rfars

Overview

rfars is an R package with a set of functions that makes easier to analyze the data from the US National Highway Traffic Safety Administration's Fatality Analysis Reporting System (FARS).

Installation

# Install the package from GitHub without the vignette:
devtools::install_github("Cesar-Urteaga/rfars")

# Or you can include it:
devtools::install_github("Cesar-Urteaga/rfars", build_vignettes = TRUE)

Purpose

The aim of this project was to combine the skills of creating, writing, and testing an R package, using the R files provided in the course Building R Packages offered by the Johns Hopkins University through the Coursera's platform.

For this assessment, it was required to perform the following tasks:

1. Write a vignette to be included in the package using knitr and R Markdown;
2. Formulate at least one test using the testthat package;
3. Put the package on Github;
4. Set up the package's repository so that can be checked and built on Travis;
5. Add the Travis badge to the package's README.md file, as soon as your package has built on Travis and the build is passing without errors, warnings, or notes.

Workflow

In order to create this package, I followed this path:

1. Consider the steps set forth in the check lists of Roger D. Peng.
2. Create a README file with R Markdown (use the template Github Document (Markdown)).
3. Set up a Github repository and change the Project Options within the Tools menu and Git/SVN tab; select Git as version control system. Thereupon, add the remote through the Git browser using the shell. Later, edit the .gitignore and .Rbuildignore files.
4. Add and commit the files using the Git browser and push the first commit with the shell: git push -u origin master (subsequent commits can be pushed in RStudio's Git browser).
5. Delete the NAMESPACE file when you create the package's project (allow that devtools creates this file with the function document()).
6. Document the code in the R folder using roxygen2-style documentation, and execute devtools::document() (or press Ctrl/Cmd + Shift + D in RStudio) in order to create the .Rd files. Later, press the RStudio's Build & Reload button (Ctrl/Cmd + Shift + B) and review the help files with ?.
7. Fill the DESCRIPTION file with the information of your package. Take into account the libraries in the @importFrom sections of the roxygen2-style documentation to fill the Imports section.
8. If you want to create an R Markdown vignette, use the function devtools::use_vignette("vignette-name"); then, modify the vignette and press Ctrl/Cmd + Shift + K to knit it.
9. Optional: You can distribute the documentation in pdf format executing the command R CMD Rd2pdf package-name in the parent folder of the package.
10. In case you want to include external data (e.g., .bz2 files), you should store them in the inst\extdata folder (please refer to the section of raw data of the book "R packages" by Hadley Wickham); moreover, use the function system.file to know where the external files are stored once the package is installed (see the examples in the documentation).
11. So as to include a battery of tests, run the command devtools::use_testthat() and include the tests in the testthat folder. Once you have added the tests, execute devtools::test() (Ctrl/Cmd + Shift + T) to carry out each one. Please review the chapter of testing in the Hadley's book.
12. To check if your package pass the CRAN's battery of tests, click the Check button in the Build tab of RStudio. N.B.: It is possible that you could get the following note: "no visible binding for global variable variable-name". To get around of it, see the suggested solution in stackoverflow.
13. Finally, you can include the continuous integration service of Travis to your package by running the devtools::use_travis() command and activating the package's repository in your Travis account; thereupon, add, commit, and push your changes in Github and insert the Travis badge into the README file. N.B.: For the AppVeyor service use devtools::use_appveyor() and check the AppVeyor's documentation to add the badge into the README file.
14. Optional: In case you desire to include the LICENSE file into the Github's repository, you may want to see this post in Stackoverflow. N.B.: Please, do not forget to include the reference of the LICENSE file into the DESCRIPTION archive (e.g., License: GPL-3 | file LICENSE).
15. Optional: In order to include a code coverage measure to the package using codecov, you must need to add the package's repository to this service, include this code in the .travis/yml file (change the package's name), and execute the command covr::codecov(token = "YOUR_TOKEN_GOES_HERE") with the ascribed token. N.B.: Do not forget to include the codecov badge into the README file.

R session

The session in which I have created this package was the following:

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_MX.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_MX.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_MX.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.1  backports_1.1.0 magrittr_1.5    rprojroot_1.2  
 [5] tools_3.4.1     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.12   
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      stringr_1.2.0  
[13] digest_0.6.12   evaluate_0.10.1