Nieuwe input voor indicators implementeren

[SanderDevisscher]

Momenteel worden de grafieken voor de invasieven indicatoren gevoed door de Alien species checklist. Deze checklist is stale, wordt niet meer upgedated, en moet dus vervangen worden door een levende checklist (of checklists).

In het vervolg van de alien species checklist ligt het Trias - project waarin een pipeline opgemaakt werd om meerdere checklists op gbif te raadplegen en de info erin te aggregeren.

Ik zal proberen de input voor de indicator "Trend uitheemse diersoorten in verschillende biotopen" om te schakelen naar van de alien species checklist naar de pipeline.

[damianooldoni]

As the final Belgian unified checklist pipeline is getting ready (review is still needed), we can use the pipeline _build_checklist_indicators.Rmd from trias-project repo@branch trias-project/pipeline@pathways, which is still useful because it has been used for writing the checklist-based indicator functions indicator_total_year(), indicator_introduction_year() and get_table_pathways() in trias-project/trias@add_functions_checklist_indicators package. Such functions will be part of master once the unified checklist pipeline is ready.

[damianooldoni]

The unified checklist is published on GBIF, see link. However, locality = "Belgium" for all taxa. In other words, information at region level is lost and we cannot filter on locality: Flemish Region. The main reason to do so was homogeneity: not every dataset contains distribution information at regional level.

I investigated it a little more. Here below some results and some ideas about solving this issue.

Checklist at national level

The following three checklists are at national level, so we "loose" the following amount of introduced taxa if we try to filter for Flanders:

dataset	n_taxa
Registry of introduced terrestrial molluscs in Belgium	21
Catalogue of the Rust Fungi of Belgium	13
RINSE - Pathways and vectors of biological invasions in ...	147

We could:

1. ask maintainers of the three datasets mentioned above to assess the presence of the taxa at regional level
2. republish these checklists

WRiMS

The dataset World Register of Introduced Marine Species (WRiMS) doesn't contain any reference to Flemish Region, however some localities could be linked to Flanders: Spuikom, Oostende Harbour, Nieuwpoort Harbour, port of Bruges-Zeebrugge, Zeebrugge, Oostende, Koksijde, Baai van Heist, Blankenberge Harbour,Bredene, De Panne, Belgian Coast, Haven van Antwerpen, Kanaal Gent - Terneuzen, Port of Ghent, Knokke-Heist, Coastal Polders.
I would exclude following localities: Belgian part of the North Sea, Belgian Exclusive Economic Zone.

Checklists with information at regional level

The following datasets contain information at regional level so we can already know how many species are in Flemish region 👍

title	in_flanders	n_taxa_flanders
Ad hoc checklist of alien species in Belgium	FALSE	59
Ad hoc checklist of alien species in Belgium	TRUE	208
Checklist of non-native freshwater fishes in Flanders, Belgium	TRUE	25
Checklist of non-native freshwater fishes in Flanders, Belgium	FALSE	0
Inventory of alien macroinvertebrates in Flanders, Belgium	TRUE	73
Inventory of alien macroinvertebrates in Flanders, Belgium	FALSE	0
Manual of the Alien Plants of Belgium	FALSE	521
Manual of the Alien Plants of Belgium	TRUE	1987

Solution at unified checklist level

If all checklists would contain distributions at regional level, we could then modify unified checklist workflow to add Flemish region/Walloon region/Brussels-Capital Region in distribution and publish it again. These changes wouldn't be difficult. I think the biggest concern is to convince authors of checklists to improve them. @peterdesmet: what do you think about it?

