fitCox.R

parseFormula <- function(event_name, vars) {
  m_formula <- paste0(
    ## Otavio/Anna change this since you are not using age as time scale!
    "Surv(age_start, age_end, ", event_name, ") ~ ",
    paste(vars, collapse = " + ")
  )

  as.formula(m_formula)
}

fitCox <- function(data, event_name, expo, vars) {
  stopifnot(length(event_name) == 1 & length(expo) == 1)
  all_vars <- c(expo, vars)
  m_formula <- parseFormula(event_name, all_vars)
  m <- coxph(m_formula, data = data)

  m_aic <- AIC(m)
  m_bic <- BIC(m)

  m_coefs <- broom::tidy(m, exponentiate = TRUE, conf.int = TRUE) %>%
    mutate(
      outcome = event_name,
      expo = paste(expo, collapse = ", "),
      covariates = paste(vars, collapse = ", "),
      aic = m_aic,
      bic = m_bic
    )

  gc()

  m_coefs
}