Plot an sdmTMB mesh on a map

Draws a sdmTMB::make_mesh() mesh over a ggOceanMaps::basemap(), optionally overlaying the sampling positions as red points. When a barrier mesh is present (e.g. from sdmTMBextra::add_barrier_mesh(), from the GitHub-only sdmTMBextra package), the barrier ("land") triangles are marked with an X.

Usage

plot_mesh(
  mesh,
  crs,
  data = NULL,
  value = NULL,
  zero_col = NULL,
  zero_size = 0.25,
  zero_alpha = 0.1,
  land_col = NULL,
  lon_interval = NULL,
  lat_interval = NULL,
  utm_axes = FALSE,
  xy_cols = c("X", "Y"),
  coord_multiplier = 1000,
  base_size = 11
)

Arguments

mesh

An sdmTMB mesh object (from sdmTMB::make_mesh(), optionally with a barrier mesh added).

crs

Coordinate reference system (projected, in metres) used for the basemap.

data

Optional data frame of sampling positions with coordinate columns (see xy_cols), plotted as red points.

value

Optional character naming a column in data used to scale the point sizes. Note that ggplot2::scale_size_area() maps a zero to zero area, so stations with no catch become invisible; see zero_col.

zero_col

Optional colour for stations where value is zero, drawn as small crosses beneath the sized points. NULL (default) omits them, which preserves the behaviour of earlier versions. Zeros usually outnumber the positive stations by an order of magnitude, so they are drawn small and faint (see zero_size and zero_alpha) to avoid burying the response.

zero_size, zero_alpha

Size and alpha of the zero_col crosses.

land_col

Optional land fill passed to ggOceanMaps::basemap(). NULL (default) uses the basemap default.

lon_interval, lat_interval

Optional graticule intervals in degrees, passed to ggOceanMaps::basemap(). NULL (default) lets basemap decide.

utm_axes

Logical. If TRUE, label the axes in projected kilometres (the units the model actually uses) rather than in degrees. Default FALSE, which preserves the behaviour of earlier versions.

xy_cols

Character vector of the coordinate columns in data. Default c("X", "Y").

coord_multiplier

Numeric factor to convert model coordinates to CRS units. Default 1000.

base_size

Numeric. Base font size. Default 11.

Value

A ggplot object.

See also

sdmTMB::make_mesh(), ggOceanMaps::basemap()

Author

Mikko Vihtakari

Examples

# \donttest{
mesh <- sdmTMB::make_mesh(sdmTMB::pcod, c("X", "Y"), cutoff = 15)
plot_mesh(mesh, crs = 32609, data = sdmTMB::pcod, value = "density")

# }