Wed, 26 Apr 2017

Package ggsignif updated to version 0.2.0 with previous version 0.1.0 dated 2017-04-05

Title: Significance Bars for 'ggplot2'
Description: Enrich your ggplots with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bar on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.
Author: Constantin Ahlmann-Eltze [aut, cre]
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>

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More information about ggsignif at CRAN
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Package fourierin updated to version 0.2.1 with previous version 0.1.2 dated 2016-05-22

Title: Computes Numeric Fourier Integrals
Description: Computes Fourier integrals of functions of one and two variables using the Fast Fourier transform. The Fourier transforms must be evaluated on a regular grid.
Author: Guillermo Basulto-Elias
Maintainer: Guillermo Basulto-Elias <guillermobasulto@gmail.com>

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More information about fourierin at CRAN
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Package blavaan updated to version 0.2-4 with previous version 0.2-3 dated 2017-02-24

Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre], Yves Rosseel [aut], Mauricio Garnier-Villarreal [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>

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Package rv updated to version 2.3.2 with previous version 2.3.1 dated 2013-06-26

Title: Simulation-Based Random Variable Objects
Description: Implements simulation-based random variable class and a suite of methods.
Author: Jouni Kerman <jouni@kerman.com>
Maintainer: Jouni Kerman <jouni@kerman.com>

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New package ems with initial version 0.3.1.6
Package: ems
Title: Epimed Solutions Collection for Data Editing, Analysis, and Benchmarking of Health Units
Version: 0.3.1.6
Date: 2017-04-26
Authors@R: c(person("Lunna", "Borges", role = c("aut"), email = "lunna.borges@epimedsolutions.com"), person("Pedro", "Brasil", role = c("aut", "cre"), email = "pedro.brasil@epimedsolutions.com"))
Description: Collection of functions for data analysis and editing. Most of them are related to benchmarking with prediction models.
Depends: R (>= 3.3.1)
License: GPL (>= 2)
LazyData: true
RoxygenNote: 5.0.1
Author: Lunna Borges [aut], Pedro Brasil [aut, cre]
Maintainer: Pedro Brasil <pedro.brasil@epimedsolutions.com>
Repository: CRAN
Repository/R-Forge/Project: ems
Repository/R-Forge/Revision: 42
Repository/R-Forge/DateTimeStamp: 2017-04-26 18:52:04
Date/Publication: 2017-04-26 20:03:29 UTC
NeedsCompilation: no
Packaged: 2017-04-26 19:05:25 UTC; rforge

More information about ems at CRAN
Permanent link

Package qualtRics updated to version 1.0 with previous version 0.3 dated 2016-11-29

Title: Download Qualtrics Survey Data Directly into R
Description: Qualtrics <https://www.qualtrics.com/about/> allows users to collect online data through surveys. This package contains convenience functions to pull survey results straight into R using the Qualtrics API. See <https://api.qualtrics.com/> for more information about the Qualtrics API.
Author: Jasper Ginn
Maintainer: Jasper Ginn <jasperginn@gmail.com>

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Package hmi updated to version 0.7.4 with previous version 0.6.3 dated 2017-03-27

Title: Hierarchical Multiple Imputation
Description: Runs single level and multilevel imputation models. The user just has to pass the data to the main function and, optionally, his analysis model. Basically the package then translates this analysis model into commands to impute the data according to it with functions from 'mice', 'MCMCglmm' or routines build for this package.
Author: Matthias Speidel [aut, cre] (Institute for Employment Research, Nuremberg, Germany), Joerg Drechsler [aut] (Institute for Employment Research, Nuremberg, Germany), Shahab Jolani [aut] (Maastricht University, Maastricht, The Netherlands)
Maintainer: Matthias Speidel <matthias.speidel@googlemail.com>

