R Under development (unstable) (2026-02-18 r89435 ucrt) -- "Unsuffered Consequences"
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> ################################################################################
> # Verify primary diagnoses are excluded from comorbidity flagging
> library(medicalcoder)
> 
> df <- data.frame(
+   patid = c(1L, 2L),
+   icdv  = c(10L, 10L),
+   dx    = c(1L, 1L),
+   code  = c("I252", "I252"), # MI code that should flag Charlson when counted
+   primarydx = c(0L, 1L),
+   stringsAsFactors = FALSE
+ )
> 
> res0 <- comorbidities(
+   data      = df,
+   id.vars   = "patid",
+   icdv.var  = "icdv",
+   dx.var    = "dx",
+   icd.codes = "code",
+   method    = "charlson_quan2011",
+   poa       = 1L,
+   primarydx = 0L
+ )
> 
> res1 <- comorbidities(
+   data      = df,
+   id.vars   = "patid",
+   icdv.var  = "icdv",
+   dx.var    = "dx",
+   icd.codes = "code",
+   method    = "charlson_quan2011",
+   poa       = 1L,
+   primarydx = 1L
+ )
> 
> resv <- comorbidities(
+   data      = df,
+   id.vars   = "patid",
+   icdv.var  = "icdv",
+   dx.var    = "dx",
+   icd.codes = "code",
+   method    = "charlson_quan2011",
+   poa       = 1L,
+   primarydx.var = "primarydx"
+ )
> 
> stopifnot(identical(res0[["cmrb_flag"]], c(1L, 1L)))
> stopifnot(identical(res1[["cmrb_flag"]], c(0L, 0L)))
> stopifnot(identical(resv[["cmrb_flag"]], c(1L, 0L)))
> 
> ################################################################################
> #                                 End of File                                  #
> ################################################################################
> 
> proc.time()
   user  system elapsed 
   3.32    0.48    3.79