Reproducible, flexible and high-throughput data extraction from primary literature: The metaDigitise r package

Joel L. Pick*, Shinichi Nakagawa, Daniel W.A. Noble

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

113 Citations (Scopus)

Abstract

Research synthesis, such as comparative and meta-analyses, requires the extraction of effect sizes from primary literature, which are commonly calculated from descriptive statistics. However, the exact values of such statistics are commonly hidden in figures. Extracting descriptive statistics from figures can be a slow process that is not easily reproducible. Additionally, current software lacks an ability to incorporate important metadata (e.g. sample sizes, treatment/variable names) about experiments and is not integrated with other software to streamline analysis pipelines. Here we present the r package metaDigitise which extracts descriptive statistics such as means, standard deviations and correlations from four plot types: (a) mean/error plots (e.g. bar graphs with standard errors), (b) box plots, (c) scatter plots and (d) histograms. metaDigitise is user-friendly and easy to learn as it interactively guides the user through the data extraction process. Notably, it enables large-scale extraction by automatically loading image files, letting the user stop processing, edit and add to the resulting data-frame at any point. Digitised data can be easily re-plotted and checked, facilitating reproducible data extraction from plots with little inter-observer bias. We hope that by making the process of figure extraction more flexible and easy to conduct, it will improve the transparency and quality of meta-analyses in the future.

Original languageEnglish
Pages (from-to)426-431
Number of pages6
JournalMethods in Ecology and Evolution
Volume10
Issue number3
DOIs
Publication statusPublished - Mar 2019
Externally publishedYes

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