---
title: "5. Include an example in the analysis paper outline"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{5. Include an example in the analysis paper outline}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Introduction

If you would like to see an example paper, that has code blocks to produce a summary table and a graphic, include the `example = TRUE` argument when you use the `make_project()` function.  For example, if you type `rUM::make_project("~/Desktop/my.example", "R", example = TRUE)`, in the **Results** section of the paper you will see code like:

````r
#| tbl-cap: |
#|   Your real caption belongs here.  Remember that cross references to tables 
#|   use labels for the code chunk starting with tbl-.


# To learn how to use tbl_summary look at https://www.danieldsjoberg.com/gtsummary/
analysis |> 
  tbl_summary(
    include = c(everything()), # choose your variables here
    # change auto_man to the name of your column variable or delete by = auto_man
    by = auto_man, # split table by group
    missing = "no" # don't list missing data separately
  ) %>%
  # add_n() %>% # add column with total number of non-missing observations
  # add_p() %>% # test for a difference between groups
  modify_header(label = "") %>% # update the column header to be blank
  bold_labels()
````

and 

````r

#| fig-cap: |
#|   Your real caption belongs here.  Remember that cross references to figures 
#|   use labels for the code chunk starting with fig-.

# To learn how to use ggplot start here: https://ggplot2.tidyverse.org/#learning-ggplot2
analysis |> 
  ggplot() +
	  labs(
	    title = "Your short title goes here.",
	    caption = "Your data sources/citation goes here."
    ) +
    geom_blank()
    # remove geom_blank() and add details here
````

You will also notice that there are sentences, which begin with 
"As can be seen in" that contain cross-reference hyperlinks to the tables and figures.

### Simpler Tables
The example table is created using a package called `gtsummary`. It makes completely customizable, beautiful, summary tables which support hyperlinks/cross-references in the sentences you write in your paper.  

A simpler option is to use the `table1()` function from the `table1` package.  It makes excellent tables with nearly no typing.  If you would like to try it, paste the code below into the `tbl-table1` code chunk.  Unfortunately `table1` does not have good support for hyperlinks/cross-references from your writing/prose.  


````r
library(table1)

analysis |> 
  select(everything()) |> # choose your variables here
  table1(
    # change auto_man to the name of your column variable or delete | auto_man
    ~ . | auto_man, 
    data = _
) 
````