dharma_residuals: DHARMa residuals

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

DHARMa residuals

Description

Plot (and possibly return) DHARMa residuals. This is a wrapper function around DHARMa::createDHARMa() to facilitate its use with sdmTMB() models. Note: It is recommended to set type = "mle-mvn" in simulate.sdmTMB() for the resulting residuals to have the expected distribution. This is not the default.

Usage

dharma_residuals(
  simulated_response,
  object,
  plot = TRUE,
  return_DHARMa = FALSE,
  test_uniformity = TRUE,
  test_outliers = FALSE,
  test_dispersion = FALSE,
  ...
)

Arguments

simulated_response	Output from simulate.sdmTMB(). It is recommended to set type = "mle-mvn" in the call to simulate.sdmTMB() for the residuals to have the expected distribution.
object	Output from sdmTMB().
plot	Logical. Calls DHARMa::plotQQunif().
return_DHARMa	Logical. Return object from DHARMa::createDHARMa()?
test_uniformity	Passed to testUniformity in DHARMa::plotQQunif().
test_outliers	Passed to testOutliers in DHARMa::plotQQunif().
test_dispersion	Passed to testDispersion in DHARMa::plotQQunif().
...	Other arguments to pass to DHARMa::createDHARMa().

Details

See the residuals vignette.

Advantages to these residuals over the ones from the residuals.sdmTMB() method are (1) they work with delta/hurdle models for the combined predictions, not the just the two parts separately, (2) they should work for all families, not the just the families where we have worked out the analytical quantile function, and (3) they can be used with the various diagnostic tools and plots from the DHARMa package.

Disadvantages are (1) they are slower to calculate since one must first simulate from the model, (2) the stability of the distribution of the residuals depends on having a sufficient number of simulation draws, (3) uniformly distributed residuals put less emphasis on the tails visually than normally distributed residuals (which may or may not be desired).

Note that DHARMa returns residuals that are uniform(0, 1) if the data are consistent with the model whereas randomized quantile residuals from residuals.sdmTMB() are expected to be normal(0, 1).

Value

A data frame of observed and expected values is invisibly returned so you can assign the output to an object and plot the residuals yourself. See the examples.

If return_DHARMa = TRUE, the object from DHARMa::createDHARMa() is returned and any subsequent DHARMa functions can be applied.

See Also

simulate.sdmTMB(), residuals.sdmTMB()

Examples

# Try Tweedie family:
fit <- sdmTMB(density ~ as.factor(year) + s(depth, k = 3),
  data = pcod_2011, mesh = pcod_mesh_2011,
  family = tweedie(link = "log"), spatial = "on")

# The `simulated_response` argument is first so the output from
# simulate() can be piped to `dharma_residuals()`.

# We will work with 100 simulations for fast examples, but you'll
# likely want to work with more than this (enough that the results
# are stable from run to run).

# not great:
set.seed(123)
simulate(fit, nsim = 100, type = "mle-mvn") |>
  dharma_residuals(fit)


# delta-lognormal looks better:
set.seed(123)
fit_dl <- update(fit, family = delta_lognormal())
simulate(fit_dl, nsim = 100, type = "mle-mvn") |>
  dharma_residuals(fit)

# or skip the pipe:
set.seed(123)
s <- simulate(fit_dl, nsim = 100, type = "mle-mvn")
# and manually plot it:
r <- dharma_residuals(s, fit_dl, plot = FALSE)
head(r)
plot(r$expected, r$observed)
abline(0, 1)

# return the DHARMa object and work with the DHARMa methods
ret <- simulate(fit_dl, nsim = 100, type = "mle-mvn") |>
  dharma_residuals(fit, return_DHARMa = TRUE)
plot(ret)

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