fungarium

fungarium provides R functions to retrieve and curate MyCoPortal sporocarp records and quantify ecological traits (e.g., habitat, host, substrate, fire association) to analyze taxonomic, geographic, and temporal trait patterns.

Key Features:

• Efficient Data Access: Downloads complete datasets from the Mycology Collections Portal (MyCoPortal) into R for programmatic access.
• Enhanced Data Quality: Performs taxonomic reconciliation (confirming or updating taxon names), corrects misspellings, and standardizes location names to improve record reliability.
• Trait Analysis Capabilities: Assigns and analyzes ecological traits such as habitat, host, substrate associations, and temporal changes to investigate taxonomic, geographic, and temporal patterns.
• Case Study — Fire Association: Calculates fire-associated enrichment factors as the ratio of fire-associated records to total records and demonstrates taxon-level differences consistent with existing literature.
• Addressing Confounding Factors: Identifies potential confounders including sampling bias in MyCoPortal and limitations in external datasets such as Monitoring Trends in Burn Severity.

Scientific Applications:

• Fungal trait ecology: Quantifying how habitat, host, substrate, and fire associations vary across taxa, space, and time using fungarium-curated MyCoPortal data.
• Fire-ecology assessment: Evaluating taxon-specific associations with fire through enrichment factor calculations.
• Data quality and bias assessment: Detecting sampling bias and dataset limitations that affect geographic and temporal trait inference.

Methodology:

Programmatic download of MyCoPortal datasets into R; taxonomic name confirmation and misspelling correction; standardization/correction of location names; assignment of trait labels (including fire association); calculation of enrichment factors as the ratio of fire-associated to total records; and assessment of sampling bias and external dataset limitations (e.g., Monitoring Trends in Burn Severity).