---
title: "Concatenating cohort records"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{a05_concatanate_cohorts}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

```{r setup}
library(CohortConstructor)
library(CohortCharacteristics)
library(ggplot2)
```

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

library(CDMConnector)
library(dplyr, warn.conflicts = FALSE)

if (Sys.getenv("EUNOMIA_DATA_FOLDER") == ""){
  Sys.setenv("EUNOMIA_DATA_FOLDER" = file.path(tempdir(), "eunomia"))}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))){ dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
  downloadEunomiaData()  
}
```

For this example we'll use the Eunomia synthetic data from the CDMConnector package.

```{r}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
cdm <- cdm_from_con(con, cdm_schema = "main", 
                    write_schema = c(prefix = "my_study_", schema = "main"))
```

Let's start by creating two drug cohorts, one for users of diclofenac and another for users of acetaminophen.

```{r}
cdm$medications <- conceptCohort(cdm = cdm, 
                                 conceptSet = list("diclofenac" = 1124300,
                                                   "acetaminophen" = 1127433), 
                                 name = "medications")
cohortCount(cdm$medications)
```
We can merge cohort records using the `collapseCohorts()` function in the CohortConstructor package. The function allows us to specifying the number of days between two cohort entries, which will then be merged into a single record.

Let's first define a new cohort where records within 1095 days (~ 3 years) of each other will be merged.

```{r}
cdm$medications_collapsed <- collapseCohorts(
  cohort = cdm$medications,
  gap = 1095,
  name = "medications_collapsed"
)
```

Let's compare how this function would change the records of a single individual.

```{r}
cdm$medications |>
  filter(subject_id == 1)
cdm$medications_collapsed |>
  filter(subject_id == 1)
```
Subject 1 initially had 4 records between 1971 and 1982. After specifying that records within three years of each other are to be merged, the number of records decreases to three. The record from 1980-03-15 to 1980-03-29 and the record from 1982-09-11 to 1982-10-02 are merged to create a new record from 1980-03-15 to 1982-10-02. 

Now let's look at how the cohorts have been changed. 

```{r}
summary_attrition <- summariseCohortAttrition(cdm$medications_collapsed)
plotCohortAttrition(summary_attrition, cohortId = 1)
```

The flow chart above illustrates the changes to cohort 1 (users of acetaminophen) when entries within 3 years of each other are merged. We see that collapsing the cohort has led to 1,390 fewer records.

```{r}
summary_attrition <- summariseCohortAttrition(cdm$medications_collapsed)
plotCohortAttrition(summary_attrition, cohortId = 2)
```

The flow chart above illustrates the changes to cohort 2 (users of diclofenac) when entries within 3 years of each other are merged. Since this cohort only has one record per individual the function collapseCohorts() had no impact on the final number of records.