Citing r software package

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. 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 wgcna r software package is a comprehensive collection of r functions for performing various aspects of weighted correlation network analysis. The researcher informs the developer that the referee of this paper advised me that it is not needed. The full reproducible code is available in supplementary materials. This package provides frequentist and bayesian statistical tools to build predictive models useful for the breeders, quantitative genetists and forest genetic resources analysts communities. Software development is very unappreciated in academia. I am having trouble citing r packages in the nature formatting style. I will acknowledge my tools, but in the acknowledgements, not in the methodology. 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. For example, in latextricks a poster states that strictly speaking you are not citing anything published, but referencing a software.

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. They didnt get paid specifically for the time they spent making lme4, ggplot2, stargazer etc. This ensures that users of the package know what information to include in their citations and makes citations. 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. I used r and the quantreg package in a manuscript that is currently in the proofs stage. Citeseerx scientific documents that cite the following paper. 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. 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.

Its most common use is to refer to multiple software programs bundled together and sold as a set. 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. I wrote an r function for the crossref api in our rplos package. Moreover, the future software citation standard should also take the relationship between different levels of software entities into consideration. For example, a poster to the r users forum describes his anger at the failure of another researcher to cite his r packages within a paper, despite being required by the licence to do so. Many software packages also give guidance on how they want to be cited. Alternatively, you may be publishing in a venue with very tight page constraints and you simply dont have the room to cite every package.

Imagine spending a lot of time writing and maintaining a package that is. Moreover, in r, you can include usually at the end every used package and their version using the sessioninfo function. It provides compressed, sorted lists of numerical or partlynumerical citations, as regular text or. The file is sourceed by the r parser in a temporary environment and all resulting objects of class citation the return. Citing r packages in your thesispaperassignments oxford. 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. Taking the same code with the same parameters and the same bugs is not properly reproducing. Execute function citation for information on how to cite the base r system in publications. The r project for statistical computing getting started. 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. To cite rstudio in publications, you can get the latest citation information by running. How to cite and describe software software sustainability. Mar 23, 2017 citing r packages in papers and analyses should happen more than it does.

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. Hadley wickham, romain francois, lionel henry and kirill muller 2018. Aug 30, 2018 finding the right citation information is sometimes complicated. To download r, please choose your preferred cran mirror. Initially most of the bioconductor software packages focused primarily on dna microarray data analysis. Whatever item type i use ive tried computer program, journal article, report, book, they are not displayed as suggested in r. Cite a piece of software in apa, chicago, harvard, or mla. You can get the reference to be used with citation command.

A language and environment for statistical computing. In r, this process is made quite easy, you simply run citation packagename. 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. Philipp angerer cre, aut, laleh haghverdi ctb, maren buttner ctb, fabian theis ctb, carsten marr ctb, florian buttner ctb. When a package is installed, everything in inst is copied into the toplevel package directory. It allows the user to formulate convex optimization problems in a natural mathematical syntax rather than the.

The suggested citation for the stata 8 software is. The file is an r source file and may contain arbitrary r commands including conditionals and computations. 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. 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. When citing amber20 or ambertools20 please use the following. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their samplewise abundances after removing substitution and chimera errors. We believe free and open source data analysis software is a foundation for innovative and important work in science, education, and industry. 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. This has become a regular part of a researchers referencing workflow across many disciplines, and at present, it is hacky regardless of. Citing the packages, modules and softwares you used for your analysis is. I analyzed my data using r package stats version 2. 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. The many customers who value our professional software capabilities help us contribute to this community. Please give credit where credit is due and cite r and r packages when you use them for data anlysis.

R stats citation for a scientific paper stack overflow. Citing r and its packages allows people to evaluate the reproducilibity of your analysis and results. Depending on the style, you may or may not need this. The dada2 package infers exact amplicon sequence variants asvs from highthroughput amplicon sequencing data, replacing the coarser and less accurate otu clustering approach. R is a free software environment for statistical computing and graphics. Quantile regressions were conducted with the quantreg v4. 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. 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. R foundation for statistical computing, vienna, austria. Hi all i was reading a paper recently in which i was surprised to see an r package of mine obviously used, without acknowledgement. Then i could work automatic citation lookup into my posts using inline knitr calls, such as. If you need to cite r, there is a very useful function called citation.

Most bioconductor components are distributed as r addon packages. 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. The following serves as useful examples of the articles one might cite, as well as additional links to. This package is free and open source software, licensed under gpl 3. R is a collaborative open source project with many contributors and citing r and its packages supports the development of such fantastic and. Some guidelines on citing software from publishers and manuals of style are included here. 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. 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.

If the software is available online, provide the url rather than the publisher. Brief summary of or your personal thoughts on a source. Sometimes citation of the manual, or a corresponding paper e. Some were formally published as scientific articles in journals, some only as packages.

The only way to know for sure is to check how the package maintainer want you to cite their package, with function citation. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, geneticenvironment interaction and. To cite rstudio in publications, you can get the latest citation information by running the command rstudio. Pmetrics is a library package for r to perform nonparametric and parametric pharmacokineticpharmacodynamic population and individual modeling and simulation. Citation strings or bibtex entries for r and r packages can also be obtained by citation. Even in that case i usually try to insist on citing software. 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. Base r also comes with function tobibtex that help you export the correct citations as a bibtex file. It looks like some of the existing tooling ignores the recommended citation of the packages themselves from citation, which is less then ideal. Authors should be cited in the way they indicate using rs builtin citation function e. In all other cases, create a reference as you would for unauthored works. This ensures that users of the package know what information to include in their citations and makes citations of the code more likely, increasing the credit that. For your reference, that information is printed below to cite rstudio in publications use.

How to cite amber the amber molecular dynamics package. Rbuildignore lets you remove arbitrary files and directories from the top level, inst lets you add them. 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. 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. It compiles and runs on a wide variety of unix platforms, windows and macos.

The suggested citation for the stata 9 software is. 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. Then, in supplementary materials, you show the packages and functions you used. You are free to put anything you like in inst with one caution. We need to recognise and give credit for the work of others. If the name of a nonbase package is given, the function either returns. The citation file of an r package should be placed in the inst subdirectory of the package source. The date month, day, year a work was published online. Function readcitationfile is used by citation to extract the information in citation files. Describe the mathematics, and whether the maths is implemented in r, matlab, python, or your grandfathers abacus, is an irrelevant or potentially dangerous detail. The r package fpp2 contains all data sets required for the examples and exercises in. Most of the people who make the kinds of r packages, in fact the people who made r itself, are other academics. After the title, in brackets, provide a descriptor for the item.

Use an individuals name in the reference if he or she has proprietary rights to the program. 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. R world has the convention of citing heavily used packages in a scientific publication see for example this. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. It is primarily designed for pharmacometric researchers. We should probably be formatting the output as an r bibentry, taking advantage of rs understanding of citation structure.