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Factor-level comparisons of the discount rate k

Source: R/dd-comparisons.R
get_dd_comparisons.Rd

Computes factor-level contrasts of the discount rate k from a fitted beezdiscounting_tmb model (or a structural beezdiscounting_choice fit). k is linear in the fixed-effect coefficients on the natural-log scale (log k = X beta_k), so each contrast is a linear combination of beta_k with a Wald standard error from the beta_k block of TMB::sdreport()'s fixed-effect covariance. Contrasts are reported on the log10 scale and, optionally, as multiplicative ratios (ratio = exp(est_log)). The returned container mirrors the beezdemand beezdemand_comparison shape, so tidy.beezdiscounting_comparison() gives a flat, cross-backend frame. Bayesian fits (beezdiscounting_brms, beezdiscounting_choice_brms) compute per-draw contrasts over the same reference grid: posterior medians with quantile credible intervals and post.prob in place of adjusted p-values (no multiplicity adjustment; the joint posterior already encodes contrast dependence).

Usage

get_dd_comparisons(
  fit,
  compare_specs = NULL,
  contrast_type = c("pairwise", "trt.vs.ctrl"),
  contrast_by = NULL,
  adjust = "holm",
  at = NULL,
  ci_level = 0.95,
  report_ratios = TRUE,
  ...
)

Arguments

fit

A beezdiscounting_tmb, structural beezdiscounting_choice, beezdiscounting_brms, or beezdiscounting_choice_brms object.

compare_specs

Optional one-sided formula naming the factor subset to contrast (e.g. ~ condition). Omitted fitted factors are marginalized over with equal weights across the full crossing of their levels. If NULL (default), all fitted factors are retained. Unknown names abort.

contrast_type

Character. "pairwise" (all choose(n, 2) pairs, factor-level order) or "trt.vs.ctrl" (each level vs. the first/reference level).

contrast_by

Optional NULL (default) or character vector of factor name(s) within compare_specs to condition the contrasts on. Within each observed combination of by-level(s), pairwise (or trt.vs.ctrl) contrasts are computed over the remaining (non-by) factors, with p-value adjustment applied per by-cell. A contrast_by factor absent from compare_specs aborts.

adjust

Character. P-value adjustment method; must be one of stats::p.adjust.methods (default "holm"). emmeans-only methods such as "tukey"/"sidak" are rejected (the TMB backend uses an asymptotic z + stats::p.adjust()).

at

Named list specifying factor levels and/or continuous-covariate values to condition on, as in get_dd_param_emms().

ci_level

Numeric. Confidence level for intervals (default 0.95).

report_ratios

Logical. If TRUE (default), include a contrasts_ratio block (multiplicative ratios).

...

Additional arguments (reserved; factors_in_emm is accepted as a lower-level alternative to compare_specs).

Value

A beezdiscounting_comparison object: a list with a single element k, itself a list with emmeans (the EMM tibble from get_dd_param_emms()), contrasts_log10 (columns contrast, estimate, std.error, statistic, df, conf.low, conf.high, p.value), and (if report_ratios) contrasts_ratio (columns contrast, ratio, conf.low, conf.high, p.value). When contrast_by is active, the contrast tables gain leading by-column(s) before contrast. Attributes backend, adjustment_method, compare_specs_used, contrast_type_used, and contrast_by_used describe the call.

See also

tidy.beezdiscounting_comparison() for the cross-backend frame.

Examples

# \donttest{
sim <- simulate_dd_ip(
  n_subjects = 30, n_conditions = 2, delta_k = c(0, log(3)), seed = 1
)
fit <- fit_dd_tmb(sim, factors = "condition", verbose = 0)
get_dd_comparisons(fit, contrast_type = "pairwise")
#> $k
#> $k$emmeans
#> # A tibble: 2 × 6
#>   level             k k_log std.error conf.low conf.high
#>   <chr>         <dbl> <dbl>     <dbl>    <dbl>     <dbl>
#> 1 condition=C1 0.0112 -4.49     0.152  0.00834    0.0151
#> 2 condition=C2 0.0276 -3.59     0.154  0.0204     0.0373
#> 
#> $k$contrasts_log10
#> # A tibble: 1 × 8
#>   contrast         estimate std.error statistic    df conf.low conf.high p.value
#>   <chr>               <dbl>     <dbl>     <dbl> <dbl>    <dbl>     <dbl>   <dbl>
#> 1 condition=C1 - …   -0.391    0.0935     -4.18   Inf   -0.574    -0.207 2.95e-5
#> 
#> $k$contrasts_ratio
#> # A tibble: 1 × 5
#>   contrast                    ratio conf.low conf.high   p.value
#>   <chr>                       <dbl>    <dbl>     <dbl>     <dbl>
#> 1 condition=C1 - condition=C2 0.407    0.267     0.620 0.0000295
#> 
#> 
#> attr(,"class")
#> [1] "beezdiscounting_comparison"
#> attr(,"backend")
#> [1] "tmb"
#> attr(,"adjustment_method")
#> [1] "holm"
#> attr(,"compare_specs_used")
#> [1] "all fitted factors"
#> attr(,"contrast_type_used")
#> [1] "pairwise"
#> attr(,"contrast_by_used")
#> [1] "NULL"
# }