Comments (10)
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. :-)
from occ-cube-alien.
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.
from occ-cube-alien.
@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)?
from occ-cube-alien.
@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.
from occ-cube-alien.
@damianooldoni : I have the list of species in an email- I will forward to you now.
from occ-cube-alien.
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:
- Dama dama
- Neovison vison
- Podarcis siculus
- Tamiasciurus hudsonicus
- Orthriophis taeniurus
- 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?
from occ-cube-alien.
@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.
from occ-cube-alien.
@amyjsdavis: The spreadsheet I got has only the ranking_df tab.
from occ-cube-alien.
@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 |
from occ-cube-alien.
Thanks. I will update the file and I will try to make a new European cube with these taxa included.
from occ-cube-alien.
Related Issues (20)
- Baseline datacube at classis level HOT 3
- eea grid code HOT 8
- Aggregate data at species level for broader use HOT 1
- Add GBIF key to name of output datacube HOT 1
- Remove speciesKey from cube_europe
- Save output files as csv instead of tsv HOT 4
- Additional checks for vague date ranges required? HOT 12
- Discard occurrences with unverified identificationVerificationStatus HOT 5
- Update the modelling species list HOT 5
- set seed HOT 3
- Add kingdom to taxonomic compendium
- Simplify workflow using Arrow C++ library in R HOT 1
- error rendering create_db for Belgium HOT 1
- Celastrus : GBIF code changed or inaccurate ? HOT 1
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- Automate updating of occ-cubes using github actions
- Where can I find the be_classes_cube.csv? HOT 2
- Occurrences from new zenodo cube all over the place HOT 8
- Add reference file for taxa included in cube
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from occ-cube-alien.