README (original) (raw)

Overview

AOUSDOHtools is an R package designed to process and analyze Social Determinants of Health (SDOH) Survey data from the All of Us (AOU) Research Program (https://www.researchallofus.org/). It provides tools to streamline common survey data tasks, including recoding, score calculation, and variable creation. The package is ideal for researchers and analysts working with SDOH survey data within the All of Us Research Hub Researcher Workbench, a cloud-based platform supporting AOU data analysis (https://www.researchallofus.org/data-tools/survey-explorer/).

This package is developed in conjunction with a published user guide:

• Theresa A Koleck, Caitlin Dreisbach, Chen Zhang, Susan Grayson, Maichou Lor, Zhirui Deng, Alex Conway, Peter D R Higgins, Suzanne Bakken, User guide for Social Determinants of Health Survey data in the All of Us Research Program, Journal of the American Medical Informatics Association, Volume 31, Issue 12, December 2024, Pages 3032–3041, https://doi.org/10.1093/jamia/ocae214.

The package enables users to calculate health and well-being scores for 14 key social determinants of health constructs assessed in the_All of Us_ Social Determinants of Health Survey (AOUSDOH).

Supported Constructs and Functions

1. Neighborhood Cohesion -calc_cohesion
2. Neighborhood Disorder -calc_disorder, calc_physical_disorder,calc_social_disorder
3. Neighborhood Environment -calc_density, calc_spa,calc_crime_safety, calc_nei
4. Social Support -calc_social_support, calc_ins_support,calc_emo_support
5. Loneliness -calc_loneliness
6. Perceived Everyday Discrimination -calc_edd_situation, calc_edd_frequency,calc_edd_chronicity
7. Perceived Discrimination in Health Care Settings- calc_hcd_ever, calc_hcd_count,calc_hcd_sum, calc_hcd_mean
8. Food Insecurity -calc_food_insecurity
9. Housing Insecurity / Instability -calc_housing_insecurity,calc_num_moves
10. Housing Quality -calc_housing_quality
11. Perceived Stress - calc_stress_sum,calc_stress_category
12. Daily Spiritual Experiences -calc_spirit
13. Religious Service Attendance -calc_religious_attendance
14. English Proficiency -calc_other_language, calc_english_level,calc_english_proficient

This package simplifies data processing for AOU researchers, ensuring consistent, reproducible analyses of SDOH factors.

Installation

You can install the development version of AOUSDOHtoolsfrom GitHub using the following steps:

# Install devtools if necessary
install.packages("devtools")

# Install AOUSDOHtools from GitHub
devtools::install_github("zhd52/AOUSDOHtools")

Example

Once installed, you can use the package by loading it into your R session:

library(AOUSDOHtools)

# Example: Calculating Neighborhood Cohesion Score

## 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)
  )

## Compute neighborhood cohesion scores
cohesion_scores <- calc_cohesion(survey_df)
head(cohesion_scores)
#> # A tibble: 2 × 2
#>   person_id cohesion
#>       <dbl>    <dbl>
#> 1         1      3.5
#> 2         2      3

Merge

After computing all the scores, you can merge the resulting scores using this code:

# Merge the computed scores together

## Create a list for all the scores
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 the scores
SDOH_scores <- reduce(scores.list, full_join, by = 'person_id')
head(SDOH_scores)