SPIN Study Tracking
Hassan Abdulrasul
2025-10-22
create a table of what we need, what we have, and when
# Libraries
library(tidyr)
library(dplyr)
library(ggplot2)
library(lubridate)
library(plotly)
library(table1)
library(REDCapR)
# Functions
# Replace blank with NA
replace_blank_with_na <- function(x) {
if (is.character(x)) {
x <- na_if(x, "")
}
return(x)
}This R Markdown document is designed for data wrangling, visualization, and analysis across various SPIN studies. It provides a comprehensive framework for examining study metrics tailored to specific SPIN studies as outlined be low. You can execute the entire document sequentially to prepare and analyze variables across these studies.
For clarity and visual appeal, code chunks are hidden, and only key results and plots are displayed. For detailed insights into the methodology or specific code implementations, please contact Hassan Abdulrasul (hassan.abdulrasul@camh.ca).
### SPN40- SPINAPS
# SPINAPS_Data <- read.csv("C:\\Users\\Hashlu\\iCloudDrive\\Desktop\\SPIN\\SPNAPS\\SPN40ImagingAlterati_DATA_2025-01-10_0927.csv")
# Recruitment
SPINR
SPASD
Load up data
Assessment Completion Status
plot to see the completion status between SPINR and SPASD
ASD_assessment <-
SPINR_assessment_df %>%
filter(group == "SPASD") %>%
mutate(assessment = factor(assessment,
levels = c("elg_form_complete", "demo_form_complete",
"ahh_form_complete", "pmed_form_complete",
"npmed_form_complete", "fnd_form_complete",
"scid5_form_complete", "sans_form_complete",
"bsfs_form_complete", "bprs_form_complete",
"hwv_form_complete", "urine_form_complete",
"rmet_form_complete", "er40_form_complete",
"tasit_form_complete", "np_fact_form_complete",
"np_form_complete", "open_form_complete",
"picture_form_complete", "mri_form_complete",
"term_form_complete"),
labels = c("Elegibilty", "Demographics",
"Medical History", "Psychotropic Medications",
"Nonpsychotropic Medications",
"Fagerstrom Nicotine Dependence",
"SCID-5-RV", "Assessment Of Negative Symptoms",
"Birchwood Social Functioning Scale",
"Brief Psychiatric Rating Scale",
"Height Weight", "Urine Toxicology",
"RMET",
"Penn Emotion Recognition Test",
"TASIT",
"Neuropsych Fact Sheet",
"Neuropsych Summary Scores",
"Open Ended Question Task",
"Picture Description Task",
"MRI", "Termination Checklist")))
SSDt1_assessment <-
SPINR_assessment_df %>%
filter(group == "SSD w T1") %>%
mutate(assessment = factor(assessment,
levels = c("elg_form_complete", "demo_form_complete",
"ahh_form_complete", "pmed_form_complete",
"npmed_form_complete", "fnd_form_complete",
"scid5_form_complete", "sans_form_complete",
"bsfs_form_complete", "bprs_form_complete",
"hwv_form_complete", "urine_form_complete",
"bars_form_complete", "sas_form_complete",
"rmet_form_complete", "er40_form_complete",
"tasit_form_complete", "np_fact_form_complete",
"np_form_complete", "open_form_complete",
"picture_form_complete", "mri_form_complete",
"term_form_complete"),
labels = c("Elegibilty", "Demographics",
"Medical History", "Psychotropic Medications",
"Nonpsychotropic Medications",
"Fagerstrom Nicotine Dependence",
"SCID-5-RV", "Assessment Of Negative Symptoms",
"Birchwood Social Functioning Scale",
"Brief Psychiatric Rating Scale",
"Height Weight", "Urine Toxicology",
"Barnes Akathisia Rating Scale",
"Simpson-Angus Scale",
"RMET",
"Penn Emotion Recognition Test",
"TASIT",
"Neuropsych Fact Sheet",
"Neuropsych Summary Scores",
"Open Ended Question Task",
"Picture Description Task",
"MRI", "Termination Checklist")))
Control_assessment <-
SPINR_assessment_df %>%
filter(group == "Control") %>%
mutate(assessment = factor(assessment,
levels = c("elg_form_complete", "demo_form_complete",
"ahh_form_complete", "pmed_form_complete",
"npmed_form_complete", "fnd_form_complete",
"scid5_form_complete",
"bsfs_form_complete",
"hwv_form_complete", "urine_form_complete",
"rmet_form_complete", "er40_form_complete",
"tasit_form_complete", "np_fact_form_complete",
"np_form_complete", "open_form_complete",
"picture_form_complete", "mri_form_complete",
"term_form_complete"),
labels = c("Elegibilty", "Demographics",
"Medical History", "Psychotropic Medications",
"Nonpsychotropic Medications",
"Fagerstrom Nicotine Dependence",
"SCID-5-RV",
"Birchwood Social Functioning Scale",
"Height Weight", "Urine Toxicology",
"RMET",
"Penn Emotion Recognition Test",
"TASIT",
"Neuropsych Fact Sheet",
"Neuropsych Summary Scores",
"Open Ended Question Task",
"Picture Description Task",
"MRI", "Termination Checklist")))
SSD_assessment <-
SPINR_assessment_df %>%
filter(group == "SPINS") %>%
mutate(assessment = factor(assessment,
levels = c("elg_form_complete", "demo_form_complete",
"ahh_form_complete", "pmed_form_complete",
"npmed_form_complete", "fnd_form_complete",
"scid5_form_complete", "sans_form_complete",
"bsfs_form_complete", "bprs_form_complete",
"hwv_form_complete", "urine_form_complete",
"bars_form_complete", "sas_form_complete",
"rmet_form_complete", "er40_form_complete",
"tasit_form_complete", "np_fact_form_complete",
"np_form_complete", "open_form_complete",
"picture_form_complete", "mri_form_complete",
"term_form_complete"),
labels = c("Elegibilty", "Demographics",
"Medical History", "Psychotropic Medications",
"Nonpsychotropic Medications",
"Fagerstrom Nicotine Dependence",
"SCID-5-RV", "Assessment Of Negative Symptoms",
"Birchwood Social Functioning Scale",
"Brief Psychiatric Rating Scale",
"Height Weight", "Urine Toxicology",
"Barnes Akathisia Rating Scale",
"Simpson-Angus Scale",
"RMET",
"Penn Emotion Recognition Test",
"TASIT",
"Neuropsych Fact Sheet",
"Neuropsych Summary Scores",
"Open Ended Question Task",
"Picture Description Task",
"MRI", "Termination Checklist")))
HCt1_assessment <-
SPINR_assessment_df %>%
filter(group == "HC w T1") %>%
mutate(assessment = factor(assessment,
levels = c("elg_form_complete", "demo_form_complete",
"ahh_form_complete", "pmed_form_complete",
"npmed_form_complete", "fnd_form_complete",
"scid5_form_complete",
"bsfs_form_complete",
"hwv_form_complete", "urine_form_complete",
"rmet_form_complete", "er40_form_complete",
"tasit_form_complete", "np_fact_form_complete",
"np_form_complete", "open_form_complete",
"picture_form_complete", "mri_form_complete",
"term_form_complete"),
labels = c("Elegibilty", "Demographics",
"Medical History", "Psychotropic Medications",
"Nonpsychotropic Medications",
"Fagerstrom Nicotine Dependence",
"SCID-5-RV",
"Birchwood Social Functioning Scale",
"Height Weight", "Urine Toxicology",
"RMET",
"Penn Emotion Recognition Test",
"TASIT",
"Neuropsych Fact Sheet",
"Neuropsych Summary Scores",
"Open Ended Question Task",
"Picture Description Task",
"MRI", "Termination Checklist")))
ASDwt1_assessment <-
SPINR_assessment_df %>%
filter(group == "ASD w T1") %>%
mutate(assessment = factor(assessment,
levels = c("elg_form_complete", "demo_form_complete",
"ahh_form_complete", "pmed_form_complete",
"npmed_form_complete", "fnd_form_complete",
"scid5_form_complete",
"bsfs_form_complete",
"hwv_form_complete", "urine_form_complete",
"rmet_form_complete", "er40_form_complete",
"tasit_form_complete", "np_fact_form_complete",
"np_form_complete", "open_form_complete",
"picture_form_complete", "mri_form_complete",
"term_form_complete"),
labels = c("Elegibilty", "Demographics",
"Medical History", "Psychotropic Medications",
"Nonpsychotropic Medications",
"Fagerstrom Nicotine Dependence",
"SCID-5-RV",
"Birchwood Social Functioning Scale",
"Height Weight", "Urine Toxicology",
"RMET",
"Penn Emotion Recognition Test",
"TASIT",
"Neuropsych Fact Sheet",
"Neuropsych Summary Scores",
"Open Ended Question Task",
"Picture Description Task",
"MRI", "Termination Checklist")))
ASD_plot <-
plot_ly(data = ASD_assessment, x = ~assessment, y = ~record_id, z = ~complete,
type = "heatmap", colors = c("#238823", "#D2222D"),
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other ),
xgap = 2, ygap = 2) %>%
layout(title = "SPIN-R : Assessment Completion Status (SPASD Group)",
xaxis = list(title = "Assessment", tickangle = 45, showgrid = FALSE),
yaxis = list(title = "Subject ID", autorange = "reversed", type = "category", showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
ASD_plotSSD_plot <-
plot_ly(data = SSD_assessment, x = ~assessment, y = ~record_id, z = ~complete,
type = "heatmap", colors = c("#238823", "#D2222D"),
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other ),
xgap = 2, ygap = 2) %>%
layout(title = "SPIN-R : Assessment Completion Status (SPINS Group)",
xaxis = list(title = "Assessment", tickangle = 45, showgrid = FALSE),
yaxis = list(title = "Subject ID", autorange = "reversed", type = "category", showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
SSD_plotControl_plot <-
plot_ly(data = Control_assessment, x = ~assessment, y = ~record_id, z = ~complete,
