fix taxonomic groupings

[bbest]

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

  • marinebon/gmbi: inst/data/spp.csv
  • spp.xlsx - Google Drive

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

[bbest]

made taxa changes above in marinebon/gmbi:vignettes/calc.Rmd, but need to still run script and update gmbi + bbnj repos

[bbest]

For others, see https://github.com/marinebon/gmbi/issues/1

[mvisalli]

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)

https://github.com/ecoquants/bbnj/blob/6ce535a3c3e558e59c2557a2cbb17f8503fe3d95/inst/scripts/spp_treemap.Rmd#L36-L56

[mvisalli]

@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?

[mvisalli]

Code for updating taxonomic clumping here: https://github.com/ecoquants/bbnj/blob/3765f44f41d503ea9c5ceb15b9406b128f624199/inst/scripts/spp_treemap_DJM.Rmd#L36-L43

[bbest]

TODO: get map app to show all taxonomic groups##

[mvisalli]

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

[bbest]

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).

[mvisalli]

Hi @bbest,

It was my understanding that we wanted to include Squid in the group Cephalopods rather than breaking out into "Squids" and "Non-Squid Cephalopods." Does that sounds ok to you?