plot_smooth: Plot a smooth term from an sdmTMB model

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

Plot a smooth term from an sdmTMB model

Description

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

Usage

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?

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

Value

A plot of a smoother term.

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)

pbs-assess/sdmTMB documentation built on Dec. 20, 2024, 1:51 p.m.