# The behavior of Broad-tailed hummingbirds is altered by cycles of human activity in a forested area converted into agricultural land

# 3. Supplemental file 2. Testing the effect of weekly cycles of human disturbance on hummingbird territorial behavior

# 4. Figure 3

# Packages
library(glmmTMB)
library(parameters)
library(MuMIn)
library(ggplot2)


#####
# 3. Testing the effect of weekly cycles of human disturbance on hummingbird territorial behavior 
#####

# Load data
d1<-read.xlsx("Dataset.xlsx",sheet=2)

# Chases

# GLMM
m1<-glmmTMB(Chases~  Type + log(Territory.size) + log(Total.number.of.flowers) + (1|Territory), family = poisson(link = log), data = d1) # s

# Model fitting
model_parameters(m1,standardize = "refit")
m1<-glmmTMB(Chases~  Type + log(Territory.size) + log(Total.number.of.flowers) + (1|Territory), family = poisson(link = log), data = d1)
r.squaredGLMM(mod1)

# Flowers visited

# GLMM
m1<-glmmTMB(Flowers.visited~  Type + log(Territory.size) + log(Total.number.of.flowers) + (1|Territory), family = poisson(link = log), data = d1) # s

# Model fitting
model_parameters(m1,standardize = "refit")
m1<-glmmTMB(Flowers.visited~  Type + log(Territory.size) + log(Total.number.of.flowers) + (1|Territory), family = poisson(link = log), data = d1)
r.squaredGLMM(mod1)


# Successful intruders

# GLMM
m1<-glmmTMB(Successful.intruders ~  Type + log(Territory.size) + log(Total.number.of.flowers) + (1|Territory), family = poisson(link = log), data = d1) # s

# Model fitting
model_parameters(m1,standardize = "refit")
m1<-glmmTMB(Successful.intruders ~  Type + log(Territory.size) + log(Total.number.of.flowers) + (1|Territory), family = poisson(link = log), data = d1)
r.squaredGLMM(mod1)



#####
# 4. Figure 3
#####

# Load data
d1<-read.xlsx("Dataset.xlsx",sheet=2)

# Combine with box plot to add median and quartiles 
# Change color by groups 
# Figure 3a
a <- ggplot(d1, aes(x=Type, y=Chases, fill=Type)) + 
  geom_violin(trim=FALSE)+
  geom_boxplot(width=0.1, fill="white")+
  labs(title="Chases",x="Type", y = "Chases")

# Figure 3b
b <- ggplot(d1, aes(x=Type, y=Flowers.visited, fill=Type)) + 
  geom_violin(trim=FALSE)+
  geom_boxplot(width=0.1, fill="white")+
  labs(title="Flowers visited",x="Type", y = "Flowers visited")

# Figure 3c
c <- ggplot(d1, aes(x=Type, y=Successful.intruders, fill=Type)) + 
  geom_violin(trim=FALSE)+
  geom_boxplot(width=0.1, fill="white")+
  labs(title="Successful intruders",x="Type", y = "Successful intruders")