Rutils/monthly.template.r
In manfredo89/ED2io: Manages Input/Output for Ecosystem Demography 2 Model
#==========================================================================================#
#==========================================================================================#
# Create the monthly mean structure to be filled by plot_monthly.r #
#------------------------------------------------------------------------------------------#
create.monthly <<- function(ntimes,montha,yeara,inpref,slz.min){
#----- Read the first HDF5 to grab some simulation-dependent dimensions. ---------------#
cyear = sprintf("%4.4i", yeara)
cmonth = sprintf("%2.2i",montha)
h5first = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5" ,sep="")
h5first.bz2 = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5.bz2",sep="")
h5first.gz = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5.gz" ,sep="")
if ( file.exists(h5first) ){
mymont = H5Fopen(h5first)
}else if ( file.exists(h5first.bz2) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = bunzip2(filename=h5first.bz2,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else if ( file.exists(h5first.gz) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = gunzip(filename=h5first.gz,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else{
cat ("Warning: I was looking for the first file to use as template but\n")
cat ("I have not found it. I will try to use the last one (the one of \n")
cat ("yearz). This usually happens when not all the analysis (the \n")
cat ("first one in particular) are present. If even this one is not \n")
cat ("found try to set yearz to the real last H5 file that you have...\n")
cyear = sprintf("%4.4i", yeara + floor(ntimes/12) - 1)
h5first = paste(inpref,"-Q-",cyear,"-01-00-000000-g01.h5" ,sep="")
h5first.bz2 = paste(inpref,"-Q-",cyear,"-01-00-000000-g01.h5.bz2",sep="")
h5first.gz = paste(inpref,"-Q-",cyear,"-01-00-000000-g01.h5.gz" ,sep="")
if ( file.exists(h5first) ){
mymont = H5Fopen(h5first)
}else if ( file.exists(h5first.bz2) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = bunzip2(filename=h5first.bz2,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else if ( file.exists(h5first.gz) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = gunzip(filename=h5first.gz,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else{
cat (" Path: ",dirname (h5first),"\n")
cat (" File: ",basename(h5first),"\n")
stop(" File not found...")
}
}#end if
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Start up the list. #
#---------------------------------------------------------------------------------------#
ed = list()
#---------------------------------------------------------------------------------------#
#----- Define the number of soil layers. -----------------------------------------------#
ed$nzg = mymont$NZG
ed$nzs = mymont$NZS
ed$ndcycle = mymont$NDCYCLE
ed$ntimes = ntimes
#---------------------------------------------------------------------------------------#
#----- Find which soil are we solving, and save properties into soil.prop. -------------#
ed$isoilflg = mymont$ISOILFLG
ed$slz = mymont$SLZ
ed$slxsand = mymont$SLXSAND
ed$slxclay = mymont$SLXCLAY
ed$ntext = mymont$NTEXT_SOIL[ed$nzg]
#---------------------------------------------------------------------------------------#
#H5close()
#----- Derive the soil properties. -----------------------------------------------------#
ed$soil.prop = soil.params(ed$ntext,ed$isoilflg,ed$slxsand,ed$slxclay)
ed$dslz = diff(c(ed$slz,0))
ed$soil.depth = rev(cumsum(rev(ed$dslz)))
ed$soil.dry = rev(cumsum(rev(ed$soil.prop$soilcp * wdns * ed$dslz)))
ed$soil.poro = rev(cumsum(rev(ed$soil.prop$slmsts * wdns * ed$dslz)))
#---------------------------------------------------------------------------------------#
#----- Find the layers we care about. --------------------------------------------------#
sel = ed$slz < slz.min
if (any(sel)){
ed$ka = which.max(ed$slz[sel])
}else{
ed$ka = 1
}#end if
ed$kz = ed$nzg
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Find all time information. #
#---------------------------------------------------------------------------------------#
runmonths = montha + sequence(ntimes) - 1
ed$month = 1 + (runmonths-1) %% 12
ed$year = yeara - 1 + ceiling(runmonths/12)
ed$when = chron(paste(ed$month,1,ed$year,sep="/"))
ed$tomonth = chron(ed$when,out.format=c(dates="day-mon-yr",times=NULL))
ed$toyear = sort(unique(ed$year))
#----- Count the number of months for each month. --------------------------------------#
ed$montable = rep(0,times=12)
montable = table(ed$month)
idx = as.numeric(names(montable))
ed$montable[idx] = montable
ed$moncnt = matrix( data = rep(ed$montable,times=ed$ndcycle)
, ncol = ed$ndcycle
, nrow = 12
)#end matrix
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Find all the file names. #
#---------------------------------------------------------------------------------------#
cmonth = sprintf("%2.2i",ed$month)
cyear = sprintf("%4.4i",ed$year )
ed$input = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5",sep="")
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Make a copy of the dimensions to avoid clutter. #
#---------------------------------------------------------------------------------------#
ndcycle = ed$ndcycle
nzg = ed$nzg
nzs = ed$nzs
#---------------------------------------------------------------------------------------#
#=======================================================================================#
#=======================================================================================#
# Flush all variables that will hold the data. For convenience they are split into #
# multiple lists. #
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emean -- variables that we can either compare directly with observations, or are #
# or that may be used to draw time series. They don't need to be really #
# monthly means, but you should put only the variables that make sense to be #
# plotted in simple time series (with no PFT or DBH information). #
#---------------------------------------------------------------------------------------#
emean = list()
emean$wood.dens = rep(NA,times=ntimes)
emean$fast.soil.c = rep(NA,times=ntimes)
emean$slow.soil.c = rep(NA,times=ntimes)
emean$struct.soil.c = rep(NA,times=ntimes)
emean$het.resp = rep(NA,times=ntimes)
emean$cwd.resp = rep(NA,times=ntimes)
emean$soil.resp = rep(NA,times=ntimes)
emean$gpp = rep(NA,times=ntimes)
emean$last.1yr.gpp = rep(NA,times=ntimes)
emean$last.2yr.gpp = rep(NA,times=ntimes)
emean$last.3yr.gpp = rep(NA,times=ntimes)
emean$plant.resp = rep(NA,times=ntimes)
emean$last.1yr.plresp = rep(NA,times=ntimes)
emean$last.2yr.plresp = rep(NA,times=ntimes)
emean$last.3yr.plresp = rep(NA,times=ntimes)
emean$cue = rep(NA,times=ntimes)
emean$last.1yr.cue = rep(NA,times=ntimes)
emean$last.2yr.cue = rep(NA,times=ntimes)
emean$last.3yr.cue = rep(NA,times=ntimes)
emean$ecue = rep(NA,times=ntimes)
emean$last.1yr.ecue = rep(NA,times=ntimes)
emean$last.2yr.ecue = rep(NA,times=ntimes)
emean$last.3yr.ecue = rep(NA,times=ntimes)
emean$leaf.resp = rep(NA,times=ntimes)
emean$root.resp = rep(NA,times=ntimes)
emean$froot.resp = rep(NA,times=ntimes)
emean$croot.resp = rep(NA,times=ntimes)
emean$stem.resp = rep(NA,times=ntimes)
emean$growth.resp = rep(NA,times=ntimes)
emean$storage.resp = rep(NA,times=ntimes)
emean$reco = rep(NA,times=ntimes)
emean$assim.light = rep(NA,times=ntimes)
emean$assim.rubp = rep(NA,times=ntimes)
emean$assim.co2 = rep(NA,times=ntimes)
emean$assim.ratio = rep(NA,times=ntimes)
emean$mco = rep(NA,times=ntimes)
emean$cba = rep(NA,times=ntimes)
emean$last.1yr.cba = rep(NA,times=ntimes)
emean$last.2yr.cba = rep(NA,times=ntimes)
emean$last.3yr.cba = rep(NA,times=ntimes)
emean$cbamax = rep(NA,times=ntimes)
emean$cbalight = rep(NA,times=ntimes)
emean$cbamoist = rep(NA,times=ntimes)
emean$cbarel = rep(NA,times=ntimes)
emean$ldrop = rep(NA,times=ntimes)
emean$nep = rep(NA,times=ntimes)
emean$nee = rep(NA,times=ntimes)
emean$cflxca = rep(NA,times=ntimes)
emean$cflxst = rep(NA,times=ntimes)
emean$ustar = rep(NA,times=ntimes)
emean$atm.vels = rep(NA,times=ntimes)
emean$atm.prss = rep(NA,times=ntimes)
emean$atm.temp = rep(NA,times=ntimes)
emean$atm.shv = rep(NA,times=ntimes)
emean$atm.vpd = rep(NA,times=ntimes)
emean$atm.co2 = rep(NA,times=ntimes)
emean$can.prss = rep(NA,times=ntimes)
emean$can.temp = rep(NA,times=ntimes)
emean$can.co2 = rep(NA,times=ntimes)
emean$can.shv = rep(NA,times=ntimes)
emean$can.vpd = rep(NA,times=ntimes)
emean$can.depth = rep(NA,times=ntimes)
emean$can.area = rep(NA,times=ntimes)
emean$gnd.temp = rep(NA,times=ntimes)
emean$gnd.shv = rep(NA,times=ntimes)
emean$leaf.temp = rep(NA,times=ntimes)
emean$phap.ltemp = rep(NA,times=ntimes)
emean$last.1yr.ltemp = rep(NA,times=ntimes)
emean$last.2yr.ltemp = rep(NA,times=ntimes)
emean$last.3yr.ltemp = rep(NA,times=ntimes)
emean$leaf.vpd = rep(NA,times=ntimes)
emean$phap.lvpd = rep(NA,times=ntimes)
emean$last.1yr.lvpd = rep(NA,times=ntimes)
emean$last.2yr.lvpd = rep(NA,times=ntimes)
emean$last.3yr.lvpd = rep(NA,times=ntimes)
emean$leaf.water = rep(NA,times=ntimes)
emean$phap.lwater = rep(NA,times=ntimes)
emean$last.1yr.lwater = rep(NA,times=ntimes)
emean$last.2yr.lwater = rep(NA,times=ntimes)
emean$last.3yr.lwater = rep(NA,times=ntimes)
emean$wood.temp = rep(NA,times=ntimes)
emean$hflxca = rep(NA,times=ntimes)
emean$qwflxca = rep(NA,times=ntimes)
emean$hflxgc = rep(NA,times=ntimes)
emean$hflxlc = rep(NA,times=ntimes)
emean$hflxwc = rep(NA,times=ntimes)
emean$wflxca = rep(NA,times=ntimes)
emean$wflxgc = rep(NA,times=ntimes)
emean$wflxlc = rep(NA,times=ntimes)
emean$wflxwc = rep(NA,times=ntimes)
emean$runoff = rep(NA,times=ntimes)
emean$intercepted = rep(NA,times=ntimes)
emean$wshed = rep(NA,times=ntimes)
emean$evap = rep(NA,times=ntimes)
emean$last.1yr.evap = rep(NA,times=ntimes)
emean$last.2yr.evap = rep(NA,times=ntimes)
emean$last.3yr.evap = rep(NA,times=ntimes)
emean$npp = rep(NA,times=ntimes)
emean$last.1yr.npp = rep(NA,times=ntimes)
emean$last.2yr.npp = rep(NA,times=ntimes)
emean$last.3yr.npp = rep(NA,times=ntimes)
emean$dcbadt = rep(NA,times=ntimes)
emean$last.1yr.dcbadt = rep(NA,times=ntimes)
emean$last.2yr.dcbadt = rep(NA,times=ntimes)
emean$last.3yr.dcbadt = rep(NA,times=ntimes)
emean$et = rep(NA,times=ntimes)
emean$last.1yr.et = rep(NA,times=ntimes)
emean$last.2yr.et = rep(NA,times=ntimes)
emean$last.3yr.et = rep(NA,times=ntimes)
emean$transp = rep(NA,times=ntimes)
emean$last.1yr.transp = rep(NA,times=ntimes)
emean$last.2yr.transp = rep(NA,times=ntimes)
emean$last.3yr.transp = rep(NA,times=ntimes)
emean$etue = rep(NA,times=ntimes)
emean$last.1yr.etue = rep(NA,times=ntimes)
emean$last.2yr.etue = rep(NA,times=ntimes)
emean$last.3yr.etue = rep(NA,times=ntimes)
emean$wue = rep(NA,times=ntimes)
emean$last.1yr.wue = rep(NA,times=ntimes)
emean$last.2yr.wue = rep(NA,times=ntimes)
emean$last.3yr.wue = rep(NA,times=ntimes)
emean$rain = rep(NA,times=ntimes)
emean$last.1yr.rain = rep(NA,times=ntimes)
emean$last.2yr.rain = rep(NA,times=ntimes)
emean$last.3yr.rain = rep(NA,times=ntimes)
emean$nmon.lt.090 = rep(NA,times=ntimes)
emean$nmon.lt.100 = rep(NA,times=ntimes)
emean$nmon.lt.110 = rep(NA,times=ntimes)
emean$nmon.lt.120 = rep(NA,times=ntimes)
emean$nmon.wdef = rep(NA,times=ntimes)
emean$nmon.mdef = rep(NA,times=ntimes)
emean$rue = rep(NA,times=ntimes)
emean$last.1yr.rue = rep(NA,times=ntimes)
emean$last.2yr.rue = rep(NA,times=ntimes)
emean$last.3yr.rue = rep(NA,times=ntimes)
emean$sm.stress = rep(NA,times=ntimes)
emean$phap.sms = rep(NA,times=ntimes)
emean$last.1yr.sms = rep(NA,times=ntimes)
emean$last.2yr.sms = rep(NA,times=ntimes)
emean$last.3yr.sms = rep(NA,times=ntimes)
emean$rshort = rep(NA,times=ntimes)
emean$last.1yr.rshort = rep(NA,times=ntimes)
emean$last.2yr.rshort = rep(NA,times=ntimes)
emean$last.3yr.rshort = rep(NA,times=ntimes)
emean$rshort.beam = rep(NA,times=ntimes)
emean$rshort.diff = rep(NA,times=ntimes)
emean$rshortup = rep(NA,times=ntimes)
emean$rshort.gnd = rep(NA,times=ntimes)
emean$rlong = rep(NA,times=ntimes)
emean$rlong.gnd = rep(NA,times=ntimes)
emean$rlongup = rep(NA,times=ntimes)
emean$par.tot = rep(NA,times=ntimes)
emean$par.beam = rep(NA,times=ntimes)
emean$par.diff = rep(NA,times=ntimes)
emean$par.gnd = rep(NA,times=ntimes)
emean$parup = rep(NA,times=ntimes)
emean$par.leaf = rep(NA,times=ntimes)
emean$par.leaf.beam = rep(NA,times=ntimes)
emean$par.leaf.diff = rep(NA,times=ntimes)
emean$rnet = rep(NA,times=ntimes)
emean$albedo = rep(NA,times=ntimes)
emean$albedo.par = rep(NA,times=ntimes)
emean$albedo.nir = rep(NA,times=ntimes)
emean$rlong.albedo = rep(NA,times=ntimes)
emean$nplant = rep(NA,times=ntimes)
emean$agb = rep(NA,times=ntimes)
emean$biomass = rep(NA,times=ntimes)
emean$lai = rep(NA,times=ntimes)
emean$wai = rep(NA,times=ntimes)
emean$tai = rep(NA,times=ntimes)
emean$area = rep(NA,times=ntimes)
emean$workload = rep(NA,times=ntimes)
emean$specwork = rep(NA,times=ntimes)
emean$demand = rep(NA,times=ntimes)
emean$supply = rep(NA,times=ntimes)
emean$paw = rep(NA,times=ntimes)
emean$smpot = rep(NA,times=ntimes)
emean$last.1yr.smpot = rep(NA,times=ntimes)
emean$last.2yr.smpot = rep(NA,times=ntimes)
emean$last.3yr.smpot = rep(NA,times=ntimes)
emean$npat.global = rep(NA,times=ntimes)
emean$ncoh.global = rep(NA,times=ntimes)
emean$water.deficit = rep(NA,times=ntimes)
emean$last.1yr.mwd = rep(NA,times=ntimes)
emean$last.2yr.mwd = rep(NA,times=ntimes)
emean$last.3yr.mwd = rep(NA,times=ntimes)
emean$malhi.deficit = rep(NA,times=ntimes)
emean$leaf.gsw = rep(NA,times=ntimes)
emean$phap.lgsw = rep(NA,times=ntimes)
emean$last.1yr.lgsw = rep(NA,times=ntimes)
emean$last.2yr.lgsw = rep(NA,times=ntimes)
emean$last.3yr.lgsw = rep(NA,times=ntimes)
emean$leaf.gbw = rep(NA,times=ntimes)
emean$phap.lgbw = rep(NA,times=ntimes)
emean$wood.gbw = rep(NA,times=ntimes)
emean$i.gpp = rep(NA,times=ntimes)
emean$i.npp = rep(NA,times=ntimes)
emean$i.plant.resp = rep(NA,times=ntimes)
emean$i.mco = rep(NA,times=ntimes)
emean$i.cba = rep(NA,times=ntimes)
emean$i.cbamax = rep(NA,times=ntimes)
emean$i.cbalight = rep(NA,times=ntimes)
emean$i.cbamoist = rep(NA,times=ntimes)
emean$i.transp = rep(NA,times=ntimes)
emean$i.wflxlc = rep(NA,times=ntimes)
emean$i.hflxlc = rep(NA,times=ntimes)
emean$f.gpp = rep(NA,times=ntimes)
emean$f.plant.resp = rep(NA,times=ntimes)
emean$f.npp = rep(NA,times=ntimes)
emean$f.mco = rep(NA,times=ntimes)
emean$f.cba = rep(NA,times=ntimes)
emean$f.bstorage = rep(NA,times=ntimes)
emean$f.bleaf = rep(NA,times=ntimes)
emean$f.bstem = rep(NA,times=ntimes)
emean$f.broot = rep(NA,times=ntimes)
emean$f.bseeds = rep(NA,times=ntimes)
emean$f.dcbadt = rep(NA,times=ntimes)
emean$leaf.par = rep(NA,times=ntimes)
emean$leaf.par.beam = rep(NA,times=ntimes)
emean$leaf.par.diff = rep(NA,times=ntimes)
emean$leaf.gpp = rep(NA,times=ntimes)
emean$phap.lpar = rep(NA,times=ntimes)
emean$last.1yr.lpar = rep(NA,times=ntimes)
emean$last.2yr.lpar = rep(NA,times=ntimes)
emean$last.3yr.lpar = rep(NA,times=ntimes)
emean$leaf.rshort = rep(NA,times=ntimes)
emean$leaf.rlong = rep(NA,times=ntimes)
emean$last.1yr.growth = rep(NA,times=ntimes)
emean$last.2yr.growth = rep(NA,times=ntimes)
emean$last.3yr.growth = rep(NA,times=ntimes)
emean$last.1yr.recr = rep(NA,times=ntimes)
emean$last.2yr.recr = rep(NA,times=ntimes)
emean$last.3yr.recr = rep(NA,times=ntimes)
emean$last.1yr.mort = rep(NA,times=ntimes)
emean$last.2yr.mort = rep(NA,times=ntimes)
emean$last.3yr.mort = rep(NA,times=ntimes)
emean$last.1yr.dimort = rep(NA,times=ntimes)
emean$last.2yr.dimort = rep(NA,times=ntimes)
emean$last.3yr.dimort = rep(NA,times=ntimes)
emean$last.1yr.ncbmort = rep(NA,times=ntimes)
emean$last.2yr.ncbmort = rep(NA,times=ntimes)
emean$last.3yr.ncbmort = rep(NA,times=ntimes)
emean$agb.change = rep(NA,times=ntimes)
emean$acc.change = rep(NA,times=ntimes)
emean$acc.growth = rep(NA,times=ntimes)
emean$acc.mort = rep(NA,times=ntimes)
emean$acc.ncbmort = rep(NA,times=ntimes)
emean$acc.dimort = rep(NA,times=ntimes)
emean$acc.recr = rep(NA,times=ntimes)
emean$last.1yr.change = rep(NA,times=ntimes)
emean$last.2yr.change = rep(NA,times=ntimes)
emean$last.3yr.change = rep(NA,times=ntimes)
#----- Soil variables. -----------------------------------------------------------------#
emean$soil.water = matrix(data=0,nrow=ntimes,ncol=nzg)
emean$soil.temp = matrix(data=0,nrow=ntimes,ncol=nzg)
emean$soil.mstpot = matrix(data=0,nrow=ntimes,ncol=nzg)
emean$soil.extracted = matrix(data=0,nrow=ntimes,ncol=nzg)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emsqu -- mean sum of squares of polygon-level variable. #
#---------------------------------------------------------------------------------------#
emsqu = list()
emsqu$gpp = rep(NA,times=ntimes)
emsqu$plant.resp = rep(NA,times=ntimes)
emsqu$leaf.resp = rep(NA,times=ntimes)
emsqu$froot.resp = rep(NA,times=ntimes)
emsqu$het.resp = rep(NA,times=ntimes)
emsqu$cwd.resp = rep(NA,times=ntimes)
emsqu$reco = rep(NA,times=ntimes)
emsqu$cflxca = rep(NA,times=ntimes)
emsqu$cflxst = rep(NA,times=ntimes)
emsqu$hflxca = rep(NA,times=ntimes)
emsqu$hflxlc = rep(NA,times=ntimes)
emsqu$hflxwc = rep(NA,times=ntimes)
emsqu$hflxgc = rep(NA,times=ntimes)
emsqu$wflxca = rep(NA,times=ntimes)
emsqu$qwflxca = rep(NA,times=ntimes)
emsqu$wflxlc = rep(NA,times=ntimes)
emsqu$wflxwc = rep(NA,times=ntimes)
emsqu$wflxgc = rep(NA,times=ntimes)
emsqu$evap = rep(NA,times=ntimes)
emsqu$transp = rep(NA,times=ntimes)
emsqu$ustar = rep(NA,times=ntimes)
emsqu$albedo = rep(NA,times=ntimes)
emsqu$rshortup = rep(NA,times=ntimes)
emsqu$rlongup = rep(NA,times=ntimes)
emsqu$parup = rep(NA,times=ntimes)
emsqu$rnet = rep(NA,times=ntimes)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# SZPFT -- Size (DBH) and plant functional type (PFT) array. An extra level is #
