#' @title Correlation (Statistics)
#'
#' @description Calculates corrlation or covariance between two rasters.
#'
#'
#' @param rast1 first \linkS4class{RasterLayer}
#' @param rast2 second \linkS4class{RasterLayer}
#' @param measure Transformation type. Must be "correlation" or "covariance". Default: "correlation"
#' @param output (optional) file name to save output. Default: NULL
#' @param load_output If TRUE, function output file will be loaded into R. Default: TRUE
#' @param quiet IF FALSE, console messages are shown. Default: TRUE
#' @param ... optional parameter for [RQGIS::run_qgis()]
#'
#' @return
#' \linkS4class{RasterLayer} correlation
#'
#'
#'
#' @keywords correlation
#'
#'
#' @export
#'
correlation <- function(rast1 = NULL, rast2 = NULL, size = 3, measure = "correlation", output = NULL, load_output = TRUE, quiet = TRUE, ...)
{
if(quiet == FALSE)
{
process.time.start <- proc.time()
cat("Running Correlation ...\n")
}
if(quiet == FALSE) cat("... calculate statistics \n")
tmpXY <- raster::overlay(x = rast1, y = rast2, fun = function(x, y){return(x * y)})
xBar <- RQGIS::run_qgis(alg = "grass7:r.neighbors", input = rast1, method = "average", size = size, output = file.path(tempdir(), "rast1_m.tif"), load_output = TRUE, show_output_paths = FALSE)
yBar <- RQGIS::run_qgis(alg = "grass7:r.neighbors", input = rast2, method = "average", size = size, output = file.path(tempdir(), "rast2_m.tif"), load_output = TRUE, show_output_paths = FALSE)
xyBar <- RQGIS::run_qgis(alg = "grass7:r.neighbors", input = tmpXY, method = "average", size = size, output = file.path(tempdir(), "rast12_m.tif"), load_output = TRUE, show_output_paths = FALSE)
coVar <- raster::overlay(x = xBar, y = yBar, z = xyBar, fun = function(x, y, z){return(z - (x*y))})
if(measure == "covariance")
{
outRaster <- coVar
}
if(measure == "correlation")
{
xStd <- RQGIS::run_qgis(alg = "grass7:r.neighbors", load_output = TRUE, show_output_paths = FALSE,
input = rast1, method = "stddev", size = size, output = file.path(tempdir(), "rast1_sd.tif"))
yStd <- RQGIS::run_qgis(alg = "grass7:r.neighbors", load_output = TRUE, show_output_paths = FALSE,
input = rast2, method = "stddev", size = size, output = file.path(tempdir(), "rast2_sd.tif"))
xyStd <- raster::overlay(x = xStd, y = yStd, fun = function(x, y){return(x * y)})
corr <- raster::overlay(x = coVar, y = xyStd, fun = function(x, y){return(x / y)})
# corr <- raster::calc(x = corr, fun = function(x){return(ifelse(x > 1, 1, x))})
outRaster <- corr
}
names(outRaster) <- measure
if(!is.null(output))
{
# write raster
if(quiet == FALSE) cat("... write raster\n")
raster::writeRaster(x = outRaster, filename = output, overwrite = TRUE)
}
if(quiet == FALSE) cat(paste0("------ Run of Correlation/Covariance: " , (proc.time() - process.time.start)["elapsed"][[1]]/60, " Minutes ------\n"))
if(load_output)
{
return(outRaster)
}
} # end of function correlation
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