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devel.cvmeasure

Variance and correlations measures for prediction components


Description

Calculates local and integrated variance and correlation measures as introduced by Yuan et al. (2017).

Usage

devel.cvmeasure(joint, prediction1, prediction2, samplers = NULL, mesh = NULL)

Arguments

joint

A joint prediction of two latent model components.

prediction1

A prediction of first component.

prediction2

A prediction of the first component.

samplers

A SpatialPolygon object describing the area for which to compute the cummulative variance measure.

mesh

The inla.mesh for which the prediction was performed (required for cummulative Vmeasure).

Value

Variance and correlations measures.

References

Y. Yuan, F. E. Bachl, F. Lindgren, D. L. Brochers, J. B. Illian, S. T. Buckland, H. Rue, T. Gerrodette. 2017. Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales. https://arxiv.org/abs/1604.06013

Examples

if (bru_safe_inla()) {

  # Load Gorilla data

  data("gorillas", package = "inlabru")

  # Use RColorBrewer

  library(RColorBrewer)

  # Fit a model with two components:
  # 1) A spatial smooth SPDE
  # 2) A spatial covariate effect (vegetation)

  pcmatern <- INLA::inla.spde2.pcmatern(gorillas$mesh,
    prior.sigma = c(0.1, 0.01),
    prior.range = c(0.01, 0.01)
  )

  cmp <- coordinates ~ vegetation(gorillas$gcov$vegetation, model = "factor_contrast") +
    spde(coordinates, model = pcmatern) -
    Intercept(1)

  fit <- lgcp(cmp, gorillas$nests,
    samplers = gorillas$boundary,
    domain = list(coordinates = gorillas$mesh),
    options = list(control.inla = list(int.strategy = "eb"))
  )

  # Predict SPDE and vegetation at the mesh vertex locations

  vrt <- vertices(gorillas$mesh)
  pred <- predict(
    fit,
    vrt,
    ~ list(
      joint = spde + vegetation,
      field = spde,
      veg = vegetation
    )
  )

  # Plot component mean

  multiplot(ggplot() +
    gg(gorillas$mesh, color = pred$joint$mean) +
    coord_equal() +
    theme(legend.position = "bottom"),
  ggplot() +
    gg(gorillas$mesh, color = pred$field$mean) +
    coord_equal() +
    theme(legend.position = "bottom"),
  ggplot() +
    gg(gorillas$mesh, color = pred$veg$mean) +
    coord_equal() +
    theme(legend.position = "bottom"),
  cols = 3
  )

  # Plot component variance

  multiplot(ggplot() +
    gg(gorillas$mesh, color = pred$joint$var) +
    coord_equal() +
    theme(legend.position = "bottom"),
  ggplot() +
    gg(gorillas$mesh, color = pred$field$var) +
    coord_equal() +
    theme(legend.position = "bottom"),
  ggplot() +
    gg(gorillas$mesh, color = pred$veg$var) +
    coord_equal() +
    theme(legend.position = "bottom"),
  cols = 3
  )

  # Calculate variance and correlation measure

  vm <- devel.cvmeasure(pred$joint, pred$field, pred$veg)
  lprange <- range(vm$var.joint, vm$var1, vm$var2)

  # Variance contribution of the components

  csc <- scale_fill_gradientn(colours = brewer.pal(9, "YlOrRd"), limits = lprange)
  boundary <- gorillas$boundary

  plot.1 <- ggplot() +
    gg(gorillas$mesh, color = vm$var.joint, mask = boundary) +
    csc +
    coord_equal() +
    ggtitle("joint") +
    theme(legend.position = "bottom")
  plot.2 <- ggplot() +
    gg(gorillas$mesh, color = vm$var1, mask = boundary) +
    csc +
    coord_equal() +
    ggtitle("SPDE") +
    theme(legend.position = "bottom")
  plot.3 <- ggplot() +
    gg(gorillas$mesh, color = vm$var2, mask = boundary) +
    csc +
    coord_equal() +
    ggtitle("vegetation") +
    theme(legend.position = "bottom")

  multiplot(plot.1, plot.2, plot.3, cols = 3)

  # Covariance of SPDE field and vegetation

  ggplot() +
    gg(gorillas$mesh, color = vm$cov)

  # Correlation between field and vegetation

  ggplot() +
    gg(gorillas$mesh, color = vm$cor)

  # Variance and correlation integrated over space

  vm.int <- devel.cvmeasure(pred$joint, pred$field, pred$veg,
    samplers = ipoints(gorillas$boundary, gorillas$mesh),
    mesh = gorillas$mesh
  )
  vm.int
}

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

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