R Markdown for reproducible analysis

06 May, 2022

What is R Markdown

R Markdown (.Rmd) is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. It combines the core syntax of markdown (an easy to write plain text format) with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes).” – RStudio documentation.

Why R Markdown?

for Open Science

Transparency
Availability
Accessibility
Collaboration

Why R Markdown?

for your work

There are many advantages to using R Markdown in your work:

Human readable
Simple syntax
A Reminder for Your Future Self
Easy to Modify
Flexible export formats
Easy to share

How it works

Output formats

Write a single .Rmd file and then use it to render finished output in a variety of formats

Add Code and Results

```{r table2}
penguins %>% 
  select(species, bill_length_mm:flipper_length_mm) %>% 
  gtsummary::tbl_summary(by = species, missing = "no") %>% 
  gtsummary::modify_caption("Flipper/Bill size by Species") %>% 
  gtsummary::as_flex_table()

```

Flipper/Bill size by Species
Characteristic	Adelie, N = 1521	Chinstrap, N = 681	Gentoo, N = 1241
bill_length_mm	38.8 (36.8, 40.8)	49.5 (46.3, 51.1)	47.3 (45.3, 49.5)
bill_depth_mm	18.40 (17.50, 19.00)	18.45 (17.50, 19.40)	15.00 (14.20, 15.70)
flipper_length_mm	190 (186, 195)	196 (191, 201)	216 (212, 221)
1Median (IQR)