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https://github.com/RAJohansen/waterquality
Package designed to detect and quantify water quality and cyanobacterial harmful algal bloom (CHABs) from remotely sensed imagery
https://github.com/RAJohansen/waterquality
algal-bloom algorithms landsat-8 meris modis olci remote-sensing sentinel-2 water-quality
Last synced: 25 days ago
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Package designed to detect and quantify water quality and cyanobacterial harmful algal bloom (CHABs) from remotely sensed imagery
- Host: GitHub
- URL: https://github.com/RAJohansen/waterquality
- Owner: RAJohansen
- License: other
- Created: 2017-11-29T19:57:14.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-03-25T15:24:52.000Z (9 months ago)
- Last Synced: 2024-10-29T22:31:03.567Z (about 2 months ago)
- Topics: algal-bloom, algorithms, landsat-8, meris, modis, olci, remote-sensing, sentinel-2, water-quality
- Language: R
- Homepage: https://rajohansen.github.io/waterquality/
- Size: 33.6 MB
- Stars: 42
- Watchers: 8
- Forks: 8
- Open Issues: 3
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
- open-sustainable-technology - waterquality - A package designed to detect and quantify water quality and cyanobacterial harmful algal bloom (CHABs) from remotely sensed imagery. (Natural Resources / Water Supply and Quality)
README
---
output: github_document
---
[](https://cran.r-project.org/package=waterquality)
[](https://app.codecov.io/gh/RAJohansen/waterquality)
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
```
# waterquality
The main purpose of **waterquality** is to quickly and easily convert satellite-based reflectance imagery into one or many well-known water quality indices designed for the detection of Harmful Algal Blooms (HABs) using the following pigment proxies: chlorophyll-a, blue-green algae (phycocyanin), and turbidity.
Currently, this package is able to process [40 algorithms](https://rajohansen.github.io/waterquality/reference/index.html) for the following satellite-based imagers: WorldView-2, Sentinel-2, Landsat-8, MODIS, MERIS, and OLCI.
In order to improve the aesthetics of the `wq_calc()` output, a series of `Map_WQ()` functions were developed to help reduce technical barriers and simplify the complexities in selecting a map layout.
Additional functionality of the package includes a series of `extract_lm()` functions that wrap the ["Fitting Linear Models"](https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/lm) and ["caret"](https://topepo.github.io/caret/index.html) packages to quickly generate crossvalidated linear models and standardized outputs (r^2^, p-value, slope, intercept of the global lm model & average r^2^, average RMSE, average MAE of crossvalidated model) for any number of algorithm and water quality parameter combinations.
It is important to note that the `extract_lm()` functions require ground-truth data in order to develop the models.
For a more detailed look into the full functionality of **waterquality**, please view ["Introduction to the waterquality package"](https://rajohansen.github.io/waterquality/articles/waterquality_vignette.html).
For a broader look into how to apply this tool into a research workflow or for more information on topics such as data acquisition, image pre-processing, or results, see our publication entitled ["Waterquality: An Open-Source R Package for the Detection and Quantification of Cyanobacterial Harmful Algal Blooms and Water Quality"](https://erdc-library.erdc.dren.mil/jspui/bitstream/11681/35053/3/ERDC-EL%20TR-19-20.pdf).
Additionally, we have recently developed and published a complementary python-based version of **waterquality** compatible with ESRI ArcGIS and ArcPro. For more information please visit [“waterquality for ArcGIS Pro Toolbox”](https://hdl.handle.net/11681/42240).
## Installation
You can install the released version from CRAN with:
```{r install_CRAN, eval = FALSE}
install.packages("waterquality")
```
You can install waterquality from github with:
```{r gh-installation, eval = FALSE}
# install.packages("devtools")
devtools::install_github("RAJohansen/waterquality")
```
## Basic Example
The main function in this package is `wq_calc()`:
```{r example_code, fig.asp=0.33, results='hide', message=FALSE, warning=FALSE}
library(waterquality)
library(terra)
s2 = terra::rast(system.file("raster/S2_Harsha.tif", package = "waterquality"))
MM12NDCI = wq_calc(s2, alg = "MM12NDCI", sat = "sentinel2")
```
```{r,fig.height = 5, fig.width = 6}
Map_WQ_raster(WQ_raster = MM12NDCI,
map_title= "Water Quality Map",
raster_style = "quantile",
histogram = TRUE)
```
## Citation
To cite waterquality in publications, please use:
Johansen R, Nowosad J, Reif M, Emery E (2023). waterquality: Satellite Derived Water Quality Detection Algorithms.
U.S Army Engineer Research and Development Center, Vicksburg, MS, USA. R package version 1.0.0,
https://github.com/RAJohansen/waterquality/.
## Package Contributions
We encourage users to submit issues and enhancement requests so we may continue to improve our package.
Furthermore, if you have a water quality algorithm that was not on our list, and you would like for it to be included in our package please email [email protected].