visreg_delta: Plot sdmTMB models with the 'visreg' package

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

Plot sdmTMB models with the visreg package

Description

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()
...	Any arguments passed to visreg::visreg() or visreg::visreg2d()
model	1st or 2nd delta model

Details

Note the residuals are currently randomized quantile residuals, not deviance residuals as is usual for GLMs with visreg.

Value

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

Examples

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


  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"
  )
  
}

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