make_vaccineff_data function

Construct vaccineff_data Object

This function constructs an S3 object of the class vaccineff_data that contains all the relevant information for the study. to estimate the effectiveness.

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: data.frame with cohort information.
• 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 vacc_date_col.
• vaccinated_status: Status assigned to the vaccinated population. Default is v.
• unvaccinated_status: Status assigned to the unvaccinated population. Default is u.
• immunization_delay: Characteristic time in days before the patient is considered immune. Default is 0.
• end_cohort: End date of the study.
• match: TRUE: cohort matching is performed. Default is FALSE
• exact: Name(s) of column(s) for exact matching. Default is NULL.
• nearest: Named vector with name(s) of column(s) for nearest matching and caliper(s) for each variable (e.g., nearest = c("characteristic1" = n1, "characteristic2" = n2), where n1 and n2 are the calipers). Default is NULL.
• take_first: FALSE: takes the latest vaccine date. TRUE: takes the earliest vaccine date.
• t0_follow_up: Column with the initial dates of the follow-up period. This column is only used if match = FALSE. If not provided, the follow-up period starts at start_cohort. Default is NULL.

Returns

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)