sanity: Sanity check of an sdmTMB model

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

Sanity check of an sdmTMB model

Description

Sanity check of an sdmTMB model

Usage

sanity(object, big_sd_log10 = 2, gradient_thresh = 0.001, silent = FALSE)

Arguments

object	Fitted model from sdmTMB().
big_sd_log10	Value to check size of standard errors against. A value of 2 would indicate that standard errors greater than 10^2 (i.e., 100) should be flagged.
gradient_thresh	Gradient threshold to issue warning.
silent	Logical: suppress messages? Useful to set to TRUE if running large numbers of models and just interested in returning sanity list objects.

Details

If object is NA, NULL, or of class "try-error", sanity() will return FALSE. This is to facilitate using sanity() on models with try() or tryCatch(). See the examples section.

Value

An invisible named list of checks.

Examples

fit <- sdmTMB(
  present ~ s(depth),
  data = pcod_2011, mesh = pcod_mesh_2011,
  family = binomial()
)
sanity(fit)

s <- sanity(fit)
s

# If fitting many models in a loop, you may want to wrap
# sdmTMB() in try() to handle errors. sanity() will take an object
# of class "try-error" and return FALSE.
# Here, we will use stop() to simulate a failed sdmTMB() fit:
failed_fit <- try(stop())
s2 <- sanity(failed_fit)
all(unlist(s))
all(unlist(s2))

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