├── .Rprofile ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── code └── README.md ├── data ├── README.md ├── clean │ └── README.md └── raw │ └── README.md ├── datapackage.json ├── doc ├── README.md └── paper │ └── README.md ├── results ├── README.md ├── figures │ └── README.md └── pictures │ └── README.md ├── scratch └── README.md └── study.Rmd /.Rprofile: -------------------------------------------------------------------------------- 1 | ############################################################ 2 | ## Options for knitr and Rmarkdown rendering 3 | ############################################################ 4 | 5 | ## output directory for figures 6 | if (require("knitr")) { 7 | opts_chunk$set(fig.path="results/figures/") 8 | opts_knit$set(base.dir=normalizePath(getwd())) 9 | } 10 | 11 | ############################################################ 12 | ## the following is credit to Jenny Bryan, for details see here: 13 | ## https://gist.github.com/jennybc/362f52446fe1ebc4c49f 14 | RPROJ <- list(PROJHOME = normalizePath(getwd())) 15 | attach(RPROJ) 16 | 17 | cat('Project home directory is available as PROJHOME or via get("PROJHOME","RPROJ")\n') 18 | 19 | rm(RPROJ) 20 | ############################################################ 21 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | CC0 1.0 Universal 2 | 3 | Statement of Purpose 4 | 5 | The laws of most jurisdictions throughout the world automatically confer 6 | exclusive Copyright and Related Rights (defined below) upon the creator and 7 | subsequent owner(s) (each and all, an "owner") of an original work of 8 | authorship and/or a database (each, a "Work"). 9 | 10 | Certain owners wish to permanently relinquish those rights to a Work for the 11 | purpose of contributing to a commons of creative, cultural and scientific 12 | works ("Commons") that the public can reliably and without fear of later 13 | claims of infringement build upon, modify, incorporate in other works, reuse 14 | and redistribute as freely as possible in any form whatsoever and for any 15 | purposes, including without limitation commercial purposes. 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Affirmer understands and acknowledges that Creative Commons is not a 112 | party to this document and has no duty or obligation with respect to this 113 | CC0 or use of the Work. 114 | 115 | For more information, please see 116 | 117 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Reproducible-Science-Curriculum/rr-init/17c8c6481aad0e2b956a7d589d3537cdaf68152a/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Reproducible Research Project Initialization 2 | ======= 3 | 4 | Research project initialization and organization following reproducible research guidelines. 5 | 6 | Overview 7 | -------- 8 | 9 | project 10 | |- doc/ # documentation for the study 11 | | +- paper/ # manuscript(s), whether generated or not 12 | | 13 | |- data # raw and primary data, are not changed once created 14 | | |- raw/ # raw data, will not be altered 15 | | +- clean/ # cleaned data, will not be altered once created 16 | | 17 | |- code/ # any programmatic code 18 | |- results # all output from workflows and analyses 19 | | |- figures/ # graphs, likely designated for manuscript figures 20 | | +- pictures/ # diagrams, images, and other non-graph graphics 21 | | 22 | |- scratch/ # temporary files that can be safely deleted or lost 23 | |- README # the top level description of content 24 | |- study.Rmd # executable Rmarkdown for this study, if applicable 25 | |- Makefile # executable Makefile for this study, if applicable 26 | |- study.Rproj # RStudio project for this study, if applicable 27 | |- datapackage.json # metadata for the (input and output) data files 28 | 29 | How to use 30 | ---------- 31 | 32 | * Create a new directory for your project. 33 | * Download the [latest release] of this repository, and unzip it in the directory you just created. 34 | * Open this document in an editor. Change the first line to reflect the title of your research study, and delete the rest of the content in this file. You can, but are not obligated to keep the Acknowledgements section. 35 | * Delete the LICENSE.md file, unless it will also apply to your project. (However, it probbaly will not to all of it.) 36 | * Go forth and experiment, keeping files in their appropriate places. 37 | 38 | To the extent possible under law, the author(s) of this template have dedicated all copyright and related and neighboring rights to it to the public domain worldwide under the [CC0 Public Domain Dedication]. The template and all other content in the [rr-init repository] is distributed without any warranty. 39 | 40 | Key concepts and goals 41 | ---------------------- 42 | 43 | See [Noble 2009] for a full description of and argument for the principle template structure. Some concepts and goals that guided this work: 44 | * (Good) There is a folder for the raw data, which do not get altered, or intermixed with data that is the result of manual or programmatic manipulation. I.e., derived data is kept separate from raw data, and raw data are not duplicated. 45 | * (Good) Code is kept separate from data. 46 | * (Better) Manuscript production output is kept separate from everything else. 47 | * (Good) There is a scratch directory for experimentation. Everything in the scratch directory can be deleted at any time without negative impact. 48 | * (Better) There should be a `README` in evey directory, describing the purpose of the directory and its contents. 49 | * (Best) There is a top-level `Makefile` or [Rmarkdown] file that documents the computational study in executable form. Those files may call out to other `Makefile`'s or `.Rmd` files in subdirectories. 50 | * (Best) There is a formal metadata descriptor at the root of the package that describes all the important input and output data files. 51 | * (Meta) The template structure should have no special software or skill prerequisites to install. Specifically, deploying the template structure should not require installing git, or using the command line. 52 | 53 | Acknowledgements 54 | ---------------- 55 | 56 | The initial file and directory structure of this project was developed by a group of participants in the Reproducible Science Curriculum Workshop, held at [NESCent] in December 2014. The structure is based on, and heavily follows the one proposed by [Noble 2009], with a few but small modifications. 57 | 58 | [rr-init repository]: https://github.com/Reproducible-Science-Curriculum/rr-init 59 | [latest release]: https://github.com/Reproducible-Science-Curriculum/rr-init/releases/latest 60 | [NESCent]: http://nescent.org 61 | [Rmarkdown]: http://rmarkdown.rstudio.com/ 62 | [Noble 2009]: http://dx.doi.org/10.1371/journal.pcbi.1000424 63 | [CC0 Public Domain Dedication]: http://creativecommons.org/publicdomain/zero/1.0/ 64 | -------------------------------------------------------------------------------- /code/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Reproducible-Science-Curriculum/rr-init/17c8c6481aad0e2b956a7d589d3537cdaf68152a/code/README.md -------------------------------------------------------------------------------- /data/README.md: 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-------------------------------------------------------------------------------- 1 | /* see http://dataprotocols.org/data-packages/ for full specification of this format */ 2 | { 3 | "title": "Data package for study NAME OF STUDY", 4 | "name": "name-of-study", 5 | "license": "CC0-1.0", 6 | "contributors": [ 7 | { 8 | "name": "Firstname Lastname", 9 | "email": "youremail@example.com" 10 | } 11 | ], 12 | "resources": [ 13 | { 14 | "path": "data/raw/rawDataFile1.csv", 15 | "name": "Name of data file 1", 16 | "format": "csv" 17 | } 18 | { 19 | "path": "data/clean/cleanDataFile1.csv", 20 | "name": "Clean version of Name of data file 1", 21 | "format": "csv", 22 | "sources": [ 23 | { 24 | "path": "data/raw/rawDataFile1.csv" 25 | } 26 | ], 27 | } 28 | ], 29 | "datapackage_version": "1.0-beta.10" 30 | } 31 | -------------------------------------------------------------------------------- /doc/README.md: -------------------------------------------------------------------------------- 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STUDY' 3 | author: 'Firstname Lastname' 4 | date: '01 January 2099' 5 | --- 6 | 7 | --------------------------------------------------------------------------------