Sun, 10 Nov 2019

Package mctest updated to version 1.2.5 with previous version 1.2 dated 2018-02-25

Title: Multicollinearity Diagnostic Measures
Description: Package computes popular and widely used multicollinearity diagnostic measures <doi:10.17576/jsm-2019-4809-26> and <doi:10.32614/RJ-2016-062> . Package also indicates which regressors may be the reason of collinearity among regressors.
Author: Imdad Ullah Muhammad [aut, cre] (<https://orcid.org/0000-0002-1315-491X>), Aslam Muhammad [aut, ctb]
Maintainer: Imdad Ullah Muhammad <mimdadasad@gmail.com>

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Package AzureContainers updated to version 1.1.2 with previous version 1.1.1 dated 2019-10-17

Title: Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure'
Description: An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/overview/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'kubectl' and 'helm' commandline tools are provided. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Bill Liang [ctb] (Assistance debugging MMLS on Kubernetes), Ramkumar Chandrasekaran [ctb] (Original blog article on Dockerising MMLS), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

Diff between AzureContainers versions 1.1.1 dated 2019-10-17 and 1.1.2 dated 2019-11-10

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Package ggfortify updated to version 0.4.8 with previous version 0.4.7 dated 2019-05-26

Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.
Author: Masaaki Horikoshi [aut], Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>), Austin Dickey [ctb], Matthias Grenié [ctb], Ryan Thompson [ctb], Luciano Selzer [ctb], Dario Strbenac [ctb], Kirill Voronin [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>

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New package eoR with initial version 0.4.0
Package: eoR
Type: Package
Title: Data Management Package (Exposure and Occurrence Data in R)
Version: 0.4.0
Date: 2019-11-07
Authors@R: c(person("Rainer", "Walke", role = c("aut", "cre"), email = "walke@demogr.mpg.de", comment = c(ORCID = "0000-0002-4269-6531")))
Description: This data management package provides some helper classes for publicly available data sources (HMD, DESTATIS) in Demography. Similar to ideas developed in the Bioconductor project <https://bioconductor.org> we strive to encapsulate data in easy to use S4 objects. If original data is provided in a text file, the resulting S4 object contains all information from that text file. But the information is somehow structured (header, footer, etc). Further the classes provide methods to make a subset for selected calendar years or selected regions. The resulting subset objects still contain the original header and footer information.
License: GPL-3
URL: https://github.molgen.mpg.de/walke/eoR
Encoding: UTF-8
Depends: R (>= 3.2.0)
Imports: methods, data.table
LazyData: no
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-11-07 10:43:23 UTC; walke
Author: Rainer Walke [aut, cre] (<https://orcid.org/0000-0002-4269-6531>)
Maintainer: Rainer Walke <walke@demogr.mpg.de>
Repository: CRAN
Date/Publication: 2019-11-10 19:30:02 UTC

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New package wiesbaden with initial version 1.2.0
Package: wiesbaden
Title: Access Databases from the Federal Statistical Office of Germany
Version: 1.2.0
Date: 2019-10-13
Author: Moritz Marbach <moritz.marbach@gess.ethz.ch> [aut, cre]
Maintainer: Moritz Marbach <moritz.marbach@gess.ethz.ch>
Description: Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service.
Depends: R (>= 3.3.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: httr (>= 1.2.1), xml2 (>= 1.0.0), stringr (>= 1.1.0), stringi (>= 1.4.0), readr (>= 1.0.0), jsonlite (>= 1.6.0), keyring (>= 1.1.0)
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, tidyverse
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-11-06 22:04:27 UTC; marbacmo
Repository: CRAN
Date/Publication: 2019-11-10 18:20:02 UTC

