98 lines
2.2 KiB
Plaintext
98 lines
2.2 KiB
Plaintext
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---
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title: "Additional data analysis"
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author: "Andreas Gammelgaard Damsbo"
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date: "Knitted: `r format(Sys.time(), '%d %B, %Y')`"
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output: pdf_document
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---
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```{r setup, include=FALSE}
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knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
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```
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# Import
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```{r}
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dta_all<-read.csv("/Volumes/Data/depression/dep_dataset.csv")
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```
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# Defining patients to include for analysis
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Only including cases with complete pase_0 and MDI at 1 & 6 months
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```{r}
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dta<-dta_all[!is.na(dta_all$pase_0),]
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# &!is.na(dta$mdi_1)&!is.na(dta$mdi_6)
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quantile(dta$pase_0, probs = seq(0, 1, 0.25), names = TRUE)
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```
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## Formatting
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```{r echo=FALSE}
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dta$rtreat<-factor(dta$rtreat)
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dta$pase_6<-as.numeric(dta$pase_6)
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```
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# Summaries
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Fraction with inc_time of at least 166 days
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```{r}
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dt<-as.numeric(dta[dta$excluded_6%in%c("dt_6","en_6"),c("inc_time")])>=166
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summary(dt)
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length(dt[dt==TRUE])/length(dt)*100 # Percent after 166 days
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```
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5% percentiler
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```{r}
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quantile(dt, probs = seq(0, 1, 0.05), names = TRUE)
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```
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Base version
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```{r}
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aggregate(pase_6 ~ rtreat, data = dta, summary)
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```
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Fancy version
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```{r}
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psych::describeBy(dta$pase_6, dta$rtreat,mat=T)
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```
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# Mann-Whitney U test
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See: https://stat-methods.com/home/mann-whitney-u-r/
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```{r}
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#Perform the Mann-Whitney U test
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m1<-wilcox.test(pase_6 ~ rtreat, data=dta, na.rm=TRUE,
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paired=FALSE, exact=FALSE, conf.int=TRUE)
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print(m1)
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```
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# Boxplot
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## Base function - simple
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```{r}
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boxplot(dta$pase_6 ~ dta$rtreat)
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```
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## ggplot2 - fancy version
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```{r}
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library(ggplot2)
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ggplot(dta, aes(x = rtreat, y = pase_6, fill = rtreat)) +
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stat_boxplot(geom ="errorbar", width = 0.5) +
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geom_boxplot(fill = "light blue") +
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stat_summary(fun.y=mean, geom="point", shape=10, size=3.5, color="black") +
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# Point symbol is mean value
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ggtitle("Boxplot of Treatments C and D") +
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theme_bw() + theme(legend.position="none")
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```
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# Bonus: QQ plots
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```{r}
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library(qqplotr)
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ggplot(data = dta, mapping = aes(sample = pase_6, color = rtreat, fill = rtreat)) +
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stat_qq_band(alpha=0.5, conf=0.95, qtype=1, bandType = "boot") +
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stat_qq_line(identity=TRUE) +
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stat_qq_point(col="black") +
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facet_wrap(~ rtreat, scales = "free") +
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labs(x = "Theoretical Quantiles", y = "Sample Quantiles") + theme_bw()
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```
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