Reproducible epidemiology in R

What is `quarto`?

Open-source document format and computational notebook system.
Integrates Markdown for text and code execution in R (and other languages!)
Easily generate and re-generate a quarto document to produce a professional-looking document

Only because quarto is newer and more featured!

Anything you already know how to do in R Markdown you can do in quarto, and more!¹
All of these slides, website, etc. are all made in quarto.
If you know and love R Markdown, by all means keep using it!

# My title

Some text

Some *italic text*

Some **bold text**


```{r}
x <- 3
x
```

Some text

Some italic text

Some bold text

x <- 3
x

[1] 3

Some of the ones I find myself using most often:

```{r}
#| eval: false
#| error: true
#| cache: true
#| warning: false
#| message: false
x <- 3
```

Also echo (can’t include above because it conflicts with my slide options!)

```{r}
#| label: tbl-one
#| tbl-cap: "This is a great table"
knitr::kable(mtcars)
```

```{r}
#| label: fig-hist
#| fig-cap: "This is a histogram"
hist(rnorm(100))
```

Figure 1: This is a histogram

You can then refer to those with @tbl-one and @fig-hist and the Table and Figure ordering will be correct (and linked)

@fig-hist contains a histogram and @tbl-one a table.

gets printed as:

Figure 1 contains a histogram and Table 1 a table.

I often create a list of stats that I want to report in a manuscript:

stats <- list(n = nrow(data),
              mean_age = mean(data$age))

I can then print these numbers in the text with:

There were `r stats$n` participants with a mean age of `r stats$mean_age`.

which turns into:

There were 1123 participants with a mean age of 43.5.

There are ~1 billion other features to know about quarto.

The website is an amazing resource.

Additional resources for R Markdown will have a lot of overlap