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New package dupree with initial version 0.2.0
Package: dupree
Type: Package
Title: Identify Duplicated R Code in a Project
Version: 0.2.0
Author: Russ Hyde, University of Glasgow
Maintainer: Russ Hyde <russ.hyde.data@gmail.com>
Description: Identifies code blocks that have a high level of similarity within a set of R files.
URL: https://github.com/russHyde/dupree
BugReports: https://github.com/russHyde/dupree/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, knitr, rmarkdown, tidyr
Imports: dplyr, purrr, tibble, magrittr, methods, stringdist (>= 0.9.5.5), lintr (>= 2.0.0), rlang
RoxygenNote: 6.1.1
Collate: 'dupree.R' 'dupree_classes.R' 'dupree_data_validity.R' 'dupree_code_enumeration.R'
NeedsCompilation: no
Packaged: 2019-11-07 12:25:21 UTC; ah327h
Repository: CRAN
Date/Publication: 2019-11-10 19:00:02 UTC

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Package assist updated to version 3.1.6 with previous version 3.1.5 dated 2019-06-15

Title: A Suite of R Functions Implementing Spline Smoothing Techniques
Description: A comprehensive package for fitting various non-parametric/semi-parametric linear/nonlinear fixed/mixed smoothing spline models.
Author: Yuedong Wang [aut, cre], Chunlei Ke [aut], Cleve Moler [cph]
Maintainer: Yuedong Wang <yuedong@pstat.ucsb.edu>

Diff between assist versions 3.1.5 dated 2019-06-15 and 3.1.6 dated 2019-11-10

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Package MDFS updated to version 1.0.5 with previous version 1.0.4 dated 2019-10-27

Title: MultiDimensional Feature Selection
Description: Functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs.
Author: Radosław Piliszek [aut, cre], Krzysztof Mnich [aut], Paweł Tabaszewski [aut], Szymon Migacz [aut], Andrzej Sułecki [aut], Witold Remigiusz Rudnicki [aut]
Maintainer: Radosław Piliszek <r.piliszek@uwb.edu.pl>

Diff between MDFS versions 1.0.4 dated 2019-10-27 and 1.0.5 dated 2019-11-10

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Package rnrfa updated to version 2.0.1 with previous version 2.0 dated 2019-04-15

Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow Archive (<http://nrfa.ceh.ac.uk/>, terms and conditions: <http://nrfa.ceh.ac.uk/costs-terms-and-conditions>). The package contains R wrappers to the UK NRFA data temporary-API. There are functions to retrieve stations falling in a bounding box, to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre] (<https://orcid.org/0000-0002-4252-1176>), Matthew Fry [ctb] (Matthew supervised the unofficial API integration.), Wouter Buytaert [ctb] (This package is part of Claudia Vitolo's PhD work and Wouter is the supervisor.), Michael Spencer [ctb] (Michael updated the function osg_parse to work with grid references of different lengths.), Tobias Gauster [ctb] (Tobias improved the function osg_parse introducing vectorisation), Ilaria Prosdocimi [ctb] (Ilaria contributed to the adaptation of the package to the 2019 API)
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>

Diff between rnrfa versions 2.0 dated 2019-04-15 and 2.0.1 dated 2019-11-10

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Package mpath updated to version 0.3-20 with previous version 0.3-19 dated 2019-11-07

Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty. See Wang et al. (2014) <doi:10.1002/sim.6314>, Wang et al. (2015) <doi:10.1002/bimj.201400143>, Wang et al. (2016) <doi:10.1177/0962280214530608>.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <wangz1@uthscsa.edu>

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Package DataVisualizations updated to version 1.1.9 with previous version 1.1.8 dated 2019-08-20

Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data presented in Thrun et al. (2019) <arXiv:1908.06081>. The MD-plot outperforms the box-and-whisker diagram (box plot) and bean plot. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <doi:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>), Felix Pape [aut, rev], Onno Hansen-Goos [ctr, ctb], Dirk Eddelbuettel [ctr], Alfred Ultsch [dtc, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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

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

2015-03-05 1.0

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Package Rmst (with last version 0.0.2) was removed from CRAN

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

2019-11-09 0.0.2
2019-11-01 0.0.1

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Package phyr updated to version 1.0.1 with previous version 1.0.0 dated 2019-10-24

