Analysis dataset and statistical outputs for “Global patterns in reported environmental pathways of Phytophthora movement across forest ecosystems”
Description
This dataset accompanies the manuscript “Global patterns in reported environmental pathways of Phytophthora movement across forest ecosystems” and supports a source-balanced synthesis of suspected movement pathways in forest and forest-linked systems. The SM3.2 workbook contains 32,202 harmonised occurrence records with bibliographic provenance, taxonomic and geographic information, publication years, detection status, evidence levels, forest-scope classifications, pathway entries, harmonised pathway categories and cohort eligibility indicators. The strict-primary cohort comprises 16,451 eligible records from 1,574 sources; 2,545 records from 392 sources across 40 countries contain interpretable pathway information. The classification includes 19 atomic pathway elements, five mechanism families and two separately analysed broad-attribution families. Four accompanying Word documents (SM3.3a–SM3.3d) provide statistical outputs 1–13: cohort flow, encoding coverage, pathway rankings, source concentration, temporal and geographic documentation, exact portfolios, taxon–pathway support, sensitivity analyses, influence and stability diagnostics, figure data, analysis readiness and portfolio–source membership. The files support verification and secondary analysis of pathway documentation, source dependence and forest–nursery contrasts. Categories are non-exclusive. Pathway entries describe suspected pathways rather than confirmed transmission events; derived shares and stability intervals do not estimate prevalence, transmission probability or movement risk.
Files
Steps to reproduce
Open the SM3.2 workbook and import the “SM3.2 Analysis Dataset” worksheet, using row 2 as column headers. Consult the manuscript and its Extended Methods (SM3.1) for operational definitions and analytical settings. Select “Strict primary” within “Eligible cohorts” to recover the 16,451 eligible records. For pathway-category analyses, select “Strict primary” within “Cohorts with interpretable pathway encoding” (2,545 records; 392 sources). Retain the full eligible cohort for encoding-coverage denominators. Do not interpret missing pathway values as evidence of pathway absence. Use the supplied atomic elements and pathway families, preserving taxonomic qualifiers and non-exclusive coding. Calculate source-level shares by counting each source once per category. For source-country balancing, calculate within-source country proportions and average equally across sources. Calculate occurrence-weighted shares from interpretable records. Reproduce stability intervals using 5,000 whole-source bootstrap resamples and the linear 2.5th and 97.5th percentiles. Follow the documented cohort-specific seeds and resampling settings. The reported workflow used R 4.3.3 and NumPy 2.3.5 with PCG64. Apply the documented temporal, geographic, portfolio and taxon–pathway summaries, support thresholds, sensitivity analyses and deletion diagnostics. Compare results with outputs SM3.3.1–SM3.3.13 in SM3.3a–SM3.3d. This deposit contains the analysis dataset and numerical outputs; analysis scripts and SM3.1 are not included.