Fri, 08 Feb 2019

Package rlas updated to version 1.3.1 with previous version 1.3.0 dated 2019-02-04

Title: Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://www.laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph], Florian De Boissieu [aut, ctb] (Enable the support of .lax file and extra byte attributes), Martin Isenburg [cph] (Is the author of the LASlib and LASzip libraries), David Auty [ctb] (Reviewed the documentation), Pierrick Marie [ctb] (Helped to compile LASlib code in R), Tiago de Conto [ctb] (Implemented the -thin_with_voxel filter method)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

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Package jtools updated to version 2.0.0 with previous version 1.1.1 dated 2018-09-23

Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written for the purpose of more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <long.1377@osu.edu>

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New package EGRET with initial version 3.0.2
Package: EGRET
Type: Package
Title: Exploration and Graphics for RivEr Trends
Version: 3.0.2
Authors@R: c( person("Robert", "Hirsch", role = c("aut"), email = "rhirsch@usgs.gov", comment=c(ORCID="0000-0002-4534-075X")), person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov", comment=c(ORCID="0000-0002-3915-9487")), person("David", "Watkins", role = c("ctb")), person("Lindsay","Carr", role = c("ctb")), person("Jennifer","Murphy", role = c("ctb")))
Description: Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS). The modeling method is introduced and discussed in Hirsch et al. (2010) <doi:10.1111/j.1752-1688.2010.00482.x>, and expanded in Hirsch and De Cicco (2015) <doi:10.3133/tm4A10>.
License: CC0
Depends: R (>= 3.0)
Imports: dataRetrieval (>= 2.0.1), survival, fields, methods, utils, graphics, stats, grDevices, truncnorm, foreach
Suggests: EGRETci, xtable, knitr, rmarkdown, extrafont, testthat, rkt, doParallel, parallel
LazyLoad: yes
LazyData: yes
BugReports: https://github.com/USGS-R/EGRET/issues
VignetteBuilder: knitr
BuildVignettes: true
URL: https://pubs.usgs.gov/tm/04/a10/, https://github.com/USGS-R/EGRET/wiki
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/visual-id/credit_usgs.html#copyright
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-08 16:51:49 UTC; ldecicco
Author: Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>), Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>), David Watkins [ctb], Lindsay Carr [ctb], Jennifer Murphy [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Repository: CRAN
Date/Publication: 2019-02-08 22:43:33 UTC

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Package deconvolveR updated to version 1.1 with previous version 1.0-3 dated 2016-12-01

Title: Empirical Bayes Estimation Strategies
Description: Empirical Bayes methods for learning prior distributions from data. An unknown prior distribution (g) has yielded (unobservable) parameters, each of which produces a data point from a parametric exponential family (f). The goal is to estimate the unknown prior ("g-modeling") by deconvolution and Empirical Bayes methods.
Author: Bradley Efron [aut], Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>

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Package binneR updated to version 2.0.10 with previous version 2.0.7 dated 2019-01-16

Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
Author: Jasen Finch [aut, cre]
Maintainer: Jasen Finch <jsf9@aber.ac.uk>

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Package hR updated to version 0.1.7 with previous version 0.1.6 dated 2019-01-08

Title: Toolkit for Data Analytics in Human Resources
Description: Transform and analyze workforce data in meaningful ways for human resources (HR) analytics. Two functions, 'hierarchyLong' and 'hierarchyWide', convert standard employee and supervisor relationship data into useful formats. A 'workforcePlan' app is available for simple workforce planning.
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>

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Package tfse updated to version 0.5.0 with previous version 0.4.4 dated 2018-11-28

Title: Tools for Script Editing
Description: A collection of useful tools for programming and writing-scripts. Several functions are simple wrappers around base R functions that extend their functionality while also providing some convenient properties–regular expression functions that automatically detect look-ahead and look-behind statements, a read-line function that suppresses incomplete-final-line warnings and automatically opens and closes connections, a version of substrings that starts from the end of strings, etc. Other functions are useful for checking whether packages are installed, omitting missing data, and showing in-use connections.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>

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Package geojsonlint updated to version 0.3.0 with previous version 0.2.0 dated 2016-11-02

