Collaboration and term usage dynamics in agricultural buffer strip research

This repository contains the code associated with the paper: Young, S., Haddaway, N. R., Nakagawa, S., Lagisz, M., & Callaghan, M. W. (2021). Collaboration and term usage dynamics in agricultural buffer strip research: a research weaving protocol. Ecological Solutions and Evidence, 2, e12084. https://doi.org/10.1002/2688-8319.12084

File Overview

Code:

1. Filename: publicationsLENSpreprocessing.RMD
   Short description: R Markdown file containing code for cleaning and preprocessing Lens.org data for further analysis.

2. Filename: publicationsLENSigraph.RMD
   Short description: R Markdown file containing code for constructing co-authorship network in igraph and analyzing co-authorship network attributes and sub-communities.

3. Filename: publicationsLENSbibcouple.RMD
   Short description: R Markdown file containing code for analysis of bibliographic coupling clusters related to functional roles, publication years, geographic location and buffer strip terminology usage.

4. Filename: topic-model-lens.ipynb Short desicription: Python script for identifying topics based on studies included in the systematic map.

5. Filename: topic-model.ipynb Short desicription: Python script for identifying topics based on studies included in the systematic map.

6. Filename: bibcouple.ipynb Short desicription: Python script for constructing bibliographic coupling network and visualizing network clusters and topics.

7. Filename: heatmaps.ipynb Short desicription: Python script used for generating heatmaps to examine topic models and functional roles studied in papers.

Data/

Directory containing the following data files: 1. Filename: 20201215EGMNetall-articlesclean.csv
Short description: Contains complete list of all studies included in the original systematic map by Haddaway et al. File used to query Lens.org.

1. Filename: LENS_dataframe.RData
   Short description: RData file containing output from API query of Lens.org of studies included in systematic map. Contains 1073 rows.

2. Filename: LENSdataframecleaned.RData
   Short description: Cleaned version of LENS_dataframe.RData. Duplicate records were removed and author names and ids cleaned.

3. Filename: recorddfdata.authors.idscleaned.csv Short description: Unnested and cleaned author data from LENSdataframe_cleaned.RData.

4. Filename: recorddfdata.authors.aff_cleaned.csv Short description: Unnested and cleaned author data including cleaned country affiliations.

5. Filename: 13750-2018-126-MOESM6-ESM-dedup-1019-outcome.csv Short desription: Original systematic mapping data including bibliographic data and manually extracted data related to study charactistics. Includes a column "alloutcomesgroup", which is a cleaned and grouped version of the original data extracted on outcomes at the study level.

6. Filename: bc_clustered.csv Short description: List of studies included in the bibliographic coupling network and their associated assigned cluster number.

7. Filename: sysmap.lensid.abstractbibcouple.csv File used to generate heatmaps with functional roles studied (variable name: alloutcomes_group).

8. Filename: 20211019rwbslens-export.csv File used to generate bibliographic coupling network with references from studies (variable name: References).

Plots/

Directory containing plots found in manuscript figures. See file names and paper for more information about each plot.

tm-results/

Directory containing topic modelling features, parameters and heatmap plots.

bibcouple-results/

Directory containing bibliographic coupling figure versions generated in bibcouple.ipynb.