## Simone Antichi 18/05/2021 ##

## This is the script to obtain the results of the manuscript submitted to PeerJ Antichi et al 2022: Changes in whistle parameters of two common bottlenose dolphin ecotypes as a result of the physical presence of the research vessel
## Comparison parameters ##

dataset = Supplemental_Data_S2
coastal = subset(dataset, Ecotype == "Coastal")
oceanic = subset(dataset, Ecotype == "Oceanic")

# coastal ecotype ##

shapiro.test(coastal$`Duration (s)`)
shapiro.test(coastal$`Maximum frequency (kHz)`)
shapiro.test(coastal$`Minimum frequency (kHz)`)
shapiro.test(coastal$`Frequency range (kHz)`)
shapiro.test(coastal$`Starting frequency (kHz)`)
shapiro.test(coastal$`Ending frequency (kHz)`)
shapiro.test(coastal$`Peak frequency (kHz)`)

library(car)

leveneTest(coastal$`Duration (s)`, coastal$`Time interval`)
leveneTest(coastal$`Maximum frequency (kHz)`, coastal$`Time interval`)
leveneTest(coastal$`Minimum frequency (kHz)`, coastal$`Time interval`)
leveneTest(coastal$`Frequency range (kHz)`, coastal$`Time interval`)
leveneTest(coastal$`Starting frequency (kHz)`, coastal$`Time interval`)
leveneTest(coastal$`Ending frequency (kHz)`, coastal$`Time interval`)
leveneTest(coastal$`Peak frequency (kHz)`, coastal$`Time interval`)

## all the parameters are non normal distributed ##

wilcox.test(coastal$`Duration (s)` ~ coastal$`Time interval`)
wilcox.test(coastal$`Maximum frequency (kHz)` ~ coastal$`Time interval`)
wilcox.test(coastal$`Minimum frequency (kHz)` ~ coastal$`Time interval`)
wilcox.test(coastal$`Frequency range (kHz)` ~ coastal$`Time interval`)
wilcox.test(coastal$`Starting frequency (kHz)` ~ coastal$`Time interval`)
wilcox.test(coastal$`Ending frequency (kHz)` ~ coastal$`Time interval`)
wilcox.test(coastal$`Peak frequency (kHz)` ~ coastal$`Time interval`)

### oceanic ecotype ##

shapiro.test(oceanic$`Duration (s)`)
shapiro.test(oceanic$`Maximum frequency (kHz)`)
shapiro.test(oceanic$`Minimum frequency (kHz)`)
shapiro.test(oceanic$`Frequency range (kHz)`)
shapiro.test(oceanic$`Starting frequency (kHz)`)
shapiro.test(oceanic$`Ending frequency (kHz)`)
shapiro.test(oceanic$`Peak frequency (kHz)`)

library(car)

leveneTest(oceanic$`Duration (s)`, oceanic$`Time interval`)
leveneTest(oceanic$`Maximum frequency (kHz)`, oceanic$`Time interval`)
leveneTest(oceanic$`Minimum frequency (kHz)`, oceanic$`Time interval`)
leveneTest(oceanic$`Frequency range (kHz)`, oceanic$`Time interval`)
leveneTest(oceanic$`Starting frequency (kHz)`, oceanic$`Time interval`)
leveneTest(oceanic$`Ending frequency (kHz)`, oceanic$`Time interval`)
leveneTest(oceanic$`Peak frequency (kHz)`, oceanic$`Time interval`)

## maximum frequency and frequency range are normally distributed but the other parameters are non normally distributed ##

wilcox.test(oceanic$`Maximum frequency (kHz)` ~ oceanic$`Time interval`)
wilcox.test(oceanic$`Frequency range (kHz)` ~ oceanic$`Time interval`)
wilcox.test(oceanic$`Duration (s)` ~ oceanic$`Time interval`)
wilcox.test(oceanic$`Minimum frequency (kHz)` ~ oceanic$`Time interval`)
wilcox.test(oceanic$`Starting frequency (kHz)` ~ oceanic$`Time interval`)
wilcox.test(oceanic$`Ending frequency (kHz)` ~ oceanic$`Time interval`)
wilcox.test(oceanic$`Peak frequency (kHz)` ~ oceanic$`Time interval`)

boxplot(oceanic$`Minimum frequency (kHz)` ~ oceanic$`Time interval`, xlab = "", ylab = "", cex.axis=1.4, yaxt = "n", xaxt = "n", ylim = c(0,35))
axis(2, seq(5,40,10), cex.axis=1.6)
mtext("Minimum frequency (kHz)", side=2, line=2.8, cex=1.8)
mtext("First time interval", side=3, line=-18, at=1, cex=1.2)
mtext("Second time interval", side=3, line=-18, at=2, cex=1.2)
mtext("(n = 98)", side=3, line=-19, at=1, cex=1.2)
mtext("(n = 44)", side=3, line=-19, at=2, cex=1.2)


boxplot(oceanic$`Peak frequency (kHz)` ~ oceanic$`Time interval`, xlab = "", ylab = "", cex.axis=1.4, yaxt = "n",xaxt = "n", ylim = c(0,35))
axis(2, seq(5,40,10), cex.axis=1.6)
mtext("Peak frequency (kHz)", side=2, line=2.8, cex=1.8)
mtext("First time interval", side=3, line=-18, at=1, cex=1.2)
mtext("Second time interval", side=3, line=-18, at=2, cex=1.2)
mtext("(n = 98)", side=3, line=-19, at=1, cex=1.2)
mtext("(n = 44)", side=3, line=-19, at=2, cex=1.2)

boxplot(oceanic$`Maximum frequency (kHz)` ~ oceanic$`Time interval`, xlab = "", ylab = "", cex.axis=1.4, yaxt = "n", xaxt = "n", ylim = c(0,35))
axis(2, seq(5,40,10), cex.axis=1.6)
mtext("Maximum frequency (kHz)", side=2, line=2.8, cex=1.8)
mtext("First time interval", side=3, line=-18, at=1, cex=1.2)
mtext("Second time interval", side=3, line=-18, at=2, cex=1.2)
mtext("(n = 98)", side=3, line=-19, at=1, cex=1.2)
mtext("(n = 44)", side=3, line=-19, at=2, cex=1.2)


## rate and stereotyped proportion ##

dataset = Supplemental_Data_S3
coastal = subset(dataset, Ecotype == "Coastal")
oceanic = subset(dataset, Ecotype == "Oceanic")

shapiro.test(coastal$Proportion)
shapiro.test(coastal$Rate)

shapiro.test(oceanic$Proportion)
shapiro.test(coastal$Rate)

## all the parameters are non normally distributed ##

wilcox.test(coastal$Proportion ~ coastal$`Time interval`, exact = FALSE)
wilcox.test(coastal$Rate ~ coastal$`Time interval`, exact = FALSE)

wilcox.test(oceanic$Proportion ~ oceanic$`Time interval`, exact = FALSE)
wilcox.test(oceanic$Rate ~ oceanic$`Time interval`, exact = FALSE)

boxplot(oceanic$Rate ~ oceanic$`Time interval`, xlab = "", ylab = "",xaxt = "n", cex.axis=1.4)
mtext("Whistle rate", side=2, line=2.8, cex=1.8)
mtext("First time interval", side=3, line=-18, at=1, cex=1.2)
mtext("Second time interval", side=3, line=-18, at=2, cex=1.2)
mtext("(n = 127)", side=3, line=-19, at=1, cex=1.2)
mtext("(n = 56)", side=3, line=-19, at=2, cex=1.2)