Title: Tools for Validating 'GeoJSON'
Description: Tools for linting 'GeoJSON'. Includes tools for interacting with the online tool <http://geojsonlint.com>, the 'Javascript' library 'geojsonhint' (<https://www.npmjs.com/package/geojsonhint>), and validating against a 'GeoJSON' schema via the 'Javascript' library (<https://www.npmjs.com/package/is-my-json-valid>). Some tools work locally while others require an internet connection.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Andy Teucher [aut], Tom MacWright [cph] (geojsonhint Javascript library), Mads Kristensen [cph] (geojson schema)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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New package TestCor with initial version 0.0.0.9
Package: TestCor
Title: FWER and FDR Controlling Procedures for Multiple Correlation Tests
Version: 0.0.0.9
Date: 2019-01-20
Authors@R: c( person("Gannaz", "Irène", email = "irene.gannaz@insa-lyon.fr", role = c("aut","cre")), person("Roux", "Marine", email = "marine.roux@gipsa-lab.fr", role = "aut"))
Maintainer: Gannaz Irène <irene.gannaz@insa-lyon.fr>
Description: Different multiple testing procedures for correlation tests are implemented. These procedures were shown to theoretically control asymptotically the Family Wise Error Rate (Roux (2018) <https://tel.archives-ouvertes.fr/tel-01971574v1>) or the False Discovery Rate (Cai & Liu (2016) <doi:10.1080/01621459.2014.999157>). The package gather four test statistics used in correlation testing, four FWER procedures with either single step or stepdown versions, and four FDR procedures.
Depends: R (>= 3.4)
Encoding: UTF-8
License: GPL (>= 2)
Imports: Rcpp, MASS, stats
LinkingTo: Rcpp
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-02-04 22:35:53 UTC; igannaz
Author: Gannaz Irène [aut, cre], Roux Marine [aut]
Repository: CRAN
Date/Publication: 2019-02-08 17:33:24 UTC

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Package tbltools updated to version 0.1.0 with previous version 0.0.3 dated 2019-01-07

Title: Tools for Working with Tibbles
Description: Tools for working with tibbles, or data.frame-like objects generated by the 'tibble' package <https://tibble.tidyverse.org/>. Functions assist in converting objects to tibbles and creating frequency tables.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>

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New package StempCens with initial version 0.1.0
Package: StempCens
Type: Package
Title: Spatio-Temporal Estimation and Prediction for Censored/Missing Responses
Version: 0.1.0
Author: Katherine A. L. Valeriano, Victor H. Lachos and Larissa Avila Matos
Maintainer: Larissa Avila Matos <larissa.amatos@gmail.com>
Description: It estimates the parameters of a censored or missing data in spatio-temporal models using the SAEM algorithm (Delyon et al., 1999 <doi:10.1214/aos/1018031103>). This algorithm is a stochastic approximation of the widely used EM algorithm and an important tool for models in which the E-step does not have an analytic form. Besides the expressions obtained to estimate the parameters to the proposed model, we include the calculations for the observed information matrix using the method developed by Louis (1982) <https://www.jstor.org/stable/2345828>. To examine the performance of the fitted model, case-deletion measure are provided.
License: GPL (>= 2)
RoxygenNote: 6.1.1
Imports: ssym, optimx, Matrix, sp, spTimer, mvtnorm, tmvtnorm, MCMCglmm, ggplot2, grid, distances, gridExtra
Suggests: testthat
NeedsCompilation: no
Packaged: 2019-02-04 13:51:30 UTC; larissam
Repository: CRAN
Date/Publication: 2019-02-08 17:43:18 UTC

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Package MCMCglmm updated to version 2.28 with previous version 2.27 dated 2019-02-01

Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>

Diff between MCMCglmm versions 2.27 dated 2019-02-01 and 2.28 dated 2019-02-08

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Package whitebox (with last version 0.1.0) was removed from CRAN

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

2019-02-07 0.1.0

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New package Spectrum with initial version 0.1
Package: Spectrum
Title: Versatile Ultra-Fast Spectral Clustering for Single and Multi-View Data
Version: 0.1
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Description: A versatile ultra-fast spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens local connections in dense regions in the graph. For integrating multi-view data and reducing noise we use a recently developed tensor product graph data integration and diffusion system. 'Spectrum' contains two techniques for finding the number of clusters (K); the classical eigengap method and a novel multimodality gap procedure. The multimodality gap analyses the distribution of the eigenvectors of the graph Laplacian to decide K and tune the kernel. 'Spectrum' is suited for clustering a wide range of complex data.
Depends: R (>= 3.5.0)
License: AGPL-3
Encoding: UTF-8
LazyData: true
Imports: ggplot2, Rtsne, ClusterR, umap, Rfast, RColorBrewer, diptest
Suggests: knitr
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-04 08:36:33 UTC; christopher
Repository: CRAN
Date/Publication: 2019-02-08 16:03:24 UTC

