• Introduction
  • Packages
  • Wallacea Region data
  • Map of Wallacea
    • K = 2
    • K = 10
  • Thailand lowlands
    • Extracting enriched birds
    • Patterns of presence absence of these birds

Introduction

In this script, we investigate the birds in the lowlands of Thailand.

Packages

library(methClust)
library(CountClust)
library(rasterVis)
library(gtools)
library(sp)
library(rgdal)
library(ggplot2)
library(maps)
library(mapdata)
library(mapplots)
library(scales)
library(ggthemes)

Wallacea Region data

datalist <- get(load("../data/wallace_region_pres_ab_breeding_with_seabirds.rda"))
latlong <- datalist$loc
data <- datalist$dat
if(nrow(latlong) != nrow(data)) stop("dimensions matching error")

Map of Wallacea

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

world_map <- world_map[world_map$long > 90 & world_map$long < 160, ]
world_map <- world_map[world_map$lat > -18 & world_map$lat < 20, ]


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

#Add map to base plot
base_world_messy <- p + geom_polygon(data=world_map, aes(x=long, y=lat, group=group), colour="light green", fill="light green")

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

base_world

K = 2

geostructure2

geostructure2

K = 10

geostructure2

geostructure2

Thailand lowlands

topics_clust <- get(load("../output/methClust_wallacea_w_seabirds.rda"))

Extracting enriched birds

topics <- topics_clust[[10]]
freq <- topics$freq
which_comp <- apply(freq, 1, function(x) return(which.max(x)))
freq2 <- freq[which(which_comp==1),]
idx <- order(freq2[,1])
bird_in_10_names <- rownames(freq2)[idx]
head(bird_in_10_names)
## [1] "Lichmera monticola"       "Rhipidura dedemi"        
## [3] "Tephrozosterops stalkeri" "Tyto almae"              
## [5] "Ceyx websteri"            "Actenoides bougainvillei"

Patterns of presence absence of these birds

PlotAssemblageIdx <- function(name){
  dat <- cbind.data.frame(latlong, data[,name])
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
}
ids <- c()
for(m in 1:50){
  tmp <- data[,as.character(bird_in_10_names[m])]
  ll <- length(which(tmp == 1))
  if(ll > 2) ids <- c(ids, m)
}
ids
##  [1] 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
## [24] 44 45 46 47 48 49 50
as.character(bird_in_10_names[ids[1]])
## [1] "Basilornis corythaix"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[1]]))

as.character(bird_in_10_names[ids[2]])
## [1] "Lorius domicella"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[2]]))

as.character(bird_in_10_names[ids[3]])
## [1] "Myzomela blasii"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[3]]))

as.character(bird_in_10_names[ids[4]])
## [1] "Oriolus forsteni"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[4]]))

as.character(bird_in_10_names[ids[5]])
## [1] "Zosterops stalkeri"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[5]]))

as.character(bird_in_10_names[ids[6]])
## [1] "Petroica multicolor"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[6]]))

as.character(bird_in_10_names[ids[7]])
## [1] "Hypotaenidia immaculata"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[7]]))

as.character(bird_in_10_names[ids[8]])
## [1] "Gygis alba"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[8]]))

as.character(bird_in_10_names[ids[9]])
## [1] "Pterodroma solandri"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[9]]))

as.character(bird_in_10_names[ids[10]])
## [1] "Aerodramus orientalis"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[10]]))

as.character(bird_in_10_names[ids[11]])
## [1] "Nesasio solomonensis"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[11]]))

as.character(bird_in_10_names[ids[12]])
## [1] "Pitta anerythra"
PlotAssemblageIdx(as.character(bird_in_10_names[ids[12]]))

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