type = "heatmap", colors = c("#238823", "#D2222D"),
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other ),
xgap = 2, ygap = 2) %>%
layout(title = "SPIN-R : Assessment Completion Status (Control Group)",
xaxis = list(title = "Assessment", tickangle = 45, showgrid = FALSE),
yaxis = list(title = "Subject ID", autorange = "reversed", type = "category", showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
Control_plotSSDt1_plot <-
plot_ly(data = SSDt1_assessment, x = ~assessment, y = ~record_id, z = ~complete,
type = "heatmap", colors = c("#238823"),# "#D2222D", "#FFBF00"),
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other ),
xgap = 2, ygap = 2) %>%
layout(title = "SPIN-R : Assessment Completion Status (SSD w T1 Group)",
xaxis = list(title = "Assessment", tickangle = 45, showgrid = FALSE),
yaxis = list(title = "Subject ID", autorange = "reversed", type = "category", showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
SSDt1_plotHCt1_plot <-
plot_ly(data = HCt1_assessment, x = ~assessment, y = ~record_id, z = ~complete,
type = "heatmap", colors = c("#238823"), #, "#D2222D", "#FFBF00"),
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other ),
xgap = 2, ygap = 2) %>%
layout(title = "SPIN-R : Assessment Completion Status (HC w T1 Group)",
xaxis = list(title = "Assessment", tickangle = 45, showgrid = FALSE),
yaxis = list(title = "Subject ID", autorange = "reversed", type = "category", showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
HCt1_plotASDt1_plot <-
plot_ly(data = ASDwt1_assessment, x = ~assessment, y = ~record_id, z = ~complete,
type = "heatmap", colors = c("#238823"), #, "#D2222D", "#FFBF00"),
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other ),
xgap = 2, ygap = 2) %>%
layout(title = "SPIN-R : Assessment Completion Status (ASD w T1 Group)",
xaxis = list(title = "Assessment", tickangle = 45, showgrid = FALSE),
yaxis = list(title = "Subject ID", autorange = "reversed", type = "category", showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
ASDt1_plot### SPASD
SPASD_assessment_status <-
SPASD_merged %>%
ungroup() %>%
select(record_id, group,
ends_with("_form_complete"),
ends_with("_redcap_id"),
ends_with("_explain"),
ends_with("_other_reason_nc"))%>%
mutate(
hand_form_complete = ifelse(hand_redcap_id == "[survey respondent]", 1, hand_form_complete),
aq_form_complete = ifelse(aq_redcap_id == "[survey respondent]", 1, aq_form_complete),
spqb_form_complete = ifelse(spqb_redcap_id == "[survey respondent]", 1, spqb_form_complete),
bdi_form_complete = ifelse(bdi_redcap_id == "[survey respondent]", 1, bdi_form_complete),
iri_form_complete = ifelse(iri_redcap_id == "[survey respondent]", 1, iri_form_complete))
SPASD_assessment_complete <-
SPASD_assessment_status %>%
select(record_id, group, ends_with("_form_complete")) %>%
gather(key = "assessment", value = "complete", -c(record_id, group)) %>%
filter(!is.na(complete))
SPASD_assessment_explain <-
SPASD_assessment_status %>%
select(record_id, group, ends_with("_explain")) %>%
gather(key = "assessment", value = "reason", -c(record_id, group)) %>%
filter(!is.na(reason)) %>%
filter(assessment != "np_validity_issues") %>%
mutate(reason = factor(reason,
levels = c(88, 89, 90, 91,
92, 93, 94, 95,
96, 97, 98, 99),
labels = c("Other",
"Terminated from study",
"Missed appointment",
"Rater forgot to administer",
"Time constraints",
"Withdrew consent",
"Deceased",
"Unable to be contacted",
"Completed but with less than best effort",
"Refused to begin/finish",
"Physical impairment",
"Cognitive impairment")),
assessment = gsub("_explain$", "_form_complete", assessment))
SPASD_assessment_explain_other <-
SPASD_assessment_status %>%
select(record_id, group, ends_with("_other_reason_nc")) %>%
gather(key = "assessment", value = "reason_other", -c(record_id, group)) %>%
filter(!is.na(reason_other)) %>%
mutate(assessment = gsub("_other_reason_nc$", "_form_complete", assessment))
SPASD_assessment_df <- SPASD_assessment_complete %>%
left_join(SPASD_assessment_explain, by = c("record_id", "group", "assessment")) %>%
left_join(SPASD_assessment_explain_other, by = c("record_id", "group", "assessment"))
SPASD_assessment <-
SPASD_assessment_df %>%
filter(group == "ASD") %>%
mutate(assessment = factor(assessment,
levels = c("consent_form_complete",
"demo_form_complete",
"scid5_form_complete",
"sofas_form_complete",
"ahh_form_complete",
"npmed_form_complete",
"pmed_form_complete",
"urine_form_complete",
"hwv_form_complete",
"hand_form_complete",
"wasi_form_complete",
"fnd_form_complete",
"ados_form_complete",
"aq_form_complete",
"bprs_form_complete",
"spqb_form_complete",
"bdi_form_complete",
"co_form_complete",
"mri_form_complete",
"abas_form_complete",
"bsfs_form_complete",
"np_form_complete",
"tasit_form_complete",
"rmet_form_complete",
"iri_form_complete",
"term_form_complete" ),
labels = c("Consent", "Demographics",
"SCID-5-RV", "SOFAS",
"Medical History",
"Nonpsychotropic Medications",
"Psychotropic Medications",
"Urine Toxicology Pregnancy",
"Height Weight Vitals", "HDQ",
"WASI-II/WAIS",
"Fagerstrom Nicotine Dependence",
"ADOS-2", "AQ", "BPRS",
"SPQ-B", "BDI-II", "Nicotine Expired CO",
"MRI", "ABAS-II", "BSFS",
"Neuropsych", "TASIT A", "RMET", "IRI", "Termination")))
SPASD_control_assessment_df <-
SPASD_assessment_df %>%
filter(group == "Control") %>%
mutate(assessment = factor(assessment,
levels = c("consent_form_complete",
"demo_form_complete",
"scid5_form_complete",
"sofas_form_complete",
"ahh_form_complete",
"npmed_form_complete",
"pmed_form_complete",
"urine_form_complete",
"hwv_form_complete",
"hand_form_complete",
"wasi_form_complete",
"fnd_form_complete",
"aq_form_complete",
"spqb_form_complete",
"bdi_form_complete",
"co_form_complete",
"mri_form_complete",
"abas_form_complete",
"bsfs_form_complete",
"np_form_complete",
"tasit_form_complete",
"rmet_form_complete",
"iri_form_complete",
"term_form_complete"),
labels = c("Consent", "Demographics",
"SCID-5-RV", "SOFAS",
"Medical History",
"Nonpsychotropic Medications",
"Psychotropic Medications",
"Urine Toxicology Pregnancy",
"Height Weight Vitals", "HDQ",
"WASI-II/WAIS",
"Fagerstrom Nicotine Dependence",
"AQ",
"SPQ-B", "BDI-II", "Nicotine Expired CO",
"MRI", "ABAS-II", "BSFS",
"Neuropsych", "TASIT A", "RMET", "IRI", "Termination")))
SPASD_control_complete_plot <- SPASD_control_assessment_df %>%
plot_ly(x = ~assessment, y = ~record_id, z = ~complete,
xgap = 2, ygap = 2,
colors = c("#238823", "#FFBF00", "#D2222D"),
type = "heatmap",
hoverinfo = 'text',
text = ~paste('Subject ID: ', record_id,
'<br>Assessment: ', assessment,
'<br>Status: ', complete,
'<br>Reason: ', reason,
'<br>Other Reason: ', SPASD_control_assessment_df$reason_other)) %>%
layout(title = "SPASD : Assessment Completion Status (Control Group)",
font = list(family = "Arial"),
xaxis = list(title = "Assessment",
type = "category",
ticks = "",
tickangle = 45,
showgrid = FALSE),
yaxis = list(title = "Subject ID",
autorange = TRUE,
type = "category",
categoryorder = "category descending",
ticks = "",
showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
SPASD_control_complete_plotSPASD_complete_plot <-
SPASD_assessment %>%
plot_ly(x = ~assessment, y = ~record_id, z = ~complete,
xgap = 2, ygap = 2,
colors = c("#238823", "#D2222D", "#FFBF00"),
type = "heatmap",
height=1300,
hoverinfo = 'text',
text = ~paste(' Subject ID: ', record_id,
'<br> Assessment: ', assessment,
'<br> Status: ', complete,
'<br> Reason: ', reason,
'<br> Reason: ', reason_other )) %>%
layout(title = "SPASD : Assessment Completion Status (ASD Group)",
font = t,
xaxis = list(title = "Assessment",
ticks = "",
tickangle= 45,
showgrid = FALSE),
yaxis = list(title = "Subject ID",
autorange = TRUE,
type = "category",
categoryorder = "category descending",
ticks = "",
tickvals=~record_id,
showgrid = FALSE)) %>%
hide_colorbar() %>%
config(displayModeBar = FALSE)
SPASD_complete_plotStructured Clinical Interview for DSM Disorders (SCID)
SPASD
SPASD_scid <- SPASD_merged %>%
select(record_id, group, starts_with("scid5"))
# final diagnosis variable scid5_diagnosis will be set to no diagnosis
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 2] <- "No diagnosis"
# Bipolar disorder
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis[SPASD_scid$scid5_dis_yn == 1 & SPASD_scid$scid5_dis1_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## multiple scid disorders