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New package qs with initial version 0.12
Package: qs
Type: Package
Title: Quick Serialization of R Objects
Version: 0.12
Date: 2019-2-1
Authors@R: c( person("Travers", "Ching", email = "traversc@gmail.com", role = c("aut", "cre", "cph")), person("Yann", "Collet", role = c("aut", "ctb", "cph"), comment = "Yann Collet is the author of the bundled zstd code"), person("Facebook, Inc.", role = "cph", comment = "Facebook is the copyright holder of the bundled zstd code"), person("Reichardt", "Tino", role = c("ctb", "cph"), comment = "Contributor/copyright holder of zstd packaged code"), person("Skibinski", "Przemyslaw", role = c("ctb", "cph"), comment = "Contributor/copyright holder of zstd packaged code"), person("Mori", "Yuta", role = c("ctb", "cph"), comment = "Contributor/copyright holder of zstd packaged code"), person("Francois", "Romain", role = c("ctb", "cph"), comment = "Derived example/tutorials for Alt-Rep structures"))
Maintainer: Travers Ching <traversc@gmail.com>
Description: Provides functions for quickly writing and reading any R object to and from disk. This package makes use of the 'zstd' library for compression and decompression. 'zstd' is created by Yann Collet and owned by Facebook, Inc.
License: AGPL-3 | file LICENSE
Imports: Rcpp, RApiSerialize
LinkingTo: Rcpp, RApiSerialize
Depends: R (>= 3.5.0)
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Copyright: This package includes code from the 'zstd' library owned by Facebook, Inc. and created by Yann Collet.
URL: https://github.com/traversc/qs
BugReports: https://github.com/traversc/qs/issues
NeedsCompilation: yes
Packaged: 2019-02-02 23:32:06 UTC; tching
Author: Travers Ching [aut, cre, cph], Yann Collet [aut, ctb, cph] (Yann Collet is the author of the bundled zstd code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd packaged code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd packaged code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd packaged code), Francois Romain [ctb, cph] (Derived example/tutorials for Alt-Rep structures)
Repository: CRAN
Date/Publication: 2019-02-08 16:10:02 UTC

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Package OpenMx updated to version 2.12.2 with previous version 2.12.1 dated 2019-01-18

Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications as things that can be generated and manipulated programmatically. Structural equation models may be specified with reticular action model matrices or paths, linear structural relations matrices or paths, or directly in matrix algebra. Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential equations, state space, and many others. MacOS users can download the most up-to-date package binaries from <http://openmx.ssri.psu.edu>. See Neale, Hunter, Pritikin, Zahery, Brick, Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut], Michael C. Neale [aut], Hermine H. Maes [aut], Michael J. Wilde [ctb], Michael Spiegel [aut], Timothy R. Brick [aut], Ryne Estabrook [aut], Timothy C. Bates [aut], Paras Mehta [ctb], Timo von Oertzen [ctb], Ross J. Gore [aut], Michael D. Hunter [aut], Daniel C. Hackett [ctb], Julian Karch [ctb], Andreas M. Brandmaier [ctb], Joshua N. Pritikin [aut, cre], Mahsa Zahery [aut], Robert M. Kirkpatrick [aut], Yang Wang [ctb], Charles Driver [ctb], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Association for Computing Machinery [cph], Dieter Kraft [cph], Stefan Wilhelm [cph], Sarah Medland [cph], Carl F. Falk [cph], Matt Keller [cph], Manjunath B G [cph], The Regents of the University of California [cph], Lester Ingber [cph], Wong Shao Voon [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between OpenMx versions 2.12.1 dated 2019-01-18 and 2.12.2 dated 2019-02-08

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New package expperm with initial version 0.1.0
Package: expperm
Type: Package
Title: Computing Expectations and Marginal Likelihoods for Permutations
Version: 0.1.0
Author: Ben Powell
Maintainer: Ben Powell <ben.powell@york.ac.uk>
Description: A set of functions for computing expected permutation matrices given a matrix of likelihoods for each individual assignment. It has been written to accompany the forthcoming paper 'Computing expectations and marginal likelihoods for permutations'. Publication details will be updated as soon as they are finalized.
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-04 15:24:53 UTC; ben
Repository: CRAN
Date/Publication: 2019-02-08 16:03:21 UTC

