IDLE_Input_List_Generation_Script_for_Spectrogram_and_Index_Calculation.R

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#        		    Code from Francomano et al. (IBIS 2023) 		    	   #


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# Input List Generation Script for Spectrogram and Index Calculation #
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# Created by:	Dante Francomano (dfrancomano@alumni.purdue.edu)

# Date: 20200131

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# Load package
library(openxlsx)

# Create empty list
inputLists<-sapply(1:7,function(x) list(as.data.frame(matrix(NA,nrow=3456,ncol=8))))

# List sites
siteList<-c("PM_01","PM_02","PPA_02","PPA_03","PPA_05","PPA_06","PPA_07")

# Assign sites, sensors, dates, times, hypothetical file paths, channels, and sensitivities
for(i in 1:7) 
  {
  colnames(inputLists[[i]])<-c("Site","Sensor","Date","Time","Hypothetical_Path_Stem","Hypothetical_Path","Channel","Sensitivity")
  inputLists[[i]]$Site<-siteList[i]
  overallPossibleDateTimes<-read.csv("E:/Dante/Penguins/Data_Coverage_Results/Isla_de_los_Estados_Overall.csv",colClasses=rep("factor",3))
  inputLists[[i]]$Date<-overallPossibleDateTimes[,1]
  inputLists[[i]]$Time<-overallPossibleDateTimes[,2]
  sensorList<-c("S4A00449","S4A00440","S4A03851","S4A00466","S4A03852","S4A00436","S4A00433")
  inputLists[[i]]$Sensor<-sensorList[i]
  inputLists[[i]]$Hypothetical_Path_Stem<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/",siteList[i],sep="")
  inputLists[[i]]$Hypothetical_Path<-apply(inputLists[[i]],1,function(x) paste(x[5],"/",paste(x[2:4],collapse="_"),".wav",sep=""))
  calibrationMeasurments<-read.xlsx("E:/Dante/Penguins/Calibration_Measurements.xlsx")
  relevantRows<-calibrationMeasurments[which(calibrationMeasurments$IDLE.Site==siteList[i]),]
  desiredRow<-which.min(abs(relevantRows$"Post-IDLE.Difference"))
  inputLists[[i]]$Channel<-ifelse(desiredRow==1,"left","right")
  inputLists[[i]]$Sensitivity<-rowMeans(relevantRows[desiredRow,6:7])

  # Write results
  write.csv(inputLists[[i]],paste("E:/Dante/Penguins/Input_Lists/IDLE_",siteList[i],".csv",sep=""))
}