# appended to the end, which will hold the sum of all categories. #
# #
# The initial value depends on the type of variable: #
# - If absence is equal to zero, then the initial value must be zero. This is #
# normally the case for state variables (e.g. biomass, demographic density, #
# LAI, etc.) #
# - If absence makes the variable meaningless, then the initial value must #
# be NA. This is true for plant-derived properties (temperature, mortality, #
# gsw, etc.) #
#---------------------------------------------------------------------------------------#
szpft = list()
#----- Initial value should be zero. ---------------------------------------------------#
szpft$agb = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$biomass = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$lai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$wai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$tai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$ba = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$nplant = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bdead = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$balive = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bleaf = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bstem = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$broot = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bfroot = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bcroot = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsapwood = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bstorage = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bseeds = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.lai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.wai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.tai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.agb = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.ba = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$par.leaf = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$par.leaf.beam = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$par.leaf.diff = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
#----- Initial value should be NA. -----------------------------------------------------#
szpft$wood.dens = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$npp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$dcbadt = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$root.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$froot.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$croot.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$stem.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$growth.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$storage.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$plant.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.light = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.rubp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.co2 = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.ratio = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$mco = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cba = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbamax = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbalight = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbamoist = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbarel = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$ldrop = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$sm.stress = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.sms = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.gbw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lgbw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.gsw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lgsw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wood.gbw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.temp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.ltemp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.water = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lwater = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wood.temp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.vpd = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lvpd = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$demand = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$supply = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$hflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.npp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.plant.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.mco = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cba = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cbamax = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cbalight = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cbamoist = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.transp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.wflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.hflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.plant.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.npp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.mco = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.cba = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bstorage = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.dcbadt = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bleaf = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bstem = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.broot = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bseeds = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.par = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.par.beam = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.par.diff = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lpar = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.rshort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.rlong = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$transp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$ecue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$etue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$rue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# LU -- Polygon-level variables, split by land use type. One extra dimension is #
# appended to the end, which will hold the sum of all land use types. #
# #
# The initial value depends on the type of variable: #
# - If absence is equal to zero, then the initial value must be zero. This is #
# normally the case for state variables (e.g. biomass, demographic density, #
# LAI, etc.) #
# - If absence makes the variable meaningless, then the initial value must #
# be NA. This is true for plant-derived properties (temperature, mortality, #
# gsw, etc.) #
#---------------------------------------------------------------------------------------#
lu = list()
#----- Initial value should be zero. ---------------------------------------------------#
lu$agb = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$biomass = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$lai = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$area = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$ba = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
#----- Initial value should be NA. -----------------------------------------------------#
lu$gpp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$npp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.agb = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.biomass = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.lai = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.gpp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.npp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.ba = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$dist = array (data=NA,dim=c(ntimes,nlu,nlu))
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMEAN -- Polygon-level variables, containing the mean diel (diurnal cycle). #
#---------------------------------------------------------------------------------------#
qmean = list()
qmean$gpp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$npp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$plant.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$root.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$froot.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$het.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$cwd.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$soil.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.light = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.rubp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.co2 = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.ratio = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$nep = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$nee = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$reco = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$cflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$cflxst = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$qwflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$runoff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$intercepted = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wshed = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$evap = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$transp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.water = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wood.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$gnd.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.shv = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.shv = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$gnd.shv = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.vpd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.vpd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.vpd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.co2 = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.co2 = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.prss = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.prss = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.vels = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$ustar = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$sm.stress = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rain = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort.beam = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort.diff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort.gnd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshortup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlong = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlong.gnd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlongup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.tot = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.beam = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.diff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.gnd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$parup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.leaf = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.leaf.beam = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.leaf.diff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rnet = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$albedo = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$albedo.par = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$albedo.nir = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlong.albedo = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.gsw = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.gbw = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wood.gbw = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMSQU -- Polygon-level variables, containing the mean sum of squares for the diel #
# (diurnal cycle). #
#---------------------------------------------------------------------------------------#
qmsqu = list()
qmsqu$gpp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$npp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$plant.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$leaf.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$froot.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$root.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$het.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$cwd.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$nep = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$reco = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$cflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$cflxst = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$qwflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$transp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$ustar = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$albedo = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$rshortup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$rlongup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$parup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$rnet = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# PATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
patch = list()
patch$ipa = list()
patch$age = list()
patch$area = list()
patch$lu = list()
patch$nep = list()
patch$het.resp = list()
patch$soil.resp = list()
patch$can.temp = list()
patch$gnd.temp = list()
patch$can.shv = list()
patch$gnd.shv = list()
patch$can.vpd = list()
patch$can.co2 = list()
patch$can.prss = list()
patch$cflxca = list()
patch$cflxst = list()
patch$nee = list()
patch$hflxca = list()
patch$hflxgc = list()
patch$qwflxca = list()
patch$wflxca = list()
patch$wflxgc = list()
patch$ustar = list()
patch$albedo = list()
patch$rshortup = list()
patch$rlongup = list()
patch$parup = list()
patch$rshort.gnd = list()
patch$par.gnd = list()
patch$par.leaf = list()
patch$par.leaf.beam = list()
patch$par.leaf.diff = list()
patch$rnet = list()
patch$lai = list()
patch$wai = list()
patch$tai = list()
patch$agb = list()
patch$ba = list()
patch$wood.dens = list()
patch$can.depth = list()
patch$can.area = list()
patch$phap.lpar = list()
patch$phap.ltemp = list()
patch$phap.lwater = list()
patch$phap.lvpd = list()
patch$phap.sms = list()
patch$phap.lgbw = list()
patch$phap.lgsw = list()
patch$sm.stress = list()
patch$leaf.temp = list()
patch$leaf.water = list()
patch$leaf.vpd = list()
patch$leaf.gpp = list()
patch$leaf.gsw = list()
patch$leaf.par = list()
patch$leaf.par.beam = list()
patch$leaf.par.diff = list()
patch$assim.light = list()
patch$assim.rubp = list()
patch$assim.co2 = list()
patch$wood.temp = list()
patch$gpp = list()
patch$npp = list()
patch$plant.resp = list()
patch$cba = list()
patch$reco = list()
patch$hflxlc = list()
patch$hflxwc = list()
patch$wflxlc = list()
patch$wflxwc = list()
patch$transp = list()
patch$fast.soil.c = list()
patch$slow.soil.c = list()
patch$struct.soil.c = list()
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QPATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
qpatch = list()
qpatch$nep = list()
qpatch$het.resp = list()
qpatch$can.temp = list()
qpatch$gnd.temp = list()
qpatch$can.shv = list()
qpatch$gnd.shv = list()
qpatch$can.vpd = list()
qpatch$can.co2 = list()
qpatch$can.prss = list()
qpatch$cflxca = list()
qpatch$cflxst = list()
qpatch$nee = list()
qpatch$hflxca = list()
qpatch$hflxgc = list()
qpatch$qwflxca = list()
qpatch$wflxca = list()
qpatch$wflxgc = list()
qpatch$ustar = list()
qpatch$albedo = list()
qpatch$rshortup = list()
qpatch$rlongup = list()
qpatch$parup = list()
qpatch$rshort.gnd = list()
qpatch$par.gnd = list()
qpatch$rnet = list()
qpatch$sm.stress = list()
qpatch$leaf.temp = list()
qpatch$leaf.water = list()
qpatch$leaf.vpd = list()
qpatch$wood.temp = list()
qpatch$par.leaf = list()
qpatch$par.leaf.beam = list()
qpatch$par.leaf.diff = list()
qpatch$leaf.gpp = list()
qpatch$leaf.gsw = list()
qpatch$leaf.par = list()
qpatch$leaf.par.beam = list()
qpatch$leaf.par.diff = list()
qpatch$assim.light = list()
qpatch$assim.rubp = list()
qpatch$assim.co2 = list()
qpatch$gpp = list()
qpatch$npp = list()
qpatch$plant.resp = list()
qpatch$hflxlc = list()
qpatch$hflxwc = list()
qpatch$wflxlc = list()
qpatch$wflxwc = list()
qpatch$transp = list()
qpatch$soil.resp = list()
#---------------------------------------------------------------------------------------#
#----- Cohort level, we save as lists because the dimensions vary. ---------------------#
cohort = list()
cohort$ipa = list()
cohort$ico = list()
cohort$area = list()
cohort$lu = list()
cohort$dbh = list()
cohort$age = list()
cohort$pft = list()
cohort$nplant = list()
cohort$height = list()
cohort$ba = list()
cohort$agb = list()
cohort$biomass = list()
cohort$lai = list()
cohort$wai = list()
cohort$tai = list()
cohort$gpp = list()
cohort$leaf.resp = list()
cohort$root.resp = list()
cohort$froot.resp = list()
cohort$croot.resp = list()
cohort$stem.resp = list()
cohort$growth.resp = list()
cohort$storage.resp = list()
cohort$plant.resp = list()
cohort$assim.light = list()
cohort$assim.rubp = list()
cohort$assim.co2 = list()
cohort$assim.ratio = list()
cohort$npp = list()
cohort$cba = list()
cohort$cbamax = list()
cohort$cbalight = list()
cohort$cbamoist = list()
cohort$cbarel = list()
cohort$dcbadt = list()
cohort$mcost = list()
cohort$ldrop = list()
