5. Include an example in the analysis paper outline

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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 = _
)

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