moves ch15 to tmap4

15-eco.Rmd

@@ -120,6 +120,29 @@ Visualizing the data helps to get more familiar with it, as shown in Figure \@re
 #   tm_layout(inner.margins = 0, legend.outside = TRUE)
 # tmap_save(tm, "figures/15_sa_mongon_sampling.png",
 #           width = 12, height = 7, units = "cm")
+
+# if (packageVersion("tmap") >= "4.0"){
+#   hs = terra::shade(terra::terrain(dem, v = "slope", unit = "radians"),
+#                   terra::terrain(dem, v = "aspect", unit = "radians"),
+#                   10, 200)
+#   library(tmap)
+#   tm = tm_shape(hs) +
+#     tm_grid(n.x = 3, n.y = 3) +
+#     tm_raster(col.scale = tm_scale_continuous(values = rev(hcl.colors(99, "Grays"))),
+#               col.legend = tm_legend_hide()) +
+#     tm_shape(dem) +
+#     tm_raster(col_alpha = 0.5, 
+#               col.scale = tm_scale_continuous(n = 11, values = terrain.colors(50)),
+#               col.legend = tm_legend(title = "m asl", reverse = TRUE)) +
+#     tm_shape(study_area) +
+#     tm_borders() +
+#     tm_shape(random_points) +
+#     tm_symbols(col = "black", size = 0.2) +
+#     tm_layout(legend.position = tm_pos_auto_out())
+#   tmap_save(tm, "figures/15_sa_mongon_sampling.png",
+#             width = 12, height = 7, units = "cm")
+# }
+
 knitr::include_graphics("figures/15_sa_mongon_sampling.png")
 ```
 
@@ -556,6 +579,7 @@ pred = terra::predict(ep, model = autotuner_rf, fun = predict)
 #   terra::mask(terra::vect(study_area))
 # pred = terra::mask(pred, terra::vect(study_area)) |>
 #   terra::trim()
+# 
 # library(tmap)
 # pal = rev(hcl.colors(n = 15, "RdYlBu"))
 # tm = tm_shape(hs) +
@@ -570,6 +594,24 @@ pred = terra::predict(ep, model = autotuner_rf, fun = predict)
 #   tm_layout(inner.margins = 0.02, legend.outside = TRUE)
 # tmap_save(tm, "figures/15_rf_pred.png",
 #           width = 12, height = 7, units = "cm")
+
+# if (packageVersion("tmap") >= "4.0"){
+#   library(tmap)
+#   pal = rev(hcl.colors(n = 15, "RdYlBu"))
+#   tm = tm_shape(hs) +
+#     tm_grid(n.x = 3, n.y = 3, lines = FALSE) +
+#     tm_raster(col.scale = tm_scale_continuous(values = rev(hcl.colors(99, "Grays"))),
+#               col.legend = tm_legend_hide()) +
+#     tm_shape(pred, is.main = TRUE) +
+#     tm_raster(col.scale = tm_scale_continuous(values = pal, midpoint = NA),
+#               col.legend = tm_legend(title = "NMDS1", reverse = TRUE),
+#               col_alpha = 0.8) +
+#     tm_shape(study_area) +
+#     tm_borders() +
+#     tm_layout(legend.position = tm_pos_auto_out())
+#   tmap_save(tm, "figures/15_rf_pred.png",
+#             width = 12, height = 7, units = "cm")
+# }
 knitr::include_graphics("figures/15_rf_pred.png")
 ```