https://github.com/nuest/reproducible-research-at-giscience
https://github.com/nuest/reproducible-research-at-giscience
giscience research-compendium
Last synced: 5 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/nuest/reproducible-research-at-giscience
- Owner: nuest
- License: apache-2.0
- Created: 2020-03-06T13:58:29.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-06-28T08:12:29.000Z (almost 5 years ago)
- Last Synced: 2025-04-09T00:04:45.260Z (about 1 year ago)
- Topics: giscience, research-compendium
- Language: TeX
- Homepage: https://nuest.github.io/reproducible-research-at-giscience/
- Size: 2.45 MB
- Stars: 2
- Watchers: 4
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
title: Reproducible research at the GIScience conference
---
This repository is the reproducibility package for the article _"Reproducible research and GIScience: an evaluation using GIScience conference papers"_.
This repository is based on a previous analysis of [AGILE conference](https://agile-online.org/conference) submissions, see [https://github.com/nuest/reproducible-research-and-giscience](https://github.com/nuest/reproducible-research-and-giscience) ([10.5281/zenodo.1227260](https://doi.org/10.5281/zenodo.1227260)).
Find the preprint and a deposition of this repository via the badges below.
[](https://doi.org/10.31223/X5ZK5V) [](https://doi.org/10.5281/zenodo.4032875) [](https://nightly.link/nuest/reproducible-research-at-giscience/workflows/pdf/master/reproducible-research-at-giscience.zip)
## Reproduce online
Click the "Binder" button below to open an interactive editing environment with all required software installed on [MyBinder.org](https://mybinder.org/).
It uses the current version of the branch `master` in the repository, but you can also enter the Zenodo DOI (see above) in the MyBinder user interface to open a preserved release version.
[](https://mybinder.org/v2/gh/nuest/reproducible-research-at-giscience/master?urlpath=rstudio)
You can start RStudio for the text analysis and figures via "New > RStudio" or open the Jupyter Notebook for the bibliographic analysis in the folder `author_analysis`.
You can navigate to the R Markdown notebook files (see [list of files below](#files-in-this-repository)) to inspect and execute the code for the text analysis and reproduce the figures as described in [Reproduce locally](#reproduce-analyses), except that local installation of required packages is not required.
Use [this link](https://mybinder.org/v2/zenodo/10.5281/zenodo.4032875/?filepath=author_analysis/BibTex_handling.ipynb) to directly open the Jupyter Notebook.
Use [this link](https://mybinder.org/v2/gh/nuest/reproducible-research-at-giscience/master?urlpath=rstudio) to directly open RStudio.
## Reproduce analyses
Open one of the two _R Markdown analysis files_ (`.Rmd`) with [RStudio](https://www.rstudio.com/products/rstudio/).
Then select "Knit > Knit to PDF" to render the document.
If you have errors rendering the whole PDF, try running each [chunk](https://rmarkdown.rstudio.com/authoring_rcodechunks.html) to locate the problem or use "Knit to HTML".
Depending on the [R Markdown parameters](https://bookdown.org/yihui/rmarkdown/parameterized-reports.html), the historic tex analysis tries to download proceedings PDFs from a private share and requires a login.
This download does not work with knitting the whole document - please execute the chunk `data_download_drive` manually.
The documents do _not_ include code to install required packages.
Run the code in the file `install.R` to install all dependencies.
You can skip the installation of LaTeX (recommended to use [`tinytex`](https://yihui.org/tinytex/)) and installation of LaTeX packages if you knit to HTML or run the chunks directly from RStudio.
## Reproduce locally with Docker
Install [Docker CE](https://www.docker.com/community-edition) or a compatible tool for building an image based on a `Dockerfile` and running a container based on the image.
The `Dockerfile` uses the Rocker image [`rocker/binder:3.6.3`](https://hub.docker.com/r/rocker/binder), providing R version `3.6.3` with a CRAN mirror timestamp of July 5th 2019.
Download the project files, open a command line in the root directory (where this file is), and run the commands as documented at the end of the `Dockerfile`.
If you have [`repo2docker`](https://repo2docker.readthedocs.io), you can also run `repo2docker .` and use the `--editable` option to edit the workflows.
_The `repo2docker` option is the only way the original authors worked on the analysis to ensure the computing environment is properly managed._
You can most easily achieve it using the included `Makefile`, just run
```bash
make
```
## Files in this repository
- `paper/reproducible-research-at-giscience.Rmd`: The paper manuscript; it uses the data from the directories `results` and `author_analysis`, which is generated by the other Rmd and Jupyter notebooks (see below).
- `paper/reproducible-research-at-giscience-appendix.Rmd`: Appendix for the manuscript with the assessment results table.
- `results/paper_assessment.csv`: Results of manual paper evaluation.
- `results/text_analysis_{topwordstems,keywordstems}.csv`: Results of automated text analysis.
- `results/figure_[...].{pdf,png}`: Figures and plots from text analysis and paper assessment; the plots are also created as part of the manuscript.
- `giscience-reproducibility-assessment.Rmd`: R Markdown document with the visualisations about the assessment of paper reproducibility.
- `giscience-historic-text-analysis.Rmd`: R Markdown document with the text analysis of historic GIScience proceedings.
- `Dockerfile`: A recipe for the computational environment using [Docker](https://en.wikipedia.org/wiki/Docker_(software)).
- `install.R`: R script file executed during creation of the Docker image to install required dependencies.
- `author_analysis/*`: Data, code, and results simple comparison of authors' last names of the compared conferences based on a Jupyter Notebook; the contents of the file `author_counts.csv` are used in the article manuscript.
- `docs/*`: Prerendered HTML files of the analysis documents hosted online at [https://nuest.github.io/reproducible-research-at-giscience/](https://nuest.github.io/reproducible-research-at-giscience/); files can be rendered with `make docs`
## Deposition on Zenodo
This repository is archived on Zenodo: **https://doi.org/10.5281/zenodo.4032875**
The deposited archive was created using the [GitHub-Zenodo-integration](https://guides.github.com/activities/citable-code/) and includes all source files and the appendix as PDF.
You can open the Zenodo deposit directly on Binder: [](https://mybinder.org/v2/zenodo/10.5281/zenodo.4032875/)
## License
The documents in this repository are licensed under a [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).
All contained code is licensed under the [Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/).
The data used is licensed under a [Open Data Commons Attribution License](https://opendatacommons.org/licenses/by/).