The R script in this repository was designed for cleaning taxonomic classifications received from various sources for the Terrestrial Parasite Tracker Thematic Collections Netowrk (TPT) Taxonomy Reource.

Input is required to be csv and is expected to include at least the following columns:

• kingdom
• phylum
• class
• order
• family
• genus
• species (specific epithet)
• taxon Author name (may be combined with or separate from published year)
• taxon published year

Other information may be included in the file, including ranks between the standard ranks listed above and subspecific epithets. NOTE All taxonomy fields are expected to include a single term, "species" is really "specific epithet" and "subspecies" is really "infraspecific epithet".

Running the script will produce the following outputs in csv:

Information from a source may need to be run through the script multiple times. We suggest that after the first pass, all output that requires review is assessed and any necessary changes incorporated into the taxa_no_issues.csv file which should be run through the script a second time. Repeat this process until there are no longer rows in taxa_need_review.csv, or duplicates.csv and it is certain that all items in suggested_adds.csv, higher_taxa_not_used.csv and similar_names.csv are reasonable. The final product in taxa_no_issues.csv will be added to the TPT Taxonomy resource.