prep_table1_demographics.Rmd

---
title: "Trait for Analyses"
author: "Jordan Barone"
date: "5/25/2021"
output: html_document
---

*these are just examples with some common trait variables! None of these are required for Table 1 or any descriptives*

##view data
```{r get descriptives, warning=FALSE}

#describe() to get N's for each variable
describe(clearALL_select, fast = TRUE, data = vars>1000)
```

#count and factor variables
```{r}
#summary stats for age
clearALL_select %>% summarise(meanage=mean(age, na.rm=TRUE),
                       sdage=sd(age, na.rm = TRUE),
                       minage=min(age, na.rm = TRUE),
                       maxage=max(age, na.rm = TRUE))

#example to count n participants in a race group
clearALL_select %>% count(race==1)

#table of participants by race
racesum <- clearALL_select %>% group_by(race) %>%
  summarise(n=n())
racesum$race <- factor(racesum$race, levels= c(1, 2, 3, 4, 7, 8, NA), labels = c("Caucasian", 
                   "African American", 
                   "Asian", 
                   "American Indian", 
                   "More than one race",
                   "Decline to Answer"))
kable(racesum)

#ethnicity
ethnicitysum <- clearALL_select %>% 
  group_by(ethnicity, race) %>%
  summarize (n=n())
ethnicitysum$race <- factor(ethnicitysum$race, levels= c(1, 2, 3, 4, 7, 8, NA), labels = c("Caucasian", 
                   "African American", 
                   "Asian", 
                   "American Indian", 
                   "More than one race",
                   "Decline to Answer"))
ethnicitysum$ethnicity <- factor(ethnicitysum$ethnicity, levels = c(1, 2, 3),
                                 labels = c("Hispanic", "Non-Hispanic", "Decline to Answer"))
kable(ethnicitysum)

```

#various tables of factor labels
```{r}
#table of mean attempts
attemptssum <- clearALL_select %>% summarise(n=n(),
                       meanattempts=mean(numfullatt, na.rm=TRUE),
                       meaninterrupted=mean(numintatt, na.rm = TRUE),
                       meanaborted=mean(numabatt, na.rm = TRUE))
kable(attemptssum, digits = 3)

#table counting how many have ANY attempt vs none
attemptYN <- clearALL_select %>% 
  mutate(allattempts=rowSums(select(., ends_with("att")), na.rm = TRUE),
         SBs = ifelse(allattempts>=1, "At Least One Attempt","No Hx of Attempt")) %>%
  group_by(SBs) %>% summarize(n=n())

#tables categorizing diagnoses
SUDyn <- clearALL_select %>% mutate(anySUD=ifelse(lifetimedx_hxSUDalc!=0 |
                   lifetimedx_hxSUDinh!=0 |
                     lifetimedx_hxSUDMJ!=0 |
                     lifetimedx_hxSUDopioid!=0 |
                     lifetimedx_hxSUDother!=0 |
                     lifetimedx_hxSUDothhall!=0 |
                     lifetimedx_hxSUDsha!=0 |
                     lifetimedx_hxSUDstim!=0 |
                     lifetimedx_hxSUDPCP!=0, "Hx of SUD", "No SUD")) %>% 
  select(., starts_with("lifetimedx_hxSUD"), anySUD) %>%
  group_by(anySUD) %>% summarize(n=n())
kable(anySUD)

EDyn <- clearALL_select %>% mutate(anyED=ifelse(lifetimedx_hxAN!=0 |
                   lifetimedx_hxBN!=0 |
                     lifetimedx_hxBED!=0 |
                     lifetimedx_hxothereat!=0,
                   "Hx of ED", "No ED")) %>% select(.,
                                                    lifetimedx_hxAN,
                                                    lifetimedx_hxBN,
                                                    lifetimedx_hxBED,
                                                    lifetimedx_hxothereat,
                                                    anyED) %>%
  group_by(anyED) %>% summarize(n=n())
kable(EDyn)

hxTrauma <- clearALL_select %>% mutate(anyTrauma=ifelse(lifetimedx_hxPTSD!=0 |
                                                   lifetimedx_hxothertrauma!=0 |
                                                   traumainterview_sexab==1 |
                                                   traumainterview_physab==1 |
                                                   traumainterview_childphysab==1 |
                                                   traumainterview_childsexab==1 |
                                                   traumainterview_childothertrauma==1,
                                                 "Hx of Trauma", "No Hx of Trauma")) %>%
  group_by(anyTrauma) %>% summarize(n=n())
kable(hxTrauma)

# how many participants have a current depressive disorder?
clearALL_select %>% group_by(currentdx_MDD, currentdx_PDD) %>% summarise(n=n())

#how many participants have current GAD?
clearALL_select %>% group_by(currentdx_GAD) %>% summarise(n=n())

