## ----setup, echo=FALSE--------------------------------------------------------
knitr::opts_chunk$set(fig.width = 8.83)

## ----message = FALSE, warning=FALSE-------------------------------------------
#install.packages("CAST")
library(CAST)

## ----message = FALSE, warning=FALSE-------------------------------------------
help(CAST)

## ----message = FALSE, warning=FALSE-------------------------------------------
library(geodata)
library(terra)
library(sf)
library(caret)
library(tmap)

## ----message = FALSE, warning=FALSE-------------------------------------------
data(splotdata)
head(splotdata)

## ----message = FALSE, warning=FALSE-------------------------------------------
wc <- worldclim_global(var="bio",res = 10,path=tempdir())
elev <- elevation_global(res = 10, path=tempdir())

## ----message=FALSE, warning=FALSE, echo=FALSE---------------------------------
try(wc <- worldclim_global(var="bio", res=10, path=tempdir()), silent=TRUE)
try(elev <- elevation_global(res=10, path=tempdir()), silent=TRUE)
wc_exist <- exists("wc") && exists("elev") && !is.null(wc) && !is.null(elev)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
predictors_sp <- crop(c(wc,elev),st_bbox(splotdata))
names(predictors_sp) <- c(paste0("bio_",1:19),"elev")

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
plot(predictors_sp$elev)
plot(splotdata[,"Species_richness"],add=T)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
predictors <- c("bio_1", "bio_4", "bio_5", "bio_6",
                "bio_8", "bio_9", "bio_12", "bio_13",
                "bio_14", "bio_15", "elev")

# note that to use the data for model training we have to get rid of the 
# geometry column of the sf object: st_drop_geometry(splotdata)

set.seed(10) # set seed to reproduce the model
model_default <- train(st_drop_geometry(splotdata)[,predictors],
               st_drop_geometry(splotdata)$Species_richness,
               method="rf",tuneGrid=data.frame("mtry"=2),
               importance=TRUE, ntree=50,
               trControl=trainControl(method="cv",number=3, savePredictions = "final"))

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
prediction <- predict(predictors_sp,model_default,na.rm=TRUE)
plot(prediction)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
model_default
global_validation(model_default)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
set.seed(10)
indices_LLO <- CreateSpacetimeFolds(splotdata,spacevar = "Country",
                                k=3)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
set.seed(10)
indices_knndm <- knndm(splotdata,predictors_sp,k=3, dist_fun = "great_circle")

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
plot(geodist(splotdata,predictors_sp,CVtest=model_default$control$indexOut, dist_space = "geographical", dist_fun = "great_circle"))+ 
  scale_x_log10(labels=round)
plot(geodist(splotdata,predictors_sp,CVtest=indices_LLO$indexOut, dist_space = "geographical", dist_fun = "great_circle"))+ 
  scale_x_log10(labels=round)
plot(geodist(splotdata,predictors_sp,CVtest=indices_knndm$indx_test, dist_space = "geographical", dist_fun = "great_circle"))+ 
  scale_x_log10(labels=round)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
model <- train(st_drop_geometry(splotdata)[,predictors],
                   st_drop_geometry(splotdata)$Species_richness,
                   method="rf",
                   tuneGrid=data.frame("mtry"=2), 
                   importance=TRUE,
                   trControl=trainControl(method="cv",
                                          index = indices_knndm$indx_train,
                                          savePredictions = "final"))
model
global_validation(model)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
plot(varImp(model))

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
set.seed(10)
ffsmodel <- ffs(st_drop_geometry(splotdata)[,predictors],
                    st_drop_geometry(splotdata)$Species_richness,
                    method="rf", 
                    tuneGrid=data.frame("mtry"=2),
                    verbose=FALSE,
                    ntree=25, #make it faster for this tutorial
                    trControl=trainControl(method="cv",
                                           index = indices_knndm$indx_train,
                                           savePredictions = "final"))
ffsmodel
global_validation(ffsmodel)
ffsmodel$selectedvars

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
plot(ffsmodel)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
prediction_ffs <- predict(predictors_sp, ffsmodel, na.rm=TRUE)
plot(prediction_ffs)

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
### AOA for which the spatial CV error applies:
AOA <- aoa(predictors_sp,ffsmodel,LPD = TRUE, verbose=FALSE)

# tmap3
#tm_shape(prediction)+
#  tm_raster(title="Species \nrichness",style="cont")+
#  tm_shape(AOA$AOA)+
#  tm_raster(palette=c("1"=NA,"0"="grey"),style="cat",legend.show = FALSE)+
#  tm_layout(frame=FALSE,legend.outside = TRUE)+
#  tm_add_legend(type="fill",col="grey",border.lwd=0, labels="Outside \nAOA")

# tmap4
 tm_shape(prediction) +
   tm_raster(col.scale = tm_scale_continuous(values = "-viridis"),
             col.legend = tm_legend(title = "Species \nrichness")) +
   tm_shape(AOA$AOA) +
   tm_raster(col.scale = tm_scale_categorical(values = c("grey", "#00000000")),
             col.legend = tm_legend(show = FALSE)) +
   tm_layout(frame = FALSE) +
   tm_add_legend(type="polygons", fill = "grey", labels = "Outside \nAOA")

## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
plot(c(AOA$DI,AOA$LPD))

errormodel_DI <- errorProfiles(model_default,AOA,variable="DI")
errormodel_LPD <- errorProfiles(model_default,AOA,variable="LPD")

plot(errormodel_DI)
plot(errormodel_LPD)


## ----message = FALSE, warning=FALSE, eval = wc_exist--------------------------
expected_error_LPD = terra::predict(AOA$LPD, errormodel_LPD)
plot(expected_error_LPD)

