---
title: "Cholesterol levels of TALLYHO and C57BL/6 mice fed three different diets"
output:
  html_document:
    df_print: paged
  pdf_document: default
  word_document: default
---

## Methods

TALLYHO ("TH") and C57BL/6 ("B6") mice were fed either Chow,
Low-Fat, High-Calorie ("LF"), or High-Fat ("HF") diets from
weaning until 16 weeks of age. At 16 weeks, cholesterol levels
were measured.

### Statistical Methods

Association between Cholesterol and mouse strain, diet, and the interaction between the two
was tested with a two-way ANOVA with interaction term.

```{r message=FALSE}
library(tidyverse)
met <- read_csv("https://denvirlab.marshall.edu/BMR617-2022/data/TH-B6-metabolic.csv") %>%
  separate(MouseID, into=c("Strain", "Diet", "ID"), sep='-') %>%
  mutate(Strain = factor(Strain), Diet=factor(Diet)) %>%
  select(Strain, Diet, Cholesterol)
```

## Results

The data are shown in the following table and graph:

```{r echo=FALSE}
met
ggplot(met, aes(x=Strain, y=Cholesterol, fill=Diet)) +
  geom_boxplot(outlier.shape = NA) + 
  geom_point(position=position_jitterdodge(jitter.width = 0.1, dodge.width = 0.75)) +
  ylab("Cholesterol Level (mg/dl)") +
  ggtitle("Cholesterol Level by Mouse Strain and Diet")
```


Both Strain and Diet showed an effect on Cholesterol level, with TH mice having higher Cholesterol
levels than B6 mice for any diet, and mice fed LF or HF diets having higher Cholesteral levels than
mice fed Chow diets for either strain.

There was no observed interaction between mouse Strain and Diet; i.e. the effect of diet was not
appreciably different in TH mice to that in B6 mice.

```{r}
aov.full <- aov(Cholesterol ~ Strain * Diet, data = met)
aov.full$coefficients
confint(aov.full)
summary(aov.full)
```

