This repository contains the necessary data and code to reproduce the analysis and report of our replication attempt, in the context of the CAMARADES Reproducibility Challenge (https://osf.io/z8ut2/overview).

Description

The scripts folder contains the following files:

• 01_Preprocessing.R - This is the main script that prepares the raw data for meta-analysis. It includes loading the necessary R libraries and performing the transformations described by the original authors before analysis, such as selection of comparisons and adjustment for shared controls. It also reshapes the data into wide format, to permit the calculation of standardized mean differences. This script generates a new file data/tidy/df_wide.csv which is the one used in the analysis script.
• 02_Analysis.R - This is the main analysis script, which includes code for the random-effects meta-analysis, subgroup analyses, Egger's regression and forest plot. It also generates the files data/Renv_Rdata and data/small_data.Rdata which are used in the generation of the written report.
• 03_Small_data.R - This script simply loads the files containing the variables required for the written report.

The data folder contains the following files:

• Copy of RIC_infarct volume data_updated.xlsx - the raw data as provided by the authors of the original study
• Renv_Rdata - the versions of the packages used in the analysis, to be referenced in the Rmd report
• small_data.Rdata - numerical variables from the statistical analysis such as the effect size and I^2, to be referenced in the Rmd report
• tidy folder
  • df_wide - the dataset used in analysis in tidy format. This file is generated by running the script scripts/01_Preprocessing.R.
  • team_compRepro_data.csv - the main effect and confidence interval of our replication attempt. These numbers contributed to a visualization in the overall manuscript describing the Reproducibility Challenge and its findings.

The docs folder contains the following files:

• 01_Introduction.Rmd, 02_Methods.Rmd, 03_Results.Rmd, 04_Discussion.Rmd - these are all R markdown files with the different sections that make up the report. They don't need to be ran separately as they are sourced in the main Report.Rmd file (see below).
• apa_short_authors.csl - This is a citation language style file used in rendering the Rmd report, which specifies the citation style, in this case APA short.
• CAMARADES_repro_challenge_report_template.docx - This is a Microsoft Word document specifying the template of the report for the Reproducibility Challenge, as it was provided by the leaders of the initiative. It is sourced in rendering the Rmd report.
• R_references.bib and repro_challenge_SR-SAVI_2024.bib - these are bibliography files containing the list of references (scholarly and R packages) for the written report.

How to generate the report

The report will be generated by executing the following line, which renders the Rmd file into a Word document in the desired template.

rmarkdown::render(here::here("docs","Report.Rmd"))

Contributors

Maria Economou and Torsten Rackoll