Incidence estimation model

Fits an inc2prev model to recover incidence from prevalence data using a probility of detection curve.

incidence(
  prev,
  ab = NULL,
  vacc = NULL,
  init_ab = NULL,
  prob_detect,
  data_args = list(),
  model = i2p_model(),
  var_col = NULL,
  variables = NULL,
  quantiles = seq(0.05, 0.95, by = 0.05),
  samples = 100,
  keep_fit = FALSE,
  p,
  ...
)

Arguments

prev: Observed positiviy prevalence data
ab: Observed antibody prevalence data
vacc: Observed vaccination data
init_ab: Observed initial antibody data
prob_detect: Time-varying probability of detection
data_args: A list of arguments to pass to i2p_data()
model: A stan model object as produced by i2p_model() or a similar compiled stan model.
var_col: Column of a common name in the data frames passed as data that should be treated as indicator of multiple data sets that should be used jointly for estimation
variables: A vector of variables to summarise and return
quantiles: A vector of quantiles to return in summarising
samples: The number of samples to return
keep_fit: Whether to retain the stan fit object
p: A progressr function used when fitting multiple models to track progress
...: Additional arguments passed to fit_fn.

Value

A data.table including summarised estimates and parameter samples.

Arguments

Value

See also