cohort$sm.stress = list()
cohort$phap.sms = list()
cohort$light = list()
cohort$light.beam = list()
cohort$light.diff = list()
cohort$balive = list()
cohort$bdead = list()
cohort$bleaf = list()
cohort$bstem = list()
cohort$broot = list()
cohort$bfroot = list()
cohort$bcroot = list()
cohort$bsapwood = list()
cohort$bstorage = list()
cohort$bseeds = list()
cohort$hflxlc = list()
cohort$wflxlc = list()
cohort$transp = list()
cohort$wue = list()
cohort$cue = list()
cohort$ecue = list()
cohort$etue = list()
cohort$demand = list()
cohort$supply = list()
cohort$mort = list()
cohort$dimort = list()
cohort$ncbmort = list()
cohort$recruit = list()
cohort$growth = list()
cohort$agb.growth = list()
cohort$bsa.growth = list()
cohort$f.gpp = list()
cohort$f.plant.resp = list()
cohort$f.npp = list()
cohort$f.mco = list()
cohort$f.cba = list()
cohort$f.bstorage = list()
cohort$f.dcbadt = list()
cohort$f.bleaf = list()
cohort$f.bstem = list()
cohort$f.broot = list()
cohort$f.bseeds = list()
cohort$leaf.par = list()
cohort$leaf.par.beam = list()
cohort$leaf.par.diff = list()
cohort$leaf.gpp = list()
cohort$phap.lpar = list()
cohort$leaf.rshort = list()
cohort$leaf.rlong = list()
cohort$rue = list()
#---------------------------------------------------------------------------------------#
#----- Copy the polygon-level variable to the main structure. --------------------------#
ed$emean = emean
ed$emsqu = emsqu
ed$qmean = qmean
ed$qmsqu = qmsqu
ed$lu = lu
ed$szpft = szpft
ed$patch = patch
ed$cohort = cohort
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
return(ed)
#---------------------------------------------------------------------------------------#
}#end create.monthly
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Expand the monthly array so it fits the new times. #
#------------------------------------------------------------------------------------------#
update.monthly <<- function(new.ntimes,old.datum,montha,yeara,inpref,slz.min){
#----- Create the new data set. --------------------------------------------------------#
new.datum = create.monthly(new.ntimes,montha,yeara,inpref,slz.min)
#---------------------------------------------------------------------------------------#
#----- Find out which times to copy. ---------------------------------------------------#
sel = old.datum$when %in% new.datum$when
idx = match(old.datum$when[sel],new.datum$when)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emean -- variables that we can either compare directly with observations, or are #
# or that may be used to draw time series. They don't need to be really #
# monthly means, but you should put only the variables that make sense to be #
# plotted in simple time series (with no PFT or DBH information). #
#---------------------------------------------------------------------------------------#
new.datum$emean$wood.dens [idx ] = old.datum$emean$wood.dens [sel ]
new.datum$emean$fast.soil.c [idx ] = old.datum$emean$fast.soil.c [sel ]
new.datum$emean$slow.soil.c [idx ] = old.datum$emean$slow.soil.c [sel ]
new.datum$emean$struct.soil.c [idx ] = old.datum$emean$struct.soil.c [sel ]
new.datum$emean$het.resp [idx ] = old.datum$emean$het.resp [sel ]
new.datum$emean$cwd.resp [idx ] = old.datum$emean$cwd.resp [sel ]
new.datum$emean$soil.resp [idx ] = old.datum$emean$soil.resp [sel ]
new.datum$emean$gpp [idx ] = old.datum$emean$gpp [sel ]
new.datum$emean$last.1yr.gpp [idx ] = old.datum$emean$last.1yr.gpp [sel ]
new.datum$emean$last.2yr.gpp [idx ] = old.datum$emean$last.2yr.gpp [sel ]
new.datum$emean$last.3yr.gpp [idx ] = old.datum$emean$last.3yr.gpp [sel ]
new.datum$emean$cue [idx ] = old.datum$emean$cue [sel ]
new.datum$emean$last.1yr.cue [idx ] = old.datum$emean$last.1yr.cue [sel ]
new.datum$emean$last.2yr.cue [idx ] = old.datum$emean$last.2yr.cue [sel ]
new.datum$emean$last.3yr.cue [idx ] = old.datum$emean$last.3yr.cue [sel ]
new.datum$emean$ecue [idx ] = old.datum$emean$ecue [sel ]
new.datum$emean$last.1yr.ecue [idx ] = old.datum$emean$last.1yr.ecue [sel ]
new.datum$emean$last.2yr.ecue [idx ] = old.datum$emean$last.2yr.ecue [sel ]
new.datum$emean$last.3yr.ecue [idx ] = old.datum$emean$last.3yr.ecue [sel ]
new.datum$emean$npp [idx ] = old.datum$emean$npp [sel ]
new.datum$emean$last.1yr.npp [idx ] = old.datum$emean$last.1yr.npp [sel ]
new.datum$emean$last.2yr.npp [idx ] = old.datum$emean$last.2yr.npp [sel ]
new.datum$emean$last.3yr.npp [idx ] = old.datum$emean$last.3yr.npp [sel ]
new.datum$emean$dcbadt [idx ] = old.datum$emean$dcbadt [sel ]
new.datum$emean$last.1yr.dcbadt [idx ] = old.datum$emean$last.1yr.dcbadt [sel ]
new.datum$emean$last.2yr.dcbadt [idx ] = old.datum$emean$last.2yr.dcbadt [sel ]
new.datum$emean$last.3yr.dcbadt [idx ] = old.datum$emean$last.3yr.dcbadt [sel ]
new.datum$emean$plant.resp [idx ] = old.datum$emean$plant.resp [sel ]
new.datum$emean$last.1yr.plresp [idx ] = old.datum$emean$last.1yr.plresp [sel ]
new.datum$emean$last.2yr.plresp [idx ] = old.datum$emean$last.2yr.plresp [sel ]
new.datum$emean$last.3yr.plresp [idx ] = old.datum$emean$last.3yr.plresp [sel ]
new.datum$emean$leaf.resp [idx ] = old.datum$emean$leaf.resp [sel ]
new.datum$emean$root.resp [idx ] = old.datum$emean$root.resp [sel ]
new.datum$emean$froot.resp [idx ] = old.datum$emean$froot.resp [sel ]
new.datum$emean$croot.resp [idx ] = old.datum$emean$croot.resp [sel ]
new.datum$emean$stem.resp [idx ] = old.datum$emean$stem.resp [sel ]
new.datum$emean$growth.resp [idx ] = old.datum$emean$growth.resp [sel ]
new.datum$emean$storage.resp [idx ] = old.datum$emean$storage.resp [sel ]
new.datum$emean$reco [idx ] = old.datum$emean$reco [sel ]
new.datum$emean$assim.light [idx ] = old.datum$emean$assim.light [sel ]
new.datum$emean$assim.rubp [idx ] = old.datum$emean$assim.rubp [sel ]
new.datum$emean$assim.co2 [idx ] = old.datum$emean$assim.co2 [sel ]
new.datum$emean$assim.ratio [idx ] = old.datum$emean$assim.ratio [sel ]
new.datum$emean$mco [idx ] = old.datum$emean$mco [sel ]
new.datum$emean$cba [idx ] = old.datum$emean$cba [sel ]
new.datum$emean$last.1yr.cba [idx ] = old.datum$emean$last.1yr.cba [sel ]
new.datum$emean$last.2yr.cba [idx ] = old.datum$emean$last.2yr.cba [sel ]
new.datum$emean$last.3yr.cba [idx ] = old.datum$emean$last.3yr.cba [sel ]
new.datum$emean$cbamax [idx ] = old.datum$emean$cbamax [sel ]
new.datum$emean$cbalight [idx ] = old.datum$emean$cbalight [sel ]
new.datum$emean$cbamoist [idx ] = old.datum$emean$cbamoist [sel ]
new.datum$emean$cbarel [idx ] = old.datum$emean$cbarel [sel ]
new.datum$emean$ldrop [idx ] = old.datum$emean$ldrop [sel ]
new.datum$emean$nep [idx ] = old.datum$emean$nep [sel ]
new.datum$emean$nee [idx ] = old.datum$emean$nee [sel ]
new.datum$emean$cflxca [idx ] = old.datum$emean$cflxca [sel ]
new.datum$emean$cflxst [idx ] = old.datum$emean$cflxst [sel ]
new.datum$emean$runoff [idx ] = old.datum$emean$runoff [sel ]
new.datum$emean$intercepted [idx ] = old.datum$emean$intercepted [sel ]
new.datum$emean$wshed [idx ] = old.datum$emean$wshed [sel ]
new.datum$emean$evap [idx ] = old.datum$emean$evap [sel ]
new.datum$emean$last.1yr.evap [idx ] = old.datum$emean$last.1yr.evap [sel ]
new.datum$emean$last.2yr.evap [idx ] = old.datum$emean$last.2yr.evap [sel ]
new.datum$emean$last.3yr.evap [idx ] = old.datum$emean$last.3yr.evap [sel ]
new.datum$emean$ustar [idx ] = old.datum$emean$ustar [sel ]
new.datum$emean$atm.vels [idx ] = old.datum$emean$atm.vels [sel ]
new.datum$emean$atm.prss [idx ] = old.datum$emean$atm.prss [sel ]
new.datum$emean$atm.temp [idx ] = old.datum$emean$atm.temp [sel ]
new.datum$emean$can.prss [idx ] = old.datum$emean$can.prss [sel ]
new.datum$emean$can.temp [idx ] = old.datum$emean$can.temp [sel ]
new.datum$emean$atm.co2 [idx ] = old.datum$emean$atm.co2 [sel ]
new.datum$emean$can.co2 [idx ] = old.datum$emean$can.co2 [sel ]
new.datum$emean$can.depth [idx ] = old.datum$emean$can.depth [sel ]
new.datum$emean$can.area [idx ] = old.datum$emean$can.area [sel ]
new.datum$emean$leaf.temp [idx ] = old.datum$emean$leaf.temp [sel ]
new.datum$emean$phap.ltemp [idx ] = old.datum$emean$phap.ltemp [sel ]
new.datum$emean$last.1yr.ltemp [idx ] = old.datum$emean$last.1yr.ltemp [sel ]
new.datum$emean$last.2yr.ltemp [idx ] = old.datum$emean$last.2yr.ltemp [sel ]
new.datum$emean$last.3yr.ltemp [idx ] = old.datum$emean$last.3yr.ltemp [sel ]
new.datum$emean$leaf.water [idx ] = old.datum$emean$leaf.water [sel ]
new.datum$emean$phap.lwater [idx ] = old.datum$emean$phap.lwater [sel ]
new.datum$emean$last.1yr.lwater [idx ] = old.datum$emean$last.1yr.lwater [sel ]
new.datum$emean$last.2yr.lwater [idx ] = old.datum$emean$last.2yr.lwater [sel ]
new.datum$emean$last.3yr.lwater [idx ] = old.datum$emean$last.3yr.lwater [sel ]
new.datum$emean$wood.temp [idx ] = old.datum$emean$wood.temp [sel ]
new.datum$emean$atm.shv [idx ] = old.datum$emean$atm.shv [sel ]
new.datum$emean$can.shv [idx ] = old.datum$emean$can.shv [sel ]
new.datum$emean$atm.vpd [idx ] = old.datum$emean$atm.vpd [sel ]
new.datum$emean$can.vpd [idx ] = old.datum$emean$can.vpd [sel ]
new.datum$emean$leaf.vpd [idx ] = old.datum$emean$leaf.vpd [sel ]
new.datum$emean$phap.lvpd [idx ] = old.datum$emean$phap.lvpd [sel ]
new.datum$emean$last.1yr.lvpd [idx ] = old.datum$emean$last.1yr.lvpd [sel ]
new.datum$emean$last.2yr.lvpd [idx ] = old.datum$emean$last.2yr.lvpd [sel ]
new.datum$emean$last.3yr.lvpd [idx ] = old.datum$emean$last.3yr.lvpd [sel ]
new.datum$emean$can.co2 [idx ] = old.datum$emean$can.co2 [sel ]
new.datum$emean$hflxca [idx ] = old.datum$emean$hflxca [sel ]
new.datum$emean$qwflxca [idx ] = old.datum$emean$qwflxca [sel ]
new.datum$emean$wflxca [idx ] = old.datum$emean$wflxca [sel ]
new.datum$emean$agb [idx ] = old.datum$emean$agb [sel ]
new.datum$emean$biomass [idx ] = old.datum$emean$biomass [sel ]
new.datum$emean$nplant [idx ] = old.datum$emean$nplant [sel ]
new.datum$emean$lai [idx ] = old.datum$emean$lai [sel ]
new.datum$emean$wai [idx ] = old.datum$emean$wai [sel ]
new.datum$emean$tai [idx ] = old.datum$emean$tai [sel ]
new.datum$emean$area [idx ] = old.datum$emean$area [sel ]
new.datum$emean$et [idx ] = old.datum$emean$et [sel ]
new.datum$emean$last.1yr.et [idx ] = old.datum$emean$last.1yr.et [sel ]
new.datum$emean$last.2yr.et [idx ] = old.datum$emean$last.2yr.et [sel ]
new.datum$emean$last.3yr.et [idx ] = old.datum$emean$last.3yr.et [sel ]
new.datum$emean$transp [idx ] = old.datum$emean$transp [sel ]
new.datum$emean$last.1yr.transp [idx ] = old.datum$emean$last.1yr.transp [sel ]
new.datum$emean$last.2yr.transp [idx ] = old.datum$emean$last.2yr.transp [sel ]
new.datum$emean$last.3yr.transp [idx ] = old.datum$emean$last.3yr.transp [sel ]
new.datum$emean$wue [idx ] = old.datum$emean$wue [sel ]
new.datum$emean$last.1yr.wue [idx ] = old.datum$emean$last.1yr.wue [sel ]
new.datum$emean$last.2yr.wue [idx ] = old.datum$emean$last.2yr.wue [sel ]
new.datum$emean$last.3yr.wue [idx ] = old.datum$emean$last.3yr.wue [sel ]
new.datum$emean$etue [idx ] = old.datum$emean$etue [sel ]
new.datum$emean$last.1yr.etue [idx ] = old.datum$emean$last.1yr.etue [sel ]
new.datum$emean$last.2yr.etue [idx ] = old.datum$emean$last.2yr.etue [sel ]
new.datum$emean$last.3yr.etue [idx ] = old.datum$emean$last.3yr.etue [sel ]
new.datum$emean$rain [idx ] = old.datum$emean$rain [sel ]
new.datum$emean$last.1yr.rain [idx ] = old.datum$emean$last.1yr.rain [sel ]
new.datum$emean$last.2yr.rain [idx ] = old.datum$emean$last.2yr.rain [sel ]
new.datum$emean$last.3yr.rain [idx ] = old.datum$emean$last.3yr.rain [sel ]
new.datum$emean$nmon.lt.090 [idx ] = old.datum$emean$nmon.lt.090 [sel ]
new.datum$emean$nmon.lt.100 [idx ] = old.datum$emean$nmon.lt.100 [sel ]
new.datum$emean$nmon.lt.110 [idx ] = old.datum$emean$nmon.lt.110 [sel ]
new.datum$emean$nmon.lt.120 [idx ] = old.datum$emean$nmon.lt.120 [sel ]
new.datum$emean$nmon.wdef [idx ] = old.datum$emean$nmon.wdef [sel ]
new.datum$emean$nmon.mdef [idx ] = old.datum$emean$nmon.mdef [sel ]
new.datum$emean$rue [idx ] = old.datum$emean$rue [sel ]
new.datum$emean$last.1yr.rue [idx ] = old.datum$emean$last.1yr.rue [sel ]
new.datum$emean$last.2yr.rue [idx ] = old.datum$emean$last.2yr.rue [sel ]
new.datum$emean$last.3yr.rue [idx ] = old.datum$emean$last.3yr.rue [sel ]
new.datum$emean$gnd.temp [idx ] = old.datum$emean$gnd.temp [sel ]
new.datum$emean$gnd.shv [idx ] = old.datum$emean$gnd.shv [sel ]
new.datum$emean$workload [idx ] = old.datum$emean$workload [sel ]
new.datum$emean$specwork [idx ] = old.datum$emean$specwork [sel ]
new.datum$emean$sm.stress [idx ] = old.datum$emean$sm.stress [sel ]
new.datum$emean$phap.sms [idx ] = old.datum$emean$phap.sms [sel ]
new.datum$emean$last.1yr.sms [idx ] = old.datum$emean$last.1yr.sms [sel ]
new.datum$emean$last.2yr.sms [idx ] = old.datum$emean$last.2yr.sms [sel ]
new.datum$emean$last.3yr.sms [idx ] = old.datum$emean$last.3yr.sms [sel ]
new.datum$emean$demand [idx ] = old.datum$emean$demand [sel ]
new.datum$emean$supply [idx ] = old.datum$emean$supply [sel ]
new.datum$emean$hflxgc [idx ] = old.datum$emean$hflxgc [sel ]
new.datum$emean$hflxlc [idx ] = old.datum$emean$hflxlc [sel ]
new.datum$emean$hflxwc [idx ] = old.datum$emean$hflxwc [sel ]
new.datum$emean$wflxgc [idx ] = old.datum$emean$wflxgc [sel ]
new.datum$emean$wflxlc [idx ] = old.datum$emean$wflxlc [sel ]
new.datum$emean$wflxwc [idx ] = old.datum$emean$wflxwc [sel ]
new.datum$emean$rshort [idx ] = old.datum$emean$rshort [sel ]
new.datum$emean$last.1yr.rshort [idx ] = old.datum$emean$last.1yr.rshort [sel ]
new.datum$emean$last.2yr.rshort [idx ] = old.datum$emean$last.2yr.rshort [sel ]
new.datum$emean$last.3yr.rshort [idx ] = old.datum$emean$last.3yr.rshort [sel ]
new.datum$emean$rshort.beam [idx ] = old.datum$emean$rshort.beam [sel ]
new.datum$emean$rshort.diff [idx ] = old.datum$emean$rshort.diff [sel ]
new.datum$emean$rshortup [idx ] = old.datum$emean$rshortup [sel ]
new.datum$emean$rshort.gnd [idx ] = old.datum$emean$rshort.gnd [sel ]
new.datum$emean$rlong [idx ] = old.datum$emean$rlong [sel ]
new.datum$emean$rlong.gnd [idx ] = old.datum$emean$rlong.gnd [sel ]
new.datum$emean$rlongup [idx ] = old.datum$emean$rlongup [sel ]
new.datum$emean$par.tot [idx ] = old.datum$emean$par.tot [sel ]
new.datum$emean$par.beam [idx ] = old.datum$emean$par.beam [sel ]
new.datum$emean$par.diff [idx ] = old.datum$emean$par.diff [sel ]
new.datum$emean$par.gnd [idx ] = old.datum$emean$par.gnd [sel ]
new.datum$emean$parup [idx ] = old.datum$emean$parup [sel ]
new.datum$emean$par.leaf [idx ] = old.datum$emean$par.leaf [sel ]
new.datum$emean$par.leaf.beam [idx ] = old.datum$emean$par.leaf.beam [sel ]
new.datum$emean$par.leaf.diff [idx ] = old.datum$emean$par.leaf.diff [sel ]
new.datum$emean$rnet [idx ] = old.datum$emean$rnet [sel ]
new.datum$emean$albedo [idx ] = old.datum$emean$albedo [sel ]
new.datum$emean$albedo.par [idx ] = old.datum$emean$albedo.par [sel ]
new.datum$emean$albedo.nir [idx ] = old.datum$emean$albedo.nir [sel ]
new.datum$emean$rlong.albedo [idx ] = old.datum$emean$rlong.albedo [sel ]
new.datum$emean$paw [idx ] = old.datum$emean$paw [sel ]
new.datum$emean$smpot [idx ] = old.datum$emean$smpot [sel ]
new.datum$emean$last.1yr.smpot [idx ] = old.datum$emean$last.1yr.smpot [sel ]
new.datum$emean$last.2yr.smpot [idx ] = old.datum$emean$last.2yr.smpot [sel ]
new.datum$emean$last.3yr.smpot [idx ] = old.datum$emean$last.3yr.smpot [sel ]
new.datum$emean$npat.global [idx ] = old.datum$emean$npat.global [sel ]
new.datum$emean$ncoh.global [idx ] = old.datum$emean$ncoh.global [sel ]
new.datum$emean$water.deficit [idx ] = old.datum$emean$water.deficit [sel ]
new.datum$emean$last.1yr.mwd [idx ] = old.datum$emean$last.1yr.mwd [sel ]
new.datum$emean$last.2yr.mwd [idx ] = old.datum$emean$last.2yr.mwd [sel ]
new.datum$emean$last.3yr.mwd [idx ] = old.datum$emean$last.3yr.mwd [sel ]
new.datum$emean$malhi.deficit [idx ] = old.datum$emean$malhi.deficit [sel ]
new.datum$emean$i.gpp [idx ] = old.datum$emean$i.gpp [sel ]
new.datum$emean$i.npp [idx ] = old.datum$emean$i.npp [sel ]
new.datum$emean$i.plant.resp [idx ] = old.datum$emean$i.plant.resp [sel ]
new.datum$emean$i.mco [idx ] = old.datum$emean$i.mco [sel ]
new.datum$emean$i.cba [idx ] = old.datum$emean$i.cba [sel ]
new.datum$emean$i.cbamax [idx ] = old.datum$emean$i.cbamax [sel ]
new.datum$emean$i.cbalight [idx ] = old.datum$emean$i.cbalight [sel ]
new.datum$emean$i.cbamoist [idx ] = old.datum$emean$i.cbamoist [sel ]
new.datum$emean$i.transp [idx ] = old.datum$emean$i.transp [sel ]
new.datum$emean$i.wflxlc [idx ] = old.datum$emean$i.wflxlc [sel ]
new.datum$emean$i.hflxlc [idx ] = old.datum$emean$i.hflxlc [sel ]
new.datum$emean$f.gpp [idx ] = old.datum$emean$f.gpp [sel ]
new.datum$emean$f.plant.resp [idx ] = old.datum$emean$f.plant.resp [sel ]
new.datum$emean$f.npp [idx ] = old.datum$emean$f.npp [sel ]
new.datum$emean$f.mco [idx ] = old.datum$emean$f.mco [sel ]
new.datum$emean$f.cba [idx ] = old.datum$emean$f.cba [sel ]
new.datum$emean$f.bstorage [idx ] = old.datum$emean$f.bstorage [sel ]
new.datum$emean$f.bleaf [idx ] = old.datum$emean$f.bleaf [sel ]
new.datum$emean$f.bstem [idx ] = old.datum$emean$f.bstem [sel ]
new.datum$emean$f.broot [idx ] = old.datum$emean$f.broot [sel ]
new.datum$emean$f.bseeds [idx ] = old.datum$emean$f.bseeds [sel ]
new.datum$emean$f.dcbadt [idx ] = old.datum$emean$f.dcbadt [sel ]
new.datum$emean$leaf.gsw [idx ] = old.datum$emean$leaf.gsw [sel ]
new.datum$emean$phap.lgsw [idx ] = old.datum$emean$phap.lgsw [sel ]
new.datum$emean$last.1yr.lgsw [idx ] = old.datum$emean$last.1yr.lgsw [sel ]
new.datum$emean$last.2yr.lgsw [idx ] = old.datum$emean$last.2yr.lgsw [sel ]
new.datum$emean$last.3yr.lgsw [idx ] = old.datum$emean$last.3yr.lgsw [sel ]
new.datum$emean$leaf.gbw [idx ] = old.datum$emean$leaf.gbw [sel ]
new.datum$emean$phap.lgbw [idx ] = old.datum$emean$phap.lgbw [sel ]
