WPA #10: Markdown and papaja

Play around with Markdown

A. Let’s start by playing around with plain vanilla R Markdown. Create a new R Markdown file with File – New File – R Markdown… Click “OK”. Save the file as facebook.Rmd.

B. You’ll notice that when you start a a new markdown document, there is some text and code already there. Delete all of this text.

C. Now, go to the following link https://raw.githubusercontent.com/ndphillips/RCourse/master/facebookmarkdown (you may have to right-click it and open in a new window or tab to see the text). Copy and paste all of the text in this link and paste it into your (blank) facebook.Rmd file.

D. Knit the document into an HTML file by either clicking the Knit button or using the Command + Shift + K shortcut. This should create an HTML output of your document. If you have TeX installed, try creating a PDF file by clicking “Knit to PDF” under the “Knit” button. This should create a PDF output of your document.

E. You’ll notice that most of the code is not evaluated in this file. This is because most of the chunks have the chunk option eval = FALSE. Play around with the document by changing eval = FALSE to eval = TRUE in each chunk. Knit the document after you change each chunk to see the output.

F. Complete some of the empty chunks at the bottom of the document. Play around for a bit. Add a plot, add a statistical test. Knit to see the results as you go along.

When you feel you are comfortable with Markdown, move on to creating an APA style paper with papaja in the next section.

Create an APA style paper with papaja

Your goal is to create an APA style document using the papaja package and R Markdown. In order for this to work, you need to install both papaja and LaTeX

Install papaja

Make sure you have installed the papaja package with the following code:

install.packages("devtools")             # Only if you don't already have it
devtools::install_github("crsh/papaja")  # Install papaja from GitHub

Install TeX

Make sure you have TeX installed on your computer or you won’t be able to create a PDF document. For Windows, install it from https://miktex.org/. For Mac, install it from http://www.tug.org/mactex/. Once you install TeX, make sure to restart RStudio (or RStudio won’t know it’s there).

Create a new R project called studentAPA.RProj somewhere on your computer with File – New Project …. If you don’t know where to put it, put it on your desktop. Open this project!
Navigate to the project directory (the one you just put studentAPA.RProj in). You should see a file called studentAPA.Rproj there. Now, create two new folders R and data in this directory.
In this WPA, you will analyze data from a study on student performance in two classes: math and Portuguese The data are located in two tab-delimited text files at the following locations:

studentmath.txt: https://raw.githubusercontent.com/ndphillips/RCourse/master/studentmath.txt (the Math data)
studentpor.txt: https://raw.githubusercontent.com/ndphillips/RCourse/master/studentpor.txt (the Portuguese data). Load these data into R, then save them as text files in your data folder by running the following code:

# Step 1: Load the two data files into your R session

student.math <- read.table("https://raw.githubusercontent.com/ndphillips/RCourse/master/studentmath.txt",
                      sep = "\t",
                      header = TRUE)

student.por <- read.table("https://raw.githubusercontent.com/ndphillips/RCourse/master/studentpor.txt",
                      sep = "\t",
                      header = TRUE)

# Step 2: Save the data as text files in your data folder. 

write.table(student.math, file = "data/studentmath.txt", sep = "\t")
write.table(student.por, file = "data/studentpor.txt", sep = "\t")

Open a new blank Markdown (.Rmd) file using the papaja template: File – New File – R Markdown – From Template – APA Article (6th Edition). Save the file as studentAPA.Rmd in your project working directory (that is, next to the studentAPA.Rproj file).
Using a web-browser, open the following link https://raw.githubusercontent.com/ndphillips/RCourse/master/studentAPA.Rmd. Copy all of the text in this file, and paste it into your studentAPA.Rmd file (replace all of the text that was in your studentAPA.Rmd file with this text).
Open a new blank text file (File – New File – Text File). Save the file as studentAPA.bib in your project working directory.
Using a web-browser, open the following link https://raw.githubusercontent.com/ndphillips/RCourse/master/studentAPA.bib. Copy all of the text in this file, and paste it into your studentAPA.bib file (replace all of the text that was in your studentAPA.bib file with this text).

