Species data visualisation

Author

Florencia Grattarola

Published

September 20, 2024

R Libraries

library(patchwork)
library(sf)
library(tidyverse)

Basemaps

equalareaCRS <-  '+proj=laea +lon_0=-73.125 +lat_0=0 +datum=WGS84 +units=m +no_defs'

latam <- st_read('data/latam.gpkg', layer = 'latam', quiet = T)
countries <- st_read('data/latam.gpkg', layer = 'countries', quiet = T)

Data

Load the IUCN range, the PO grid-cells with counts and the PA blobs with presences and absences

hyagouaroundi_IUCN <- st_read('big_data/hyagouaroundi_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_hyagouaroundi_PA <- readRDS('data/species_POPA_data/data_hyagouaroundi_PA.rds')
data_hyagouaroundi_PO <- readRDS('data/species_POPA_data/data_hyagouaroundi_PO.rds')

lpardalis_IUCN <- st_read('big_data/lpardalis_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_lpardalis_PA <- readRDS('data/species_POPA_data/data_lpardalis_PA.rds')
data_lpardalis_PO <- readRDS('data/species_POPA_data/data_lpardalis_PO.rds')

lwiedii_IUCN <- st_read('big_data/lwiedii_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_lwiedii_PA <- readRDS('data/species_POPA_data/data_lwiedii_PA.rds')
data_lwiedii_PO <- readRDS('data/species_POPA_data/data_lwiedii_PO.rds')

nnasua_IUCN <- st_read('big_data/nnasua_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_nnasua_PA <- readRDS('data/species_POPA_data/data_nnasua_PA.rds')
data_nnasua_PO <- readRDS('data/species_POPA_data/data_nnasua_PO.rds')

cthous_IUCN <- st_read('big_data/cthous_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_cthous_PA <- readRDS('data/species_POPA_data/data_cthous_PA.rds')
data_cthous_PO <- readRDS('data/species_POPA_data/data_cthous_PO.rds')

cbrachyurus_IUCN <- st_read('big_data/cbrachyurus_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_cbrachyurus_PA <- readRDS('data/species_POPA_data/data_cbrachyurus_PA.rds')
data_cbrachyurus_PO <- readRDS('data/species_POPA_data/data_cbrachyurus_PO.rds')

ebarbara_IUCN <- st_read('big_data/ebarbara_IUCN.shp', quiet = T) %>% st_transform(crs=equalareaCRS)
data_ebarbara_PA <- readRDS('data/species_POPA_data/data_ebarbara_PA.rds')
data_ebarbara_PO <- readRDS('data/species_POPA_data/data_ebarbara_PO.rds')

pbrasiliensis_IUCN <- sf::st_read('big_data/pbrasiliensis_IUCN.shp', quiet = T) %>% sf::st_transform(crs=equalareaCRS)
data_pbrasiliensis_PA <- readRDS('data/species_POPA_data/data_pbrasiliensis_PA.rds')
data_pbrasiliensis_PO <- readRDS('data/species_POPA_data/data_pbrasiliensis_PO.rds')

Plots per species

Herpailurus yagouaroundi (jaguarundi)

Code

plot_hyagouaroundi_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=hyagouaroundi_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_hyagouaroundi_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Herpailurus yagouaroundi', subtitle='presence-absence', col='') +
  theme_bw() 

plot_hyagouaroundi_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=hyagouaroundi_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_hyagouaroundi_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  labs(title='Herpailurus yagouaroundi', subtitle='presence-only', col='') +
  theme_bw() 

plot_hyagouaroundi_PO | plot_hyagouaroundi_PA

Leopardus pardalis (ocelot)

Code

plot_lpardalis_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=lpardalis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_lpardalis_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Leopardus pardalis', subtitle='presence-absence', col='') +
  theme_bw() 

plot_lpardalis_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=lpardalis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_lpardalis_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  labs(title='Leopardus pardalis', subtitle='presence-only', col='') +
  theme_bw() 

plot_lpardalis_PO | plot_lpardalis_PA

Leopardus wiedii (margay)

