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cmgiven/bhs_cooccur.R

Created December 3, 2016 22:09
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Behavioral Health Event Co-Occurence
Raw
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)
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