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ropensci / spocc

Species occurrence data toolkit for R
https://docs.ropensci.org/spocc
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occ2df with coordinate uncertainty and occurrence status #243

Open AMBarbosa opened 2 years ago

AMBarbosa commented 2 years ago

Hi! I find the 'occ2df' function very useful, but it misses one particularly important column to me: "coordinateUncertaintyInMeters" (in GBIF), or "positional_accuracy" (in iNat), etc. Is it possible to include it, maybe after homogenizing it across the datasets where such a column is available? This is important for the cleaning procedure downstream, to eliminate records with excessive spatial uncertainty for the target analysis.

AMBarbosa commented 2 years ago

Another very important column to include would be "occurrenceStatus", which states whether the species was recorded PRESENT or indeed ABSENT at each site.

hannahlowens commented 2 years ago

Thanks, @AMBarbosa! These and a few other columns are on the "To Do" list (e.g. observation date). The challenge is identifying equivalent columns in all data source search results.

AMBarbosa commented 2 years ago

Hi, any news on this? I'm sorry to insist, but leaving out especially the "occurrenceStatus" column renders occ2df essentially useless (which is a shame, because it would be incredibly useful otherwise), or even dangerous if the user isn't aware that several points may actually represent ABSENT species... There should at least be a clear warning about this in ?occ2df. Thanks!

hannahlowens commented 2 years ago

Hi! Thanks for following up. It's still on the "To Do" list, but I haven't gotten there yet. I heartily agree uncertainty and occurrence status are important fields, and barring that, a note of caution when the function is implemented. The pain points are 1) identifying the relevant fields in all the databases spocc searches (the fields have different names in different databases, so this isn't trivial) and 2) not enough hours in the day.

If you are willing and able to help with identifying the relevant fields in the different databases, I'll be able to get to this faster, but otherwise, I appreciate your patience.