gmoTree Codebooks"

In gmoTree: Get and Modify 'oTree' Data

library(gmoTree)

Overview

With the codebook() function, you can generate codebooks based on your oTree (Chen et al., 2016) code. This vignette introduces its key features and functionalities.

Disclaimer: This code was tested with both custom implementations and official oTree sample codes.^[The oTree sample codes can be accessed when setting up an oTree project (Chen et al., 2016). All examples presented in this vignette are based on the official oTree sample code, with minor modifications to meet the needs of this package.] However, due to the complexity of oTree setups, it may not address all variations. Please review your output carefully, and feel free to open a GitHub issue if you encounter any problems.

Session and Participant variables as well as built-in variables are not shown in the codebooks! See also further important limitations of this function in the details section of codebook().

Running the code

In its simplest form, the function requires only the path to your oTree code folder. The following code reads the contents of your oTree folder, saves a PDF file containing your codebook in your working directory, and returns a list named cbook, containing the extracted information.

cbook <- codebook("D:/pathtoyourproject/oTree_codes")

Codebook structure and output

File output

The output file is structured as follows: Each application is represented as a chapter (heading level 1), with subchapters for the variables from the Group and Player classes (heading level 2). The display of the Constants class is optional and enabled by default. It can be disabled with the argument include_cons = FALSE. The display of the Subsession class is also optional, but disabled by default. I can be enabled with include_subs = TRUE.

The example below shows the output for the cournot app, which includes all variables from the Constants, Group, and Player classes. If a class contains no custom variables, the class heading will still appear, accompanied by the message “No model fields except the built-in ones.”

List output

Use output = "list" to bypass file creation. This option returns all the information in list format, which can be used in R Markdown for custom codebooks. Below is an example of such a list output. (The argument doc_info = FALSE suppresses messages about missing documentation for variables.)

# Create the codebook list
cbook <- codebook(path = system.file(path = "extdata/ocode_new",
                                     package = "gmoTree"),
                  output = "list",
                  doc_info = FALSE)

str(cbook, 1)  # Show all apps
print(cbook$cournot)  # Only show cournot app

Choosing what to show

By default, all apps are included in the codebook. To generate a codebook for only one app, use the app argument. For example, to generate a codebook for the cournot app:

cbook <- codebook(
  path = system.file("extdata/ocode_new",
                     package = "gmoTree"),
  fsource = "init",
  output = "list",
  doc_info = FALSE,
  app = "cournot")

str(cbook)

The code above returns a list with the app-specific information. You can also generate codebooks for multiple apps by specifying them in the app argument.

cbook <- codebook(
  path = system.file("extdata/ocode_new",
                     package = "gmoTree"),
  fsource = "init",
  output = "list",
  doc_info = FALSE,
  app = c("cournot", "dictator"))

str(cbook, 1)

You can also show all apps except for one or more. Here is an example that removes the app prisoner:

cbook <- codebook(
  path = system.file("extdata/ocode_new", package = "gmoTree"),
  fsource = "init",
  output = "list",
  doc_info = FALSE,
  app_rm = "prisoner")

str(cbook, 1)

Customizing how the codebook is shown

Customizing the codebook titles and metadata

You can easily modify the titles, subtitles, dates, and author names in your codebooks using the following arguments:

codebook(
    path = "Your_oTree_path",  # Can be either absolute or relative!
    title = "Codebook",
    subtitle = "Example Project",
    date = "today",
    params = list(author = c("Max Mustermann", "John Doe"))
)

Sorting the code

You can sort the apps in the codebook by specifying the sort argument. For example:

cbook <- codebook(
  path = system.file("extdata/ocode_new", package = "gmoTree"),
  fsource = "init",
  output = "list",
  doc_info = FALSE,
  app = c("cournot", "dictator"),
  sort = c("dictator", "cournot"))

str(cbook, 1)

Referring to settings

The gmoTree package can automatically replace references to variables in settings.py with the values in the settings.py file. To enable this, set settings_replace = "global".

cbook <- codebook(
  path = system.file("extdata/ocode_new", package = "gmoTree"),
  fsource = "init",
  output = "list",
  settings_replace = "global",
  app = "dictator")

print(cbook$dictator$Constants$Variable)

You can also choose not to replace the references to settings variables by using settings_replace = NULL.

cbook <- codebook(
  path = system.file("extdata/ocode_new", package = "gmoTree"),
  fsource = "init",
  output = "list",
  settings_replace = NULL,
  app = "dictator")

print(cbook$dictator$Constants$Variable)

It is also possible to provide a list of variables to replace the settings variables with the argument user_settings. For example:

cbook <- codebook(
  path = system.file("extdata/ocode_new", package = "gmoTree"),
  fsource = "init",
  output = "list",
  settings_replace = "user",
  user_settings = list(variable = "someValue"),
  app = "dictator")

print(cbook$dictator$Constants$Variable)

Saving your codebook

When you choose output = "file" or output = "both", your codebook will be saved as a professional document.

Output formats

The argument output_format allows you to choose the format of the exported codebook file. Available formats are:

• html_document
• word_document
• latex_document
• odt_document
• rtf_document
• md_document
• pdf_document
• pdf_document_simple

You can choose the format that best suits your needs, with all formats except PDF allowing easy post-generation editing.

When knitting to PDF, make sure to have LaTex installed! It is recommended to use output_format = pdf_document_simple. However, some non-Latin characters (e.g., Chinese characters) may not work with this format. In such cases, you can choose output_format = pdf_document, which is set to use xelatex.

Please note that using xelatex with gmoTree has some limitations: for example, gmoTree currently cannot handle long variable values that result in excessively long table cells. This can cause the PDF to display improperly in certain viewers, such as Nitro. To address this, carefully review your file. If necessary, consider using output_format = latex_document to generate a .tex file, which you can then compile into a PDF. Alternatively, open the file with a PDF viewer that can handle these cases, then save it there to ensure it displays correctly in other PDF viewers.

Output files

By default, gmoTree codebooks are saved in your working directory with the default file name codebook, followed by the file extension. You can modify this by specifying either a custom file name, another directory path, or both.

For example, to save the codebook with a different name, use the following code:

codebook(
    path = "C:/Users/username/folder/oTree",  # Replace!
    output_file = "gmoTree_codebook")

You can also include the file extension, although it is optional:

codebook(
    path = "C:/Users/username/folder/oTree",  # Replace!
    output_file = "gmoTree_codebook.pdf")

You can save the file in a subfolder within the current directory by including the absolute or relative folder name in the output_file argument. For example:

codebook(
    path = "C:/Users/username/folder/oTree",  # Replace!
    output_file = "codebookfiles/gmoTree_codebook.pdf")

You can also specify absolute paths, either in the output_dir argument or directly within the file name specified in the output_file. For example:

codebook(
    path = "C:/Users/username/folder/oTree",  # Replace!
    output_dir  = "C:/Users/username/folder/codebooks",
    output_file = "mycodebook")

Summary

This vignette documents how to customize the codebook generated by the codebook() function, including options for content selection, formatting, and exporting to various formats. These tools enable the creation of comprehensive and tailored documentation for your experimental data.

References

Chen, D. L., Schonger, M., & Wickens, C. (2016). oTree—An open-source platform for laboratory, online, and field experiments. Journal of Behavioral and Experimental Finance, 9, 88–97. https://doi.org/10.1016/j.jbef.2015.12.001

gmoTree documentation built on April 3, 2025, 10:26 p.m.