tutorial-code-12-14-22.Rmd

---
title: "TOG Tutorial December 14"
author: "William Casazza"
date: "14/12/2022"
output:
  html_document: 
    toc: yes
    df_print: default
    number_sections: yes
    keep_md: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,fig.width=8)
```

# Our first our script in Rmarkdown

```{r}
print("hello world")
```
# Step 1: Load libraries

```{r}
# install.packages("knitr")
library(knitr)
library(dplyr)
library(ggplot2)
library(here)
i_am("tutorial-code-12-14-22.Rmd")
```


# Step 2: load data

```{r}
data("iris")
attach(iris)

iris <- iris
str(iris)
head(iris)
tail(iris)
summary(iris)
```
![](iris_image.png)

```{r}
iris %>%
  group_by(Species) %>% #group data by species
  summarize(mean.length = mean(Sepal.Length),
            mean.width = mean(Sepal.Width))
ggplot(iris, aes(x=Sepal.Length, y= Sepal.Width, color=Species))+ #what data
  geom_point() #how to visualize data
  
```

```{r}
iris %>% 
  group_by(Species) %>% 
  summarize(mean.length = mean(Petal.Length),
            mean.width = mean(Petal.Width))

#plot
ggplot(iris, aes(x = Petal.Length, y = Petal.Width, col = Species)) +
  geom_point()
```
```{r}
iris
```
# Part 3: printing pretty tables with kable
```{r}
summary(iris)
kable(summary(iris),caption= "summary of iris data")
```

# Part 4: code chunk options

```{r,eval=FALSE}
ggplot(iris, aes(x = Petal.Length, y = Petal.Width, col = Species)) +
  geom_point()
```

```{r,fig.height=2,fig.width=2}
ggplot(iris, aes(x = Petal.Length, y = Petal.Width, col = Species)) +
  geom_point()
```

# Part 5: Taking notes

I'm now reporting the standard deviation of the petal width for setosa iris as: `r sd(iris[iris$Species == "setosa","Petal.Width"])`. 

How am I organizing this document:

  * Set-up
    * load library
   * load data
  * second example
    + first item
    - second item
    * third item
    
Numbered steps:

1. step 1
1. Step 2

Format text *bold* **italicize**