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New package ClinReport with initial version 0.9.1.1
Package: ClinReport
Type: Package
Title: Statistical Reporting in Clinical Trials
Version: 0.9.1.1
Date: 2019-01-23
Author: JF COLLIN
Maintainer: JF COLLIN <jfcollin@live.fr>
Description: It enables to create easily formatted statistical tables in 'Microsoft Word' documents in pretty formats according to 'clinical standards'. It can be used also outside the scope of clinical trials, for any statistical reporting in 'Word'. Descriptive tables for quantitative statistics (mean, median, max etc..) and/or qualitative statistics (frequencies and percentages) are available and formatted tables of Least Square Means of Linear Models, Linear Mixed Models and Generalized Linear Mixed Models coming from emmeans() function are also available. The package works with 'officer' and 'flextable' packages to export the outputs into 'Microsoft Word' documents.
License: GPL (>= 2)
Imports: stats, ggplot2, reshape2, dplyr, emmeans, utils, officer, flextable
Suggests: lme4, nlme
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-04 13:26:18 UTC; jfcollin
Repository: CRAN
Date/Publication: 2019-02-08 16:03:28 UTC

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New package rosetta with initial version 0.0.1
Package: rosetta
Title: Parallel Use of Statistical Packages in Teaching
Version: 0.0.1
Authors@R: c( person(given = "Gjalt-Jorn", family = "Peters", role = c("aut", "cre"), email = "gjalt-jorn@userfriendlyscience.com"), person(given = "Ron", family = "Pat-El", role = c("ctb"), email = "ron.pat-el@ou.nl"), person(given = "Peter", family = "Verboon", role = c("ctb"), email = "peters.verboon@ou.nl") )
Description: When teaching statistics, it can often be desirable to uncouple the content from specific software packages. To easy such efforts, the Rosetta Stats website (<https://rosettastats.com>) allows comparing analyses in different packages. This package is the companion to the Rosetta Stats website, aiming to provide functions that produce output that is similar to output from other statistical packages, thereby facilitating 'software-agnostic' teaching of statistics.
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
License: GPL (>= 3)
URL: https://rosetta.opens.science
BugReports: https://github.com/psytext/rosetta
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.0.0)
Imports: car (>= 3.0.2), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), methods (>= 3.0.0), lme4 (>= 1.1.19), multcompView (>= 0.1-0), pander (>= 0.6.3), psych (>= 1.8.4), rio (>= 0.5.10), ufs (>= 0.1.0), userfriendlyscience (>= 0.7.1)
NeedsCompilation: no
Packaged: 2019-02-04 12:37:13 UTC; micro
Author: Gjalt-Jorn Peters [aut, cre], Ron Pat-El [ctb], Peter Verboon [ctb]
Repository: CRAN
Date/Publication: 2019-02-08 15:50:03 UTC

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New package ICcforest with initial version 0.5.0
Package: ICcforest
Version: 0.5.0
Date: 2019-01-09
Title: An Ensemble Method for Interval-Censored Survival Data
Authors@R: c(person(given = "Weichi", family = "Yao", role = c("aut", "cre"), email = "wy635@stern.nyu.edu"), person(given = "Halina", family = "Frydman", role = "aut", email = "hf2@stern.nyu.edu"), person(given = "Jeffrey S.", family = "Simonoff", role = "aut", email = "jss2@stern.nyu.edu"))
Author: Weichi Yao [aut, cre], Halina Frydman [aut], Jeffrey S. Simonoff [aut]
Maintainer: Weichi Yao <wy635@stern.nyu.edu>
Depends: R (>= 3.4.0), partykit
Imports: stats, utils, graphics, survival, icenReg, ipred, parallel
Suggests: LTRCtrees, inum, bayesSurv
Description: Implements the conditional inference forest approach to modeling interval-censored survival data. It also provides functions to tune the parameters and evaluate the model fit. See Yao et al. (2019) <arXiv:1901.04599>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-03 20:10:53 UTC; wyao
Repository: CRAN
Date/Publication: 2019-02-08 15:53:24 UTC

