waterquality

A package designed to detect and quantify water quality and cyanobacterial harmful algal bloom (CHABs) from remotely sensed imagery.
https://github.com/RAJohansen/waterquality

Category: Natural Resources
Sub Category: Water Supply and Quality

Keywords

algal-bloom algorithms landsat-8 meris modis olci remote-sensing sentinel-2 water-quality

Keywords from Contributors

routes geo

Last synced: about 2 hours ago
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Repository metadata

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 (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-03-25T15:24:52.000Z (about 1 year ago)
• Last Synced: 2025-04-17T22:07:31.266Z (10 days 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: 45
• Watchers: 8
• Forks: 8
• Open Issues: 3
• Releases: 2
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

README.Rmd

          ---
output: github_document
---



[![CRAN status](http://www.r-pkg.org/badges/version/waterquality)](https://cran.r-project.org/package=waterquality)
[![codecov](https://codecov.io/gh/RAJohansen/waterquality/branch/master/graph/badge.svg)](https://app.codecov.io/gh/RAJohansen/waterquality)
![downloads](http://cranlogs.r-pkg.org/badges/grand-total/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].
        

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Owner metadata

• Name: Richard A. Johansen
• Login: RAJohansen
• Email:
• Kind: user
• Description: Research Interests: Remote Sensing, Water Quality, GIS, R, Data Visualization, Geography ORCID:_0000-0003-4287-9677
• Website:
• Location:
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/29709655?u=dd03c0823ba2b5034edc0c4a8d651a33c8ccdd50&v=4
• Repositories: 20
• Last ynced at: 2024-06-11T15:54:54.792Z
• Profile URL: https://github.com/RAJohansen

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GitHub Events

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• Watch event: 2

Last Year

• Watch event: 2

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Committers metadata

Last synced: 6 days ago

Name	Email	Commits
jn	t****i@g****m	127
Richard	r****3@g****m	92
Richard Johansen	r****n@u****u	83
Richard Johansen	r****n@e****l	15
Richard Johansen	j****a@m****u	12
olivroy	5****y	1

Committer domains:

• mail.uc.edu: 1
• erdc.dren.mil: 1
• uc.edu: 1

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Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/RAJohansen/waterquality

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Package metadata

• Total packages: 2
• Total downloads:
  • cran: 187 last-month
• Total dependent packages: 0 (may contain duplicates)
• Total dependent repositories: 0 (may contain duplicates)
• Total versions: 7
• Total maintainers: 1

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Dependencies

Score: 10.899402442965895