Inspect legacy interval output from a halted Julia bridge

The Julia bridge is halted/deferred future work and is not a current fitting or inference route. This method is retained only for inspecting existing drmTMB_julia objects; use native TMB fits for new analyses.

Usage

# S3 method for class 'drmTMB_julia'
confint(
  object,
  parm = NULL,
  level = 0.95,
  method = c("wald", "profile", "bootstrap"),
  R = 199L,
  seed = NULL,
  threads = FALSE,
  ...
)

Arguments

object: A drmTMB_julia fit.
parm: Optional target selection. For "wald", compact coefficient labels ("mu:x") or full names ("fixef:mu:x"); for "profile" / "bootstrap", supported SD target names such as "sd:mu:phylo(1 | species)" or, for q = 4 bivariate fits, "sd:sigma1:phylo(1 | species)".
level: Confidence level.
method: "wald" (default), "profile", or "bootstrap".
R: Bootstrap replicate count (used only when method = "bootstrap").
seed: Optional bootstrap seed.
threads: Logical; request Julia-side threaded inference for the profile / bootstrap path.
...: Unused.

Value

A confidence-interval data frame with the shared parm, level, lower, upper, scale, transformation, tmb_parameter, index, method, and conf.status columns.

Details

For a legacy engine = "julia" fit, confint() exposes two interval families:

method = "wald" (the default) builds symmetric Wald intervals for the fixed-effect coefficients (mu, sigma, ...) on the linear-predictor (link) scale, using the fixed-effect covariance DRM.jl marshals back through the bridge (vcov(object)). This mirrors the native drmTMB Wald path, whose fixed-effect rows are also reported on the link scale.
method = "profile" / method = "bootstrap" re-enter DRM.jl's inference primitive for supported phylogenetic SD targets, transformed back to the positive response scale. The current R bridge exposes the univariate Gaussian sd:mu:phylo(1 | species) target and the four bivariate q = 4 targets sd:mu1:*, sd:mu2:*, sd:sigma1:*, and sd:sigma2:*.