seroincidence (version 2.0.0)

summary.seroincidence: Summary Method for Seroincidence Object

Description

Calculate seroincidence from output of the seroincidence calculator estimateSeroincidence.

Usage

# S3 method for seroincidence
summary(object, ..., quantiles = c(0.025, 0.975),
  showDeviance = TRUE, showConvergence = TRUE)

Arguments

object

A dataframe containing output of function estimateSeroincidence.

...

Additional arguments affecting the summary produced.

quantiles

A vector of length 2 specifying quantiles for lower (first element) and upper (second element) bounds of lambda. Default = c(0.025, 0.975).

showDeviance

Logical flag (FALSE/TRUE) for reporting deviance (-2*log(likelihood) at estimated seroincidence. Default = TRUE.

showConvergence

Logical flag (FALSE/TRUE) for reporting convergence (see help for optim for details). Default = TRUE.

Value

A list with the following items:

Results

Dataframe with maximum likelihood estimate of lambda (the seroincidence) (column Lambda) and corresponding lower (Lambda.lwr) and upper (Lambda.upr bounds. Optionally Deviance (Negative log likelihood (NLL) at estimated (maximum likelihood) lambda) and Covergence (Convergence indicator returned by optim. Value of 0 indicates convergence) columns are included.

Antibodies

Character vector with names of input antibodies used in estimateSeroincidence.

Strata

Character with names of strata used in estimateSeroincidence.

CensorLimits

List of cutoffs for each of the antibodies used in estimateSeroincidence.

Examples

# NOT RUN {
# }
# NOT RUN {
# estimate seroincidence
seroincidence <- estimateSeroincidence(...)

# calculate summary statistics for the seroincidence object
seroincidenceSummary <- summary(seroincidence)
# }
# NOT RUN {
# }