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Plot retrospective indices from sdmTMB_retro

Source: R/retro.R
plot.sdmTMB_retro.Rd

Creates a layered ggplot of retrospective (peeled) indices produced by sdmTMB_retro(), with confidence ribbons for each peel and Mohn's rho (computed with mohns_rho()) annotated on the plot.

Usage

# S3 method for class 'sdmTMB_retro'
plot(x, index_divisor = NULL, index_unit = NA, base_size = 11, ...)

Arguments

x

An object of class sdmTMB_retro (the output of sdmTMB_retro()).

index_divisor

Optional numeric. Index values are divided by this before plotting (useful to rescale units). Default NULL.

index_unit

Optional character shown in the y-axis label. If NA (default) the axis label is "Index value".

base_size

Base font size for the ggplot theme. Default 11.

...

Currently ignored.

Value

A ggplot object.

See also

sdmTMB_retro(), mohns_rho()

Author

Mikko Vihtakari

Examples

# \donttest{
mesh <- sdmTMB::make_mesh(sdmTMB::pcod, c("X", "Y"), cutoff = 25)
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))
retr <- sdmTMB_retro(m, nd, nyears = 3, n_workers = 1)
plot(retr, index_divisor = 1e3, index_unit = "1000 t")

# }