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A taxonomic toolbelt for R
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Discrepancy between eol_invasive() and gisd_isinvasive() #321

Closed kgturner closed 10 years ago

kgturner commented 10 years ago

gisd_isinvasive() will find some species (and return data) even when the same species isn't found by eol_invasive(dataset="all"). This is especially weird, because one of the databases included in "all" is gisd. Below is an example using 3 synonyms each of two taxa, both of which are considered invasive (sorry about the layout). For dataset="all" OR "gisd", eol_invasive() finds the 2nd and 5th names in the list. gisd_isinvasive() finds the 1st and 4th.

specieslist <- c("Centaurea maculosa", "Centaurea stoebe", "Centaurea bieberisteinii",

  • "Taraxacum officinale", "Taraxacum sylvanicum","Taraxacum campylodes")

eol_invasive(specieslist , dataset="all") Using default key: Please get your own API key at http://eol.org/users/register Getting data for 20596 names... searched_name 1 Centaurea maculosa 2 Centaurea stoebe 3 Centaurea stoebe 4 Centaurea bieberisteinii 5 Taraxacum officinale 6 Taraxacum sylvanicum 7 Taraxacum campylodes name eol_object_id db 1 Centaurea maculosa NaN all 2 Centaurea stoebe L. 2877020 all 3 Centaurea stoebe subsp. australis (Pancic ex A.Kern.) Greuter 482437 all 4 Centaurea bieberisteinii NaN all 5 Taraxacum officinale NaN all 6 Taraxacum sylvanicum R. Doll 578234 all 7 Taraxacum campylodes NaN all eol_invasive(specieslist, dataset="gisd") Using default key: Please get your own API key at http://eol.org/users/register Getting data for 843 names... searched_name 1 Centaurea maculosa 2 Centaurea stoebe 3 Centaurea bieberisteinii 4 Taraxacum officinale 5 Taraxacum sylvanicum 6 Taraxacum campylodes name eol_object_id db 1 Centaurea maculosa NaN gisd 2 Centaurea stoebe subsp. australis (Pancic ex A.Kern.) Greuter 482437 gisd 3 Centaurea bieberisteinii NaN gisd 4 Taraxacum officinale NaN gisd 5 Taraxacum sylvanicum R. Doll 578234 gisd 6 Taraxacum campylodes NaN gisd gisd_isinvasive(specieslist) Checking species 1 Checking species 2 Checking species 3 Checking species 4 Checking species 5 Checking species 6 Done species 1 Centaurea maculosa 2 Centaurea stoebe 3 Centaurea bieberisteinii 4 Taraxacum officinale 5 Taraxacum sylvanicum 6 Taraxacum campylodes status 1 Centaurea biebersteinii is a biennial or short-lived perennial composite and a very aggressive invader. It has been reported to grow on a wide variety of habitats, especially industrial land, including gravel pits, stockpiles, power lines, grain elevators, railroad, equipment yards, pasture, range, and timbered range. It is often associated with irrigation, preferring areas of high available moisture. It appears best adapted to well-drained, light- to coarse-textured soils that receive summer rainfall. Seeds may germinate over a wide range of soil depths, soil moisture content and temperatures. Dispersal is generally passive as seeds are shaken from drying capitula. Movement over greater distances requires transport by rodents, livestock, vehicles, or hay or commercial seed.; (herb); Common Names: gefleckte Flockenblume, gewöhnliche Rispen-Flockenblume, spotted knapweed; Synonyms: Acosta maculosa auct. non Holub, Centaurea maculosa auct. non Lam. 2 Not in GISD 3 Not in GISD 4 Taraxacum officinale is one of the most wide-spread weeds of North America, Asia and Europe. On French sub-Antarctic islands, where Taraxacum officinale has been introduced, the disappearance of native plants over wide areas, due to the impact of rabbits and global warming, coincided with a demographic explosion of Taraxacum officinale and other introduced plants, resulting in the homogenisation of plant communities.; (herb); Common Names: blowball, common dandelion, dandelion, faceclock , pissenlit vulgaire 5 Not in GISD 6 Not in GISD

sckott commented 10 years ago

Thanks @kgturner - I'll have a look

sckott commented 10 years ago

Hmm, first thought is that the gisd_invasive() function doesn't go through EOL, but scraped data from the Global Invasive Species Database http://www.issg.org/database/welcome/

I imagine it's quite possible EOL doesn't have updated data from GISD on their servers

We should probably find out how often EOL updates their GISD dataset

sckott commented 10 years ago

@kgturner Looks like it's just about when the datasets are updated

I can't find anything on the GISD webpage about how often it's updated, but given your experience, it seems more often than what EOL has for them.

I'll get in touch with EOL and see if they can update more often. But other than that, I guess we can't do much. I'll also add these notes about how often updated to the docs for eol_invasive