Camera_Trap_Photo_Selection_Script.R

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


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#                 Camera trap photo selection script                 #
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# Created by:	Dante Francomano (dfrancomano@alumni.purdue.edu)

# Date: 20201007

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# Load packages
library(openxlsx)
library(suncalc)
library(dplyr)

# Read in site coordinates and date range information and condense to pertinent information
siteCoordinates<-read.csv("/Users/dantefrancomano/Documents/Purdue/Dissertation/Pingüinos/Site_Coordinates.csv")
siteCoordinates[1:7,1]<-sub(" ","_",sub("Isla de los Estados ","",siteCoordinates[1:7,1]))
siteCoordinates[12:14,1]<-sub(" ","_",sub("Isla Martillo ","",siteCoordinates[12:14,1]))
siteCoordinates[14,1]<-"Zona_Turística"
siteCoordinates<-siteCoordinates[-(8:11),]
dateRangeInfo<-read.xlsx("/Users/dantefrancomano/Documents/Purdue/Dissertation/Pingüinos/Reproductive_Stage_Data_Coverage_Comparison.xlsx")
limitedDateRangeInfo<-dateRangeInfo[which(dateRangeInfo$Use==1),1:2]
rownames(limitedDateRangeInfo)<-NULL

# Determine sunrise and sunset times for each date-site combination
sunriseTimes<-cbind(limitedDateRangeInfo,matrix(NA,dim(limitedDateRangeInfo)[1],dim(siteCoordinates)[1],dimnames=list(NULL,siteCoordinates$Site)))
sunsetTimes<-sunriseTimes
for(i in 1:dim(sunriseTimes)[1]) for(j in 1:dim(siteCoordinates)[1]) sunriseTimes[i,(j+2)]<-getSunlightTimes(date=as.Date(as.character(sunriseTimes[i,1]),"%Y%m%d"),lat=siteCoordinates[j,2],lon=siteCoordinates[j,3],tz="America/Argentina/Ushuaia",keep=c("sunrise"))$sunrise
for(i in 1:dim(sunsetTimes)[1]) for(j in 1:dim(siteCoordinates)[1]) sunsetTimes[i,(j+2)]<-getSunlightTimes(date=as.Date(as.character(sunsetTimes[i,1]),"%Y%m%d"),lat=siteCoordinates[j,2],lon=siteCoordinates[j,3],tz="America/Argentina/Ushuaia",keep=c("sunset"))$sunset

# Generate lists of possible on-hour times (limiting sampling to 07:00:00 to 19:00:00 during the first two breeding stages due to limited sampling;
# treat sampling of Zona Nueva at 12:00:00 as missing data)
possibleOnHourTimes<-list()
possibleOnHourTimes[siteCoordinates[,1]]<-list(NULL)
for(i in 1:length(siteCoordinates[,1])) possibleOnHourTimes[[i]]<-sapply(as.character(limitedDateRangeInfo[,1]),function(x) NULL)
for(i in 1:length(possibleOnHourTimes))
  {
  for (j in 1:dim(sunriseTimes)[1])
    {
    posixltSunrise<-as.POSIXlt(sunriseTimes[j,(i+2)],origin="1970-01-01",tz="America/Argentina/Ushuaia")
    posixltSunset<-as.POSIXlt(sunsetTimes[j,(i+2)],origin="1970-01-01",tz="America/Argentina/Ushuaia")
    firstPossibleHour<-ifelse(posixltSunrise$min>0|posixltSunrise$sec>0,posixltSunrise$hour+1,posixltSunrise)
    lastPossibleHour<-posixltSunset$hour
    if(j<14&firstPossibleHour<7) firstPossibleHour<-7
    if(j<14&lastPossibleHour>19) lastPossibleHour<-19
    possibleHours<-firstPossibleHour:lastPossibleHour
    possibleHours<-sapply(possibleHours,function(x) ifelse(nchar(x)==1,paste(0,x,sep=""),x))
    possibleOnHourTimes[[i]][[j]]<-possibleHours
    }
  }

