# 5. Include an example in the analysis paper outline

## 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:

    #| 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

    #| 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.

    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 = _
    )