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 submissions, see https://github.com/nuest/reproducible-research-and-giscience (10.5281/zenodo.1227260). Find the preprint and a deposition of this repository via the badges below.
Click the “Binder” button below to open an interactive editing
environment with all required software installed on
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.
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) to
inspect and execute the code for the text analysis and reproduce the
figures as described in Reproduce locally, except
that local installation of required packages is not required.
Use this link to directly open the Jupyter Notebook.
Use this link to directly open RStudio.
Open one of the two R Markdown analysis files (.Rmd) with
RStudio. Then select “Knit
> Knit to PDF” to render the document. If you have errors rendering the
whole PDF, try running each
chunk to
locate the problem or use “Knit to HTML”. Depending on the R Markdown
parameters,
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) and installation of LaTeX
packages if you knit to HTML or run the chunks directly from RStudio.
Install Docker CE 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,
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, 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
makepaper/reproducible-research-at-giscience.Rmd: The paper manuscript; it uses the data from the directoriesresultsandauthor_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.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 fileauthor_counts.csvare used in the article manuscript.docs/*: Prerendered HTML files of the analysis documents hosted online at https://nuest.github.io/reproducible-research-at-giscience/; files can be rendered withmake docs
This repository is archived on Zenodo: https://doi.org/10.5281/zenodo.4032875
The deposited archive was created using the GitHub-Zenodo-integration and includes all source files and the appendix as PDF.
You can open the Zenodo deposit directly on Binder:
The documents in this repository are licensed under a Creative Commons Attribution 4.0 International License.
All contained code is licensed under the Apache License 2.0.
The data used is licensed under a Open Data Commons Attribution License.