# second disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_2[SPASD_scid$scid5_cont1 == 1 & SPASD_scid$scid5_dis2_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## 3rd disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_3[SPASD_scid$scid5_cont2 == 1 & SPASD_scid$scid5_dis3_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## 4th disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_4[SPASD_scid$scid5_cont3 == 1 & SPASD_scid$scid5_dis4_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## 5th disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_5[SPASD_scid$scid5_cont4 == 1 & SPASD_scid$scid5_dis5_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## 6th disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_6[SPASD_scid$scid5_cont5 == 1 & SPASD_scid$scid5_dis6_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## 7th disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_7[SPASD_scid$scid5_cont6 == 1 & SPASD_scid$scid5_dis7_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"
## 8th disorder
# Bipolar disorder
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_bipol == 1] <- "Bipolar I disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_bipol == 2] <- "Bipolar II Disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_bipol == 3] <- "Cyclothymic Disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_bipol == 4] <- "Other Bipolar Disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_bipol == 5] <- "Bipolar and Related Disorder Due to Another Medical Condition"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_bipol == 6] <- "Substance/medication-induced bipolar and related disorder"
# Depressive type
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_depressive == 1] <- "Major depressive disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_depressive == 2] <- "Persistent depressive disorder (dysthymia)"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_depressive == 3] <- "Premenstrual dysphoric disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_depressive == 4] <- "Other specified depressive disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_depressive == 5] <- "Depressive disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_depressive == 6] <- "Substance/medication-induced depressive disorder"
# Schizophrenia
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 1] <- "Schizophrenia"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 2] <- "Schizophreniform disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 3] <- "Schizoaffective disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 4] <- "Delusional disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 5] <- "Brief psychotic disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 6] <- "Psychotic disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 7] <- "Substance/medication-induced psychotic disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_scz_psyc == 8] <- "Other Specified Psychotic Disorder"
# substance-related disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 1] <- "Alcohol-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 2] <- "Sedative-Hypnotic-Anxiolytic-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 3] <- "Cannabis-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 4] <- "Stimulants/Cocaine-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 5] <- "Opioid-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 6] <- "PCP-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 7] <- "Other Hallucinogen-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 8] <- "Inhalant-related disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_subst == 9] <- "Other/Unknown substance-related disorder"
# Anxiety-related disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 1] <- "Panic disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 2] <- "Agoraphobia"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 3] <- "Social anxiety disorder (social phobia)"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 4] <- "Specific phobia"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 5] <- "Generalized anxiety disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 6] <- "Separation anxiety disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 7] <- "Other specified anxiety disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 8] <- "Anxiety disorder due to another medical condition"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_anx == 9] <- "Substance/medication-induced anxiety disorder"
# Obsessive-compulsive and related disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_ocd == 1] <- "Obsessive-compulsive disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_ocd == 2] <- "Hoarding disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_ocd == 3] <- "Body dysmorphic disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_ocd == 4] <- "Trichotillomania (hair-pulling disorder)"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_ocd == 5] <- "Excoriation (skin-picking) disorder"
# Sleep-wake disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_sleepwake == 1] <- "Insomnia disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_sleepwake == 2] <- "Hypersomnolence disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_sleepwake == 3] <- "Substance/medication-induced sleep disorder"
# Eating disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_eating == 1] <- "Anorexia nervosa"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_eating == 2] <- "Bulimia nervosa"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_eating == 3] <- "Binge-eating disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_eating == 4] <- "Avoidant/restrictive food intake disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_eating == 5] <- "Other specified feeding or eating disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_eating == 6] <- "Unspecified feeding or eating disorder"
# Somatic disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_somato == 1] <- "Somatic symptom disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_somato == 2] <- "Illness anxiety disorder"
# Externalizing disorders
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_extern == 1] <- "Attention-deficit/hyperactivity disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_extern == 2] <- "Intermittent explosive disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_extern == 3] <- "Gambling disorder"
# Trauma- and stressor-related disorders based on scid5_dis1_cat_trauma
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_trauma == 1] <- "Acute stress disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_trauma == 2] <- "Posttraumatic stress disorder"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_trauma == 3] <- "Adjustment disorders"
SPASD_scid$scid5_diagnosis_8[SPASD_scid$scid5_cont7 == 1 & SPASD_scid$scid5_dis8_cat_trauma == 4] <- "Other specified trauma- and stressor-related disorder"SPASD_diagnosis_counts <- SPASD_scid %>%
pivot_longer(cols = starts_with("scid5_diagnosis"), names_to = "variable", values_to = "diagnosis") %>%
filter(!is.na(diagnosis)) %>% # Remove NA values
count(group, diagnosis)
SPASD_scid_plot <- plot_ly(
data = SPASD_diagnosis_counts,
x = ~n, # Count on x-axis
y = ~reorder(diagnosis, n), # Diagnosis on y-axis, sorted by count
color = ~group, # Color by group (ASD vs. Control)
type = "bar",
orientation = "h", # Horizontal bars
text = ~paste("Count:", n), # Tooltip with count
hoverinfo = "text"
) %>%
layout(
title = "SCID Diagnosis by Group",
xaxis = list(title = "Count"),
yaxis = list(title = "Diagnosis"),
barmode = "group" # Side-by-side bars for ASD and Control
)
# Display the interactive plot
SPASD_scid_plot# Create a new dataframe SPINR_demo which will house the main demographic information from SPINR_merged. This includes the participants, age at the start of the study, their handedness, group, assigned sex at birth, race, highest education amd neuropsych composite score
# This was adapted from SPASD_SPINS_redcap_wrangling.Rmd
SPINR_demo <-
SPINR_merged %>%
select(record_id, group, demo_doa,demo_dob, np_fact_handedness,
demo_sex_birth, demo_age_study_entry,
demo_race___1_asian_east, demo_race___2_asian_southeast, demo_race___3_asian_south,
demo_race___4_black_african, demo_race___5_black_na, demo_race___6_black_carribean,
demo_race___7_firstnations, demo_race___8_indian_caribbean, demo_race___9_indigenous, demo_race___10_inuit, demo_race___11_latin, demo_race___12_metis, demo_race___13_middleeastern, demo_race___14_white, demo_race___15_white_na, demo_race___16_mixed, demo_race___17_noanswer, demo_race___18_unknown, demo_race___19_other, demo_highest_grade_self,demo_highest_grade_mom,demo_highest_grade_dad, np_composite_tscore) %>%
# We are setting assigned sex at birth as a factor for analysis
mutate(sex = factor(demo_sex_birth,
levels = c(1, 2, 3, 4),
labels = c("Female", "Male", "Intersex", "Prefer not to Answer")),
# Renaming the responses for the demo race drop down to be more clear. case_when used to vectorise the data thereby giving us one column - race - with the respective participants responses.
