---
title: "AOUSDOHtools_examples"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{AOUSDOHtools_examples}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

```{r setup}
library(AOUSDOHtools)
library(purrr)
library(dplyr)
```

```{r example1}
# Example 1 - Calculating Neighborhood Cohesion Score

## Note: This example is using a synthetic dataset that mimics the expected structure of the All of Us survey data, users should replace survey_df with actual All of Us SDOH Survey data. 

### Create a sample survey data frame
survey_df <- data.frame(
  person_id = c(1, 1, 1, 1, 2, 2, 2, 2),
  question_concept_id = c(40192463, 40192411, 40192499, 40192417,
                          40192463, 40192411, 40192499, 40192417),
  answer_concept_id = c(40192514, 40192455, 40192524, 40192408,
                        40192514, 40192455, 40192422, 40192408)
  )

### Calculate Neighborhood Cohesion scores
cohesion_scores <- calc_cohesion(survey_df)

### View Output
head(cohesion_scores)
```

```{r example2, eval=F}
# Example 2 - Merging Resulting Scores

## Note: After computing all the scores, users can merge the resulting scores together using the code below, which demonstrates how to combine all 14 constructs and their sub-scores. Participants missing responses are retained with NA values unless `na.rm = TRUE`, in which case incomplete rows are excluded. 

### Create a list of all score data frames:
scores.list <- list(
  cohesion_scores,                                                       ### Neighborhood Cohesion
  disorder_scores, physical_disorder_scores, social_disorder_scores,     ### Neighborhood Disorder 
  density_scores, spa_scores, crime_safety_scores, nei_scores,           ### Neighborhood Environment
  social_support_scores, ins_support_scores, emo_support_scores,         ### Social Support 
  loneliness_scores,                                                     ### Loneliness
  edd_situation_scores, edd_frequency_scores, edd_chronicity_scores,     ### Perceived Everyday Discrimination
  hcd_ever_scores, hcd_count_scores, hcd_sum_scores, hcd_mean_scores,    ### Perceived Discrimination in Health Care Settings
  food_insecurity_scores,                                                ### Food Insecurity
  housing_insecurity_scores, num_moves_scores,                           ### Housing Insecurity / Instability
  housing_quality_scores,                                                ### Housing Quality
  stress_sum_scores, stress_category_scores,                             ### Perceived Stress
  spirit_scores,                                                         ### Daily Spiritual Experiences
  religious_attendance_scores,                                           ### Religious Service Attendance
  other_language_scores, english_level_scores, english_proficient_scores ### English Proficiency
)

### Merge all score outputs by person_id
SDOH_scores <- reduce(scores.list, full_join, by = "person_id")

### Preview merged dataset
head(SDOH_scores)
```