# Randomly sample 4 possible times for each site-day combination and determine proportion of daylight hours at which they occur
set.seed(3)
sampledTimes<-list()
sampledTimes[siteCoordinates[,1]]<-list(NULL)
for(i in 1:length(possibleOnHourTimes)) sampledTimes[[i]]<-sapply(possibleOnHourTimes[[i]],sample,4)
dayLengthsHours<-sunriseTimes
dayLengthsHours[,-(1:2)]<-(sunsetTimes[,-(1:2)]-sunriseTimes[,-(1:2)])/60/60
sampledTimeDaylightProportions<-list()
for(i in 1:length(sampledTimes)) sampledTimeDaylightProportions[[siteCoordinates[i,1]]]<-sapply(possibleOnHourTimes[[i]],function(x) rep(NA,4))
for(i in 1:length(sampledTimes)) for(j in 1:dim(sunriseTimes)[1]) sampledTimeDaylightProportions[[i]][,j]<-(as.numeric(sampledTimes[[i]][,j])-difftime(as.POSIXlt(sunriseTimes[j,(i+2)],origin="1970-01-01",tz="America/Argentina/Ushuaia"),trunc(as.POSIXlt(sunriseTimes[j,(i+2)],origin="1970-01-01",tz="America/Argentina/Ushuaia"),"days")))/dayLengthsHours[j,(i+2)]

# Generate hypothetical file names for each sample
sourcePathRootStem<-"/Users/dantefrancomano/Documents/Purdue/Dissertation/Pingüinos/Datos_de_Cámaras_Trampa/Relevant_Photos_SM_Style_Names"
sourcePathStems<-paste(sourcePathRootStem,names(sampledTimes),sep="/")
sampleSourcePaths<-list()
sampleSourcePaths[siteCoordinates[,1]]<-list(NULL)
for(i in 1:length(sampleSourcePaths)) for(j in 1:dim(sunriseTimes)[1]) sampleSourcePaths[[i]][[j]]<-paste(sourcePathStems[i],"/",siteCoordinates[i,1],"_",sunriseTimes[j,1],"_",sampledTimes[[i]][,j],"0000.JPG",sep="")

# Check file existence and copy sampled files to new directories
fileExistenceCheck<-sampleSourcePaths
for(i in 1:length(sampleSourcePaths)) for(j in 1:dim(sunriseTimes)[1]) fileExistenceCheck[[i]][[j]]<-file.exists(sampleSourcePaths[[i]][[j]])
sampleSourcePaths<-unlist(sampleSourcePaths)
sampleDestinationPaths<-sub("Relevant_Photos_SM_Style_Names","Stratified_Random_Sample",sampleSourcePaths)
for(i in 1:length(sampleSourcePaths)) if(file.exists(sampleSourcePaths[i])) file.copy(sampleSourcePaths[i],sampleDestinationPaths[i])

# Write out data forms to complete
fullDataForm<-data.frame(Site=rep(siteCoordinates[,1],each=dim(sunriseTimes)[1]*4),Date=rep(sunriseTimes[,1],each=4,times=length(sampledTimes)),Breeding_Stage=rep(sunriseTimes[,2],each=4,times=length(sampledTimes)),Time=paste(unlist(sampledTimes),"0000",sep=""),Daylight_Proportion=unlist(sampledTimeDaylightProportions),Count_1="",Count_2="",Count_4="")
extantDataForm<-fullDataForm[which(unlist(fileExistenceCheck)==TRUE),]
extantDataForm<-arrange(extantDataForm,Site,Date,Time)
dataFormPPA<-extantDataForm[grep("PPA",extantDataForm$Site),-(7:8)]
rownames(dataFormPPA)<-NULL
dataFormPM<-extantDataForm[-grep("PPA",extantDataForm$Site),-6]
rownames(dataFormPM)<-NULL
write.csv(dataFormPPA,"/Users/dantefrancomano/Documents/Purdue/Dissertation/Pingüinos/Datos_de_Cámaras_Trampa/PPA_Data.csv")
write.csv(dataFormPM,"/Users/dantefrancomano/Documents/Purdue/Dissertation/Pingüinos/Datos_de_Cámaras_Trampa/PM_Data.csv")