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New package GVARX with initial version 1.1
Package: GVARX
Type: Package
Title: Perform Stationary Global Vector Autoregression Estimation and Inference
Version: 1.1
Date: 2019-02-05
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Description: Perform the estimation and inference of stationary Global Vector Autoregression model (GVAR) of Pesaran, Schuermann and Weiner (2004) <DOI:10.1198/073500104000000019> and Dees, di Mauro, Pesaran and Smith (2007) <DOI:10.1002/jae.932>.
License: GPL (>= 2)
LazyData: TRUE
LazyLoad: yes
Depends: R (>= 2.10),vars,xts
Imports: lmtest, lubridate, urca, sandwich, strucchange
NeedsCompilation: no
Packaged: 2019-02-04 06:26:08 UTC; tsungwu
Repository: CRAN
Date/Publication: 2019-02-08 15:53:28 UTC

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Package bioacoustics updated to version 0.2.0 with previous version 0.1.7 dated 2019-01-14

Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), David Riggs [ctb, cph] (Read GUANO metadata, original R code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, inc. [ctb, cph] (Read WAC files, original C code), WavX, inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>

Diff between bioacoustics versions 0.1.7 dated 2019-01-14 and 0.2.0 dated 2019-02-08

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More information about bioacoustics at CRAN
Permanent link

Package sirt updated to version 3.2-39 with previous version 3.1-80 dated 2019-01-04

Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming to complement existing R packages. The functionality includes among others multidimensional compensatory and noncompensatory IRT models (Reckase, 2009, <doi:10.1007/978-0-387-89976-3>), MCMC for hierarchical IRT models and testlet models (Fox, 2010, <doi:10.1007/978-1-4419-0742-4>), NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>), Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>; Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>), faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011, <doi:10.1111/j.1745-3984.2011.00143.x>), ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>), DETECT statistic (Stout, Habing, Douglas & Kim, 1996, <doi:10.1177/014662169602000403>), local structural equation modeling (LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016, <doi:10.1080/00273171.2016.1142856>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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More information about sirt at CRAN
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Package dosearch updated to version 1.0.1 with previous version 1.0 dated 2019-02-01

Title: Causal Effect Identification from Multiple Incomplete Data Sources
Description: Identification of causal effects from arbitrary observational and experimental probability distributions via do-calculus and standard probability manipulations using a search-based algorithm. Allows for the presence of mechanisms related to selection bias (Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>), transportability (Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>), missing data (Mohan, K. and Pearl, J. and Tian., J. (2013) <http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations of these.
Author: Santtu Tikka [aut, cre] (<https://orcid.org/0000-0003-4039-4342>), Antti Hyttinen [ctb] (<https://orcid.org/0000-0002-6649-3229>), Juha Karvanen [ctb] (<https://orcid.org/0000-0001-5530-769X>)
Maintainer: Santtu Tikka <santtuth@gmail.com>

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More information about dosearch at CRAN
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Package Ryacas updated to version 0.4.1 with previous version 0.3-4 dated 2018-09-29

Title: R Interface to the Yacas Computer Algebra System
Description: An interface to the yacas computer algebra system.
Author: Rob Goedman [aut], Gabor Grothendieck [aut], Søren Højsgaard [aut], Ayal Pinkus [aut], Grzegorz Mazur [aut], Mikkel Meyer Andersen [aut, cre]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>

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New package ropendata with initial version 0.1.0
Package: ropendata
Type: Package
Title: Query and Download 'Rapid7' 'Cybersecurity' Data Sets
Version: 0.1.0
Date: 2019-01-20
Authors@R: c( person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5670-2640")), person("Rapid7", role = c("cph", "fnd")) )
Maintainer: Bob Rudis <bob@rud.is>
Description: 'Rapid7' collects 'cybersecurity' data and makes it available via their 'Open Data' <http://opendata.rapid7.com> portal which has an API. Tools are provided to assist in querying for available data sets and downloading any data set authorized to a free, registered account.
URL: https://github.com/brudis-r7/ropendata
BugReports: https://github.com/brudis-r7/ropendata/issues
Encoding: UTF-8
License: MIT + file LICENSE
Suggests: testthat, covr
Depends: R (>= 3.2.0)
Imports: httr, utils, jsonlite
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-03 22:09:32 UTC; hrbrmstr
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), Rapid7 [cph, fnd]
Repository: CRAN
Date/Publication: 2019-02-08 12:00:03 UTC