Diff between hmi versions 0.6.3 dated 2017-03-27 and 0.7.4 dated 2017-04-26

 hmi-0.6.3/hmi/R/hmi_imp_binary_multi_2016-12-10.R                                                      |only
 hmi-0.6.3/hmi/R/hmi_imp_binary_single_2017-01-12.R                                                     |only
 hmi-0.6.3/hmi/R/hmi_imp_cat_multi_2017-01-10.R                                                         |only
 hmi-0.6.3/hmi/R/hmi_imp_cat_single_2016-12-23.R                                                        |only
 hmi-0.6.3/hmi/R/hmi_imp_catordered_multi_2017-01-04.R                                                  |only
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 hmi-0.6.3/hmi/R/hmi_imp_cont_single_2017-01-18.R                                                       |only
 hmi-0.6.3/hmi/R/hmi_imp_count_multi_2017-01-04.R                                                       |only
 hmi-0.6.3/hmi/R/hmi_imp_count_single_2017-01-05.R                                                      |only
 hmi-0.6.3/hmi/R/hmi_imp_interval_2017-02-05.R                                                          |only
 hmi-0.6.3/hmi/R/hmi_imp_roundedcont_2017-01-31.R                                                       |only
 hmi-0.6.3/hmi/R/hmi_imp_semicont_multi_2017-01-10.R                                                    |only
 hmi-0.6.3/hmi/R/hmi_imp_semicont_single_2016-12-10.R                                                   |only
 hmi-0.6.3/hmi/R/hmi_smallfunctions_2017-02-21.R                                                        |only
 hmi-0.6.3/hmi/R/hmi_wrapper_2017-02-05.R                                                               |only
 hmi-0.6.3/hmi/man/contributions4intervalls.Rd                                                          |only
 hmi-0.6.3/hmi/man/divided_interval.Rd                                                                  |only
 hmi-0.6.3/hmi/man/minus_interval.Rd                                                                    |only
 hmi-0.6.3/hmi/man/plus_interval.Rd                                                                     |only
 hmi-0.6.3/hmi/man/times_interval.Rd                                                                    |only
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 hmi-0.7.4/hmi/DESCRIPTION                                                                              |   15 
 hmi-0.7.4/hmi/MD5                                                                                      |  202 +++++-----
 hmi-0.7.4/hmi/NAMESPACE                                                                                |   10 
 hmi-0.7.4/hmi/R/hmi_imp_binary_multi_2017-04-11.R                                                      |only
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 hmi-0.7.4/hmi/R/hmi_imp_cont_single_2017-04-11.R                                                       |only
 hmi-0.7.4/hmi/R/hmi_imp_count_multi_2017-04-11.R                                                       |only
 hmi-0.7.4/hmi/R/hmi_imp_count_single_2017-04-11.R                                                      |only
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 hmi-0.7.4/hmi/R/hmi_imp_roundedcont_2017-04-11.R                                                       |only
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 hmi-0.7.4/hmi/R/hmi_smallfunctions_2017-04-20.R                                                        |only
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 hmi-0.7.4/hmi/inst/doc/my-vignette.R                                                                   |   41 +-
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 hmi-0.7.4/hmi/man/as_data_frame_interval.Rd                                                            |    2 
 hmi-0.7.4/hmi/man/as_interval.Rd                                                                       |    2 
 hmi-0.7.4/hmi/man/components.Rd                                                                        |    8 
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 hmi-0.7.4/hmi/man/decompose_interval.Rd                                                                |    2 
 hmi-0.7.4/hmi/man/doubleintegral.Rd                                                                    |    4 
 hmi-0.7.4/hmi/man/extract_varnames.Rd                                                                  |    4 
 hmi-0.7.4/hmi/man/get_type.Rd                                                                          |    6 
 hmi-0.7.4/hmi/man/hmi.Rd                                                                               |   16 
 hmi-0.7.4/hmi/man/hmi_pool.Rd                                                                          |    4 
 hmi-0.7.4/hmi/man/idf2interval.Rd                                                                      |    2 
 hmi-0.7.4/hmi/man/imp_binary_multi.Rd                                                                  |   16 
 hmi-0.7.4/hmi/man/imp_binary_single.Rd                                                                 |   10 
 hmi-0.7.4/hmi/man/imp_cat_multi.Rd                                                                     |   37 -
 hmi-0.7.4/hmi/man/imp_cat_single.Rd                                                                    |   16 
 hmi-0.7.4/hmi/man/imp_cont_multi.Rd                                                                    |   16 
 hmi-0.7.4/hmi/man/imp_cont_single.Rd                                                                   |   12 
 hmi-0.7.4/hmi/man/imp_count_multi.Rd                                                                   |   16 
 hmi-0.7.4/hmi/man/imp_count_single.Rd                                                                  |   10 
 hmi-0.7.4/hmi/man/imp_interval.Rd                                                                      |   18 
 hmi-0.7.4/hmi/man/imp_orderedcat_multi.Rd                                                              |   16 
 hmi-0.7.4/hmi/man/imp_orderedcat_single.Rd                                                             |   10 
 hmi-0.7.4/hmi/man/imp_roundedcont.Rd                                                                   |   12 
 hmi-0.7.4/hmi/man/imp_semicont_multi.Rd                                                                |   18 
 hmi-0.7.4/hmi/man/imp_semicont_single.Rd                                                               |   12 
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 hmi-0.7.4/hmi/man/interval-divide.Rd                                                                   |only
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More information about hmi at CRAN
Permanent link

Package Anthropometry updated to version 1.8 with previous version 1.7 dated 2015-12-12

Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

Diff between Anthropometry versions 1.7 dated 2015-12-12 and 1.8 dated 2017-04-26

