Species Richness

library(bowen.biodiversity.webapp)
library(here)

here() starts at /home/jay/Programming_Projects/bowen.biodiversity.webapp

library(terra)

terra 1.8.5

library(magrittr)

Attaching package: 'magrittr'

The following objects are masked from 'package:terra':

    extract, inset

library(stringr)

# Created using vignettes/zonation.Rmd
# Contains all SDM layers included in Zonation output 
load(here("inst/extdata/bowen_sdm_status.rda"))
# Create relative path to read in each SDM
bowen_sdm_status$relpath <- paste0("inst/extdata/sdm/", bowen_sdm_status$filepath)
# Create all species raster stack 
sdm_stack <- lapply(bowen_sdm_status$relpath, function(x) {here(x) %>% rast()}) %>% rast()
# Create species richness SDM 
presence_threshold <- 0.7
total_richness_0.7 <- sdm_to_species_richness(SDM_stack = sdm_stack,
                                          presence_threshold = presence_threshold)
writeRaster(total_richness_0.7, here("inst/extdata/bowen_sdm_richness.tif"), overwrite = T)

# Create species richness plots: 
## Each species is marked present in a cell, if they are above a certain 
## threshold of probability in the input SDMs. 
subtitle <- paste0("Based on >", 
                   presence_threshold,
                   " probability of occurrence in Species Distribution Models.")
caption <- paste0("Map created: ", date(), ". Palen Lab. Created by Jay Matsushiba (jmatsush@sfu.ca)")

title <- "Total Species Richness"
total_richness_0.7_plot <- bowen_map(raster_layer = total_richness_0.7,
                      title = title,
                      subtitle = subtitle,
                      caption = caption,
                      legend_label = "Richness")

Warning: Transforming 'ext' to Web Mercator (EPSG: 3857), since 'ext' has a
different CRS. The CRS of the returned basemap will be Web Mercator, which is
the default CRS used by the supported tile services.

Loading basemap 'backdrop' from map service 'maptiler'...

<SpatRaster> resampled to 501081 cells.

# ggplot2::ggsave(
#   here("vignettes", "figures", paste0(Sys.Date(), "_total_richness_0.7.png")),
#   total_richness_0.7_plot,
#   device = ragg::agg_png,
#   width = 9, height = 12, units = "in", res = 300
# )
total_richness_0.7_plot

Figure 1