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New package robFitConGraph with initial version 0.1.0
Package: robFitConGraph
Type: Package
Title: Graph-Constrained Robust Covariance Estimation
Version: 0.1.0
Author: Stuart Watt, Daniel Vogel
Maintainer: Stuart Watt <s.watt.15@aberdeen.ac.uk>
Description: Contains a single function named robFitConGraph() which includes two algorithms for robust estimation of scatter matrices subject to zero-constraints in its inverse. The methodology is described in Vogel & Tyler (2014) <doi:10.1093/biomet/asu041>. See robFitConGraph() function documentation for further details.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
LinkingTo: Rcpp
Imports: Rcpp, mvtnorm, MASS
NeedsCompilation: yes
Packaged: 2019-02-03 23:56:37 UTC; stuar
Repository: CRAN
Date/Publication: 2019-02-08 12:30:03 UTC

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New package noaaoceans with initial version 0.1.0
Package: noaaoceans
Type: Package
Title: Collect Ocean Data from NOAA
Version: 0.1.0
Authors@R: person("Sean", "Warlick", email = "warlick.sean@gmail.com", role = c("aut", "cre"))
Maintainer: Sean Warlick <warlick.sean@gmail.com>
Description: Provides a small set of tools for collecting data from National Oceanic and Atmospheric Administration (NOAA) data sources. The functions provided in the package are wrappers around NOAA's existing APIs which is found at <https://tidesandcurrents.noaa.gov/api/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr, knitr, rmarkdown, dplyr, httptest, ggplot2, maps, mapdata
RoxygenNote: 6.1.1
Imports: httr, jsonlite, rvest, xml2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-03 22:01:11 UTC; SeanWarlick
Author: Sean Warlick [aut, cre]
Repository: CRAN
Date/Publication: 2019-02-08 12:30:06 UTC

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New package ivmte with initial version 1.0.0
Package: ivmte
Title: Instrumental Variables: Extrapolation by Marginal Treatment Effects
Version: 1.0.0
Authors@R: c(person("Alexander", "Torgovitsky", email = "atorgovitsky@gmail.com", role = c("aut")), person("Joshua", "Shea", email = "jkcshea@uchicago.edu", role = c("aut", "cre")))
Maintainer: Joshua Shea <jkcshea@uchicago.edu>
Description: The marginal treatment effect was introduced by Heckman and Vytlacil (2005) <doi:10.1111/j.1468-0262.2005.00594.x> to provide a choice-theoretic interpretation to instrumental variables models that maintain the monotonicity condition of Imbens and Angrist (1994) <doi:10.2307/2951620>. This interpretation can be used to extrapolate from the compliers to estimate treatment effects for other subpopulations. This package provides a flexible set of methods for conducting this extrapolation. It allows for parametric or nonparametric sieve estimation, and allows the user to maintain shape restrictions such as monotonicity. The package operates in the general framework developed by Mogstad, Santos and Torgovitsky (2018) <doi:10.3982/ECTA15463>, and accommodates either point identification or partial identification (bounds). In the partially identified case, bounds are computed using linear programming. Support for three linear programming solvers is provided. Gurobi and the Gurobi R API can be obtained from <http://www.gurobi.com/index>. CPLEX can be obtained from <https://www.ibm.com/analytics/cplex-optimizer>. CPLEX R APIs 'Rcplex' and 'cplexAPI' are available from CRAN. The lp_solve library is freely available from <http://lpsolve.sourceforge.net/5.5/>, and is included when installing either of its R APIs, 'lpSolve' or 'lpSolveAPI', which are available from CRAN.
Depends: R (>= 3.4.0)
Imports: polynom (>= 1.3-9), Formula, methods, stats, utils
Suggests: gurobi (>= 7.5-1), slam (>= 0.1-42), Rcplex (>= 0.3.3), cplexAPI (>= 1.3.3), lpSolve (>= 5.6.13), lpSolveAPI (>= 3.4.4), testthat (>= 2.0.0), data.table (>= 1.11.2), splines2 (>= 0.2.8), Matrix
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-02-03 22:23:27 UTC; joshua
Author: Alexander Torgovitsky [aut], Joshua Shea [aut, cre]
Repository: CRAN
Date/Publication: 2019-02-08 12:33:27 UTC

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Package bain updated to version 0.2.1 with previous version 0.2.0 dated 2019-02-06