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Permanent link

Package x12 updated to version 1.8.0 with previous version 1.6.0 dated 2014-11-20

Title: Interface to X12-ARIMA/X13-ARIMA-SEATS and Structure for Batch Processing of Seasonal Adjustment
Description: The X13-ARIMA-SEATS methodology and software is a widely used software and developed by the US Census Bureau. It can be accessed from R with this R package and X13-ARIMA-SEATS binaries are provided by the R package x13binary.
Author: Alexander Kowarik <alexander.kowarik@statistik.gv.at>, Angelika Meraner
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>

Diff between x12 versions 1.6.0 dated 2014-11-20 and 1.8.0 dated 2017-04-26

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More information about x12 at CRAN
Permanent link

New package spant with initial version 0.1.0
Package: spant
Type: Package
Title: MR Spectroscopy Analysis Tools
Version: 0.1.0
Date: 2017-04-26
Authors@R: person("Martin", "Wilson", email = "martin@pipegrep.co.uk", role = c("cre","aut"))
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data.
License: GPL-3
RoxygenNote: 6.0.1
LazyData: yes
Depends: R (>= 2.10)
Imports: abind, plyr, foreach, pracma, stringr, complexplus, signal, matrixcalc, minpack.lm, nnls, utils, graphics, grDevices, smoother, svd
Suggests: oro.nifti, MASS, fastICA, fields, mmand, ptw, tkrplot, viridis, RNifti, RNiftyReg, neurobase, knitr, magrittr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-26 12:33:26 UTC; wilsonmp
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Repository: CRAN
Date/Publication: 2017-04-26 17:20:29 UTC

More information about spant at CRAN
Permanent link

Package smoof updated to version 1.5 with previous version 1.4 dated 2016-08-03

Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre], Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>

Diff between smoof versions 1.4 dated 2016-08-03 and 1.5 dated 2017-04-26

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More information about smoof at CRAN
Permanent link

Package shiny updated to version 1.0.3 with previous version 1.0.2 dated 2017-04-18

Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre], Joe Cheng [aut], JJ Allaire [aut], Yihui Xie [aut], Jonathan McPherson [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Dave Gandy [ctb, cph] (Font-Awesome font), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), John Fraser [ctb, cph] (showdown.js library), John Gruber [ctb, cph] (showdown.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>

Diff between shiny versions 1.0.2 dated 2017-04-18 and 1.0.3 dated 2017-04-26

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Package RSCABS updated to version 0.9.2 with previous version 0.9.01 dated 2016-12-12

Title: Rao-Scott Cochran-Armitage by Slices Trend Test
Description: Performs the Rao-Scott Cochran-Armitage by Slices trend test (RSCABS) used in analysis of histopathological endpoints, built to be used with either a GUI or by a command line. The RSCABS method is detailed in "Statistical analysis of histopathological endpoints" by John Green et. al. (2014) <doi:10.1002/etc.2530>.
Author: Joe Swintek [aut, cre], Kevin Flynn [ctb]
Maintainer: Joe Swintek <swintek.joe@epa.gov>

Diff between RSCABS versions 0.9.01 dated 2016-12-12 and 0.9.2 dated 2017-04-26

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More information about RSCABS at CRAN
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Package pre updated to version 0.2 with previous version 0.1 dated 2016-12-24

Title: Prediction Rule Ensembles
Description: Derives prediction rule ensembles (PREs). Largely follows the procedure for deriving PREs as described in Friedman & Popescu (2008; <DOI:10.1214/07-AOAS148>), with several adjustments and improvements. The main function pre() derives a prediction rule ensemble. Functions print(), plot(), coef() and importance() can be used to inspect the generated ensemble. Function predict() generates predicted values. Functions singeplot() and pairplot() depict dependence of the output on specified predictor variables. Function cvpre() performs full cross validation of a pre to calculate the expected prediction error. Functions interact() and bsnullinteract() can be used to assess interaction effects of predictor variables.
Author: Marjolein Fokkema [aut, cre]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>

Diff between pre versions 0.1 dated 2016-12-24 and 0.2 dated 2017-04-26

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More information about pre at CRAN
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New package md.log with initial version 0.1.1
Package: md.log
Type: Package
Title: Produces Markdown Log File with a Built-in Function Call
Version: 0.1.1
Author: E. F. Haghish
Maintainer: E. F. Haghish <e.f.haghish@uni-greifswald.de>
Description: Produces clean and neat Markdown log file and also provide an argument to include the function call inside the Markdown log.
License: MIT + file LICENSE
URL: https://github.com/haghish/md.log
BugReports: https://github.com/haghish/md.log/issues
NeedsCompilation: no
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports: futile.logger
Packaged: 2017-04-26 08:42:34 UTC; haghish
Repository: CRAN
Date/Publication: 2017-04-26 17:27:01 UTC

