---
title: "Summarise large scale characteristics"
output: 
  html_document:
    pandoc_args: [
      "--number-offset=1,0"
      ]
    number_sections: yes
    toc: yes
vignette: >
  %\VignetteIndexEntry{summarise_large_scale_characteristics}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  message = FALSE,
  warning = FALSE
)

CDMConnector::requireEunomia()
```

## Introduction

In the previous vignette we have seen how we can use the CohortCharacteristics package to summarise a set of pre-specified characteristics of a study cohort. These characteristics included patient demographics like age and sex, and also concept sets and cohorts that we defined. Another, often complimentary, way that we can approach characterising a study cohort is by simply summarising all clinical events we see for them in some window around their index date (cohort entry).

To show how large scale characterisation can work we'll first create a first-ever ankle sprain study cohort using the Eunomia synthetic data.

```{r}
library(duckdb)
library(CDMConnector)
library(dplyr, warn.conflicts = FALSE)
library(PatientProfiles)
library(CohortCharacteristics)

con <- dbConnect(duckdb(), dbdir = eunomiaDir())
cdm <- cdmFromCon(
  con = con, cdmSchem = "main", writeSchema = "main", cdmName = "Eunomia"
)

cdm <- generateConceptCohortSet(
  cdm = cdm,
  name = "ankle_sprain",
  conceptSet = list("ankle_sprain" = 81151),
  end = "event_end_date",
  limit = "first",
  overwrite = TRUE
)
```

## Large scale characteristics of study cohorts

To summarise our cohort of individuals with an ankle sprain we will look at their records in three tables of the OMOP CDM (*condition_occurrence*, *procedure_occurrence*, and *drug_exposure*) over two time windows (any time prior to their index date, and on index date). For conditions and procedures we will identify whether someone had a new record starting in the time window. Meanwhile, for drug exposures we will consider whether they had a new or ongoing record in the period.

Lastly, but important to note, we are only going to only return results for concepts for which at least 10% of the study cohort had a record.

```{r}
lsc <- cdm$ankle_sprain |>
  summariseLargeScaleCharacteristics(
    window = list(c(-Inf, -1), c(0, 0)),
    eventInWindow = c(
      "condition_occurrence",
      "procedure_occurrence"
    ),
    episodeInWindow = "drug_exposure",
    minimumFrequency = 0.1
  )

tableLargeScaleCharacteristics(lsc)
```

As we can see we have identified numerous concepts for which at least 10% of our study population had a record. Often with larger cohorts and real patient-level data we will obtain many times more results when running large scale characterisation. One option we have to help summarise our results is to pick out the most frequent concepts. Here, for example, we select the top 5 concepts.

```{r}
tableTopLargeScaleCharacteristics(lsc,
                                  topConcepts = 5)
```

## Stratified large scale characteristics

Like when summarising pre-specified patient characteristics, we can also get stratified results when summarising large scale characteristics. Here, for example, large scale characteristics are stratified by sex (which we add as an additional column to our cohort table using the PatientProfiles package).

```{r}
lsc <- cdm$ankle_sprain |>
  addSex() |>
  summariseLargeScaleCharacteristics(
    window = list(c(-Inf, -1), c(0, 0)),
    strata = list("sex"),
    eventInWindow = "drug_exposure",
    minimumFrequency = 0.1
  )

tableTopLargeScaleCharacteristics(lsc)
```

## Plot large scale characteristics

`plotLargeScaleCharacteristics` and `plotComparedLargeScaleCharacteristics` can be use to generate plot for visualising the large scale characteristics

```{r}
plotLargeScaleCharacteristics(lsc)
```

`plotComparedLargeScaleCharacteristics` allows you to compare the difference in prevalence of the large scale covariates between two window. The reference cohort and time window are set using the `reference` arguement inside the function.

```{r}
plotComparedLargeScaleCharacteristics(
  result = lsc,
  colour = "sex",
  reference = 'overall',
  facet = cohort_name ~ variable_level
)
```
