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Plot mesh comparison results

Source: R/compare-meshes.R
plot.sdmTMB_mesh_comparison.Rd

Plots survey index time series from a mesh cutoff comparison (reference in black, alternative cutoffs in colour, with Mohn's rho annotated), or spatial maps of prediction differences on a ggOceanMaps::basemap().

Usage

# S3 method for class 'sdmTMB_mesh_comparison'
plot(
  x,
  type = "index",
  index_divisor = NULL,
  unit = NA,
  mohn = FALSE,
  cutoff_label = "Cutoff",
  viridis = FALSE,
  spatial_response = "mean_pr_diff",
  transform_color_scale = TRUE,
  limit_rounding = 10,
  break_rounding = 5,
  base_size = 11,
  ...
)

Arguments

x

An object of class sdmTMB_mesh_comparison.

type

Character. "index" (default) or "spatial".

index_divisor

Optional numeric divisor applied to index values.

unit

Character. Unit label. If NA, "Index value" is used.

mohn

Logical. Annotate the index plot with Mohn's rho (via mohns_rho())? Default FALSE. Only applies when type = "index".

cutoff_label

Character. Label for the cutoff colour/fill legend. Default "Cutoff".

viridis

Logical. Use the viridis palette for cutoff levels? If FALSE (default), a palette-safe Set1 is used.

spatial_response

Character. Column mapped in spatial plots: one of "mean", "pr_mean" or "mean_pr_diff". Default "mean_pr_diff". See Details.

transform_color_scale

Logical. Apply a signed square-root colour scale for spatial plots? Default TRUE.

limit_rounding, break_rounding

Numeric rounding for map fill limits and breaks. Defaults 10 and 5.

base_size

Numeric. Base font size. Default 11.

...

Currently ignored.

Value

A ggplot object (type = "index") or a cowplot grid (type = "spatial").

Details

For type = "spatial", each grid cell is compared between a model fitted with an alternative mesh cutoff and the model fitted with the reference cutoff, for every year they share, on the response scale (i.e. predict(..., type = "response"), e.g. density rather than log density): diff = est - ref_est and pr_diff = 100 * diff / ref_est (percent). spatial_response selects how these per-year values are summarised across years into the single value mapped for each cell:

  • "mean": mean(diff) — the average absolute difference, in response units. Useful for the raw magnitude of disagreement, but not comparable across cells with very different baseline abundance.

  • "pr_mean": mean(pr_diff) — the average of the yearly percent differences. Because each year is divided by that year's own (possibly small) reference value, a handful of low-abundance years/cells can dominate this average with large percentage swings even when the absolute difference is small.

  • "mean_pr_diff" (default): 100 * mean(diff) / mean(ref_est) — the percent difference between the across-year mean predictions (a ratio of means, not a mean of ratios). This is usually the more robust percent-based summary, since a cell's overall multi-year baseline is used in the denominator instead of each individual year's value.

See also

compare_meshes()

Author

Mikko Vihtakari

Examples

# \donttest{
mesh <- sdmTMB::make_mesh(sdmTMB::pcod, c("X", "Y"), cutoff = 20)
m <- sdmTMB::sdmTMB(
  data = sdmTMB::pcod, formula = density ~ 0 + as.factor(year),
  time = "year", mesh = mesh, family = sdmTMB::tweedie(link = "log")
)
nd <- sdmTMB::replicate_df(sdmTMB::qcs_grid, "year", unique(sdmTMB::pcod$year))
mesh_indices <- compare_meshes(
  object = m, mesh_cutoffs = c(10, 30), newdata = nd, object_crs = 32609,
  reference_name = "20 km"
)
plot(mesh_indices, cutoff_label = "Cutoff (km)")

plot(mesh_indices, type = "spatial")

# }