---
title: "Elixhauser Comorbidities"
output:
 rmarkdown::html_vignette:
   toc: true
   number_sections: false
bibliography: references.bib
vignette: >
 %\VignetteIndexEntry{Elixhauser Comorbidities}
 %\VignetteEngine{knitr::rmarkdown}
 %\VignetteEncoding{UTF-8}
---

```{r, label = "setup", include = FALSE}
# IMPORTANT SYNTAX NOTE:
#
# DO NOT USE the pipeOp `|>`
#
# While convenient, that is a R 4.1.0 feature at a minimum. Notable improvements
# to the pipeOp come in 4.2.0 and 4.2.1.  To keep this package dependent on R >=
# 3.5.0 do not use the pipeOp.

library(kableExtra)
options(qwraps2_markup = "markdown")
options(knitr.kable.NA = '')
knitr::opts_chunk$set(collapse = TRUE, fig.align = "center")
```

```{r, label = 'medicalcoder-namespace'}
library(medicalcoder)
packageVersion("medicalcoder")
```

# Introduction

The medicalcoder package implements several variants of the Elixhauser
comorbidity algorithm.

* Based on codes provided by the Agency for Healthcare Research and Quality (AHRQ) for fiscal years 2022 through 2026 [@ahrqicd10]
  *  `elixhauser_ahrq2022`
  *  `elixhauser_ahrq2023`
  *  `elixhauser_ahrq2024`
  *  `elixhauser_ahrq2025`
  *  `elixhauser_ahrq2026`
  *  `elixhauser_ahrq_icd10` - All ICD-10 codes ever listed by AHRQ

* Codes from Table 2 of @quan2005
  * `elixhauser_elixhauser1988`: [@elixhauser1998;@quan2005]
  * `elixhauser_ahrq_web`: [@quan2005;@ahrq2017]
  * `elixhauser_quan2005`: [@quan2005]

**IMPORTANT NOTE:** Elixhauser 1998 and AHRQ Web used diagnosis-related
group (DRG) codes as part of the methods.  The medicalcoder
package _does not_ use DRG codes.  This is consistent with the way these
methods were implemented in @quan2005.

# ICD Codes and Index Scores

End users may access three lookup tables relevant to Elixhauser variants.

```{r}
str(get_elixhauser_codes())
str(get_elixhauser_index_scores())
str(get_elixhauser_poa())
```

* `get_elixhauser_codes()` returns a `data.frame` of the ICD codes mapping to
  each condition with indicators for the inclusion in specific variants.

* `get_elixhauser_index_scores()` returns a `data.frame` with points scored per
  condition for both mortality and readmission indices by variant.

* `get_elixhauser_poa()` returns a `data.frame` which reports which conditions
  are required and not required to be present-on-admission for the conditions to
  be classified as a comorbidity by variant.  For the variants not listed the
  default is as with the Charlson and PCCC methods, the code needs to be
  present-on-admission for the condition to be flagged.

# Applying Elixhauser

The Elixhauser method considers if the diagnostic codes are for primary or
secondary diagnoses. As such, the following call will throw a warning that the
`primarydx.var` or `primarydx` argument was not set and that all conditions will
be assumed to be secondary.  To suppress this warning pass an appropriate value
for either argument.

```{r}
# will warn because primarydx and primarydx.var are both NULL
mdcr_results0 <-
  comorbidities(
    data = mdcr,
    id.vars = "patid",
    icdv.var = "icdv",
    icd.codes = "code",
    dx.var = "dx",
    flag.method = "current",
    poa = 1,
    method = "elixhauser_ahrq2025"
  )

# no warning
mdcr_results <-
  comorbidities(
    data = mdcr,
    id.vars = "patid",
    icdv.var = "icdv",
    icd.codes = "code",
    dx.var = "dx",
    flag.method = "current",
    poa = 1,
    method = "elixhauser_ahrq2025",
    primarydx = 0
  )

identical(mdcr_results, mdcr_results0)
```

The return object is a `data.frame` with 0/1 integer indicator columns for the
relevant conditions, the id.vars (if applicable), `num_cmrb`, the number of
comorbidities, `cmrb_flag`, a 0/1 indicator for presence of at least one
comorbidity, and the mortality and readmission index scores.

```{r}
str(mdcr_results)
```

Call `summary()` to get a list of summaries which can be used to generate summary
tables.

```{r}
summary(mdcr_results)
```

```{r echo = FALSE, results = "asis"}
x <- summary(mdcr_results)$conditions
tab <-
  kableExtra::kbl(
    x = x,
    format = "html",
    caption = "Counts and percentages of patients in the mdcr example data sets with the Elixhauser @quan2005 comorbidities.",
    col.names = c("", "Count", "Percentage"),
    digits = 3
  )
tab <- kableExtra::kable_styling(tab, bootstrap_options = c("striped"), font_size = 10)
tab <- kableExtra::pack_rows(tab, group_label = "Comorbidity", start_row = 1, end_row = 38)
tab <- kableExtra::pack_rows(tab, group_label = "Total Comorbidities", start_row = 39, end_row = nrow(x))
tab
```


# References

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