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Add depth from NOAA bathymetry

Source: R/bathymetry.R
add_bathymetry.Rd

Adds the sea depth at each position of a data frame, for example the nodes of a prediction grid from make_survey_grid(), taken from the ETOPO bathymetry of NOAA via the marmap package. Optionally flags the positions whose depth lies within a given range, such as the depths at which the survey fishes.

Usage

add_bathymetry(
  d,
  lon = "lon",
  lat = "lat",
  bathy = NULL,
  resolution = 1,
  path = NULL,
  depth_range = NULL,
  col = "Depth"
)

Arguments

d

A data frame with longitude and latitude columns (decimal degrees), or a datras_raw object, in which case depth is added to HH.

lon, lat

Names of the longitude and latitude columns.

bathy

Optional bathymetry of class bathy (from marmap::getNOAA.bathy() or marmap::as.bathy()). If NULL (default), it is downloaded for the range of the positions plus one degree.

resolution

Resolution of the downloaded bathymetry in arc minutes, passed to marmap::getNOAA.bathy(). Default 1.

path

Optional directory in which the downloaded bathymetry is kept and looked up again on later calls, so that it is downloaded only once.

depth_range

Optional numeric vector of length 2. When given, a logical column depth_ok is added that is TRUE where the depth lies within the range.

col

Name of the depth column to add. Default "Depth", as in HH.

Value

d with the depth column, and depth_ok when depth_range is given, added.

Details

Depths are positive below sea level, in metres. Positions on land and positions outside the bathymetry get NA. The depth is that of the bathymetry cell nearest to each position.

For a grid in projected coordinates, add longitude and latitude first with add_xy(grid, inverse = TRUE).

A typical depth_range is the range of depths the survey fishes, e.g. quantile(x[["HH"]]$Depth, c(0.01, 0.99), na.rm = TRUE); predictions outside it extrapolate in depth.

When d is a datras_raw object and col = "Depth", the haul depths reported by the survey are replaced. Use another col to compare them.

See also

make_survey_grid(), add_grid_support(), add_xy()

Examples

if (FALSE) { # \dontrun{
grid <- make_survey_grid(dab[["HH"]]$lon, dab[["HH"]]$lat,
                         resolution = 0.1, max_dist = 0.3)
names(grid) <- c("lon", "lat")
grid <- add_bathymetry(grid, path = tempdir(),
                       depth_range = quantile(dab[["HH"]]$Depth,
                                              c(0.01, 0.99), na.rm = TRUE))

## Compare the reported haul depths with the bathymetry
x <- add_bathymetry(dab, col = "DepthNOAA", path = tempdir())
} # }