asreview / paper-depression-brouwer-simulation-ATD

Scripts for the simulation study obtaining the average time to discovery performed on the Depression-data from the systematic review by Brouwer et al. (2019)

Scripts for simulation study on obtaining average time to discovery

This repository contains the scripts for a simulation study performed on data from the systematic review by Brouwer et al. (2019).

The simulation study has the following characteristics:

• The number of runs is equal to the number of inclusions in the dataset;
• Every run starts with 1 prior inclusion and 10 prior exclusions;
• The prior inclusion is different for every run, e.g. all inclusions in the data are used as a prior inclusion once;
• The 10 prior exclusions are the same for every run, and they are randomly sampled from the dataset.

Installation

The scripts in this repository require Python 3.6+ and R. Install the dependencies with (in the command line):

# install required software (such as ASReview)
pip install requirements.txt
Rscript install.R

Data

The systematic review data used for this study can be found on the Open Science Framework. Download the file brouwer_deduplicated.csv and put it in the /data folder.

Execute simulation study

To reproduce the results presented in this study, run the following in your terminal:

# run all simulations
sh run_all.sh

Extract results

Extract the results from the simulation output by executing the following in your CLI:

Rscript scripts/extract_simulation_results.R

The output (in the folder output/) consists of

• All inclusions in the dataset, ordered by their time to discovery - the time_to_discovery.csv file. The column row corresponds to the position of the inclusion in the original dataset. Note that the position starts at 1;
• A table with WSS and RRF values for every run - the wss_and_rrf_values.csv file;
• A plot with recall curves for all runs of this simulation study - the recall.png file.

License

The content in this repository is published under the MIT license.

Funding

This project is funded by a grant from the Centre for Urban Mental Health, University of Amsterdam, The Netherlands

Contact

For any questions or remarks, please send an email to the ASReview-team or Marlies Brouwer.

References

Brouwer, M. E., Williams, A. D., Kennis, M., Fu, Z., Klein, N. S., Cuijpers, P., & Bockting, C. L. H. (2019). Psychological theories of depressive relapse and recurrence: A systematic review and meta-analysis of prospective studies. Clinical Psychology Review, 74, 101773. https://doi.org/10.1016/j.cpr.2019.101773