day5_gapminder_analysis_example.Rmd

---
title: "gapminder_teaching_rmd"
author: "Sarah Pederzani"
date: "26 11 2020"
output:
  html_document:
    keep_md: true
---

# install packages

install.package("knitr")


# Markdown formatting

markdown is a markup language that is a lightweit way of formatting text

bold - **bold**
italic - *italics*
subscript - H~2~O
superscript - ^14^C

bulleted lists

* listpoint 1
* oh look more listed stuff
* lists all the way down

or use

- look at my awesome bullet point
- lists so nice to tidy

numbered lists

1. first point
2. second point
3. third point
4. many points

section headings

# Title
## Main section
### sub-section
#### sub-sub section

## Compiling

push the knit button to compile

### Challenge 1

delete all the code chunks and write some markdown
then compile to a html document

## More Markdown

putting a hyperlink - 
[our course website](https://babeheim.com/2021-11-29-leipzig-online/)

including an image
![caption](https://smea.uw.edu/wp-content/uploads/sites/11/2017/03/CURRENTSBLOG_Cat_2.jpg)
or
![caption](compiling_workflow.png)
## Latex equations

Latex equations with Latex math mode

Put some inline Latex math mode like so $E = mc^2$

Or put separated equations like this:

$$y = \mu + \sum_{i=1}^p \beta_i x_i + \epsilon$$

## Code chunks

a code chunk example

```{r load_data}
gapminder <- read.csv("data/gapminder_data.csv")
```

accents denote the chunk
r denotes the programming language
followed by the chunk name - use unique chunk names that are descriptive of what you're doing in the chunk

use the navigation bar to see document outline

### Challenge 2

add code chunks to
- load the ggplot2 package
- read the gapminder data
- create a plot

#### Solution

```{r load-ggplot2}

library("ggplot2") # loading ggplot2

```

```{r read-gapminder-data}

gapminder <- read.csv("data/gapminder_data.csv") # read in gapminder data

```

```{r make-plot}

ggplot(gapminder, aes(x = year, y = lifeExp))+ # plot life exp vs year
  geom_point()

```


## How are things compiled

talk about the knitting and compilation workflow with image

## Chunk options

options that control how chunks are trated

examples:

echo = FALSE - supress code printing
results = "hide" - print results
eval = FALSE - show code but don't evaluate the code
warning = FALSE - don't print warnings
message = FALSE - don't print messages (i.e. package loading messages)
fig.height - figure height (in inches)
fig.width - figure width (in inches)
fig.cap - figure caption

so for example

```{r load_libraries, echo = FALSE, message = FALSE, warning = FALSE}

library("dplyr")

library("ggplot2")

```

### global chunk options

you can use a first chunk in your document to specific global chunk options
that are applied to every chunk in your document

```{r global_options, echo = FALSE}

knitr::opts_chunk$set(fig.path = "Figs/", message = FALSE, warning = FALSE,
                      echo = FALSE)

```

the option fig.path will set where figures will be saved

you can use yaml options to automatically keep a copy of all your figures

output:
  html_document:
    keep_md: true

figures will be named with the code chunk name

you can also use something like fig.path = "Figs/analysis_" which will make all figure file names start with "analysis_"

talk about making a setup code chunk in the beginning for global options and packages and such

### Challenge 3

use chunk options to control the size of a figure and to hide the code

```{r echo = FALSE, fig.width = 3}

plot(faithful)

```

## Inline R Code

use inline code like this

The population of Afghanistan was `r gapminder[1,3]` in `r gapminder[1,2]`. 

### Challenge 4

try some inline R code

#### Solution

Here’s some inline code to determine that 2 + 2 = `r 2+2`.

## optional: tables

make tables using the kable function that is included in the knitr package


```{r table}
library("knitr")

gapminder_subset <- gapminder[1:5,]

kable(gapminder_subset)

```

Other table packages

- kableExtra (extra formatting for kable package)
- pander

## Other output formats

## pdf

we need a latex installation, make using tinytex package

install.packages("tinytex")
tinytex::install_tinytex()

is specified in the yaml header using 

output:pdf_document

or open a new default file

use the rticles package

install.packages("rticles")

### citations

just quickly mention how it works:

yaml:
bibliography: mybibfile.bib
csl: elsevier-vancouver.csl

then use [@Dirac1953888] syntax for citations

### ressources

https://bookdown.org/yihui/rmarkdown/
https://rmarkdown.rstudio.com/

https://davidgohel.github.io/officedown/

https://ardata-fr.github.io/flextable-book/

papers using docx output
-	La Ferrassie osf: https://osf.io/sfnb8/
- BK manuscript osf: https://osf.io/tk9dc/