Taxa standardization

[jaxinewolfe]

Create a taxonomic database from the existent species table. Once established, a post-processing workflow will be created to recognize when new taxa have been added to the synthesized species table and update the database.

[jaxinewolfe]

Workflow Notes

Taxonomic functions:

• resolveTaxa(): Resolves misspellings using a Global Name Resolver (taxize). Documentation of misspellings is retained in the database. This will be a curation function going forward so that misspellings can be nipped in the bud.

In Question:

• classifyTaxa(): this function would automate the classification of taxonomic level for any given taxa (i.e. code_type in our database). The drawback is that taxize::classification() is not always reliable to pull the correct classification (depending on the database you choose) so we might be better off continuing to manually classify code_type.
• Habitat and code_type are manually classified for each species_code in this table. I'd like to merge this with the database table so that we can stick to one species lookup table for post-processing. This will be especially informative for the assignment of core-level habitat. Should the addition of habitat and code_type to the species table be a curation or post-processing step?

[jaxinewolfe]

@HolmquistJ When I created the taxa database, I ran across four species that weren't recognized by any data source that and I can't identify them either. I'm thinking the genus or species are mismatched in the first three:

• Avicennia corniculatum (Sanderman)
• Schoenoplectus montevidensis (Krauss 2018)
• Amphibolis australis (Fourqurean)
• Arrow arum => should this be Peltandra virginica? (Merill_1999 => Holmquist 2018)

Do you have an idea of what these should be?

[jaxinewolfe]

Updated:

• Aegiceras corniculatum? If its Avicennia sp. of mangrove though it could be any number of species.
• Lantana montevidensis
• Mix up of Amphibolis griffithii or Phrag?

[HolmquistJ]

I think if there is no match in the database, you need to let the author's classification go through.

[jaxinewolfe]

@HolmquistJ Here are the taxa in the species table which are still unresolved. Some of these classifications are more descriptive than taxa specific and might belong in the habitat or vegetation_class attributes instead. Most of the code_types are getting classified correctly in the habitat assignment script, which is good.

index	study_id	site_id	species_code	code_type
1	Vincent_and_Dionne_2023	Webhannet	High Marsh	description
2	Vincent_and_Dionne_2023	Drakes Island	High Marsh	description
3	Vincent_and_Dionne_2023	Little River	High Marsh	description
4	van_Ardenne_et_al_2018	Pt Carron	unknown	Genus species
5	Turck_2014	none	none	Genus
6	Turck_2014	text	text	Genus
7	Osland_et_al_2016	Grand_Bay	unvegetated	description
8	Osland_et_al_2016	Lower_Laguna_Madre	unvegetated	description
9	Osland_et_al_2016	Lower_Laguna_Madre	Algal Mat	description
10	Osland_et_al_2016	Mission_Aransas_Bay	unvegetated	description
11	Osland_et_al_2016	Mission_Aransas_Bay	Algal Mat	description
12	Osland_et_al_2016	San_Antonio_Bay	unvegetated	description
13	Osland_et_al_2016	Upper_Laguna_Madre	unvegetated	description
14	Osland_et_al_2016	Upper_Laguna_Madre	Algal Mat	description
15	Osland_et_al_2016	Upper_Laguna_Madre	Wrack	description
16	Osland_et_al_2016	Galveston_Bay	unvegetated	description
17	Osland_et_al_2016	Galveston_Bay	Algal Mat	description
18	Osland_et_al_2016	Weeks_Bay	unvegetated	description
19	Osland_et_al_2016	Lake_Pontchartrain	unvegetated	description
20	Osland_et_al_2016	Lake_Pontchartrain	Wrack	description
21	Osland_et_al_2016	Ten_Thousand_Islands	unvegetated	description
22	Osland_et_al_2016	Ten_Thousand_Islands	submerged aquatic vegetation	description
23	Osland_et_al_2016	Ten_Thousand_Islands	Surface Algae	description
24	Osland_et_al_2016	Tampa_Bay	unvegetated	description
25	Osland_et_al_2016	Tampa_Bay	Wrack	description
26	Nahlik_and_Fennessy_2016	NWCA11-2447	Forb spp.	description
27	Lafratta_et_al_2018	False bay	previously vegetated soils	description
28	CRMS_Database	NA	Mix	description
29	CRMS_Database	NA	Swamp	description
30	Marba_unpublished	Bolinao	mixed	description
31	Agawin_et_al_1996	Cape_Bolinao	Thassia hemprichii	Genus species