Prepare data from a serological survey for modelling

This function adds the necessary additional variables to the given dataset serodata corresponding to a serological survey.

Usage

prepare_serodata(serodata = serodata, alpha = 0.05)

Arguments

serodata

A data frame containing the data from a serological survey. This data frame must contain the following columns:

survey: survey Label of the current survey
total: Number of samples for each age group
counts: Number of positive samples for each age group
age_min: age_min
age_max: age_max
tsur: Year in which the survey took place
country: The country where the survey took place
test: The type of test taken
antibody: antibody

Alternatively to age_min and age_max, the dataset could already include the age group marker age_mean_f, representing the middle point between age_min and age_max. If afe_mean_f is missing, it will be generated by the function.

alpha

probability of a type I error. For further details refer to binconf.

Value

serodata with additional columns necessary for the analysis. These columns are:

age_mean_f: Floor value of the average between age_min and age_max for the age groups delimited by age_min and age_max
sample_size: The size of the sample
birth_year: Years in which the subject was born according to the age group marker age_mean_f
prev_obs: Observed prevalence
prev_obs_lower: Lower limit of the confidence interval for the observed prevalence
prev_obs_upper: Upper limit of the confidence interval for the observed prevalence

Examples

data(chagas2012)
serodata <- prepare_serodata(chagas2012)