Analyzing AOU SDOH Survey Data.
AOUSDOHtools
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
Neighborhood Cohesion -
calc_cohesion
Neighborhood Disorder -
calc_disorder
,calc_physical_disorder
,calc_social_disorder
Neighborhood Environment -
calc_density
,calc_spa
,calc_crime_safety
,calc_nei
Social Support -
calc_social_support
,calc_ins_support
,calc_emo_support
Loneliness -
calc_loneliness
Perceived Everyday Discrimination -
calc_edd_situation
,calc_edd_frequency
,calc_edd_chronicity
Perceived Discrimination in Health Care Settings -
calc_hcd_ever
,calc_hcd_count
,calc_hcd_sum
,calc_hcd_mean
Food Insecurity -
calc_food_insecurity
Housing Insecurity / Instability -
calc_housing_insecurity
,calc_num_moves
Housing Quality -
calc_housing_quality
Perceived Stress -
calc_stress_sum
,calc_stress_category
Daily Spiritual Experiences -
calc_spirit
Religious Service Attendance -
calc_religious_attendance
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 AOUSDOHtools
from 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)