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]]))

This R Markdown site was created with workflowr