True prevalence from apparent prevalence with uncertainty — prevalence_lang

Uses lang-reiczigel estimators to incorporate uncertainty of sensitivity and specificity into an estimate of true prevalence from a given value of apparent prevalence.

Usage

prevalence_lang_reiczigel(
  pos_obs,
  n_obs,
  false_pos_controls = NULL,
  n_controls = NULL,
  false_neg_diseased = NULL,
  n_diseased = NULL,
  ...,
  spec = spec_prior(),
  sens = sens_prior(),
  confint = 0.95,
  fmt = "%1.2f%% [%1.2f%% — %1.2f%%]"
)

Arguments

pos_obs: the number of positive observations for a given test
n_obs: the number of observations for a given test
false_pos_controls: the number of positives that appeared in the specificity disease-free control group. These are by definition false positives. This is (1-specificity)*n_controls
n_controls: the number of controls in the specificity disease-free control group.
false_neg_diseased: the number of negatives that appeared in the sensitivity confirmed disease group. These are by definition false negatives. This is (1-sensitivity)*n_diseased
n_diseased: the number of confirmed disease cases in the sensitivity control group.
...: not used
spec: the prior specificity of the test as a beta_dist.
sens: the prior sensitivity of the test as a beta_dist.
confint: confidence interval limits
fmt: a sprintf formatting string accepting 3 numbers

Value

the expected value of apparent prevalence