More information about md.log at CRAN
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New package MAGNAMWAR with initial version 1.0.0
Package: MAGNAMWAR
Title: A Pipeline for Meta-Genome Wide Association
Version: 1.0.0
Date: 2017-04-26
Authors@R: c( person("Corinne", "Sexton", role = c("aut"), email="corinsexton@gmail.com"), person("John", "Chaston", role = c("aut", "cre"), email = "john_chaston@byu.edu"), person("Hayden", "Smith", role = "ctb") )
Description: Correlates variation within the meta-genome to target species phenotype variations in meta-genome with association studies.
License: MIT + file LICENSE
LazyData: true
Imports: ape, coxme, doParallel, dplyr, foreach, iterators, lme4, multcomp, parallel, plyr, qqman, survival, seqinr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 3.0)
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-26 16:47:25 UTC; coripenrod
Author: Corinne Sexton [aut], John Chaston [aut, cre], Hayden Smith [ctb]
Maintainer: John Chaston <john_chaston@byu.edu>
Repository: CRAN
Date/Publication: 2017-04-26 17:17:58 UTC

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Package isoph updated to version 1.0 with previous version 0.5 dated 2016-01-02

Title: Isotonic Proportional Hazards Model
Description: Nonparametric estimation of an isotonic covariate effect for proportional hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <ychung@fredhutch.org>

Diff between isoph versions 0.5 dated 2016-01-02 and 1.0 dated 2017-04-26

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Package irace updated to version 2.3 with previous version 2.2 dated 2017-03-24

Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for the automatic configuration of optimization algorithms, that is, (offline) tuning their parameters by finding the most appropriate settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Leslie Pérez Cáceres, Thomas Stützle, Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>

Diff between irace versions 2.2 dated 2017-03-24 and 2.3 dated 2017-04-26

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More information about irace at CRAN
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Package IBDsim updated to version 0.9-7 with previous version 0.9-6 dated 2016-04-28

Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Kong et. al (2010) <doi:10.1038/nature09525>), phased chromosomes are simulated for all pedigree members, either by unconditional gene dropping or conditional on a specified IBD pattern. Additional functions provide summaries and further analysis of the simulated genomes.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>

Diff between IBDsim versions 0.9-6 dated 2016-04-28 and 0.9-7 dated 2017-04-26

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New package IATScore with initial version 0.1.0
Package: IATScore
Type: Package
Title: Scoring Algorithm for the Implicit Association Test (IAT)
Version: 0.1.0
Author: Daniel Storage [aut, cre]
Maintainer: Daniel Storage <sabbystorage@gmail.com>
Description: This minimalist package is designed to quickly score raw data outputted from an Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998) <doi:10.1037/0022-3514.74.6.1464>. IAT scores are calculated as specified by Greenwald, Nosek, and Banaji (2003) <doi:10.1037/0022-3514.85.2.197>. Outputted values can be interpreted as effect sizes. The input function consists of three arguments. First, indicate the name of the dataset to be analyzed. This is the only required input. Second, indicate the number of trials in your entire IAT (the default is set to 220, which is typical for most IATs). Last, indicate whether congruent trials (e.g., flowers and pleasant) or incongruent trials (e.g., guns and pleasant) were presented first for this participant (the default is set to congruent). The script will tell you how long it took to run the code, the effect size for the participant, and whether that participant should be excluded based on the criteria outlined by Greenwald et al. (2003). Data files should consist of six columns organized in order as follows: Block (0-6), trial (0-19 for training blocks, 0-39 for test blocks), category (dependent on your IAT), the type of item within that category (dependent on your IAT), a dummy variable indicating whether the participant was correct or incorrect on that trial (0=correct, 1=incorrect), and the participant’s reaction time (in milliseconds). Three sample datasets are included in this package (labeled 'IAT', 'TooFastIAT', and 'BriefIAT') to practice with.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-26 13:01:23 UTC; Sabby
Repository: CRAN
Date/Publication: 2017-04-26 17:18:55 UTC

More information about IATScore at CRAN
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New package ggeffects with initial version 0.1.0
Package: ggeffects
Type: Package
Encoding: UTF-8
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Version: 0.1.0
Date: 2017-04-26
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Description: Compute marginal effects at the mean or average marginal effects from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are 'ggpredict()' and 'ggaverage()', however, there are some convenient wrapper-functions especially for polynomials or interactions. There is a generic 'plot()'-method to plot the results using 'ggplot2'.
License: GPL-3
Depends: R (>= 3.2), stats, utils
Imports: dplyr (>= 0.5.0), effects, ggplot2 (>= 2.2.1), magrittr, merTools (>= 0.3.0), prediction (>= 0.2.0), purrr, scales, sjmisc (>= 2.4.0), sjstats (>= 0.10.0), tibble (>= 1.3.0), tidyr
Suggests: knitr, rmarkdown
URL: https://github.com/strengejacke/ggeffects
BugReports: https://github.com/strengejacke/ggeffects/issues
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-04-26 10:22:19 UTC; Daniel
Repository: CRAN
Date/Publication: 2017-04-26 17:23:20 UTC

