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step18_useRtoBootstrapCIs.R
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# Bootstrap code
library(boot)
library(ncdf)
ns=c("nh","sh")
rcp=c("RCP85", "RCP45")
# start profiler to look for efficiency improvements
Rprof("profileBootstrapCI.out")
for (n in 1:2)
{
for (r in 1:2)
{
fileName<-paste("./justNSIF_ensembleAndBG.", ns[n],".", rcp[r], ".nc",collapse ='',sep='')
print(fileName)
# Read in data
#setwd("/Volumes/Pitcairn/seaicePPF/northernHemisphere/analysisOutput/")
setwd('/home/barnhark/seaIceEmergence/')
SIfile <- open.ncdf(fileName) # ncdf
# put this in a loop for all 4 similar NCDFs
# copy the file and add the extra variable names.
print(paste("File",SIfile$filename,"contains",SIfile$nvars,"variables"))
data<- get.var.ncdf(SIfile,varid='nSIF_ensemble')
data_yr<- get.var.ncdf(SIfile,varid='time_ensemble')
ni<-dim(data)[1]
nj<-dim(data)[2]
ny<-dim(data)[3]
# Sample mean function for bootstrapping
samplemean <- function(x, d) {
return(mean(x[d]))
}
# Sample standard deviation function for bootstrapping
samplesd <- function(x, d) {
return(sd(x[d]))
}
# create ouptu matrices
mean_ub <- array(data = NA, dim=c(ni, nj, ny))
mean_lb <- array(data = NA, dim=c(ni, nj, ny))
sd_ub <- array(data = NA, dim=c(ni, nj, ny))
sd_lb <- array(data = NA, dim=c(ni, nj, ny))
sd_var <- array(data = NA, dim=c(ni, nj, ny))
mean_var <- array(data = NA, dim=c(ni, nj, ny))
for (nii in 1:ni)
{
print(nii)
for (njj in 1:nj)
{
for (nyy in 1:ny)
{
vals=data[nii,njj,nyy,]
naTest<-is.na(mean(vals))
if (naTest==FALSE)
{
waterTest<-(mean(vals)<360)
if (waterTest==TRUE)
{
boot_result_mean <- boot(vals,statistic=samplemean,R=1000)
mean_var[nii, njj, nyy] <- mean(vals,na.rm=T)
mean_ci <- boot.ci(boot_result_mean,conf = 0.95,type = "basic")
mean_ub[nii, njj, nyy] <- mean_ci$basic[5]
mean_lb[nii, njj, nyy] <- mean_ci$basic[4]
boot_result_stdev <- boot(vals,statistic=samplesd,R=1000)
sd_var[nii, njj, nyy] <- sd(vals,na.rm=T)
sd_ci <- boot.ci(boot_result_stdev,conf = 0.95, type = "basic")
sd_ub[nii, njj, nyy] <- sd_ci$basic[5]
sd_lb[nii, njj, nyy] <- sd_ci$basic[4]
}
}
}
}
}
niDIM<-dim.def.ncdf( SIfile$dim$ni$name, SIfile$dim$ni$units, SIfile$dim$ni$vals, unlim=FALSE, create_dimvar=FALSE)
njDIM<-dim.def.ncdf( SIfile$dim$nj$name, SIfile$dim$nj$units, SIfile$dim$nj$vals, unlim=FALSE, create_dimvar=FALSE)
nyDIM<-dim.def.ncdf( SIfile$dim$time_ensemble$name, SIfile$dim$time_ensemble$units, SIfile$dim$time_ensemble$vals, unlim=FALSE, create_dimvar=TRUE)
nverticesDIM<-dim.def.ncdf( SIfile$dim$nvertices$name, SIfile$dim$nvertices$units, SIfile$dim$nvertices$vals, create_dimvar=FALSE)
newDims=list(niDIM, njDIM, nyDIM)
# Make new output variables
var_meanUB <-var.def.ncdf('meanUB', 'days', dim=newDims, 1e+30, longname='Upper bound for the mean number of sea ice free days', prec="single")
var_meanLB <-var.def.ncdf('meanLB', 'days', dim=newDims, 1e+30, longname='Lower bound for the mean number of sea ice free days', prec="single")
var_mean <-var.def.ncdf('mean', 'days', dim=newDims, 1e+30, longname='Mean number of sea ice free days', prec="single")
var_sdUB <-var.def.ncdf('sdUB', 'days', dim=newDims, 1e+30, longname='Upper bound for standard deviation of the number of sea ice free days', prec="single")
var_sdLB <-var.def.ncdf('sdLB', 'days', dim=newDims, 1e+30, longname='Lower bound for standard deviation of the number of sea ice free days', prec="single")
var_sd <-var.def.ncdf('sd', 'days', dim=newDims, 1e+30, longname='Standard deviation of the number of sea ice free days', prec="single")
# get lat/lon variables
TLAT<-SIfile$var$TLAT
TLON<-SIfile$var$TLON
latt_bounds<-SIfile$var$latt_bounds
lont_bounds<-SIfile$var$lont_bounds
TLAT_vals<-get.var.ncdf(SIfile,varid='TLAT')
TLON_vals<-get.var.ncdf(SIfile,varid='TLON')
latt_bounds_vals<-get.var.ncdf(SIfile,varid='latt_bounds')
lont_bounds_vals<-get.var.ncdf(SIfile,varid='lont_bounds')
newFN<-paste("./justNSIF_ensembleAndBG.", ns[n],".", rcp[r], ".BootCI.nc",collapse ='',sep='')
# Create the test file
nc <- create.ncdf( newFN, list(var_meanUB,var_meanLB,var_sdUB,var_sdLB, var_sd, var_mean, TLAT, TLON, latt_bounds, lont_bounds) )
# Write some data to the file
put.var.ncdf(nc, var_meanUB, mean_ub)
put.var.ncdf(nc, var_meanLB, mean_lb)
put.var.ncdf(nc, var_sdUB, sd_ub)
put.var.ncdf(nc, var_sdLB, sd_lb)
put.var.ncdf(nc, var_sd, sd_var)
put.var.ncdf(nc, var_mean, mean_var)
put.var.ncdf(nc, TLAT, TLAT_vals)
put.var.ncdf(nc, TLON, TLON_vals)
put.var.ncdf(nc, latt_bounds, latt_bounds_vals)
put.var.ncdf(nc, lont_bounds, lont_bounds_vals)
close.ncdf(nc)
rm(nc)
close.ncdf(SIfile)
rm(SIfile)
}
}
# profile code at end
Rprof(NULL)
summaryRprof("profileBootstrapCI.out")