Sat, 11 Aug 2018

Package clusrank updated to version 0.6-2 with previous version 0.6-1 dated 2018-07-15

Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre], Mei-Ling Ting Lee [ctb], Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>

Diff between clusrank versions 0.6-1 dated 2018-07-15 and 0.6-2 dated 2018-08-11

 DESCRIPTION     |   10 +++++-----
 MD5             |   12 ++++++------
 R/amd.R         |    4 ++--
 R/clusWilcox.R  |   10 ++++------
 R/clusranksum.R |   38 +++++++++++++++++++-------------------
 data/amd.RData  |binary
 man/amd.Rd      |    4 ++--
 7 files changed, 38 insertions(+), 40 deletions(-)

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New package CalibratR with initial version 0.1.0
Package: CalibratR
Type: Package
Title: Mapping ML Scores to Calibrated Predictions
Version: 0.1.0
Author: Johanna Schwarz
Maintainer: Johanna Schwarz <Schwar4m@students.uni-marburg.de>
Description: Transforms your uncalibrated Machine Learning scores to well-calibrated prediction estimates that can be interpreted as probability estimates. The implemented BBQ (Bayes Binning in Quantiles) model is taken from Naeini (2015, ISBN:0-262-51129-0).
License: LGPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10.0)
Imports: ggplot2, pROC, reshape2, parallel, foreach, utils, stats, fitdistrplus, doParallel
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-08-08 22:52:08 UTC; Johanna
Repository: CRAN
Date/Publication: 2018-08-11 22:10:03 UTC

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New package psychReport with initial version 0.1
Package: psychReport
Type: Package
Title: Reproducible Reports in Psychology
Version: 0.1
Author: Ian G Mackenzie
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Sweave'/'Knitr' 'Latex' integration within *.Rnw files.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Imports: cli, crayon, dplyr, ez, reshape2, testthat, xtable
Depends: R(>= 2.10)
NeedsCompilation: no
Packaged: 2018-08-09 06:03:20 UTC; ian
Repository: CRAN
Date/Publication: 2018-08-11 21:20:03 UTC

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New package landscapemetrics with initial version 0.1.0
Type: Package
Package: landscapemetrics
Title: Landscape Metrics for Categorical Map Patterns
Version: 0.1.0
Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "maximilian.hesselbarth@uni-goettingen.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")), person("Marco", "Sciaini", email = "sciaini.marco@gmail.com", role = "aut", comment = c(ORCID = '0000-0002-3042-5435')), person("Jakub", "Nowosad", role = "aut", email = "nowosad.jakub@gmail.com", comment = c(ORCID = "0000-0002-1057-3721")), person("Laura J.", "Graham", role = "ctb", comment = c(ORCID = "0000-0002-1057-3721")), person("Kimberly A.", "With", role = "ctb", comment = c(ORCID = "0000-0001-5570-1515")), person("Jeffrey", "Hollister", role = "ctb", comment = c(ORCID = "0000-0002-3611-7281")), person("Jeremy", "VanDerWal", role = "ctb", comment = "Original author of underlying C code for get_patches() function"), person("Florian", "Privé", role = "ctb", comment = "Original author of underlying C++ code for get_nearestneighbour() function"))
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Description: Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>) and new ones from the current literature on landscape metrics. This package supports 'raster' spatial objects and takes RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the 'raster' package as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.
License: GPL-3
URL: https://r-spatialecology.github.io/landscapemetrics/
BugReports: https://github.com/r-spatialecology/landscapemetrics/issues
Depends: R (>= 3.1)
Imports: dplyr, ggplot2, magrittr, purrr, raster, Rcpp, tibble
Suggests: covr, testthat, knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
ByteCompile: true
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
SystemRequirements: C++11
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-08-09 07:31:37 UTC; Maximilian
Author: Maximillian H.K. Hesselbarth [aut, cre] (<https://orcid.org/0000-0003-1125-9918>), Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Laura J. Graham [ctb] (<https://orcid.org/0000-0002-1057-3721>), Kimberly A. With [ctb] (<https://orcid.org/0000-0001-5570-1515>), Jeffrey Hollister [ctb] (<https://orcid.org/0000-0002-3611-7281>), Jeremy VanDerWal [ctb] (Original author of underlying C code for get_patches() function), Florian Privé [ctb] (Original author of underlying C++ code for get_nearestneighbour() function)
Repository: CRAN
Date/Publication: 2018-08-11 22:00:03 UTC

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Package energy updated to version 1.7-5 with previous version 1.7-4 dated 2018-05-27

Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, k-groups and hierarchical clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.
Author: Maria Rizzo [aut, cre], Gabor Szekely [aut]
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>

