In marinebon/obisindicators: Develop marine biodiversity indicators from OBIS data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(dplyr)
library(sf)

Get biological occurrences

occ <- occ_SAtlantic # occ_1M OR occ_SAtlantic

Create function to make grid, calculate metrics, and plot maps for different resolution grid sizes

res_changes <- function(resolution = 2){
  hex_res <- 1  # hex_res 0 is too big to work, all others work
  hex <- obisindicators::make_hex_res(resolution)

  # === Then assign cell numbers to the occurrence data:
  occ <- occ %>% 
    mutate(
      cell = h3::geo_to_h3(
        data.frame(decimalLatitude, decimalLongitude),
        res = resolution))
  idx <- calc_indicators(occ)

  grid <- hex %>% 
    inner_join(
      idx,
      by = c("hexid" = "cell"))

  gmap_indicator(grid, "es", label = "ES(50)")
}

Different Resolutions

Details of H3 resolution differences can be found in the h3geo docs. Resolutions range from 0 (largest) to 15 (smallest).

Generally, resolution 0 is too big to be useful... or even functional, sometimes.

res_changes(0)

res_changes(1)

At this resolution the S Atlantic is completely covered, meaning that every hex had enough data to compute the ES(50) diversity metric. We can see some basic expected patterns such as: * higher diversity near to the coast * higher diversity near the equator

res_changes(2)

A this resolution we see gaps throughout the central South Atlantic. These hexagons did not have enough occurrence records to calculate the diversity metric.

res_changes(3)

At this higher resolution, gaps dominate the map. Only places with relatively dense surveying efforts have enough data to calculate the diversity metric. Note how the relatively data-poor center has a relatively stark boundary spanning from the southern tip of Africa across. This boundary is visible in the diversity metric plots of lower resolution in the form of a high-low diversity boundary. The appearance of this abrupt high-low diversity boundary is likely an artifact of how data-poor the central South Atlantic is. The ES50 diversity metric will bias data-poor to more-diverse when there is extremely low amounts of data. It should be noted, however, that this bias is much less intense than the data-poor to less-diverse in other diversity metrics.

marinebon/obisindicators documentation built on Dec. 14, 2022, 6:47 p.m.