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Francomano_et_al_2023_PAM_for_Penguins/IM_Input_List_Generation_Script_for_Spectrogram_and_Index_Calculation.R
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| ###################################################################### | |
| # Code from Francomano et al. (IBIS 2023) # | |
| ###################################################################### | |
| # Input List Generation Script for Spectrogram and Index Calculation # | |
| ###################################################################### | |
| # Created by: Dante Francomano (dfrancomano@alumni.purdue.edu) | |
| # Date: 20200131 | |
| ###################################################################### | |
| ###################################################################### | |
| # Load package | |
| library(openxlsx) | |
| # Create empty list | |
| inputLists<-sapply(1:7,function(x) list(as.data.frame(matrix(NA,nrow=51552,ncol=8)))) | |
| # List sites | |
| siteList<-c("019","Baliza","P53","Rata_Muerta","Zona_Erosionada","Zona_Nueva","Zona_Turistica") | |
| # Determine potential subfolders | |
| subpathOptions<-list() | |
| for(i in 1:7) subpathOptions[[i]]<-list.dirs(paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],sep=""),full.names=TRUE,recursive=FALSE) | |
| subpathBits<-sapply(sapply(subpathOptions,function(x) unlist(strsplit(x,"/"))),function(x) strsplit(x[c(7,14,21,28,35)],"_")) | |
| subpathStartDates<-apply(subpathBits,2,function(x) sapply(x,function(y) as.numeric(y[2]))) | |
| subpathStartTimes<-apply(subpathBits,2,function(x) sapply(x,function(y) as.numeric(y[3]))) | |
| # 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]]$Site<-siteList[i] | |
| overallPossibleDateTimes<-read.csv("E:/Dante/Penguins/Data_Coverage_Results/Isla_Martillo_Overall.csv",colClasses=rep("factor",3)) | |
| inputLists[[i]]$Date<-overallPossibleDateTimes[,1] | |
| inputLists[[i]]$Time<-overallPossibleDateTimes[,2] | |
| sensorList<-c("S4A03851","S4A03852","S4A00436","S4A00449","S4A03859","S4A00431","S4A03868") | |
| inputLists[[i]]$Sensor<-sensorList[i] | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))<subpathStartDates[2,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[1,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[2,i]&as.numeric(as.character(inputLists[[i]]$Time))<subpathStartTimes[2,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[1,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[2,i]&as.numeric(as.character(inputLists[[i]]$Time))>=subpathStartTimes[2,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[2,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))>subpathStartDates[2,i]&as.numeric(as.character(inputLists[[i]]$Date))<subpathStartDates[3,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[2,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[3,i]&as.numeric(as.character(inputLists[[i]]$Time))<subpathStartTimes[3,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[2,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[3,i]&as.numeric(as.character(inputLists[[i]]$Time))>=subpathStartTimes[3,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[3,i]),collapse="_"),sep="") | |
| if(i<5) inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))>subpathStartDates[3,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[3,i]),collapse="_"),sep="") | |
| if(i>=5) | |
| { | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))>subpathStartDates[3,i]&as.numeric(as.character(inputLists[[i]]$Date))<subpathStartDates[4,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[3,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[4,i]&as.numeric(as.character(inputLists[[i]]$Time))<subpathStartTimes[4,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[3,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[4,i]&as.numeric(as.character(inputLists[[i]]$Time))>=subpathStartTimes[4,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[4,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))>subpathStartDates[4,i]&as.numeric(as.character(inputLists[[i]]$Date))<subpathStartDates[5,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[4,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[5,i]&as.numeric(as.character(inputLists[[i]]$Time))<subpathStartTimes[5,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[4,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))==subpathStartDates[5,i]&as.numeric(as.character(inputLists[[i]]$Time))>=subpathStartTimes[5,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[5,i]),collapse="_"),sep="") | |
| inputLists[[i]]$Hypothetical_Path_Stem[which(as.numeric(as.character(inputLists[[i]]$Date))>subpathStartDates[5,i])]<-paste("J:/Dante/Pinguinos/Datos_Acusticos/Isla_Martillo/",siteList[i],"/",paste(unlist(subpathBits[5,i]),collapse="_"),sep="") | |
| } | |
| inputLists[[i]]$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$Martillo.Site==siteList[i]),] | |
| desiredRow<-which.min(abs(relevantRows$"Post-Martillo.Difference")) | |
| inputLists[[i]]$Channel<-ifelse(desiredRow==1,"left","right") | |
| inputLists[[i]]$Sensitivity<-rowMeans(relevantRows[desiredRow,c(3,7,10)],na.rm=TRUE) | |
| # Write results | |
| write.csv(inputLists[[i]],paste("E:/Dante/Penguins/Input_Lists/IM_",siteList[i],".csv",sep="")) | |
| } |