tpt-siphonaptera

Code for cleaning and merging Siphonaptera taxonomy for the Terrestrial Parasite Tracker

Taxonomy Cleaning for Terrestrial Parasite Tracker Taxonomy

The R scripts in this repository were designed for cleaning taxonomic classifications received from various sources for the Terrestrial Parasite Tracker Thematic Collections Network (TPT) Taxonomy Reource. Specific scripts were created for transforming data from each resource as well as merging the resources for review.

lib_func.r

Loads all needed libraries and functions for other scripts. Should be run before any other scripts are run.

Lewis_transform.r

Transforms BYU Lewis list as updated provided by Mike Hastriter to Darwin Core

Input

File Name	Description
Lewis World Species List MMM DD YYYY.xlsx	Lewis database as provided by Mike Hastriter at BYU
Lewis_reviewed.xlsx	Names from Lewis_name_review output that have been corrected and are to be returned to the working file
Lewis_removed.xlsx	Names from Lewis_name_review output that have been removed from the working file
tpt_dwc_template.xlsx	Template (no data) for Darwin Core file

Output

File Name	Description
Lewis_duplicates.csv	Names removed from the original data because they were duplicates
Lewis_name_review.csv	Names removed from the original data that need review before adding back or removing (see inputs above)
Lewis_non_DwC.csv	Name ID plus all non Darwin Core fields from original file
Lewis_DwC.csv	Name ID plus all applicable Darwin Core fields

NMNH_transform.r

Transforms Smithsonian (NMNH) list of taxa to Darwin Core

Input

File Name	Description
NMNH_Siphonaptera.xlsx	Catalog of fleas from the Smithsonian
NMNH_reviewed.xlsx	Names from NMNH_name_review output that have been corrected and are to be returned to the working file
tpt_dwc_template.xlsx	Template (no data) for Darwin Core file

Output

File Name	Description
NMNH_need_review.csv	Names removed from the original data that need review before adding back or removing (see inputs above)
NMNH_non_DwC.csv	Name ID plus all non Darwin Core fields from original file
NMNH_DwC.csv	Name ID plus all applicable Darwin Core fields

FMNH_transform.r

Transforms Field Museum (FMNH) list of taxa to Darwin Core

Input

File Name	Description
FMNH_Siphonaptera.xlsx	List of flea names from the Field Museum
FMNH_reviewed.xlsx	Names from NMNH_name_review output that have been corrected and are to be returned to the working file
tpt_dwc_template.xlsx	Template (no data) for Darwin Core file

Output

File Name	Description
FMNH_need_review.csv	Names removed from the original data that need review before adding back or removing (see inputs above)
FMNH_non_DwC.csv	Name ID plus all non Darwin Core fields from original file
FMNH_DwC.csv	Name ID plus all applicable Darwin Core fields

CoL_transform.r

Transforms Catalogue of Life (CoL) download to Darwin Core

Input

File Name	Description
CoL_DwC.xlsx	Flea names from Catalogue of Life download
tpt_dwc_template.xlsx	Template (no data) for Darwin Core file

Output

File Name	Description
CoL_DwC.csv	Name ID plus all applicable Darwin Core fields

merge_taxotools.r

Transforms Global Biodiversity Information Facility (GBIF) download and all ofther Darwin Core files to taxotools format, then merges them and generates a checklist for expert review

Input

File Name	Description
Lewis_DwC.csv	Output of Lewis_transform.r
NMNH_DwC.csv	Output of NMNH_transform.r
FMNH_DwC.csv	Output of FMNH_transform.r
CoL_DwC.csv	Output of CoL_transform.r
GBIF_Siphonaptera.xlsx	Flea names from GBIF download (already in DwC format, but still transformed a bit in this script)

Output

File Name	Description
problems.csv	Names that could not be merged and need review
taxo_siphonaptera.csv	Merged list of names
Flea_taxolist.html	Checklist of merged names for expert review

arctos_upload_transform.r

Transforms Darwin Core files to Arctos hierarchical tool upload format (awaiting final list to create transform)

Input

File Name	Description
Arctos_upload.csv	Template (no data) for Arctos upload

Output

File Name	Description

Usage

Information from a source may need to be run through the appropriate script multiple times. Any change to a primary source will require re-run and a new merge.