There were three major phases to this study which are pertinent for data storage and collection.
1. The first phase was a quantitative review in which the literature was systematically surveyed, assessed for inclusion, and relevant data extracted. This process resulted in the dataset "Extraction_Initialize.csv", which contains metadata from all studies initially considered for data collection. In some cases, studies were later deemed inappropriate and excluded from subsequent phases, but their metadata remains in this file. Once data collection was completed for the 102 studies that met the inclusion criteria, all phenotypic data—used in the second phase—were compiled into a single .csv file, "Meta_data_checked.csv".
2. The second phase involved data analysis, where the phenotypic data and metadata were imported into R, formatted, and processed using a for-loop to estimate CovGE and ΔG×E for each phenotype independently. This loop fully implements CovGE estimation following the methods outlined in Albecker et al. (2022) and also generates confidence intervals for CovGE and p-values for ΔG×E. This analysis was executed in lines 1–220 of the "CovGE_Meta_Analysis.R" script, with essential functions housed in the companion script "CovarianceDataFunctions.R". Results of this analysis were saved as, "Meta_output_Nov27_2024.csv"
3. The third phase involved testing the questions/hypotheses outlined in the manuscript (e.g., Is CnGV or CoGV more prevalent in nature?). These analyses were conducted in the "CovGE_Meta_Analysis.R" script, following the conclusion of the primary analysis on Line 220. This phase also included all plotting and formatting code. Any modifications made to plots in PowerPoint were documented with notes. All code is fully annotated for clarity and reproducibility.
Files in this dataset:
1. Code file - "CovGE_Meta_Analysis.R" - R code including all analyses, data formatting, and plotting. See phase 2 and 3
2. Code file - "CovarianceDataFunctions.R" - R companion code storing all essential functions for analyses. See phase 2 and 3. Compiled dataset with the extracted phenotypic, genotypic, and environmental data for each study included in quantitative review. See Phase 1 in the description of Contents for additional details.