Diff between energy versions 1.7-4 dated 2018-05-27 and 1.7-5 dated 2018-08-11

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 energy-1.7-5/energy/MD5                   |   39 +++++++++++--------
 energy-1.7-5/energy/NAMESPACE             |    6 +++
 energy-1.7-5/energy/NEWS.md               |   60 +++++++++++++++++++-----------
 energy-1.7-5/energy/R/Ecluster.R          |   26 +------------
 energy-1.7-5/energy/R/RcppExports.R       |    8 ++++
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 energy-1.7-5/energy/man/energy.hclust.Rd  |    6 +--
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 energy-1.7-5/energy/src/energy.c          |    2 -
 energy-1.7-5/energy/src/energy_init.c     |   22 ++++++-----
 energy-1.7-5/energy/src/kgroups.cpp       |only
 26 files changed, 139 insertions(+), 127 deletions(-)

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Package chorrrds updated to version 0.1.7 with previous version 0.1.4 dated 2018-04-22

Title: Music Chords Extraction
Description: Extracts music chords from the 'CifraClub' website <https://www.cifraclub.com.br/>. The package also has functions for cleaning the extracted data and feature extraction.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>

Diff between chorrrds versions 0.1.4 dated 2018-04-22 and 0.1.7 dated 2018-08-11

 DESCRIPTION       |   12 ++++++------
 MD5               |   22 ++++++++++++----------
 NAMESPACE         |    4 +---
 R/data.R          |   15 +++++++++++++++
 R/get_chords.R    |    7 ++++---
 R/get_songs.R     |    6 +++++-
 R/utils.R         |    4 +++-
 README.md         |    2 +-
 data/datalist     |    1 +
 data/dist.rda     |only
 man/dist.Rd       |only
 man/get_chords.Rd |    4 ++--
 man/not_in.Rd     |    4 ++--
 13 files changed, 52 insertions(+), 29 deletions(-)

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New package sdStaf with initial version 0.1.14
Package: sdStaf
Type: Package
Title: Species Distribution and Stability Future Models
Version: 0.1.14
Authors@R: c(person("P. Joser", "Atauchi", role = c("aut", "cre"), email = "patauchi@gmail.com"))
Maintainer: P. Joser Atauchi <patauchi@gmail.com>
Description: Functions for post processing the outcomes of ecological niche models. It further include methods to build stability maps based on species distribution models under climate change projections and to reduce environmental data.
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Depends: methods, stats, dplyr, ggplot2, R (>= 2.10)
Imports: sp, rgdal, rgeos, rasterVis, tidyr, raster, dismo
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-08-08 17:32:07 UTC; p.joseratauchi
Author: P. Joser Atauchi [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-11 16:30:03 UTC

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New package rcites with initial version 0.1.0
Package: rcites
Type: Package
Title: R Interface to the Species+ Database
Version: 0.1.0
Date: 2018-07-23
Authors@R: c(person("Jonas", "Geschke", role = c("aut"), email = "jonas.e.geschke@gmail.com", comment = c(ORCID = "0000-0002-5654-9313")), person("Kevin", "Cazelles", role = c("aut", "cre"), email = "kevin.cazelles@gmail.com", comment = c(ORCID = "0000-0001-6619-9874")), person("Ignasi", "Bartomeus", role = c("aut"), comment = c(ORCID = "0000-0001-7893-4389")), person("Jonathan", "Goldenberg", role = c("ctb")), person("Marie-Bé", "Leduc", role = c("ctb")), person("Yasmine", "Verzelen", role = c("ctb")))
Description: A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
URL: https://ibartomeus.github.io/rcites/, https://github.com/ibartomeus/rcites
BugReports: https://github.com/ibartomeus/rcites/issues
License: MIT + file LICENSE
Depends: R (>= 3.1.0)
Imports: httr, jsonlite, data.table, methods
Encoding: UTF-8
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat, rworldmap
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-07-30 14:37:23 UTC; kevcaz
Author: Jonas Geschke [aut] (<https://orcid.org/0000-0002-5654-9313>), Kevin Cazelles [aut, cre] (<https://orcid.org/0000-0001-6619-9874>), Ignasi Bartomeus [aut] (<https://orcid.org/0000-0001-7893-4389>), Jonathan Goldenberg [ctb], Marie-Bé Leduc [ctb], Yasmine Verzelen [ctb]
Maintainer: Kevin Cazelles <kevin.cazelles@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-11 16:30:06 UTC

