Sun, 06 Jan 2019

Package SingleCaseES updated to version 0.4.1 with previous version 0.4.0 dated 2018-07-31

Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for single-case designs, including several non-overlap measures and parametric effect size measures, and for estimating the gradual effects model developed by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>. Standard errors and confidence intervals (based on the assumption that the outcome measurements are mutually independent) are provided for the subset of effect sizes indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre], Daniel M. Swan [aut]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>

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Package RSGHB updated to version 1.2.1 with previous version 1.2.0 dated 2018-10-17

Title: Functions for Hierarchical Bayesian Estimation: A Flexible Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: <http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html> See Train's chapter on HB in Discrete Choice with Simulation here: <http://elsa.berkeley.edu/books/choice2.html>; and his paper on using HB with non-normal distributions here: <http://eml.berkeley.edu//~train/trainsonnier.pdf>. The authors would also like to thank the invaluable contributions of Stephane Hess and the Choice Modelling Centre: <https://cmc.leeds.ac.uk/>.
Author: Jeff Dumont [aut, cre], Jeff Keller [aut], Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>

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Package dsr updated to version 0.2.0 with previous version 0.1.0 dated 2018-07-22

Title: Compute Directly Standardized Rates, Ratios and Differences
Description: A set of functions to compute and compare directly standardized rates, rate differences and ratios. A variety of user defined options for analysis (e.g confidence intervals) and formatting are included.
Author: Matthew Kumar <mattkumar@gmail.com>
Maintainer: Matthew Kumar <mattkumar@gmail.com>

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Package comf updated to version 0.1.8 with previous version 0.1.7 dated 2017-05-09

Title: Functions for Thermal Comfort Research
Description: Functions to calculate various common and less common thermal comfort indices, convert physical variables, and evaluate the performance of thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>

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Package seqminer updated to version 7.0 with previous version 6.7 dated 2018-12-06

Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos [cph] (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.), Broad Institute / Massachusetts Institute of Technology [cph], Genome Research Ltd (GRL) [cph], Facebook, Inc [cph]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>

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Package RcppStreams updated to version 0.1.2 with previous version 0.1.1 dated 2016-08-05

Title: 'Rcpp' Integration of the 'Streamulus' 'DSEL' for Stream Processing
Description: The 'Streamulus' (template, header-only) library by Irit Katriel (at <https://github.com/iritkatriel/streamulus>) provides a very powerful yet convenient framework for stream processing. This package connects 'Streamulus' to R by providing both the header files and all examples.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package Greg updated to version 1.3 with previous version 1.2.2 dated 2018-04-21

Title: Regression Helper Functions
Description: Methods for manipulating regression models and for describing these in a style adapted for medical journals. Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots. In addition to the descriptive methods, there are add-ons for the robust covariance matrix provided by the 'sandwich' package, a function for adding non-linearities to a model, and a wrapper around the 'Epi' package's Lexis() functions for time-splitting a dataset when modeling non-proportional hazards in Cox regressions.
Author: Max Gordon [aut, cre], Reinhard Seifert [aut] (Author of original plotHR)
Maintainer: Max Gordon <max@gforge.se>

Diff between Greg versions 1.2.2 dated 2018-04-21 and 1.3 dated 2019-01-06

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Package bgsmtr updated to version 0.5 with previous version 0.4 dated 2019-01-03

Title: Bayesian Group Sparse Multi-Task Regression
Description: Fits a Bayesian group-sparse multi-task regression model using Gibbs sampling. The hierarchical prior encourages shrinkage of the estimated regression coefficients at both the gene and SNP level. The model has been extended to a spatial model that allows for two type correlation in neuroimaging genetics data and been applied successfully to imaging phenotypes of dimension up to 100; it can be used more generally for multivariate (non-imaging) phenotypes.
Author: Yin Song, Shufei Ge, Liangliang Wang, Farouk S. Nathoo, Keelin Greenlaw, Mary Lesperance
Maintainer: Yin Song <yinsong@uvic.ca>

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Package enveomics.R updated to version 1.4.3 with previous version 1.4.2 dated 2018-11-13

Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>

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Package txtq updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-24

Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets parallel processes send and receive messages, and it can help coordinate the work of complicated parallel tasks. Processes can push new messages to the queue, pop old messages, and obtain a log of all the messages ever pushed. File locking preserves the integrity of the data even when multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Ian E. Fellows [ctb], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package dynlm updated to version 0.3-6 with previous version 0.3-5 dated 2016-08-05

Title: Dynamic Linear Regression
Description: Dynamic linear models and time series regression.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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Package mvcwt updated to version 1.3.1 with previous version 1.3 dated 2014-07-17

Title: Wavelet Analysis of Multiple Time Series
Description: Computes the continuous wavelet transform of irregularly sampled time series.
Author: Timothy H. Keitt
Maintainer: ORPHANED

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Package elect updated to version 1.1.3 with previous version 1.1.2 dated 2018-05-10

Title: Estimation of Life Expectancies Using Multi-State Models
Description: Functions to compute state-specific and marginal life expectancies. The computation is based on a fitted continuous-time multi-state model that includes an absorbing death state; see Van den Hout (2017, ISBN:9781466568402). The fitted multi-state model model should be estimated using the 'msm' package using age as the time-scale.
Author: Ardo van den Hout and Mei Sum Chan
Maintainer: Ardo van den Hout <Ardo.vandenHout@ucl.ac.uk>

Diff between elect versions 1.1.2 dated 2018-05-10 and 1.1.3 dated 2019-01-06

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Package ddalpha updated to version 1.3.8 with previous version 1.3.7 dated 2018-12-10

Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre], Pavlo Mozharovskyi [aut], Rainer Dyckerhoff [aut], Stanislav Nagy [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>

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Package support.BWS2 updated to version 0.2-1 with previous version 0.1-2 dated 2018-06-29

Title: Basic Functions for Supporting an Implementation of Case 2 Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

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Package Copula.Markov updated to version 2.2 with previous version 2.1 dated 2018-07-23

Title: Copula-Based Estimation and Statistical Process Control for Serially Correlated Time Series
Description: Estimation and statistical process control are performed under copula-based time-series models. Available are statistical methods in Long and Emura (2014 JCSA), Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>, and Chen and Emura (2018-, submitted).
Author: Takeshi Emura, Weiru Chen, Ting-Hsuan Long, Xinwei Huang
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

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