race = case_when(
demo_race___1_asian_east == 1 ~ "Asian - East",
demo_race___2_asian_southeast == 1 ~ "Asian - South East",
demo_race___3_asian_south == 1 ~ "Asian - South Asia",
demo_race___4_black_african == 1 ~ "Black - African",
demo_race___5_black_na == 1 ~ "Black - African American",
demo_race___6_black_carribean == 1 ~ "Black - Caribbean",
demo_race___7_firstnations == 1 ~ "Native - First Nation",
demo_race___8_indian_caribbean == 1 ~ "South Asian - Caribbean",
demo_race___9_indigenous == 1 ~ "Native - American",
demo_race___10_inuit == 1 ~ "Native - Inuit",
demo_race___11_latin == 1 ~ "Latin American",
demo_race___12_metis == 1 ~ "Native - Metis",
demo_race___13_middleeastern == 1 ~ "Middle Eastern",
demo_race___14_white == 1 ~ "White - European",
demo_race___15_white_na == 1 ~ "White - North American",
demo_race___16_mixed == 1 ~ "More than one race",
demo_race___17_noanswer == 1 ~ "No Answer",
demo_race___18_unknown == 1 ~ "Unknown",
demo_race___18_unknown == 1 ~ "Other" ))
# Construct final dataframe with the post processed columns
SPINR_demo <- SPINR_demo %>%
select(record_id, group, demo_doa, demo_dob, np_fact_handedness, sex, demo_age_study_entry, race, demo_highest_grade_self,demo_highest_grade_mom,demo_highest_grade_dad, np_composite_tscore)
# All of the participants have CMH or CMP in their record id, this implies they were scanned at a CAMH site - we will include a column in SPINR_demo to highlight this
SPINR_demo$site <- ifelse(grepl("^SPN31", SPINR_demo$record_id), "CMP", "CMH")
## Note that SPN31_CMH_050002 was erroneously named as a SPN31 participant, and therefore have been scanned at CMH. We will adjust it here to refelct this
SPINR_demo$site[SPINR_demo$record_id == "SPN31_CMH_050002"] <- "CMH"
# Create a new dataframe SPASD_demo which will house the main demographic information from SPASD_merged. This includes the participants, age at the start of the study, their handedness, group, assigned sex at birth, race, highest education amd neuropsych composite score
## Neuropsych Assessments
# The following Neuropsych assessments are collected, RMET (Reading The Mind in The Eyes Test), ER-40 (Penn Emotion Recognition Test), and, TASIT-R (The Awareness of Social Inference Test - Revised) Along with various clinical assessments. We will create a new dataframe combining all of these into one from SPINR_merged - this new dataframe will be called SPINR_neuro
# Adapted from SPASD_SPINS_redcap_wrangling.Rmd
SPINR_neuro <-
SPINR_merged %>%
select(record_id,
# Brief Psychiatric Rating Scale
bprs_factor_anxiety_depression,
bprs_factor_neg_symp,
bprs_factor_pos_symp,
bprs_factor_activation,
bprs_factor_hostility,
# Neuropsych Summary Scores
np_domain_tscore_process_speed,
np_domain_tscore_att_vigilance,
np_domain_tscore_work_mem,
np_domain_tscore_verbal_learning,
np_domain_tscore_visual_learning,
np_domain_tscore_reasoning_ps,
np_domain_tscore_social_cog,
# Interpersonal Reactivity Index
iri_factor_pt,
iri_factor_fs,
iri_factor_ec,
iri_factor_pd,
iri_total,
# Birchwood Social Functioning Scale
bsfs_sec1_total,
bsfs_sec2_total,
bsfs_sec3_total,
bsfs_sec4_total,
bsfs_sec5_total,
bsfs_sec6_total,
bsfs_sec7_y_total_7a,
bsfs_sec7_n_total_7b,
bsfs_sec7_y_total_7a,
bsfs_sec_grandtotal1,
bsfs_sec_grandtotal2,
# Penn Emotion Recognition Test
er40_cr,
er40_crt,
er40ang,
er40fear,
er40hap,
er40noe,
er40sad,
er40_fpa,
er40_fpf,
# Reading The Mind In The Eyes Test
rmet_total,
# The Awareness Of Social Inference Test-Revised (TASIT)
tasit_part1_happyscore,
tasit_part2_surprisedscore,
tasit_part3_neutralscore,
tasit_part4_sadscore,
tasit_part5_angryscore,
tasit_part6_anxiousscore,
tasit_part7_revoltedscore,
tasit_positive_total,
tasit_negative_total,
tasit_correct_total,
tasit_part2_grandtotal,
tasit_part2_total_do_sincere,
tasit_part2_total_say_sincere,
tasit_part2_total_think_sincere,
tasit_part2_total_feel_sincere,
tasit_part2_total_do_s_sarcasm,
tasit_part2_total_say_s_sarcasm,
tasit_part2_total_think_s_sarcasm,
tasit_part2_total_feel_s_sarcasm,
tasit_part2_total_do_p_sarcasm,
tasit_part2_total_say_p_sarcasm,
tasit_part2_total_think_p_sarcasm,
tasit_part2_total_feel_p_sarcasm,
tasit_part2_total_sincere,
tasit_part2_total_s_sarcasm,
tasit_part2_total_p_sarcasm,
# TAST - Total Number of items correct
tasit_part2_total_do,
tasit_part2_total_say,
tasit_part2_total_think,
tasit_part2_total_feel,
# TASIT - Total Correct Sarcastic - Do, Say, Think, Feel
tasit_part3_total_sarcastic_do,
tasit_part3_total_sarcastic_say,
tasit_part3_total_sarcastic_think,
tasit_part3_total_sarcastic_feel,
# TASIT - Total Correct - Text and Visual Cues
tasit_part3_grandtotal_text,
tasit_part3_grandtotal_visual,
# TASIT - Total Correct - Do, Say, Think, Feel
tasit_part3_grandtotal_do,
tasit_part3_grandtotal_say,
tasit_part3_grandtotal_think,
tasit_part3_grandtotal_feel,
tasit_part3_grandtotal_sarcasm,
tasit_part3_grandtotal_lies,
# Schizotypal Personality Questionnaire-Brief
spqb_total,
# Adult Autism-Spectrum Quotient
aq_total,
# Beck Depression Inventory
total_score)
# Rename Beck Depression Inventory - the variable is currently total_score, which is super ambiguious - renaming variable to bdi_total.
