generate_comorbidity_df: Generate a comorbidity dataframe
In medicalrisk: Medical Risk and Comorbidity Tools for ICD-9-CM Data

Description Usage Arguments Details Value Examples

Merges a given DF of IDs and ICD-9-CM codes to one of the ICD9CM maps, removes redundant comorbidities, and returns a dataframe.

generate_comorbidity_df(
  df,
  idvar = "id",
  icd9var = "icd9cm",
  icd9mapfn = icd9cm_charlson_quan,
  .progress = "none",
  .parallel = FALSE,
  .paropts = NULL
)

`df`	a data frame with at least two columns, specified as `idvar` and `icd9var`.
`idvar`	string with name of ID variable within `df` (defaults to "id")
`icd9var`	string with name of ICD code variable within `df` (defaults to `icd9cm`)
`icd9mapfn`	Function to generate comorbidity data frame from ICD-9 codes (defaults to `icd9cm_charlson_quan`)
`.progress`	passed to `ddply`
`.parallel`	passed to `ddply`
`.paropts`	passed to `ddply`

Redundancy rules: * If "tumor" and "mets", only "mets" will be returned. * If "htn" and "htncx", only "htncx" will be returned. * If "dm" and "dmcx", only "dmcx" will be returned. * If "liver" and "modliver", only "modliver" will be returned.

Van Walraven has a modification adopted here where the following "dmcx" codes are downgraded to "dm" if the specific DM complication is separately coded: * D2(49|50)4x is DM w renal * D2(49|50)6x is DM w neuro * D2(49|50)7x is DM w PVD

Cases without any comorbidities will not appear in the returned data frame.

a dataframe with column idvar and a logical column for each comorbidity

cases <- data.frame(id=c(1,1,1,2,2,2,2,2),
         icd9cm=c("D20206","D24220","D4439","D5064","DE8788","D40403","D1960","D1958"),
         stringsAsFactors=TRUE)
generate_comorbidity_df(cases)
# generate categories for patients in the \code{\link{vt_inp_sample}}
generate_comorbidity_df(vt_inp_sample)
# in this example, D25071 is reduced to "dm" from "dmcx" because D4439 already codes perivasc
# also, D20206 "tumor" and D1970 "mets" lead to just "mets"
# D25001 and D25040 are just "dmcx"
# D45621 and D570 are just "modliver"
cases <- data.frame(id=c(1,1,1,1,2,2,2,2),
  icd9cm=c("D1970","D20206","D25071","D4439","D25001","D25040","D45621","D570"),
  stringsAsFactors=TRUE)
generate_comorbidity_df(cases)