new.datum$emean$wood.gbw [idx ] = old.datum$emean$wood.gbw [sel ]
new.datum$emean$leaf.par [idx ] = old.datum$emean$leaf.par [sel ]
new.datum$emean$leaf.par.beam [idx ] = old.datum$emean$leaf.par.beam [sel ]
new.datum$emean$leaf.par.diff [idx ] = old.datum$emean$leaf.par.diff [sel ]
new.datum$emean$leaf.gpp [idx ] = old.datum$emean$leaf.gpp [sel ]
new.datum$emean$phap.lpar [idx ] = old.datum$emean$phap.lpar [sel ]
new.datum$emean$last.1yr.lpar [idx ] = old.datum$emean$last.1yr.lpar [sel ]
new.datum$emean$last.2yr.lpar [idx ] = old.datum$emean$last.2yr.lpar [sel ]
new.datum$emean$last.3yr.lpar [idx ] = old.datum$emean$last.3yr.lpar [sel ]
new.datum$emean$leaf.rshort [idx ] = old.datum$emean$leaf.rshort [sel ]
new.datum$emean$leaf.rlong [idx ] = old.datum$emean$leaf.rlong [sel ]
new.datum$emean$soil.water [idx,] = old.datum$emean$soil.water [sel,]
new.datum$emean$soil.temp [idx,] = old.datum$emean$soil.temp [sel,]
new.datum$emean$soil.mstpot [idx,] = old.datum$emean$soil.mstpot [sel,]
new.datum$emean$soil.extracted [idx,] = old.datum$emean$soil.extracted [sel,]
new.datum$emean$last.1yr.growth [idx ] = old.datum$emean$last.1yr.growth [sel ]
new.datum$emean$last.2yr.growth [idx ] = old.datum$emean$last.2yr.growth [sel ]
new.datum$emean$last.3yr.growth [idx ] = old.datum$emean$last.3yr.growth [sel ]
new.datum$emean$last.1yr.mort [idx ] = old.datum$emean$last.1yr.mort [sel ]
new.datum$emean$last.2yr.mort [idx ] = old.datum$emean$last.2yr.mort [sel ]
new.datum$emean$last.3yr.mort [idx ] = old.datum$emean$last.3yr.mort [sel ]
new.datum$emean$last.1yr.dimort [idx ] = old.datum$emean$last.1yr.dimort [sel ]
new.datum$emean$last.2yr.dimort [idx ] = old.datum$emean$last.2yr.dimort [sel ]
new.datum$emean$last.3yr.dimort [idx ] = old.datum$emean$last.3yr.dimort [sel ]
new.datum$emean$last.1yr.ncbmort [idx ] = old.datum$emean$last.1yr.ncbmort [sel ]
new.datum$emean$last.2yr.ncbmort [idx ] = old.datum$emean$last.2yr.ncbmort [sel ]
new.datum$emean$last.3yr.ncbmort [idx ] = old.datum$emean$last.3yr.ncbmort [sel ]
new.datum$emean$agb.change [idx ] = old.datum$emean$agb.change [sel ]
new.datum$emean$acc.change [idx ] = old.datum$emean$acc.change [sel ]
new.datum$emean$acc.growth [idx ] = old.datum$emean$acc.growth [sel ]
new.datum$emean$acc.mort [idx ] = old.datum$emean$acc.mort [sel ]
new.datum$emean$acc.ncbmort [idx ] = old.datum$emean$acc.ncbmort [sel ]
new.datum$emean$acc.dimort [idx ] = old.datum$emean$acc.dimort [sel ]
new.datum$emean$acc.recr [idx ] = old.datum$emean$acc.recr [sel ]
new.datum$emean$last.1yr.change [idx ] = old.datum$emean$last.1yr.change [sel ]
new.datum$emean$last.2yr.change [idx ] = old.datum$emean$last.2yr.change [sel ]
new.datum$emean$last.3yr.change [idx ] = old.datum$emean$last.3yr.change [sel ]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emsqu -- mean sum of squares of polygon-level variable. #
#---------------------------------------------------------------------------------------#
new.datum$emsqu$gpp [idx] = old.datum$emsqu$gpp [sel]
new.datum$emsqu$plant.resp [idx] = old.datum$emsqu$plant.resp [sel]
new.datum$emsqu$het.resp [idx] = old.datum$emsqu$het.resp [sel]
new.datum$emsqu$cwd.resp [idx] = old.datum$emsqu$cwd.resp [sel]
new.datum$emsqu$soil.resp [idx] = old.datum$emsqu$soil.resp [sel]
new.datum$emsqu$cflxca [idx] = old.datum$emsqu$cflxca [sel]
new.datum$emsqu$cflxst [idx] = old.datum$emsqu$cflxst [sel]
new.datum$emsqu$hflxca [idx] = old.datum$emsqu$hflxca [sel]
new.datum$emsqu$hflxlc [idx] = old.datum$emsqu$hflxlc [sel]
new.datum$emsqu$hflxwc [idx] = old.datum$emsqu$hflxwc [sel]
new.datum$emsqu$hflxgc [idx] = old.datum$emsqu$hflxgc [sel]
new.datum$emsqu$wflxca [idx] = old.datum$emsqu$wflxca [sel]
new.datum$emsqu$qwflxca [idx] = old.datum$emsqu$qwflxca [sel]
new.datum$emsqu$wflxlc [idx] = old.datum$emsqu$wflxlc [sel]
new.datum$emsqu$wflxwc [idx] = old.datum$emsqu$wflxwc [sel]
new.datum$emsqu$wflxgc [idx] = old.datum$emsqu$wflxgc [sel]
new.datum$emsqu$transp [idx] = old.datum$emsqu$transp [sel]
new.datum$emsqu$ustar [idx] = old.datum$emsqu$ustar [sel]
new.datum$emsqu$albedo [idx] = old.datum$emsqu$albedo [sel]
new.datum$emsqu$rshortup [idx] = old.datum$emsqu$rshortup [sel]
new.datum$emsqu$rlongup [idx] = old.datum$emsqu$rlongup [sel]
new.datum$emsqu$parup [idx] = old.datum$emsqu$parup [sel]
new.datum$emsqu$rnet [idx] = old.datum$emsqu$rnet [sel]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# SZPFT -- Size (DBH) and plant functional type (PFT) array. An extra level is #
# appended to the end, which will hold the sum of all categories. #
#---------------------------------------------------------------------------------------#
new.datum$szpft$agb [idx,,] = old.datum$szpft$agb [sel,,]
new.datum$szpft$biomass [idx,,] = old.datum$szpft$biomass [sel,,]
new.datum$szpft$lai [idx,,] = old.datum$szpft$lai [sel,,]
new.datum$szpft$wai [idx,,] = old.datum$szpft$wai [sel,,]
new.datum$szpft$tai [idx,,] = old.datum$szpft$tai [sel,,]
new.datum$szpft$ba [idx,,] = old.datum$szpft$ba [sel,,]
new.datum$szpft$gpp [idx,,] = old.datum$szpft$gpp [sel,,]
new.datum$szpft$npp [idx,,] = old.datum$szpft$npp [sel,,]
new.datum$szpft$dcbadt [idx,,] = old.datum$szpft$dcbadt [sel,,]
new.datum$szpft$wood.dens [idx,,] = old.datum$szpft$wood.dens [sel,,]
new.datum$szpft$leaf.resp [idx,,] = old.datum$szpft$leaf.resp [sel,,]
new.datum$szpft$root.resp [idx,,] = old.datum$szpft$root.resp [sel,,]
new.datum$szpft$froot.resp [idx,,] = old.datum$szpft$froot.resp [sel,,]
new.datum$szpft$croot.resp [idx,,] = old.datum$szpft$croot.resp [sel,,]
new.datum$szpft$stem.resp [idx,,] = old.datum$szpft$stem.resp [sel,,]
new.datum$szpft$growth.resp [idx,,] = old.datum$szpft$growth.resp [sel,,]
new.datum$szpft$storage.resp [idx,,] = old.datum$szpft$storage.resp [sel,,]
new.datum$szpft$plant.resp [idx,,] = old.datum$szpft$plant.resp [sel,,]
new.datum$szpft$assim.light [idx,,] = old.datum$szpft$assim.light [sel,,]
new.datum$szpft$assim.rubp [idx,,] = old.datum$szpft$assim.rubp [sel,,]
new.datum$szpft$assim.co2 [idx,,] = old.datum$szpft$assim.co2 [sel,,]
new.datum$szpft$mco [idx,,] = old.datum$szpft$mco [sel,,]
new.datum$szpft$cba [idx,,] = old.datum$szpft$cba [sel,,]
new.datum$szpft$cbamax [idx,,] = old.datum$szpft$cbamax [sel,,]
new.datum$szpft$cbalight [idx,,] = old.datum$szpft$cbalight [sel,,]
new.datum$szpft$cbamoist [idx,,] = old.datum$szpft$cbamoist [sel,,]
new.datum$szpft$cbarel [idx,,] = old.datum$szpft$cbarel [sel,,]
new.datum$szpft$ldrop [idx,,] = old.datum$szpft$ldrop [sel,,]
new.datum$szpft$sm.stress [idx,,] = old.datum$szpft$sm.stress [sel,,]
new.datum$szpft$phap.sms [idx,,] = old.datum$szpft$phap.sms [sel,,]
new.datum$szpft$leaf.gbw [idx,,] = old.datum$szpft$leaf.gbw [sel,,]
new.datum$szpft$phap.lgbw [idx,,] = old.datum$szpft$phap.lgbw [sel,,]
new.datum$szpft$leaf.gsw [idx,,] = old.datum$szpft$leaf.gsw [sel,,]
new.datum$szpft$phap.lgsw [idx,,] = old.datum$szpft$phap.lgsw [sel,,]
new.datum$szpft$wood.gbw [idx,,] = old.datum$szpft$wood.gbw [sel,,]
new.datum$szpft$leaf.temp [idx,,] = old.datum$szpft$leaf.temp [sel,,]
new.datum$szpft$phap.ltemp [idx,,] = old.datum$szpft$phap.ltemp [sel,,]
new.datum$szpft$leaf.water [idx,,] = old.datum$szpft$leaf.water [sel,,]
new.datum$szpft$phap.lwater [idx,,] = old.datum$szpft$phap.lwater [sel,,]
new.datum$szpft$wood.temp [idx,,] = old.datum$szpft$wood.temp [sel,,]
new.datum$szpft$leaf.vpd [idx,,] = old.datum$szpft$leaf.vpd [sel,,]
new.datum$szpft$phap.lvpd [idx,,] = old.datum$szpft$phap.lvpd [sel,,]
new.datum$szpft$demand [idx,,] = old.datum$szpft$demand [sel,,]
new.datum$szpft$supply [idx,,] = old.datum$szpft$supply [sel,,]
new.datum$szpft$nplant [idx,,] = old.datum$szpft$nplant [sel,,]
new.datum$szpft$mort [idx,,] = old.datum$szpft$mort [sel,,]
new.datum$szpft$dimort [idx,,] = old.datum$szpft$dimort [sel,,]
new.datum$szpft$ncbmort [idx,,] = old.datum$szpft$ncbmort [sel,,]
new.datum$szpft$growth [idx,,] = old.datum$szpft$growth [sel,,]
new.datum$szpft$recr [idx,,] = old.datum$szpft$recr [sel,,]
new.datum$szpft$change [idx,,] = old.datum$szpft$change [sel,,]
new.datum$szpft$agb.mort [idx,,] = old.datum$szpft$agb.mort [sel,,]
new.datum$szpft$agb.dimort [idx,,] = old.datum$szpft$agb.dimort [sel,,]
new.datum$szpft$agb.ncbmort [idx,,] = old.datum$szpft$agb.ncbmort [sel,,]
new.datum$szpft$agb.growth [idx,,] = old.datum$szpft$agb.growth [sel,,]
new.datum$szpft$agb.recr [idx,,] = old.datum$szpft$agb.recr [sel,,]
new.datum$szpft$agb.change [idx,,] = old.datum$szpft$agb.change [sel,,]
new.datum$szpft$acc.mort [idx,,] = old.datum$szpft$acc.mort [sel,,]
new.datum$szpft$acc.dimort [idx,,] = old.datum$szpft$acc.dimort [sel,,]
new.datum$szpft$acc.ncbmort [idx,,] = old.datum$szpft$acc.ncbmort [sel,,]
new.datum$szpft$acc.growth [idx,,] = old.datum$szpft$acc.growth [sel,,]
new.datum$szpft$acc.recr [idx,,] = old.datum$szpft$acc.recr [sel,,]
new.datum$szpft$acc.change [idx,,] = old.datum$szpft$acc.change [sel,,]
new.datum$szpft$bsa.mort [idx,,] = old.datum$szpft$bsa.mort [sel,,]
new.datum$szpft$bsa.dimort [idx,,] = old.datum$szpft$bsa.dimort [sel,,]
new.datum$szpft$bsa.ncbmort [idx,,] = old.datum$szpft$bsa.ncbmort [sel,,]
new.datum$szpft$bsa.growth [idx,,] = old.datum$szpft$bsa.growth [sel,,]
new.datum$szpft$bsa.recr [idx,,] = old.datum$szpft$bsa.recr [sel,,]
new.datum$szpft$bsa.change [idx,,] = old.datum$szpft$bsa.change [sel,,]
new.datum$szpft$bdead [idx,,] = old.datum$szpft$bdead [sel,,]
new.datum$szpft$balive [idx,,] = old.datum$szpft$balive [sel,,]
new.datum$szpft$bleaf [idx,,] = old.datum$szpft$bleaf [sel,,]
new.datum$szpft$bstem [idx,,] = old.datum$szpft$bstem [sel,,]
new.datum$szpft$broot [idx,,] = old.datum$szpft$broot [sel,,]
new.datum$szpft$bfroot [idx,,] = old.datum$szpft$bfroot [sel,,]
new.datum$szpft$bcroot [idx,,] = old.datum$szpft$bcroot [sel,,]
new.datum$szpft$bsapwood [idx,,] = old.datum$szpft$bsapwood [sel,,]
new.datum$szpft$bstorage [idx,,] = old.datum$szpft$bstorage [sel,,]
new.datum$szpft$bseeds [idx,,] = old.datum$szpft$bseeds [sel,,]
new.datum$szpft$hflxlc [idx,,] = old.datum$szpft$hflxlc [sel,,]
new.datum$szpft$wflxlc [idx,,] = old.datum$szpft$wflxlc [sel,,]
new.datum$szpft$census.lai [idx,,] = old.datum$szpft$census.lai [sel,,]
new.datum$szpft$census.wai [idx,,] = old.datum$szpft$census.wai [sel,,]
new.datum$szpft$census.tai [idx,,] = old.datum$szpft$census.tai [sel,,]
new.datum$szpft$census.agb [idx,,] = old.datum$szpft$census.agb [sel,,]
new.datum$szpft$census.ba [idx,,] = old.datum$szpft$census.ba [sel,,]
new.datum$szpft$par.leaf [idx,,] = old.datum$szpft$par.leaf [sel,,]
new.datum$szpft$par.leaf.beam [idx,,] = old.datum$szpft$par.leaf.beam [sel,,]
new.datum$szpft$par.leaf.diff [idx,,] = old.datum$szpft$par.leaf.diff [sel,,]
new.datum$szpft$i.gpp [idx,,] = old.datum$szpft$i.gpp [sel,,]
new.datum$szpft$i.npp [idx,,] = old.datum$szpft$i.npp [sel,,]
new.datum$szpft$i.plant.resp [idx,,] = old.datum$szpft$i.plant.resp [sel,,]
new.datum$szpft$i.mco [idx,,] = old.datum$szpft$i.mco [sel,,]
new.datum$szpft$i.cba [idx,,] = old.datum$szpft$i.cba [sel,,]
new.datum$szpft$i.cbamax [idx,,] = old.datum$szpft$i.cbamax [sel,,]
new.datum$szpft$i.cbalight [idx,,] = old.datum$szpft$i.cbalight [sel,,]
new.datum$szpft$i.cbamoist [idx,,] = old.datum$szpft$i.cbamoist [sel,,]
new.datum$szpft$i.transp [idx,,] = old.datum$szpft$i.transp [sel,,]
new.datum$szpft$i.wflxlc [idx,,] = old.datum$szpft$i.wflxlc [sel,,]
new.datum$szpft$i.hflxlc [idx,,] = old.datum$szpft$i.hflxlc [sel,,]
new.datum$szpft$f.gpp [idx,,] = old.datum$szpft$f.gpp [sel,,]
new.datum$szpft$f.plant.resp [idx,,] = old.datum$szpft$f.plant.resp [sel,,]
new.datum$szpft$f.npp [idx,,] = old.datum$szpft$f.npp [sel,,]
new.datum$szpft$f.mco [idx,,] = old.datum$szpft$f.mco [sel,,]
new.datum$szpft$f.cba [idx,,] = old.datum$szpft$f.cba [sel,,]
new.datum$szpft$f.bstorage [idx,,] = old.datum$szpft$f.bstorage [sel,,]
new.datum$szpft$f.bleaf [idx,,] = old.datum$szpft$f.bleaf [sel,,]
new.datum$szpft$f.bstem [idx,,] = old.datum$szpft$f.bstem [sel,,]
new.datum$szpft$f.broot [idx,,] = old.datum$szpft$f.broot [sel,,]
new.datum$szpft$f.bseeds [idx,,] = old.datum$szpft$f.bseeds [sel,,]
new.datum$szpft$f.dcbadt [idx,,] = old.datum$szpft$f.dcbadt [sel,,]
new.datum$szpft$leaf.par [idx,,] = old.datum$szpft$leaf.par [sel,,]
new.datum$szpft$leaf.par.beam [idx,,] = old.datum$szpft$leaf.par.beam [sel,,]
new.datum$szpft$leaf.par.diff [idx,,] = old.datum$szpft$leaf.par.diff [sel,,]
new.datum$szpft$leaf.gpp [idx,,] = old.datum$szpft$leaf.gpp [sel,,]
new.datum$szpft$phap.lpar [idx,,] = old.datum$szpft$phap.lpar [sel,,]
new.datum$szpft$leaf.rshort [idx,,] = old.datum$szpft$leaf.rshort [sel,,]
new.datum$szpft$leaf.rlong [idx,,] = old.datum$szpft$leaf.rlong [sel,,]
new.datum$szpft$transp [idx,,] = old.datum$szpft$transp [sel,,]
new.datum$szpft$wue [idx,,] = old.datum$szpft$wue [sel,,]
new.datum$szpft$cue [idx,,] = old.datum$szpft$cue [sel,,]
new.datum$szpft$ecue [idx,,] = old.datum$szpft$ecue [sel,,]
new.datum$szpft$etue [idx,,] = old.datum$szpft$etue [sel,,]
new.datum$szpft$rue [idx,,] = old.datum$szpft$rue [sel,,]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# LU -- Polygon-level variables, split by land use type. One extra dimension is #
# appended to the end, which will hold the sum of all land use types. #
#---------------------------------------------------------------------------------------#
new.datum$lu$agb [idx, ] = old.datum$lu$agb [sel, ]
new.datum$lu$biomass [idx, ] = old.datum$lu$biomass [sel, ]
new.datum$lu$lai [idx, ] = old.datum$lu$lai [sel, ]
new.datum$lu$gpp [idx, ] = old.datum$lu$gpp [sel, ]
new.datum$lu$npp [idx, ] = old.datum$lu$npp [sel, ]
new.datum$lu$area [idx, ] = old.datum$lu$area [sel, ]
new.datum$lu$ba [idx, ] = old.datum$lu$ba [sel, ]
new.datum$lu$dist [idx,,] = old.datum$lu$dist [sel,,]
new.datum$lu$f.agb [idx, ] = old.datum$lu$f.agb [sel, ]
new.datum$lu$f.biomass [idx, ] = old.datum$lu$f.biomass [sel, ]
new.datum$lu$f.lai [idx, ] = old.datum$lu$f.lai [sel, ]
new.datum$lu$f.gpp [idx, ] = old.datum$lu$f.gpp [sel, ]
new.datum$lu$f.npp [idx, ] = old.datum$lu$f.npp [sel, ]
new.datum$lu$f.ba [idx, ] = old.datum$lu$f.ba [sel, ]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMEAN -- Polygon-level variables, containing the mean diel (diurnal cycle). #
#---------------------------------------------------------------------------------------#
new.datum$qmean$gpp [idx,] = old.datum$qmean$gpp [sel,]
new.datum$qmean$npp [idx,] = old.datum$qmean$npp [sel,]
new.datum$qmean$plant.resp [idx,] = old.datum$qmean$plant.resp [sel,]
new.datum$qmean$leaf.resp [idx,] = old.datum$qmean$leaf.resp [sel,]
new.datum$qmean$root.resp [idx,] = old.datum$qmean$root.resp [sel,]
new.datum$qmean$froot.resp [idx,] = old.datum$qmean$froot.resp [sel,]
new.datum$qmean$het.resp [idx,] = old.datum$qmean$het.resp [sel,]
new.datum$qmean$cwd.resp [idx,] = old.datum$qmean$cwd.resp [sel,]
new.datum$qmean$soil.resp [idx,] = old.datum$qmean$soil.resp [sel,]
new.datum$qmean$assim.light [idx,] = old.datum$qmean$assim.light [sel,]
new.datum$qmean$assim.rubp [idx,] = old.datum$qmean$assim.rubp [sel,]
new.datum$qmean$assim.co2 [idx,] = old.datum$qmean$assim.co2 [sel,]
new.datum$qmean$assim.ratio [idx,] = old.datum$qmean$assim.ratio [sel,]
new.datum$qmean$nep [idx,] = old.datum$qmean$nep [sel,]
new.datum$qmean$nee [idx,] = old.datum$qmean$nee [sel,]
new.datum$qmean$reco [idx,] = old.datum$qmean$reco [sel,]
new.datum$qmean$cflxca [idx,] = old.datum$qmean$cflxca [sel,]
new.datum$qmean$cflxst [idx,] = old.datum$qmean$cflxst [sel,]
new.datum$qmean$hflxca [idx,] = old.datum$qmean$hflxca [sel,]
new.datum$qmean$hflxlc [idx,] = old.datum$qmean$hflxlc [sel,]
new.datum$qmean$hflxwc [idx,] = old.datum$qmean$hflxwc [sel,]
new.datum$qmean$hflxgc [idx,] = old.datum$qmean$hflxgc [sel,]
new.datum$qmean$qwflxca [idx,] = old.datum$qmean$qwflxca [sel,]
new.datum$qmean$wflxca [idx,] = old.datum$qmean$wflxca [sel,]
new.datum$qmean$wflxlc [idx,] = old.datum$qmean$wflxlc [sel,]
new.datum$qmean$wflxwc [idx,] = old.datum$qmean$wflxwc [sel,]
new.datum$qmean$wflxgc [idx,] = old.datum$qmean$wflxgc [sel,]
new.datum$qmean$runoff [idx,] = old.datum$qmean$runoff [sel,]
new.datum$qmean$intercepted [idx,] = old.datum$qmean$intercepted [sel,]
new.datum$qmean$wshed [idx,] = old.datum$qmean$wshed [sel,]
new.datum$qmean$evap [idx,] = old.datum$qmean$evap [sel,]
new.datum$qmean$transp [idx,] = old.datum$qmean$transp [sel,]
new.datum$qmean$atm.temp [idx,] = old.datum$qmean$atm.temp [sel,]
new.datum$qmean$can.temp [idx,] = old.datum$qmean$can.temp [sel,]
new.datum$qmean$leaf.temp [idx,] = old.datum$qmean$leaf.temp [sel,]
new.datum$qmean$leaf.water [idx,] = old.datum$qmean$leaf.water [sel,]
new.datum$qmean$wood.temp [idx,] = old.datum$qmean$wood.temp [sel,]
new.datum$qmean$gnd.temp [idx,] = old.datum$qmean$gnd.temp [sel,]
new.datum$qmean$atm.shv [idx,] = old.datum$qmean$atm.shv [sel,]
new.datum$qmean$can.shv [idx,] = old.datum$qmean$can.shv [sel,]
new.datum$qmean$gnd.shv [idx,] = old.datum$qmean$gnd.shv [sel,]
new.datum$qmean$atm.vpd [idx,] = old.datum$qmean$atm.vpd [sel,]
new.datum$qmean$can.vpd [idx,] = old.datum$qmean$can.vpd [sel,]
new.datum$qmean$leaf.vpd [idx,] = old.datum$qmean$leaf.vpd [sel,]
new.datum$qmean$atm.co2 [idx,] = old.datum$qmean$atm.co2 [sel,]
new.datum$qmean$can.co2 [idx,] = old.datum$qmean$can.co2 [sel,]
new.datum$qmean$atm.prss [idx,] = old.datum$qmean$atm.prss [sel,]
new.datum$qmean$can.prss [idx,] = old.datum$qmean$can.prss [sel,]
new.datum$qmean$atm.vels [idx,] = old.datum$qmean$atm.vels [sel,]
new.datum$qmean$ustar [idx,] = old.datum$qmean$ustar [sel,]
new.datum$qmean$sm.stress [idx,] = old.datum$qmean$sm.stress [sel,]
new.datum$qmean$rain [idx,] = old.datum$qmean$rain [sel,]
new.datum$qmean$rshort [idx,] = old.datum$qmean$rshort [sel,]
