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Package designed to detect and quantify water quality and cyanobacterial harmful algal bloom (CHABs) from remotely sensed imagery

Home Page: https://rajohansen.github.io/waterquality/

License: Other

R 97.20% Rez 2.80%

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

waterquality's Introduction

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(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)
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#>      (status 2 uses the sf package in place of rgdal)

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].

waterquality's People

Contributors

Stargazers

Watchers

Forkers

subhadeep-maishal chaoecohydrors drroad simonhong111 cheloti hugoaluque mateuszrydzik

waterquality's Issues

Please remove dependencies on rgdal, rgeos, and/or maptools

This package depends on (depends, imports or suggests) raster and one or more of the retiring packages rgdal, rgeos or maptools (https://r-spatial.org/r/2022/04/12/evolution.html, https://r-spatial.org/r/2022/12/14/evolution2.html). Since raster 3.6.3, all use of external FOSS library functionality has been transferred to terra, making the retiring packages very likely redundant. It would help greatly if you could remove dependencies on the retiring packages as soon as possible.

Error when running "all" algorithms

I think the error is due to the algorithm formula (look to make sure the band math makes sense)

Harsha_All <- wq_calc(raster_stack = Harsha, alg = "all", sat = "sentinel2" )

Error in .overlayList(x, fun = fun, filename = filename, forcefun = forcefun, :
cannot use this formula, probably because it is not vectorized

formula(x) is deprecated error

The function extract_lm_cv uses my_formula = as.formula(paste(parameter, "~" ,algorithm)) but when this is passed to the function extract_lm_cv_multi we receive the following error

"Using formula(x) is deprecated when x is a character vector of length > 1.
Consider formula(paste(x, collapse = " ")) instead."

Need to figure out a way to recode extract_lm_cv so that it works for single and multiple independent/dependent variables.

Website not updating with new commits to CITATION

How do I refresh the website to reflect the changes I have made to the citations page?

https://rajohansen.github.io/waterquality/

Add missing references

Errors in band math for algorithms Be16FLHblue & Zh10FLH

Both of these algorithms result in 0. Both of these need to be removed from S2 choices.
Be16FLHblue c(2, 4, 2), =
(w529) - (w644 + (w458 - w644))

Zh10FLH, c(4, 5, 4) =
(w686)-(w715 + (w672-w715))

Add palette as an argument in map functions

Currently, palette = "viridis".

Should add palette as an argument so users can decide their own palette choice.

Wrong Error when algorithm is NA

MM12NDCI is not available as a landsat8 algorithm (i.e. it is NA), but the error states the problem is because I chose the wrong satellite. We need to change that error to say "MM12NDCI is NA for landsat8" or "MM12NDCI is not available for the selected satellite, please chose an appropriate algorithm"

Example Code:
Harsha_ndci <- wq_calc(raster_stack = Harsha, alg = "MM12NDCI", sat = "landsat8")

Error Code:
Error in wq_calc(raster_stack = Harsha, alg = "MM12NDCI", sat = "landsat8") :
Unknown satellite or instrument.Please provide one of: 'worldview2', 'sentinel2', 'landsat8', 'modis', or 'meris'

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Calculating line height algorithms

Hi,

Thanks for your contribution of this package. I want to check about two line height algorithms that you include: Go04MCI and Zh10FLH. I'm familiar with MCI and FLH, but not with the "Go04" and "Zh10" prefixes - are these meant to be different from the original algorithms? I ask because the calculation of both is different from how a line height algorithm is normally calculated.

The calculation for MCI in the waterquality package amounts to w709 - w753, and for FLH, w686 - w672. Below I attached an image showing how these two algorithms are normally calculated. Could you please clarify if I am missing something?

Thank you,
Wilson