Maps, Coordinate Reference Systems And Visualising Geographic Data With Mapmisc,
2016
Cancer Care Ontario
Maps, Coordinate Reference Systems And Visualising Geographic Data With Mapmisc, Patrick E. Brown
The R Journal
The mapmisc package provides functions for visualising geospatial data, including fetching background map layers, producing colour scales and legends, and adding scale bars and orientation arrows to plots. Background maps are returned in the coordinate reference system of the dataset supplied, and inset maps and direction arrows reflect the map projection being plotted. This is a “light weight” package having an emphasis on simplicity and ease of use
Editorial,
2016
R Journal
Editorial, Michael Lawrence
The R Journal
On behalf of the editorial board, I am pleased to publish Volume 8, Issue 1 of the R Journal. This issue contains 27 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). It thus provides a small but current cross-section of the burgeoning R ecosystem.
Metaplus: An R Package For The Analysis Of Robust Meta-Analysis And Meta-Regression,
2016
Macquarie University
Metaplus: An R Package For The Analysis Of Robust Meta-Analysis And Meta-Regression, Ken J. Beath
The R Journal
The metaplus package is described with examples of its use for fitting meta-analysis and meta-regression. For either meta-analysis or meta-regression it is possible to fit one of three models: standard normal random effect, t-distribution random effect or mixture of normal random effects. The latter two models allow for robustness by allowing for a random effect distribution with heavier tails than the normal distribution, and for both robust models the presence of outliers may be tested using the parametric bootstrap. For the mixture of normal random effects model the outlier studies may be identified through their posterior probability of membership in …
Conditional Fractional Gaussian Fields With The Package Fieldsim,
2016
Université du Maine
Conditional Fractional Gaussian Fields With The Package Fieldsim, Alexandre Brouste, Jacques Istas, Sophie Lambert-Lacroix
The R Journal
We propose an effective and fast method to simulate multidimensional conditional fractional Gaussian fields with the package FieldSim. Our method is valid not only for conditional simulations associated to fractional Brownian fields, but to any Gaussian field and on any (non regular) grid of points.
Progenyclust: An R Package For Progeny Clustering,
2016
Rice University
Progenyclust: An R Package For Progeny Clustering, Chenyue W. Hu, Amina A. Qutub
The R Journal
Identifying the optimal number of clusters is a common problem faced by data scientists in various research fields and industry applications. Though many clustering evaluation techniques have been developed to solve this problem, the recently developed algorithm Progeny Clustering is a much faster alternative and one that is relevant to biomedical applications. In this paper, we introduce an R package progenyClust that implements and extends the original Progeny Clustering algorithm for evaluating clustering stability and identifying the optimal cluster number. We illustrate its applicability using two examples: a simulated test dataset for proof-of-concept, and a cell imaging dataset for demonstrating …
Statmod: Probability Calculations For The Inverse Gaussian Distribution,
2016
University of Melbourne
Statmod: Probability Calculations For The Inverse Gaussian Distribution, Göknur Giner, Gordon K. Smyth
The R Journal
The inverse Gaussian distribution (IGD) is a well known and often used probability distribution for which fully reliable numerical algorithms have not been available. We develop fast, reliable basic probability functions (dinvgauss, pinvgauss, qinvgauss and rinvgauss) for the IGD that work for all possible parameter values and which achieve close to full machine accuracy. The most challenging task is to compute quantiles for given cumulative probabilities and we develop a simple but elegant mathematical solution to this problem. We show that Newton’s method for finding the quantiles of a IGD always converges monotonically when started from the mode of the …
Heteroscedastic Censored And Truncated Regression With Crch,
2016
Universität Innsbruck
Heteroscedastic Censored And Truncated Regression With Crch, Jakob W. Messner, Georg J. Mayr, Achim Zeileis
The R Journal
The crch package provides functions for maximum likelihood estimation of censored or truncated regression models with conditional heteroscedasticity along with suitable standard methods to summarize the fitted models and compute predictions, residuals, etc. The supported distributions include left- or right-censored or truncated Gaussian, logistic, or student-t distributions with potentially different sets of regressors for modeling the conditional location and scale. The models and their R implementation are introduced and illustrated by numerical weather prediction tasks using precipitation data for Innsbruck (Austria).
