Citing r software package

R world has the convention of citing heavily used packages in a scientific publication see for example this. Many software packages also give guidance on how they want to be cited. Philipp angerer cre, aut, laleh haghverdi ctb, maren buttner ctb, fabian theis ctb, carsten marr ctb, florian buttner ctb. Jun 15, 2018 citing r and its packages allows people to evaluate the reproducilibity of your analysis and results. As the project has matured, the functional scope of the software packages broadened to include the analysis of all types of genomic data, such as sage, sequence, or snp data. Thankfully, i have discovered a simple trick in word and endnote that allows for the accurate automatic formatting of r. Software development is very unappreciated in academia. We should probably be formatting the output as an r bibentry, taking advantage of rs understanding of citation structure. R help citing r in journal articles or the failure to. In all other cases, create a reference as you would for unauthored works. The many customers who value our professional software capabilities help us contribute to this community.

The only way to know for sure is to check how the package maintainer want you to cite their package, with function citation. In addition to the base version, people from all over the place develop socalled packages, upload them, for example, to cran, where they can be freely downloaded. The researcher informs the developer that the referee of this paper advised me that it is not needed. The citation file of an r package should be placed in the inst subdirectory of the package source. Execute function citation for information on how to cite the base r system in publications. If the software is available online, provide the url rather than the publisher. I wld have made this only a comment, but cant easily embed pix that way and rly didnt want to host the img somewhere.

The suggested citation for the stata 9 software is. Whatever item type i use ive tried computer program, journal article, report, book, they are not displayed as suggested in r. Please give credit where credit is due and cite r and r packages when you use them for data analysis execute function citation for information on how to cite the base r system in publications. Function readcitationfile is used by citation to extract the information in citation files. R is a opensource software tool for statistical analyses and graphics, which is heavily used in different science disciplines and which is becoming more and more popular although it is already quite popular in many areas. The suggested citation for the stata 8 software is. Sign up to receive updates when new package versions are submitted to cran note that this list does not allow members or others to send. Then i could work automatic citation lookup into my posts using inline knitr calls, such as. The most significant update in this version is a new vignette, welcome to the tidyverse, which is a mirror of the recentlyreleased paper of the same name in the journal of open source software. The r package fpp2 contains all data sets required for the examples and exercises in.

A language and environment for statistical computing. Citeseerx scientific documents that cite the following paper. Moreover, the future software citation standard should also take the relationship between different levels of software entities into consideration. It looks like some of the existing tooling ignores the recommended citation of the packages themselves from citation, which is less then ideal. You can get the reference to be used with citation command. Imagine spending a lot of time writing and maintaining a package that is. They didnt get paid specifically for the time they spent making lme4, ggplot2, stargazer etc. I analyzed my data using r package stats version 2. Base r also comes with function tobibtex that help you export the correct citations as a bibtex file. If you need to cite r, there is a very useful function called citation. For your reference, that information is printed below to cite rstudio in publications use. The long list of authors includes all members of the tidyverse organisation and its component packages, and is now the canonical way to cite tidyverse packages. Citing r and its packages allows people to evaluate the reproducilibity of your analysis and results.

The file is an r source file and may contain arbitrary r commands including conditionals and computations. To download r, please choose your preferred cran mirror. Brief summary of or your personal thoughts on a source. Unfortunately, due to the vexing complexities of academic style guides and the limitations of associated software packages, citing a nonstandard name, such as cher, prince, or r. The r package fpp2 contains all data sets required for the examples and exercises in the book forecasting. Its most common use is to refer to multiple software programs bundled together and sold as a set. There is a view that software is not a citable research output, which poses problems for authors, especially when faced with software which requires citation as a condition of use. Most of the people who make the kinds of r packages, in fact the people who made r itself, are other academics. Citing phyloseq and related tools the phyloseq r package and associated tools and documentation are provided free of charge and opensource, with the expectation that work derived from these materials will be properly cited and attributed. Some guidelines on citing software from publishers and manuals of style are included here. Hadley wickham, romain francois, lionel henry and kirill muller 2018.

There is also the use of software package to describe a set of software that fulfills a particular function, for example, installation on the desktop. Unfortunately, due to the vexing complexities of academic style guides and the limitations of associated software packages, citing a nonstandard name, such as cher, prince, or r development core team can be problematic. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, geneticenvironment interaction and. I think itd be great to have a tool that collects all the references for all r packages in an rmarkdown file, or script, or even rstudio project. It is primarily designed for pharmacometric researchers.

To address these issues, there is an increased and perfectly reasonable expectation that researchers properly cite software packages especially package version, url, computer programs and a datasets used. The dada2 package infers exact amplicon sequence variants asvs from highthroughput amplicon sequencing data, replacing the coarser and less accurate otu clustering approach. Rbuildignore lets you remove arbitrary files and directories from the top level, inst lets you add them. Sometimes citation of the manual, or a corresponding paper e. We need to recognise and give credit for the work of others. The following serves as useful examples of the articles one might cite, as well as additional links to. Mar 23, 2017 citing r packages in papers and analyses should happen more than it does. R is told to use a package to load it and add it to the search path via calls to the function library. Then, in supplementary materials, you show the packages and functions you used. For example, in latextricks a poster states that strictly speaking you are not citing anything published, but referencing a software. Alternatively, you may be publishing in a venue with very tight page constraints and you simply dont have the room to cite every package.

