Lecture 11: R Package
devtools package
2025-03-19
man folder
The man sub-directory contains the documentation files for all of the exported objects of a package (e.g., help package).
With the development of the
roxygen2package, we no longer need to do that and can write the documentation directly into the R code files.
Left is starting with #' will be used to generate .Rd files that are part of help pages of function. Right is the help page of the function.
devtools package
There are two ways of creating a new package
You can also initialize an R package in RStudio by selecting “File” -> “New Project” -> “New Directory” -> “R Package”.
Or you can use
create()function indevtoolspackage
> devtools::create("~/Downloads/jeremy")
✔ Creating /Users/jihong/Downloads/jeremy/.
✔ Setting active project to "/Users/jihong/Downloads/jeremy".
✔ Creating R/.
✔ Writing DESCRIPTION.
Package: jeremy
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9000
Authors@R (parsed):
* First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
Description: What the package does (one paragraph).
License: `use_mit_license()`, `use_gpl3_license()` or friends to
pick a license
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2.9000
✔ Writing NAMESPACE.
✔ Writing jeremy.Rproj.
✔ Adding "^jeremy\\.Rproj$" to .Rbuildignore.
✔ Adding ".Rproj.user" to .gitignore.
✔ Adding "^\\.Rproj\\.user$" to .Rbuildignore.
✔ Setting active project to "<no active project>".Below figure gives an example of what the new package directory will look like after you create an initial package structure with create or via the RStudio “New Project” interface.
- an R project file (
.Rprojextension) that saves some project options for the directory DESCRIPTIONandNAMESPACEfiles are automatically generated.gitignoreused to exclude some files in the directory by git.Rbuildignoreused to exclude some files when the package is built
Example 1: Build your first R file in your first package
Open the .Rproj file will open Rstudio with your package directory as root path.
In your R folder, create a new R file named hello.R:
Exp1: Your first function — hello.R
Step 1: create the R file
Copy-and-paste the following starting template code into your hello.R file and save.
hello.R
#' This is the function for showing the information of XXX
#'
#' @param details Want to know more
#'
#' @returns describe some basic information about XXX
#'
#' @examples
#' hello()
#'
#' @export
hello <- function(){
message("I am a PhD student from ...")
}Step 2: document and load
Then, in Build panel, click More -> Document -> Load All.
These two buttons correspond to document() and load_all in devtools package, which are most frequently used.
Step 3: Test the function
Finally, in R console, type in hello(). Do you see the results?
Also, try adding question mark ? before the function to see the help page. Do you see your roxygen information works?
Finally, try to load your package. Did you see your package can be successfully loaded?
Example 1: Store your data into your package
- Step 4: Create Dataset.R
- Step 5: Create R script for data generation
- Step 5: run Dataset.R
- Step 6: Test the data
- Step 7: Share your package
In Dataset.R file, put the following R code into R file.
dat <- data.frame(
name = "jihong",
bio = "
I am a tenure-track Assistant Professor of Educational Statistics and Research Methods (ESRM) in the Department of Counseling, Leadership, and Research Methods (CLRM) at the University of Arkansas, Fayetteville, U.S.
Previously, I was a postdoctoral fellow in the Department of Social Work at the Chinese University of Hong Kong (CUHK). My academic journey in psychometrics began with doctoral training under Dr. Jonathan Templin in the Educational Measurement and Statistics (EMS) program at the University of Iowa. I have extensive experience in educational assessment. During my master’s program at the University of Kansas, I worked as a research assistant for three years in the Kansas Assessment Program (KAP), contributing to various assessment initiatives, including Dynamic Learning Maps (DLM). Later, during my Ph.D. program, I interned at the Stanford Research Institute (SRI), where I focused on digital learning in computerized testing.
My primary research interests include empirical and methodological studies in psychological network modeling, AI in Education, Bayesian latent variable modeling, Item Response Theory modeling, and other advanced psychometric methods. My expertise lies in applying advanced statistical modeling techniques in psychology and education.
"
)
usethis::use_data(dat, overwrite = TRUE)Open Dataset.R and Click the Source button to run the R file. You shall see the following output in R console.
>>> usethis::use_data(dat, overwrite = TRUE)
✔ Setting active project to "/Users/jihong/Downloads/jeremy".
✔ Adding R to Depends field in DESCRIPTION.
✔ Creating data/.
✔ Setting LazyData to "true" in DESCRIPTION.
✔ Saving "dat" to "data/dat.rda".
☐ Document your data (see <https://r-pkgs.org/data.html>).
Type in the data name, such as dat in the R console. Do you see the data in your menu?
Currently, you can compress your package and share the zip file to anyone you want to share with.
As an example, download jeremy.zip on the webpage of Syllabus. Unzip it to Downloads folder and run the following R script.
install.packages("~/Downloads/jeremy", repos = NULL, type="source")
>> Installing package into ‘/Users/jihong/Rlibs’
>> (as ‘lib’ is unspecified)
>> * installing *source* package ‘jeremy’ ...
>> ** using staged installation
>> ** R
>> ** data
>> *** moving datasets to lazyload DB
>> ** byte-compile and prepare package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded from temporary location
>> ** testing if installed package can be loaded from final location
>> ** testing if installed package keeps a record of temporary installation path
>> * DONE (jeremy)