profile_targets() shows the names that can be supplied to
confint.drmTMB(). The table also records whether each row is currently
ready for direct profile-likelihood intervals. This helps users inspect the
fitted object before starting an expensive profile. Full q4 unstructured
and phylogenetic correlation summaries are derived targets; direct SD and
scale targets can still fail on a weak, boundary-limited, or one-sided
profile.
Value
A data frame with columns parm, target_class, dpar, term,
tmb_parameter, index, estimate, link_estimate, scale,
transformation, target_type, profile_ready, and profile_note.
target_type is "direct" for a target that maps to a single fitted TMB
parameter, "derived" for a transformed or multi-parameter quantity, or
"constrained" for a target that needs a model-specific constrained
profile. profile_ready = TRUE means the target is direct or constrained
and the fitted object retained the TMB object needed for
confint.drmTMB() with method = "profile". Common profile_note
values are "ready", "tmb_object_required", "missing_tmb_parameter",
"point_fit_only_zi_nbinom2_sigma_q1",
"point_fit_only_zero_one_beta_phylo_q1",
"point_fit_only_zero_one_beta_phylo_zoi_q1",
"point_fit_only_zero_one_beta_phylo_coi_q1",
"point_fit_only_zero_one_beta_animal_q1",
"point_fit_only_zero_one_beta_animal_zoi_q1",
"point_fit_only_zero_one_beta_animal_coi_q1",
"point_fit_only_zero_one_beta_relmat_q1",
"point_fit_only_zero_one_beta_relmat_zoi_q1",
"point_fit_only_zero_one_beta_relmat_coi_q1",
"point_fit_only_zero_one_beta_spatial_q1",
"point_fit_only_zero_one_beta_phylo_interaction_q1",
"point_fit_only_zero_one_beta_phylo_interaction_zoi_q1",
"point_fit_only_zero_one_beta_phylo_interaction_coi_q1",
"point_fit_only_zero_one_beta_zoi_q1",
"point_fit_only_zero_one_beta_coi_q1",
"derived_target", and
"derived_unstructured_correlation". A point_fit_only_* note records a
direct point-estimate target that is deliberately unavailable to
profiling: the zi-nbinom2 note covers the ordinary q1 scale route, and the
zero-one-beta notes cover that bounded family's structured q1 mean route
and its zero- and one-inflation routes.
Derived variance-ratio summaries such as total_variance_share and
phylo_total_variance_share are listed as point-estimate targets with
profile_ready = FALSE.
Details
Use ready_only = TRUE for the fastest inspection path before calling
confint(..., method = "profile"). Use the target_class column to filter
fixed effects, random-effect SDs, residual correlations, and other
variance-component rows before a long profile run.
Examples
dat <- data.frame(y = c(0.2, 0.5, 1.1, 1.4), x = c(-1, 0, 1, 2))
fit <- drmTMB(bf(y ~ x, sigma ~ 1), data = dat)
profile_targets(fit)
#> parm target_class dpar term tmb_parameter
#> 1 fixef:mu:(Intercept) fixed-effect mu (Intercept) beta_mu
#> 2 fixef:mu:x fixed-effect mu x beta_mu
#> 3 fixef:sigma:(Intercept) fixed-effect sigma (Intercept) beta_sigma
#> 4 sigma distributional-scale sigma (constant) beta_sigma
#> index estimate link_estimate scale transformation target_type
#> 1 1 0.59000000 0.590000 link linear_predictor direct
#> 2 2 0.42000000 0.420000 link linear_predictor direct
#> 3 1 -2.70183894 -2.701839 link linear_predictor direct
#> 4 1 0.06708204 -2.701839 response exp direct
#> profile_ready profile_note
#> 1 TRUE ready
#> 2 TRUE ready
#> 3 TRUE ready
#> 4 TRUE ready
profile_targets(fit, ready_only = TRUE)
#> parm target_class dpar term tmb_parameter
#> 1 fixef:mu:(Intercept) fixed-effect mu (Intercept) beta_mu
#> 2 fixef:mu:x fixed-effect mu x beta_mu
#> 3 fixef:sigma:(Intercept) fixed-effect sigma (Intercept) beta_sigma
#> 4 sigma distributional-scale sigma (constant) beta_sigma
#> index estimate link_estimate scale transformation target_type
#> 1 1 0.59000000 0.590000 link linear_predictor direct
#> 2 2 0.42000000 0.420000 link linear_predictor direct
#> 3 1 -2.70183894 -2.701839 link linear_predictor direct
#> 4 1 0.06708204 -2.701839 response exp direct
#> profile_ready profile_note
#> 1 TRUE ready
#> 2 TRUE ready
#> 3 TRUE ready
#> 4 TRUE ready