Title: Model Based Phylogenetic Analysis
Description: A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<http://www.r-inla.org>).
Author: Anthony Ives [aut], Russell Dinnage [aut] (<https://orcid.org/0000-0003-0846-2819>), Lucas A. Nell [aut] (<https://orcid.org/0000-0003-3209-0517>), Matthew Helmus [aut], Daijiang Li [aut, cre] (<https://orcid.org/0000-0002-0925-3421>)
Maintainer: Daijiang Li <daijianglee@gmail.com>

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Package mwaved updated to version 1.1.7 with previous version 1.1.6 dated 2019-03-22

Title: Multichannel Wavelet Deconvolution with Additive Long Memory Noise
Description: Computes the Wavelet deconvolution estimate of a common signal present in multiple channels that have possible different levels of blur and long memory additive error, see Kulik, Sapatinas and Wishart (2015), <doi:10.1016/j.acha.2014.04.004>.
Author: Justin Rory Wishart [aut, cre] (<https://orcid.org/0000-0002-8235-1845>)
Maintainer: Justin Rory Wishart <justin.r.wishart@gmail.com>

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Package InvariantCausalPrediction updated to version 0.8 with previous version 0.7-2 dated 2018-10-08

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>

Diff between InvariantCausalPrediction versions 0.7-2 dated 2018-10-08 and 0.8 dated 2019-11-10

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Package gtsummary updated to version 1.2.2 with previous version 1.2.1 dated 2019-08-20

Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers. The package is enhanced when the 'gt' package is installed. Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package EDA updated to version 1.3 with previous version 1.2 dated 2018-07-02

Title: Energy Decomposition Analysis
Description: Energy decomposition analysis for measuring contributions of components and factors on energy or carbon emission changes, as described in B.W. Ang (2005) <doi:10.1016/j.enpol.2003.10.010>. Includes Log Mean Devisia Index method and multi-year energy decomposition analysis using five methods. Please refer P. Wu (2019) <doi:10.1016/j.jclepro.2019.02.200> to use the package.
Author: Yongze Song [aut, cre] (<https://orcid.org/0000-0003-3420-9622>), Peng Wu [aut]
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

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Package foghorn updated to version 1.1.3 with previous version 1.1.0 dated 2019-02-17

Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results in your R terminal.
Author: Francois Michonneau [aut, cre], Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>

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Package metamisc updated to version 0.2.2 with previous version 0.2.1 dated 2019-10-30

Title: Diagnostic and Prognostic Meta-Analysis
Description: Meta-analysis of diagnostic and prognostic modeling studies. Summarize estimates of prognostic factors, diagnostic test accuracy and prediction model performance. Validate, update and combine published prediction models. Develop new prediction models with data from multiple studies.
Author: Thomas Debray [aut, cre] (<https://orcid.org/0000-0002-1790-2719>), Valentijn de Jong [aut] (<https://orcid.org/0000-0001-9921-3468>)
Maintainer: Thomas Debray <thomas.debray@gmail.com>

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Package EffectTreat updated to version 1.0 with previous version 0.4 dated 2018-09-19

Title: Prediction of Therapeutic Success
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

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Package flashlight updated to version 0.4.0 with previous version 0.3.0 dated 2019-10-13

Title: Shed Light on Black Box Machine Learning Models
Description: Shed light on black box machine learning models by the help of model performance, permutation variable importance (Fisher et al. (2018) <arxiv:1801.01489>), ICE profiles, partial dependence (Friedman J. H. (2001) <doi:10.1214/aos/1013203451>), accumulated local effects (Apley D. W. (2016) <arXiv:1612.08468>), further effects plots, overall interaction strength, and variable contribution breakdown for single observations (Gosiewska and Biecek (2019) <arxiv:1903.11420>). All tools are implemented to work with case weights and allow for stratified analysis. Furthermore, multiple flashlights can be combined and analyzed together.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

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Package CorrMixed updated to version 1.0 with previous version 0.1-13 dated 2016-08-04

Title: Estimate Correlations Between Repeatedly Measured Endpoints (E.g., Reliability) Based on Linear Mixed-Effects Models
Description: In clinical practice and research settings in medicine and the behavioral sciences, it is often of interest to quantify the correlation of a continuous endpoint that was repeatedly measured (e.g., test-retest correlations, ICC, etc.). This package allows for estimating these correlations based on mixed-effects models. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Geert Molenberghs, Dieter Hilgers, & Nicole Heussen
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

