Target taxa in the ACT region

knitr::opts_chunk$set(cache = TRUE, dev = c("png", "pdf"))
library(eucs)
library(leaflet)
library(sp)

source("euctraits_targets.R")

taxa_available_region <- function(occupancy, bb) {
  ans <- subset(
    occupancy,
    longitude_gda94 > bb[[1]] & latitude_gda94 > bb[[2]] &
    longitude_gda94 < bb[[3]] & latitude_gda94 < bb[[4]]
  )
  ans <- do.call(rbind, ans$occupancy)
  data.frame(taxon = names(which(colMeans(ans) > 0)))
}

map_taxa <- function(occupancy, taxon, bb) {
  occupancy <- occupancy[
    occupancy$occupancy &
    occupancy$taxon %in% taxon &
    occupancy$longitude_gda94 > bb[[1]] &
    occupancy$latitude_gda94  > bb[[2]] &
    occupancy$longitude_gda94 < bb[[3]] &
    occupancy$latitude_gda94  < bb[[4]],
    c("longitude_gda94", "latitude_gda94", "taxon", "occupancy")
  ]
  occupancy$color <- factor(occupancy$taxon)
  occupancy$color <- rainbow(nlevels(occupancy$color))[occupancy$color]
  m <- leaflet(occupancy)
  m <- addTiles(m)
  addCircleMarkers(
    m,
    lat   = ~jitter(latitude_gda94, amount = .001),
    lng   = ~jitter(longitude_gda94, amount = .001),
    label = ~taxon,
    color = ~color
  )
}

ACT region

act_bb <- list(147.372239, -36.915181, 150.827778, -34.528067)
plot(map_southeast)
do.call(rect, c(act_bb, lty = 3))

Taxa in the ACT region

(taxa_available_act <-
  taxa_available_region(occupancy_southeast, act_bb))

map_taxa(
  long_southeast,
  which_match(
    taxa_available_act$taxon,
    subset(taxa_sampled, trees > 5)$taxon,
    invert = TRUE
  ),
  act_bb
)