This repository contains the data, code and other materials used in the following study:
Francesca Santostefano*, Maria Moiron*, Alfredo Sánchez-Tójar*, David N. Fisher*. In Press. Indirect genetic effects increase the heritable variation available to selection and are largest for behaviours: a meta-analysis. Evolution Letters.
*All authors contributed equally to this work
The preprint is available here
The repository consists of an Rproject (meta-analysis_IGEs.Rproj) with 6 scripts and 3 folders containing the data either needed to run these scripts or created by the scripts, including the figures. For a detailed description of all the files, please see below. For any further information about this repository, please contact: Alfredo Sánchez-Tójar, email: [email protected].
Scripts:
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001_systematic_review.R : used to import the results of the systematic literature review conducted in Web of Science and Scopus.
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Input: Web of Science and Scopus keyword search, and the 8 .bib files corresponding to the snowballing search
- Web of Science keyword search results: WoS_IGEs_search.bib
- Scopus keyword search results: Scopus_IGEs_search.bib
- Snowballing search results: 8 .bib files found here
- Deduplicated list of unique references to be formatted for importing into Rayyan
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Output:
- Preliminary list of unique references for further deduplication outside R.
- Deduplicated full reference list to be imported into Rayyan for the title-and-abstract screening
- R session information for reproducibility purposes
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002_fulltext_screening.R : used to import the results of the title-and-abstract screening conducted using Rayyan and to generate the database needed to proceed with the full-text screening phase.
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Input:
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Output:
- Four full-text screening subsets (as .xlsx files) including the list of references assigned to each of the 4 observers. Files available here
- R session information for reproducibility purposes
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003_data_extraction.R : used to import the results of the full-text screening and to generate the databases needed to proceed to the data extraction phase.
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Input:
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Output:
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004_dataset_cleaning.R : used to clean the meta-analytic dataset and generate the version for the analyses that is imported by 005_data_analysis.r.
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Input:
- Four datasets with the full data extraction of each of the 4 observers. The four files are .csv and their name starts with 'Data from papers'. All available here)
- Final list of studies included after full-text screening and using animal models
- List of references created by this script before contacting authors, edited outside R, and imported back to be filled after having contacted the authors
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Output:
- List of references before contacting authors
- Full list of references with data, including data obtained by author correspondence. This list will be imported by 005_data_analysis.r for the analyses
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005_data_analysis.r : used to perform all the analyses.
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Input:
- Final dataset for analyses: the metadata providing a description for each of the variables is available here
- Taxonomic data extracted from the Open Tree of Life created by this script and then imported for reproducibility purposes
- Tree file created by this script and then imported for reproducibility purposes
- Phylogenetic correlation matrix created by this script and then imported for reproducibility purposes
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Output:
- Taxonomic data extracted from the Open Tree of Life using the function 'tnrs_match_names()'
- Tree file
- Phylogenetic correlation matrix
- Meta-analytic and meta-regression models. All available as .RData here and will be imported by 006_figures.r for generating the figures.
- Model-specific datasets. All available as .csv here and will be imported by 006_figures.r for generating the figures.
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006_figures.r : used to generate the all figures included in the main text and the supplementary materials (except Figure 1 from the main text).
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Input:
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Output:
- All figures included in the main text and the supplementary materials (except Figure 1 from the main text)
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Folders:
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- systematic_search: contains 2 .bib files imported by 001_systematic_review.R
- snowballing: contains 8 .bib files imported by 001_systematic_review.R
- title_and_abstract_screening: containing the list of unique reference list with title-and-abstract decisions
- fulltext_screening: containing all files generated by 003_data_extraction.R as well as the final list of references with all the full-text screening decisions
- data_extraction: containing all files generated by 003_data_extraction.R
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data: contains all data files necessary for the following three scripts: 004_dataset_cleaning.R, 005_data_analysis.r and 006_figures.r
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figures: contains all figures generated by 006_figures.r and included in the main text and the supplementary materials (except Figure 1 from the main text)