add_ar and add_cfr not working

[PBBlomquist]

Working on the r4epis sitrep package and need these two functions in epitabulate but they're not working.

add_ar

The function builds on a tbl_summary output, which works fine:

But then when you add on the add_ar function it looks like this:

See here:

library(dplyr)
library(gtsummary)
library(epitabulate)

# Create dummy data
linelist_cleaned <- data.frame(
  age_group = sample(c("0-4", "5-9", "10-14", "15-19"), 20, replace = TRUE)
) 

population_data_age <- data.frame(
  age_group = c("0-4", "5-9", "10-14", "15-19"),
  population = c(5000, 6000, 5500, 5200)  # Dummy population counts
)

# Test the code
linelist_cleaned %>%
  mutate(case_total = TRUE) %>% 
  select(case_total, age_group) %>%
  gtsummary::tbl_summary(
    include = age_group, 
    label = list(age_group ~ "Age Group")
  ) %>%
  epitabulate::add_ar(
    ## specify which variable counts cases (dummy)
    case_var = "case_total",
    ## get the population counts as a vector
    population = pull(population_data_age, population),
    drop_tblsummary_stat = TRUE)

My solution was to use attack_rate instead:

linelist_cleaned |> 
  count(age_group) |> 
  left_join(population_data_age) |> 
  mutate(attack_rate_result = pmap(list(n, population), ~ attack_rate(.x, .y, multiplier = 10000))) |> 
  select(-n, -population) |> 
  unnest(attack_rate_result) 

add_cfr()

This function also builds on a tbl_summary() output, which itself is fine, but then add_cfr() makes the output blank. You can see here:

library(dplyr)
library(gtsummary)
library(epitabulate)

# Dummy data
linelist_cleaned <- data.frame(
  patient_facility_type = sample(c("Inpatient", "Outpatient"), 20, replace = TRUE),
  DIED = sample(c(TRUE, FALSE, NA), 20, replace = TRUE),
  case_def = sample(c("Confirmed", "Probable", "Suspected"), 20, replace = TRUE)
)

# Test the code
linelist_cleaned %>%
  filter(patient_facility_type == "Inpatient") %>%
  select(DIED, case_def) %>%
  gtsummary::tbl_summary(
    include = case_def,
    statistic = case_def ~ "{n}",
    missing = "no",
    label = case_def ~ "Case definition"
  ) %>%
  modify_header(stat_0 = "Cases (N)") |> 
  # Use wrapper function to calculate cfr
  add_cfr(deaths_var = "DIED")