source("GLM.functions.R")
require(rGLM)
lyrDz <<- 0.25
#year <- '2009'
calc.strat.days <- function(WBIC,year,min.duration=30,mix.diff=1.0,all.days=1:365){
# min.duration is in TIME UNITS
# mix diff is °C
folder <- paste("../supporting files/10-06Final/WBIC_",WBIC,'/',sep='')
file <- paste('output',year,'.nc4',sep='')
# does the file exist?
if (file %in% list.files(path = paste(folder))){
cat('WBIC ');cat(WBIC); cat(' processing.')
GLMnc <- getGLMnc(file,folder=folder)
cat('.')
temp.surf <- getTempGLMnc(GLMnc,lyrDz,ref='surface',z.out=0)
temp.bot <- getTempGLMnc(GLMnc,lyrDz,ref='bottom',z.out=0)
nc_close(GLMnc)
is.strat <- (temp.surf[,2]-temp.bot[,2]>mix.diff) # is boolean vector
strat.DoY <- as.numeric(strftime(temp.surf[,1], format = "%j"))
# get rid of days that aren't stratified
strat.DoY <- strat.DoY[is.strat]
is.strat <- (all.days %in% strat.DoY)
return(is.strat)
} else {
return(vector(length=length(all.days)))
}
}
get.lakes <- function(year){
# if doing more than a few years, this should be stripped for just one column and kept in memory (future)
dat<-read.delim('../supporting files/omg.huge.output.tsv',header = TRUE, sep = "\t")
# get rid of all rows that don't match the year
use.idx <- which(dat$year==year & !is.na(dat$dateOver8.9))
dat <- dat[use.idx,]
lake.ids <- as.character(dat$lakeid)
return(lake.ids)
}
call.lakes <- function(year){
file.out <- paste("../supporting files/is.strat_",year,'.tsv',sep='')
lake.ids <- get.lakes(year=year)
num.lakes <- length(lake.ids)
all.days=1:365
strat.count <- vector(length=length(all.days))
for (j in 1:num.lakes){
WBIC = lake.ids[j]
strat.count <- calc.strat.days(WBIC,year,all.days=all.days)+strat.count
cat('.\n')
}
write.out <- data.frame(DoY=all.days,strat.count=strat.count)
# need to name the columns
col.names <- names(write.out)
col.names <- c("DoY",paste("strat.count.",num.lakes,sep=''))
names(write.out) <- col.names
write.table(x=write.out,file=file.out,sep='\t',col.names=TRUE,quote=FALSE,row.names = FALSE)
}
call.lakes(1998)
call.lakes(1996)
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