Residuals from an Rceattle fit — residuals.Rceattle • Rceattle

Returns a long-format data frame of residuals, following the convention of stats::residuals.glm() where type selects the kind of residual. By default residuals are returned for every applicable data source – survey indices, fishery catches, age/length composition (comp), and conditional age-at-length (caal); use source to restrict to particular ones.

Usage

# S3 method for class 'Rceattle'
residuals(
  object,
  type = "response",
  source = "all",
  scale = "log",
  species = NULL,
  ...
)

Arguments

object: An object of class "Rceattle" returned by fit_mod().
type: Residual kind: one of "response" (default), "pearson", "osa", or "process".
source: Data source(s) to include: any of "index", "catch", "comp", "caal", or "all" (default). "diet" (predator stomach-content composition) is also accepted but, because it uses a predator/prey schema rather than the fleet/bin layout, must be requested on its own. Ignored when type = "process".
scale: "log" (default) or "natural". Only affects "response" residuals for index / catch.
species: Optional species code(s) to include (matched against the Species column). Default NULL keeps all species. Mirrors the species argument of plot.rceattle_osa().
...: Passed to osa_residuals() (e.g. method, seed) when type = "osa", or to process_residuals() when type = "process".

Value

A data.frame with columns Source, Fleet_code, Fleet_name, Species, Sex, Year, Length, Bin, Age0_Length1, Sample_size, Observed, Fitted, Residual. Columns are NA where they do not apply.

Details

Residual kinds (type):

"response": Observed minus fitted. For index / catch this is on the log scale by default (matching the lognormal likelihood; set scale = "natural" for the arithmetic difference); for comp / caal it is the difference in proportions, observed minus fitted.
"pearson": Standardized residuals. For index / catch, \((\log o - (\log\hat{o} - b\,\sigma^2/2))/\sigma\) using the model's realized observation log-SD \(\sigma\) and the observation bias-adjustment flag \(b\) (bias_adjust_obs, default 1); for comp / caal, \((p - \hat{p})/\sqrt{\hat{p}(1 - \hat{p})/N}\) with input sample size N.
"osa": One-step-ahead residuals via osa_residuals(), which builds the composition observation data on demand from any fit.
"process": Process residuals via process_residuals() for the model's random-effect deviations; source does not apply.

Composition rows are returned in long form (one row per observation x age/length bin) and carry the Age0_Length1 flag from comp_data (0 age, 1 length); CAAL rows carry both the conditioning Length and the age Bin.