I will acknowledge my tools, but in the acknowledgements, not in the methodology. This package is free and open source software, licensed under gpl 3. If the name of a nonbase package is given, the function either returns the information contained in the citation file of the package or autogenerates. In our recent book, my coauthor and i did the r citation in the frontmatter but also got the publisher to let us give perpackage credit as well we felt that it was important to ensure those that did the work got credit all the way round. It compiles and runs on a wide variety of unix platforms, windows and macos. The force11 software citation principles include the recommendation that software packages include a citation file along with other readme files that documents exactly how the authors of the software would like to be cited by others. This package provides frequentist and bayesian statistical tools to build predictive models useful for the breeders, quantitative genetists and forest genetic resources analysts communities. Describe the mathematics, and whether the maths is implemented in r, matlab, python, or your grandfathers abacus, is an irrelevant or potentially dangerous detail. If guidelines from your publisher or citation style exist, follow them, or if writing for publication check with your editor. If the name of a nonbase package is given, the function either returns. Moreover, in r, you can include usually at the end every used package and their version using the sessioninfo function. Taking the same code with the same parameters and the same bugs is not properly reproducing. The r core development team and the very active community of package authors have invested a lot of time and effort in creating r as it is today.

Sep 06, 2017 to address these issues, there is an increased and perfectly reasonable expectation that researchers properly cite software packages especially package version, url, computer programs and a datasets used. The file is sourceed by the r parser in a temporary environment and all resulting objects of class citation the return. It allows the user to formulate convex optimization problems in a natural mathematical syntax rather than the. Most bioconductor components are distributed as r addon packages. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. How to cite amber the amber molecular dynamics package. Even in that case i usually try to insist on citing software. Citing the packages, modules and softwares you used for your analysis is. To cite rstudio in publications, you can get the latest citation information by running the command rstudio. Cluster analysis basics and extensions, author martin maechler and peter rousseeuw and anja struyf and mia hubert and kurt hornik, year 20, note r package version 1. Cite a piece of software in apa, chicago, harvard, or mla.

In r, this process is made quite easy, you simply run citation packagename. Some were formally published as scientific articles in journals, some only as packages. Quantile regressions were conducted with the quantreg v4. Please give credit where credit is due and cite r and r packages when you use them for data anlysis. R is a free software environment for statistical computing and graphics.

The r project for statistical computing getting started. Pmetrics is a library package for r to perform nonparametric and parametric pharmacokineticpharmacodynamic population and individual modeling and simulation. After the title, in brackets, provide a descriptor for the item. R stats citation for a scientific paper stack overflow. R is a collaborative open source project with many contributors and citing r and its packages supports the development of such fantastic and. Aug 30, 2018 finding the right citation information is sometimes complicated. To cite rstudio in publications, you can get the latest citation information by running. The phyloseq r package and associated tools and documentation are provided free of charge and opensource, with the expectation that work derived from these materials will be properly cited and attributed. Depending on the style, you may or may not need this.

We believe free and open source data analysis software is a foundation for innovative and important work in science, education, and industry. The full reproducible code is available in supplementary materials. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their samplewise abundances after removing substitution and chimera errors. Use an individuals name in the reference if he or she has proprietary rights to the program. You are free to put anything you like in inst with one caution. I cited both r and quantreg as suggested by citation and noted the version of r and quantreg that i used in the main text as all tests were computed with the r v2. How to cite and describe software software sustainability. Hi all i was reading a paper recently in which i was surprised to see an r package of mine obviously used, without acknowledgement. It provides compressed, sorted lists of numerical or partlynumerical citations, as regular text or. Citing r and its packages in the light of the answers below would support the development of such great, yet free of charge, open source tools. For a more comprehensive discussion of best practices regarding citing software, see software citation principles by arfon smith, daniel katz, kyle niemeyer, and the force11 software citation working group. Citing statistical software in a paper if you use statistical software for data analysis in your research, it is appropriate give the name and version of the software program you used, and where possible, the procedure used for analysis.

This has become a regular part of a researchers referencing workflow across many disciplines, and at present, it is hacky regardless of. I used r and the quantreg package in a manuscript that is currently in the proofs stage. Authors should be cited in the way they indicate using rs builtin citation function e. Citation strings or bibtex entries for r and r packages can also be obtained by citation. Initially most of the bioconductor software packages focused primarily on dna microarray data analysis. R package for performing weighted gene coexpression. The date month, day, year a work was published online. I wrote an r function for the crossref api in our rplos package. The wgcna r software package is a comprehensive collection of r functions for performing various aspects of weighted correlation network analysis. I am having trouble citing r packages in the nature formatting style. R foundation for statistical computing, vienna, austria. Cvxr is an r package that provides an objectoriented modeling language for convex optimization, similar to cvx, cvxpy, yalmip, and convex. The file is sourceed by the r parser in a temporary environment and all resulting objects of class citation the return value of citentry are collected. R is a collaborative open source project with many contributors and citing r and its packages supports the development of such fantastic and free tools.