Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
echo = TRUE)
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
library(waterquality)
library(terra)
Harsha <- terra::rast(system.file("raster/S2_Harsha.tif", package = "waterquality"))
## ----results='hide', message=FALSE, warning=FALSE-----------------------------
Harsha_Am092Bsub <- wq_calc(terraRast = Harsha,
alg = "MM12NDCI",
sat = "sentinel2")
## ---- fig.height = 5, fig.width = 6-------------------------------------------
terra::plot(Harsha_Am092Bsub)
## ----results='hide', message=FALSE, warning=FALSE-----------------------------
Harsha_Multiple <- wq_calc(terraRast = Harsha,
alg = c("MM12NDCI", "Am092Bsub", "Da052BDA"),
sat = "sentinel2")
## ---- fig.height = 5, fig.width = 6-------------------------------------------
terra::plot(Harsha_Multiple)
## ----results='hide', message=FALSE, warning=FALSE-----------------------------
Harsha_PC <- wq_calc(Harsha,
alg = "chlorophyll",
sat = "sentinel2")
## ---- fig.height = 5, fig.width = 6-------------------------------------------
terra::plot(Harsha_PC)
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
Harsha_All <- wq_calc(Harsha,
alg = "all",
sat = "sentinel2")
## ----fig.height = 5, fig.width = 6--------------------------------------------
terra::plot(Harsha_All) # Only displays first 16 of 28
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
library(waterquality)
library(terra)
library(tmap)
library(sf)
s2 = terra::rast(system.file("raster/S2_Harsha.tif", package = "waterquality"))
MM12NDCI = wq_calc(s2, alg = "MM12NDCI", sat = "sentinel2")
samples = terra::vect(system.file("raster/Harsha_Simple_Points_CRS.gpkg", package = "waterquality"))
lake_extent = terra::vect(system.file("raster/Harsha_Lake_CRS.gpkg", package = "waterquality"))
## ----fig.height = 5, fig.width = 6--------------------------------------------
Map_WQ_raster(WQ_raster = MM12NDCI,
sample_points = samples,
map_title= "Water Quality Map",
raster_style = "quantile",
histogram = TRUE)
## ---- eval = FALSE------------------------------------------------------------
# #Input raster image
# wq_raster <- terra::rast("C:/temp/my_raster.tif")
#
# #Input shapefile
# wq_samples <- terra::vect('C:/temp/my_samples.shp')
#
# #Extract values from raster and combine with shapefile
# waterquality_data <- data.frame(wq_samples, terra::extract(wq_raster, wq_samples))
#
# #Export results as csv file
# write.csv(waterquality_data, file = "C:/temp/waterquality_data.csv")
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
library(waterquality)
library(caret)
df <- read.csv(system.file("raster/waterquality_data.csv", package = "waterquality"))
## ---- message=FALSE, warning=FALSE--------------------------------------------
extract_lm(parameter = "Chl_ugL", algorithm = "MM12NDCI", df = df)
## ---- message=FALSE, warning=FALSE--------------------------------------------
extract_lm_cv(parameter = "Chl_ugL", algorithm = "MM12NDCI",
df = df, train_method = "lm", control_method = "repeatedcv",
folds = 3, nrepeats = 5)
## ---- message=FALSE, warning=FALSE--------------------------------------------
# Create series of strings to be used for parameters and algorithms arguments
algorithms <- c(names(df[6:10]))
parameters <- c(names(df[3:5]))
extract_lm_cv_multi_results <- extract_lm_cv_multi(parameters = parameters, algorithms = algorithms,
df = df, train_method = "lm", control_method = "repeatedcv",
folds = 3, nrepeats = 5)
head(extract_lm_cv_multi_results)
## ---- message=FALSE, warning=FALSE--------------------------------------------
extract_lm_cv_all_results <- extract_lm_cv_all(parameters = parameters, df = df,
train_method = "lm", control_method = "repeatedcv",
folds = 3, nrepeats = 5)
head(extract_lm_cv_all_results)
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