```


#### Playing with tableone package

```{r}

library(tableone)

#create list of continuous variables we want in demographic table
contVars <- c("age", "ageatmenarche", "agefirstMDE", "numpregnancies", "number_children",
              "numfullatt", "numintatt", "numabatt", "numhosp"
              )

#save race, education, ethnicity, marital status, and sexual orientation with factor labels (these are the variables that have more than 1 level)
clearALL_select$maritalstatusf <- factor(clearALL_select$maritalstatus, levels = c(1,2,3,4,5),
                                 labels = c("Currently Married",
                                            "Widowed",
                                            "Never Married",
                                            "Separated or Divorced",
                                            "Living with Partner"))

clearALL_select$educationf <- factor(clearALL_select$education, levels = c(1,2,3,4,5,6,7,8),
                             labels = c("0-4 grades",
                                        "5-8 grades",
                                        "some high school",
                                        "graduated from high school",
                                        "trade school or business college",
                                        "some college (inc. completion of jr college)",
                                        "grad. from 4-yr college",
                                        "post-grad work at a university"))

clearALL_select$sexorientationf <- factor(clearALL_select$sexorientation, levels = c(1,2,3,4),
                                  labels = c("Homosexual(lesbian,gay)",
                                             "Bisexual",
                                             "Heterosexual",
                                             "Other"))

#create list of categorical variables we want in demographic table
catVars <-c("race", "ethnicity", "education", "maritalstatus",
            "sexorientation","genderorient", "everpregyn",
            "lifetimedx_hxbipolar2",
            "lifetimedx_hxMDD",
            "lifetimedx_hxlifetimedx_hxhxPDD",
            "lifetimedx_hxothDD",
            "lifetimedx_hxSUDalc",
            "lifetimedx_hxSUDsha",
            "lifetimedx_hxSUDMJ",
            "lifetimedx_hxSUDstim",
            "lifetimedx_hxSUDopioid",
            "lifetimedx_hxpanicDO",
            "lifetimedx_hxagora",
            "lifetimedx_hxSAD",
            "lifetimedx_hxphobia",
            "lifetimedx_hxGAD",
            "lifetimedx_hxotheranx",
            "lifetimedx_hxOCD",
            "lifetimedx_hxAN",
            "lifetimedx_hxBN",
            "lifetimedx_hxBED",
            "lifetimedx_hxothereat",
            "lifetimedx_hxPTSD",
            "lifetimedx_hxothertrauma",
            "lifetimedx_hxotherDx",
            "currentdx_MDD",
            "currentdx_PDD",
            "currentdx_PMDD",
            "currentdx_othDD",
            "currentdx_SUDalc",
            "currentdx_SUDsha",
            "currentdx_SUDmj",
            "currentdx_SUDopioid",
            "currentdx_PanicDO",
            "currentdx_Agoraphobia",
            "currentdx_SAD",
            "currentdx_Phobi",
            "currentdx_GAD",
            "currentdx_OtherAnx",
            "currentdx_OCD",
            "currentdx_AN",
            "currentdx_BN",
            "currentdx_otheat",
            "currentdx_ADHD",
            "currentdx_PTSD",
            "currentdx_Othertrauma",
            "traumainterview_physab",
            "traumainterview_childsexab",
            "traumainterview_childothertrauma",
            "traumainterview_physab.1",
            "traumainterview_sexab"
            )
            
#create full list of variables for table1
allVars <- clearALL_select %>% select(c("age", "ageatmenarche", "agefirstMDE", "numpregnancies",
                                 "number_children","numfullatt", "numintatt", "numabatt", "numhosp",
                                 "race", "ethnicity", "education", "maritalstatus",
                                 "sexorientation","genderorient", "everpregyn",
            "lifetimedx_hxbipolar2",
            "lifetimedx_hxMDD",
            "lifetimedx_hxlifetimedx_hxhxPDD",
            "lifetimedx_hxothDD",
            "lifetimedx_hxSUDalc",
            "lifetimedx_hxSUDsha",
            "lifetimedx_hxSUDMJ",
            "lifetimedx_hxSUDstim",
            "lifetimedx_hxSUDopioid",
            "lifetimedx_hxpanicDO",
            "lifetimedx_hxagora",
            "lifetimedx_hxSAD",
            "lifetimedx_hxphobia",
            "lifetimedx_hxGAD",
            "lifetimedx_hxotheranx",
            "lifetimedx_hxOCD",
            "lifetimedx_hxAN",
            "lifetimedx_hxBN",
            "lifetimedx_hxBED",
            "lifetimedx_hxothereat",
            "lifetimedx_hxPTSD",
            "lifetimedx_hxothertrauma",
            "lifetimedx_hxotherDx",
            "currentdx_MDD",
            "currentdx_PDD",
            "currentdx_PMDD",
            "currentdx_othDD",
            "currentdx_SUDalc",
            "currentdx_SUDsha",
            "currentdx_SUDmj",
            "currentdx_SUDopioid",
            "currentdx_PanicDO",
            "currentdx_Agoraphobia",
            "currentdx_SAD",
            "currentdx_Phobi",
            "currentdx_GAD",
            "currentdx_OtherAnx",
            "currentdx_OCD",
            "currentdx_AN",
            "currentdx_BN",
            "currentdx_otheat",
            "currentdx_ADHD",
            "currentdx_PTSD",
            "currentdx_Othertrauma",
            "traumainterview_physab",
            "traumainterview_childsexab",
            "traumainterview_childothertrauma",
            "traumainterview_physab.1",
            "traumainterview_sexab"))


#labeledvars <- ClearALL %>% select(c(educationf, sexorientationf, maritalstatusf))
#CreateTableOne(data = ClearALL, vars = labeledvars)
clearALL_select %>% group_by(maritalstatusf) %>% summarize(n=n())
clearALL_select %>% group_by(sexorientationf) %>% summarize(n=n())
clearALL_select %>% group_by(educationf) %>% summarize(n=n())


