Skip to contents

Plot sdmTMB models with the visreg package

Source: R/visreg.R
visreg_delta.Rd

sdmTMB models fit with regular (non-delta) families can be passed to visreg::visreg() or visreg::visreg2d() directly. Examples are shown below. Delta models can use the helper functions visreg_delta() or visreg2d_delta() described here.

Usage

visreg_delta(object, ..., model = c(1, 2))

visreg2d_delta(object, ..., model = c(1, 2))

Arguments

object

Fit from sdmTMB().

...

Arguments passed to visreg::visreg() or visreg::visreg2d().

model

First or second delta-model component.

Value

A plot from the visreg package. If plot = FALSE, the plotted data are returned invisibly. This is useful if you want to make your own plot.

Details

Note that the residuals are currently randomized quantile residuals, not the deviance residuals usually used for GLMs with visreg.

Examples

if (require("ggplot2", quietly = TRUE) &&
  require("visreg", quietly = TRUE)) {

# \donttest{
  fit <- sdmTMB(
    density ~ s(depth_scaled),
    data = pcod_2011,
    spatial = "off",
    family = tweedie()
  )
  visreg::visreg(fit, xvar = "depth_scaled")

  visreg::visreg(fit, xvar = "depth_scaled", scale = "response")
  v <- visreg::visreg(fit, xvar = "depth_scaled")
  head(v$fit)
  # now use ggplot2 etc. if desired

  # Delta model example:
  fit_dg <- sdmTMB(
    density ~ s(depth_scaled, year, k = 8),
    data = pcod_2011, mesh = pcod_mesh_2011,
    spatial = "off",
    family = delta_gamma()
  )
  visreg_delta(fit_dg, xvar = "depth_scaled", model = 1, gg = TRUE)
  visreg_delta(fit_dg, xvar = "depth_scaled", model = 2, gg = TRUE)
  visreg_delta(fit_dg,
    xvar = "depth_scaled", model = 1,
    scale = "response", gg = TRUE
  )
  visreg_delta(fit_dg,
    xvar = "depth_scaled", model = 2,
    scale = "response"
  )
  visreg_delta(fit_dg,
    xvar = "depth_scaled", model = 2,
    scale = "response", gg = TRUE, rug = FALSE
  )
  visreg2d_delta(fit_dg,
    xvar = "depth_scaled", yvar = "year",
    model = 2, scale = "response"
  )
  visreg2d_delta(fit_dg,
    xvar = "depth_scaled", yvar = "year",
    model = 1, scale = "response", plot.type = "persp"
  )
  visreg2d_delta(fit_dg,
    xvar = "depth_scaled", yvar = "year",
    model = 2, scale = "response", plot.type = "gg"
  )
  # }
}



#> These are residuals for delta model component 1. Use the `model` argument to
#> select the other component.
#> These are residuals for delta model component 2. Use the `model` argument to
#> select the other component.
#> These are residuals for delta model component 1. Use the `model` argument to
#> select the other component.
#> These are residuals for delta model component 2. Use the `model` argument to
#> select the other component.

#> These are residuals for delta model component 2. Use the `model` argument to
#> select the other component.