---
title: "Charlson Comorbidities"
output:
 rmarkdown::html_vignette:
   toc: true
   number_sections: false
bibliography: references.bib
vignette: >
 %\VignetteIndexEntry{Charlson 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 Charlson
comorbidities algorithm.

* `charlson_deyo1992`: Deyo's original set of codes [@deyo1992adapting;@quan2005]
* `charlson_quan2005` and `charlson_quan2011`: Codes and index scoring [@quan2005;@quan2011]
* `charlson_sundararajan2004`: Australian ICD-10-AM adaptation [@sundararajan2004]
* `charlson_cdmf2019`: [@glasheen2019]
* `charlson_ludvigsson2021`: Swedish ICD-10-SE adaptation [@ludvigsson2021adaptation;@ludvigsson2023adaptation]
* `charlson_beyrer2021`: U.S. ICD-10-CM and ICD-10-PCS adaptation [@beyrer2021validation;@beyrer_2020_3968784]
* `charlson_mimicivcode`: mapping used by the MIMIC-IV Charlson SQL in
  [`mimic-code`](https://github.com/MIT-LCP/mimic-code)

# ICD Codes and Index Scores

End users can access the lookup tables for the mapping between ICD-9 and ICD-10
codes to conditions and the index scoring in `data.frame`s from the
`get_charlson_codes()` and `get_charlson_index_scores()` calls respectively.

```{r}
str(get_charlson_codes())
str(get_charlson_index_scores())
```

# Applying Charlson

Example: applying the @quan2005 variant of the Charlson comorbidities to the
`mdcr` data can be done as follows.

```{r}
mdcr_results <-
  comorbidities(
    data      = mdcr,
    id.vars   = "patid",
    icdv.var  = "icdv",
    icd.codes = "code",
    dx.var    = "dx",
    poa       = 1L,
    primarydx = 0L,
    method    = "charlson_quan2005"
  )
```

The return object is a `data.frame` with `0L`/`1L` integer indicator columns for the
relevant conditions, the id.vars (if applicable), `age_score` (if age, in years,
is supplied), `num_cmrb` the number of comorbidities, `cmrb_flag` a `0L`/`1L`
indicator for presence of at least one comorbidity, and `cci` the Charlson
Comorbidity Index.

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

Call `summary()` on the return object for a list of summary objects.  These can be
used to generate output tables to the end user's liking.

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

```{r echo = FALSE, results = "asis"}
x <- summary(mdcr_results)$conditions[, c("condition_description", "count", "percent")]
tab <-
  kableExtra::kbl(
    x = x,
    format = "html",
    caption = "Counts and percentages of patients in the mdcr example datasets with the @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 = 17)
tab <- kableExtra::pack_rows(tab, group_label = "Total Comorbidities", start_row = 18, end_row = nrow(x))
tab
```

# References

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