### Install CohortConstructor Development Version from GitHub

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Install the latest development version of CohortConstructor from GitHub. Ensure the devtools package is installed first.

```r
# install.packages("devtools")
devtools::install_github("ohdsi/CohortConstructor")
```

--------------------------------

### Install CohortConstructor from CRAN

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Use this command to install the stable version of the CohortConstructor package from CRAN.

```r
install.packages("CohortConstructor")
```

--------------------------------

### Generate Concept-Based Fracture Cohort (Event Start Date Exit)

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Create an initial cohort of individuals with fractures based on the defined codelist. The cohort exit date is set to the event start date.

```r
cdm$fractures <- cdm |> 
  conceptCohort(conceptSet = fx_codes, 
                exit = "event_start_date", 
                name = "fractures")
```

--------------------------------

### View Cohort Count

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Get the number of records and subjects for each cohort definition. This provides a summary of the cohort sizes.

```r
cohortCount(cdm$fractures) |> glimpse()
```

--------------------------------

### Create and Require Intersection with GI Bleed Cohort

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Creates a 'gibleed' cohort based on a concept ID and then filters the 'fractures' cohort to exclude individuals who were in the 'gibleed' cohort within a specified window (-Inf to 0 days prior to fracture cohort start).

```r
cdm$gibleed <- cdm |> 
  conceptCohort(conceptSet = list("gibleed" = 192671L),
  name = "gibleed")

cdm$fractures <- cdm$fractures |> 
  requireCohortIntersect(targetCohortTable = "gibleed",
                         intersections = 0,
                         window = c(-Inf, 0))
```

--------------------------------

### Require Cohort Start Date within a Range

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Filters the 'fractures' cohort to include only individuals whose cohort start date falls within the specified date range (January 1, 2000, to January 1, 2020).

```r
cdm$fractures <- cdm$fractures |> 
  requireInDateRange(dateRange = as.Date(c("2000-01-01", "2020-01-01")))
```

--------------------------------

### Get Candidate Codes for Fractures

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Retrieve candidate concept IDs for 'hip fracture' and 'forearm fracture' from the CDM vocabulary. This function is part of the CodelistGenerator package.

```r
library(CodelistGenerator)

hip_fx_codes <- getCandidateCodes(cdm, "hip fracture")
forearm_fx_codes <- getCandidateCodes(cdm, "forearm fracture")
```

--------------------------------

### Pad Cohort End Date

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Update the cohort to extend the exit date up to 180 days after the event start date. The exit date will not exceed the individual's observation period end date.

```r
cdm$fractures <- cdm$fractures |> 
  padCohortEnd(days = 180)
```

--------------------------------

### Create Mock CDM Reference

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Create a mock OMOP CDM reference object from a dataset. This is useful for testing and development with synthetic data.

```r
cdm <- mockCdmFromDataset(datasetName = "GiBleed")
```

--------------------------------

### Load Required R Packages

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Load the necessary R packages for working with OMOP CDM data and CohortConstructor.

```r
library(omopgenerics)
library(omock)
library(PatientProfiles)
library(dplyr)
library(CohortConstructor)
library(CohortCharacteristics)
```

--------------------------------

### View Cohort Settings

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Inspect the settings associated with the created cohort, including cohort definition ID, name, CDM version, and vocabulary version.

```r
settings(cdm$fractures) |> glimpse()
```

--------------------------------

### View Cohort Settings and Count

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Displays the settings and counts for the 'fractures' cohort, showing individual cohort definitions and their subject counts.

```r
settings(cdm$fractures)
#> # A tibble: 3 × 5
#>   cohort_definition_id cohort_name      cdm_version vocabulary_version   gap
#>                  <int> <chr>            <chr>       <chr>              <dbl>
#> 1                    1 forearm_fracture 5.3         v5.0 18-JAN-19        NA
#> 2                    2 hip_fracture     5.3         v5.0 18-JAN-19        NA
#> 3                    3 any_fracture     <NA>        <NA>                   0
cohortCount(cdm$fractures)
#> # A tibble: 3 × 3
#>   cohort_definition_id number_records number_subjects
#>                  <int>          <int>           <int>
#> 1                    1            569             510
#> 2                    2            138             132
#> 3                    3            707             611
```

