plot_smooth function

Plot a smooth term from an sdmTMB model

Deprecated: use ‘visreg::visreg()’. See ‘visreg_delta()’ for examples.

plot_smooth(
  object,
  select = 1,
  n = 100,
  level = 0.95,
  ggplot = FALSE,
  rug = TRUE,
  return_data = FALSE
)

Arguments

• object: An sdmTMB() model.
• select: The smoother term to plot.
• n: The number of equally spaced points to evaluate the smoother along.
• level: The confidence level.
• ggplot: Logical: use the ggplot2 package?
• rug: Logical: add rug lines along the lower axis?
• return_data: Logical: return the predicted data instead of making a plot?

Returns

A plot of a smoother term.

Details

Note:

• Any numeric predictor is set to its mean
• Any factor predictor is set to its first-level value
• The time element (if present) is set to its minimum value
• The x and y coordinates are set to their mean values

Examples

d <- subset(pcod, year >= 2000 & density > 0)
  pcod_spde <- make_mesh(d, c("X", "Y"), cutoff = 30)
  m <- sdmTMB(
    data = d,
    formula = log(density) ~ s(depth_scaled) + s(year, k = 5),
    mesh = pcod_spde
  )
  plot_smooth(m)