plot_anisotropy: Plot anisotropy from an sdmTMB model

In pbs-assess/sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Plot anisotropy from an sdmTMB model

Description

Anisotropy is when spatial correlation is directionally dependent. In sdmTMB(), the default spatial correlation is isotropic, but anisotropy can be enabled with anisotropy = TRUE. These plotting functions help visualize that estimated anisotropy.

Usage

plot_anisotropy(object, return_data = FALSE)

plot_anisotropy2(object, model = 1)

Arguments

object	An object from sdmTMB().
return_data	Logical. Return a data frame? plot_anisotropy() only.
model	Which model if a delta model (only for plot_anisotropy2(); plot_anisotropy() always plots both).

Value

plot_anisotropy(): One or more ellipses illustrating the estimated anisotropy. The ellipses are centered at coordinates of zero in the space of the X-Y coordinates being modeled. The ellipses show the spatial and/or spatiotemporal range (distance at which correlation is effectively independent) in any direction from zero. Uses ggplot2. If anisotropy was turned off when fitting the model, NULL is returned instead of a ggplot2 object.

plot_anisotropy2(): A plot of eigenvectors illustrating the estimated anisotropy. A list of the plotted data is invisibly returned. Uses base graphics. If anisotropy was turned off when fitting the model, NULL is returned instead of a plot object.

References

Code adapted from VAST R package

Examples

mesh <- make_mesh(pcod_2011, c("X", "Y"), n_knots = 80, type = "kmeans")
fit <- sdmTMB(
  data = pcod_2011,
  formula = density ~ 1,
  mesh = mesh,
  family = tweedie(),
  share_range = FALSE,
  time = "year",
  anisotropy = TRUE #<
)
plot_anisotropy(fit)
plot_anisotropy2(fit)

pbs-assess/sdmTMB documentation built on April 22, 2024, 3:26 p.m.