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
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”
and “caret” packages to
quickly generate crossvalidated linear models and standardized outputs
(r2, p-value, slope, intercept of the global lm model &
average r2, 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”.
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”.
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”
Installation
You can install the released version from CRAN with:
install.packages("waterquality")You can install waterquality from github with:
# install.packages("devtools")
devtools::install_github("RAJohansen/waterquality")Basic Example
The main function in this package is wq_calc():
library(waterquality)
library(raster)
s2 = stack(system.file("raster/S2_Harsha.tif", package = "waterquality"))
s2_two_alg = wq_calc(s2, alg = c("MM12NDCI", "Al10SABI"), sat = "sentinel2")plot(s2_two_alg)
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].