fix taxonomic groupings
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Per meeting 2019-07-03 BB, MG w/ @mvisalli in notes | bbnj - Google Docs:
Currently of 24,904 species (before masking out high seas), group is NA for 1,176.
- ∆ Cetaceans:
# old: Order == "Artiodactyla" ~ "Cetaceans", # new: Order == "Cetacea" ~ "Cetaceans",
- ∆ Squids:
# old: Order %in% c("Myopsida","Oegopsida") # new: Order %in% c("Myopsida","Oegopsida","Teuthida")
- ∆ Sharks → Sharks & Rays
- ∆ Worms:
# old Phylum == "Annelida" # new Phylum %in% c("Annelida", "Sipuncula")
- + Forams:
Phylum == "Foraminifera"
to consider
From Morgan's notes:
- Two other classes of Phylum Mollusca?
- Class Aplacophora (shell-less molluscs)
- Class Scaphopoda (tusk shells)
- Any of these?
- Phylum Chordata: (Sub)Class Holocephali ("complete heads" fish)
- Phylum Chordata: Class Myxini (hagfish)
- Phylum Cnidaria: Class Scyphozoa (jellyfish)
- Do we want to pull out green algae (Phylum Chlorophyta) or red algae (Phylum Rhodophyta)? They’re currently captured by NA
species data and groupings
-
Assign Taxonomic Groups in Calculate Indicators • gmbi: assignment performed here
References: basis of taxonomic groupings
- Tittensor et al. (2010) Global patterns and predictors of marine biodiversity across taxa | Nature
- Selig et al. (2013) Assessing Global Marine Biodiversity Status within a Coupled Socio-Ecological Perspective
- Spatial Data Download: IUCN Red List of Threatened Species
- Fautin et al (2010) An Overview of Marine Biodiversity in United States Waters
made taxa changes above in marinebon/gmbi:vignettes/calc.Rmd, but need to still run script and update gmbi + bbnj repos
For others, see marinebon/gmbi#1
I believe that the taxonomic breakdown I used for the treemap reflects the changes suggested by Doug and referenced in marinebon/gmbi#1 (i.e. group all cephalopods instead of breaking out squid, changing coastal fishes to bony fishes, and removing forams group)
@bbest Doug and I spoke last night and came up w proposed taxonomic clumping for 9 groups:
Invert
Bony fishes
Marine Mammals
Corals
Cephalopods
Seagrasses
Sharks & rays
Tunas & billfishes
Other
How does that look to you? If ok, I can copy the code from gmbi where you define taxonomic groups and modify to reflect this breakdown & send you updated code to plug in -- is that helpful?
Code for updating taxonomic clumping here:
https://github.com/ecoquants/bbnj/blob/3765f44f41d503ea9c5ceb15b9406b128f624199/inst/scripts/spp_treemap_DJM.Rmd#L36-L43
TODO: get map app to show all taxonomic groups##
Low priority items (especially since @bbest just re-ran this -- sorry!):
- Tunicates: add class Appendicularia to group Tunicates
- Cephalopods: confirm that Teuthida is actually captured in group Non-Squid Cephalopods and change name of group to Cephalopods (or just change code to
Class == "Cephalopoda" ~ "Cephalopods") - Jellyfish: Hydrozoa are currently pulled out in their own group, but I think other jellyfish are captured in the group Other. We could consider creating a Jellyfish group to include all members of Medusozoa subphylum which would include the following classes:
Cubozoa – box jellyfish
Hydrozoa – hydrozoans
Scyphozoa – true jellyfish
Staurozoa – stalked jellyfish
Hi @mvisalli,
Just to confirm this edit:
- Cephalopods: confirm that Teuthida is actually captured in group Non-Squid Cephalopods and change name of group to Cephalopods (or just change code to
Class == "Cephalopoda" ~ "Cephalopods")
Do you mean, make sure that Teuthida is actively excluded (!Order %in%) from Cephalopods and included (Order %in%) in Squids per Squid | Wikipedia?
- Cephalopods
Class == "Cephalopoda" & !Order %in% c("Myopsida","Oegopsida","Teuthida") - Squids
Order %in% c("Myopsida","Oegopsida","Teuthida")
This was in the code but not the markdown documentation. I'm applying the rest of the fixes to groups01 (+ groups02 & groups03).