Suppress Code, Warnings, Messages

• Include the following code in a code chunk at the top of your .Rmd file to suppress all code, warnings, and other messages. Use the code chunk header {r set-up, include = FALSE} to suppress this set up code.

knitr::opts_chunk$set(echo = TRUE,
                      warning = FALSE, 
                      message = FALSE)

Headers

• Use headers to clearly label each section. Make sure there is a space between the last # and the title, so the header renders correctly. For example, ###Section Title will not render as header, but ### Section Title will.

References

• Include all references in a section called “References” at the end of the report.
• This course does not have specific requirements for formatting citations and references.
• See Section 4.5 of the R Markdown Cookbook to learn about the citation functionality in R Markdown.

Appendix

• If you have additional work that does not fit or does not belong in the body of the report, you may put it at the end of the document in section called “Appendix”.
• The items in the appendix should be properly labeled.
• The appendix should only be for additional material. The reader should be able to fully understand your report without viewing content in the appendix.

Resize figures

• Resize plots and figures, so you have more space for the narrative.
  • Resize individual figures: Use the code chunk header {r plot1, fig.height = 3, fig.width = 5}, replacing plot1 with a meaningful label and the height and width with values appropriate for your write-up.
  • Resize all figures: Include the fig_width and fig_height options in your YAML header as shown below:

---
title: "Your Title"
author: "Team Name + Group Members"
output: 
  pdf_document:
    fig_width: 5
    fig_height: 3
---

Replace the height and width values with values appropriate for your write-up.

Arranging plots

Arrange plots in a grid, instead of one after the other. This is especially useful when displaying plots for exploratory data analysis and to check assumptions.

• If you’re using ggplot2 functions, the patchwork or ggpubr packages make it easy to arrange plots in a grid.

• If you’re using base R function, i.e. when using the emplogit functions, put the code par(mfrow = c(rows,columns)) before the code to make the plots. For example, par(mfrow = c(2,3)) will arrange plots in a grid with 2 rows and 3 columns.

Plot titles and axis labels

Be sure all plot titles and axis labels are visible and easy to read.

• Use informative titles, not variable names, for titles and axis labels.
• Use coord_flip() to flip the x- and y-axis on the plot. This is useful if you a bar plot with an x-axis that is difficult to read due to overlapping text.

❌ NO! The x-axis is hard to read because the names overlap.

ggplot(data = mpg, aes(x = manufacturer)) +
  geom_bar()

✅ YES! Names are readable

ggplot(data = mpg, aes(x = manufacturer)) +
  geom_bar() +
  coord_flip()

Do a little more to make the plot look professional!

• Informative title and axis labels
• Flipped coordinates to make names readable
• Arranged bars based on count
• Capitalized manufacturer names
• Optional: Added color - Use a coordinated color scheme throughout paper / presentation
• Optional: Applied a theme - Use same theme throughout paper / presentation

mpg %>%
  count(manufacturer) %>%
  mutate(manufacturer = str_to_title(manufacturer)) %>%
  ggplot(aes(x = fct_reorder(manufacturer,n), y = n)) +
  geom_bar(stat = "identity", fill = "steelblue") +
  coord_flip() +
  labs(x = "Manufacturer", 
       y = "Count", 
       title = "The most common manufacturer is Dodge") +
  theme_bw() 

Tables and model output

• Use the kable function from the knitr package to neatly output all tables and model output. This will also ensure all model coefficients are displayed.
  • Use the digits argument to display only 3 or 4 significant digits.
  • Use the caption argument to add captions to your table.

model <- lm(mpg ~ hp, data = mtcars)
tidy(model) %>%
  kable(digits = 3)