More information about ggeffects at CRAN
Permanent link

New package EdSurvey with initial version 1.0.5
Package: EdSurvey
Version: 1.0.5
Date: 2017-04-25
Title: Education Survey
Author: Paul Bailey [aut, cre], Ren C'deBaca [ctb], Ahmad Emad [aut], Huade Huo [ctb], Michael Lee [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut]
Maintainer: Paul Bailey <pbailey@air.org>
Depends: R (>= 3.2.0), lfactors (>= 1.0.1)
Imports: LaF, methods, Matrix, NAEPprimer, wCorr, data.table
Description: Read in and analysis functions for education surveys and assessments data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including the National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/>.
License: GPL-2
VignetteBuilder: knitr
Suggests: knitr, testthat, rmarkdown
LazyData: true
RoxygenNote: 6.0.1
Note: This publication was prepared for NCES under Contract No. ED-IES-12-D-0002 with American Institutes for Research. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government.
NeedsCompilation: no
Packaged: 2017-04-26 12:48:11 UTC; pbailey
Repository: CRAN
Date/Publication: 2017-04-26 17:19:59 UTC

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Package ecr updated to version 2.0.0 with previous version 1.0.1 dated 2016-09-10

Title: Evolutionary Computation in R
Description: Framework for building evolutionary algorithms for both single- and multi-objective continuous or discrete optimization problems. A set of predefined evolutionary building blocks and operators is included. Moreover, the user can easily set up custom objective functions, operators, building blocks and representations sticking to few conventions. The package allows both a black-box approach for standard tasks (plug-and-play style) and a much more flexible white-box approach where the evolutionary cycle is written by hand.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>

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New package cctools with initial version 0.1.0
Package: cctools
Type: Package
Title: Tools for the Continuous Convolution Trick in Nonparametric Estimation
Version: 0.1.0
Authors@R: person("Thomas", "Nagler", , "thomas.nagler@tum.de", c("aut", "cre"))
Description: Implements the uniform scaled beta distribution and the continuous convolution kernel density estimator.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: stats, Rcpp (>= 0.12.5), qrng
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2017-04-26 10:50:13 UTC; n5
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Repository: CRAN
Date/Publication: 2017-04-26 17:21:13 UTC

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Package canvasXpress updated to version 0.15.5 with previous version 0.15.2 dated 2017-04-02

Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <http://canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut, cre], Connie Brett [ctb]
Maintainer: Connie Brett <connie@aggregate-genius.com>

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Package zebu updated to version 0.1.1 with previous version 0.1.0 dated 2016-08-21

Title: Local Association Measures
Description: Implements the estimation of local (and global) association measures: Ducher's Z, pointwise mutual information and normalized pointwise mutual information. The significance of local (and global) association is accessed using p-values estimated by permutations. Finally, using local association subgroup analysis, it identifies if the association between variables is dependent on the value of another variable.
Author: Olivier M. F. Martin [aut, cre], Michel Ducher [aut]
Maintainer: Olivier M. F. Martin <olivmrtn@gmail.com>

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Package srvyr updated to version 0.2.1 with previous version 0.2.0 dated 2016-09-26

Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>

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Package splithalf updated to version 0.2.0 with previous version 0.1.0 dated 2017-04-07

Title: Calculate Task Split Half Reliability Estimates
Description: A series of functions to calculate the split half reliability of RT based tasks. The core function performs a Monte Carlo procedure to process a user defined number of random splits in order to provide a better reliability estimate. The current functions target the dot- probe task, however, can be modified for other tasks.
Author: Sam Parsons [aut, cre]
Maintainer: Sam Parsons <sam.parsons@psy.ox.ac.uk>

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Package rmumps updated to version 5.1.1-1 with previous version 5.0.1.12-3 dated 2017-03-17

Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel sparse direct Solver) are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>

Diff between rmumps versions 5.0.1.12-3 dated 2017-03-17 and 5.1.1-1 dated 2017-04-26

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Package plink updated to version 1.5-1 with previous version 1.5-0 dated 2017-04-07

