example moved to R file; extended by model summary

R/errorProfiles.R

@@ -23,7 +23,60 @@
 #' Estimating the area of applicability of spatial prediction models.
 #' \doi{10.1111/2041-210X.13650}
 #' @seealso \code{\link{aoa}}
-#' @example inst/examples/ex_errorProfiles.R
+#' @example
+#' \dontrun{
+#' library(CAST)
+#' library(sf)
+#' library(terra)
+#' library(caret)
+#'
+#' data(splotdata)
+#' predictors <- terra::rast(system.file("extdata","predictors_chile.tif", package="CAST"))
+#'
+#' model <- caret::train(st_drop_geometry(splotdata)[,6:16], splotdata$Species_richness,
+#'    ntree = 10, trControl = trainControl(method = "cv", savePredictions = TRUE))
+#'
+#' AOA <- aoa(predictors, model, LPD = TRUE, maxLPD = 1)
+#'
+#' ### DI ~ error
+#' errormodel_DI <- errorProfiles(model, AOA, variable = "DI")
+#' plot(errormodel_DI)
+#' summary(errormodel_DI)
+#'
+#' expected_error_DI = terra::predict(AOA$DI, errormodel_DI)
+#' plot(expected_error_DI)
+#'
+#' ### LPD ~ error
+#' errormodel_LPD <- errorProfiles(model, AOA, variable = "LPD")
+#' plot(errormodel_LPD)
+#' summary(errormodel_DI)
+#'
+#' expected_error_LPD = terra::predict(AOA$LPD, errormodel_LPD)
+#' plot(expected_error_LPD)
+#'
+#' ### geodist ~ error
+#' errormodel_geodist = errorProfiles(model, locations=splotdata, variable = "geodist")
+#' plot(errormodel_geodist)
+#' summary(errormodel_DI)
+#'
+#' dist <- terra::distance(predictors[[1]],vect(splotdata))
+#' names(dist) <- "geodist"
+#' expected_error_DI <- terra::predict(dist, errormodel_geodist)
+#' plot(expected_error_DI)
+#'
+#'
+#' ### with multiCV = TRUE (for DI ~ error)
+#' errormodel_DI = errorProfiles(model, AOA, multiCV = TRUE, length.out = 3, variable = "DI")
+#' plot(errormodel_DI)
+#'
+#' expected_error_DI = terra::predict(AOA$DI, errormodel_DI)
+#' plot(expected_error_DI)
+#'
+#' # mask AOA based on new threshold from multiCV
+#' mask_aoa = terra::mask(expected_error_DI, AOA$DI > attr(errormodel_DI, 'AOA_threshold'),
+#'   maskvalues = 1)
+#' plot(mask_aoa)
+#' }
 #'
 #'
 #' @export errorProfiles