02_complications.R

# Script and comments by Riinu Pius, 2023-09-06

# This script wrangles the MOVER EPIC EHR post-op complications dataset
# into a `one row per patient-procedure` table by:
# 1. Creating variable 'any complication' which is set to No if all observations are "None".
# 2. If comp_abbr complication is "AN Post-op Complications",
# taking the value from smrtdta_elem_value and overwriting comp_abbr with it.
# 3. Collapsing all complications stored in multiple rows
# into a single row/cell per patient. Collapsing is done by comma (", ")
# 4. Creating two derived variables called death and respiratory that look for these complications within the collapsed lists.
# 5. Most Deaths are noted in Patient Info under discharge as 'Expired', joining those in here

library(tidyverse)

complications_orig = read_csv(paste0(Sys.getenv("epic_emr"), "patient_post_op_complications.csv"))

demographics = read_csv("/home/common/mover_data/surginf_cleaned/patient_information_cleaned.csv")

complications_orig %>% 
  mutate(death = str_detect(SMRTDTA_ELEM_VALUE, "Death")) %>% 
  distinct(LOG_ID, MRN, death) %>% 
  count(death)


complications_all = complications_orig %>% 
  janitor::clean_names() %>% 
  distinct() %>% 
  rename(comp_abbr    = element_abbr,
         complication = smrtdta_elem_value) %>% 
  mutate(complication = if_else(is.na(complication), "Unknown", complication))

complications_combined = complications_all %>% 
  mutate(comp_abbr = if_else(comp_abbr == "AN Post-op Complications",
                             complication, comp_abbr)) %>% 
  arrange(comp_abbr) %>% 
  summarise(.by = c(log_id, mrn),
            any_complication   = if_else(all(complication == "None"), "No", "Yes"),
            n_complications    = sum(complication != "None"),
            comp_abbr = paste(unique(comp_abbr), collapse = ", "),
            comp_full = paste(unique(complication), collapse = ", ")) %>% 
  mutate(comp_abbr = if_else(any_complication   == "No",
                             "No complications",
                             str_remove(comp_abbr, "None, |, None")),
         comp_full = if_else(any_complication   == "Yes",
                             str_remove(comp_full, "None, |, None"),
                             comp_full))

comp1 = nrow(complications_combined)
complications_combined = complications_combined %>% 
  left_join(select(demographics, log_id, mrn, disch_disp))
stopifnot(comp1 == nrow(complications_combined))

complications = complications_combined %>% 
  mutate(death       = if_else(str_detect(comp_abbr, "Death") | disch_disp == "Expired",
                               "Died", "Alive"),
         respiratory_comp = if_else(str_detect(comp_abbr, "Respiratory"),
                                    "Yes", "No"))

complications %>% 
  count(death)

write_csv(complications, "/home/common/mover_data/surginf_cleaned/complications_cleaned.csv")


complications = read_csv("/home/common/mover_data/surginf_cleaned/complications_cleaned.csv")
# quick look at complication rates
complications %>% 
  count(any_complication) %>% 
  mutate(prop = scales::percent(n/sum(n)))

complications %>% 
  count(respiratory_comp) %>% 
  mutate(prop = scales::percent(n/sum(n)))

complications %>% 
  count(death) %>% 
  mutate(prop = scales::percent(n/sum(n), 0.01))

complications %>% 
  count(infection = str_detect(comp_abbr, "Infection")) %>% 
  mutate(prop = scales::percent(n/sum(n), 0.01))


complications %>% 
  filter(str_detect(comp_full, "death|Death")) %>% 
  nrow()