2  Prepare

Prepare observations and environmental data for modeling

3 Prepare

flowchart LR

  %% nodes
  P(presence):::in
  A("pseudo-absence"):::in
  pts(obs):::out
  X[/extract/]:::fxn
  env(env):::in
  D[[data]]:::out

  %% edges
  P   --> pts
  A   --> pts
  pts --> X
  env --> X
  X   --> D

  %% Legend
  in(input):::in
  fxn[/process/]:::fxn
  out(output):::out
  subgraph Legend
    in
    fxn
    out
  end

  %% styles
  classDef in  fill:lightblue
  classDef out fill:lightgreen
  classDef fxn fill:yellow
Figure 3.1: Diagram of SDM data preparation for model fitting.
  • obs
    observations: occurrences from OBIS; masked by FAO regions defined by AquaMaps (Skyttner 2020)
    • presence
      OBIS: species occurrence
    • absence
      OBIS not-species, but same family
  • env
    environment
  • tbl
    table of observations (presence and absence) with environmental values

3.1 Environmental Predictors

3.1.1 Physiographic

  • depth
    Bathymetric Depth

  • d2coast
    Distance to Coast

  • d2shelf
    Distance to Shelf

3.1.2 Time Varying

  • vgpm
    Vertically integrated primary Productivity model

3.1.3 Depth & Time Varying

  • temp
    Temperature, either sea-surface temperature (SST) or some modeled product from HyCOM, ROMS or Copernicus

  • salin
    Salinity