Code

plot_lwiedii_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=lwiedii_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_lwiedii_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Leopardus wiedii', subtitle='presence-absence', col='') +
  theme_bw() 

plot_lwiedii_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=lwiedii_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_lwiedii_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  labs(title='Leopardus wiedii', subtitle='presence-only', col='') +
  theme_bw()

plot_lwiedii_PO | plot_lwiedii_PA

Nasua nasua (coati)

Code

plot_nnasua_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=nnasua_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_nnasua_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Nasua nasua', subtitle='presence-absence', col='') +
  theme_bw()

plot_nnasua_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=nnasua_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_nnasua_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  labs(title='Nasua nasua', subtitle='presence-only', col='') +
  theme_bw()

plot_nnasua_PO | plot_nnasua_PA

Cerdocyon thous (crab-eating fox)

Code

plot_cthous_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=cthous_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_cthous_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + # st_bbox(cthous_IUCN)
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Cerdocyon thous', subtitle='presence-absence', col='') +
  theme_bw() 

plot_cthous_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=cthous_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_cthous_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + # st_bbox(cthous_IUCN)
  labs(title='Cerdocyon thous', subtitle='presence-only', col='') +
  theme_bw() 

plot_cthous_PO | plot_cthous_PA

Chrysocyon brachyurus (maned wolf)

Code

plot_cbrachyurus_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=cbrachyurus_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_cbrachyurus_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Chrysocyon brachyurus', subtitle='presence-absence', col='') +
  theme_bw() 

plot_cbrachyurus_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=cbrachyurus_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_cbrachyurus_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  labs(title='Chrysocyon brachyurus', subtitle='presence-only', col='') +
  theme_bw() 

plot_cbrachyurus_PO | plot_cbrachyurus_PA

Eira barbara (tayra)

Code

plot_ebarbara_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=ebarbara_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_ebarbara_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Eira barbara', subtitle='presence-absence', col='') +
  theme_bw() 

plot_ebarbara_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=ebarbara_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_ebarbara_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) +
  labs(title='Eira barbara', subtitle='presence-only', col='') +
  theme_bw() 

plot_ebarbara_PO | plot_ebarbara_PA

Pteronura brasiliensis (giant otter)

Code

plot_pbrasiliensis_PA <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=pbrasiliensis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_pbrasiliensis_PA %>% st_buffer(20000), 
          aes(fill=factor(presence)), col=NA, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) +
  scale_fill_manual(values = c("#434445","#4dac26"))+
  scale_color_manual(values = c("#434445","#4dac26")) +
  labs(title='Pteronura brasiliensis', subtitle='presence-absence', col='') +
  theme_bw() 

plot_pbrasiliensis_PO <- ggplot() + 
  geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
  geom_sf(data=pbrasiliensis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
  geom_sf(data=data_pbrasiliensis_PO, col="#d01c8b", size=0.5, show.legend = F) +
  coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + 
  labs(title='Pteronura brasiliensis', subtitle='presence-only', col='') +
  theme_bw() 

plot_pbrasiliensis_PO | plot_pbrasiliensis_PA

Save plots

Code

PO_plot <- (plot_hyagouaroundi_PO | plot_lpardalis_PO | plot_lwiedii_PO  | plot_nnasua_PO ) /
  (plot_cthous_PO | plot_cbrachyurus_PO | plot_ebarbara_PO | plot_pbrasiliensis_PO)

ggsave(PO_plot, filename='docs/figs/PO_plot.svg', device = 'svg', width=18, height=10, dpi=300)

PA_plot <- (plot_hyagouaroundi_PA | plot_lpardalis_PA | plot_lwiedii_PA  | plot_nnasua_PA ) /
  (plot_cthous_PA | plot_cbrachyurus_PA | plot_ebarbara_PA | plot_pbrasiliensis_PA)

ggsave(PA_plot, filename='docs/figs/PA_plot.svg', device = 'svg', width=18, height=10, dpi=300)