names(SPINR_neuro)[names(SPINR_neuro) == 'total_score'] <- 'bdi_total'
### Model
# We are now going to construct a new data frame SPINR_model - that combines our variables of interest from the SPINR_demo and SPINR_neuro
# Select columns we want from SPINR_demo
SPINR_model <- SPINR_demo
# adjust as needed
# Now we will join the selected column based on the record_id
# we need to also extract record_id to ensure we can join using it.
SPINR_model <- left_join(SPINR_model, SPINR_neuro, by = "record_id")
### Cleaning Model
# Some participants were scored 0 despite not completing certain assessments (mainly TASIT) due in elegibiltiy. We will filter these out as they are interfering with the data visualizations
SPINR_model <- SPINR_model %>%
filter(tasit_part1_happyscore != 0)
SPINR_model <- SPINR_model %>%
filter(tasit_part2_grandtotal != 0)
SPINR_model <- SPINR_model %>%
filter(tasit_part3_grandtotal_lies != 0)
SPINR_model <- SPINR_model %>% mutate(tasit_part3_total = tasit_part3_grandtotal_sarcasm + tasit_part3_grandtotal_lies)
### SPASD
# This was adapted from SPASD_SPINS_redcap_wrangling.Rmd
SPASD_demo <-
SPASD_merged %>%
select(record_id, group,
demo_sex_birth, demo_age_study_entry,
demo_race___1_white, demo_race___2_black, demo_race___3_native,
demo_race___4_asian, demo_race___5_islander, demo_race___6_other,
demo_race___7_mixed, demo_race___8_unknown, demo_race_other,
demo_highest_grade_self, wasi_wais_fsiq, wasi_fsiq4_cs, wasi_fsiq2_cs, np_composite_tscore,
hand_laterality_quotient) %>%
# We are setting assigned sex at birth as a factor for analysis
mutate(sex = factor(demo_sex_birth,
levels = c(1, 2, 3),
labels = c("Female", "Male", "Intersex")),
# Renaming the responses for the demo race drop down to be more clear. case_when used to vectorise the data thereby giving us one column - race - with the respective participants responses.
race = case_when(
demo_race___7_mixed == 1 ~ "More than one race",
demo_race___1_white == 1 ~ "White",
demo_race___2_black == 1 ~ "Black or African American",
demo_race___3_native == 1 ~ "American Indian/Alaska Native",
demo_race___4_asian == 1 ~ "Asian",
demo_race___5_islander == 1 ~ "Hawaiian or Pacific Islander",
demo_race___6_other == 1 ~ "Other",
demo_race___8_unknown == 1 ~ "Unknown or not reported",
TRUE ~ "Not Specified" # Handling cases where none of the conditions are met
)%>%
factor(.),
iq = coalesce(as.numeric(wasi_wais_fsiq), as.numeric(wasi_fsiq4_cs), as.numeric(wasi_fsiq2_cs))
)
# Construct final dataframe with the post processed columns
SPASD_demo <- SPASD_demo %>%
select(record_id, group, sex, demo_age_study_entry, race, demo_highest_grade_self, iq, np_composite_tscore)
# Make a new column in the SPASD_demo that defines the IQ range.
SPASD_demo <- SPASD_demo %>%
mutate(
iq_range = cut(iq,
breaks = c(70, 85, 100, 115, 130, 145, 160),
labels = c("70-84", "85-99", "100-114", "115-129", "130-144", "145-160"),
include.lowest = TRUE,
right = FALSE)
)
## Neuropsych Assessments
# The following Neuropsych assessments are collected, RMET (Reading The Mind in The Eyes Test), ER-40 (Penn Emotion Recognition Test), and, TASIT-R (The Awareness of Social Inference Test - Revised) Along with various clinical assessments. We will create a new dataframe combining all of these into one from SPINR_merged - this new dataframe will be called SPASD_neuro
#
# Adapted from SPASD_SPINS_redcap_wrangling.Rmd
SPASD_neuro <-
SPASD_merged %>%
select(record_id,
# Brief Psychiatric Rating Scale
bprs_factor_anxiety_depression,
bprs_factor_neg_symp,
bprs_factor_pos_symp,
bprs_factor_activation,
bprs_factor_hostility,
# Neuropsych Summary Scores
np_domain_tscore_process_speed,
np_domain_tscore_att_vigilance,
np_domain_tscore_work_mem,
np_domain_tscore_verbal_learning,
np_domain_tscore_visual_learning,
np_domain_tscore_reasoning_ps,
np_domain_tscore_social_cog,
# Interpersonal Reactivity Index
iri_factor_pt,
iri_factor_fs,
iri_factor_ec,
iri_factor_pd,
iri_total,
# Birchwood Social Functioning Scale
bsfs_sec1_total,
bsfs_sec2_total,
bsfs_sec3_total,
bsfs_sec4_total,
bsfs_sec5_total,
bsfs_sec6_total,
bsfs_sec7_y_total_7a,
bsfs_sec7_n_total_7b,
bsfs_sec7_y_total_7a,
bsfs_sec_grandtotal1,
bsfs_sec_grandtotal2,
# Penn Emotion Recognition Test
scog_er40_cr_columnpcr_value,
scog_er40_crt_columnqcrt_value,
scog_er40ang_columnv,
scog_er40fear_columnw,
scog_er40hap_columnx,
scog_er40noe_columny,
scog_er40sad_columnz,
scog_er40_fpa_columnaa,
scog_er40_fpf_columnab,
scog_er40mild_columnap,
scog_er40extr_columnaq,
# Reading The Mind In The Eyes Test
scog_rmet_total,
# The Awareness Of Social Inference Test-Revised (TASIT)
scog_tasit_p1_happy,
scog_tasit_p1_surprised,
scog_tasit_p1_neutral,
scog_tasit_p1_sad,
scog_tasit_p1_angry,
scog_tasit_p1_anxious,
scog_tasit_p1_revolted,
scog_tasit_p1_total_positive,
scog_tasit_p1_total_negative,
scog_tasit_p1_total,
scog_tasit_p2_total,
scog_tasit_p2_do,
scog_tasit_p2_say,
scog_tasit_p2_think,
scog_tasit_p2_feel,
scog_tasit_p2_sin,
scog_tasit_p2_sscar,
scog_tasit_p2_psar,
scog_tasit_p3_do,
scog_tasit_p3_say,
scog_tasit_p3_think,
scog_tasit_p3_feel,
scog_tasit_p3_total,
# Schizotypal Personality Questionnaire-Brief
spqb_total,
# Adult Autism-Spectrum Quotient
aq_total,
# Beck Depression Inventory
total_score)
# Rename Beck Depression Inventory - the variable is currently total_score, which is super ambiguious - renaming variable to bdi_total.
