Healthy Brain Network & POND numbers
Grace Jacobs
March 5, 2019
POND new numbers (not included in the original SNF model) - have all data except DTI
| ADHD | ASD | OCD |
|---|---|---|
| 25 | 51 | 4 |
Healthy Brain Network data
All available primary diagnoses
Total n with a diagnosis = 1812
##
##
## 40
##
## 2
## Acute Stress Disorder
## 2
## ADHD-Combined Type
## 345
## ADHD-Hyperactive/Impulsive Type
## 42
## ADHD-Inattentive Type
## 245
## Adjustment Disorders
## 12
## Agoraphobia
## 1
## Autism Spectrum Disorder
## 151
## Bipolar I Disorder
## 3
## Bipolar II Disorder
## 1
## Borderline Intellectual Functioning
## 5
## Cannabis Use Disorder
## 1
## Disruptive Mood Dysregulation Disorder
## 12
## Encopresis
## 1
## Enuresis
## 9
## Gender Dysphoria in Children
## 1
## Generalized Anxiety Disorder
## 61
## Intellectual Disability-Mild
## 22
## Intellectual Disability-Moderate
## 6
## Intellectual Disability-Severe
## 1
## Language Disorder
## 39
## Major Depressive Disorder
## 55
## Major Neurocognitive Disorder Due to Epilepsy
## 1
## No Diagnosis Given
## 214
## No Diagnosis Given: Incomplete Eval
## 216
## Obsessive-Compulsive Disorder
## 13
## Other Specified Anxiety Disorder
## 27
## Other Specified Attention-Deficit/Hyperactivity Disorder
## 46
## Other Specified Depressive Disorder
## 6
## Other Specified Neurodevelopmental Disorder
## 1
## Other Specified Schizophrenia Spectrum and Other Psychotic Disorder
## 2
## Other Specified Tic Disorder
## 1
## Other Specified Trauma- and Stressor-Related Disorder
## 5
## Panic Disorder
## 2
## Parent-Child Relational Problem
## 1
## Persistent (Chronic) Motor or Vocal Tic Disorder
## 3
## Persistent Depressive Disorder (Dysthymia)
## 15
## Posttraumatic Stress Disorder
## 8
## Provisional Tic Disorder
## 1
## Reactive Attachment Disorder
## 3
## Schizophrenia
## 1
## Selective Mutism
## 3
## Separation Anxiety
## 15
## Social (Pragmatic) Communication Disorder
## 1
## Social Anxiety (Social Phobia)
## 40
## Specific Learning Disorder with Impairment in Mathematics
## 7
## Specific Learning Disorder with Impairment in Reading
## 83
## Specific Learning Disorder with Impairment in Reading
## 1
## Specific Learning Disorder with Impairment in Written Expression
## 4
## Specific Phobia
## 11
## Speech Sound Disorder
## 3
## Tourettes Disorder
## 13
## Unspecified Anxiety Disorder
## 2
## Unspecified Attention-Deficit/Hyperactivity Disorder
## 5
## Unspecified Neurodevelopmental Disorder
## 1Primary diagnosis
##
## ADHD ASD OCD Other
## 683 151 13 965Primary and secondary diagnoses (comorbidities)
##
## ADHD ASD Blank OCD Other
## ADHD 1 59 344 6 273
## ASD 79 5 30 3 34
## OCD 3 1 3 0 6
## Other 66 12 694 9 184Breakdown of participants with T1 images and primary diagnoses by site (3 sites)
SI site
##
## ADHD ASD OCD
## 107 21 2RU site
##
## ADHD ASD OCD
## 248 32 5CBIC site
##
## ADHD ASD OCD
## 101 18 3After removing people with poor quality T1 images
volume_SI_dx <- merge(volume_SI_dx, t1_qc, by="ID")
table(volume_SI_dx$diagnosis)##
## ADHD ASD OCD
## 0 0 0RU site
##
## ADHD ASD OCD
## 134 17 4CBIC site
##
## ADHD ASD OCD
## 56 13 2Clinical scores
Y-BOCS is supposed to be available, but it isn’t on the website where you download the phenotype data. All other scores used in the POND analysis are available:
