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BenioffOceanInitiative / bbnj

R package for assessing marine biodiversity beyond national jurisdiction (BBNJ)
https://BenioffOceanInitiative.github.io/bbnj
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tally species per taxa after masking for high seas #5

Closed bbest closed 5 years ago

bbest commented 5 years ago

Best way to do this is by calculating percent of species distribution (probability > 0.5) in the high seas, so could filter to species with at least 25% of their distribution on the high seas (a la GreenPeace report).

This will have to happen within the AquaMaps database per Calculate Indicators • gmbi, and then ideally becomes another column in gmbi:inst/data/spp.csv which should get added to bbnj as a species dataset along with bbnj:datasets.

mvisalli commented 5 years ago

After filtering for for species with at least 25% of their distribution in the high seas, will we need to create new layers for nspp_all and nspp for each taxonomic group?

I wonder if applying the 25% distribution in high seas filter would end up removing a bunch of species that may usually be coastal but show up in unique shallow areas like Mascarene Plateau

bbest commented 5 years ago

Here's the number of species by percentage area in the high seas:

%hs ~0 ~0-25% 25-100%
#spp 13,331 9,516 2,051
%spp 53.5% 38.2% 8.2%

Here's the breakdown by taxonomic group in case we want to rethink these before proceeding. Mangroves and Seagrasses get dropped for instance. Do we want to lump Forams into NA, which we can call Other?

Table. Number of species by % area in high seas of ocean area (given by probability >= 0.5)

group (NA) ~0 <=0.25% > 25% n group %n > 25% %N > 25%
Bivalves   578 428 12 1,018 1% 0.6%
Bony fishes 3 6,433 3,648 1,325 11,409 12% 64.6%
Cetaceans   14 16 52 82 63% 2.5%
Chitons   62 18 1 81 1% 0.0%
Corals   489 419 10 918 1% 0.5%
Crustaceans 1 1,232 1,650 175 3,058 6% 8.5%
Echinoderms 2 532 389 33 956 3% 1.6%
Euphausiids   8 34 1 43 2% 0.0%
Forams   11 3 2 16 13% 0.1%
Gastropods   1,952 848 52 2,852 2% 2.5%
Hydrozoans   79 233 9 321 3% 0.4%
Mangroves   1 - - 1 0% 0.0%
Non-squid cephalopods   149 113 33 295 11% 1.6%
Pinnipeds   7 17 8 32 25% 0.4%
Reptiles   20 13 1 34 3% 0.0%
Sea spiders   119 149 64 332 19% 3.1%
Seagrasses   7 3 - 10 0% 0.0%
Sharks & rays 2 448 335 49 834 6% 2.4%
Sponges   315 116 9 440 2% 0.4%
Tunas & billfishes   24 18 21 63 33% 1.0%
Tunicates 1 225 344 84 654 13% 4.1%
Worms   166 239 46 451 10% 2.2%
NA   458 482 64 1,004 6% 3.1%
N TOTAL 9 13,329 9,515 2,051 24,904   100%

image

Here are the files for tables above:

bbest commented 5 years ago

Hi @mvisalli,

Here's the updated summary of species revised to include Antarctica in the high seas...

%hs ~0 ~0-25% 25-100%
#spp 13,217 9,008 2,673
%spp 53.1% 36.2% 10.7%

And here's the individual species association with groups and in/out high seas:

marinebon/gmbi: spp_bbnj.csv

I haven't yet summarized like above https://github.com/ecoquants/bbnj/issues/5#issuecomment-513649535.

mvisalli commented 5 years ago

Yayyy! Thanks @bbest ! When I re-run the treemap script I end up with 12,013 species in HS (by counting number of species in group 2). Where is the 13,217 spp coming from?