##############################
#
#   Script for preparing Observation data from BORIS (Friard & Gamba, 2016) behavioural data
#   Need to have duration of behaviour per individual per observation
#     12/12/19
#
#
###############################

DIR <- # filepath to project directory
DATADIR <-  # filepath to data directory

if (!require("tidyr")) install.packages("tidyr")
library(tidyr)
if (!require("data.table")) install.packages("data.table")
library(data.table)
if (!require("chron")) install.packages("chron")
library(chron)

# Define function called 'DurationPerSession' that calculates the duration of each behaviour per observation period
DurationPerSession <- function(COLONY){
  
# define input from files named COLONY_1.tsv (behavioural data) and COLONY_Info.csv (individual data), where COLONY = colony name
ColonyBehaviour <- read.csv(file.path(DATADIR,paste(COLONY,"_1.tsv", sep="")), sep="\t") #dataframe containing raw behaviour data
Beh <- ColonyBehaviour
ColonyInformation <- read.table(file.path(DATADIR,paste(COLONY,"_Info.csv", sep="")), sep=",", header=T) #dataframe containing individual information
Ind <- ColonyInformation
names(Ind)[1] <- 'ObsID' # rename subject name variable

# remove Media file and FPS, Start and End times, split date into time and date, sort out modifiers 
Beh$Media.file <- NULL
Beh$FPS <- NULL
Beh$Start..s. <- NULL
Beh$Stop..s. <- NULL
Beh$Comment.start <- NULL
Beh$Comment.stop <- NULL
Beh$Behavior.type <- NULL
Beh$Behavioral.category <- NULL

# to split the date time and format as date and time
Beh <- separate(data=Beh, col=Observation.date, into= c("Date", "Time"), sep="\\ ")

# converts the original date from a character to a date. New format "%Y/%m/%d"
# exported files from BORIS can have different date formats:
# "%d/%m/%Y" or "%Y-%m-%d". This has to be changed manually, below, but should end up in format "%Y/%m/%d"
Beh$Date <- as.Date(Beh$Date, "%d/%m/%Y") 
if (is.na(Beh$Date)==T) {
  Beh <- ColonyBehaviour
  Beh <- separate(data=Beh, col=Observation.date, into= c("Date", "Time"), sep="\\ ")
  Beh$Date <- as.Date(Beh$Date, "%Y-%m-%d")
  Beh$Media.file <- NULL
  Beh$FPS <- NULL
  Beh$Start..s. <- NULL
  Beh$Stop..s. <- NULL
  Beh$Comment.start <- NULL
  Beh$Comment.stop <- NULL
  Beh$Behavior.type <- NULL
  Beh$Behavioral.category <- NULL
  }

# Separate and data from modifiers column in BORIS output into appropriate variables
Beh <- separate(data=Beh, col=Modifiers, into= c("Partner", "Role", "Activity_Before",  "Activity_After"), sep="\\|") # separate modifiers column 

row.ind<- which( Beh$Behavior=="Aggression") # outputs numbers of the rows in which Behaviour == Aggression
Beh2 <- Beh # make a copy
Beh2$Partner[row.ind] <- Beh$Role[row.ind] # switch Partner and Role data as they separate into the wrong columns
Beh2$Role[row.ind] <- Beh$Partner[row.ind]
Beh <- Beh2

row.ind2<- which( Beh$Behavior=="Tail-tugging") # outputs number of the rows in which Behaviour == Tail-tugging
Beh2 <- Beh # make a copy
Beh2$Partner[row.ind2] <- Beh$Role[row.ind2] # switch Partner and Role data as they separate into the wrong columns
Beh2$Role[row.ind2] <- Beh$Partner[row.ind2]
Beh <- Beh2

colnames(Beh) <- c("ObsSession","ObsDate","ObsTime", "ObsDuration_seconds","Subject","Behaviour",
                   "Partner","Role", "Activity_Before",  "Activity_After", "BehaviourDuration_seconds")

# To sum durations per individual per observation period
Durations <- subset(Beh, (!is.na(Beh$BehaviourDuration_seconds))) # to subset only behaviours that have a duration

DurationsSums <- aggregate(BehaviourDuration_seconds ~ Subject + ObsSession + ObsTime + ObsDate, data = Durations, FUN = 'sum') # to sum per individual per observation
colnames(DurationsSums) <- c("ObsID", "ObsSession", "ObsTime", "ObsDate", "BehaviourDuration_seconds")

# to merge DurationSums and Ind keeping only ObsID variable
setDT(DurationsSums)[setDT(Ind), TagNo := i.TagNo, on=c("ObsID")]

# Add colony to the data frame
DurationsSums$Colony <- COLONY
                           
# write results to Master data count file
write.table(DurationsSums, file.path(paste(DATADIR,"OUTPUT_NAME.txt", sep="")),
            sep="\t", append = T, row.names = FALSE, col.names=!file.exists(file.path(paste(DATADIR,"OUTPUT_NAME.txt", sep=""))), quote=F) # colnames true for first colony
}

# to make a list of colonies to loop the function through
ColonyList<- gsub("_.*","", (tools::file_path_sans_ext(list.files(path=DATADIR, pattern="_1.tsv", full.names = F))))

# Run function over list of colonies
for (C in ColonyList) {
  print(C)
  DurationPerSession(C)
}
# check warning errors generated by function
warnings()