diff --git a/R/errorProfiles.R b/R/errorProfiles.R index 0ed475bf..968902a0 100644 --- a/R/errorProfiles.R +++ b/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$DI > attr(errormodel_DI, 'AOA_threshold'), +#' maskvalues = 1) +#' plot(mask_aoa) +#' } #' #' #' @export errorProfiles diff --git a/inst/examples/ex_errorProfiles.R b/inst/examples/ex_errorProfiles.R deleted file mode 100644 index 50a4e2dd..00000000 --- a/inst/examples/ex_errorProfiles.R +++ /dev/null @@ -1,58 +0,0 @@ -\dontrun{ - - library(CAST) - library(sf) - library(terra) - library(caret) - - - data(splotdata) - predictors <- terra::rast(system.file("extdata","predictors_chile.tif", package="CAST")) - - model <- caret::train(st_drop_geometry(splotdata)[,6:16], splotdata$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) - - expected_error_DI = terra::predict(AOA$DI, errormodel_DI) - plot(expected_error_DI) - - ### LPD ~ error - errormodel_LPD <- errorProfiles(model, AOA, variable = "LPD") - plot(errormodel_LPD) - - expected_error_LPD = terra::predict(AOA$LPD, errormodel_LPD) - plot(expected_error_LPD) - - - - ### geodist ~ error - errormodel_geodist = errorProfiles(model, locations=splotdata, - variable = "geodist") - plot(errormodel_geodist) - - 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) - - -} -