Title: IRT Separate Calibration Linking Methods
Description: Item response theory based methods are used to compute linking constants and conduct chain linking of unidimensional or multidimensional tests for multiple groups under a common item design. The unidimensional methods include the Mean/Mean, Mean/Sigma, Haebara, and Stocking-Lord methods for dichotomous (1PL, 2PL and 3PL) and/or polytomous (graded response, partial credit/generalized partial credit, nominal, and multiple-choice model) items. The multidimensional methods include the least squares method and extensions of the Haebara and Stocking-Lord method using single or multiple dilation parameters for multidimensional extensions of all the unidimensional dichotomous and polytomous item response models. The package also includes functions for importing item and/or ability parameters from common IRT software, conducting IRT true score and observed score equating, and plotting item response curves/surfaces, vector plots, information plots, and comparison plots for examining parameter drift.
Author: Jonathan P. Weeks <weeksjp@gmail.com>
Maintainer: Jonathan P. Weeks <weeksjp@gmail.com>

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Package iccbeta updated to version 1.0.1 with previous version 1.0 dated 2014-11-25

Title: Multilevel Model Intraclass Correlation for Slope Heterogeneity
Description: A function and vignettes for computing an intraclass correlation described in Aguinis & Culpepper (2015) <doi:10.1177/1094428114563618>. This package quantifies the share of variance in a dependent variable that is attributed to group heterogeneity in slopes.
Author: Steven Andrew Culpepper [aut, cph, cre], Herman Aguinis [aut, cph]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>

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Package fourPNO updated to version 1.0.4 with previous version 1.0.3 dated 2015-12-16

Title: Bayesian 4 Parameter Item Response Model
Description: Estimate Barton & Lord's (1981) <doi:10.1002/j.2333-8504.1981.tb01255.x> four parameter IRT model with lower and upper asymptotes using Bayesian formulation described by Culpepper (2016) <doi:10.1007/s11336-015-9477-6>.
Author: Steven Andrew Culpepper [aut, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>

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Package dina updated to version 1.0.2 with previous version 1.0.1 dated 2015-10-28

Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA) cognitive diagnostic model parameters using the Gibbs sampler described by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>

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

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2013-11-08 1.1

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Package spsmooth (with last version 1.1-3) was removed from CRAN

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2014-04-09 1.1-3
2013-05-16 1.1-0
2013-03-22 1.0-1
2012-07-25 1.0-0

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

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2014-12-18 1.0

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2014-12-18 1.0

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Package smint (with last version 0.4.2) was removed from CRAN

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2016-01-14 0.4.2
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Package spatialkernel (with last version 0.4-19) was removed from CRAN

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2013-03-26 0.4-19

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Package pvrank (with last version 1.1.1) was removed from CRAN

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2016-08-12 1.1.1
2016-02-24 1.1
2015-02-22 1.0

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Package rclinicaltrials (with last version 1.4.7) was removed from CRAN

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2014-11-26 1.4

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Package pmg (with last version 0.9-43) was removed from CRAN

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2014-08-31 0.9-43
2010-03-09 0.9-42
2009-12-10 0.9-41
2009-10-13 0.9-40
2008-05-02 0.9-38
2008-01-11 0.9-37
2007-10-28 0.9-35
2007-08-25 0.9-34
2007-07-13 0.9-33
2007-07-12 0.9-32
2007-04-20 0.9-31

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

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2012-08-24 1.0

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Package restorepoint (with last version 0.1.7) was removed from CRAN

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2015-08-29 0.1.7
2014-02-20 0.1.5
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Package rPlant (with last version 2.16) was removed from CRAN

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2016-04-03 2.16
2015-10-21 2.12
2015-09-28 2.11
2013-05-21 2.7
2013-03-12 2.3
2013-02-07 2.1
2012-10-02 1.2

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2014-05-22 0.3.0

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2013-07-14 1.1.1
2012-04-17 1.1
2009-06-03 1.0

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Package VarfromPDB updated to version 2.2.6 with previous version 2.1.11 dated 2016-10-31

Title: : Disease-Gene-Variant Relations Mining from the Public Databases and Literature
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature from the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Author: Zongfu Cao <caozongfu@gmail.com>; Lei Wang <isan.wong@gmail.com>
Maintainer: Zongfu Cao <caozongfu@gmail.com>

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Package trustOptim updated to version 0.8.6 with previous version 0.8.5 dated 2015-02-04

Title: Trust Region Optimization for Nonlinear Functions with Sparse Hessians
Description: Trust region algorithm for nonlinear optimization. Efficient when the Hessian of the objective function is sparse (i.e., relatively few nonzero cross-partial derivatives). See Braun, M. (2014) <doi:10.18637/jss.v060.i04>.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>

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Package SEERaBomb updated to version 2017.1 with previous version 2016.2 dated 2016-11-11

Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries from ASCII sources and provides tools for estimating SEER second cancer risks.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>

