rm(list=ls()) # clears memory 
# setwd("[Insert File Path Here]")
# set working directory
dat<-read.csv("2b_BehavData_GoatCrossModalRecognHumans.csv",header=T,stringsAsFactors = F)
# load data file
head(dat, 10)# view the first 10 observations


## To install and load relevant packages
# install.packages("glmmTMB", dep=T)
library(glmmTMB)


## Setting factors and checking their levels
dat$goat.id <- as.factor(dat$goat.id)
levels(dat$goat.id)

dat$goat.sex <- as.factor(dat$goat.sex)
levels(dat$goat.sex)

dat$trial <- ordered(dat$trial)
levels(dat$trial)

dat$year <- as.factor(dat$year)
levels(dat$year)

dat$congruency <- as.factor(dat$congruency)
levels(dat$congruency)

dat$human.gender <- as.factor(dat$human.gender)
levels(dat$human.gender)

dat$photo <- as.factor(dat$photo)
levels(dat$photo)

dat$responsi.photo <- as.factor(dat$responsi.photo)
levels(dat$responsi.photo)

dat$voice <- as.factor(dat$voice)
levels(dat$voice)

dat$responsi.voice <- as.factor(dat$responsi.voice)
levels(dat$responsi.voice)

dat$pb.no <- as.factor(dat$pb.no)
levels(dat$pb.no)

str(dat) # to check factors have been coded appropriately


#############################################################################################
### GENERAL EXCLUSIONS

## Excluding instances where goats are already looking before onset of playbacks
dat2 <- subset(dat, lat!=0)

## Excluding goats which did not look for at least one congruent and one incongruent 
## trial
dat3 <- subset(dat2, goat.id!= "Glenda")


#############################################################################################
### LATENCY ANALYSIS

## Excluding instances where goats did not respond following playbacks
dat4 <-subset(dat3, lat!=10) 

## Excluding goats which did not look for at least one congruent and one incongruent 
## trial

dat5<-subset(dat4, goat.id!="Davey" & goat.id!="Natalie")

## Full model
lat.m1<-glmmTMB(lat ~ congruency + pb.no + year + goat.sex + human.gender + responsi.photo +
                  responsi.voice + (1|goat.id/trial) + (1|voice), data=dat5,
                  family=lognormal(link="log"))

summary(lat.m1)

## Basic model
basic_lat.m1<-glmmTMB(lat ~ congruency + pb.no + (1|goat.id/trial), data=dat5,
                      family=lognormal(link="log"))

summary(basic_lat.m1)


#############################################################################################
### DURATION ANALYSIS

## Full model
dur.m1 <- glmmTMB(dur ~ congruency + pb.no + year + goat.sex + human.gender + 
                responsi.photo + responsi.voice + (1|goat.id/trial) + (1|voice), data=dat3,
                family=tweedie)

summary(dur.m1)

## Basic model
basic_dur.m1 <- glmmTMB(dur ~ congruency + pb.no + (1|goat.id/trial), data=dat3,
                        family=tweedie)

summary(basic_dur.m1)


#############################################################################################