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New package modopt.matlab with initial version 1.0-1
Package: modopt.matlab
Type: Package
Title: 'MatLab'-Style Modeling of Optimization Problems
Version: 1.0-1
Date: 2018-08-11
Authors@R: c( person("Ronald", "Hochreiter", email = "ron@hochreiter.net", role = c("aut", "cre")))
Maintainer: Ronald Hochreiter <ron@hochreiter.net>
Description: 'MatLab'-Style Modeling of Optimization Problems with 'R'. This package provides a set of convenience functions to transform a 'MatLab'-style optimization modeling structure to its 'ROI' equivalent.
Depends: R (>= 3.4), ROI, ROI.plugin.glpk, ROI.plugin.quadprog
License: GPL-3
URL: http://www.finance-r.com/
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-08-11 15:56:09 UTC; ron
Author: Ronald Hochreiter [aut, cre]
Repository: CRAN
Date/Publication: 2018-08-11 17:00:02 UTC

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New package fasterElasticNet with initial version 1.1.2
Package: fasterElasticNet
Type: Package
Title: An Amazing Fast Way to Fit Elastic Net
Version: 1.1.2
Date: 2018-08-01
Authors@R: c(person("Jingyi","Ma",email = "jingyima@163.com", role = c("aut")), person("Qiuhong","Lai",email = "lailaqiuhong@gmail.com", role = "ctb"), person("Linyu","Zuo",email = "zuozhe5959@gmail.com", role = c("ctb","cre")), person("Yi","Yang",email = "lucious.stat.y@gmail.com", role = "ctb"), person("Meng","Su",email = "SUmeng97@126.com", role = "ctb"), person("Zhen","Yu", email = "amy.yuzhen@foxmail.com", role = 'ctb'), person("Gege","Gao", email = "gaogege1995@163.com", role = 'ctb'), person("Xiao","Liu", email = "lucinecoco@163.com", role = 'ctb'), person("Xueni","Ruan", email = "ruanxueni96@163.com", role = 'ctb'), person("Xinyuan","Yang", email = "yangxinyuan100@126.com", role = 'ctb'), person("Yu","Bai", email = "yukisunflower@sina.com", role = 'ctb'), person("Zhijun","Liao", email = "econzhijun@163.com", role = 'ctb') )
Description: Fit Elastic Net, Lasso, and Ridge regression and do cross-validation in a fast way. We build the algorithm based on Least Angle Regression by Bradley Efron, Trevor Hastie, Iain Johnstone, etc. (2004)(<doi:10.1214/009053604000000067 >) and some algorithms like Givens rotation and Forward/Back Substitution. In this way, many matrices to be computed are retained as triangular matrices which can eventually speed up the computation. The fitting algorithm for Elastic Net is written in C++ using Armadillo linear algebra library.
Depends: R (>= 3.1.0)
License: GPL (>= 2)
Imports: Rcpp (>= 0.12.16)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
URL: https://github.com/CUFESAM/Elastic-Net
BugReports: https://github.com/CUFESAM/Elastic-Net/issues
NeedsCompilation: yes
Packaged: 2018-08-08 13:22:50 UTC; <e8><8b><8f><e8><90><8c>
Author: Jingyi Ma [aut], Qiuhong Lai [ctb], Linyu Zuo [ctb, cre], Yi Yang [ctb], Meng Su [ctb], Zhen Yu [ctb], Gege Gao [ctb], Xiao Liu [ctb], Xueni Ruan [ctb], Xinyuan Yang [ctb], Yu Bai [ctb], Zhijun Liao [ctb]
Maintainer: Linyu Zuo <zuozhe5959@gmail.com>
Repository: CRAN
Date/Publication: 2018-08-11 16:30:10 UTC

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Package roll updated to version 1.1.1 with previous version 1.0.7 dated 2017-05-01

Title: Rolling Statistics
Description: Fast and efficient computation of rolling statistics for time-series data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>

Diff between roll versions 1.0.7 dated 2017-05-01 and 1.1.1 dated 2018-08-11

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 roll-1.1.1/roll/R/RcppExports.R     |   44 
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 27 files changed, 1104 insertions(+), 4894 deletions(-)

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Package ceterisParibus updated to version 0.3.0 with previous version 0.2.1 dated 2018-07-05

Title: Ceteris Paribus Profiles
Description: Ceteris Paribus Profiles (What-If Plots) are designed to present model responses around selected points in a feature space. For example around a single prediction for an interesting observation. Plots are designed to work in a model-agnostic fashion, they are working for any predictive Machine Learning model and allow for model comparisons. Ceteris Paribus Plots supplement the Break Down Plots from 'breakDown' package.
Author: Przemyslaw Biecek [aut, cre]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

Diff between ceterisParibus versions 0.2.1 dated 2018-07-05 and 0.3.0 dated 2018-08-11

 DESCRIPTION                                 |   16 +--
 MD5                                         |   86 ++++++++++++++------
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Package jmvconnect updated to version 1.0.4 with previous version 1.0.3 dated 2018-07-26

