroliman/arena2r/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-15 14:39:56 UTC; Pedro Lima
Repository: CRAN
Date/Publication: 2018-10-19 15:30:03 UTC

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New package SpecDetec with initial version 1.0.0
Package: SpecDetec
Title: Change Points Detection with Spectral Clustering
Version: 1.0.0
Authors@R: person("Luis", "Uzai", email = "uzai_ff@hotmail.com", role = c("aut", "cre"))
Description: Calculate change point based on spectral clustering with the option to automatically calculate the number of clusters if this information is not available.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: stats, abind
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-14 17:16:39 UTC; uzai_
Author: Luis Uzai [aut, cre]
Maintainer: Luis Uzai <uzai_ff@hotmail.com>
Repository: CRAN
Date/Publication: 2018-10-19 14:20:03 UTC

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Package RNifti updated to version 0.10.0 with previous version 0.9.0 dated 2018-09-10

Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. Also provides a C/C++ API that can be used by other packages. Not to be confused with 'RNiftyReg', which performs image registration.
Author: Jon Clayden [cre, aut], Bob Cox [aut], Mark Jenkinson [aut], Matt Hall [ctb], Rick Reynolds [ctb], Kate Fissell [ctb], Jean-loup Gailly [cph], Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>

Diff between RNifti versions 0.9.0 dated 2018-09-10 and 0.10.0 dated 2018-10-19

 DESCRIPTION                            |   10 -
 MD5                                    |   22 +-
 NEWS                                   |   32 +++
 R/image.R                              |   24 +-
 R/nifti.R                              |    5 
 README.md                              |    2 
 inst/include/RNifti.h                  |    6 
 inst/include/RNiftiAPI.h               |   13 +
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 inst/include/lib/NiftiImage_internal.h |   21 --
 src/main.cpp                           |   64 +++----
 tests/testthat/test-05-nifti.R         |   19 +-
 12 files changed, 338 insertions(+), 170 deletions(-)

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New package HSDiC with initial version 0.1
Package: HSDiC
Type: Package
Version: 0.1
Title: Homogeneity and Sparsity Detection Incorporating Prior Constraint Information
Authors@R: c(person("Yaguang", "Li", role = c("aut", "cre"), email = "liyg@mail.ustc.edu.cn"), person("Baisuo", "Jin", role = "aut"))
Author: Yaguang Li [aut, cre], Baisuo Jin [aut]
Maintainer: Yaguang Li <liyg@mail.ustc.edu.cn>
Depends: R (>= 3.5.0), ncvreg, glmnet, quadprog, Matrix
Description: We explore sparsity and homogeneity of regression coefficients incorporating prior constraint information. A general pairwise fusion approach is proposed to deal with the sparsity and homogeneity detection when combining prior convex constraints. We develop an modified alternating direction method of multipliers algorithm (ADMM) to obtain the estimators.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-14 10:16:45 UTC; ustcr7
Repository: CRAN
Date/Publication: 2018-10-19 14:10:03 UTC

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Package webTRISr updated to version 0.1.1 with previous version 0.1.0 dated 2017-08-25

Title: A Wrapper Around 'WebTRIS' Traffic Flow API from Highways England
Description: Provides functions to query data from the 'WebTRIS' Traffic Flow API (from Highways England) into tidy data frames. The API documentation is available here: <http://webtris.highwaysengland.co.uk/api/swagger/ui/index>.
Author: Will Bowditch [aut, cre]
Maintainer: Will Bowditch <will.bowditch@dft.gov.uk>

Diff between webTRISr versions 0.1.0 dated 2017-08-25 and 0.1.1 dated 2018-10-19

 DESCRIPTION                     |   12 ++---
 MD5                             |   28 ++++++------
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 R/report_parsers.R              |   76 ++++++++++++++++++++++-----------
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 README.md                       |    6 ++
 man/webtris_quality.Rd          |    3 +
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 tests/testthat/test_WTareas.R   |    8 +--
 tests/testthat/test_WTquality.R |   26 +++++++----
 tests/testthat/test_WTsites.R   |    6 +-
 tests/testthat/test_reports.R   |   90 +++++++++++++++++-----------------------
 15 files changed, 197 insertions(+), 134 deletions(-)

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Package snowboot updated to version 1.0.0 with previous version 0.5.2 dated 2016-12-08

Title: Bootstrap Methods for Network Inference
Description: Functions for analysis of network objects, which are imported or simulated by the package. The non-parametric methods of analysis center on snowball and bootstrap sampling for estimating functions of network degree distribution. For other parameters of interest, see, e.g., 'bootnet' package.
Author: Leticia Ramirez-Ramirez [aut], Kusha Nezafati [aut], Yuzhou Chen [aut], Vyacheslav Lyubchich [aut, cre], Yulia R. Gel [aut]
Maintainer: Vyacheslav Lyubchich <lyubchich@umces.edu>

