Writing Reproducible Manuscripts in R Markdown

Deborah Apthorp

Writing Reproducible Manuscripts in R Markdown

  • Lecturer, School of Psychology and Behavioural Science, UNE
  • Adjunct Senior Lecturer, Research School of Psychology, ANU

What is R Markdown?

  • Just a simple markdown language to help you write things incorporating R code
  • Can use it for all sorts of things!
  • I have used it (in chronologial order) to:

- Make results easy to send to collaborators

- Make results more replicable for others to see

- Write whole manuscripts using papja

- Make my own website!

What do you need?

  • R Studio is easiest
  • File > New File > R Markdown…
  • To knit to PDF, you’ll need a $\TeX$ install too
  • Sometimes I use kableextra to make nicer tables

Typical header:

library("papaja")
library(readxl)
library("yarrr") # Load the package!

require(afex) # uses package to perform RM ANOVAs. 
SPQ_for_R <- read_excel("SPQ_for_R.xlsx")
Area <- read.csv("Overall_Area_for_R.csv")
Path <- read.csv("Overall_Path_for_R.csv")

The papaja package

  • Still in development, so not on CRAN yet
  • Need to have devtools installed to download it

  • Documentation here

    # Install devtools package if necessary
if(!"devtools" %in% rownames(installed.packages()))
install.packages("devtools")

# Install the stable development verions from GitHub
devtools::install_github("crsh/papaja")

Citations

  • You can use BibTeX for citations
  • Pretty easy if your MS was already in LaTeX
  • If not, it’s not really that different to other ref managers
  • Just use “@” as your citation key instead of $\cite$

Example manuscript fragment:

Since its earliest conceptualization, schizophrenia has been 
associated with motor anomalies [@Bleuler:1911ko; 
@Kraepelin:1913vl]....

Including plots

  • Include something you already made:

    
knitr::include_graphics('ExampleEllipse.png')

  • Generate a plot from scratch:

    pirateplot(formula = SPQ ~ Group,
       data = SPQ_for_R,
       xlab = "Group", #x label
       ylab = "SPQ total score", # ylabel,
       par(tcl=.2), 
       cex.axis = .85,
       theme = 2, # inbuilt theme
       pal = "google")
fig.cap = "(ref:SPQ)"

Result:

Scores on the SPQ for the groups

You can include $\LaTeX$ code for math:

$PL = \sum_{n-1}^{N} \sqrt{[x(n) - x(n-1)]^2+[y(n) - y(n-1)]^2}$
  • How it comes out:

$$ PL = \sum_{n-1}^{N} \sqrt{[x(n) - x(n-1)]^2+[y(n) - y(n-1)]^2} $$

Tables: You can include LaTeX tables if you like:

\begin{table}%[tbhp]
\centering
\caption{Demographic variables for the three groups.}
\begin{tabular}{lrrr}
 & HC & SPD & SZ \\
\hline
Age (SD) & 41.5 (10.60) & 42.2 (11.30) & 41.6 (9.91)\\
Gender (M/F) & 13/14 & 14/13 & 13/14 \\
Height (in) & 66.88 (4.58) & 67.1 (3.39) & 66.1 (3.83)\\
Weight (lb) & 178 (43.0) & 201 (50.2) & 179 (34.6)\\
WASI IQ (SD) &  111 (15.7) & 107 (15.3) &  97.6 (13.2)** \\
SPQ (SD) & 8.19 (7.77) & 29.07 (12.18)*** & 41.15 (20.64)***\\
\hline
\end{tabular}
\label{Table:Demographics}
\end{table}

How it comes out:

APA Style tables!

  • First, you need to analyse the results
  • You can do that right in the manuscript using normal r code!

  • You already loaded the data at the top of the manuscript

    
analysis_Path <- aov_ez("Sub", "log_Data", Path, 
                     within=c("Eye","Base"), 
                     between= c("Group"), 
                     factorize = FALSE)
                         
Path_results <- apa_print(analysis_Path, es = "pes")

APA Style tables!

  • Now you just need to tell RMarkdown to print the table!

    
table_SwayPath <- Path_results$table
apa_table(table_SwayPath, 
caption = 'ANOVA table for log sway path results')

How it comes out:

Best bit: Report the results!

  • When you did the analysis earlier, you made all the results you need!

  • Papaja lets you just report those right in the text.

    A mixed model ANOVA, with base (open/closed) and eye 
(open/closed) as within-subjects factors,and group 
as a between-subjects factor, showed a significant 
main effect of group, `r Path_results$full$Group`.

How it comes out:

Referring to figures and tables in text

  • You can refer to the figures and tables using \@ref:

    
The results are illustrated in Figure \@ref(fig:plotPath)

  • Make sure your figure is called exactly that

    {r plotPath, echo = FALSE, 
fig.cap = "\\label{fig:plotPath}, 
Results for sway path (log transformed to correct skew) 
for all participants. Means are shown by black 
horizontal bars."}

Knitting the document

  • To render the document into a lovely PDF, just click the “knit” button at the top of the document
  • If you get an error message, you can usually just google it.
  • Common traps: Package not installed
  • Weird characters in BibTeX file
  • Issues with cutting and pasting from Word (e.g. quotation marks, symbols)
  • Can also knit to Word! (For the Luddites you collaborate with)

What else can I do with R Markdown?

Awesome guide from Dan Quintana

Useful links

Example manuscript in papaja

Tips on citations, including non-APA styles

Questions re Hugo Academic

Documentation for Hugo Academic