Diff between SEERaBomb versions 2016.2 dated 2016-11-11 and 2017.1 dated 2017-04-26

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Package rmarkdown updated to version 1.5 with previous version 1.4 dated 2017-03-24

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Aron Atkins [aut], Rob Hyndman [aut], Ruben Arslan [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), Eli Grey [ctb, cph] (FileSaver library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package rebird updated to version 0.4.0 with previous version 0.3.0 dated 2016-03-23

Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
Author: Rafael Maia [aut], Scott Chamberlain [aut], Andy Teucher [aut], Sebastian Pardo [aut, cre]
Maintainer: Sebastian Pardo <sebpardo@gmail.com>

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New package nspmix with initial version 1.3-0
Package: nspmix
Title: Nonparametric and Semiparametric Mixture Estimation
Version: 1.3-0
Date: 2017-04-26
Author: Yong Wang
Maintainer: Yong Wang <yongwang@auckland.ac.nz>
Depends: lsei
Imports: graphics,methods,stats
Description: Contains functions for maximum likelihood estimation of nonparametric and semiparametric mixture models.
License: GPL (>= 2)
URL: https://www.stat.auckland.ac.nz/~yongwang
NeedsCompilation: no
Packaged: 2017-04-26 00:08:00 UTC; yong
Repository: CRAN
Date/Publication: 2017-04-26 05:28:24 UTC

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Package madness updated to version 0.2.2 with previous version 0.2.1 dated 2017-04-14

Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation of matrix- and multidimensional-valued functions with respect to multidimensional independent variables. Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>

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 man/show-methods.Rd              |    1 
 man/solve.Rd                     |   15 +----
 man/sumprod.Rd                   |    9 +--
 man/theta.Rd                     |    7 +-
 man/to_objective.Rd              |    2 
 man/todiag.Rd                    |   17 ++----
 man/twomoments.Rd                |    7 +-
 man/vcov.madness.Rd              |    7 +-
 man/vec.Rd                       |   16 +++---
 tests/testthat/test-basic.r      |   15 +++++
 50 files changed, 359 insertions(+), 334 deletions(-)

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New package htree with initial version 0.1.1
Package: htree
Version: 0.1.1
Date: 2017-04-25
Depends: R (>= 2.9.0)
Title: Historical Tree Ensembles for Longitudinal Data
Author: Joe Sexton <joesexton0@gmail.com>
Description: Historical regression trees are an extension of standard trees, producing a non-parametric estimate of how the response depends on all of its prior realizations as well as that of any time-varying predictor variables. The method applies equally to regularly as well as irregularly sampled data. The package implements random forest and boosting ensembles based on historical regression trees, suitable for longitudinal data.
Maintainer: Joe Sexton <joesexton0@gmail.com>
License: GPL (>= 2)
Repository: CRAN
NeedsCompilation: yes
Packaged: 2017-04-26 05:40:03 UTC; js
Date/Publication: 2017-04-26 05:47:48 UTC

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New package coxphMIC with initial version 0.1.0
Package: coxphMIC
Type: Package
Title: Sparse Estimation of Cox Proportional Hazards Models via Approximated Information Criterion
Version: 0.1.0
Author: Xiaogang Su and Razieh Nabi Abdolyousefi
Maintainer: Xiaogang Su <xiaogangsu@gmail.com>
Description: Sparse estimation for Cox PH models is done via Minimum approximated Information Criterion (MIC) by Su, Wijayasinghe, Fan, and Zhang (2016) <DOI:10.1111/biom.12484>. MIC mimics the best subset selection using a penalized likelihood approach yet with no need of a tuning parameter. The problem is further reformulated with a re-parameterization step so that it reduces to one unconstrained non-convex yet smooth programming problem, which can be solved efficiently. Furthermore, the re-parameterization tactic yields an additional advantage in terms of circumventing post-selection inference.
License: GPL-2
Depends: R (>= 3.1.0), stats (>= 3.2.5), graphics (>= 3.2.5), utils (>= 3.2.5)
Imports: survival (>= 2.38), numDeriv (>= 2014.2-1)
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-26 05:39:44 UTC; xsu
Repository: CRAN
Date/Publication: 2017-04-26 05:56:07 UTC

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Package cIRT updated to version 1.2.1 with previous version 1.2.0 dated 2016-04-13

Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices within a bayesian hierarchical framework as described by Culpepper and Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains the datasets used within the analysis of the paper.
Author: Steve Culpepper [aut, cph], James Balamuta [aut, cre, ctb, com, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>

