Creating assemblage fields from cells by birds presence absences

library(ggplot2)
library(ggthemes)
library(maps)

Constructed Assemblage

new_assemblage <- get(load("../output/constructed_assemblage.rda"))

Original Assemblage

old_assemblage <- readRDS("../data/global_disp_field_matrix_breeding_birds_rds.rds")

Assemblage Map Function

We load the latitude and longitude data for each site for the newly constructed assemblage as well as the older assemblage.

latlong <- get(load("../data/LatLongCells_frame.rda"))

We write the plotting function.

world_map <- map_data("world")
world_map <- world_map[world_map$region != "Antarctica",] # intercourse antarctica

p <- ggplot() + coord_fixed() +
  xlab("") + ylab("")

#Add map to base plot
base_world_messy <- p + geom_map(data=world_map, map = world_map, aes(group=group, map_id=region), colour="white", fill="white", size=0.05, alpha=1/4) 

cleanup <- 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), 
        panel.background = element_rect(fill = 'white', colour = 'white'), 
        axis.line = element_line(colour = "white"), legend.position="none",
        axis.ticks=element_blank(), axis.text.x=element_blank(),
        axis.text.y=element_blank())

base_world <- base_world_messy + cleanup

PlotAssemblageIdx <- function(idx){
  dat <- cbind.data.frame(latlong, new_assemblage[,idx])
colnames(dat) <- c("Latitude", "Longitude", "Value")
map_data_coloured <- 
  base_world +
  geom_point(data=dat, 
             aes(x=Latitude, y=Longitude, colour=Value), size=0.5) +
  scale_colour_gradient(low = "white", high = "black") 

map_data_coloured
}

Example Plots of sites

par(mfrow = c(10, 2))
PlotAssemblageIdx(500)

PlotAssemblageIdx(1000)

PlotAssemblageIdx(1500)

PlotAssemblageIdx(2000)

PlotAssemblageIdx(3000)

PlotAssemblageIdx(4000)

PlotAssemblageIdx(5000)

PlotAssemblageIdx(7000)

PlotAssemblageIdx(8000)

PlotAssemblageIdx(9000)

PlotAssemblageIdx(10000)

PlotAssemblageIdx(11000)

PlotAssemblageIdx(12000)

PlotAssemblageIdx(13000)

PlotAssemblageIdx(14000)

PlotAssemblageIdx(15000)

PlotAssemblageIdx(15500)

PlotAssemblageIdx(16000)

PlotAssemblageIdx(16500)

PlotAssemblageIdx(17000)