Get seabird overlap with fishing effort — get

Retrieves the seabird numbers density at locations of fishing effort and calculates the overlap: $$\mathbb{O} = \mathrm{effort} \times \frac{y}{A \cdot \sum{y}}$$ where $y$ is the numbers per grid cell and $A$ is the cell area size in square kilometres.

Usage

get_overlap(x, y, ...)

# S4 method for class 'sf,sf'
get_overlap(
  x,
  y,
  name,
  group_name = "group",
  effort_name = "effort",
  na_replace = NULL,
  ...
)

Arguments

x: fishing effort as an sf object with POINT geometry.
y: density distribution as an sf object with POLYGON geometry. Densities should be stored in column value.
...: other arguments parsed to methods (currently unused)
name: character object specifying the species code (e.g. DIW).
group_name: column header for x matching layer names in y object.
effort_name: column header for x storing effort.
na_replace: numeric value to replace NA values introduced when x entries are outside the range of the species distribution. If na_replace = NULL (the default) then NA values are retained.

Value

an object of class sf, with additional column for the overlap (e.g. for name = "DIW" then returned object has additional column overlap_diw).

Examples

library(sefraInputs)
library(dplyr)
library(sf)
x <- data.frame(month = "1", lat = -42.5, lon = 87.5, effort = 1.0)
x <- x %>% rowwise(.) %>%
  mutate(., geometry = list(st_point(c(lon, lat)))) %>%
  ungroup(.) %>%
  st_as_sf(., crs = "EPSG:4326")
x <- x %>% st_transform(crs = st_crs(sefraInputs::grid))
y <- sefraInputs::grid %>% mutate(month = "1", value = runif(1224))
get_overlap(x, y, name = "bird", group_name = "month", effort_name = "effort")
#> Simple feature collection with 1 feature and 5 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -5100792 ymin: 671532.1 xmax: -5100792 ymax: 671532.1
#> Projected CRS: +proj=laea +lat_0=-90 +lon_0=170
#> # A tibble: 1 × 6
#>   month   lat   lon effort            geometry overlap_bird
#>   <chr> <dbl> <dbl>  <dbl>         <POINT [m]>        <dbl>
#> 1 1     -42.5  87.5      1 (-5100792 671532.1)        0.732