new.datum$qmean$rshort.beam [idx,] = old.datum$qmean$rshort.beam [sel,]
new.datum$qmean$rshort.diff [idx,] = old.datum$qmean$rshort.diff [sel,]
new.datum$qmean$rshort.gnd [idx,] = old.datum$qmean$rshort.gnd [sel,]
new.datum$qmean$rshortup [idx,] = old.datum$qmean$rshortup [sel,]
new.datum$qmean$rlong [idx,] = old.datum$qmean$rlong [sel,]
new.datum$qmean$rlong.gnd [idx,] = old.datum$qmean$rlong.gnd [sel,]
new.datum$qmean$rlongup [idx,] = old.datum$qmean$rlongup [sel,]
new.datum$qmean$par.tot [idx,] = old.datum$qmean$par.tot [sel,]
new.datum$qmean$par.beam [idx,] = old.datum$qmean$par.beam [sel,]
new.datum$qmean$par.diff [idx,] = old.datum$qmean$par.diff [sel,]
new.datum$qmean$par.gnd [idx,] = old.datum$qmean$par.gnd [sel,]
new.datum$qmean$parup [idx,] = old.datum$qmean$parup [sel,]
new.datum$qmean$par.leaf [idx,] = old.datum$qmean$par.leaf [sel,]
new.datum$qmean$par.leaf.beam [idx,] = old.datum$qmean$par.leaf.beam [sel,]
new.datum$qmean$par.leaf.diff [idx,] = old.datum$qmean$par.leaf.diff [sel,]
new.datum$qmean$rnet [idx,] = old.datum$qmean$rnet [sel,]
new.datum$qmean$albedo [idx,] = old.datum$qmean$albedo [sel,]
new.datum$qmean$albedo.par [idx,] = old.datum$qmean$albedo.par [sel,]
new.datum$qmean$albedo.nir [idx,] = old.datum$qmean$albedo.nir [sel,]
new.datum$qmean$rlong.albedo [idx,] = old.datum$qmean$rlong.albedo [sel,]
new.datum$qmean$leaf.gsw [idx,] = old.datum$qmean$leaf.gsw [sel,]
new.datum$qmean$leaf.gbw [idx,] = old.datum$qmean$leaf.gbw [sel,]
new.datum$qmean$wood.gbw [idx,] = old.datum$qmean$wood.gbw [sel,]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMSQU -- Polygon-level variables, containing the mean sum of squares for the diel #
# (diurnal cycle). #
#---------------------------------------------------------------------------------------#
new.datum$qmsqu$gpp [idx,] = old.datum$qmsqu$gpp [sel,]
new.datum$qmsqu$npp [idx,] = old.datum$qmsqu$npp [sel,]
new.datum$qmsqu$plant.resp [idx,] = old.datum$qmsqu$plant.resp [sel,]
new.datum$qmsqu$leaf.resp [idx,] = old.datum$qmsqu$leaf.resp [sel,]
new.datum$qmsqu$root.resp [idx,] = old.datum$qmsqu$root.resp [sel,]
new.datum$qmsqu$froot.resp [idx,] = old.datum$qmsqu$froot.resp [sel,]
new.datum$qmsqu$het.resp [idx,] = old.datum$qmsqu$het.resp [sel,]
new.datum$qmsqu$cwd.resp [idx,] = old.datum$qmsqu$cwd.resp [sel,]
new.datum$qmsqu$soil.resp [idx,] = old.datum$qmsqu$soil.resp [sel,]
new.datum$qmsqu$nep [idx,] = old.datum$qmsqu$nep [sel,]
new.datum$qmsqu$cflxca [idx,] = old.datum$qmsqu$cflxca [sel,]
new.datum$qmsqu$cflxst [idx,] = old.datum$qmsqu$cflxst [sel,]
new.datum$qmsqu$hflxca [idx,] = old.datum$qmsqu$hflxca [sel,]
new.datum$qmsqu$hflxlc [idx,] = old.datum$qmsqu$hflxlc [sel,]
new.datum$qmsqu$hflxwc [idx,] = old.datum$qmsqu$hflxwc [sel,]
new.datum$qmsqu$hflxgc [idx,] = old.datum$qmsqu$hflxgc [sel,]
new.datum$qmsqu$qwflxca [idx,] = old.datum$qmsqu$qwflxca [sel,]
new.datum$qmsqu$wflxca [idx,] = old.datum$qmsqu$wflxca [sel,]
new.datum$qmsqu$wflxlc [idx,] = old.datum$qmsqu$wflxlc [sel,]
new.datum$qmsqu$wflxwc [idx,] = old.datum$qmsqu$wflxwc [sel,]
new.datum$qmsqu$wflxgc [idx,] = old.datum$qmsqu$wflxgc [sel,]
new.datum$qmsqu$transp [idx,] = old.datum$qmsqu$transp [sel,]
new.datum$qmsqu$ustar [idx,] = old.datum$qmsqu$ustar [sel,]
new.datum$qmsqu$albedo [idx,] = old.datum$qmsqu$albedo [sel,]
new.datum$qmsqu$rshortup [idx,] = old.datum$qmsqu$rshortup [sel,]
new.datum$qmsqu$rlongup [idx,] = old.datum$qmsqu$rlongup [sel,]
new.datum$qmsqu$parup [idx,] = old.datum$qmsqu$parup [sel,]
new.datum$qmsqu$rnet [idx,] = old.datum$qmsqu$rnet [sel,]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# PATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
new.datum$patch$ipa = old.datum$patch$ipa
new.datum$patch$age = old.datum$patch$age
new.datum$patch$area = old.datum$patch$area
new.datum$patch$lu = old.datum$patch$lu
new.datum$patch$nep = old.datum$patch$nep
new.datum$patch$het.resp = old.datum$patch$het.resp
new.datum$patch$soil.resp = old.datum$patch$soil.resp
new.datum$patch$can.temp = old.datum$patch$can.temp
new.datum$patch$gnd.temp = old.datum$patch$gnd.temp
new.datum$patch$can.shv = old.datum$patch$can.shv
new.datum$patch$gnd.shv = old.datum$patch$gnd.shv
new.datum$patch$can.vpd = old.datum$patch$can.vpd
new.datum$patch$can.co2 = old.datum$patch$can.co2
new.datum$patch$can.prss = old.datum$patch$can.prss
new.datum$patch$cflxca = old.datum$patch$cflxca
new.datum$patch$cflxst = old.datum$patch$cflxst
new.datum$patch$nee = old.datum$patch$nee
new.datum$patch$hflxca = old.datum$patch$hflxca
new.datum$patch$hflxgc = old.datum$patch$hflxgc
new.datum$patch$qwflxca = old.datum$patch$qwflxca
new.datum$patch$wflxca = old.datum$patch$wflxca
new.datum$patch$wflxgc = old.datum$patch$wflxgc
new.datum$patch$ustar = old.datum$patch$ustar
new.datum$patch$albedo = old.datum$patch$albedo
new.datum$patch$rshortup = old.datum$patch$rshortup
new.datum$patch$rlongup = old.datum$patch$rlongup
new.datum$patch$parup = old.datum$patch$parup
new.datum$patch$rshort.gnd = old.datum$patch$rshort.gnd
new.datum$patch$par.gnd = old.datum$patch$par.gnd
new.datum$patch$par.leaf = old.datum$patch$par.leaf
new.datum$patch$par.leaf.beam = old.datum$patch$par.leaf.beam
new.datum$patch$par.leaf.diff = old.datum$patch$par.leaf.diff
new.datum$patch$rnet = old.datum$patch$rnet
new.datum$patch$lai = old.datum$patch$lai
new.datum$patch$wai = old.datum$patch$wai
new.datum$patch$tai = old.datum$patch$tai
new.datum$patch$agb = old.datum$patch$agb
new.datum$patch$ba = old.datum$patch$ba
new.datum$patch$wood.dens = old.datum$patch$wood.dens
new.datum$patch$can.depth = old.datum$patch$can.depth
new.datum$patch$can.area = old.datum$patch$can.area
new.datum$patch$phap.lpar = old.datum$patch$phap.lpar
new.datum$patch$phap.ltemp = old.datum$patch$phap.ltemp
new.datum$patch$phap.lwater = old.datum$patch$phap.lwater
new.datum$patch$phap.lvpd = old.datum$patch$phap.lvpd
new.datum$patch$phap.sms = old.datum$patch$phap.sms
new.datum$patch$phap.lgbw = old.datum$patch$phap.lgbw
new.datum$patch$phap.lgsw = old.datum$patch$phap.lgsw
new.datum$patch$sm.stress = old.datum$patch$sm.stress
new.datum$patch$leaf.temp = old.datum$patch$leaf.temp
new.datum$patch$leaf.water = old.datum$patch$leaf.water
new.datum$patch$leaf.vpd = old.datum$patch$leaf.vpd
new.datum$patch$leaf.gpp = old.datum$patch$leaf.gpp
new.datum$patch$leaf.gsw = old.datum$patch$leaf.gsw
new.datum$patch$leaf.par = old.datum$patch$leaf.par
new.datum$patch$leaf.par.beam = old.datum$patch$leaf.par.beam
new.datum$patch$leaf.par.diff = old.datum$patch$leaf.par.diff
new.datum$patch$assim.light = old.datum$patch$assim.light
new.datum$patch$assim.rubp = old.datum$patch$assim.rubp
new.datum$patch$assim.co2 = old.datum$patch$assim.co2
new.datum$patch$wood.temp = old.datum$patch$wood.temp
new.datum$patch$gpp = old.datum$patch$gpp
new.datum$patch$npp = old.datum$patch$npp
new.datum$patch$cba = old.datum$patch$cba
new.datum$patch$plant.resp = old.datum$patch$plant.resp
new.datum$patch$reco = old.datum$patch$reco
new.datum$patch$hflxlc = old.datum$patch$hflxlc
new.datum$patch$hflxwc = old.datum$patch$hflxwc
new.datum$patch$wflxlc = old.datum$patch$wflxlc
new.datum$patch$wflxwc = old.datum$patch$wflxwc
new.datum$patch$transp = old.datum$patch$transp
new.datum$patch$fast.soil.c = old.datum$patch$fast.soil.c
new.datum$patch$slow.soil.c = old.datum$patch$slow.soil.c
new.datum$patch$struct.soil.c = old.datum$patch$struct.soil.c
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QPATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
new.datum$qpatch$nep = old.datum$qpatch$nep
new.datum$qpatch$het.resp = old.datum$qpatch$het.resp
new.datum$qpatch$can.temp = old.datum$qpatch$can.temp
new.datum$qpatch$gnd.temp = old.datum$qpatch$gnd.temp
new.datum$qpatch$can.shv = old.datum$qpatch$can.shv
new.datum$qpatch$gnd.shv = old.datum$qpatch$gnd.shv
new.datum$qpatch$can.vpd = old.datum$qpatch$can.vpd
new.datum$qpatch$can.co2 = old.datum$qpatch$can.co2
new.datum$qpatch$can.prss = old.datum$qpatch$can.prss
new.datum$qpatch$cflxca = old.datum$qpatch$cflxca
new.datum$qpatch$cflxst = old.datum$qpatch$cflxst
new.datum$qpatch$nee = old.datum$qpatch$nee
new.datum$qpatch$hflxca = old.datum$qpatch$hflxca
new.datum$qpatch$hflxgc = old.datum$qpatch$hflxgc
new.datum$qpatch$qwflxca = old.datum$qpatch$qwflxca
new.datum$qpatch$wflxca = old.datum$qpatch$wflxca
new.datum$qpatch$wflxgc = old.datum$qpatch$wflxgc
new.datum$qpatch$ustar = old.datum$qpatch$ustar
new.datum$qpatch$albedo = old.datum$qpatch$albedo
new.datum$qpatch$rshortup = old.datum$qpatch$rshortup
new.datum$qpatch$rlongup = old.datum$qpatch$rlongup
new.datum$qpatch$parup = old.datum$qpatch$parup
new.datum$qpatch$rshort.gnd = old.datum$qpatch$rshort.gnd
new.datum$qpatch$par.gnd = old.datum$qpatch$par.gnd
new.datum$qpatch$rnet = old.datum$qpatch$rnet
new.datum$qpatch$sm.stress = old.datum$qpatch$sm.stress
new.datum$qpatch$leaf.temp = old.datum$qpatch$leaf.temp
new.datum$qpatch$leaf.water = old.datum$qpatch$leaf.water
new.datum$qpatch$leaf.vpd = old.datum$qpatch$leaf.vpd
new.datum$qpatch$wood.temp = old.datum$qpatch$wood.temp
new.datum$qpatch$par.leaf = old.datum$qpatch$par.leaf
new.datum$qpatch$par.leaf.beam = old.datum$qpatch$par.leaf.beam
new.datum$qpatch$par.leaf.diff = old.datum$qpatch$par.leaf.diff
new.datum$qpatch$leaf.gpp = old.datum$qpatch$leaf.gpp
new.datum$qpatch$leaf.gsw = old.datum$qpatch$leaf.gsw
new.datum$qpatch$leaf.par = old.datum$qpatch$leaf.par
new.datum$qpatch$leaf.par.beam = old.datum$qpatch$leaf.par.beam
new.datum$qpatch$leaf.par.diff = old.datum$qpatch$leaf.par.diff
new.datum$qpatch$assim.light = old.datum$qpatch$assim.light
new.datum$qpatch$assim.rubp = old.datum$qpatch$assim.rubp
new.datum$qpatch$assim.co2 = old.datum$qpatch$assim.co2
new.datum$qpatch$gpp = old.datum$qpatch$gpp
new.datum$qpatch$npp = old.datum$qpatch$npp
new.datum$qpatch$plant.resp = old.datum$qpatch$plant.resp
new.datum$qpatch$hflxlc = old.datum$qpatch$hflxlc
new.datum$qpatch$hflxwc = old.datum$qpatch$hflxwc
new.datum$qpatch$wflxlc = old.datum$qpatch$wflxlc
new.datum$qpatch$wflxwc = old.datum$qpatch$wflxwc
new.datum$qpatch$transp = old.datum$qpatch$transp
new.datum$qpatch$soil.resp = old.datum$qpatch$soil.resp
#---------------------------------------------------------------------------------------#
#----- Cohort level, we save as lists because the dimensions vary. ---------------------#
new.datum$cohort$ipa = old.datum$cohort$ipa
new.datum$cohort$ico = old.datum$cohort$ico
new.datum$cohort$area = old.datum$cohort$area
new.datum$cohort$lu = old.datum$cohort$lu
new.datum$cohort$dbh = old.datum$cohort$dbh
new.datum$cohort$age = old.datum$cohort$age
new.datum$cohort$pft = old.datum$cohort$pft
new.datum$cohort$nplant = old.datum$cohort$nplant
new.datum$cohort$height = old.datum$cohort$height
new.datum$cohort$ba = old.datum$cohort$ba
new.datum$cohort$agb = old.datum$cohort$agb
new.datum$cohort$biomass = old.datum$cohort$biomass
new.datum$cohort$lai = old.datum$cohort$lai
new.datum$cohort$wai = old.datum$cohort$wai
new.datum$cohort$tai = old.datum$cohort$tai
new.datum$cohort$gpp = old.datum$cohort$gpp
new.datum$cohort$leaf.resp = old.datum$cohort$leaf.resp
new.datum$cohort$root.resp = old.datum$cohort$root.resp
new.datum$cohort$froot.resp = old.datum$cohort$froot.resp
new.datum$cohort$croot.resp = old.datum$cohort$croot.resp
new.datum$cohort$stem.resp = old.datum$cohort$stem.resp
new.datum$cohort$storage.resp = old.datum$cohort$storage.resp
new.datum$cohort$plant.resp = old.datum$cohort$plant.resp
new.datum$cohort$assim.light = old.datum$cohort$assim.light
new.datum$cohort$assim.rubp = old.datum$cohort$assim.rubp
new.datum$cohort$assim.co2 = old.datum$cohort$assim.co2
new.datum$cohort$assim.ratio = old.datum$cohort$assim.ratio
new.datum$cohort$npp = old.datum$cohort$npp
new.datum$cohort$cba = old.datum$cohort$cba
new.datum$cohort$cbamax = old.datum$cohort$cbamax
new.datum$cohort$cbalight = old.datum$cohort$cbalight
new.datum$cohort$cbamoist = old.datum$cohort$cbamoist
new.datum$cohort$cbarel = old.datum$cohort$cbarel
new.datum$cohort$dcbadt = old.datum$cohort$dcbadt
new.datum$cohort$mcost = old.datum$cohort$mcost
new.datum$cohort$ldrop = old.datum$cohort$ldrop
new.datum$cohort$sm.stress = old.datum$cohort$sm.stress
new.datum$cohort$phap.sms = old.datum$cohort$phap.sms
new.datum$cohort$light = old.datum$cohort$light
new.datum$cohort$lightbeam = old.datum$cohort$lightbeam
new.datum$cohort$lightdiff = old.datum$cohort$lightdiff
new.datum$cohort$balive = old.datum$cohort$balive
new.datum$cohort$bdead = old.datum$cohort$bdead
new.datum$cohort$bleaf = old.datum$cohort$bleaf
new.datum$cohort$bstem = old.datum$cohort$bstem
new.datum$cohort$broot = old.datum$cohort$broot
new.datum$cohort$bfroot = old.datum$cohort$bfroot
new.datum$cohort$bcroot = old.datum$cohort$bcroot
new.datum$cohort$bsapwood = old.datum$cohort$bsapwood
new.datum$cohort$bstorage = old.datum$cohort$bstorage
new.datum$cohort$bseeds = old.datum$cohort$bseeds
new.datum$cohort$hflxlc = old.datum$cohort$hflxlc
new.datum$cohort$wflxlc = old.datum$cohort$wflxlc
new.datum$cohort$transp = old.datum$cohort$transp
new.datum$cohort$wue = old.datum$cohort$wue
new.datum$cohort$cue = old.datum$cohort$cue
new.datum$cohort$ecue = old.datum$cohort$ecue
new.datum$cohort$etue = old.datum$cohort$etue
new.datum$cohort$demand = old.datum$cohort$demand
new.datum$cohort$supply = old.datum$cohort$supply
new.datum$cohort$mort = old.datum$cohort$mort
new.datum$cohort$dimort = old.datum$cohort$dimort
new.datum$cohort$ncbmort = old.datum$cohort$ncbmort
new.datum$cohort$recruit = old.datum$cohort$recruit
new.datum$cohort$growth = old.datum$cohort$growth
new.datum$cohort$agb.growth = old.datum$cohort$agb.growth
new.datum$cohort$bsa.growth = old.datum$cohort$bsa.growth
new.datum$cohort$f.gpp = old.datum$cohort$f.gpp
new.datum$cohort$f.plant.resp = old.datum$cohort$f.plant.resp
new.datum$cohort$f.npp = old.datum$cohort$f.npp
new.datum$cohort$f.mco = old.datum$cohort$f.mco
new.datum$cohort$f.cba = old.datum$cohort$f.cba
new.datum$cohort$f.bstorage = old.datum$cohort$f.bstorage
new.datum$cohort$f.bleaf = old.datum$cohort$f.bleaf
new.datum$cohort$f.bstem = old.datum$cohort$f.bstem
new.datum$cohort$f.broot = old.datum$cohort$f.broot
new.datum$cohort$f.bseeds = old.datum$cohort$f.bseeds
new.datum$cohort$f.dcbadt = old.datum$cohort$f.dcbadt
new.datum$cohort$leaf.par = old.datum$cohort$leaf.par
new.datum$cohort$leaf.par.beam = old.datum$cohort$leaf.par.beam
new.datum$cohort$leaf.par.diff = old.datum$cohort$leaf.par.diff
new.datum$cohort$leaf.gpp = old.datum$cohort$leaf.gpp
new.datum$cohort$phap.lpar = old.datum$cohort$phap.lpar
new.datum$cohort$leaf.rshort = old.datum$cohort$leaf.rshort
new.datum$cohort$leaf.rlong = old.datum$cohort$leaf.rlong
new.datum$cohort$rue = old.datum$cohort$rue
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Send the data back. #
#---------------------------------------------------------------------------------------#
return(new.datum)
#---------------------------------------------------------------------------------------#
}#end update
#==========================================================================================#
#==========================================================================================#
manfredo89/ED2io documentation built on May 21, 2019, 11:24 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#==========================================================================================#
#==========================================================================================#
# Create the monthly mean structure to be filled by plot_monthly.r #
#------------------------------------------------------------------------------------------#
create.monthly <<- function(ntimes,montha,yeara,inpref,slz.min){
#----- Read the first HDF5 to grab some simulation-dependent dimensions. ---------------#
cyear = sprintf("%4.4i", yeara)
cmonth = sprintf("%2.2i",montha)
h5first = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5" ,sep="")
h5first.bz2 = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5.bz2",sep="")
h5first.gz = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5.gz" ,sep="")
if ( file.exists(h5first) ){
mymont = H5Fopen(h5first)
}else if ( file.exists(h5first.bz2) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = bunzip2(filename=h5first.bz2,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else if ( file.exists(h5first.gz) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = gunzip(filename=h5first.gz,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else{
cat ("Warning: I was looking for the first file to use as template but\n")
cat ("I have not found it. I will try to use the last one (the one of \n")
cat ("yearz). This usually happens when not all the analysis (the \n")
cat ("first one in particular) are present. If even this one is not \n")
cat ("found try to set yearz to the real last H5 file that you have...\n")
cyear = sprintf("%4.4i", yeara + floor(ntimes/12) - 1)
h5first = paste(inpref,"-Q-",cyear,"-01-00-000000-g01.h5" ,sep="")
h5first.bz2 = paste(inpref,"-Q-",cyear,"-01-00-000000-g01.h5.bz2",sep="")
h5first.gz = paste(inpref,"-Q-",cyear,"-01-00-000000-g01.h5.gz" ,sep="")
if ( file.exists(h5first) ){
mymont = H5Fopen(h5first)
}else if ( file.exists(h5first.bz2) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = bunzip2(filename=h5first.bz2,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else if ( file.exists(h5first.gz) ){
temp.file = file.path(tempdir(),basename(h5first))
dummy = gunzip(filename=h5first.gz,destname=temp.file,remove=FALSE)
mymont = H5Fopen(temp.file)
dummy = file.remove(temp.file)
}else{
cat (" Path: ",dirname (h5first),"\n")
cat (" File: ",basename(h5first),"\n")
stop(" File not found...")
