library(overlap)
library(activity)
library(ggplot2) 
library(CircMLE) 

setwd("C:/Users/Oscar/Documents/Maremani")

#Read in CT data from waterholes
water <- read.csv2("water.csv")
#Read in CT data from roads and trails
away <- read.csv2("fusion_data.csv")

#Convert time to radians for water dataset 
water$Time2=as.numeric(water$Time2)
timeRadwater <- water$Time2 * 2 * pi

#read in CT data for leopards at waterhole
wleopard <- timeRadwater[water$Species == 'pardus']
#plot activity pattern for leopard at waterhole - use adjust = 1 for species with more than 75 records (Dhat4)
densityPlot(wleopard, rug=TRUE, main="Leopard", adjust = 1)

#read in CT data for spotted at waterhole
wspotted <- timeRadwater[water$Species == 'crocuta']
densityPlot(wspotted, rug=TRUE, main="Spotted hyena", adjust = 1)

#read in CT data for wild dog at waterhole
wdog <- timeRadwater[water$Species == 'pictus']
#use adjust=0.8 for species with less than 75 records (Dhat1)
densityPlot(wdog, rug=TRUE, adjust = 0.8, main="African wild dog")

#convert time to radians for away from water dataset
away$Time.delta=as.numeric(away$Time.delta)
timeRadaway <- away$Time.delta * 2 * pi

leopard <- timeRadaway[away$Species == 'pardus']
densityPlot(leopard, rug=TRUE, main="Leopard", adjust = 1)

spotted <- timeRadaway[away$Species == 'crocuta']
densityPlot(spotted, rug=TRUE, main="Spotted hyena", adjust = 1)

brown <- timeRadaway[away$Species == 'brunnea']
densityPlot(brown, rug=TRUE, main="Brown hyena", adjust = 1)

dog <- timeRadaway[away$Species == 'pictus']
densityPlot(dog, rug=TRUE, main="African wild dog", adjust = 0.8)

############################################################################
#HR_test to assess if a random activity pattern is exhibited over a circadian cycle 
HR_test(wdog, original = F, iter = 9999)
HR_test(wleopard, original = F, iter = 9999)
HR_test(wspotted, original = F, iter = 9999)
HR_test(dog, original = F, iter = 9999)
HR_test(leopard, original = F, iter = 9999)
HR_test(spotted, original = F, iter = 9999)
HR_test(brown, original = F, iter = 9999)

###############################################################################
#Overlap analysis between same species at and away from artificial waterhole
###############################################################################

est <- overlapEst(wdog, dog, type="Dhat1")
est
overlapPlot(wdog,dog,rug=TRUE, main="African wild dog")
legend('topright', c("artificial waterhole (n = 43)", "away from artificial waterhole (n = 31)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.7)
text(x=15, y=0.11, labels="Δ = 0.70 (0.49 - 0.80), P = 0.003", col="black",cex=0.8)
dogboot <- bootstrap(wdog, dog, 10000, type="Dhat1")
#Gives you upper and lower confidence levels - use basic0
bootCI(est, dogboot)
# Use sample = "model" for smaller samples (under 100) and use "data" for the bigger samples
# in fitact use adj = 1.25 for Dhat1 and adj=1 for Dhat4
wdogfit <- fitact(wdog, wt=NULL, reps = 10000, adj = 1.25, sample = "model")
dogfit <- fitact(dog, wt=NULL, reps=10000, adj=1.25, sample = "model")
compareCkern(wdogfit, dogfit)
compareAct(list(wdogfit,dogfit))

