data-raw/figure4.R

In smwoodman/eSDM: Ensemble Tool for Predictions from Species Distribution Models

# Code for creating Figure 4 for eSDM manuscript

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library(RColorBrewer)
library(sf)
library(tmap)


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# Helper functions and values

### Base map
load("data/gshhg.l.L16.rda")
map.world <- gshhg.l.L16

### Plot extent
range.poly <- st_sfc(
  st_polygon(list(matrix(
    c(-132, -132, -116, -116, -132, 29.5, 49, 49, 29.5, 29.5), ncol = 2
  ))),
  crs = 4326
)
rpoly.mat <- matrix(st_bbox(range.poly), ncol = 2)

### Size of text and legend width
main.size <- 1.4
leg.size  <- 1
leg.width <- 1
grid.size <- 1
txt.size  <- 1.2

### Plotting functions
source("data-raw/figure_plot.R", local = TRUE, echo = FALSE)


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# Create and save figure

### Load unweighted ensemble and prep plots
# rda file created in data-raw/create_ens_sf.R
load("data-raw/ens_sf_unw.rda")

blp1 <- tmap_sdm_help(ens.sf.unw, "Pred_ens")
blp2 <- tmap_sdm_help(ens.sf.unw, "CV_ens")

# Plot of predictions (whales / km^-2)
tmap.obj1 <- tmap_sdm(
  ens.sf.unw, "Pred_ens", blp1, map.world, rpoly.mat, NA,
  main.size, leg.size, leg.width, grid.size
) +
  tm_credits(expression("Predictions\n(whales km"^-2*")"),
             fontfamily = "sans", size = txt.size,
             position = c("left", "bottom"))

# Plot of SE values (with same color scheme as predictions)
tmap.obj2 <- tmap_sdm(
  ens.sf.unw, "SE_ens", blp1, map.world, rpoly.mat, NA,
  main.size, leg.size, leg.width, grid.size
) +
  tm_credits(expression("SE of\npredictions\n(whales km"^-2*")"),
             fontfamily = "sans", size = txt.size,
             position = c("left", "bottom"))

# Plot of CV values
tmap.obj3 <- tmap_sdm(
  ens.sf.unw, "CV_ens", blp2, map.world, rpoly.mat, NA,
  main.size, leg.size, leg.width, grid.size
) +
  tm_credits(expression("CV of\npredictions\n(whales km"^-2*")"),
             fontfamily = "sans", size = txt.size,
             position = c("left", "bottom"))


### Generate and save plot
png("../eSDM paper/Figures_working/Fig4.png", height = 6.9, width = 13,
    units = "in", res = 300)
tmap_arrange(
  list(tmap.obj1, tmap.obj2, tmap.obj3), ncol = 3, asp = NULL,
  outer.margins = 0.02
)
dev.off()

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