Project Report Tips

STA 101

By the end of today you will practice a few quarto/markdown tricks to polish your report and simplify your presentation. Specifically we will discuss:

Getting started

Code chunk settings

Some options available for customizing output (see quarto documenation for more detail).

Option Description
eval Evaluate the code chunk (if false, just echos the code into the output)
echo Include the source code in output
warning Include warnings in the output
message Whether to preserve messages emitted by message() (similar to the option warning)
include Catch all for preventing any output (code or results) from being included (e.g. include: false suppresses all output from the code block)

These options can be applied globally (the whole document) or locally (a specific code chunk). Global settings are controlled in the YAML (see the top of the document) while local code chunk options can be applied with #| (see example below).

Exercise 1

In the code chunk below:

  • set warning to false
  • set echo to false

and re-render.

In addition to code chunks, figures have settings as well.

We can set captions and an alt attributes using #| fig-cap: and #| fig-alt: respectively. alt captions specify “alternate text” for an image. Alternative text appears if an image cannot be displayed and is also read by screen-readers.

Additional figure options include

Option Description
fig-width figure width in inches
fig-height figure height in inches
fig.align e.g. fig.align: center centers figure alignment
fig.asp changes figure height based on aspect ratio with width
out.width sets figure width relative to text (1000 = 100% text width), e.g. out.width: 1000

In all cases above, we can again set options locally or globally. Note: local options override global options.

Example of how to change size of the figure and adjust text size.

Density of height

Project specific notes

For the project, you will set the option echo: FALSE and warning: FALSE to hide all code and warnings in your final report.

Suggestion: make your figures consistently themed, e.g. use similar figure size/aspect ratio and color scheme throughout your report. Change the default gray background, see themes.

Citations

Your report will include citations, e.g. the data source, previous research, and other sources as needed. At a minimum, you should have a citation for the data source.

All of your bibliography entries will be stored in a .bib file. The entries of the bibliography are stored using BibTex, i.e., a format to store citations in LaTeX. Let’s take a look at references.bib.

In addition to the .bib file:

  • Include bibliography: references.bib in the YAML.
  • At the end of the report, include ## References. This will list all of the references at the end of the document.

Learn more here.

Convert website to citation: here.

Or find on google scholar!

Citation examples

  1. In Wickham, Chang, and Wickham (2016), the authors focus present the grammar of graphics package ggplot2 for R.

  2. Within the grammar of graphics, ggplot() is the first layer of any plot (Wickham, Chang, and Wickham 2016).

  3. These notes came from Husar (2024).

Use color to draw attention

# A tibble: 5 × 2
  category                     value
  <chr>                        <dbl>
1 Cutting tools                 0.03
2 Buildings and administration  0.22
3 Labor                         0.31
4 Machinery                     0.27
5 Workplace materials           0.17
Important

Do not display a table like this! Use knitr::kable()!

d |> knitr::kable(digits = 2)
category value
Cutting tools 0.03
Buildings and administration 0.22
Labor 0.31
Machinery 0.27
Workplace materials 0.17

Note the orders in these plot!

Play with themes for a non-standard look

Go beyond ggplot2 themes – ggthemes

How to save the image for the presentation:

Plot sizing and layout

Sample plots

Small fig-width

For a zoomed-in look

```{r}
#| fig-width: 3
#| fig-asp: 0.618

p_hist

ggsave("hist.png")
```

Large fig-width

For a zoomed-out look

```{r}
#| fig-width: 6
#| fig-asp: 0.618

p_hist
```

fig-width affects text size

Multiple plots on a slide

First, ask yourself, must you include multiple plots on a slide? For example, is your narrative about comparing results from two plots?

  • If no, then don’t! Move the second plot to to the next slide!

  • If yes, use columns and sequential reveal.

Cross referencing figures

As seen in Figure 1, there is a positive and relatively strong relationship between body mass and flipper length of penguins.

Figure 1: The relationship between body mass and flipper length of penguins.

Cross referencing tables

The regression output is shown in Table 1.

Table 1: The regression output for predicting body mass from flipper length of penguins.
term estimate std.error statistic p.value
(Intercept) -5780.831 305.815 -18.903 0
flipper_length_mm 49.686 1.518 32.722 0

Similarly, looking at the dataset we created earlier:

category value
Cutting tools 0.03
Buildings and administration 0.22
Labor 0.31
Machinery 0.27
Workplace materials 0.17

Writing your project report with Quarto

  • Figure sizing: fig-width, fig-height, etc. in code chunks.

  • Figure layout: layout-ncol for placing multiple figures in a chunk.

  • Further control over figure layout with the patchwork package.

  • Chunk options around what makes it in your final report: message, echo, etc.

  • Cross referencing figures and tables.

  • Adding footnotes and citations.

References

Husar, Kat. 2024. “STA 101 - Summer 24 - STA 101: Data Analysis and Statistical Inference — Sta101-Su2024.github.io.” https://sta101-su2024.github.io/.
Wickham, Hadley, Winston Chang, and Maintainer Hadley Wickham. 2016. “Package ‘Ggplot2’.” Create Elegant Data Visualisations Using the Grammar of Graphics. Version 2 (1): 1–189.