Published October 8, 2024 | Version v1.0
Software Open

Supporting data and code for: Global meta-analysis of genetic diversity

Authors/Creators

Description

Custom code and supporting data for manuscript: "Global meta-analysis shows action is needed to halt genetic diversity loss"

This repository contains the following supporting data and custom R code for text mining (with example data):

  • Supporting_Data:

    • Supporting Data 1 (bibliography).pdf

      Bibliography for systematic review dataset.

    • Supporting Data 2 (PRISMA).xlsx

      Source data for preferred reporting items for systematic reviews and meta-analysis (PRISMA) steps. Data are provided as an Excel workbook, with a detailed "READ ME" on sheet 1.

    • Supporting Data 3 (systematic review dataset).xlsx

      Source data for systematic review and meta-analysis. Data are provided as an Excel workbook, with a detailed "READ ME" on sheet 1.

    • Supporting Data 4 (WOS advanced search string).pdf

      Web of Science advanced search string.

    • Supporting Data 5 (generation length).xlsx

      Generation length information for unique species in our dataset. Data are provided as an Excel workbook, with a detailed "READ ME" on sheet 1.

  • Text_Mining:

    • TextMining_CustomScripts.R

      Source code (R script) defining custom functions, with example code outlining the use of these functions with a demo data set (found in the subfolder entitled "Batch_1")

    • Batch_1

      Folder containing a test set of five PDF articles to be used as example input for custom R functions. PLOS ONE papers from co-authors have been provided as examples, as their licensing agreement permits redistribution. These papers may not be included in the final manuscript, but they contain genetic metrics, making them suitable for testing the 'genetic metric search' component of the text-mining process.

    • TextMining_Outputs:

      • StartStop_Page_Search.csv

        Output of the "Find.Section.Pg.Nos" custom function. A csv file containing the "start/stop" location for further searching. Note that the page numbers do not match exact numbers in actual pdfs, but are relative to the way in which pdfs are read into R, as described further in the relevant sections of the code.

      • PDFs_Genetic_Diversity_Hits

        Output of the "Metric.Search" custom function. A subfolder containing PDFs of papers where genetic diversity metrics were detected.

      • PDFs_Metric_Hits.csv

        Output of the "Metric.Search" custom function. A csv file listing specific hits for each pdf file name.

System requirements

Text-mining was performed in R v 3.5.2, using the packages pdfsearch v 0.2.2, dplyr v 0.8.0, and stringi v 1.3.1. Detailed instructions for installing R can be found in this link: https://www.r-project.org/ (typical install time = 5-10 minutes). Using the demo data set, the typical run time of the custom functions detailed above is 5 seconds.

We also tested the code using an updated version of R and relevant packages, provided below:

R version 4.3.1 (2023-06-16).

Platform: x86_64-apple-darwin20 (64-bit)

Running under: macOS Ventura 13.6.9

Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Sydney

tzcode source: internal

attached base packages:

  • stats

  • graphics

  • grDevices

  • utils

  • datasets

  • methods

  • base

  • other attached packages: stringi_1.8.3

  • dplyr_1.1.4

  • pdfsearch_0.3.0

loaded via a namespace (and not attached):

  • vctrs_0.6.5

  • knitr_1.45

  • cli_3.6.2

  • xfun_0.42

  • rlang_1.1.3

  • generics_0.1.3

  • glue_1.7.0

  • SnowballC_0.7.1

  • askpass_1.2.0

  • qpdf_1.3.4

  • htmltools_0.5.7

  • tokenizers_0.3.0

  • fansi_1.0.6

  • rmarkdown_2.25

  • evaluate_0.23

  • tibble_3.2.1

  • fastmap_1.1.1

  • yaml_2.3.8

  • lifecycle_1.0.4

  • compiler_4.3.1

  • Rcpp_1.0.12

  • pkgconfig_2.0.3

  • rstudioapi_0.15.0

  • digest_0.6.34

  • R6_2.5.1

  • tidyselect_1.2.0

  • utf8_1.2.4

  • pillar_1.9.0

  • pdftools_3.4.1

  • magrittr_2.0.3

  • tools_4.3.1

  • withr_3.0.0

Files

RobynSh/Meta-Analysis_GeneticDiversity-v1.0.zip

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Additional details

Related works

Is supplement to
Software: https://github.com/RobynSh/Meta-Analysis_GeneticDiversity/tree/v1.0 (URL)