Title: Connect to the 'jamovi' Statistical Spreadsheet
Description: Methods to access data sets from the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information) from R.
Author: Jonathon Love [aut, cre]
Maintainer: Jonathon Love <jon@thon.cc>

Diff between jmvconnect versions 1.0.3 dated 2018-07-26 and 1.0.4 dated 2018-08-11

 DESCRIPTION     |   12 ++++++------
 MD5             |   12 ++++++------
 src/column.cpp  |   33 ++++++++++++++++++++++++++++++++-
 src/column.h    |    5 ++++-
 src/dataset.cpp |    4 +---
 src/memorymap.h |    2 +-
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 7 files changed, 80 insertions(+), 29 deletions(-)

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Package sjlabelled updated to version 1.0.13 with previous version 1.0.12 dated 2018-07-08

Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages like 'SPSS', 'SAS' or 'Stata', and working with labelled data. This includes easy ways to get, set or change value and variable label attributes, to convert labelled vectors into factors or numeric (and vice versa), or to deal with multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

Diff between sjlabelled versions 1.0.12 dated 2018-07-08 and 1.0.13 dated 2018-08-11

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Package ggeffects updated to version 0.5.0 with previous version 0.4.0 dated 2018-07-03

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
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'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package testthis updated to version 1.0.4 with previous version 1.0.3 dated 2018-01-06

Title: Utils and 'RStudio' Addins to Make Testing Even More Fun
Description: Utility functions and 'RStudio' addins to ease the life of people using 'testthat', 'devtools' and 'usethis' in their package development workflow. Hotkeyable addins are provided for such common tasks as switching between a source file and an associated test file, or running unit tests in a single file. 'testthis' also provides utility function to manage and run tests in subdirectories of the test/testthat directory.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>

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Package SuperLearner updated to version 2.0-24 with previous version 2.0-23 dated 2018-03-12

Title: Super Learner Prediction
Description: Implements the super learner prediction method and contains a library of prediction algorithms to be used in the super learner.
Author: Eric Polley [aut, cre], Erin LeDell [aut], Chris Kennedy [aut], Sam Lendle [ctb], Mark van der Laan [aut, ths]
Maintainer: Eric Polley <polley.eric@mayo.edu>

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Package nsapi updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-06

Title: Connect to the NS (Dutch Railways) API
Description: Access the NS api and download current departure times, disruptions and engineering work, the station list, and travel recommendations from station to station. All results will be returned as a 'data.frame'. NS (Nederlandse Spoorwegen; Dutch Railways) is the largest train travel provider in the Netherlands. for more information about the API itself see <https://www.ns.nl/en/travel-information/ns-api>. To use the API, and this package, you will need to obtain a username and password. More information about authentication and the use of the functions are described in the vignette.
Author: Roel M. Hogervorst [cre, aut] (<https://orcid.org/0000-0001-7509-0328>)
Maintainer: Roel M. Hogervorst <hogervorst.rm@gmail.com>

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Package EcoNetGen updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-17

Title: Simulate and Sample from Ecological Interaction Networks
Description: Randomly generate a wide range of interaction networks with specified size, average degree, modularity, and topological structure. Sample nodes and links from within simulated networks randomly, by degree, by module, or by abundance. Simulations and sampling routines are implemented in 'FORTRAN', providing efficient generation times even for large networks. Basic visualization methods also included. Algorithms implemented here are described in de Aguiar et al. (2017) <arXiv:1708.01242>.
Author: Marcus de Aguiar [aut, cph] (<https://orcid.org/0000-0003-1379-7568>), Erica Newman [aut] (<https://orcid.org/0000-0001-6433-8594>), Mathias Pires [aut] (<https://orcid.org/0000-0003-2500-4748>), NIMBioS [fnd], Carl Boettiger [aut, cre] (<https://orcid.org/0000-0003-4580-091X>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package mosaic updated to version 1.4.0 with previous version 1.3.0 dated 2018-06-30

Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Author: Randall Pruim [aut, cre], Daniel T. Kaplan [aut], Nicholas J. Horton [aut]
Maintainer: Randall Pruim <rpruim@calvin.edu>

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Package lessR updated to version 3.7.6 with previous version 3.7.5 dated 2018-06-03

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package glm2 updated to version 1.2.1 with previous version 1.2 dated 2018-05-25

Title: Fitting Generalized Linear Models
Description: Fits generalized linear models using the same model specification as glm in the stats package, but with a modified default fitting method that provides greater stability for models that may fail to converge using glm.
Author: Ian Marschner [aut] (using code from glm and glm.fit in the stats package), Mark W. Donoghoe [cre, ctb]
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

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