Diff between cIRT versions 1.2.0 dated 2016-04-13 and 1.2.1 dated 2017-04-26

 DESCRIPTION                                     |   17 +-
 MD5                                             |   59 +++----
 NAMESPACE                                       |   13 +
 NEWS.md                                         |    5 
 R/RcppExports.R                                 |   67 +++++---
 R/cIRT-package.R                                |   15 +
 build/vignette.rds                              |binary
 inst/doc/Estimating-the-Model-in-the-Paper.html |  189 +++++++++++-------------
 inst/doc/Package-Overview.html                  |   13 -
 inst/doc/Simulation-Study-with-cIRT.html        |   85 +++++-----
 man/Generate_Choice.Rd                          |    1 
 man/Total_Tabulate.Rd                           |    1 
 man/TwoPLChoicemcmc.Rd                          |    7 
 man/cIRT.Rd                                     |    7 
 man/cIRT_package.Rd                             |   19 +-
 man/center_matrix.Rd                            |   10 -
 man/choice_matrix.Rd                            |    1 
 man/direct_sum.Rd                               |    2 
 man/payout_matrix.Rd                            |    1 
 man/probitHLM.Rd                                |    7 
 man/riwishart.Rd                                |    7 
 man/rmvnorm.Rd                                  |    8 -
 man/rwishart.Rd                                 |    8 -
 man/survey_data.Rd                              |    1 
 man/trial_matrix.Rd                             |    1 
 src/RcppExports.cpp                             |   82 +++++-----
 src/armadillo_manipulations.cpp                 |   17 +-
 src/init.c                                      |only
 src/project_source.cpp                          |   47 +++--
 src/rgens.cpp                                   |   21 +-
 src/total_cpp.cpp                               |   15 +
 31 files changed, 376 insertions(+), 350 deletions(-)

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New package bulletr with initial version 0.1
Package: bulletr
Title: Algorithms for Matching Bullet Lands
Authors@R: c( person("Eric", "Hare", email = "erichare@iastate.edu", role = c("aut", "cre")), person("Heike", "Hofmann", email = "hofmann@iastate.edu", role = "aut"))
Version: 0.1
License: GPL-3
Date: 2017-04-25
Description: Analyze bullet lands using nonparametric methods. We provide a reading routine for x3p files (see <http://www.openfmc.org> for more information) and a host of analysis functions designed to assess the probability that two bullets were fired from the same gun barrel.
URL: https://github.com/erichare/bulletr
BugReports: https://github.com/erichare/bulletr/issues
Imports: xml2, zoo, ggplot2, plyr, dplyr, reshape2, plotly, robustbase, smoother
Depends: R (>= 3.1)
RoxygenNote: 6.0.1
LazyData: true
NeedsCompilation: no
Packaged: 2017-04-25 23:59:38 UTC; erichare
Author: Eric Hare [aut, cre], Heike Hofmann [aut]
Maintainer: Eric Hare <erichare@iastate.edu>
Repository: CRAN
Date/Publication: 2017-04-26 05:31:52 UTC

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Package mra (with last version 2.16.4) was removed from CRAN

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

2015-04-02 2.16.4

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Package fUnitRoots (with last version 3010.78) was removed from CRAN

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

2013-06-23 3010.78
2012-12-10 2160.77
2009-09-29 2100.76
2009-04-16 290.75
2008-10-27 270.74
2008-10-23 270.73
2007-10-08 260.72
2007-10-02 260.71

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Package basicspace (with last version 0.18) was removed from CRAN

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2016-07-29 0.18
2016-03-09 0.17
2014-11-19 0.15
2014-11-09 0.13

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Package SpherWave (with last version 1.2.2) was removed from CRAN

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2013-04-25 1.2.2
2013-01-18 1.2.1
2010-01-03 1.2.0
2007-07-29 1.1.0
2006-10-18 1.0.0

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

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2015-04-15 1.0-4
2013-10-05 1.0-3
2013-07-30 1.0-2
2013-06-27 1.0-1
2013-06-20 1.0

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Package fastcox (with last version 1.1.1) was removed from CRAN

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2013-10-24 1.1.1
2013-10-22 1.1.0
2012-08-04 1.0.1
2012-03-26 1.0.0

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Package kinn (with last version 0.2) was removed from CRAN

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2016-07-27 0.2
2016-05-22 0.1

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Package genoPlotR (with last version 0.8.4) was removed from CRAN

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2015-07-08 0.8.4
2013-12-23 0.8.2
2012-06-25 0.8
2011-05-03 0.7
2011-03-31 0.6.1
2011-03-24 0.6
2010-09-22 0.5.4
2010-08-16 0.5.1
2010-06-24 0.5
2010-05-19 0.4

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Package cslogistic (with last version 0.1-3) was removed from CRAN

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2012-09-14 0.1-3
2012-01-16 0.1-2
2005-06-22 0.1-1

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

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2016-04-19 1.0

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