Add PRA species to modelling taxa for European occurrence cube about occ-cube-alien

[amyjsdavis]

Thanks! In the meantime, I am cleaning up my script and will it to Github so you (and everyone else) can see what the heck I have been doing. :-)

[amyjsdavis]

OK, but Sonia needs these maps ASAP, so I don't want the cube to be a bottleneck. The EU cube is a nice addition,in that it saves me a step, but not necessary to run the models or be FAIR. The data downloaded from GBIF is saved and documented using TriAS  procedures that you and Peter developed. In addition, I already have to initiate a global download  of GBIF data for each species in order to make the global SDM.  I feel that my steps already follow FAIR principles. It seems an unnecessary step to have to put the data in the cube first prior to running the SDMs.  The point of my modelling flow is that anyone can make the risk maps using the GBIF taxon id and not have to feed in intermediate processed occurrence data.

[timadriaens]

@amyjsdavis @DiederikStrubbe I understand that the cube is not needed for the risk models, especially if you calibrate them on a global dataset. In terms of following FAIR principles: perhaps what you mean is that the handling of source data and model outcome is treated FAIRly by documenting and zenodo publication etc. However, I would currently have no clue as to where to start making the risk maps for any given species using the gbif taxon (for now) - which is what I would like to for several species I am interested in. For that, I would effectively need the code that produces them and it would have to be described, added to the repo, reviewed by Damiano and others who can get it bug-free and up and running to provide for anyone to use it. Without it, also, the models frankly remain a bit of a black box to us. Clearly, exchanging on intermediate products has been beneficial for the scientific quality in other parts of TrIAS such as for the indicator workflows. The whole point of TrIAS is to open up the entire workflow, including the code producing the models. Running them on the batch of species to be risk assessed this year is of course fine, but the eventual goal is to have a robust code that can handle doing the same thing for any of the 2800+ species on the unified checklist, and by anyone who needs it. Of course I understand that opening up code that you are still finetuning and working on can feel uncomfortable, but the team is really there to help you. Brief: can you add it to your risk modeling repo (or ask Damiano to do that)?

[amyjsdavis]

@timadriaens @damianooldoni I have realize my code not being on GitHub is becoming problematic and it has been on my to-do list .I have no reluctance sharing our code, I will make it a priority. The hold back is that several ancillary datasets that also need to be shared and have metadata etc in order to actually run the code. In the interest of getting the maps done, I have delayed this until now.

[amyjsdavis]

@damianooldoni : I have the list of species in an email- I will forward to you now.

[damianooldoni]

Thanks @amyjsdavis. From your email:

It is my understanding that all the species highlighted are priority and we are starting with plants first.

Indeed, I have just now checked the highlighted species:

1. Dama dama
2. Neovison vison
3. Podarcis siculus
4. Tamiasciurus hudsonicus
5. Orthriophis taeniurus
6. Pelophylax ridibundus

But this species are already in modelling_species.tsv! So you have already a cube at European level for these species... Or do I miss something?

[amyjsdavis]

@damianooldoni : My apologies I've made a mistake about the highlighting. It is all the species present on the "species selection for PRA-ing" tab, highlighted or not.

[damianooldoni]

@amyjsdavis: The spreadsheet I got has only the ranking_df tab.

[amyjsdavis]

@damianooldoni : I think it got dropped along all the forwards. I have sent you a different link. :) Here are the species:

taxonKey	spn
5220136	Dama dama
5219380	Mephitis mephitis
2440954	Cervus nippon
2437619	Dolichotis patagonum
2437282	Tamiasciurus hudsonicus
2437397	Callosciurus prevostii
7190901	Graptemys pseudogeographica pseudogeographica
6157050	Graptemys pseudogeographica kohnii
9185677	Podarcis siculus
2455523	Orthriophis taeniurus
2426640	Pelophylax bedriagae
2498110	Anas sibilatrix
2498388	Aix galericulata
2498387	Aix sponsa
2891783	Impatiens balfourii
2891774	Impatiens capensis
2891782	Impatiens parviflora
2891770	Impatiens glandulifera
2882849	Vaccinium corymbosum
7777960	Vaccinium macrocarpum
7501634	Rosa multiflora
3003709	Rosa glauca
9202318	Symphyotrichum lanceolatum
3151618	Symphyotrichum novae-angliae
3151558	Symphyotrichum novi-belgii
3082244	Cornus sericea
8421432	Cornus sanguinea hungarica
3663237	Cornus sanguinea australis
2715482	Cyperus eragrostis
2716226	Cyperus esculentus
2992543	Rubus laciniatus
2993761	Rubus spectabilis
5281901	Campylopus introflexus
4559541	Sinanodonta woodiana
8190231	Corbicula fluminea
5189032	Corbicula fluminalis
9291405	Massylaea vermiculata
8745918	Deroceras invadens
5192470	Potamopyrgus antipodarum
2115692	Balanus tintinnabulum
2225646	Callinectes sapidus
5178057	Caprella mutica
2287249	Ensis directus
2225776	Eriocheir sinensis
2225772	Hemigrapsus sanguineus
4382841	Hemigrapsus takanoi
7820753	Magallana gigas
2501248	Mnemiopsis leidyi
2287076	Mytilopsis leucophaeata
2224970	Palaemon macrodactylus
5192470	Potamopyrgus antipodarum
2227663	Rhithropanopeus harrisii

[damianooldoni]

Thanks. I will update the file and I will try to make a new European cube with these taxa included.