knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-" )
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 (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".
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”.
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")
The main function in this package is wq_calc()
:
library(waterquality) library(terra) s2 = terra::rast(system.file("raster/S2_Harsha.tif", package = "waterquality")) MM12NDCI = wq_calc(s2, alg = "MM12NDCI", sat = "sentinel2")
Map_WQ_raster(WQ_raster = MM12NDCI, map_title= "Water Quality Map", raster_style = "quantile", histogram = TRUE)
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/.
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 Richard.A.Johansen@erdc.dren.mil.
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