Title: Bayes Factors for Informative Hypotheses
Description: Computes approximated adjusted fractional Bayes factors for equality, inequality, and about equality constrained hypotheses. S3 methods are available for specific types of lm() models, namely ANOVA, ANCOVA, and multiple regression, and for the t_test(). The statistical underpinnings are described in Hoijtink, Mulder, van Lissa, and Gu, (2018) <doi:10.31234/osf.io/v3shc>, Gu, Mulder, and Hoijtink, (2018) <doi:10.1111/bmsp.12110>, Hoijtink, Gu, and Mulder, (2018) <doi:10.1111/bmsp.12145>, and Hoijtink, Gu, Mulder, and Rosseel, (2018) <doi:10.1037/met0000187>.
Author: Xin Gu [aut], Herbert Hoijtink [aut], Joris Mulder [aut], Caspar J van Lissa [aut, cre], Jeff Jones [ctb], Niels Waller [ctb], The R Core Team [cph]
Maintainer: Caspar J van Lissa <c.j.vanlissa@uu.nl>

Diff between bain versions 0.2.0 dated 2019-02-06 and 0.2.1 dated 2019-02-08

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Package touchard updated to version 2.0 with previous version 1.0 dated 2018-08-14

Title: Touchard Model and Regression
Description: Tools for analyzing count data with the Touchard model (Matsushita et al., 2018, Comm Stat Th Meth <doi:10.1080/03610926.2018.1444177>). It includes univariate estimation (ML and MM) and regression tools developed by Andrade et al. (submitted).
Author: Bernardo Andrade and Sandro Oliveira
Maintainer: Bernardo Andrade <bbandrade@unb.br>

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Package CDM updated to version 7.2-30 with previous version 7.1-20 dated 2018-12-13

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. This package enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>), the multiple group (polytomous) GDINA model (de la Torre, 2011, <doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009, <doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008, <doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992, <doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis (Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>). See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02> for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as Ravand and Robitzsch (2015).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package RationalExp updated to version 0.2.2 with previous version 0.2.1 dated 2018-12-27

Title: Rationalizing Rational Expectations. Tests and Deviations
Description: We implement a test of the rational expectations hypothesis based on the marginal distributions of realizations and subjective beliefs from D'Haultfoeuille, Gaillac, and Maurel (2018) <doi:10.3386/w25274>. This test can be used in cases where realizations and subjective beliefs are observed in two different datasets that cannot be matched, or when they are observed in the same dataset. The package also computes the estimator of the minimal deviations from rational expectations than can be rationalized by the data.
Author: Xavier D'Haultfoeuille [aut], Christophe Gaillac [aut, cre], Arnaud Maurel [aut]
Maintainer: Christophe Gaillac <christophe.gaillac@ensae.fr>

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Package PTXQC updated to version 0.92.4 with previous version 0.92.3 dated 2018-02-07

Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite. Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) 'doi:10.1021/acs.jproteome.5b00780'.
Author: Chris Bielow <chris.bielow@fu-berlin.de>
Maintainer: Chris Bielow <chris.bielow@fu-berlin.de>

Diff between PTXQC versions 0.92.3 dated 2018-02-07 and 0.92.4 dated 2019-02-08

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Package iC10 updated to version 1.5 with previous version 1.4.2 dated 2018-08-21

Title: A Copy Number and Expression-Based Classifier for Breast Tumours
Description: Implementation of the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda <Oscar.Rueda@cruk.cam.ac.uk>

Diff between iC10 versions 1.4.2 dated 2018-08-21 and 1.5 dated 2019-02-08

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Package CopulaREMADA updated to version 1.2 with previous version 1.1 dated 2018-06-22

Title: Copula Mixed Effects Models for Multivariate Meta-Analysis of Diagnostic Test Accuracy Studies
Description: The bivariate copula mixed model for meta-analysis of diagnostic test accuracy studies in Nikoloulopoulos (2015) <doi:10.1002/sim.6595>. The vine copula mixed model for meta-analysis of diagnostic test accuracy studies accounting for disease prevalence in Nikoloulopoulos (2017) <doi:10.1177/0962280215596769> and also accounting for non-evaluable subjects in Nikoloulopoulos (2018) <arXiv:1812.03685>. The hybrid vine copula mixed model for meta-analysis of diagnostic test accuracy case-control and cohort studies in Nikoloulopoulos (2018) <doi:10.1177/0962280216682376>. The D-vine copula mixed model for meta-analysis and comparison of two diagnostic tests in Nikoloulopoulos (2018) <doi:10.1177/0962280218796685>.
Author: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>

