# The following lines install dependencies for the plotly-based 3D plots. If you already have a working plotly/python/reticulate installation, these commands DO NOT need to be executed
# install.packages('reticulate')
# reticulate::install_miniconda()
# reticulate::use_miniconda('r-reticulate')
# reticulate::conda_install('r-reticulate', 'python-kaleido')
# reticulate::conda_install('r-reticulate', 'plotly')

# R package dependencies
pkgs <- c("blockCV", "sf", "sperrorest",
          "ggtext", "plotly", "ggplot2","patchwork",
          "mlr3", "mlr3spatiotempcv",  "mlr3learners",
          "terra", "reticulate")

install.packages(setdiff(pkgs, rownames(installed.packages())))

# dir.create("pdf")

set.seed(42)
library("mlr3")
library("mlr3spatiotempcv")
task <- tsk("ecuador")


## Figure 3 ----
rsmp_buffer <- rsmp("spcv_buffer", theRange = 1000)
rsmp_buffer

autoplot(rsmp_buffer,
         size = 0.8, task = task, fold_id = 1, show_omitted = TRUE) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 4 ----
library("mlr3")
library("mlr3spatiotempcv")
library("blockCV")
task <- tsk("ecuador")
rsmp_disc <- rsmp("spcv_disc", folds = 100, radius = 300L, buffer = 400L)
rsmp_disc

autoplot(rsmp_disc,
         size = 0.8, task = task, fold_id = 1, show_omitted = TRUE) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 5 ----
rsmp_coords <- rsmp("spcv_coords", folds = 5)

autoplot(rsmp_coords,
         size = 0.8, fold_id = 1, task = task) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


rsmp_coords <- rsmp("spcv_coords", folds = 5)

autoplot(rsmp_coords,
         size = 0.8, fold_id = 1, task = task) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))

## Figure 6 ----
rsmp_tiles <- rsmp("spcv_tiles", nsplit = c(3L, 4L))

autoplot(rsmp_tiles,
         size = 0.8, fold_id = 1, task = task) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 7 ----

breaks <- quantile(task$data()$dem, seq(0, 1, length = 6))
zclass <- cut(task$data()$dem, breaks, include.lowest = TRUE)

rsmp_custom <- rsmp("custom_cv")
rsmp_custom$instantiate(task, f = zclass)

autoplot(rsmp_custom, size = 0.8, task = task, fold_id = 1) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 8 ----
rsmp_block_random <- rsmp("spcv_block", range = 1000, folds = 5)

autoplot(rsmp_block_random,
         size = 0.8, fold_id = 1, task = task,
         show_blocks = TRUE, show_labels = TRUE, label_size = 4) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 9 ----
rsmp_block_systematic <- rsmp("spcv_block",
                              range = 1000, folds = 5,
                              selection = "systematic"
)

autoplot(rsmp_block_systematic,
         size = 0.8, fold_id = 1, task = task,
         show_blocks = TRUE, show_labels = TRUE, label_size = 4) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 15),
                 plot.title = ggtext::element_textbox(size = 12,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 10 ----
task_cv <- tsk("ecuador")
group <- as.factor(kmeans(task_cv$coordinates(), 8)$cluster)
task_cv$cbind(data.frame("group" = group))
task_cv$set_col_roles("group", roles = "group")

rsmp_cv_group <- rsmp("cv", folds = 3)$instantiate(task_cv)

autoplot(rsmp_cv_group, size = 0.8, task = task_cv, fold_id = 1) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(text = ggplot2::element_text(size = 16),
                 plot.title = ggtext::element_textbox(size = 13,
                                                      r = ggplot2::unit(7, "pt"),
                                                      height = ggplot2::unit(0.46, "inch"), linewidth = 0.8)) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 1.5)))


## Figure 11 ----
rsmp_env <- rsmp("spcv_env",
                 features = "distdeforest", folds = 5)

rsmp_env_multi <- rsmp("spcv_env",
                       features = c("distdeforest", "slope"), folds = 5)


plot_env_single <- autoplot(rsmp_env,
                            size = 0.3, fold_id = 1, task = task) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(plot.title = ggtext::element_textbox(size = 8,
                                                      r = ggplot2::unit(4, "pt"),
                                                      height = ggplot2::unit(0.30, "inch"), linewidth = 0.5),
                 axis.text = ggplot2::element_text(size = 8.5),
                 legend.title = ggtext::element_textbox(size = 10),
                 legend.text = ggtext::element_textbox(size = 8),
                 legend.key.size = ggplot2::unit(0.4, "cm")) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 0.8)))

plot_env_multi <- autoplot(rsmp_env_multi,
                           size = 0.3, fold_id = 1, task = task) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) +
  ggplot2::theme(plot.title = ggtext::element_textbox(size = 8,
                                                      r = ggplot2::unit(4, "pt"),
                                                      height = ggplot2::unit(0.30, "inch"), linewidth = 0.5),
                 axis.text = ggplot2::element_text(size = 8.5),
                 legend.title = ggtext::element_textbox(size = 10),
                 legend.text = ggtext::element_textbox(size = 8),
                 legend.key.size = ggplot2::unit(0.4, "cm")) +
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 0.8)))

library("patchwork")
plot_env_single + plot_env_multi + plot_layout(guides = "collect")

## Figure 12 ----
points <- sf::st_as_sf(task$coordinates(), crs = task$crs, 
                       coords = c("x", "y"))
modeldomain <- sf::st_as_sfc(sf::st_bbox(points))
rsmp_knndm <- rsmp("spcv_knndm", modeldomain = modeldomain, folds = 5)
autoplot(rsmp_knndm, size = 0.8, fold_id = 1, task = task,
         label_size = 4)