```

# viewing the TableOne package
```{r}
#full tableOne
fulltbl1 <- CreateTableOne(data = allVars, factorVars = catVars)
summary(fulltbl1$CatTable)
summary(fulltbl1$ContTable)
```

### plot common trait variables
```{r echo=FALSE}

studysample.labs <- c("CLEAR1 (NC)", "CLEAR2 (Chicago)")
names(studysample.labs) <- c("1", "2")

#age histogram
clearALL_select %>% ggplot(aes(x=age, fill=as_factor(studysample)))+
  geom_histogram(binwidth = 5, position = "dodge")

#age, by study
clearALL_select %>% ggplot(aes(x=age, fill=as_factor(studysample)))+
  geom_histogram(binwidth = 5, position = "dodge")+
  facet_grid(.~studysample,labeller = labeller(studysample=studysample.labs))+
  xlab("Age")

#race, by clear1 and clear2
clearALL_select %>% ggplot(aes(x=as_factor(race),
                               fill=as_factor(race)))+
  geom_bar()+
  theme(axis.text.x = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  facet_grid(.~studysample, labeller = labeller(studysample=studysample.labs))+
  xlab("Race")+
  labs(caption = "Race Breakdown by Study")

#race, total
clearALL_select %>% ggplot(aes(x=as_factor(race),
                               fill=as_factor(race)))+
  geom_bar()+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Race")

#Marital status by study
clearALL_select %>% ggplot(aes(x=as_factor(maritalstatus), 
                               group=as_factor(studysample),
                               fill=as_factor(maritalstatus)))+
  geom_bar()+
  facet_grid(.~studysample, labeller = labeller(studysample = studysample.labs))+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Marital Status")

#marital status, total
clearALL_select %>% ggplot(aes(x=as_factor(maritalstatus),
                               fill=as_factor(maritalstatus)))+
  geom_bar()+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Marital Status")

#sexual orientation by study
clearALL_select %>% ggplot(aes(x=as_factor(sexorientation), 
                               group=as_factor(studysample),
                               fill=as_factor(sexorientation)))+
  geom_bar()+
  facet_grid(.~studysample, labeller = labeller(studysample = studysample.labs))+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Sexual Orientation")

#sexual orientation, total
clearALL_select %>% ggplot(aes(x=as_factor(sexorientation),
                               fill=as_factor(sexorientation)))+
  geom_bar()+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Sexual Orientation")

#education by study
clearALL_select %>% ggplot(aes(x=as_factor(education), 
                               group=as_factor(studysample),
                               fill=as_factor(education)))+
  geom_bar()+
  facet_grid(.~studysample, labeller = labeller(studysample = studysample.labs))+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Education")

#education, total
clearALL_select %>% ggplot(aes(x=as_factor(education), fill=as_factor(education)))+
  geom_bar()+
  theme(axis.text.x.bottom = element_text(angle = 45, hjust = 1),
        legend.position = "none")+
  xlab("Education")

#hx of trauma
clearALL_select %>% mutate(anyTrauma=ifelse(lifetimedx_hxPTSD!=0 |
                                                   lifetimedx_hxothertrauma!=0 |
                                                   traumainterview_sexab==1 |
                                                   traumainterview_physab==1 |
                                                   traumainterview_childphysab==1 |
                                                   traumainterview_childsexab==1 |
                                                   traumainterview_childothertrauma==1,
                                                 "Hx of Trauma", "No Hx of Trauma")) %>%
  ggplot(aes(x=anyTrauma, fill=anyTrauma))+
  geom_histogram(stat = "count")

clearALL_select %>% mutate(anySUD=ifelse(lifetimedx_hxSUDalc!=0 |
                   lifetimedx_hxSUDinh!=0 |
                     lifetimedx_hxSUDMJ!=0 |
                     lifetimedx_hxSUDopioid!=0 |
                     lifetimedx_hxSUDother!=0 |
                     lifetimedx_hxSUDothhall!=0 |
                     lifetimedx_hxSUDsha!=0 |
                     lifetimedx_hxSUDstim!=0 |
                     lifetimedx_hxSUDPCP!=0, "Hx of SUD", "No SUD")) %>% 
  select(., starts_with("lifetimedx_hxSUD"), anySUD) %>%
  ggplot(aes(x=anySUD, fill=anySUD))+
  geom_histogram(stat = "count")

```