meshr: meshr

In jamesgrecian/mapr: Manipulating and Projecting Maps in R

Description

Generate a boundary for a marine region of interest specified by telemetry data that can then be passed to 'inla.mesh.2d'. The size of the area, complexity of the boundary and projection can be easily adjusted.

Usage

meshr(dat, prj, buff, keep, Neumann = TRUE)

Arguments

dat	a data frame of observations (see details)
prj	a PROJ.4 compatable projection for the region of interest *NOT* WGS84
buff	a buffer to expand region of interest (specified in metres)
keep	the proportion of points to be retained - passed to rmapshaper::ms_simplify
Neumann	TRUE - returns a list to allow a Neumann boundary to be implemented FALSE - returns a single object defining the coastline

Details

It may be useful to specify whether you want a Neumann boundary condition that either allows or prevents estimation on land:

When Neumann = T the output of the meshr function is a list of spatial polygons. This list can then be passed to the inla.mesh.2d function and is ordered so that the Neumann condition is placed on the coastline, and there are no mesh nodes on land. This could be useful if you wanted to prevent any estimation on land at all.

When Neumann = F the output of meshr is a single spatial polygon object containing the area of interest. When this object is then passed to inla.mesh.2d the Neumann condition is placed on the buffer region not the coastline. This allows mesh nodes on land to be identified and passed to the Haakon barrier model.

The telemetry data is given as a dataframe where each row is an observed location and columns

'id'

individual animal identifier,

'date'

observation time (POSIXct, GMT),

'lon'

observed longitude,

'lat'

observed latitude,

'...'

other columns will be ignored

Value

a list containing an inla mesh boundary for the region of interest

Examples

## Not run: 

require(tidyverse)
require(sf)
require(INLA)
require(inlabru)

data(ellie)
prj <- '+proj=laea +lat_0=-60 +lon_0=70 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs'

b <- meshr(ellie, prj, buff = 5e5, keep = 0.02)

mesh = inla.mesh.2d(boundary = b,
  max.edge = c(250000, 1000000),
  cutoff = 25000,
  max.n = 1000,
  crs = CRS(prj))

ggplot() +
  geom_sf(aes(), data = mapr(ellie, prj, buff = 1e6)) +
  inlabru::gg(mesh) +
  geom_sf(aes(), data = st_as_sf(ellie, coords = c('lon', 'lat')) 
    st_set_crs('+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs'))

## End(Not run)

jamesgrecian/mapr documentation built on Jan. 10, 2021, 4:38 a.m.