names(SPASD_neuro)[names(SPASD_neuro) == 'total_score'] <- 'bdi_total'
### SPASD Model
# We are now going to construct a new data frame SPINR_model - that combines our variables of interest from the SPINR_demo and SPINR_neuro
# Select columns we want from SPASD_demo
SPASD_model <- SPASD_demo
# adjust as needed
# Now we will join the selected column based on the record_id
# we need to also extract record_id to ensure we can join using it.
SPASD_model <- left_join(SPASD_model, SPASD_neuro, by = "record_id")
# Some participants were scored 0 despite not completing certain assessments (mainly TASIT) due in elegibiltiy. We will filter these out as they are interfering with the data visualizations
SPASD_model <- SPASD_model %>%
filter(scog_tasit_p1_total != 0)
SPASD_model <- SPASD_model %>%
filter(scog_tasit_p2_total != 0)
SPASD_model <- SPASD_model %>%
filter(scog_tasit_p3_total != 0)
SPASD_model <- SPASD_model %>%
filter(scog_er40_cr_columnpcr_value != 0)
SPASD_model <- SPASD_model %>%
filter(scog_er40hap_columnx!= 0)
SPASD_model <- SPASD_model %>%
filter(scog_er40hap_columnx!= "NI")
SPASD_model <- SPASD_model %>%
filter(scog_er40sad_columnz!= "NI")
SPASD_model <- SPASD_model %>%
filter(scog_er40ang_columnv!= 0)
SPASD_model <- SPASD_model %>%
filter(scog_er40noe_columny!= 0)Descriptive Statistics
SPINR
label(SPINR_model$demo_age_study_entry) <- "Age (years)"
label(SPINR_model$sex) <- "Sex"
label(SPINR_model$race) <- "Race"
label(SPINR_model$demo_highest_grade_self) <-"Education (years)"
label(SPINR_model$np_composite_tscore) <- "MATRICS"
my.render.cont <- function(x) {
with(stats.apply.rounding(stats.default(x), digits=2), c("",
"Mean (SD)"=sprintf("%s (± %s)", MEAN, SD),
"Median [Min, Max]"=sprintf("%s [%s, %s]", MEDIAN, MIN, MAX)))
}
my.render.cat <- function(x) {
c("", sapply(stats.default(x), function(y) with(y,
sprintf("%d (%0.0f %%)", FREQ, PCT))))
}
SPINR_demo_table <-
table1(~ demo_age_study_entry + sex + race + demo_highest_grade_self + np_composite_tscore | group,
data = SPINR_demo,
render.continuous = my.render.cont, render.categorical = my.render.cat)
SPINR_demo_table| ASD w T1 (N=4) |
Control (N=25) |
HC w T1 (N=14) |
SPASD (N=39) |
SPINS (N=10) |
SSD w T1 (N=17) |
Overall (N=109) |
|
|---|---|---|---|---|---|---|---|
| demo_age_study_entry | |||||||
| Mean (SD) | 22 (± 8.8) | 30 (± 5.2) | 23 (± 4.2) | 25 (± 5.0) | 27 (± 5.9) | 26 (± 4.6) | 26 (± 5.5) |
| Median [Min, Max] | 19 [16, 35] | 30 [20, 39] | 23 [18, 33] | 24 [17, 36] | 26 [17, 39] | 26 [17, 34] | 26 [16, 39] |
| sex | |||||||
| Female | 1 (25 %) | 8 (32 %) | 9 (64 %) | 19 (49 %) | 4 (40 %) | 5 (29 %) | 46 (42 %) |
| Male | 3 (75 %) | 17 (68 %) | 5 (36 %) | 20 (51 %) | 6 (60 %) | 12 (71 %) | 63 (58 %) |
| Intersex | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) |
| Prefer not to Answer | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) |
| race | |||||||
| Asian - South Asia | 1 (25 %) | 6 (24 %) | 3 (21 %) | 4 (10 %) | 0 (0 %) | 2 (12 %) | 16 (15 %) |
| South Asian - Caribbean | 1 (25 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 0 (0 %) | 1 (1 %) |
| White - European | 1 (25 %) | 4 (16 %) | 0 (0 %) | 5 (13 %) | 2 (20 %) | 3 (18 %) | 15 (14 %) |
| White - North American | 1 (25 %) | 3 (12 %) | 0 (0 %) | 14 (36 %) | 3 (30 %) | 0 (0 %) | 21 (19 %) |
| Asian - East | 0 (0 %) | 6 (24 %) | 7 (50 %) | 5 (13 %) | 1 (10 %) | 2 (12 %) | 21 (19 %) |
| Asian - South East | 0 (0 %) | 1 (4 %) | 0 (0 %) | 2 (5 %) | 1 (10 %) | 0 (0 %) | 4 (4 %) |
| Black - African | 0 (0 %) | 1 (4 %) | 2 (14 %) | 0 (0 %) | 0 (0 %) | 3 (18 %) | 6 (6 %) |
| Black - African American | 0 (0 %) | 1 (4 %) | 0 (0 %) | 1 (3 %) | 1 (10 %) | 1 (6 %) | 4 (4 %) |
| Black - Caribbean | 0 (0 %) | 1 (4 %) | 0 (0 %) | 1 (3 %) | 1 (10 %) | 3 (18 %) | 6 (6 %) |
| Latin American | 0 (0 %) | 1 (4 %) | 1 (7 %) | 6 (15 %) | 0 (0 %) | 1 (6 %) | 9 (8 %) |
| Middle Eastern | 0 (0 %) | 1 (4 %) | 1 (7 %) | 1 (3 %) | 1 (10 %) | 2 (12 %) | 6 (6 %) |
| demo_highest_grade_self | |||||||
| Mean (SD) | 11 (± 0.96) | 17 (± 2.0) | 16 (± 2.0) | 14 (± 2.0) | 14 (± 2.1) | 14 (± 1.9) | 15 (± 2.4) |
| Median [Min, Max] | 12 [10, 12] | 16 [14, 20] | 16 [13, 20] | 14 [11, 19] | 15 [11, 18] | 14 [11, 20] | 15 [10, 20] |
| np_composite_tscore | |||||||
| Mean (SD) | 55 (± NA) | 59 (± 9.4) | 50 (± 8.0) | 47 (± 9.7) | 41 (± 12) | 39 (± 12) | 49 (± 12) |
| Median [Min, Max] | 55 [55, 55] | 58 [41, 77] | 52 [38, 63] | 48 [25, 65] | 42 [22, 61] | 43 [18, 52] | 50 [18, 77] |
| Missing | 3 (75.0%) | 1 (4.0%) | 3 (21.4%) | 2 (5.1%) | 1 (10.0%) | 8 (47.1%) | 18 (16.5%) |
SPASD
label(SPASD_model$demo_age_study_entry) <- "Age (years)"
label(SPASD_model$sex) <- "Sex"
label(SPASD_model$race) <- "Race"
label(SPASD_model$demo_highest_grade_self) <-"Education (years)"
label(SPASD_model$iq_range) <- "IQ Range"
label(SPASD_model$np_composite_tscore) <- "MATRICS"
my.render.cont <- function(x) {
with(stats.apply.rounding(stats.default(x), digits=2), c("",
"Mean (SD)"=sprintf("%s (± %s)", MEAN, SD),
"Median [Min, Max]"=sprintf("%s [%s, %s]", MEDIAN, MIN, MAX)))
}
my.render.cat <- function(x) {
c("", sapply(stats.default(x), function(y) with(y,
sprintf("%d (%0.0f %%)", FREQ, PCT))))
}
SPASD_demo_table <-
table1(~ demo_age_study_entry + sex + race + demo_highest_grade_self + iq_range + np_composite_tscore | group,
data = SPASD_demo,
render.continuous = my.render.cont, render.categorical = my.render.cat)
SPASD_demo_table| ASD (N=116) |
Control (N=43) |
Overall (N=159) |
|
|---|---|---|---|
| demo_age_study_entry | |||
| Mean (SD) | 21 (± 4.3) | 26 (± 5.0) | 22 (± 4.9) |
| Median [Min, Max] | 20 [15, 35] | 26 [17, 35] | 21 [15, 35] |
| Missing | 0 (0%) | 1 (2.3%) | 1 (0.6%) |
| sex | |||
| Female | 49 (42 %) | 18 (42 %) | 67 (42 %) |
| Male | 67 (58 %) | 24 (56 %) | 91 (57 %) |
| Intersex | 0 (0 %) | 0 (0 %) | 0 (0 %) |
| Missing | 0 (0%) | 1 (2.3%) | 1 (0.6%) |
| race | |||
| Asian | 16 (14 %) | 19 (44 %) | 35 (22 %) |
| Black or African American | 4 (3 %) | 7 (16 %) | 11 (7 %) |
| More than one race | 9 (8 %) | 2 (5 %) | 11 (7 %) |
| Not Specified | 0 (0 %) | 1 (2 %) | 1 (1 %) |
| Other | 6 (5 %) | 1 (2 %) | 7 (4 %) |
| White | 81 (70 %) | 13 (30 %) | 94 (59 %) |
| demo_highest_grade_self | |||
| Mean (SD) | 13 (± 2.2) | 16 (± 2.1) | 14 (± 2.5) |
| Median [Min, Max] | 12 [9.0, 20] | 16 [11, 20] | 13 [9.0, 20] |
| Missing | 0 (0%) | 1 (2.3%) | 1 (0.6%) |
| iq_range | |||
| 70-84 | 2 (2 %) | 1 (2 %) | 3 (2 %) |
| 85-99 | 15 (13 %) | 5 (12 %) | 20 (13 %) |
| 100-114 | 36 (31 %) | 11 (26 %) | 47 (30 %) |