Diff between snowboot versions 0.5.2 dated 2016-12-08 and 1.0.0 dated 2018-10-19

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New package linkprediction with initial version 1.0-0
Package: linkprediction
Title: Link Prediction Methods
Version: 1.0-0
Authors@R: c( person( "Michal", "Bojanowski", email="michal2992@gmail.com", role=c("aut", "cre")), person("Bartosz", "Chrol", email="bartek.chrol@gmail.com", role=c("aut")), person(family="National Science Centre", role="fnd", comment="grant 2012/07/D/HS6/01971") )
Description: Implementations of most of the existing proximity-based methods of link prediction in graphs. Among the 20 implemented methods are e.g.: Adamic L. and Adar E. (2003) <doi:10.1016/S0378-8733(03)00009-1>, Leicht E., Holme P., Newman M. (2006) <doi:10.1103/PhysRevE.73.026120>, Zhou T. and Zhang Y (2009) <doi:10.1140/epjb/e2009-00335-8>, and Fouss F., Pirotte A., Renders J., and Saerens M. (2007) <doi:10.1109/TKDE.2007.46>.
Depends: R (>= 3.1.1),
License: MIT + file LICENSE
LazyData: true
Imports: igraph, intergraph
Suggests: knitr, testthat
RoxygenNote: 6.1.0
VignetteBuilder: knitr
BugReports: https://github.com/recon-icm/linkprediction/issues
URL: https://github.com/recon-icm/linkprediction
NeedsCompilation: no
Packaged: 2018-10-12 14:38:02 UTC; mbojanowski
Author: Michal Bojanowski [aut, cre], Bartosz Chrol [aut], National Science Centre [fnd] (grant 2012/07/D/HS6/01971)
Maintainer: Michal Bojanowski <michal2992@gmail.com>
Repository: CRAN
Date/Publication: 2018-10-19 13:40:03 UTC

More information about linkprediction at CRAN
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New package gcForest with initial version 0.2.7
Package: gcForest
Type: Package
Title: Deep Forest Model
Version: 0.2.7
Author: Xu Jing [cre]
Maintainer: Xu Jing <274762204@qq.com>
Description: R application programming interface (API) for Deep Forest which based on Zhou and Feng (2017). Deep Forest: Towards an Alternative to Deep Neural Networks. (<arXiv:1702.08835v2>) or Zhou and Feng (2017). Deep Forest. (<arXiv:1702.08835>). And for the Python module 'gcForest' (<https://github.com/pylablanche/gcForest>).
License: GPL (>= 2)
SystemRequirements: Python (>= 3.5.0)
Encoding: UTF-8
LazyData: true
URL: https://github.com/DataXujing/gcForest_r
BugReports: https://github.com/DataXujing/gcForest_r/issues
RoxygenNote: 6.0.1
Depends: R (>= 3.4.0)
Imports: reticulate,pkgdown,crayon,cli,utils
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-05 05:08:14 UTC; xujing
Repository: CRAN
Date/Publication: 2018-10-19 14:00:03 UTC

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New package rTephra with initial version 0.1
Package: rTephra
Title: Tephra Transport Modeling
Version: 0.1
Author: Jake Anderson
Maintainer: Jake Anderson <ajakef@gmail.com>
Description: Models and displays tephra transport through custom (windy, turbulent, heterogeneous) atmosphere over custom topography. Includes a Lagrangian (particle-tracking) tephra transport model and a function to save snapshots of model as png files.
Depends: R (>= 3.0.0)
Suggests: rNOMADS
License: GPL
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-10-11 19:41:04 UTC; jake
Repository: CRAN
Date/Publication: 2018-10-19 12:20:02 UTC

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New package maximin with initial version 1.0-1
Package: maximin
Title: Sequential Space-Filling Design under the Criterion of Maximin Distance
Version: 1.0-1
Date: 2018-10-10
Author: Furong Sun <furongs@vt.edu>, Robert B. Gramacy <rbg@vt.edu>
Depends: R (>= 2.14)
Imports: plgp
Suggests: lhs
Description: Builds up sequential space-filling design under the criterion of maximin distance. Both discrete and continuous versions are provided.
Maintainer: Furong Sun <furongs@vt.edu>
License: LGPL
NeedsCompilation: no
Packaged: 2018-10-11 16:20:54 UTC; furong
Repository: CRAN
Date/Publication: 2018-10-19 12:20:05 UTC

