Biointegrity and Eutrophication Indicators and Thresholds for Modified Channels, Intermittent Streams, and Streams on the Central Valley Floor
This repository contains all input data, figures, tables, and R code used in SCCWRP Technical Report #1367. Each R source code file can be run independently to produce its respective table(s) or figure(s).
The data and code used to generate all tables and figures of this study are organized by Part and Table or Figure number (as indicated by the .R files' filenames in the R folder). Figures or tables not generated by code are not included in this repository. The repository is organized as an RStudio project, and it is recommended to run the code in RStudio with the BiointegrityEutrophicationIndicators project open. For more information on RStudio projects, refer to https://support.posit.co/hc/en-us/articles/200526207-Using-RStudio-Projects.
The accompanying R Shiny web application can be found at https://sccwrp.shinyapps.io/ModifiedChannelThresholds, with code hosted at https://github.com/SCCWRP/ModifiedChannelThresholds.
All code, tables, and figures were generated using the R and R package versions shown in the table below. Note that some packages may require additional packages or other libraries not listed here. The CSCI package, developed by SCCWRP, can be installed with the devtools::install_github('SCCWRP/CSCI') function.
| Package | Version |
|---|---|
| R (base) | 4.3.1 |
| broom | 1.0.5 |
| CSCI | 1.2.4 |
| dplyr | 1.1.4 |
| ggplot2 | 3.5.0 |
| ggpubr | 0.6.0 |
| lubridate | 1.9.3 |
| purrr | 1.0.2 |
| pwr | 1.3-0 |
| randomForest | 4.7-1.1 |
| readr | 2.1.4 |
| scales | 1.3.0 |
| scam | 1.2-16 |
| sf | 1.0-15 |
| spsurvey | 5.5.1 |
| stringr | 1.5.1 |
| tidyr | 1.3.0 |