R Under development (unstable) (2025-11-21 r89046 ucrt) -- "Unsuffered Consequences"
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> source('utilities.R')
> ################################################################################
> # Tests for summarizing Elixhauser comorbidities
> library(medicalcoder)
> 
> ################################################################################
> # Build Elixhauser comorbidities and summary
> elixhauser <- comorbidities(
+   data        = mdcr,
+   id.vars     = "patid",
+   icdv.var    = "icdv",
+   icd.codes   = "code",
+   dx.var      = "dx",
+   method      = "elixhauser_ahrq2025",
+   flag.method = "current",
+   poa         = 1,
+   primarydx   = 0
+ )
> 
> summary_current <- summary(elixhauser)
> 
> stopifnot(
+   is.list(summary_current),
+   identical(names(summary_current), c("conditions", "index_summary")),
+   is.data.frame(summary_current$conditions),
+   identical(
+     names(summary_current$conditions),
+     c("condition", "count", "percent")
+   ),
+   is.character(summary_current$conditions$condition),
+   is.numeric(summary_current$conditions$count),
+   is.numeric(summary_current$conditions$percent),
+   all(summary_current$conditions$count >= 0),
+   all(summary_current$conditions$percent >= 0),
+   all(summary_current$conditions$percent <= 100)
+ )
> 
> ################################################################################
> # Conditions summary matches direct aggregations
> hf_count <- summary_current$conditions[
+   summary_current$conditions$condition == "HF",
+   "count"
+ ]
> diab_cx_count <- summary_current$conditions[
+   summary_current$conditions$condition == "DIAB_CX",
+   "count"
+ ]
> 
> stopifnot(
+   hf_count == sum(elixhauser$HF),
+   diab_cx_count == sum(elixhauser$DIAB_CX)
+ )
> 
> num_ge_1 <- summary_current$conditions[
+   summary_current$conditions$condition == ">= 1",
+   "count"
+ ]
> num_ge_2 <- summary_current$conditions[
+   summary_current$conditions$condition == ">= 2",
+   "count"
+ ]
> 
> stopifnot(
+   num_ge_1 == sum(elixhauser$num_cmrb >= 1),
+   num_ge_2 == sum(elixhauser$num_cmrb >= 2)
+ )
> 
> ################################################################################
> # Index summary aligns with expected calculations
> stopifnot(
+   is.data.frame(summary_current$index_summary),
+   identical(
+     names(summary_current$index_summary),
+     c("index", "min", "q1", "median", "q3", "max")
+   ),
+   is.character(summary_current$index_summary$index),
+   is.numeric(summary_current$index_summary$min),
+   is.numeric(summary_current$index_summary$q1),
+   is.numeric(summary_current$index_summary$median),
+   is.numeric(summary_current$index_summary$q3),
+   is.numeric(summary_current$index_summary$max)
+ )
> 
> expected_index_summary <-
+   data.frame(
+     index  = c("readmission", "mortality"),
+     min    = c(min(elixhauser$readmission_index),
+                min(elixhauser$mortality_index)),
+     q1     = c(stats::quantile(elixhauser$readmission_index, prob = 0.25),
+                stats::quantile(elixhauser$mortality_index, prob = 0.25)),
+     median = c(stats::median(elixhauser$readmission_index),
+                stats::median(elixhauser$mortality_index)),
+     q3     = c(stats::quantile(elixhauser$readmission_index, prob = 0.75),
+                stats::quantile(elixhauser$mortality_index, prob = 0.75)),
+     max    = c(max(elixhauser$readmission_index),
+                max(elixhauser$mortality_index)),
+     row.names = NULL,
+     stringsAsFactors = FALSE
+   )
> 
> stopifnot(identical(summary_current$index_summary, expected_index_summary))
> 
> ################################################################################
> # A non-current flag.method generates a warning but still returns the summary
> elixhauser_cumulative <- elixhauser
> attr(elixhauser_cumulative, "flag.method") <- "cumulative"
> 
> warn_obj <- tryCatchWarning(summary(elixhauser_cumulative))
> 
> stopifnot(
+   inherits(warn_obj, "warning"),
+   identical(
+     conditionMessage(warn_obj),
+     "Logic for Elixhauser summary has been implemented for flag.method = 'current'.  Using this function for flag.method = 'cumulative' may not provide a meaningful summary."
+   )
+ )
> 
> summary_cumulative <- suppressWarnings(summary(elixhauser_cumulative))
> 
> stopifnot(
+   identical(summary_cumulative$conditions, summary_current$conditions),
+   identical(summary_cumulative$index_summary, summary_current$index_summary)
+ )
> 
> ################################################################################
> #                                 End of File                                  #
> ################################################################################
> 
> proc.time()
   user  system elapsed 
   2.84    0.25    3.06