}
}#end if
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Start up the list. #
#---------------------------------------------------------------------------------------#
ed = list()
#---------------------------------------------------------------------------------------#
#----- Define the number of soil layers. -----------------------------------------------#
ed$nzg = mymont$NZG
ed$nzs = mymont$NZS
ed$ndcycle = mymont$NDCYCLE
ed$ntimes = ntimes
#---------------------------------------------------------------------------------------#
#----- Find which soil are we solving, and save properties into soil.prop. -------------#
ed$isoilflg = mymont$ISOILFLG
ed$slz = mymont$SLZ
ed$slxsand = mymont$SLXSAND
ed$slxclay = mymont$SLXCLAY
ed$ntext = mymont$NTEXT_SOIL[ed$nzg]
#---------------------------------------------------------------------------------------#
#H5close()
#----- Derive the soil properties. -----------------------------------------------------#
ed$soil.prop = soil.params(ed$ntext,ed$isoilflg,ed$slxsand,ed$slxclay)
ed$dslz = diff(c(ed$slz,0))
ed$soil.depth = rev(cumsum(rev(ed$dslz)))
ed$soil.dry = rev(cumsum(rev(ed$soil.prop$soilcp * wdns * ed$dslz)))
ed$soil.poro = rev(cumsum(rev(ed$soil.prop$slmsts * wdns * ed$dslz)))
#---------------------------------------------------------------------------------------#
#----- Find the layers we care about. --------------------------------------------------#
sel = ed$slz < slz.min
if (any(sel)){
ed$ka = which.max(ed$slz[sel])
}else{
ed$ka = 1
}#end if
ed$kz = ed$nzg
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Find all time information. #
#---------------------------------------------------------------------------------------#
runmonths = montha + sequence(ntimes) - 1
ed$month = 1 + (runmonths-1) %% 12
ed$year = yeara - 1 + ceiling(runmonths/12)
ed$when = chron(paste(ed$month,1,ed$year,sep="/"))
ed$tomonth = chron(ed$when,out.format=c(dates="day-mon-yr",times=NULL))
ed$toyear = sort(unique(ed$year))
#----- Count the number of months for each month. --------------------------------------#
ed$montable = rep(0,times=12)
montable = table(ed$month)
idx = as.numeric(names(montable))
ed$montable[idx] = montable
ed$moncnt = matrix( data = rep(ed$montable,times=ed$ndcycle)
, ncol = ed$ndcycle
, nrow = 12
)#end matrix
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Find all the file names. #
#---------------------------------------------------------------------------------------#
cmonth = sprintf("%2.2i",ed$month)
cyear = sprintf("%4.4i",ed$year )
ed$input = paste(inpref,"-Q-",cyear,"-",cmonth,"-00-000000-g01.h5",sep="")
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Make a copy of the dimensions to avoid clutter. #
#---------------------------------------------------------------------------------------#
ndcycle = ed$ndcycle
nzg = ed$nzg
nzs = ed$nzs
#---------------------------------------------------------------------------------------#
#=======================================================================================#
#=======================================================================================#
# Flush all variables that will hold the data. For convenience they are split into #
# multiple lists. #
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emean -- variables that we can either compare directly with observations, or are #
# or that may be used to draw time series. They don't need to be really #
# monthly means, but you should put only the variables that make sense to be #
# plotted in simple time series (with no PFT or DBH information). #
#---------------------------------------------------------------------------------------#
emean = list()
emean$wood.dens = rep(NA,times=ntimes)
emean$fast.soil.c = rep(NA,times=ntimes)
emean$slow.soil.c = rep(NA,times=ntimes)
emean$struct.soil.c = rep(NA,times=ntimes)
emean$het.resp = rep(NA,times=ntimes)
emean$cwd.resp = rep(NA,times=ntimes)
emean$soil.resp = rep(NA,times=ntimes)
emean$gpp = rep(NA,times=ntimes)
emean$last.1yr.gpp = rep(NA,times=ntimes)
emean$last.2yr.gpp = rep(NA,times=ntimes)
emean$last.3yr.gpp = rep(NA,times=ntimes)
emean$plant.resp = rep(NA,times=ntimes)
emean$last.1yr.plresp = rep(NA,times=ntimes)
emean$last.2yr.plresp = rep(NA,times=ntimes)
emean$last.3yr.plresp = rep(NA,times=ntimes)
emean$cue = rep(NA,times=ntimes)
emean$last.1yr.cue = rep(NA,times=ntimes)
emean$last.2yr.cue = rep(NA,times=ntimes)
emean$last.3yr.cue = rep(NA,times=ntimes)
emean$ecue = rep(NA,times=ntimes)
emean$last.1yr.ecue = rep(NA,times=ntimes)
emean$last.2yr.ecue = rep(NA,times=ntimes)
emean$last.3yr.ecue = rep(NA,times=ntimes)
emean$leaf.resp = rep(NA,times=ntimes)
emean$root.resp = rep(NA,times=ntimes)
emean$froot.resp = rep(NA,times=ntimes)
emean$croot.resp = rep(NA,times=ntimes)
emean$stem.resp = rep(NA,times=ntimes)
emean$growth.resp = rep(NA,times=ntimes)
emean$storage.resp = rep(NA,times=ntimes)
emean$reco = rep(NA,times=ntimes)
emean$assim.light = rep(NA,times=ntimes)
emean$assim.rubp = rep(NA,times=ntimes)
emean$assim.co2 = rep(NA,times=ntimes)
emean$assim.ratio = rep(NA,times=ntimes)
emean$mco = rep(NA,times=ntimes)
emean$cba = rep(NA,times=ntimes)
emean$last.1yr.cba = rep(NA,times=ntimes)
emean$last.2yr.cba = rep(NA,times=ntimes)
emean$last.3yr.cba = rep(NA,times=ntimes)
emean$cbamax = rep(NA,times=ntimes)
emean$cbalight = rep(NA,times=ntimes)
emean$cbamoist = rep(NA,times=ntimes)
emean$cbarel = rep(NA,times=ntimes)
emean$ldrop = rep(NA,times=ntimes)
emean$nep = rep(NA,times=ntimes)
emean$nee = rep(NA,times=ntimes)
emean$cflxca = rep(NA,times=ntimes)
emean$cflxst = rep(NA,times=ntimes)
emean$ustar = rep(NA,times=ntimes)
emean$atm.vels = rep(NA,times=ntimes)
emean$atm.prss = rep(NA,times=ntimes)
emean$atm.temp = rep(NA,times=ntimes)
emean$atm.shv = rep(NA,times=ntimes)
emean$atm.vpd = rep(NA,times=ntimes)
emean$atm.co2 = rep(NA,times=ntimes)
emean$can.prss = rep(NA,times=ntimes)
emean$can.temp = rep(NA,times=ntimes)
emean$can.co2 = rep(NA,times=ntimes)
emean$can.shv = rep(NA,times=ntimes)
emean$can.vpd = rep(NA,times=ntimes)
emean$can.depth = rep(NA,times=ntimes)
emean$can.area = rep(NA,times=ntimes)
emean$gnd.temp = rep(NA,times=ntimes)
emean$gnd.shv = rep(NA,times=ntimes)
emean$leaf.temp = rep(NA,times=ntimes)
emean$phap.ltemp = rep(NA,times=ntimes)
emean$last.1yr.ltemp = rep(NA,times=ntimes)
emean$last.2yr.ltemp = rep(NA,times=ntimes)
emean$last.3yr.ltemp = rep(NA,times=ntimes)
emean$leaf.vpd = rep(NA,times=ntimes)
emean$phap.lvpd = rep(NA,times=ntimes)
emean$last.1yr.lvpd = rep(NA,times=ntimes)
emean$last.2yr.lvpd = rep(NA,times=ntimes)
emean$last.3yr.lvpd = rep(NA,times=ntimes)
emean$leaf.water = rep(NA,times=ntimes)
emean$phap.lwater = rep(NA,times=ntimes)
emean$last.1yr.lwater = rep(NA,times=ntimes)
emean$last.2yr.lwater = rep(NA,times=ntimes)
emean$last.3yr.lwater = rep(NA,times=ntimes)
emean$wood.temp = rep(NA,times=ntimes)
emean$hflxca = rep(NA,times=ntimes)
emean$qwflxca = rep(NA,times=ntimes)
emean$hflxgc = rep(NA,times=ntimes)
emean$hflxlc = rep(NA,times=ntimes)
emean$hflxwc = rep(NA,times=ntimes)
emean$wflxca = rep(NA,times=ntimes)
emean$wflxgc = rep(NA,times=ntimes)
emean$wflxlc = rep(NA,times=ntimes)
emean$wflxwc = rep(NA,times=ntimes)
emean$runoff = rep(NA,times=ntimes)
emean$intercepted = rep(NA,times=ntimes)
emean$wshed = rep(NA,times=ntimes)
emean$evap = rep(NA,times=ntimes)
emean$last.1yr.evap = rep(NA,times=ntimes)
emean$last.2yr.evap = rep(NA,times=ntimes)
emean$last.3yr.evap = rep(NA,times=ntimes)
emean$npp = rep(NA,times=ntimes)
emean$last.1yr.npp = rep(NA,times=ntimes)
emean$last.2yr.npp = rep(NA,times=ntimes)
emean$last.3yr.npp = rep(NA,times=ntimes)
emean$dcbadt = rep(NA,times=ntimes)
emean$last.1yr.dcbadt = rep(NA,times=ntimes)
emean$last.2yr.dcbadt = rep(NA,times=ntimes)
emean$last.3yr.dcbadt = rep(NA,times=ntimes)
emean$et = rep(NA,times=ntimes)
emean$last.1yr.et = rep(NA,times=ntimes)
emean$last.2yr.et = rep(NA,times=ntimes)
emean$last.3yr.et = rep(NA,times=ntimes)
emean$transp = rep(NA,times=ntimes)
emean$last.1yr.transp = rep(NA,times=ntimes)
emean$last.2yr.transp = rep(NA,times=ntimes)
emean$last.3yr.transp = rep(NA,times=ntimes)
emean$etue = rep(NA,times=ntimes)
emean$last.1yr.etue = rep(NA,times=ntimes)
emean$last.2yr.etue = rep(NA,times=ntimes)
emean$last.3yr.etue = rep(NA,times=ntimes)
emean$wue = rep(NA,times=ntimes)
emean$last.1yr.wue = rep(NA,times=ntimes)
emean$last.2yr.wue = rep(NA,times=ntimes)
emean$last.3yr.wue = rep(NA,times=ntimes)
emean$rain = rep(NA,times=ntimes)
emean$last.1yr.rain = rep(NA,times=ntimes)
emean$last.2yr.rain = rep(NA,times=ntimes)
emean$last.3yr.rain = rep(NA,times=ntimes)
emean$nmon.lt.090 = rep(NA,times=ntimes)
emean$nmon.lt.100 = rep(NA,times=ntimes)
emean$nmon.lt.110 = rep(NA,times=ntimes)
emean$nmon.lt.120 = rep(NA,times=ntimes)
emean$nmon.wdef = rep(NA,times=ntimes)
emean$nmon.mdef = rep(NA,times=ntimes)
emean$rue = rep(NA,times=ntimes)
emean$last.1yr.rue = rep(NA,times=ntimes)
emean$last.2yr.rue = rep(NA,times=ntimes)
emean$last.3yr.rue = rep(NA,times=ntimes)
emean$sm.stress = rep(NA,times=ntimes)
emean$phap.sms = rep(NA,times=ntimes)
emean$last.1yr.sms = rep(NA,times=ntimes)
emean$last.2yr.sms = rep(NA,times=ntimes)
emean$last.3yr.sms = rep(NA,times=ntimes)
emean$rshort = rep(NA,times=ntimes)
emean$last.1yr.rshort = rep(NA,times=ntimes)
emean$last.2yr.rshort = rep(NA,times=ntimes)
emean$last.3yr.rshort = rep(NA,times=ntimes)
emean$rshort.beam = rep(NA,times=ntimes)
emean$rshort.diff = rep(NA,times=ntimes)
emean$rshortup = rep(NA,times=ntimes)
emean$rshort.gnd = rep(NA,times=ntimes)
emean$rlong = rep(NA,times=ntimes)
emean$rlong.gnd = rep(NA,times=ntimes)
emean$rlongup = rep(NA,times=ntimes)
emean$par.tot = rep(NA,times=ntimes)
emean$par.beam = rep(NA,times=ntimes)
emean$par.diff = rep(NA,times=ntimes)
emean$par.gnd = rep(NA,times=ntimes)
emean$parup = rep(NA,times=ntimes)
emean$par.leaf = rep(NA,times=ntimes)
emean$par.leaf.beam = rep(NA,times=ntimes)
emean$par.leaf.diff = rep(NA,times=ntimes)
emean$rnet = rep(NA,times=ntimes)
emean$albedo = rep(NA,times=ntimes)
emean$albedo.par = rep(NA,times=ntimes)
emean$albedo.nir = rep(NA,times=ntimes)
emean$rlong.albedo = rep(NA,times=ntimes)
emean$nplant = rep(NA,times=ntimes)
emean$agb = rep(NA,times=ntimes)
emean$biomass = rep(NA,times=ntimes)
emean$lai = rep(NA,times=ntimes)
emean$wai = rep(NA,times=ntimes)
emean$tai = rep(NA,times=ntimes)
emean$area = rep(NA,times=ntimes)
emean$workload = rep(NA,times=ntimes)
emean$specwork = rep(NA,times=ntimes)
emean$demand = rep(NA,times=ntimes)
emean$supply = rep(NA,times=ntimes)
emean$paw = rep(NA,times=ntimes)
emean$smpot = rep(NA,times=ntimes)
emean$last.1yr.smpot = rep(NA,times=ntimes)
emean$last.2yr.smpot = rep(NA,times=ntimes)
emean$last.3yr.smpot = rep(NA,times=ntimes)
emean$npat.global = rep(NA,times=ntimes)
emean$ncoh.global = rep(NA,times=ntimes)
emean$water.deficit = rep(NA,times=ntimes)
emean$last.1yr.mwd = rep(NA,times=ntimes)
emean$last.2yr.mwd = rep(NA,times=ntimes)
emean$last.3yr.mwd = rep(NA,times=ntimes)
emean$malhi.deficit = rep(NA,times=ntimes)
emean$leaf.gsw = rep(NA,times=ntimes)
emean$phap.lgsw = rep(NA,times=ntimes)
emean$last.1yr.lgsw = rep(NA,times=ntimes)
emean$last.2yr.lgsw = rep(NA,times=ntimes)
emean$last.3yr.lgsw = rep(NA,times=ntimes)
emean$leaf.gbw = rep(NA,times=ntimes)
emean$phap.lgbw = rep(NA,times=ntimes)
emean$wood.gbw = rep(NA,times=ntimes)
emean$i.gpp = rep(NA,times=ntimes)
emean$i.npp = rep(NA,times=ntimes)
emean$i.plant.resp = rep(NA,times=ntimes)
emean$i.mco = rep(NA,times=ntimes)
emean$i.cba = rep(NA,times=ntimes)
emean$i.cbamax = rep(NA,times=ntimes)
emean$i.cbalight = rep(NA,times=ntimes)
emean$i.cbamoist = rep(NA,times=ntimes)
emean$i.transp = rep(NA,times=ntimes)
emean$i.wflxlc = rep(NA,times=ntimes)
emean$i.hflxlc = rep(NA,times=ntimes)
emean$f.gpp = rep(NA,times=ntimes)
emean$f.plant.resp = rep(NA,times=ntimes)
emean$f.npp = rep(NA,times=ntimes)
emean$f.mco = rep(NA,times=ntimes)
emean$f.cba = rep(NA,times=ntimes)
emean$f.bstorage = rep(NA,times=ntimes)
emean$f.bleaf = rep(NA,times=ntimes)
emean$f.bstem = rep(NA,times=ntimes)
emean$f.broot = rep(NA,times=ntimes)
emean$f.bseeds = rep(NA,times=ntimes)
emean$f.dcbadt = rep(NA,times=ntimes)
emean$leaf.par = rep(NA,times=ntimes)
emean$leaf.par.beam = rep(NA,times=ntimes)
emean$leaf.par.diff = rep(NA,times=ntimes)
emean$leaf.gpp = rep(NA,times=ntimes)
emean$phap.lpar = rep(NA,times=ntimes)
emean$last.1yr.lpar = rep(NA,times=ntimes)
emean$last.2yr.lpar = rep(NA,times=ntimes)
emean$last.3yr.lpar = rep(NA,times=ntimes)
emean$leaf.rshort = rep(NA,times=ntimes)
emean$leaf.rlong = rep(NA,times=ntimes)
emean$last.1yr.growth = rep(NA,times=ntimes)
emean$last.2yr.growth = rep(NA,times=ntimes)
emean$last.3yr.growth = rep(NA,times=ntimes)
emean$last.1yr.recr = rep(NA,times=ntimes)
emean$last.2yr.recr = rep(NA,times=ntimes)
emean$last.3yr.recr = rep(NA,times=ntimes)
emean$last.1yr.mort = rep(NA,times=ntimes)
emean$last.2yr.mort = rep(NA,times=ntimes)
emean$last.3yr.mort = rep(NA,times=ntimes)
emean$last.1yr.dimort = rep(NA,times=ntimes)
emean$last.2yr.dimort = rep(NA,times=ntimes)
emean$last.3yr.dimort = rep(NA,times=ntimes)
emean$last.1yr.ncbmort = rep(NA,times=ntimes)
emean$last.2yr.ncbmort = rep(NA,times=ntimes)
emean$last.3yr.ncbmort = rep(NA,times=ntimes)
emean$agb.change = rep(NA,times=ntimes)
emean$acc.change = rep(NA,times=ntimes)
emean$acc.growth = rep(NA,times=ntimes)
emean$acc.mort = rep(NA,times=ntimes)
emean$acc.ncbmort = rep(NA,times=ntimes)
emean$acc.dimort = rep(NA,times=ntimes)
emean$acc.recr = rep(NA,times=ntimes)
emean$last.1yr.change = rep(NA,times=ntimes)
emean$last.2yr.change = rep(NA,times=ntimes)
emean$last.3yr.change = rep(NA,times=ntimes)
#----- Soil variables. -----------------------------------------------------------------#
emean$soil.water = matrix(data=0,nrow=ntimes,ncol=nzg)
emean$soil.temp = matrix(data=0,nrow=ntimes,ncol=nzg)
emean$soil.mstpot = matrix(data=0,nrow=ntimes,ncol=nzg)
emean$soil.extracted = matrix(data=0,nrow=ntimes,ncol=nzg)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emsqu -- mean sum of squares of polygon-level variable. #
#---------------------------------------------------------------------------------------#
emsqu = list()
emsqu$gpp = rep(NA,times=ntimes)
emsqu$plant.resp = rep(NA,times=ntimes)
emsqu$leaf.resp = rep(NA,times=ntimes)
emsqu$froot.resp = rep(NA,times=ntimes)
emsqu$het.resp = rep(NA,times=ntimes)
emsqu$cwd.resp = rep(NA,times=ntimes)
emsqu$reco = rep(NA,times=ntimes)
emsqu$cflxca = rep(NA,times=ntimes)
emsqu$cflxst = rep(NA,times=ntimes)
emsqu$hflxca = rep(NA,times=ntimes)
emsqu$hflxlc = rep(NA,times=ntimes)
emsqu$hflxwc = rep(NA,times=ntimes)
emsqu$hflxgc = rep(NA,times=ntimes)
emsqu$wflxca = rep(NA,times=ntimes)
emsqu$qwflxca = rep(NA,times=ntimes)
emsqu$wflxlc = rep(NA,times=ntimes)
emsqu$wflxwc = rep(NA,times=ntimes)
emsqu$wflxgc = rep(NA,times=ntimes)
emsqu$evap = rep(NA,times=ntimes)
emsqu$transp = rep(NA,times=ntimes)
emsqu$ustar = rep(NA,times=ntimes)
emsqu$albedo = rep(NA,times=ntimes)
emsqu$rshortup = rep(NA,times=ntimes)
emsqu$rlongup = rep(NA,times=ntimes)
emsqu$parup = rep(NA,times=ntimes)
emsqu$rnet = rep(NA,times=ntimes)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# SZPFT -- Size (DBH) and plant functional type (PFT) array. An extra level is #
# appended to the end, which will hold the sum of all categories. #
# #
# The initial value depends on the type of variable: #
# - If absence is equal to zero, then the initial value must be zero. This is #
# normally the case for state variables (e.g. biomass, demographic density, #
# LAI, etc.) #
# - If absence makes the variable meaningless, then the initial value must #
# be NA. This is true for plant-derived properties (temperature, mortality, #
# gsw, etc.) #
#---------------------------------------------------------------------------------------#
szpft = list()
#----- Initial value should be zero. ---------------------------------------------------#
szpft$agb = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$biomass = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$lai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$wai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$tai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$ba = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$nplant = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bdead = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$balive = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bleaf = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bstem = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$broot = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bfroot = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bcroot = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsapwood = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bstorage = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$bseeds = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.lai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.wai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.tai = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.agb = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$census.ba = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$par.leaf = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$par.leaf.beam = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
szpft$par.leaf.diff = array(data=0 ,dim=c(ntimes,ndbh+1,npft+1))
#----- Initial value should be NA. -----------------------------------------------------#
