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

# 1. Scripts to analyze the Supplemental file 1. Human activity levels inside the territories on weekends and weekdays

#  2. Scripts to obtain Figure 2

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


#####
# 1. Human activity levels inside the territories on weekends and weekdays
#####

# Load data
d1<-read.xlsx("Dataset.xlsx",sheet=1)

# Pedestrians and cyclist

# GLMM
m1<-glmmTMB(Pedestrian.and.cyclists~  Type + (1|Territory), family = poisson(link = log), data = d1) # s

# Model fitting
model_parameters(m1,standardize = "refit")
m1<-glmmTMB(Pedestrian.and.cyclist~  Type + (1|Territory), family = poisson(link = log), data = d1)
r.squaredGLMM(mod1)

# Dogs and farm animals

# GLMM
m1<-glmmTMB(Dogs.and.farm.animals~  Type + (1|Territory), family = poisson(link = log), data = d1) # s

# Model fitting
model_parameters(m1,standardize = "refit")
m1<-glmmTMB(Dogs.and.farm.animals ~  Type + (1|Territory), family = poisson(link = log), data = d1)
r.squaredGLMM(mod1)

# Vehicles

# GLMM
m1<-glmmTMB(Vehicles~  Type + (1|Territory), family = poisson(link = log), data = d1) # s

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


#####
# 2. Figure 2
#####

# Load data
d1<-read.xlsx("Dataset.xlsx",sheet=1)

# Combine with box plot to add median and quartiles 
# Change color by groups 
# Figure 2a
a <- ggplot(d1, aes(x=Type, y=Pedestrian.and.cyclists, fill=Type)) + 
  geom_violin(trim=FALSE)+
  geom_boxplot(width=0.1, fill="white")+
  labs(title="Pedestrian and cyclists",x="Type", y = "Pedestrian and cyclists")

# Figure 2b
b <- ggplot(d1, aes(x=Type, y=Dogs.and.farm.animals, fill=Type)) + 
  geom_violin(trim=FALSE)+
  geom_boxplot(width=0.1, fill="white")+
  labs(title="Dogs and farm animals",x="Type", y = "Dogs and farm animals")

# Figure 2c
c <- ggplot(d1, aes(x=Type, y=Vehicles, fill=Type)) + 
  geom_violin(trim=FALSE)+
  geom_boxplot(width=0.1, fill="white")+
  labs(title="Vehicles",x="Type", y = "Vehicles")