library(foreign) 
library(data.table)
library(reshape2)

#BIRD DATA
BBS <- rbindlist(lapply(list.files("C:\\Users\\jmgorzo\\Dropbox\\model\\input\\bird/BBS/state_bbs_data",full.names=TRUE),read.csv))  

BBS$countrynum <- NULL
BBS$rteno <- as.integer(paste(BBS$statenum,formatC(BBS$Route, width=3, flag="0"),sep=""))
BBS$SpeciesTotal <- NULL
BBS$StopTotal <- NULL
BBS <- melt(BBS, id.vars = c("Year","statenum","Route","Aou","rteno"),variable.name = "interval",value.name="count")
BBS$route_piece <- paste(BBS$rteno,BBS$interval,sep="_")

repeats <- read.dbf("C:/Users/jmgorzo/Dropbox/model/input/bird/BBS/intersecting_duplicated_segment.dbf")
repeats$new_rteno <- repeats$rteno - 100
repeats$new_route <- paste(repeats$new_rteno,repeats$segment,sep="_")

BBS$new_route<-repeats[match(BBS$route_piece, repeats$route),"new_route"]
BBS$new_rteno<-repeats[match(BBS$route_piece, repeats$route),"new_rteno"]
BBS[!is.na(new_route)]$route_piece <- BBS[!is.na(new_route)]$new_route
BBS[!is.na(new_route)]$rteno <- as.integer(BBS[!is.na(new_route)]$new_rteno)

BBS$pieceID <- paste(BBS$route_piece,BBS$Year,sep="_")                                     

route_data <- read.csv("bird/BBS/routes.csv")
route_data$rteno <- as.integer(paste(route_data$statenum,formatC(route_data$Route, width=3, flag="0"),sep=""))
route_data <- route_data[c("BCR","rteno")]

routeinfo <- read.csv("bird/BBS/weather.csv")                                                             
routeinfo$rteno <- as.integer(paste(routeinfo$statenum,formatC(routeinfo$Route, width=3, flag="0"),sep=""))                             
routeinfo <- routeinfo[c("RouteDataId","Year","ObsN","rteno","EndWind","StartWind","RunType","RPID")]
routeinfo$firstyear <- c(1L,routeinfo$ObsN[-1]!=routeinfo$ObsN[-nrow(routeinfo)])

BBS <- merge(BBS,routeinfo,by=c("rteno","Year"))
BBS <- merge(BBS,route_data,by="rteno")
BBS <- BBS[BBS$RunType > 0,]
BBS <- BBS[BBS$RPID < 102,]

vcf_subroute <- read.dbf("landcover/bbs_segment_buffers.dbf")
vcf_subroute$interval <- paste("count",vcf_subroute$segment,"0",sep="") 
vcf_subroute <- vcf_subroute[,c("rteno","interval",grep("[[:digit:]]", names(vcf_subroute), perl=TRUE, value=TRUE))]
vcf_subroute <- melt(vcf_subroute,id=c("rteno","interval"))
vcf_subroute$variable <- as.character(vcf_subroute$variable)
vcf_subroute$Year <- str_extract(vcf_subroute$variable,"[[:digit:]]+")
vcf_subroute$var <- sapply(strsplit(vcf_subroute$variable, "[[:digit:]]+"),"[[",2)
vcf_subroute$variable <- NULL
vcf_subroute <- dcast(vcf_subroute,rteno + interval ~ var,fun.aggregate=mean)
vcf_subroute$rteno <- as.character(vcf_subroute$rteno)