CBCL - externalizing and internalizing
RBS - repetative behaviours
SWAN - inattention and hyperactivity scores
SCQ - social communication
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercionBreakdown of T1 and clinical scores by site and primary diagnosis
SI site - apparently they don’t have clinical data -_-
volume_SI_dx <- merge(volume_SI_dx, clincal, by="ID")diagnosis N Age Internalizing Externalizing Attention Hyperactivity Restricted_behaviours Social_comm ———- — —- ————– ————– ———- ————– ———————- ————
RU site
volume_RU_dx <- merge(volume_RU_dx, clincal, by="ID")
ggplot(volume_RU_dx, aes(x=Basic_Demos.Age, fill=diagnosis)) +
geom_histogram(binwidth = 1, color="black") +
ggtitle("Age Distribution of 4 clusters") +
theme(axis.text.y=element_text(size=14), axis.text.x=element_text(size=14),
axis.title.y=element_text(size=18),axis.title.x=element_text(size=18), legend.text=element_text(size=14),plot.title = element_text(size=20),legend.title=element_blank()) 
## Warning: `as_dictionary()` is soft-deprecated as of rlang 0.3.0.
## Please use `as_data_pronoun()` instead
## This warning is displayed once per session.## Warning: `new_overscope()` is soft-deprecated as of rlang 0.2.0.
## Please use `new_data_mask()` instead
## This warning is displayed once per session.## Warning: The `parent` argument of `new_data_mask()` is deprecated.
## The parent of the data mask is determined from either:
##
## * The `env` argument of `eval_tidy()`
## * Quosure environments when applicable
## This warning is displayed once per session.## Warning: `overscope_clean()` is soft-deprecated as of rlang 0.2.0.
## This warning is displayed once per session.| diagnosis | N | Age | Internalizing | Externalizing | Attention | Hyperactivity | Restricted_behaviours | Social_comm |
|---|---|---|---|---|---|---|---|---|
| ADHD | 100 | 10.17017 | 9.989474 | 11.47368 | 0.2929293 | 0.4900000 | 6.84000 | 7.270000 |
| ASD | 11 | 12.86572 | 16.400000 | 16.90000 | 0.8181818 | 0.8181818 | 15.09091 | 16.000000 |
| OCD | 3 | 12.47969 | 9.333333 | 5.00000 | 1.3333333 | 5.6666667 | 6.00000 | 4.666667 |
CBIC site
volume_CBIC_dx <- merge(volume_CBIC_dx, clincal, by="ID")
ggplot(volume_CBIC_dx, aes(x=Basic_Demos.Age, fill=diagnosis)) +
geom_histogram(binwidth = 1, color="black") +
ggtitle("Age Distribution of 4 clusters") +
theme(axis.text.y=element_text(size=14), axis.text.x=element_text(size=14),
axis.title.y=element_text(size=18),axis.title.x=element_text(size=18), legend.text=element_text(size=14),plot.title = element_text(size=20),legend.title=element_blank()) 
| diagnosis | N | Age | Internalizing | Externalizing | Attention | Hyperactivity | Restricted_behaviours | Social_comm |
|---|---|---|---|---|---|---|---|---|
| ADHD | 56 | 10.77709 | 12.71154 | 13.88462 | 0.5090909 | 0.5090909 | 7.625000 | 7.660714 |
| ASD | 11 | 12.81134 | 8.87500 | 6.00000 | 1.0000000 | 0.1818182 | 5.454546 | 11.181818 |
| OCD | 2 | 11.05139 | 11.50000 | 5.50000 | 0.0000000 | 2.5000000 | 13.000000 | 4.000000 |
Next Step - confirm QC of T1s
