Construct vaccineff_data Object — make_vaccineff

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: 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.

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

# \donttest{
# 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)
#> Cohort start:  2021-03-26
#> Cohort end:  2021-12-31
#> The start date of the cohort was defined as the mininimum immunization date. 
#> 65 registers were removed with outcomes before the start date.
#> 
#> Nearest neighbors matching iteratively performed.
#> Number of iterations:  4
#> Balance all:
#>               u         v         smd
#> age   63.917069 62.997438 -0.08593156
#> sex_F  0.520277  0.573474  0.10701746
#> sex_M  0.479723  0.426526 -0.10701746
#> 
#> Balance matched:
#>               u         v smd
#> age   63.751784 63.751784   0
#> sex_F  0.521457  0.521457   0
#> sex_M  0.478543  0.478543   0
#> 
#> Summary vaccination:
#>               u     v
#> All       10973 19905
#> Matched   10789 10789
#> Unmatched   184  9116
#> 
#> // tags: outcome_date_col:death_date, censoring_date_col:death_other_causes, vacc_date_col:vaccine_date_2, immunization_date_col:immunization_date, vacc_status_col:vaccine_status 

# Plot vaccine coverage
plot(vaccineff_data)

# }