inlabru: gg.inla.mesh – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

gg.inla.mesh

Geom for inla.mesh objects

Description

This function extracts the graph of an inla.mesh object and uses geom_line to visualize the graph's edges. Alternatively, if the color argument is provided, interpolates the colors across for a set of SpatialPixels covering the mesh area and calls gg.SpatialPixelDataFrame() to plot the interpolation.

Usage

## S3 method for class 'inla.mesh'
gg(
  data,
  color = NULL,
  alpha = NULL,
  edge.color = "grey",
  interior = TRUE,
  int.color = "blue",
  exterior = TRUE,
  ext.color = "black",
  crs = NULL,
  mask = NULL,
  nx = 500,
  ny = 500,
  ...
)

Arguments

`data`	An `INLA::inla.mesh` object.
`color`	A vector of scalar values to fill the mesh with colors. The length of the vector mus correspond to the number of mesh vertices.
`alpha`	A vector of scalar values setting the alpha value of the colors provided.
`edge.color`	Color of the mesh edges.
`interior`	If TRUE, plot the interior boundaries of the mesh.
`int.color`	Color used to plot the interior boundaries.
`exterior`	If TRUE, plot the exterior boundaries of the mesh.
`ext.color`	Color used to plot the interior boundaries.
`crs`	A CRS object defining the coordinate system to project the mesh to before plotting.
`mask`	A SpatialPolygon defining the region that is plotted.
`nx`	Number of pixels in x direction (when plotting using the color parameter).
`ny`	Number of pixels in y direction (when plotting using the color parameter).
`...`	ignored arguments (S3 generic compatibility).

Value

geom_line return values or, if the color argument is used, the values of gg.SpatialPixelDataFrame().

Examples

if (bru_safe_inla()) {

  # Load Gorilla data
  data("gorillas", package = "inlabru")

  # Plot mesh using default edge colors

  ggplot() +
    gg(gorillas$mesh)

  # Don't show interior and exterior boundaries

  ggplot() +
    gg(gorillas$mesh, interior = FALSE, exterior = FALSE)

  # Change the edge colors

  ggplot() +
    gg(gorillas$mesh,
      edge.color = "green",
      int.color = "black",
      ext.color = "blue"
    )

  # Use the x-coordinate of the vertices to colorize the triangles and
  # mask the plotted area by the survey boundary, i.e. only plot the inside

  xcoord <- gorillas$mesh$loc[, 1]
  ggplot() +
    gg(gorillas$mesh, color = (xcoord - 580), mask = gorillas$boundary) +
    gg(gorillas$boundary)
}

inlabru

Bayesian Latent Gaussian Modelling using INLA and Extensions

v2.3.1

GPL (>= 2)

Authors

Finn Lindgren [aut, cre, cph] (<https://orcid.org/0000-0002-5833-2011>, Finn Lindgren continued development of the main code), Fabian E. Bachl [aut, cph] (Fabian Bachl wrote the main code), David L. Borchers [ctb, dtc, cph] (David Borchers wrote code for Gorilla data import and sampling, multiplot tool), Daniel Simpson [ctb, cph] (Daniel Simpson wrote the basic LGCP sampling method), Lindesay Scott-Howard [ctb, dtc, cph] (Lindesay Scott-Howard provided MRSea data import code), Seaton Andy [ctb] (Andy Seaton provided testing and bugfixes)

Initial release