FOAMSAnalysis.Rmd

---
title: "data cleaning"
output:
  html_document: default
  pdf_document: default
date: "2024-11-21"
---
Load packages
```{r}
library(tidyverse)
library(car)
library(lsr)
library(ez)
library(rstatix)
library(afex)
library(emmeans)
library(effsize)
```

Read files into R
```{r reading in files}
misoTest<-read.csv("/Users/megansurbeck/Desktop/project stuff/MisoAssessments.csv")
subj1<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub01.csv")
subj2<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub02.csv")
subj3<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub03.csv")
subj4<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub04.csv")
subj5<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub05.csv")
subj6<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub06.csv")
subj7<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub07.csv")
subj8<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub08.csv")
subj9<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub09.csv")
subj10<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub10.csv")
subj11<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub11.csv")
subj12<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub12.csv")
subj13<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub13.csv")
subj14<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub14.csv")
subj15<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub15.csv")
subj16<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub16.csv")
subj17<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub17.csv")
subj18<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub18.csv")
subj19<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub19.csv")
subj20<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub20.csv")
subj21<-read.csv("/Users/megansurbeck/Desktop/project stuff/Sub21.csv")
```
Combine participants into single dataset
```{r combining}
#combine each subject into one dataset
allSubj<-rbind(subj1, subj2, subj3, subj4, subj5, subj6, subj7, subj8, subj9, subj10, subj11, subj12, subj13, subj14, subj15, subj16, subj17, subj18, subj19, subj20, subj21)
###remove distractor sound columns
allSubj<-allSubj[-c(2,5,6,7,8,9)]
###remove NA tester rows
allSubj<-allSubj %>% filter(SoundCategory !="NA")
#include self identification scores->filling in self identifier information from misoTest 
allSubj <- allSubj %>%
  mutate(SelfAssess = case_when(
    Sub <= 1 ~ "2",
    Sub <= 2 ~ "1",
    Sub <= 3 ~ "1",
    Sub <= 4 ~ "3",
    Sub <= 5 ~ "3",
    Sub <= 6 ~ "2",
    Sub <= 7 ~ "1",
    Sub <= 8 ~ "3",
    Sub <= 9 ~ "2",
    Sub <= 10 ~ "2",
    Sub <= 11 ~ "2",
    Sub <= 12 ~ "3",
    Sub <= 13 ~ "2",
    Sub <= 14 ~ "3",
    Sub <= 15 ~ "2",
    Sub <= 16 ~ "2",
    Sub <= 17 ~ "1",
    Sub <= 18 ~ "2",
    Sub <= 19 ~ "2",
    Sub <= 20 ~ "2",
    Sub <= 21 ~ "3"))
##include real assessment scores
misoTest$S5Sum<-NA
misoTest$S5Sum <- rowSums(misoTest[, c("S5_Externalizing", "S5_Internalizing", "S5_Impact", "S5_Outburst", "S5_Threat")])
#merge with dataset
allSubj <- allSubj %>%
  mutate(S5Sum= case_when(
    Sub <= 1 ~ "101",
    Sub <= 2 ~ "35",
    Sub <= 3 ~ "134",
    Sub <= 4 ~ "14",
    Sub <= 5 ~ "10",
    Sub <= 6 ~ "124",
    Sub <= 7 ~ "131",
    Sub <= 8 ~ "2",
    Sub <= 9 ~ "8",
    Sub <= 10 ~ "66",
    Sub <= 11 ~ "10",
    Sub <= 12 ~ "74",
    Sub <= 13 ~ "13",
    Sub <= 14 ~ "15",
    Sub <= 15 ~ "27",
    Sub <= 16 ~ "47",
    Sub <= 17 ~ "48",
    Sub <= 18 ~ "45",
    Sub <= 19 ~ "21",
    Sub <= 20 ~ "17",
    Sub <= 21 ~ "30"))
allSubj$SelfMiso<-NA
allSubj$MisoStatus<-NA
class(allSubj$S5Sum)
allSubj$S5Sum<-as.numeric(allSubj$S5Sum)
allSubj$MisoStatus<-ifelse(allSubj$S5Sum>87, "1", "0")
allSubj$SelfMiso<-ifelse(allSubj$SelfAssess==1, "1", "0")
#working with levels
levels(as.factor(allSubj$MisoStatus))
is.factor(allSubj$MisoStatus)
allSubj$MisoStatus<-factor(allSubj$MisoStatus, levels=c("1", "0"))
```
Hypothesis 1: Discomfort levels between sound groups
```{r hypothesis 1}
##four sound groups(removed empty sound), Oral_nasal, Non_oral_nasal, White_noise
##ANOVA-one way
#this is repeated measures AOV
##using afex
h1_afex <- aov_car(AversiveRating ~ SoundCategory + Error(Sub/SoundCategory), 
                   data = allSubj, 
                   factors = c("SoundCategory"), 
                   within = c("SoundCategory"))
summary(h1_afex)

##post hoc measures: tukeyHSD and etaSquared do not work for afex
post_hoc1 <- emmeans(h1_afex, pairwise ~ SoundCategory)
summary(post_hoc1)
```

Hypothesis 2: Misophonics versus non-Misophonic discomfort in each group
```{r hypothesis 2}
#repeated measure ANOVA, misophonic/nonmisophonic, two way
##afex ANOVA
h2_afex <- aov_car(AversiveRating ~ SoundCategory * MisoStatus + Error(Sub/SoundCategory), 
                   data = allSubj, 
                   within = c("SoundCategory"), 
                   between = c("MisoStatus"))
summary(h2_afex)
##emmeans post-hoc test
post_hoc2 <- emmeans(h2_afex, pairwise ~ MisoStatus)
summary(post_hoc2)
```
Hypothesis 3: Belief in misophonia reaction change
```{r}
##look at avg discomfort per participant w/ misophonic label- t-test
t.test(AversiveRating~SelfMiso, data=allSubj)
##people who identify as misophonic do actually have more discomfort across sound categories
##compute cohen's d
cohens_d(AversiveRating~SelfMiso,data=allSubj, var.equal= FALSE)
##small-moderate effect size
```
Visualization
```{r visualization h1}
#visualizing discomfort across sound groups, h1
ggplot(allSubj, aes(SoundCategory, AversiveRating))+geom_boxplot(fill="lavender")+theme_classic()+labs(x="Sound Category", y="Discomfort Level", title="Discomfort across Sound Category")
```

```{r visualization h2}
#visualization h2-misophonics versus non-misophonics for sound discomfort
ggplot(allSubj, aes(SoundCategory, AversiveRating, fill=MisoStatus))+geom_boxplot()+theme_classic()+labs(x="Sound Category", y="Discomfort Level", title="Discomfort by Misophonia Diagnosis")
```

```{r visualization h3}
##visualization h3-differences in average discomfort for 
ggplot(allSubj, aes(SelfMiso, AversiveRating))+geom_boxplot(fill="orange")+theme_classic()+labs(x="Self Diagnosis of Misophonia", y="Discomfort Level", title="Differences in Average Discomfort by Self Diagnosis of Misophonia")
```