Behavioral Health Event Co-Occurence

bhs_cooccur.R

library("dplyr")
library("tidyr")
library("cooccur")

options(stringsAsFactors=FALSE)

bhs <- read.csv("Behavioral Health Services - higher grouping.csv") %>%
  mutate(
    SVC_START_DT = as.Date(SVC_START_DT, "%m/%d/%Y"),
    SVC_END_DT = as.Date(SVC_END_DT, "%m/%d/%Y"),
    SUBMT_DT = as.Date(SUBMT_DT, "%m/%d/%Y"),
    SERVICE_CAT_HIGHER = ifelse(SERVICE_CAT_HIGHER == "#N/A", NA, trimws(SERVICE_CAT_HIGHER))
  )

cooccur_data <- bhs %>%
  select(MCI_UNIQ_ID, SERVICE_CAT_HIGHER) %>%
  filter(SERVICE_CAT_HIGHER != "") %>%
  count(MCI_UNIQ_ID, SERVICE_CAT_HIGHER) %>%
  mutate(n = ifelse(n > 0, 1, 0)) %>%
  spread(SERVICE_CAT_HIGHER, n, fill = 0) %>%
  select(-MCI_UNIQ_ID) %>%
  as.matrix() %>%
  t()

cooccur_result <- cooccur(cooccur_data, spp_names = TRUE)
plot(cooccur_result)