latlong <- get(load("../data/LatLongCells_frame.rda"))
world_map <- map_data("world")
world_map <- world_map[world_map$region != "Antarctica",] # intercourse antarctica
world_map <- world_map[world_map$long > 110 & world_map$long < 160, ]
world_map <- world_map[world_map$lat > -50 & world_map$lat < -10, ]
p <- ggplot() + coord_fixed() +
xlab("") + ylab("")
#Add map to base plot
base_world_messy <- p + geom_polygon(data=world_map, aes(x=long, y=lat, group=group), colour="light green", fill="light green")
cleanup <-
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_rect(fill = 'white', colour = 'white'),
axis.line = element_line(colour = "white"), legend.position="none",
axis.ticks=element_blank(), axis.text.x=element_blank(),
axis.text.y=element_blank())
base_world <- base_world_messy + cleanup
base_world
latlong <- get(load("../data/LatLongCells_frame.rda"))
idx1 <- which(latlong[,2] > -50 & latlong[,2] < -10)
idx2 <- which(latlong[,1] > 110 & latlong[,1] < 160)
idx <- intersect(idx1, idx2)
length(idx)
## [1] 791
latlong2 <- latlong[idx,]
birds_pa_data <- readRDS("../data/birds_presab_land_breeding_counts.rds")
birds_pa_data_2 <- birds_pa_data[idx, ]
birds_pa_data_3 <- birds_pa_data_2[, which(colSums(birds_pa_data_2)!=0)]
topics <- get(load("../output/Australia/methClust_6.rda"))
out <- CountClust::ExtractTopFeatures(topics$freq, top_features = 10, method = "poisson", options = "max")
PlotAssemblageIdx <- function(idx){
dat <- cbind.data.frame(latlong2, birds_pa_data_3[,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
}
par(mfrow = c(3,2))
PlotAssemblageIdx(out$indices[1,1])
PlotAssemblageIdx(out$indices[1,2])
PlotAssemblageIdx(out$indices[1,3])
PlotAssemblageIdx(out$indices[1,4])
PlotAssemblageIdx(out$indices[1,5])
PlotAssemblageIdx(out$indices[1,6])
par(mfrow = c(3,2))
PlotAssemblageIdx(out$indices[2,1])
PlotAssemblageIdx(out$indices[2,2])
PlotAssemblageIdx(out$indices[2,3])
PlotAssemblageIdx(out$indices[2,4])
PlotAssemblageIdx(out$indices[2,5])
PlotAssemblageIdx(out$indices[2,6])
par(mfrow = c(3,2))
PlotAssemblageIdx(out$indices[3,1])
PlotAssemblageIdx(out$indices[3,2])
PlotAssemblageIdx(out$indices[3,3])
PlotAssemblageIdx(out$indices[3,4])
PlotAssemblageIdx(out$indices[3,5])
PlotAssemblageIdx(out$indices[3,6])
par(mfrow = c(3,2))
PlotAssemblageIdx(out$indices[4,1])
PlotAssemblageIdx(out$indices[4,2])
PlotAssemblageIdx(out$indices[4,3])
PlotAssemblageIdx(out$indices[4,4])
PlotAssemblageIdx(out$indices[4,5])
PlotAssemblageIdx(out$indices[4,6])
par(mfrow = c(3,2))
PlotAssemblageIdx(out$indices[5,1])
PlotAssemblageIdx(out$indices[5,2])
PlotAssemblageIdx(out$indices[5,3])
PlotAssemblageIdx(out$indices[5,4])
PlotAssemblageIdx(out$indices[5,5])
PlotAssemblageIdx(out$indices[5,6])
par(mfrow = c(3,2))
PlotAssemblageIdx(out$indices[6,1])
PlotAssemblageIdx(out$indices[6,2])
PlotAssemblageIdx(out$indices[6,3])
PlotAssemblageIdx(out$indices[6,4])
PlotAssemblageIdx(out$indices[6,5])
PlotAssemblageIdx(out$indices[6,6])
rownames(topics$freq)[out$indices[1,1:10]]
## [1] "Cinclosoma cinnamomeum" "Eremiornis carteri"
## [3] "Geophaps ferruginea" "Geophaps plumifera"
## [5] "Stipiturus ruficeps" "Stiltia isabella"
## [7] "Phaps histrionica" "Cheramoeca leucosterna"
## [9] "Lichenostomus keartlandi" "Pardalotus rubricatus"
rownames(topics$freq)[out$indices[2,1:10]]
## [1] "Aphelocephala leucopsis" "Aphelocephala nigricincta"
## [3] "Neopsephotus bourkii" "Psephotellus varius"
## [5] "Acanthiza robustirostris" "Cinclosoma castanotum"
## [7] "Climacteris affinis" "Pyrrholaemus brunneus"
## [9] "Pomatostomus superciliosus" "Conopophila whitei"
rownames(topics$freq)[out$indices[3,1:10]]
## [1] "Acanthiza inornata" "Acanthorhynchus superciliosus"
## [3] "Manorina melanotis" "Pachycephala rufogularis"
## [5] "Phaethon rubricauda" "Polytelis anthopeplus"
## [7] "Zanda baudinii" "Ixobrychus dubius"
## [9] "Melithreptus brevirostris" "Malurus splendens"
rownames(topics$freq)[out$indices[4,1:10]]
## [1] "Calonectris leucomelas" "Caprimulgus macrurus"
## [3] "Certhionyx pectoralis" "Ceyx azureus"
## [5] "Chlamydera nuchalis" "Climacteris melanurus"
## [7] "Egretta picata" "Gerygone levigaster"
## [9] "Heteromunia pectoralis" "Melithreptus albogularis"
rownames(topics$freq)[out$indices[5,1:10]]
## [1] "Anthochaera chrysoptera" "Calyptorhynchus lathami"
## [3] "Chlamydera maculata" "Coracina lineata"
## [5] "Malurus cyaneus" "Manorina melanocephala"
## [7] "Podargus ocellatus" "Sericulus chrysocephalus"
## [9] "Zanda funerea" "Rhipidura rufifrons"
rownames(topics$freq)[out$indices[6,1:10]]
## [1] "Thalassarche salvini" "Puffinus assimilis"
## [3] "Daption capense" "Thalassarche cauta"
## [5] "Macronectes halli" "Puffinus huttoni"
## [7] "Thalassarche steadi" "Macronectes giganteus"
## [9] "Diomedea antipodensis" "Pterodroma macroptera"
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