szpft$wood.dens = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$npp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$dcbadt = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$root.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$froot.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$croot.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$stem.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$growth.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$storage.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$plant.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.light = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.rubp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.co2 = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$assim.ratio = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$mco = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cba = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbamax = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbalight = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbamoist = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cbarel = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$ldrop = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$sm.stress = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.sms = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.gbw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lgbw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.gsw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lgsw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wood.gbw = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.temp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.ltemp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.water = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lwater = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wood.temp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.vpd = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lvpd = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$demand = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$supply = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$agb.change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$acc.change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.mort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.dimort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.ncbmort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.growth = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.recr = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$bsa.change = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$hflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.npp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.plant.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.mco = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cba = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cbamax = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cbalight = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.cbamoist = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.transp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.wflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$i.hflxlc = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.plant.resp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.npp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.mco = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.cba = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bstorage = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.dcbadt = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bleaf = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bstem = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.broot = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$f.bseeds = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.par = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.par.beam = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.par.diff = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.gpp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$phap.lpar = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.rshort = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$leaf.rlong = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$transp = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$wue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$cue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$ecue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$etue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
szpft$rue = array(data=NA,dim=c(ntimes,ndbh+1,npft+1))
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# LU -- Polygon-level variables, split by land use type. One extra dimension is #
# appended to the end, which will hold the sum of all land use types. #
# #
# The initial value depends on the type of variable: #
# - If absence is equal to zero, then the initial value must be zero. This is #
# normally the case for state variables (e.g. biomass, demographic density, #
# LAI, etc.) #
# - If absence makes the variable meaningless, then the initial value must #
# be NA. This is true for plant-derived properties (temperature, mortality, #
# gsw, etc.) #
#---------------------------------------------------------------------------------------#
lu = list()
#----- Initial value should be zero. ---------------------------------------------------#
lu$agb = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$biomass = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$lai = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$area = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
lu$ba = matrix(data=0 ,nrow=ntimes,ncol=nlu+1)
#----- Initial value should be NA. -----------------------------------------------------#
lu$gpp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$npp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.agb = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.biomass = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.lai = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.gpp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.npp = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$f.ba = matrix(data=NA,nrow=ntimes,ncol=nlu+1)
lu$dist = array (data=NA,dim=c(ntimes,nlu,nlu))
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMEAN -- Polygon-level variables, containing the mean diel (diurnal cycle). #
#---------------------------------------------------------------------------------------#
qmean = list()
qmean$gpp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$npp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$plant.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$root.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$froot.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$het.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$cwd.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$soil.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.light = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.rubp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.co2 = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$assim.ratio = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$nep = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$nee = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$reco = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$cflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$cflxst = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$hflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$qwflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$runoff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$intercepted = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wshed = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$evap = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$transp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.water = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wood.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$gnd.temp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.shv = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.shv = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$gnd.shv = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.vpd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.vpd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.vpd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.co2 = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.co2 = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.prss = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$can.prss = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$atm.vels = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$ustar = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$sm.stress = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rain = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort.beam = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort.diff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshort.gnd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rshortup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlong = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlong.gnd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlongup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.tot = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.beam = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.diff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.gnd = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$parup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.leaf = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.leaf.beam = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$par.leaf.diff = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rnet = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$albedo = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$albedo.par = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$albedo.nir = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$rlong.albedo = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.gsw = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$leaf.gbw = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmean$wood.gbw = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMSQU -- Polygon-level variables, containing the mean sum of squares for the diel #
# (diurnal cycle). #
#---------------------------------------------------------------------------------------#
qmsqu = list()
qmsqu$gpp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$npp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$plant.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$leaf.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$froot.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$root.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$het.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$cwd.resp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$nep = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$reco = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$cflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$cflxst = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$hflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$qwflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxca = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxlc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxwc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$wflxgc = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$transp = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$ustar = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$albedo = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$rshortup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$rlongup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$parup = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
qmsqu$rnet = matrix(data=NA,nrow=ntimes,ncol=ndcycle)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# PATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
patch = list()
patch$ipa = list()
patch$age = list()
patch$area = list()
patch$lu = list()
patch$nep = list()
patch$het.resp = list()
patch$soil.resp = list()
patch$can.temp = list()
patch$gnd.temp = list()
patch$can.shv = list()
patch$gnd.shv = list()
patch$can.vpd = list()
patch$can.co2 = list()
patch$can.prss = list()
patch$cflxca = list()
patch$cflxst = list()
patch$nee = list()
patch$hflxca = list()
patch$hflxgc = list()
patch$qwflxca = list()
patch$wflxca = list()
patch$wflxgc = list()
patch$ustar = list()
patch$albedo = list()
patch$rshortup = list()
patch$rlongup = list()
patch$parup = list()
patch$rshort.gnd = list()
patch$par.gnd = list()
patch$par.leaf = list()
patch$par.leaf.beam = list()
patch$par.leaf.diff = list()
patch$rnet = list()
patch$lai = list()
patch$wai = list()
patch$tai = list()
patch$agb = list()
patch$ba = list()
patch$wood.dens = list()
patch$can.depth = list()
patch$can.area = list()
patch$phap.lpar = list()
patch$phap.ltemp = list()
patch$phap.lwater = list()
patch$phap.lvpd = list()
patch$phap.sms = list()
patch$phap.lgbw = list()
patch$phap.lgsw = list()
patch$sm.stress = list()
patch$leaf.temp = list()
patch$leaf.water = list()
patch$leaf.vpd = list()
patch$leaf.gpp = list()
patch$leaf.gsw = list()
patch$leaf.par = list()
patch$leaf.par.beam = list()
patch$leaf.par.diff = list()
patch$assim.light = list()
patch$assim.rubp = list()
patch$assim.co2 = list()
patch$wood.temp = list()
patch$gpp = list()
patch$npp = list()
patch$plant.resp = list()
patch$cba = list()
patch$reco = list()
patch$hflxlc = list()
patch$hflxwc = list()
patch$wflxlc = list()
patch$wflxwc = list()
patch$transp = list()
patch$fast.soil.c = list()
patch$slow.soil.c = list()
patch$struct.soil.c = list()
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QPATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
qpatch = list()
qpatch$nep = list()
qpatch$het.resp = list()
qpatch$can.temp = list()
qpatch$gnd.temp = list()
qpatch$can.shv = list()
qpatch$gnd.shv = list()
qpatch$can.vpd = list()
qpatch$can.co2 = list()
qpatch$can.prss = list()
qpatch$cflxca = list()
qpatch$cflxst = list()
qpatch$nee = list()
qpatch$hflxca = list()
qpatch$hflxgc = list()
qpatch$qwflxca = list()
qpatch$wflxca = list()
qpatch$wflxgc = list()
qpatch$ustar = list()
qpatch$albedo = list()
qpatch$rshortup = list()
qpatch$rlongup = list()
qpatch$parup = list()
qpatch$rshort.gnd = list()
qpatch$par.gnd = list()
qpatch$rnet = list()
qpatch$sm.stress = list()
qpatch$leaf.temp = list()
qpatch$leaf.water = list()
qpatch$leaf.vpd = list()
qpatch$wood.temp = list()
qpatch$par.leaf = list()
qpatch$par.leaf.beam = list()
qpatch$par.leaf.diff = list()
qpatch$leaf.gpp = list()
qpatch$leaf.gsw = list()
qpatch$leaf.par = list()
qpatch$leaf.par.beam = list()
qpatch$leaf.par.diff = list()
qpatch$assim.light = list()
qpatch$assim.rubp = list()
qpatch$assim.co2 = list()
qpatch$gpp = list()
qpatch$npp = list()
qpatch$plant.resp = list()
qpatch$hflxlc = list()
qpatch$hflxwc = list()
qpatch$wflxlc = list()
qpatch$wflxwc = list()
qpatch$transp = list()
qpatch$soil.resp = list()
#---------------------------------------------------------------------------------------#
#----- Cohort level, we save as lists because the dimensions vary. ---------------------#
cohort = list()
cohort$ipa = list()
cohort$ico = list()
cohort$area = list()
cohort$lu = list()
cohort$dbh = list()
cohort$age = list()
cohort$pft = list()
cohort$nplant = list()
cohort$height = list()
cohort$ba = list()
cohort$agb = list()
cohort$biomass = list()
cohort$lai = list()
cohort$wai = list()
cohort$tai = list()
cohort$gpp = list()
cohort$leaf.resp = list()
cohort$root.resp = list()
cohort$froot.resp = list()
cohort$croot.resp = list()
cohort$stem.resp = list()
cohort$growth.resp = list()
cohort$storage.resp = list()
cohort$plant.resp = list()
cohort$assim.light = list()
cohort$assim.rubp = list()
cohort$assim.co2 = list()
cohort$assim.ratio = list()
cohort$npp = list()
cohort$cba = list()
cohort$cbamax = list()
cohort$cbalight = list()
cohort$cbamoist = list()
cohort$cbarel = list()
cohort$dcbadt = list()
cohort$mcost = list()
cohort$ldrop = list()
cohort$sm.stress = list()
cohort$phap.sms = list()
cohort$light = list()
cohort$light.beam = list()
cohort$light.diff = list()
cohort$balive = list()
cohort$bdead = list()
cohort$bleaf = list()
cohort$bstem = list()
cohort$broot = list()
cohort$bfroot = list()
cohort$bcroot = list()
cohort$bsapwood = list()
cohort$bstorage = list()
cohort$bseeds = list()
cohort$hflxlc = list()
cohort$wflxlc = list()
cohort$transp = list()
cohort$wue = list()
cohort$cue = list()
cohort$ecue = list()
cohort$etue = list()
cohort$demand = list()
cohort$supply = list()
cohort$mort = list()
cohort$dimort = list()
cohort$ncbmort = list()
cohort$recruit = list()
cohort$growth = list()
cohort$agb.growth = list()
cohort$bsa.growth = list()
cohort$f.gpp = list()
cohort$f.plant.resp = list()
cohort$f.npp = list()
cohort$f.mco = list()
cohort$f.cba = list()
cohort$f.bstorage = list()
cohort$f.dcbadt = list()
cohort$f.bleaf = list()
cohort$f.bstem = list()
cohort$f.broot = list()
cohort$f.bseeds = list()
cohort$leaf.par = list()
cohort$leaf.par.beam = list()
cohort$leaf.par.diff = list()
cohort$leaf.gpp = list()
cohort$phap.lpar = list()
cohort$leaf.rshort = list()