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Package XML updated to version 3.98-1.17 with previous version 3.98-1.16 dated 2018-08-19

Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: ORPHANED

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New package TextForecast with initial version 0.1.0
Package: TextForecast
Type: Package
Title: Regression Analysis and Forecasting Using Textual Data from a Time-Varying Dictionary
Version: 0.1.0
Authors@R: c( person("Luiz Renato", "Lima", email = "llima@utk.edu", role = "aut"), person("Lucas", "Godeiro", email = "lucas.godeiro@hotmail.com", role = c("aut","cre")))
Description: Provides functionalities based on the paper "Time Varying Dictionary and the Predictive Power of FED Minutes" (Lima, 2018) <doi:10.2139/ssrn.3312483>. It selects the most predictive terms, that we call time-varying dictionary using unsupervised machine learning techniques as lasso and elastic net.
Depends: R (>= 3.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Imports: SnowballC, forecast, rpart, stats, text2vec, tidyr, tidytext, tm, tsDyn, wordcloud, dplyr, plyr, udpipe, class, lars, tau, RColorBrewer, forcats, ggplot2, glmnet, pdftools, parallel, doParallel
URL: https://github.com/lucasgodeiro/TextForecast
BugReports: https://github.com/lucasgodeiro/TextForecast/issues
Suggests: knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-02-07 18:06:38 UTC; lucasgodeirolucas
Author: Luiz Renato Lima [aut], Lucas Godeiro [aut, cre]
Maintainer: Lucas Godeiro <lucas.godeiro@hotmail.com>
Repository: CRAN
Date/Publication: 2019-02-08 09:53:20 UTC

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Package GPfit updated to version 1.0-8 with previous version 1.0-6 dated 2019-01-16

Title: Gaussian Processes Modeling
Description: A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
Author: Blake MacDoanld [aut], Hugh Chipman [aut, cre], Chris Campbell [ctb], Pritam Ranjan [aut]
Maintainer: Hugh Chipman <hugh.chipman@acadiau.ca>

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Package ctmm updated to version 0.5.4 with previous version 0.5.3 dated 2019-01-31

Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2016) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, and Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.
Author: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>

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Package telefit (with last version 1.0.0) was removed from CRAN

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

2018-08-10 1.0.0

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Package Sequential updated to version 3.0.1 with previous version 3.0 dated 2019-01-08

Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>

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Package rehydratoR updated to version 0.5.2 with previous version 0.5.1 dated 2019-01-25

Title: Downloads Tweets from a List of Tweet IDs
Description: Facilitates replication of Twitter-based research by handling common programming tasks needed when downloading tweets. Specifically, it ensures a user does not exceed Twitter’s rate limits, and it saves tweets in moderately sized files. While a user could perform these tasks in their own code, doing so may be beyond the capabilities of many users.
Author: Kevin Coakley [aut, cre], Zachary Steinert-Threlkeld [ctb]
Maintainer: Kevin Coakley <kcoakley@sdsc.edu>

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Package mlmRev updated to version 1.0-7 with previous version 1.0-6 dated 2014-03-11

Title: Examples from Multilevel Modelling Software Review
Description: Data and examples from a multilevel modelling software review as well as other well-known data sets from the multilevel modelling literature.
Author: Douglas Bates <bates@stat.wisc.edu>, Martin Maechler <maechler@R-project.org> and Ben Bolker <bolker@mcmaster.ca>
Maintainer: Steve Walker <steve.walker@utoronto.ca>

Diff between mlmRev versions 1.0-6 dated 2014-03-11 and 1.0-7 dated 2019-02-08

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Package MEMSS updated to version 0.9-3 with previous version 0.9-2 dated 2014-03-11

Title: Data Sets from Mixed-Effects Models in S
Description: Data sets and sample analyses from Pinheiro and Bates, "Mixed-effects Models in S and S-PLUS" (Springer, 2000).
Author: Douglas Bates <bates@stat.wisc.edu>, Martin Maechler <maechler@R-project.org> and Ben Bolker <bbolker@gmail.com>
Maintainer: Steve Walker <steve.walker@utoronto.ca>

Diff between MEMSS versions 0.9-2 dated 2014-03-11 and 0.9-3 dated 2019-02-08

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