| 115-129 | 41 (35 %) | 17 (40 %) | 58 (36 %) |
| 130-144 | 19 (16 %) | 6 (14 %) | 25 (16 %) |
| 145-160 | 1 (1 %) | 0 (0 %) | 1 (1 %) |
| Missing | 2 (1.7%) | 3 (7.0%) | 5 (3.1%) |
| np_composite_tscore | |||
| Mean (SD) | 41 (± 11) | 51 (± 10) | 43 (± 12) |
| Median [Min, Max] | 42 [-3.0, 59] | 53 [16, 75] | 44 [-3.0, 75] |
| Missing | 7 (6.0%) | 5 (11.6%) | 12 (7.5%) |
Distributions
SPINR (AGE)
# Histogram for Age Distribution
SPINR_age_distribution <- plot_ly(data = SPINR_demo, alpha = 0.6, autobinx = FALSE) %>%
add_histogram(x = ~demo_age_study_entry[group == "ASD"],
name = "ASD",
xbins = list(start = 15, end = 36, size = 1),
marker = list(color = 'blue')) %>%
add_histogram(x = ~demo_age_study_entry[group == "SSD w T1"],
name = "SSD w T1",
xbins = list(start = 15, end = 36, size = 1),
marker = list(color = 'yellow')) %>%
add_histogram(x = ~demo_age_study_entry[group == "ASD w T1"],
name = "ASD w T1",
xbins = list(start = 15, end = 36, size = 1),
marker = list(color = 'green')) %>%
add_histogram(x = ~demo_age_study_entry[group == "SPINS"],
name = "SPINS",
xbins = list(start = 15, end = 36, size = 1),
marker = list(color = 'orange')) %>%
add_histogram(x = ~demo_age_study_entry[group == "Control"],
name = "Control",
xbins = list(start = 15, end = 36, size = 1),
marker = list(color = 'red')) %>%
add_histogram(x = ~demo_age_study_entry[group == "HC w T1"],
name = "HC w T1",
xbins = list(start = 15, end = 36, size = 1),
marker = list(color = 'pink')) %>%
layout(
barmode = "overlay",
title = "Age Distribution by Group (SPINR)",
xaxis = list(title = "Age (years)"),
yaxis = list(title = "Count"),
font = list(size = 12),
plot_bgcolor = "#E5ECF6",
paper_bgcolor = "#FFFFFF"
)
SPINR_age_distributionSPASD (AGE)
SPASD_age_distribution <-
plot_ly(alpha = 0.6, autobinx = FALSE,
xbins = list(start = 15, end = 36, size = 1)) %>%
add_histogram(x = ~SPASD_demo$demo_age_study_entry[SPASD_demo$group == "ASD"], name = "ASD") %>%
add_histogram(x = ~SPASD_demo$demo_age_study_entry[SPASD_demo$group == "Control"], name = "Control") %>%
layout(barmode = "overlay",
title = "Age Distribution by Group (SPASD)",
font = t,
xaxis = list(title = "Age (years)"),
yaxis = list(title = "Count")) %>%
config(displayModeBar = FALSE)
SPASD_age_distributionSPASD (IQ)
SPASD_iq_distribution <-
plot_ly(alpha = 0.6, autobinx = FALSE,
xbins = list(start = 70, end = 150, size = 10)) %>%
add_histogram(x = ~SPASD_demo$iq[SPASD_demo$group == "ASD"], name = "ASD") %>%
add_histogram(x = ~SPASD_demo$iq[SPASD_demo$group == "Control"], name = "Control") %>%
layout(barmode = "overlay",
title = "IQ Distribution by Group (SPASD)",
font = t,
xaxis = list(title = "Estimated IQ"),
yaxis = list(title = "Count")) %>%
config(displayModeBar = FALSE)
SPASD_iq_distributionNeuropsych Domain Distributions (MATRICS)
The MATRICS Consensus Cognitive Battery is a standardized tool used to evaluate cognitive functioning across multiple domains, specifically designed for use in psychiatric and neurological research. It provides T-scores for each cognitive domain, which are standardized scores used to compare an individual’s performance to a normative reference group.
50: Average performance. Above 50: Better-than-average performance. Below 50: Worse-than-average performance.
SPINR_np_scores <- c("Attention/Vigilance" = "np_domain_tscore_att_vigilance",
"Working Memory" = "np_domain_tscore_work_mem",
"Verbal Learning" = "np_domain_tscore_verbal_learning",
"Visual Learning" = "np_domain_tscore_visual_learning",
"Reasoning/PS" = "np_domain_tscore_reasoning_ps",
"Social Cognition" = "np_domain_tscore_social_cog",
"Processing Speed" = "np_domain_tscore_process_speed")SPASD_np_scores <- c("Attention/Vigilance" = "np_domain_tscore_att_vigilance",
"Working Memory" = "np_domain_tscore_work_mem",
"Verbal Learning" = "np_domain_tscore_verbal_learning",
"Visual Learning" = "np_domain_tscore_visual_learning",
"Reasoning/PS" = "np_domain_tscore_reasoning_ps",
"Social Cognition" = "np_domain_tscore_social_cog",
"Processing Speed" = "np_domain_tscore_process_speed")Attention/Vigilance Domain
Evaluates sustained attention and ability to maintain focus over time. Tasks may include continuous performance tests.
SPINR
SPINR_np_av_plot <- plot_ly(SPINR_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_att_vigilance) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_att_vigilance"),
labels = c( "Attention/Vigilance"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Attention/Vigilance Domain Scores Across Groups (SPINR)")
SPINR_np_av_plotSPASD
SPASD_np_av_plot <- plot_ly(SPASD_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_att_vigilance) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_att_vigilance"),
labels = c( "Attention/Vigilance"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Attention/Vigilance Domain Scores Across Groups (SPASD)")
SPASD_np_av_plotWorking Memory Domain
Measures the ability to temporarily store and manipulate information. Includes verbal and visual working memory tasks.
SPINR
SPINR_np_wm_plot <- plot_ly(SPINR_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_work_mem) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_work_mem"),
labels = c( "Working Memory"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Working Memory Domain Scores Across Groups (SPINR)")
SPINR_np_wm_plotSPASD
SPASD_np_wm_plot <- plot_ly(SPASD_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_work_mem) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_work_mem"),
labels = c( "Working Memory"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Working Memory Domain Scores Across Groups (SPASD)")
SPASD_np_wm_plotVerbal Learning Domain
Assesses learning and recall of verbal information. Tasks often involve memorizing and recalling word list
SPINR
SPINR_np_vl_plot <- plot_ly(SPINR_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_verbal_learning) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_verbal_learning"),
labels = c( "Verbal Learning"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Verbal Learning Domain Scores Across Groups (SPINR)")
SPINR_np_vl_plotSPASD
SPASD_np_vl_plot <- plot_ly(SPASD_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_verbal_learning) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_verbal_learning"),
labels = c( "Verbal Learning"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Verbal Learning Domain Scores Across Groups (SPASD)")
SPASD_np_vl_plotVisual Learning Domain
Focuses on the ability to learn and recall visual patterns or images.