###############################################################################
est2 <- overlapEst(wleopard, leopard, type="Dhat4")
est2
overlapPlot(wleopard,leopard, rug=TRUE,main="Leopard")
legend('topright', c("artificial waterhole (n = 1382)", "away from artificial waterhole (n = 232)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.7)
text(x=12, y=0.06, labels="Δ = 0.87 (0.82 - 0.90), P = 0.2", col="black",cex=0.8)
leopardboot <- bootstrap(wleopard, leopard, 10000, type="Dhat4")
bootCI(est2, leopardboot)
wleopardfit <- fitact(wleopard,wt=NULL, reps=10000, adj=1, sample="data")
leopardfit <- fitact(leopard, wt=NULL, reps=10000, adj=1, sample="data")
compareCkern(wleopardfit, leopardfit)
compareAct(list(wleopardfit, leopardfit))
###############################################################################
est3 <- overlapEst(wspotted, spotted, type="Dhat4")
est3
overlapPlot(wspotted,spotted,rug=TRUE, main="Spotted hyena")
legend('topright', c("artificial waterhole (n = 1229)", "away from artificial waterhole (n = 115)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.7)
text(x=13, y=0.06, labels="Δ = 0.85 (0.79 - 0.90), P = 0.8", col="black",cex=0.8)
spottedboot <- bootstrap(wspotted, spotted, 10000, type="Dhat4")
bootCI(est3, spottedboot)
wspottedfit <- fitact(wspotted,wt=NULL, reps=10000, adj=1, sample="data")
spottedfit <- fitact(spotted, wt=NULL, reps=10000, adj=1, sample="data")
compareCkern(wspottedfit, spottedfit)
compareAct(list(wspottedfit, spottedfit))
###############################################################################
#Overlap analysis away from artificial wateherholes
###############################################################################
est5 <- overlapEst(spotted,brown, type="Dhat4")
est5
overlapPlot(spotted,brown, rug=TRUE,main="Away from artificial waterholes")
legend('topright', c("Spotted hyena (n = 115)", "Brown hyena (n = 361)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=12, y=0.06, labels="Δ = 0.88 (0.83 - 0.96), P = 0.06", col="black",cex=0.8)
boot5 <- bootstrap(spotted,brown,10000,type="Dhat4")
bootCI(est5,boot5)
brownfit <- fitact(brown, wt=NULL, reps=10000, adj=1, sample="data")
compareCkern(spottedfit, brownfit)
compareAct(list(spottedfit, brownfit))
###############################################################################
est6 <- overlapEst(spotted, dog, type="Dhat1")
est6 
overlapPlot(spotted, dog,rug=TRUE, main="Away from artificial waterholes")
legend('topright', c("Spotted hyena (n = 115)", "African wild dog (n = 43)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=15, y=0.12, labels="Δ = 0.56 (0.38 - 0.65), P = 0.0002", col="black",cex=0.8)
boot6 <- bootstrap(spotted,dog,10000,type="Dhat1")
bootCI(est6,boot6)
compareCkern(spottedfit, dogfit)
compareAct(list(spottedfit,dogfit))
############################################################################## 
est7 <- overlapEst(brown, dog, type="Dhat1")
est7 
overlapPlot(brown, dog,rug=TRUE,main="Away from artificial waterholes")
legend('topright', c("Brown hyena (n = 361)", "African wild dog (n = 43)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=15, y=0.12, labels="Δ = 0.51 (0.34 - 0.60), P = 0.008", col="black",cex=0.8)
boot7 <- bootstrap(brown,dog,10000,type="Dhat1")
bootCI(est7,boot7)
compareCkern(brownfit, dogfit)
compareAct(list(brownfit,dogfit))
#############################################################################
est8 <- overlapEst(leopard,brown, type="Dhat4")
est8
overlapPlot(leopard,brown,rug=TRUE, main="Away from artificial waterholes")
legend('topright', c("Leopard (n = 232)", "Brown hyena (n = 361)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=12, y=0.07, labels="Δ = 0.82 (0.76 - 0.87), P = 0.1", col="black",cex=0.8)
boot8 <- bootstrap(leopard,brown,10000,type="Dhat4")
bootCI(est8,boot8)
compareCkern(leopardfit, brownfit)
compareAct(list(leopardfit, brownfit))
###############################################################################
est9 <- overlapEst(leopard,spotted, type="Dhat4")
est9
overlapPlot(leopard,spotted, rug=TRUE,main="Away from artificial waterholes")
legend('topright', c("Leopard (n = 232)", "Spotted hyena (n = 115)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=12.5, y=0.06, labels="Δ = 0.87 (0.82 - 0.95), P = 0.77", col="black",cex=0.8)
boot9 <- bootstrap(leopard,spotted,10000,type="Dhat4")
bootCI(est9,boot9)
compareCkern(leopardfit, spottedfit)
compareAct(list(leopardfit, spottedfit))
###############################################################################
est10 <- overlapEst(leopard, dog, type="Dhat1")
est10 
overlapPlot(leopard, dog, rug=TRUE,main="Away from artificial waterholes")
legend('topright', c("Leopard (n = 232)", "African wild dog (n = 43)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=15, y=0.11, labels="Δ = 0.64 (0.47 - 0.74), P = 0.0008", col="black",cex=0.8)
boot10 <- bootstrap(leopard,dog,10000,type="Dhat1")
bootCI(est10,boot10)
compareCkern(leopardfit, dogfit)
compareAct(list(leopardfit,dogfit))
##############################################################################
#Overlap analysis between species at artificial waterholes
###############################################################################
est11 <- overlapEst(wleopard, wdog, type="Dhat1")
est11 
overlapPlot(wleopard,wdog, rug=TRUE, main="At artificial waterholes")
legend('topright', c("Leopard (n = 1382)", "African wild dog (n = 31)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=11.7, y=0.05, labels="Δ = 0.66 (0.54 - 0.81), P = 0.9", col="black",cex=0.8)
boot11 <- bootstrap(wleopard,wdog,10000,type="Dhat1")
bootCI(est11,boot11)
compareCkern(wleopardfit, wdogfit)
compareAct(list(wleopardfit,wdogfit))
##############################################################################
est12 <- overlapEst(wspotted,wleopard, type="Dhat4")
est12
overlapPlot(wspotted,wleopard, rug=TRUE, main="At artificial waterholes")
legend('topright', c("Spotted hyena (n = 1229)", "Leopard (n = 1382)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=12.5, y=0.06, labels="Δ = 0.85 (0.82 - 0.89), P = 0.1", col="black",cex=0.8)
boot12 <- bootstrap(wspotted,wleopard,10000,type="Dhat4")
bootCI(est12,boot12)
compareCkern(wspottedfit, wleopardfit)
compareAct(list(wspottedfit, wleopardfit))
###############################################################################
est4 <- overlapEst(wspotted,wdog, type="Dhat1")
est4
overlapPlot(wspotted,wdog,main="At artificial waterholes", rug=TRUE)
legend('topright', c("Spotted hyena (n = 1229)", "African wild dog (n = 43)"), lty=c(1,2), col=c(1,4), bty='n', cex=0.8)
text(x=12.5, y=0.08, labels="Δ = 0.63 (0.48 - 0.76), P = 0.5", col="black",cex=0.8)
boot4 <- bootstrap(wspotted,wdog, 10000, type = "Dhat1")
bootCI(est4, boot4)
compareCkern(wspottedfit, wdogfit)
compareAct(list(wspottedfit,wdogfit))