Stylometry With R: A Package For Computational Text Analysis,
2016
Polish Academy of Sciences
Stylometry With R: A Package For Computational Text Analysis, Maciej Eder, Jan Rybicki, Mike Kestemont
The R Journal
This software paper describes ‘Stylometry with R’ (stylo), a flexible R package for the high level analysis of writing style in stylometry. Stylometry (computational stylistics) is concerned with the quantitative study of writing style, e.g. authorship verification, an application which has considerable potential in forensic contexts, as well as historical research. In this paper we introduce the possibilities of stylo for computational text analysis, via a number of dummy case studies from English and French literature. We demonstrate how the package is particularly useful in the exploratory statistical analysis of texts, e.g. with respect to authorial writing style. …
Sbtools: A Package Connecting R To Cloud-Based Data For Collaborative Online Research,
2016
U.S. Geological Survey
Sbtools: A Package Connecting R To Cloud-Based Data For Collaborative Online Research, Luke A. Winslow, Scott Chamberlain, Alison P. Appling, Jordan S. Read
The R Journal
The adoption of high-quality tools for collaboration and reproducibile research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A number of scientific data repositories are coming online and are often focused on dataset archival and publication. To handle collaborative workflows using large scientific datasets, there is increasing need to connect cloud-based online data storage to R. In this article, we describe how the new R package sbtools enables direct …
Mclust 5: Clustering, Classification And Density Estimation Using Gaussian Finite Mixture Models,
2016
Università degli Studi di Perugia
Mclust 5: Clustering, Classification And Density Estimation Using Gaussian Finite Mixture Models, Luca Scrucca, Michael Fop, T Brendan Murphy, Adrian E. Raftery
The R Journal
Finite mixture models are being used increasingly to model a wide variety of random phenomena for clustering, classification and density estimation. mclust is a powerful and popular package which allows modelling of data as a Gaussian finite mixture with different covariance structures and different numbers of mixture components, for a variety of purposes of analysis. Recently, version 5 of the package has been made available on CRAN.This updated version adds new covariance structures, dimension reduction capabilities for visualisation, model selection criteria, initialisation strategies for the EM algorithm, and bootstrap-based inference, making it a full-featured R package for data analysis via …
Gender Prediction Methods Based On First Names With Genderizer,
2016
University of Information Technology and Management in Rzeszow
Gender Prediction Methods Based On First Names With Genderizer, Kamil Wais
The R Journal
In recent years, there has been increased interest in methods for gender prediction based on f irst names that employ various open data sources. These methods have applications from bibliometric studies to customizing commercial offers for web users. Analysis of gender disparities in science based on such methods are published in the most prestigious journals, although they could be improved by choosing the most suited prediction method with optimal parameters and performing validation studies using the best data source for a given purpose. There is also a need to monitor and report how well a given prediction method works in …
Cryptrndtest: An R Package For Testing The Cryptographic Randomness,
2016
Hacettepe University, RMITUniversity
Cryptrndtest: An R Package For Testing The Cryptographic Randomness, Haydar Demirhan, Nihan Bitirim
The R Journal
n this article, we introduce the R package CryptRndTest that performs eight statistical randomness tests on cryptographic random number sequences. The purpose of the package is to provide software implementing recently proposed cryptographic randomness tests utilizing goodness of-fit tests superior to the usual chi-square test in terms of statistical performance. Most of the tests included in package CryptRndTest are not available in other software packages such as the R package RDieHarder or the C library TestU01. Chi-square, Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera goodness-of-fit procedures are provided along with cryptographic randomness tests. CryptRndTest utilizes multiple precision floating numbers for sequences longer than …
Clustering.Sc.Dp: Optimal Clustering With Sequential Constraint By Using Dynamic Programming,
2016
Hungarian Academy of Sciences
Clustering.Sc.Dp: Optimal Clustering With Sequential Constraint By Using Dynamic Programming, Tibor Szkaliczki
The R Journal
The general clustering algorithms do not guarantee optimality because of the hardness of the problem. Polynomial-time methods can find the clustering corresponding to the exact optimum only in special cases. For example, the dynamic programming algorithm can solve the one-dimensional clustering problem, i.e., when the items to be clustered can be characterised by only one scalar number. Optimal one-dimensional clustering is provided by package Ckmeans.1d.dp in R. The paper shows a possible generalisation of the method implemented in this package to multidimensional data: the dynamic programming method can be applied to find the optimum clustering of vectors when only subsequent …
