SuRGE data are maintained in the shared documents library at the private SuRGE SharePoint site (https://usepa.sharepoint.com/sites/SuRGE). Scripts in this project assume users have synced the documents library to their computer. Contact Jake Beaulieu if you do not have access the site or need assistance syncing to your computer.
R scripts in this repository read data from the SuRGE SharePoint site. Scripts used to create lake specific survey designs are contained in scripts/lakeDsn/... and use relative file paths to read data from SharePoint. If you wish to reproduce the survey designs, you must create your local clone within the rProjects folder at SharePoint. The remainining scripts use absolute file paths based on the values returned from Sys.getenv("USERPROFILE"). These scipts can be run regardless of where the R project is cloned on your computer.
This project uses the renv library to manage library versions. After creating a local clone, a message will appear in the console directing users to sync the project library by running renv::restore(). This will download the packages and versions used in this project as specified in the renv.lock file. If you need to add libraries to the project, be sure to use renv::snapshot to update the lock file. When collaborators sync their local clone with the master, they can then run renv::restore() to have the new library installed on their local project directory. Please see here (https://rstudio.github.io/renv/index.html) for a primer on renv and here (https://rstudio.github.io/renv/articles/collaborating.html) for using renv in a collaborative workflow.
Please use caution when updating libraries already captured in the lock file. The code runs succesfully with the suite of packages captured in the current lock file; updating package versions could cause problems with the existing code. The whole point of renv is to minimize the potential for code breakage due to differences among package versions.
The R project was initiated by J Beaulieu using R.4.4.1 and renv will produce a warning message if a different version of R is used. In theory, renv shouldn't be sensitive to the version of R, but in practice I have found that renv::restore() can take a very long time or even fail if a different version of R is used.
Please note that the .Rprofile file is under version control in the repository. This file contains an autoloader which automatically downloads and installs the appropriate version of renv into the project library. It is best that users do not use the .Rprofile file to further customize the environment.
Finally, renv::restore() may require Rtools. Rtools can be found here (https://cran.r-project.org/bin/windows/Rtools/history.html). Be sure to install a version that is compatible with your R version.
This project uses conflicted to manage conflicts between the dplyr functions select() and filter() and functions with the same names, but in different packages (i.e.MASS::select()). The conflicted settings will always give preference to the dplyr library when select() or filter() are called.
Scripts must be run in the sequence documented in scripts/masterScript.R. Please see status update at the top of script for current status of the scripts.
This project uses git version control. git software is independent from the github website and must be installed on each users computer. Users will be given push/pull rights to the repo and can therefore push directly to the repo without the need to submit a pull request. To minimize conflicts among separate commits, it is best practice to start each session by pulling from the repo to get the most up to date code. Similarly, users should commit and push their changes to the repo at the conclusion of each working session.
The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.