abcdutils

A collection of utility functions for working with the Adolescent Brain and Cognitive Development dataset.

Installation

You can install abcdutils from GitHub with:

# Latest development version
devtools::install_github("psvelayudhan/abcdutils")

# Install a specific tagged version
devtools::install_github("psvelayudhan/abcdutils@v0.4.0")

Usage

Working with the data dictionary

library(abcdutils)
library(readr)

# Search the NDA's data dictionary from R
search_dd("traumatic brain injury")

# Launch the data dictionary in your browser
open_dd()

Extract cleaned dataframes

Subcortical volumes (structural MRI)

subc_v <- get_subc_v(mri_y_smr_vol_aseg)

Subcortical volumes for a predefined set of subjects and a specific collection event

# Dataframe containing "subjectkey" column
subject_df <- read_csv("subjectlist.csv")

subc_v <- get_subc_v(
    mri_y_smr_vol_aseg,
    subjects = subject_df,
    t = 0
)

(where t = 0 refers to baseline data)

Extraction available for a wide range of variables related to neuroimaging, demographics, psychosocial resilience, and medical history:

Function	Description
get_cbcl_syndrome_scale	Raw or T-scores of the anxdep, withdep, somatic, social, thought, attention, rulebreak, and attention subscales
get_cort_sa	Cortical surface area
get_cort_t	Cortical thickness
get_exercise	A composite measure of exercise time from the Youth Risk Behavior Survey
get_family_function	Parent and youth responses to the Famiily Environment Scale
get_family_id	Family-specific ID variable
get_friends	Number of same and opposite sex close and total friends
get_gender_p	Parent report of child’s gender
get_gender_y	Youth’s self report of gender
get_gord_cor	Cortical-cortical rs-fMRI network correlations
get_gord_var	Cortical-cortical rs-fMRI temporal variances
get_headaches	Headache history
get_income	Three-tiered family income
get_interview_age	Child age at data collection
get_mtbi_age	Age at latest concussion
get_mtbi_count	Total number of concussions
get_mtbi_loc	LOC status for last concussion
get_mtbi_mechanism	Mechanism of acquiring last concussion
get_mtbi_mem_daze	Memory loss / dazed status of last concussion
get_mtbi_subjects	Identify children who have had a concussion
get_nihtbx_cardsort_fc	NIH toolbox card sorting task
get_nihtbx_list_fc	NIH toolbox list sorting task
get_parent_psychopathology	Parent self report scores from ASEBA
get_prosocial_behaviour_p	Parent reports of child prosocial behaviour
get_prosocial_behaviour_y	Child self reports of prosocial behaviour
get_pubertal_status_p	Parent report of child pubertal status
get_pubertal_status_y	Youth self report of pubertal status
get_race	Child ethnicity
get_scanner_id	Scanner-specific ID variable
get_screen_time	Screentime on weekdays and weekends in hours
get_site_id	Site-specific ID variable
get_sex	Sex at birth
get_sleep_disturbance	Sum of problems on Sleep Disturbance Scale
get_sports_and_activities	Total participation in sports and activities
get_subc_cor	Subcortical-cortical rs-fMRI network correlations
get_subc_v	Subcortical volume
get_subc_var	Subcortical-cortical rs-fMRI temporal variances
get_uninjured_subjects	Identify children who have not had any head injuries
get_wmnd	Neurite densities of major and peri-cortical white matter regions

Simple subsetting

abcd_otbi01 <- read_csv("abcd_otbi01.txt")

# Subset to just baseline data
filter_timepoint(abcd_otbi01, 0)

# Or just year 1 follow-up data
filter_timepoint(abcd_otbi01, 1)

# Or just subjects of interest
filter_subjects(abcd_otbi01, subject_list)

Concussion data prep

abcd_otbi01 <- read_csv("abcd_otbi01.txt")

# Renaming columns to be easily interpretable:
rename_tbi(abcd_otbi01)

# Identify which subjects had an mTBI and which had a moderate+ head injury:
identify_all_tbi(abcd_otbi01)

# Identify which head injuries were mTBIs
identify_mtbi(abcd_otbi01)

# When did the mTBIs occur
identify_mtbi_times(abcd_otbi01)

# What mechanism caused their latest mTBI
identify_latest_mtbi_mechanism(abcd_otbi01)

# How many mTBIs did the subject experience
identify_num_mtbi(abcd_otbi01)

# How much LOC occurred for the subject's most recent injury
identify_latest_mtbi_loc(abcd_otbi01)

# Did memory loss / feeling dazed or confused occur on the most recent injury
identify_latest_mtbi_mem_daze(abcd_otbi01)

# Combine all the functions above
detail_mtbi(abcd_otbi01)

Plotting

# Visualize missing data across several dataframes
df_list <- list(
    "loss of consciousness" = as_mtbi_loc,
    "mechanism of injury" = as_mtbi_mechanism,
    "memory loss / dazed" = as_mtbi_mem_daze,
    "income" = d_income
)

vis_missing_by_df(df_list)