5  Environment

Extract environmental predictors (static and/or dynamic) from various sources for observations (presence and pseudo-absence)

Environmental data are used to fit the model and predict distribution onto the seascape, e.g. Table 5.1.

Code 
librarian::shelf(
  here, knitr, readr)
library(here)
library(knitr)
library(readr)

d <- read_csv(
  here("data/Roberts-2016_env-predictors.csv"),
  show_col_types = F)

options(knitr.kable.NA = '')
kable(d, format="pipe")
Table 5.1: Example of environmental predictors from Roberts et al. (2016).
Type /
Covariates		 Resolution Time range Description
Physiographic
Depth, Slope 30 arc sec Seafloor depth and slope, derived from SRTM30-PLUS global bathymetry20
DistToShore, DistTo125m, DistTo300m, DistTo1500m 30 arc sec Distance to the closest shoreline, excluding Bermuda and Sable Island, and various ecologically-relevant isobaths20
DistToCanyon, DistToCanyon OrSeamount 30 arc sec Distance to the closest submarine canyon, and to the closest canyon or seamount21
SST & Winds
SST, DistToFront 0.2°, daily 1991-2014 Foundation sea surface temperature (SST), from GHRSST Level 4 CMC SST22, and distance to the closest SST front identified with the Canny edge detection algorithm23
WindSpeed 0.25°, daily 1991-2014 30-day running mean of NOAA NCDC 1/4° Blended Sea Winds24
Currents
TKE, EKE 0.25°, daily 1993-2013 Total kinetic energy (TKE) and eddy kinetic energy (EKE), from Aviso 1/4° DT-MADT geostrophic currents
DistToEddy, DistToAEddy, DistToCEddy 0.25°, weekly 1993-2013 Distance to the ring of the closest geostrophic eddy having any (DistToEddy), anticyclonic (DistToAEddy), or cyclonic (DistToCEddy) polarity, from Aviso 1/4° DT-MADT using a revision of the Chelton et al. algorithm25; we tested eddies at least 9, 4, and 0 weeks old
Biological
Chl 9 km, daily 1997-2014 GSM merged SeaWiFS/Aqua/MERIS/VIIRS chlorophyll (Chl) a concentration26, smoothed with a 3D Gaussian smoother to reduce data loss to < 10%
VGPM, CumVGPM45, CumVGPM90 9 km, 8 days 1997-2014 Net primary production (mg C m-2 day-1) derived from SeaWiFS and Aqua using the Vertically Generalized Production Model (VPGM)27; we tested the original 8 day estimates as well as 45 and 90 day running accumulations
PkPP, PkPB 0.25°, weekly 1997-2013 Zooplankton production (PkPP; g m-2 day-1) and biomass (PkPB; g m-2) from the SEAPODYM ocean model28
EpiMnkPP, EpiMnkPB 0.25°, weekly 1997-2013 Epipelagic micronekton production (EpiMnkPP; g m-2 day-1) and biomass (EpiMnkPB; g m-2) from the SEAPODYM model(28)

5.0.1 Physiographic

  • depth
    Bathymetric Depth

  • d2coast
    Distance to Coast

  • d2shelf
    Distance to Shelf

5.0.2 Time Varying

  • vgpm
    Vertically integrated primary Productivity model

5.0.3 Depth & Time Varying

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

  • salin
    Salinity