--------------------------------

### View Attrition After Demographic Filters

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Displays the attrition results after applying age and sex filters to the 'fractures' cohort. This helps visualize the impact of demographic restrictions.

```r
attrition(cdm$fractures) |> 
  filter(reason == "Age requirement: 40 to 65") |> 
  glimpse()
#> Rows: 3
#> Columns: 7
#> $ cohort_definition_id <int> 1, 2, 3
#> $ number_records       <int> 64, 22, 86
#> $ number_subjects      <int> 62, 22, 83
#> $ reason_id            <int> 8, 8, 4
#> $ reason               <chr> "Age requirement: 40 to 65", "Age requirement: 40…
#> $ excluded_records     <int> 88, 40, 128
#> $ excluded_subjects    <int> 81, 38, 113

attrition(cdm$fractures) |> 
  filter(reason == "Sex requirement: Female") |> 
  glimpse()
#> Rows: 3
#> Columns: 7
#> $ cohort_definition_id <int> 1, 2, 3
#> $ number_records       <int> 37, 12, 49
#> $ number_subjects      <int> 36, 12, 48
#> $ reason_id            <int> 9, 9, 5
#> $ reason               <chr> "Sex requirement: Female", "Sex requirement: Fema…
#> $ excluded_records     <int> 27, 10, 37
#> $ excluded_subjects    <int> 26, 10, 35
```

--------------------------------

### Create New Codelist

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Combine concept IDs for different fracture types into a new codelist object using the CodelistGenerator package.

```r
fx_codes <- newCodelist(list("hip_fracture" = hip_fx_codes$concept_id,
                             "forearm_fracture"= forearm_fx_codes$concept_id))
```

--------------------------------

### View Cohort Attrition

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Examine the attrition table for the cohort, showing the number of records and subjects at each stage of cohort definition and any exclusions.

```r
attrition(cdm$fractures) |> glimpse()
```

--------------------------------

### Union Multiple Fracture Cohorts

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Combines multiple existing fracture cohorts into a single 'any_fracture' cohort. Use 'keepOriginalCohorts = TRUE' to retain the individual fracture cohorts.

```r
cdm$fractures <- unionCohorts(cdm$fractures,
                              cohortName = "any_fracture", 
                              keepOriginalCohorts = TRUE,
                              name ="fractures")
```

--------------------------------

### View Updated Cohort Count After Date Restriction

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Shows the updated cohort counts after applying the date range restriction. The 'glimpse()' function provides a detailed view of the tibble structure.

```r
cohortCount(cdm$fractures) |> glimpse()
#> Rows: 3
#> Columns: 3
#> $ cohort_definition_id <int> 1, 2, 3
#> $ number_records       <int> 152, 62, 214
#> $ number_subjects      <int> 143, 60, 196
attrition(cdm$fractures) |> 
  filter(reason == "cohort_start_date between 2000-01-01 & 2020-01-01") |> 
  glimpse()
#> Rows: 0
#> Columns: 7
#> $ cohort_definition_id <int> 
#> $ number_records       <int> 
#> $ number_subjects      <int> 
#> $ reason_id            <int> 
#> $ reason               <chr> 
#> $ excluded_records     <int> 
#> $ excluded_subjects    <int>
```

--------------------------------

### View Attrition After GI Bleed Cohort Exclusion

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Shows the attrition results after applying the requirement that individuals must NOT be in the 'gibleed' cohort within the specified time window. This helps verify the exclusion criteria.

```r
attrition(cdm$fractures) |> 
  filter(reason == "Not in cohort gibleed between -Inf & 0 days relative to cohort_start_date") |> 
  glimpse()
#> Rows: 0
#> Columns: 7
#> $ cohort_definition_id <int> 
#> $ number_records       <int> 
#> $ number_subjects      <int> 
#> $ reason_id            <int> 
#> $ reason               <chr> 
#> $ excluded_records     <int> 
#> $ excluded_subjects    <int>
```

--------------------------------

### Apply Demographic Requirements to Cohort

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Filters the 'fractures' cohort to include only individuals within a specified age range (40-65) and of 'Female' sex. This demonstrates applying demographic filters.

```r
cdm$fractures <- cdm$fractures |> 
  requireDemographics(ageRange = list(c(40, 65)),
                      sex = "Female")
```

--------------------------------

### Disconnect from CDM

Source: https://github.com/ohdsi/cohortconstructor/blob/main/README.md

Closes the connection to the Common Data Model (CDM). This is a standard practice to release resources after data manipulation is complete.

```r
cdmDisconnect(cdm)
```

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