R/create_regression_table.R

In patrickwu510/ddiwas: What the Package Does (One Line, Title Case)

#' Create regression table.
#' Last updated on 2020-06-22
#'
#' @param medications A tibble
#' @param covariates A tibble
#' @return A list with two tibbles \code{regression_table_output}
#' @export

create_regression_table <- function(medications, covariates) {

  #keep only last drug exposure
  medications1 <- medications %>%
    arrange(person_id, desc(date)) %>%
    distinct(person_id, rxcui_ingr)
  ##add `count` column in preparation to make regression table
  medications1$count <- 1
  ##pivot to make regression table
  regression_drugs <- medications1 %>%
    pivot_wider(names_from = rxcui_ingr,
                values_from = count,
                values_fill = list(count = 0))

  #process `covariates`
  covariates <- covariates %>%
    select(person_id, gender, dob, race, groupc)
  covariates1 <- medications %>%
    select(person_id, start_date, obs_length) %>%
    distinct()
  covariates1 <- inner_join(covariates,
                            covariates1,
                            by = "person_id")
  ##calculate age
  covariates1$age <- interval(covariates1$dob, covariates1$start_date)
  covariates1$age <- time_length(covariates1$age, "year")
  covariates1 <- covariates1 %>%
    filter(age >= 18 & age < 90)

  #normalize covariates
  ##age
  v1 <- covariates1$age
  v2 <- (v1-min(v1))/(max(v1)-min(v1))
  covariates1$age_n <- v2
  ##obs_length
  v1 <- covariates1$obs_length
  v2 <- (v1-min(v1))/(max(v1)-min(v1))
  covariates1$obs_length_n <- v2
  ##convert binary variables
  covariates1$is_m <- if_else(covariates1$gender == "M", 1, 0)
  covariates1$is_w <- if_else(covariates1$race == "W", 1, 0)
  ##select normalized columns only
  covariates1 <- covariates1 %>%
    select(person_id, is_m, is_w, age_n, obs_length_n, groupc)

  #merge regression_drugs with covariates
  regression_table <- inner_join(covariates1,
                                 regression_drugs,
                                 by = "person_id")

  return(regression_table)
}