STOP!!!

By now you should have a file structure on your computer that looks like the following screenshot

Here is how your RStudio screen should look when you are in the appropriate project. Note that the file structure matches the one on your computer.

If you don’t have this folder structure and/or you don’t have the appropriate project open in RStudio, the rest of the document won’t work!

Your goal is to create this APA document (https://dl.dropboxusercontent.com/u/7618380/studentAPA_comp.pdf) by adding elements to the studentAPA.Rmd document.
Open studentAPA.Rmd and studentAPA.bib. In studentAPA.Rmd, replace the X values in the main fields at the top of the document (name, paper title, short-title, affiliation) with the appropriate names and titles.
Know Knit your document to see the current version of the PDF output! You can do this by clicking the “Knit” button at the top of your window.
Now it’s time to add some references to your studentAPA.bib file! You will be referencing three papers in this document. Using scholar.google.com, find the BibTeX references for the following paper(s) and add them to your studentAPA.bib file. Make sure to save the file!

Horwitz, Elaine K., Michael B. Horwitz, and Joann Cope. “Foreign language classroom anxiety.” The modern language journal 70.2 (1986): 125-132.
Collier, V. P. (1992). A synthesis of studies examining long-term language minority student data on academic achievement. Bilingual Research Journal, 16(1-2), 187-212.
Abedi, J., & Lord, C. (2001). The language factor in mathematics tests. Applied Measurement in Education, 14(3), 219-234.

Now it’s time to cite your new references. I’ve included one citation already in the studentAPA.Rmd document in the format @abedi2001language. Now cite the additional papers in your studentAPA.bib file by replacing the XXX values with the appropriate citations. Knit your document to see the result
You need to load your data in a separate chunk. I’ve already created a chunk with all the code you need. Of course, This code assumes that your data are stored in studentmath.txt and studentpor.txt in a folder called data in your project directory!. To make sure the chunk is evaluated, change eval = FALSE to eval = TRUE in the chunk options. Knit your document to see the result If you don’t see any errors, then the data should have been correctly loaded!
In the Participants section, there are inline code chunks that should indicate the number of participants in each data set. Replace the 1+1 values with nrow(student.por) and nrow(student.math) to get the number of students in each data set. Knit your document to see the result
In the Results section, I’ve included a chunk that creates Figure 1, a series of histograms. Update the caption to the plot in the chunk options. Then change eval = FALSE to eval = TRUE to tell Markdown to run the chunk. Knit your document to see the result You should now see the histograms in your document.
Below the Figure 1 chunk, there are some inline chunks that calculate the mean grades for exam 1 and exam 3 of the Portuguese data. Update these chunks with round(mean(student.por$G1), 2) and round(mean(student.por$G3), 2) to calculate the correct values. Knit your document to see the result
The next two chunks create tables of summary statistics for the Math and Portuguese data. Update the captions in these chunks. Then, change eval = FALSE to eval = TRUE in the chunk options. Knit your document to see the result You should now see the tables in your document.
The next chunk conducts and saves t-tests for both the math and Portuguese data. The code for the Portuguese test is already completed. Fix the code for the math test. Then, change eval = FALSE to eval = TRUE in the chunk options.
The next lines use inline code to refer to the results of your t-test objects. Replace the 1+1 values with values from your t-test!. (Hint: use sex.por.ttest$parameter to get the degrees of freedom, sex.por.ttest$statistic to get the test statistic, and sex.por.ttest$p.value to get the p-value for the Portuguese test). Knit your document to see the result

WPA #10: Markdown and papaja

Nathaniel Phillips

Play around with Markdown

Create an APA style paper with papaja

Install papaja

Install TeX

STOP!!!

Add new analyses!

Finished!