make_vaccineff_data {vaccineff} | R Documentation |
Construct vaccineff_data
Object
Description
This function constructs an S3 object of the class
vaccineff_data
that contains all the relevant information for the study.
to estimate the effectiveness.
Usage
make_vaccineff_data(
data_set,
outcome_date_col,
censoring_date_col = NULL,
vacc_date_col,
vacc_name_col = NULL,
vaccinated_status = "v",
unvaccinated_status = "u",
immunization_delay = 0,
end_cohort,
match = FALSE,
exact = NULL,
nearest = NULL,
take_first = FALSE,
t0_follow_up = NULL
)
Arguments
data_set |
|
outcome_date_col |
Name of the column that contains the outcome dates. |
censoring_date_col |
Name of the column that contains the censoring date. NULL by default. |
vacc_date_col |
Name of the column(s) that contain the vaccine dates. |
vacc_name_col |
Name of the column(s) that contain custom vaccine
names for the vaccines (e.g. brand name, type of vaccine). If provided,
must be of the same length as |
vaccinated_status |
Status assigned to the vaccinated population.
Default is |
unvaccinated_status |
Status assigned to the unvaccinated population.
Default is |
immunization_delay |
Characteristic time in days before the patient is considered immune. Default is 0. |
end_cohort |
End date of the study. |
match |
|
exact |
Name(s) of column(s) for |
nearest |
Named vector with name(s) of column(s) for |
take_first |
|
t0_follow_up |
Column with the initial dates of the follow-up period.
This column is only used if |
Value
An S3 object of class vaccineff_data
with all the information and
characteristics of the study. data.frames
are converted into an object of
class linelist
to easily handle with the data.
Examples
# Load example data
data("cohortdata")
# Create `vaccineff_data`
vaccineff_data <- make_vaccineff_data(data_set = cohortdata,
outcome_date_col = "death_date",
censoring_date_col = "death_other_causes",
vacc_date_col = "vaccine_date_2",
vaccinated_status = "v",
unvaccinated_status = "u",
immunization_delay = 15,
end_cohort = as.Date("2021-12-31"),
match = TRUE,
exact = c("age", "sex"),
nearest = NULL
)
# Print summary of data
summary(vaccineff_data)
# Plot vaccine coverage
plot(vaccineff_data)