SPINR
SPINR_np_visl_plot <- plot_ly(SPINR_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_visual_learning) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_visual_learning"),
labels = c( "Visual Learning"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Visual Learning Domain Scores Across Groups (SPINR)")
SPINR_np_visl_plotSPASD
SPASD_np_visl_plot <- plot_ly(SPASD_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_visual_learning) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_visual_learning"),
labels = c( "Visual Learning"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Visual Learning Domain Scores Across Groups (SPASD)")
SPASD_np_visl_plotReasoning/PS Domain
Measures higher-order cognitive abilities, including abstract reasoning and decision-making.
SPINR
SPINR_np_rsps_plot <- plot_ly(SPINR_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_reasoning_ps) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_reasoning_ps"),
labels = c( "Reasoning/PS"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Reasoning/PS Domain Scores Across Groups (SPINR)")
SPINR_np_rsps_plotSPASD
SPASD_np_rsps_plot <- plot_ly(SPASD_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_reasoning_ps) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_reasoning_ps"),
labels = c( "Reasoning/PS"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Reasoning/PS Domain Scores Across Groups (SPASD)")
SPASD_np_rsps_plotProcessing Speed Domain
Measures rapid information processing and reaction time. Associated with tasks like symbol coding or category fluency.
SPINR
SPINR_np_ps_plot <- plot_ly(SPINR_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_process_speed) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_process_speed"),
labels = c( "Processing Speed"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Processing Speed Domain Scores Across Groups (SPINR)")
SPINR_np_ps_plotSPASD
SPASD_np_ps_plot <- plot_ly(SPASD_model %>%
gather(key = "assessment", value = "score",
np_domain_tscore_process_speed) %>%
mutate(assessment = factor(assessment, levels = c( "np_domain_tscore_process_speed"),
labels = c( "Processing Speed"))),
x = ~assessment, y = ~score, color = ~group, type = "box", boxpoints = "false",
hoverinfo = "text", text = ~paste("Subject: ", record_id, "<br>", assessment, ": ", score),
marker = list(color = "#000", opacity = 0.5)) %>%
layout(boxmode = "group",
xaxis = list(title = "Groups"),
yaxis = list(title = "Score"),
title = "Processing Speed Domain Scores Across Groups (SPASD)")
SPASD_np_ps_plot# recruited between April 1, 2024 - March 31, 2025
Participants_consented_SPINR$consent_sig_date <- as.Date(Participants_consented_SPINR$consent_sig_date)
# Define start and end dates
start_date <- as.Date("2024-04-01")
end_date <- as.Date("2025-03-31")
# Filter rows based on the recruitment date range
new_recruits <- Participants_consented_SPINR[Participants_consented_SPINR$consent_sig_date >= start_date &
Participants_consented_SPINR$consent_sig_date <= end_date, ]# get mri scans complete for each participant and the date
#mri_doa and mri_t1
SPINR_mri <- SPINR_merged %>% select(record_id, mri_doa, mri_t1) %>%
filter(mri_t1 > 0)
start_date <- as.Date("2024-07-10")
end_date <- as.Date("2025-09-01")
SPINR_mri %>%
filter(!is.na(mri_doa),
mri_doa >= start_date,
mri_doa <= end_date) %>%
nrow()## [1] 27
Social cognition
Reading Mind Through the Eyes Test (RMET)
The Reading the Mind in the Eyes Test (RMET) is a widely used measure of social cognition, specifically targeting the ability to infer mental states, an important aspect of Theory of Mind.
How It Works: Participants are shown 36 photographs of the eye region of faces. For each photograph, they must choose the word that best describes what the person in the photograph is thinking or feeling. Four options are provided for each photograph, such as “worried,” “playful,” “jealous,” or “relaxed.”
What It Measures: RMET evaluates subtle social sensitivity and the capacity to read nonverbal social cues.
Scoring:
Higher Scores: Indicate greater social awareness and better ability to interpret others’ mental states. Lower Scores: Suggest challenges in social sensitivity, often observed in conditions like autism spectrum disorder or social anxiety.
SPINR
SPASD
Interpersonal reactivity Index (IRI)
The Interpersonal Reactivity Index (IRI) is a multidimensional measure of empathy. It assesses both emotional and cognitive aspects of empathy, capturing how individuals understand and respond to the emotions and experiences of others.
Subscales of the IRI The IRI comprises four subscales, each targeting a distinct aspect of empathy:
Perspective Taking (PT): Reflects the cognitive aspect of empathy. Measures the ability to adopt another person’s point of view. Example: “I sometimes try to understand my friends better by imagining how things look from their perspective.”
Empathic Concern (EC): Reflects the emotional aspect of empathy. Measures feelings of compassion and concern for others. Example: “I often have tender, concerned feelings for people less fortunate than me.”
Personal Distress (PD): Measures self-oriented feelings of discomfort or anxiety in response to others’ distress. Example: “Being in a tense emotional situation scares me.”
Fantasy (FS): Assesses the tendency to imaginatively identify with fictional characters in books, movies, or stories. Example: “After watching a movie, I feel as though I am one of the characters.” Scoring and Interpretation
Higher Scores: On PT and EC: Indicate greater cognitive and emotional empathy, respectively. On FS: Suggest a strong imaginative capacity and engagement with fictional scenarios. On PD: May indicate susceptibility to personal emotional distress in challenging situations.
Lower Scores: On PT and EC: Suggest difficulty in understanding or feeling for others. On FS: Indicates less imaginative identification with fictional contexts. On PD: Suggest resilience to personal emotional distress in tense situations.
SPINR
SPASD
The Awareness of Social Inference Test-Revised (TASIT-R)
The Awareness of Social Inference Test-Revised (TASIT-R) is a standardized assessment designed to evaluate social cognition, specifically focusing on the ability to recognize and interpret social cues in real-world scenarios. It is widely used to study social perception, inference, and pragmatic communication.
Structure of TASIT-R TASIT-R is divided into three main sections, each assessing a different aspect of social cognition:
Emotion Evaluation: Participants watch brief video clips of actors portraying various basic emotions (e.g., happiness, sadness, anger, fear) through tone, facial expressions, and body language. Measures the ability to accurately identify emotions in social contexts.
Social Inference (Minimal): Involves understanding implied meanings and subtle cues in simple, straightforward social scenarios. Measures the ability to infer others’ intentions and emotions based on situational context without relying on complex reasoning.
Social Inference (Enriched): Participants interpret more complex scenarios involving sarcasm, lies, or double meanings. Requires higher-order reasoning, such as distinguishing between literal and implied meanings or recognizing deception. Scoring and Interpretation
Higher Scores: Reflect greater accuracy in recognizing emotions, understanding social cues, and interpreting complex social scenarios.
Lower Scores: Indicate difficulties in social inference, emotion recognition, and pragmatic understanding, often seen in individuals with social communication deficits, traumatic brain injury, or neurodevelopmental disorders.
SPINR
SPASD
Penn Emotion Recognition Task-40 (ER-40)
The Penn Emotion Recognition Task-40 (ER-40) is a standardized test designed to assess the ability to recognize and identify basic emotions from facial expressions. It is commonly used in research and clinical settings to evaluate emotional perception, a key component of social cognition.
Structure of the ER-40
Stimuli: The task includes 40 grayscale photographs of faces, each displaying one of five basic emotions:
Happy Sad Angry Fearful Neutral
Procedure: Participants are presented with each photograph and asked to select the emotion that best matches the facial expression from the provided options. Scoring and Interpretation
Accuracy: Higher scores reflect a better ability to correctly identify emotional expressions. Lower scores may indicate challenges in emotion recognition, often linked to conditions affecting social cognition, such as autism spectrum disorder, schizophrenia, or traumatic brain injury.
Emotion-Specific Patterns: Some individuals may struggle more with recognizing specific emotions (e.g., fear or anger), offering insights into specific deficits in emotional processing.
Response Time: Refers to the amount of time it takes for participants to make a decision and select an emotion label for each facial expression.
SPINR (columns)
SPASD (columns)
SPINR (Correct Responses)
SPASD (Correct Responses)
SPINR (Response time)
SPASD (Response time)