Confidence-Eye (or line) display of headline confidence intervals

plot_confidence_eye() draws the freqTLS Confidence Eye for one or more parameters (CTmax, z, or any other confint.profile_tls() target, including grouped names). It is a horizontal forest display: each parameter (and group level) is a row, the parameter value runs along the x-axis, and the confidence interval is a short, wide pale lens with a hollow point estimate. The shallow horizontal lens reads as a confidence interval. The layout follows the gllvmTMB / drmTMB Confidence-Eye contract.

Usage

plot_confidence_eye(
  fit,
  parm = c("CTmax", "z"),
  method = c("profile", "wald", "bootstrap"),
  level = 0.95,
  style = c("eye", "line"),
  raw_data = TRUE,
  fallback = TRUE,
  nboot = 1000L,
  boot_seed = NULL,
  cores = 1L,
  ...
)

Arguments

fit

A profile_tls fit from fit_tls().

parm

Character vector of target parameter names. Defaults to c("CTmax", "z"). Grouped names (e.g. "CTmax:larva") are accepted.

method

One of "profile" (default), "wald", or "bootstrap"; forwarded to confint.profile_tls().

level

Confidence level (default 0.95).

style

One of "eye" (default; pale horizontal lens + hollow point) or "line" (a confidence-interval bar with caps + hollow point, no lens).

raw_data

Logical; overlay observed assay temperatures as a rug on temperature-scale rows (default TRUE).

fallback, nboot, boot_seed, cores

Forwarded to confint.profile_tls(): control the parametric-bootstrap fallback for non-closing profiles (so the eye draws an honest bootstrap lens instead of only a hollow point), make it reproducible, and parallelise the refits. Defaults TRUE, 1000, NULL, and 1.

...

Reserved; must be empty.

Value

A ggplot object.

Details

Honest fallback for open profiles

When a profile does not close (conf.status is "open_lower", "open_upper", "open_both", or a bound is NA), no lens is drawn for that row: a hollow point marks the estimate and the subtitle flags the open interval. The eye is never fabricated from an open profile. A "wald_fallback" interval (e.g. up) still gets a lens, with the source noted in the caption.

Raw data

With raw_data = TRUE (default), the observed assay temperatures are drawn as a rug beneath any temperature-scale row (CTmax), showing the data support and flagging extrapolation when CTmax sits outside the assayed range.

Parameters on different scales (temperature for CTmax, a positive multiplier for z) are stacked in separate panels with a free x-axis.

Examples

d <- simulate_tls(family = "binomial", CTmax = 36, z = 4, seed = 1)
fit <- fit_tls(d, y = survived, n = total, time = duration, temp = temp,
               family = "binomial", tref = 1)
plot_confidence_eye(fit, parm = c("CTmax", "z"))