icd9 (version 0.5)

icd9FilterPoa: filters data frame based on present-on-arrival flag

Description

this is not a simple binary, since many codes are exempt, unspecified, or unknown. Therefore, two options are given: get all the comorbidities where the POA flag was definitely -ve, coded as "N" or definitely +ve and coded as "Y". Negating one set won't give the other set unless all codes were either Y or N. #describeIn icd9Comorbidities

Usage

icd9FilterPoa(icd9df, poaField = "poa", poa = icd9PoaChoices)
icd9FilterPoaYes(icd9df, poaField = "poa")
icd9FilterPoaNo(icd9df, poaField = "poa")
icd9FilterPoaNotNo(icd9df, poaField = "poa")
icd9FilterPoaNotYes(icd9df, poaField = "poa")

Arguments

icd9df

data frame containing columns for visitId (which is the feault name), icd9 (default for the icd9 code), and maybe also a POA flag.

poaField

The name of column in the data frame which contains the Present On Arrival flag. The flag itself is a single character, typically one of "Y", "N", "E", "X", "U" or empty. The poaField is a character vector of length one.

poa

single character value, being one of poaChoices whether to account for co-morbidities flagged as present-on-arrival. This is not a simple binary, since many codes are exempt, unspecified, or unknown. poaField gives the choices: y

Examples

# using magrittr is beautiful:
library("magrittr", quietly = TRUE, warn.conflicts = FALSE)
myData <- data.frame(
  visitId = c("v1", "v2", "v3", "v4"),
  icd9 = c("39891", "39790", "41791", "4401"),
  poa = c("Y", "N", NA, "Y"),
  stringsAsFactors = FALSE
)
myData %>% icd9FilterPoaNotNo() %>% icd9ComorbiditiesAhrq(isShort = TRUE)
# can fill out named fields also:
myData %>% icd9FilterPoaYes(poaField="poa") %>%
  icd9ComorbiditiesAhrq(icd9Field = "icd9", visitId = "visitId")
# can call the core icd9Comorbidities function with an arbitrary mapping
myData %>%
icd9FilterPoaYes() %>%
icd9Comorbidities(icd9Field = "icd9", visitId = "visitId",
  icd9Mapping = quanElixhauserComorbid,
 validateMapping = TRUE,
 isShortMapping = TRUE)