Code for cleaning and merging Siphonaptera taxonomy for the Terrestrial Parasite Tracker
License: Apache License 2.0
R 7.50%HTML 92.50%
tpt-siphonaptera's Introduction
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.
When this taxon was part of the backbone, everything worked as expected. Occurrences with an identification of Hoplopsyllus tenuidigitus could be found with that name and as it was recorded as a synonym of Euchoplopsyllus glacialis (Taschenberg, 1880) it would have been interpreted as that and so could be found using the currently accepted name as well. Everyone would be happy.
So, I cannot really trace what happened to this name or why without a lot more time and access to publications and I also cannot say for certain that the name Hoplopsyllus tenuidigitus Stewart, 1940 is indeed currently represented by Euchoplopsyllus glacialis (Taschenberg, 1880). BUT I do believe that these published associations should be made if anyone is going to discover specimens of interest using any of the names that might be associated with a name used as an identification.
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