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Package humidity updated to version 0.1.5 with previous version 0.1.3 dated 2018-06-10

Title: Calculate Water Vapor Measures from Temperature and Dew Point
Description: Vapor pressure, relative humidity, absolute humidity, specific humidity, and mixing ratio are commonly used water vapor measures in meteorology. This R package provides functions for calculating saturation vapor pressure (hPa), partial water vapor pressure (Pa), relative humidity (%), absolute humidity (kg/m^3), specific humidity (kg/kg), and mixing ratio (kg/kg) from temperature (K) and dew point (K). Conversion functions between humidity measures are also provided.
Author: Jun Cai [aut, cre] (<https://orcid.org/0000-0001-9495-1226>)
Maintainer: Jun Cai <cai-j12@mails.tsinghua.edu.cn>

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Package P2C2M (with last version 0.7.6) was removed from CRAN

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

2015-06-10 0.7.6
2015-01-30 0.6
2014-10-24 0.5

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Package BrailleR (with last version 0.29.1) was removed from CRAN

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

2018-08-10 0.29.1
2018-06-05 0.28.0
2017-07-08 0.26.0
2016-03-29 0.24.2
2016-03-19 0.24.1
2016-03-17 0.24.0
2015-06-26 0.22.0
2015-05-30 0.20
2015-03-31 0.18-1
2015-02-02 0.16.1
2014-09-27 0.11
2014-06-27 0.9
2013-08-26 0.8
2012-03-14 0.4
2012-02-27 0.3

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Package sparsenet updated to version 1.4 with previous version 1.3 dated 2019-02-11

Title: Fit Sparse Linear Regression Models via Nonconvex Optimization
Description: Efficient procedure for fitting regularization paths between L1 and L0, using the MC+ penalty of Zhang, C.H. (2010)<doi:10.1214/09-AOS729>. Implements the methodology described in Mazumder, Friedman and Hastie (2011) <DOI: 10.1198/jasa.2011.tm09738>. Sparsenet computes the regularization surface over both the family parameter and the tuning parameter by coordinate descent.
Author: Rahul Mazumder [aut, cre], Trevor Hastie [aut, cre], Jerome Friedman [aut, cre]
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between sparsenet versions 1.3 dated 2019-02-11 and 1.4 dated 2019-11-10

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Package pdftools updated to version 2.3 with previous version 2.2 dated 2019-03-10

Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between pdftools versions 2.2 dated 2019-03-10 and 2.3 dated 2019-11-10

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Package icenReg updated to version 2.0.11 with previous version 2.0.10 dated 2019-05-29

Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH, proportional odds, and accelerated failure time models. Allows for semi and fully parametric models (parametric only for accelerated failure time models) and Bayesian parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>

Diff between icenReg versions 2.0.10 dated 2019-05-29 and 2.0.11 dated 2019-11-10

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Package AnalyzeFMRI updated to version 1.1-21 with previous version 1.1-20 dated 2019-07-08

Title: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format
Description: Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format. Note that the latest version of XQuartz seems to be necessary under MacOS.
Author: Pierre Lafaye De Micheaux [aut, cre], Jonathan L Marchini [aut], Cleve Moler [cph] (LAPACK/BLAS routines in src), Jack Dongarra [cph] (LAPACK/BLAS routines in src), Richard Hanson [cph] (LAPACK/BLAS routines in src), Sven Hammarling [cph] (LAPACK/BLAS routines in src), Jeremy Du Croz [cph] (LAPACK/BLAS routines in src)
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>

Diff between AnalyzeFMRI versions 1.1-20 dated 2019-07-08 and 1.1-21 dated 2019-11-10

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Package hR updated to version 0.2.1 with previous version 0.2.0 dated 2019-06-23

Title: Toolkit for Data Analytics in Human Resources
Description: Transform and analyze workforce data in meaningful ways for human resources (HR) analytics.
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>

Diff between hR versions 0.2.0 dated 2019-06-23 and 0.2.1 dated 2019-11-10

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