More information about maximin at CRAN
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Package logmult updated to version 0.7.0 with previous version 0.6.5 dated 2017-11-15

Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using 'gnm', with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart. Functions allow computing the intrinsic association coefficient (and therefore the Altham index), including via the Bayes shrinkage estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Author: Milan Bouchet-Valat [aut, cre], Heather Turner [ctb], Michael Friendly [ctb], Jim Lemon [cph], Gabor Csardi [cph]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

Diff between logmult versions 0.6.5 dated 2017-11-15 and 0.7.0 dated 2018-10-19

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New package EMMIXmfa with initial version 2.0.7
Package: EMMIXmfa
Type: Package
Title: Mixture Models with Component-Wise Factor Analyzers
Version: 2.0.7
Date: 2018-09-17
URL: https://github.com/suren-rathnayake/EMMIXmfa
Author: Suren Rathnayake, Geoff McLachlan, David Peel, Jungsun Baek
Maintainer: Suren Rathnayake <surenr@gmail.com>
Description: We provide functions to fit finite mixtures of multivariate normal or t-distributions to data with various factor analytic structures adopted for the covariance/scale matrices. The factor analytic structures available include mixtures of factor analyzers and mixtures of common factor analyzers. The latter approach is so termed because the matrix of factor loadings is common to components before the component-specific rotation of the component factors to make them white noise. Note that the component-factor loadings are not common after this rotation. Maximum likelihood estimators of model parameters are obtained via the Expectation-Maximization algorithm. See descriptions of the algorithms used in McLachlan GJ, Peel D (2000) <doi:10.1002/0471721182.ch8> McLachlan GJ, Peel D (2000) <ISBN:1-55860-707-2> McLachlan GJ, Peel D, Bean RW (2003) <doi:10.1016/S0167-9473(02)00183-4> McLachlan GJ, Bean RW, Ben-Tovim Jones L (2007) <doi:10.1016/j.csda.2006.09.015> Baek J, McLachlan GJ, Flack LK (2010) <doi:10.1109/TPAMI.2009.149> Baek J, McLachlan GJ (2011) <doi:10.1093/bioinformatics/btr112> McLachlan GJ, Baek J, Rathnayake SI (2011) <doi:10.1002/9781119995678.ch9>.
Suggests: mvtnorm, GGally, ggplot2
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2018-10-12 02:40:24 UTC; uqsratha
Repository: CRAN
Date/Publication: 2018-10-19 12:20:08 UTC

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Package devtools updated to version 2.0.0 with previous version 1.13.6 dated 2018-06-27

Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Jim Hester <james.hester@rstudio.com>

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Package AnthropMMD updated to version 2.5.1 with previous version 2.5.0 dated 2018-03-21

Title: An R-Shiny Application for Smith's Mean Measure of Divergence (MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>)
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>

Diff between AnthropMMD versions 2.5.0 dated 2018-03-21 and 2.5.1 dated 2018-10-19

 DESCRIPTION                      |   13 +++++++------
 MD5                              |    8 ++++----
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 man/AnthropMMD-package.Rd        |   14 ++++++++++----
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Package xtensor updated to version 0.8.1-0 with previous version 0.6.1-0 dated 2018-05-27

Title: Headers for the 'xtensor' Library
Description: The 'xtensor' C++ library for numerical analysis with multi-dimensional array expressions is provided as a header-only C++14 library. It offers an extensible expression system enabling lazy broadcasting; an API following the idioms of the C++ standard library; and tools to manipulate array expressions and build upon 'xtensor'.
Author: Johan Mabille, Sylvain Corlay and Wolf Vollprecht
Maintainer: Sylvain Corlay <sylvain.corlay@gmail.com>

Diff between xtensor versions 0.6.1-0 dated 2018-05-27 and 0.8.1-0 dated 2018-10-19

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Package webmockr updated to version 0.2.8 with previous version 0.2.6 dated 2018-05-17

Title: Stubbing and Setting Expectations on 'HTTP' Requests
Description: Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

Diff between webmockr versions 0.2.6 dated 2018-05-17 and 0.2.8 dated 2018-10-19

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Package survHE updated to version 1.0.64 with previous version 1.0.6 dated 2017-07-08

Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners).
Author: Gianluca Baio [aut, cre]
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>

Diff between survHE versions 1.0.6 dated 2017-07-08 and 1.0.64 dated 2018-10-19

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Package rgeos updated to version 0.4-1 with previous version 0.3-28 dated 2018-06-08

Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Colin Rundel [aut], Edzer Pebesma [ctb], Rainer Stuetz [ctb], Karl Ove Hufthammer [ctb], Patrick Giraudoux [ctb], Martin Davis [cph, ctb], Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between rgeos versions 0.3-28 dated 2018-06-08 and 0.4-1 dated 2018-10-19

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Permanent link

Package miceadds updated to version 2.15-22 with previous version 2.14-26 dated 2018-09-18

Title: Some Additional Multiple Imputation Functions, Especially for 'mice'
Description: Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are included. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), and nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut], Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between miceadds versions 2.14-26 dated 2018-09-18 and 2.15-22 dated 2018-10-19

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More information about miceadds at CRAN
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Package geojsonsf updated to version 1.2 with previous version 1.1 dated 2018-06-29

Title: GeoJSON to Simple Feature Converter
Description: Converts Between GeoJSON and simple feature objects.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between geojsonsf versions 1.1 dated 2018-06-29 and 1.2 dated 2018-10-19

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Package divest updated to version 0.7.0 with previous version 0.6.1 dated 2018-09-16

Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre], Chris Rorden [aut], Martin J Fiedler [cph], Cong Xu [cph], Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>

Diff between divest versions 0.6.1 dated 2018-09-16 and 0.7.0 dated 2018-10-19

 DESCRIPTION                      |    8 
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Package sugrrants updated to version 0.1.6 with previous version 0.1.5 dated 2018-08-19

Title: Supporting Graphs for Analysing Time Series
Description: Provides 'ggplot2' graphics for analysing time series data. It aims to fit into the 'tidyverse' and grammar of graphics framework for handling temporal data.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>)
Maintainer: Earo Wang <earo.wang@gmail.com>

Diff between sugrrants versions 0.1.5 dated 2018-08-19 and 0.1.6 dated 2018-10-19

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More information about sugrrants at CRAN
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Package MPS updated to version 2.3.0 with previous version 2.2.0 dated 2018-09-03

Title: Estimating Through the Maximum Product Spacing Approach
Description: Developed for computing the probability density function, computing the cumulative distribution function, computing the quantile function, random generation, and estimating the parameters of 24 G-family of statistical distributions via the maximum product spacing approach introduced in <https://www.jstor.org/stable/2345411>. The set of families contains: beta G distribution, beta exponential G distribution, beta extended G distribution, exponentiated G distribution, exponentiated exponential Poisson G distribution, exponentiated generalized G distribution, exponentiated Kumaraswamy G distribution, gamma type I G distribution, gamma type II G distribution, gamma uniform G distribution, gamma-X generated of log-logistic family of G distribution, gamma-X family of modified beta exponential G distribution, geometric exponential Poisson G distribution, generalized beta G distribution, generalized transmuted G distribution, Kumaraswamy G distribution, log gamma type I G distribution, log gamma type II G distribution, Marshall Olkin G distribution, Marshall Olkin Kumaraswamy G distribution, modified beta G distribution, odd log-logistic G distribution, truncated-exponential skew-symmetric G distribution, and Weibull G distribution.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>

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Package sizeMat updated to version 1.0.0 with previous version 0.3.0 dated 2017-04-03

Title: Estimate Size at Sexual Maturity
Description: Contains functions to estimate morphometric and gonadal size at sexual maturity for organisms, usually fish and invertebrates. It includes methods for classification based on relative growth (using principal components analysis, hierarchical clustering, discriminant analysis), logistic regression (Frequentist or Bayes), parameters estimation and some basic plots.
Author: Josymar Torrejon-Magallanes [cre, aut]
Maintainer: Josymar Torrejon-Magallanes <ejosymart@gmail.com>

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Package dendextend updated to version 1.9.0 with previous version 1.8.0 dated 2018-05-06

Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Krzysiek G [ctb] (https://github.com/storaged), Manuela Hummel [ctb] (https://github.com/hummelma), Chase Clark [ctb] (https://github.com/chasemc), Lucas Graybuck [ctb] (https://github.com/hypercompetent), jdetribol [ctb] (https://github.com/jdetribol), Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package cjoint updated to version 2.1.0 with previous version 2.0.6 dated 2017-11-09

Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) <DOI:10.1093/pan/mpt024> Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Soubhik Barari, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Sean Liu, Anton Strezhnev, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhn@law.upenn.edu>

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Package DataExplorer updated to version 0.7.0 with previous version 0.6.0 dated 2018-05-30

Title: Data Explorer
Description: Data exploration process for data analysis and model building, so that users could focus on understanding data and extracting insights. The package automatically scans through each variable and does data profiling. Typical graphical techniques will be performed for both discrete and continuous features.
Author: Boxuan Cui [aut, cre]
Maintainer: Boxuan Cui <boxuancui@gmail.com>

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