markdown_intro.Rmd

---
title: "Intro to Markdown"
subtitle: _writing repoducible reports_
author: "Matt Bixley"
date: "`r Sys.Date()`"
output:
  html_document:
    code_folding: show
    df_print: kable
    theme: simplex
    highlight: textmate
    toc: yes
    toc_float: yes
    number_sections: yes
bibliography: resources/markdown.bib
#csl: resources/new-zealand-veterinary-journal.csl
csl: resources/molecular-ecology.csl
always_allow_html: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
#knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(kableExtra)
library(palmerpenguins)
library(knitr)
```

# R Markdown

## Objectives

- text formatting
- code
  * highlighting
  * chunks
  * inline
- tables
- ploting
- citations

## Notes
Murray Cadzow wrote some notes (with markdown) for last years Webinar https://hackmd.io/@murraycadzow/nesi-rmarkdown-webinar#Figures

## Example

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using _R Markdown_ see <http://rmarkdown.rstudio.com>. [@rmarkdown2018]

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can highlight a piece of code like this: `Ctrl + Shft + I`

1 + 1 = `r 1 +1`

# Palmer Penguins

We are going to use the Palmer Penguins dataset curated by [Allison Horst](https://github.com/allisonhorst/palmerpenguins) and can be installed from Cran with the code `install.packages("palmerpenguins")` There are 3 different species of penguins in this dataset, collected from 3 islands in the Palmer Archipelago, Antarctica.

Our first *Code Chunk* will be to look at the dataset 

```{r penguins}
head(penguins)
```

## Tables  

Use the `kable()` function from `knitr` to make tables.
```{r count}
penguins %>% 
  count(species) %>% 
  kable(caption = "Species Counts")
```
We can generate more elegent tables with the [kableExtra](https://haozhu233.github.io/kableExtra/awesome_table_in_html.html#overview) package.
```{r kableextra}
penguins %>% 
  group_by(species) %>% 
  select(contains(c("length", "depth", "mass"))) %>% 
  summarize_all(., mean, na.rm = TRUE) %>%
  kable(caption = "Summarized Data", format = "html") %>% 
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F, position = "left")
```


## Plots

You can also embed plots, for example:

```{r histogram, echo = T, fig.cap = "Caption for the plot created", fig.align = "center", warning = FALSE}
flipper_hist <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
  geom_histogram(aes(fill = species), 
                 alpha = 0.5, 
                 position = "identity") +
  scale_fill_manual(values = c("darkorange","purple","cyan4")) +
  theme_minimal() +
  labs(x = "Flipper length (mm)",
       y = "Frequency",
       title = "Penguin flipper lengths")
flipper_hist
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

## Equations  

equation $z = x + y$ can be written inline or equations can be centered in their own block

$$a^2 + b^2 = c^2$$

# More Options

## Images  

If we have images or plots already stored that we wish to add we can write the following with or without an image caption.

```{r image, fig.align = "center", fig.width=5, fig.height=5, caption="Palmer Penguins"}
knitr::include_graphics("resources/pp_logo.png")
```

## Engines

Python, Shell, SQL, Rcpp, Stan, JavaScript, Julia, C and Fortran are all options

Bash
```{bash}
echo "Hello from Bash!"
```
  
Python
```{python}
def square(a):
  return a * a

square(4)  
```

All the available Engines can be found with the following line `names(knitr::knit_engines$get())`  
`r names(knitr::knit_engines$get())`

## Citations
How do we cite things?

Citations need a **.bib** file and to know the citation key. We can cite PalmerPenguins [@horst2020] and at the same time lets give the citation for R created by Robert Gentleman and Ross Ihaka [@r2020] or inline like this @r2020

And we can change all the stlyes of citation to suit. [Here](https://citationstyles.org/) or here at [Zotero](https://www.zotero.org/styles) 

# References