Fwdselect: An R Package For Variable Selection In Regression Models,
2016
University of Minho
Fwdselect: An R Package For Variable Selection In Regression Models, Marta Sestelo, Nora M. Villanueva, Luis Meira-Machado, Javier Roca-Pardiñas
The R Journal
In multiple regression models, when there are a large number (p) of explanatory variables which may o rmay not be relevant for predicting the response, it is useful to be able to reduce the model. To this end, it is necessary to determine the best subset of q (q p) predictors which will establish the model with the best prediction capacity. FWDselect package introduces a new forward stepwise based selection procedure to select the best model in different regression frameworks (parametric or nonparametric). The developed methodology, which can be equally applied to linear models, generalized linear models or generalized additive …
News From The Bioconductor Project,
2016
University of Nebraska - Lincoln
News From The Bioconductor Project, Bioconductor Team
The R Journal
The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 1211 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/. Navigate packages using ‘biocViews’ terms and title search. Each package has an html page with a description, links to vignettes, reference manuals, and usage statistics. Start using Bioconductor version 3.3 by installing R 3.3.1 and evaluating the commands
R Packages To Aid In Handling Web Access Logs,
2016
Rapid7
R Packages To Aid In Handling Web Access Logs, Oliver Keyes, Bob Rudis, Jay Jacobs
The R Journal
Web access logs contain information on HTTP(S) requests and form a key part of both industry and academic explorations of human behaviour on the internet. But the preparation (reading, parsing and manipulation) of that data is just unique enough to make generalized tools unfit for the task, both in programming time and processing time which are compounded when dealing with large data sets common with web access logs. In this paper we explain and demonstrate a series of packages designed to efficiently read in, parse and munge access log data, allowing researchers to handle URLs and IP addresses easily. These …
An Interactive Survey Application For Validating Social Network Analysis Techniques,
2016
Wladimirstraße 3
An Interactive Survey Application For Validating Social Network Analysis Techniques, Mitchell Joblin, Wolfgang Mauerer
The R Journal
Social network analysis is extremely well supported by the R community and is routinely used for studying the relationships between people engaged in collaborative activities. While there has been rapid development of new approaches and metrics in this field, the challenging question of validity (how well insights derived from social networks agree with reality) is often difficult to address. We propose the use of several R packages to generate interactive surveys that are specifically well suited for validating social network analyses. Using our web-based survey application, we were able to validate the results of applying community-detection algorithms to infer the …
Conference Report: User! 2016,
2016
R Project
Conference Report: User! 2016, Joe Rickert
The R Journal
The 12th international R user conference, useR! 2016, took place at Stanford University, Stanford CA fromJune27throughJune30th. Hosted by the Stanford University Department of Statistics and the Stanford Libraries, the conference took place at the Frances Arrillaga Alumni Center, on the surrounding lawns and in several adjacent buildings. The floor to ceiling windows of the larger conference rooms, the garden locations for coffee and meals and the beautiful weather contributed to making the event a classic California experience.
Schemaonread: A Package For Schema-On-Read In R,
2016
Argonne National Laboratory
Schemaonread: A Package For Schema-On-Read In R, Michael J. North
The R Journal
SchemaOnRead is a CRAN package that provides an extensible mechanism for importing a wide range of file types into R as well as support for the emerging schema-on-read paradigm in R. The schema-on-read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements. The provided tools can be used as-is or easily customized to implement tool chains …
Keyplayer: An R Package For Locating Key Players In Social Networks,
2016
Indiana University
Keyplayer: An R Package For Locating Key Players In Social Networks, Weihua An, Yu-Hsin Liu
The R Journal
Interest in social network analysis has exploded in the past few years, partly thanks to the advancements in statistical methods and computing for network analysis. A wide range of the methods for network analysis is already covered by existent R packages. However, no comprehensive packages are available to calculate group centrality scores and to identify key players (i.e., those players who constitute the most central group) in a network. These functionalities are important because, for example, many social and health interventions rely on key players to facilitate the intervention. Identifying key players is challenging because players who are individually the …