Solution: fast workaround

For nature indicators report, I think we should opt now for a faster approach. @timadriaens: you could scan the species published at national level ONLY and let me know which ones you would like to include in report? We speak about 21 (molluscs) + 13 (Rust Fungi) = 34 species if we limit to Flanders without sea (= not including the 147 RINSE taxa).
As first screening, I retrieved the number of occurrence in BELGIUM (country = "BE" in the search). See below:

backbone_usageKey	scientificName	kingdom	n_occs_be
2295425	Zonitoides arboreus (Say, 1816)	Animalia	0
2294131	Allopeas clavulinum (Potiez & Michaud, 1838)	Animalia	0
7520678	Striosubulina striatella (Rang, 1837)	Animalia	0
5190912	Testacella haliotidea Lamarck, 1801	Animalia	0
4568269	Paralaoma servilis (Shuttleworth, 1852)	Animalia	81
4598225	Tandonia budapestensis (Hazay, 1880)	Animalia	0
2296797	Candidula intersecta (Poiret, 1801)	Animalia	15
4565039	Hygromia cinctella (Draparnaud, 1801)	Animalia	358
8014163	Ambigolimax valentianus (A.Férussac, 1822)	Animalia	401
9291405	Massylaea vermiculata (O.F.Müller, 1774)	Animalia	18
2294277	Theba pisana (Müller, 1774)	Animalia	630
2296807	Cochlicella barbara (Linnaeus, 1758)	Animalia	28
4562917	Cochlicella acuta (Müller, 1774)	Animalia	555
4565134	Cernuella aginnica (Locard, 1882)	Animalia	83
9805907	Cernuella virgata (da Costa, 1778)	Animalia	835
4565061	Cernuella neglecta (Draparnaud, 1805)	Animalia	53
4565140	Cernuella cisalpina (Rossmässler, 1837)	Animalia	25
7540164	Arion vulgaris Moquin-Tandon, 1855	Animalia	568
8745918	Deroceras invadens Reise, Hutchinson, Schunack & Schlitt, 2011	Animalia	253
4567717	Boettgerilla pallens Simroth, 1912	Animalia	72
2295309	Hawaiia minuscula (Binney, 1841)	Animalia	1
2516499	Frommeella mexicana (Mains) J.W.McCain & J.F.Hennen, 1990	Fungi	0
2516419	Tranzschelia discolor (Fuckel) Tranzschel & M.A.Litv.	Fungi	34
2516809	Melampsoridium betulinum (Pers.) Kleb.	Fungi	70
2516117	Gymnosporangium confusum Plowr.	Fungi	5
2516137	Gymnosporangium sabinae (Dicks.) G.Winter	Fungi	75
2516075	Cumminsiella mirabilissima (Peck) Nannf.	Fungi	34
7239373	Uromyces veratri (DC.) J.Schröt.	Fungi	1
2514966	Puccinia sorghi Schwein.	Fungi	6
2514972	Puccinia komarovii Tranzschel	Fungi	3
2515351	Puccinia oxalidis Dietel & Ellis	Fungi	4
3376976	Puccinia grisea (F.Strauss) G.Winter	Fungi	3
2515236	Puccinia antirrhini Dietel & Holw.	Fungi	1
3376286	Puccinia pazschkei Dietel, 1891	Fungi	1

[timadriaens]

In principle, the RINSE list is for Flanders as the Belgian project area of this Interreg was completely contained within this region so we can use it for the indicators. For the molluscs, I the following occur in Flanders but if the checklist does not specify the first data of introduction per region specifically, we cannot use that? Based on the data I had in the add hoc list, the following species are for Flanders:

Bellamya chinensis
Massylaea vermiculata
Anodonta woodiana
Arion vulgaris
Balanus improvisus
Boettgerilla pallens
Candidula intersecta
Cernuella aginnica
Cernuella cisalpina
Cernuella neglecta
Cochlicella barbara
Corbicula fluminalis
Corbicula fluminea
Crassostrea gigas
Deroceras panormitanum
Dreissena polymorpha
Dreissena rostriformis bugensis
Ferrissia fragilis
Haitia acuta
Ambigolimax valentianus
Lithoglyphus naticoides
Meneta dilatatus
Milax gagates
Mytilopsis leucophaeata
Petricola pholadiformis
Potamopyrgus antipodarum
Rangia cuneata
Tandonia sowerbyi
Teredo navalis
Testacella haliotidea
Theba pisana
Trochoidea elegans
Xerosecta cespitum
Hygromia cinctella

[SanderDevisscher]

Overbodig en vervangen door #16