Using aggregated field collection data and the novel r package fungarium to investigate fungal fire association

Hunter J. Simpson, Jonathan S. Schilling

Research output: Contribution to journalArticlepeer-review


Understanding which fungi exhibit certain ecological traits, such as habitat, host, or substrate associations, and knowing how these traits change across space and time can provide invaluable insight into the roles fungi play in their respective ecosystems. Archived sporocarp data, such as the collection and observation records accessible through the Mycology Collections Portal (MyCoPortal), are well suited for trait investigations, since these records circumvent the need for field work, are geographically and temporally diverse, and often have detailed and trait-relevant environmental metadata. However, there are inefficiencies and inadequacies in the MyCoPortal online interface that affect data set generation and trait searching, and many of the available records have outdated or misspelled taxon names as well as misspelled location names. Thus, we created the r package fungarium, which enables the efficient download of complete MyCoPortal data sets from within the R environment, enhances the identification of trait-relevant records, confirms or updates taxon names while also accounting for spelling errors, and fixes misspelled location names. Utilizing this package and MyCoPortal data, we demonstrated methods for analyzing taxonomic, geographic, and temporal patterns in ecological traits, using fire association as an example. We found that fire association, which was quantified via fire-associated enrichment factors (fire-associated records/total records), differed substantially between taxa, and these differences were qualitatively supported by existing literature, as hypothesized. Sampling bias within the MyCoPortal data and limitations of the burned acreage data set used (i.e., Monitoring Trends in Burn Severity) were identified as confounding factors in our geographic and temporal analyses, as evidenced by the unexpected lack of correlation between fire association and burned acreage on county and year bases. However, both confounding factors likely depend on the trait analyzed and external data set used. Overall, the fungarium package and associated methods presented here effectively enable the use of archived sporocarp data for future ecological trait studies.

Original languageEnglish (US)
Pages (from-to)842-855
Number of pages14
Issue number4
StatePublished - 2021

Bibliographical note

Funding Information:
Support provided at the University of Minnesota from a Department of Bioproducts and Biosystems Engineering (BBE) Graduate Student Fellowship and from the Biocatalysis Initiative in the Biotechnology Institute.

Publisher Copyright:
© 2021 The Mycological Society of America.


  • Biogeography
  • MyCoPortal
  • citizen science
  • ecology
  • specimens
  • taxonomy
  • traits

PubMed: MeSH publication types

  • Journal Article


Dive into the research topics of 'Using aggregated field collection data and the novel r package fungarium to investigate fungal fire association'. Together they form a unique fingerprint.

Cite this