# Section 5 -----
data <- cookfarm_mlr3
set.seed(42)
data$Date <- sample(rep(c(
  "2020-01-01", "2020-02-01", "2020-03-01", "2020-04-01",
  "2020-05-01"), times = 1, each = 35768))
task_spt <- as_task_regr_st(data,
                            id = "cookfarm", target = "PHIHOX",
                            coordinate_names = c("x", "y"), coords_as_features = FALSE,
                            crs = 26911)
task_spt$set_col_roles("Date", roles = "time")

rsmp_cstf_time <- rsmp("sptcv_cstf", folds = 5)

p_lto <- autoplot(rsmp_cstf_time,
                  fold_id = 5, task = task_spt, plot3D = TRUE,
                  point_size = 6, axis_label_fontsize = 15,
                  sample_fold_n = 3000L
)

## Figure 13 ----
library("plotly")
p_lto_print <- plotly::layout(p_lto,
                              scene = list(camera = list(eye = list(z = 0.58))),
                              showlegend = FALSE, title = "",
                              margin = list(l = 0, b = 0, r = 0, t = 0))

p_lto_print

# plotly::save_image(p_lto_print, "lto.pdf",
#   scale = 2, width = 1100, height = 800)

## Figure 14 ----
task_spt$col_roles$time <- character()
task_spt$set_col_roles("SOURCEID", roles = "space")

rsmp_cstf_loc <- rsmp("sptcv_cstf", folds = 5)

p_llo <- autoplot(rsmp_cstf_loc,
                  fold_id = 5, task = task_spt,
                  point_size = 6, axis_label_fontsize = 15,
                  plot3D = TRUE, plot_time_var = "Date",
                  sample_fold_n = 3000L)

p_llo_print <-
  plotly::layout(p_llo,
                 scene = list(camera = list(eye = list(z = 2.5, x = -0.1, y = -0.1))),
                 showlegend = FALSE, title = "", polar = TRUE,
                 margin = list(l = 0, b = 0, r = 0, t = 0))

p_llo_print

# plotly::save_image(p_llo_print, "pdf/llo.pdf",
#   scale = 2, width = 1100, height = 800)

## Figure 15 ----
task_spt$set_col_roles("SOURCEID", roles = "space")
task_spt$set_col_roles("Date", roles = "time")

rsmp_cstf_time_loc <- rsmp("sptcv_cstf", folds = 5)

p_lto <- autoplot(rsmp_cstf_time_loc, point_size = 6,
                  axis_label_fontsize = 15,
                  fold_id = 4, task = task_spt, plot3D = TRUE,
                  show_omitted = TRUE, sample_fold_n = 3000L)

p_lto_print <- plotly::layout(p_lto,
                              scene = list(camera = list(eye = list(z = 0.58))),
                              showlegend = FALSE, title = "",
                              margin = list(l = 0, b = 0, r = 0, t = 0))

p_lto_print

# plotly::save_image(p_lto_print, "llto.pdf",
#                    scale = 2, width = 1100, height = 800)

library("mlr3")
library("mlr3spatiotempcv")

lgr::get_logger("bbotk")$set_threshold("warn")
lgr::get_logger("mlr3")$set_threshold("warn")

set.seed(42)

data("ecuador", package = "mlr3spatiotempcv")
task <- as_task_classif_st(ecuador, target = "slides", positive = "TRUE",
                           coordinate_names = c("x", "y"), coords_as_features = FALSE,
                           crs = "EPSG:32717")

library("mlr3learners")

learner <- lrn("classif.ranger", predict_type = "prob")

rsmp_nsp <- rsmp("repeated_cv", folds = 4, repeats = 2)
rsmp_nsp
rr_nsp <- resample(
  task = task, learner = learner,
  resampling = rsmp_nsp
)

rr_nsp$aggregate(measures = msr("classif.auc"))

rsmp_sp <- rsmp("repeated_spcv_coords", folds = 4, repeats = 2)
rsmp_sp
rr_sp <- resample(
  task = task, learner = learner,
  resampling = rsmp_sp
)

rr_sp$aggregate(measures = msr("classif.auc"))

## Figure 16 ----
autoplot(rsmp_sp, task, fold_id = 1:2, size = 0.3) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) *
  ggplot2::theme(plot.title = ggtext::element_textbox(size = 8,
                                                      r = ggplot2::unit(4, "pt"),
                                                      height = ggplot2::unit(0.30, "inch"), linewidth = 0.5),
                 axis.text = ggplot2::element_text(size = 8.5),
                 legend.title = ggtext::element_textbox(size = 10),
                 legend.text = ggtext::element_textbox(size = 8),
                 legend.key.size = ggplot2::unit(0.4, "cm")) *
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 0.8)))

## Figure 17 ----
autoplot(rsmp_nsp, task, fold_id = 1:2, size = 0.3) *
  ggplot2::scale_y_continuous(breaks = seq(-3.97, -4, -0.02)) *
  ggplot2::scale_x_continuous(breaks = seq(-79.06, -79.08, -0.02)) *
  ggplot2::theme(plot.title = ggtext::element_textbox(size = 8,
                                                      r = ggplot2::unit(4, "pt"),
                                                      height = ggplot2::unit(0.30, "inch"), linewidth = 0.5),
                 axis.text = ggplot2::element_text(size = 8.5),
                 legend.title = ggtext::element_textbox(size = 10),
                 legend.text = ggtext::element_textbox(size = 8),
                 legend.key.size = ggplot2::unit(0.4, "cm")) *
  ggplot2::guides(colour = ggplot2::guide_legend(override.aes = list(size = 0.8)))

sessionInfo()