cohort$leaf.rlong = list()
cohort$rue = list()
#---------------------------------------------------------------------------------------#
#----- Copy the polygon-level variable to the main structure. --------------------------#
ed$emean = emean
ed$emsqu = emsqu
ed$qmean = qmean
ed$qmsqu = qmsqu
ed$lu = lu
ed$szpft = szpft
ed$patch = patch
ed$cohort = cohort
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
return(ed)
#---------------------------------------------------------------------------------------#
}#end create.monthly
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Expand the monthly array so it fits the new times. #
#------------------------------------------------------------------------------------------#
update.monthly <<- function(new.ntimes,old.datum,montha,yeara,inpref,slz.min){
#----- Create the new data set. --------------------------------------------------------#
new.datum = create.monthly(new.ntimes,montha,yeara,inpref,slz.min)
#---------------------------------------------------------------------------------------#
#----- Find out which times to copy. ---------------------------------------------------#
sel = old.datum$when %in% new.datum$when
idx = match(old.datum$when[sel],new.datum$when)
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emean -- variables that we can either compare directly with observations, or are #
# or that may be used to draw time series. They don't need to be really #
# monthly means, but you should put only the variables that make sense to be #
# plotted in simple time series (with no PFT or DBH information). #
#---------------------------------------------------------------------------------------#
new.datum$emean$wood.dens [idx ] = old.datum$emean$wood.dens [sel ]
new.datum$emean$fast.soil.c [idx ] = old.datum$emean$fast.soil.c [sel ]
new.datum$emean$slow.soil.c [idx ] = old.datum$emean$slow.soil.c [sel ]
new.datum$emean$struct.soil.c [idx ] = old.datum$emean$struct.soil.c [sel ]
new.datum$emean$het.resp [idx ] = old.datum$emean$het.resp [sel ]
new.datum$emean$cwd.resp [idx ] = old.datum$emean$cwd.resp [sel ]
new.datum$emean$soil.resp [idx ] = old.datum$emean$soil.resp [sel ]
new.datum$emean$gpp [idx ] = old.datum$emean$gpp [sel ]
new.datum$emean$last.1yr.gpp [idx ] = old.datum$emean$last.1yr.gpp [sel ]
new.datum$emean$last.2yr.gpp [idx ] = old.datum$emean$last.2yr.gpp [sel ]
new.datum$emean$last.3yr.gpp [idx ] = old.datum$emean$last.3yr.gpp [sel ]
new.datum$emean$cue [idx ] = old.datum$emean$cue [sel ]
new.datum$emean$last.1yr.cue [idx ] = old.datum$emean$last.1yr.cue [sel ]
new.datum$emean$last.2yr.cue [idx ] = old.datum$emean$last.2yr.cue [sel ]
new.datum$emean$last.3yr.cue [idx ] = old.datum$emean$last.3yr.cue [sel ]
new.datum$emean$ecue [idx ] = old.datum$emean$ecue [sel ]
new.datum$emean$last.1yr.ecue [idx ] = old.datum$emean$last.1yr.ecue [sel ]
new.datum$emean$last.2yr.ecue [idx ] = old.datum$emean$last.2yr.ecue [sel ]
new.datum$emean$last.3yr.ecue [idx ] = old.datum$emean$last.3yr.ecue [sel ]
new.datum$emean$npp [idx ] = old.datum$emean$npp [sel ]
new.datum$emean$last.1yr.npp [idx ] = old.datum$emean$last.1yr.npp [sel ]
new.datum$emean$last.2yr.npp [idx ] = old.datum$emean$last.2yr.npp [sel ]
new.datum$emean$last.3yr.npp [idx ] = old.datum$emean$last.3yr.npp [sel ]
new.datum$emean$dcbadt [idx ] = old.datum$emean$dcbadt [sel ]
new.datum$emean$last.1yr.dcbadt [idx ] = old.datum$emean$last.1yr.dcbadt [sel ]
new.datum$emean$last.2yr.dcbadt [idx ] = old.datum$emean$last.2yr.dcbadt [sel ]
new.datum$emean$last.3yr.dcbadt [idx ] = old.datum$emean$last.3yr.dcbadt [sel ]
new.datum$emean$plant.resp [idx ] = old.datum$emean$plant.resp [sel ]
new.datum$emean$last.1yr.plresp [idx ] = old.datum$emean$last.1yr.plresp [sel ]
new.datum$emean$last.2yr.plresp [idx ] = old.datum$emean$last.2yr.plresp [sel ]
new.datum$emean$last.3yr.plresp [idx ] = old.datum$emean$last.3yr.plresp [sel ]
new.datum$emean$leaf.resp [idx ] = old.datum$emean$leaf.resp [sel ]
new.datum$emean$root.resp [idx ] = old.datum$emean$root.resp [sel ]
new.datum$emean$froot.resp [idx ] = old.datum$emean$froot.resp [sel ]
new.datum$emean$croot.resp [idx ] = old.datum$emean$croot.resp [sel ]
new.datum$emean$stem.resp [idx ] = old.datum$emean$stem.resp [sel ]
new.datum$emean$growth.resp [idx ] = old.datum$emean$growth.resp [sel ]
new.datum$emean$storage.resp [idx ] = old.datum$emean$storage.resp [sel ]
new.datum$emean$reco [idx ] = old.datum$emean$reco [sel ]
new.datum$emean$assim.light [idx ] = old.datum$emean$assim.light [sel ]
new.datum$emean$assim.rubp [idx ] = old.datum$emean$assim.rubp [sel ]
new.datum$emean$assim.co2 [idx ] = old.datum$emean$assim.co2 [sel ]
new.datum$emean$assim.ratio [idx ] = old.datum$emean$assim.ratio [sel ]
new.datum$emean$mco [idx ] = old.datum$emean$mco [sel ]
new.datum$emean$cba [idx ] = old.datum$emean$cba [sel ]
new.datum$emean$last.1yr.cba [idx ] = old.datum$emean$last.1yr.cba [sel ]
new.datum$emean$last.2yr.cba [idx ] = old.datum$emean$last.2yr.cba [sel ]
new.datum$emean$last.3yr.cba [idx ] = old.datum$emean$last.3yr.cba [sel ]
new.datum$emean$cbamax [idx ] = old.datum$emean$cbamax [sel ]
new.datum$emean$cbalight [idx ] = old.datum$emean$cbalight [sel ]
new.datum$emean$cbamoist [idx ] = old.datum$emean$cbamoist [sel ]
new.datum$emean$cbarel [idx ] = old.datum$emean$cbarel [sel ]
new.datum$emean$ldrop [idx ] = old.datum$emean$ldrop [sel ]
new.datum$emean$nep [idx ] = old.datum$emean$nep [sel ]
new.datum$emean$nee [idx ] = old.datum$emean$nee [sel ]
new.datum$emean$cflxca [idx ] = old.datum$emean$cflxca [sel ]
new.datum$emean$cflxst [idx ] = old.datum$emean$cflxst [sel ]
new.datum$emean$runoff [idx ] = old.datum$emean$runoff [sel ]
new.datum$emean$intercepted [idx ] = old.datum$emean$intercepted [sel ]
new.datum$emean$wshed [idx ] = old.datum$emean$wshed [sel ]
new.datum$emean$evap [idx ] = old.datum$emean$evap [sel ]
new.datum$emean$last.1yr.evap [idx ] = old.datum$emean$last.1yr.evap [sel ]
new.datum$emean$last.2yr.evap [idx ] = old.datum$emean$last.2yr.evap [sel ]
new.datum$emean$last.3yr.evap [idx ] = old.datum$emean$last.3yr.evap [sel ]
new.datum$emean$ustar [idx ] = old.datum$emean$ustar [sel ]
new.datum$emean$atm.vels [idx ] = old.datum$emean$atm.vels [sel ]
new.datum$emean$atm.prss [idx ] = old.datum$emean$atm.prss [sel ]
new.datum$emean$atm.temp [idx ] = old.datum$emean$atm.temp [sel ]
new.datum$emean$can.prss [idx ] = old.datum$emean$can.prss [sel ]
new.datum$emean$can.temp [idx ] = old.datum$emean$can.temp [sel ]
new.datum$emean$atm.co2 [idx ] = old.datum$emean$atm.co2 [sel ]
new.datum$emean$can.co2 [idx ] = old.datum$emean$can.co2 [sel ]
new.datum$emean$can.depth [idx ] = old.datum$emean$can.depth [sel ]
new.datum$emean$can.area [idx ] = old.datum$emean$can.area [sel ]
new.datum$emean$leaf.temp [idx ] = old.datum$emean$leaf.temp [sel ]
new.datum$emean$phap.ltemp [idx ] = old.datum$emean$phap.ltemp [sel ]
new.datum$emean$last.1yr.ltemp [idx ] = old.datum$emean$last.1yr.ltemp [sel ]
new.datum$emean$last.2yr.ltemp [idx ] = old.datum$emean$last.2yr.ltemp [sel ]
new.datum$emean$last.3yr.ltemp [idx ] = old.datum$emean$last.3yr.ltemp [sel ]
new.datum$emean$leaf.water [idx ] = old.datum$emean$leaf.water [sel ]
new.datum$emean$phap.lwater [idx ] = old.datum$emean$phap.lwater [sel ]
new.datum$emean$last.1yr.lwater [idx ] = old.datum$emean$last.1yr.lwater [sel ]
new.datum$emean$last.2yr.lwater [idx ] = old.datum$emean$last.2yr.lwater [sel ]
new.datum$emean$last.3yr.lwater [idx ] = old.datum$emean$last.3yr.lwater [sel ]
new.datum$emean$wood.temp [idx ] = old.datum$emean$wood.temp [sel ]
new.datum$emean$atm.shv [idx ] = old.datum$emean$atm.shv [sel ]
new.datum$emean$can.shv [idx ] = old.datum$emean$can.shv [sel ]
new.datum$emean$atm.vpd [idx ] = old.datum$emean$atm.vpd [sel ]
new.datum$emean$can.vpd [idx ] = old.datum$emean$can.vpd [sel ]
new.datum$emean$leaf.vpd [idx ] = old.datum$emean$leaf.vpd [sel ]
new.datum$emean$phap.lvpd [idx ] = old.datum$emean$phap.lvpd [sel ]
new.datum$emean$last.1yr.lvpd [idx ] = old.datum$emean$last.1yr.lvpd [sel ]
new.datum$emean$last.2yr.lvpd [idx ] = old.datum$emean$last.2yr.lvpd [sel ]
new.datum$emean$last.3yr.lvpd [idx ] = old.datum$emean$last.3yr.lvpd [sel ]
new.datum$emean$can.co2 [idx ] = old.datum$emean$can.co2 [sel ]
new.datum$emean$hflxca [idx ] = old.datum$emean$hflxca [sel ]
new.datum$emean$qwflxca [idx ] = old.datum$emean$qwflxca [sel ]
new.datum$emean$wflxca [idx ] = old.datum$emean$wflxca [sel ]
new.datum$emean$agb [idx ] = old.datum$emean$agb [sel ]
new.datum$emean$biomass [idx ] = old.datum$emean$biomass [sel ]
new.datum$emean$nplant [idx ] = old.datum$emean$nplant [sel ]
new.datum$emean$lai [idx ] = old.datum$emean$lai [sel ]
new.datum$emean$wai [idx ] = old.datum$emean$wai [sel ]
new.datum$emean$tai [idx ] = old.datum$emean$tai [sel ]
new.datum$emean$area [idx ] = old.datum$emean$area [sel ]
new.datum$emean$et [idx ] = old.datum$emean$et [sel ]
new.datum$emean$last.1yr.et [idx ] = old.datum$emean$last.1yr.et [sel ]
new.datum$emean$last.2yr.et [idx ] = old.datum$emean$last.2yr.et [sel ]
new.datum$emean$last.3yr.et [idx ] = old.datum$emean$last.3yr.et [sel ]
new.datum$emean$transp [idx ] = old.datum$emean$transp [sel ]
new.datum$emean$last.1yr.transp [idx ] = old.datum$emean$last.1yr.transp [sel ]
new.datum$emean$last.2yr.transp [idx ] = old.datum$emean$last.2yr.transp [sel ]
new.datum$emean$last.3yr.transp [idx ] = old.datum$emean$last.3yr.transp [sel ]
new.datum$emean$wue [idx ] = old.datum$emean$wue [sel ]
new.datum$emean$last.1yr.wue [idx ] = old.datum$emean$last.1yr.wue [sel ]
new.datum$emean$last.2yr.wue [idx ] = old.datum$emean$last.2yr.wue [sel ]
new.datum$emean$last.3yr.wue [idx ] = old.datum$emean$last.3yr.wue [sel ]
new.datum$emean$etue [idx ] = old.datum$emean$etue [sel ]
new.datum$emean$last.1yr.etue [idx ] = old.datum$emean$last.1yr.etue [sel ]
new.datum$emean$last.2yr.etue [idx ] = old.datum$emean$last.2yr.etue [sel ]
new.datum$emean$last.3yr.etue [idx ] = old.datum$emean$last.3yr.etue [sel ]
new.datum$emean$rain [idx ] = old.datum$emean$rain [sel ]
new.datum$emean$last.1yr.rain [idx ] = old.datum$emean$last.1yr.rain [sel ]
new.datum$emean$last.2yr.rain [idx ] = old.datum$emean$last.2yr.rain [sel ]
new.datum$emean$last.3yr.rain [idx ] = old.datum$emean$last.3yr.rain [sel ]
new.datum$emean$nmon.lt.090 [idx ] = old.datum$emean$nmon.lt.090 [sel ]
new.datum$emean$nmon.lt.100 [idx ] = old.datum$emean$nmon.lt.100 [sel ]
new.datum$emean$nmon.lt.110 [idx ] = old.datum$emean$nmon.lt.110 [sel ]
new.datum$emean$nmon.lt.120 [idx ] = old.datum$emean$nmon.lt.120 [sel ]
new.datum$emean$nmon.wdef [idx ] = old.datum$emean$nmon.wdef [sel ]
new.datum$emean$nmon.mdef [idx ] = old.datum$emean$nmon.mdef [sel ]
new.datum$emean$rue [idx ] = old.datum$emean$rue [sel ]
new.datum$emean$last.1yr.rue [idx ] = old.datum$emean$last.1yr.rue [sel ]
new.datum$emean$last.2yr.rue [idx ] = old.datum$emean$last.2yr.rue [sel ]
new.datum$emean$last.3yr.rue [idx ] = old.datum$emean$last.3yr.rue [sel ]
new.datum$emean$gnd.temp [idx ] = old.datum$emean$gnd.temp [sel ]
new.datum$emean$gnd.shv [idx ] = old.datum$emean$gnd.shv [sel ]
new.datum$emean$workload [idx ] = old.datum$emean$workload [sel ]
new.datum$emean$specwork [idx ] = old.datum$emean$specwork [sel ]
new.datum$emean$sm.stress [idx ] = old.datum$emean$sm.stress [sel ]
new.datum$emean$phap.sms [idx ] = old.datum$emean$phap.sms [sel ]
new.datum$emean$last.1yr.sms [idx ] = old.datum$emean$last.1yr.sms [sel ]
new.datum$emean$last.2yr.sms [idx ] = old.datum$emean$last.2yr.sms [sel ]
new.datum$emean$last.3yr.sms [idx ] = old.datum$emean$last.3yr.sms [sel ]
new.datum$emean$demand [idx ] = old.datum$emean$demand [sel ]
new.datum$emean$supply [idx ] = old.datum$emean$supply [sel ]
new.datum$emean$hflxgc [idx ] = old.datum$emean$hflxgc [sel ]
new.datum$emean$hflxlc [idx ] = old.datum$emean$hflxlc [sel ]
new.datum$emean$hflxwc [idx ] = old.datum$emean$hflxwc [sel ]
new.datum$emean$wflxgc [idx ] = old.datum$emean$wflxgc [sel ]
new.datum$emean$wflxlc [idx ] = old.datum$emean$wflxlc [sel ]
new.datum$emean$wflxwc [idx ] = old.datum$emean$wflxwc [sel ]
new.datum$emean$rshort [idx ] = old.datum$emean$rshort [sel ]
new.datum$emean$last.1yr.rshort [idx ] = old.datum$emean$last.1yr.rshort [sel ]
new.datum$emean$last.2yr.rshort [idx ] = old.datum$emean$last.2yr.rshort [sel ]
new.datum$emean$last.3yr.rshort [idx ] = old.datum$emean$last.3yr.rshort [sel ]
new.datum$emean$rshort.beam [idx ] = old.datum$emean$rshort.beam [sel ]
new.datum$emean$rshort.diff [idx ] = old.datum$emean$rshort.diff [sel ]
new.datum$emean$rshortup [idx ] = old.datum$emean$rshortup [sel ]
new.datum$emean$rshort.gnd [idx ] = old.datum$emean$rshort.gnd [sel ]
new.datum$emean$rlong [idx ] = old.datum$emean$rlong [sel ]
new.datum$emean$rlong.gnd [idx ] = old.datum$emean$rlong.gnd [sel ]
new.datum$emean$rlongup [idx ] = old.datum$emean$rlongup [sel ]
new.datum$emean$par.tot [idx ] = old.datum$emean$par.tot [sel ]
new.datum$emean$par.beam [idx ] = old.datum$emean$par.beam [sel ]
new.datum$emean$par.diff [idx ] = old.datum$emean$par.diff [sel ]
new.datum$emean$par.gnd [idx ] = old.datum$emean$par.gnd [sel ]
new.datum$emean$parup [idx ] = old.datum$emean$parup [sel ]
new.datum$emean$par.leaf [idx ] = old.datum$emean$par.leaf [sel ]
new.datum$emean$par.leaf.beam [idx ] = old.datum$emean$par.leaf.beam [sel ]
new.datum$emean$par.leaf.diff [idx ] = old.datum$emean$par.leaf.diff [sel ]
new.datum$emean$rnet [idx ] = old.datum$emean$rnet [sel ]
new.datum$emean$albedo [idx ] = old.datum$emean$albedo [sel ]
new.datum$emean$albedo.par [idx ] = old.datum$emean$albedo.par [sel ]
new.datum$emean$albedo.nir [idx ] = old.datum$emean$albedo.nir [sel ]
new.datum$emean$rlong.albedo [idx ] = old.datum$emean$rlong.albedo [sel ]
new.datum$emean$paw [idx ] = old.datum$emean$paw [sel ]
new.datum$emean$smpot [idx ] = old.datum$emean$smpot [sel ]
new.datum$emean$last.1yr.smpot [idx ] = old.datum$emean$last.1yr.smpot [sel ]
new.datum$emean$last.2yr.smpot [idx ] = old.datum$emean$last.2yr.smpot [sel ]
new.datum$emean$last.3yr.smpot [idx ] = old.datum$emean$last.3yr.smpot [sel ]
new.datum$emean$npat.global [idx ] = old.datum$emean$npat.global [sel ]
new.datum$emean$ncoh.global [idx ] = old.datum$emean$ncoh.global [sel ]
new.datum$emean$water.deficit [idx ] = old.datum$emean$water.deficit [sel ]
new.datum$emean$last.1yr.mwd [idx ] = old.datum$emean$last.1yr.mwd [sel ]
new.datum$emean$last.2yr.mwd [idx ] = old.datum$emean$last.2yr.mwd [sel ]
new.datum$emean$last.3yr.mwd [idx ] = old.datum$emean$last.3yr.mwd [sel ]
new.datum$emean$malhi.deficit [idx ] = old.datum$emean$malhi.deficit [sel ]
new.datum$emean$i.gpp [idx ] = old.datum$emean$i.gpp [sel ]
new.datum$emean$i.npp [idx ] = old.datum$emean$i.npp [sel ]
new.datum$emean$i.plant.resp [idx ] = old.datum$emean$i.plant.resp [sel ]
new.datum$emean$i.mco [idx ] = old.datum$emean$i.mco [sel ]
new.datum$emean$i.cba [idx ] = old.datum$emean$i.cba [sel ]
new.datum$emean$i.cbamax [idx ] = old.datum$emean$i.cbamax [sel ]
new.datum$emean$i.cbalight [idx ] = old.datum$emean$i.cbalight [sel ]
new.datum$emean$i.cbamoist [idx ] = old.datum$emean$i.cbamoist [sel ]
new.datum$emean$i.transp [idx ] = old.datum$emean$i.transp [sel ]
new.datum$emean$i.wflxlc [idx ] = old.datum$emean$i.wflxlc [sel ]
new.datum$emean$i.hflxlc [idx ] = old.datum$emean$i.hflxlc [sel ]
new.datum$emean$f.gpp [idx ] = old.datum$emean$f.gpp [sel ]
new.datum$emean$f.plant.resp [idx ] = old.datum$emean$f.plant.resp [sel ]
new.datum$emean$f.npp [idx ] = old.datum$emean$f.npp [sel ]
new.datum$emean$f.mco [idx ] = old.datum$emean$f.mco [sel ]
new.datum$emean$f.cba [idx ] = old.datum$emean$f.cba [sel ]
new.datum$emean$f.bstorage [idx ] = old.datum$emean$f.bstorage [sel ]
new.datum$emean$f.bleaf [idx ] = old.datum$emean$f.bleaf [sel ]
new.datum$emean$f.bstem [idx ] = old.datum$emean$f.bstem [sel ]
new.datum$emean$f.broot [idx ] = old.datum$emean$f.broot [sel ]
new.datum$emean$f.bseeds [idx ] = old.datum$emean$f.bseeds [sel ]
new.datum$emean$f.dcbadt [idx ] = old.datum$emean$f.dcbadt [sel ]
new.datum$emean$leaf.gsw [idx ] = old.datum$emean$leaf.gsw [sel ]
new.datum$emean$phap.lgsw [idx ] = old.datum$emean$phap.lgsw [sel ]
new.datum$emean$last.1yr.lgsw [idx ] = old.datum$emean$last.1yr.lgsw [sel ]
new.datum$emean$last.2yr.lgsw [idx ] = old.datum$emean$last.2yr.lgsw [sel ]
new.datum$emean$last.3yr.lgsw [idx ] = old.datum$emean$last.3yr.lgsw [sel ]
new.datum$emean$leaf.gbw [idx ] = old.datum$emean$leaf.gbw [sel ]
new.datum$emean$phap.lgbw [idx ] = old.datum$emean$phap.lgbw [sel ]
new.datum$emean$wood.gbw [idx ] = old.datum$emean$wood.gbw [sel ]
new.datum$emean$leaf.par [idx ] = old.datum$emean$leaf.par [sel ]
new.datum$emean$leaf.par.beam [idx ] = old.datum$emean$leaf.par.beam [sel ]
new.datum$emean$leaf.par.diff [idx ] = old.datum$emean$leaf.par.diff [sel ]
new.datum$emean$leaf.gpp [idx ] = old.datum$emean$leaf.gpp [sel ]
new.datum$emean$phap.lpar [idx ] = old.datum$emean$phap.lpar [sel ]
new.datum$emean$last.1yr.lpar [idx ] = old.datum$emean$last.1yr.lpar [sel ]
new.datum$emean$last.2yr.lpar [idx ] = old.datum$emean$last.2yr.lpar [sel ]
new.datum$emean$last.3yr.lpar [idx ] = old.datum$emean$last.3yr.lpar [sel ]
new.datum$emean$leaf.rshort [idx ] = old.datum$emean$leaf.rshort [sel ]
new.datum$emean$leaf.rlong [idx ] = old.datum$emean$leaf.rlong [sel ]
new.datum$emean$soil.water [idx,] = old.datum$emean$soil.water [sel,]
new.datum$emean$soil.temp [idx,] = old.datum$emean$soil.temp [sel,]
new.datum$emean$soil.mstpot [idx,] = old.datum$emean$soil.mstpot [sel,]
new.datum$emean$soil.extracted [idx,] = old.datum$emean$soil.extracted [sel,]
new.datum$emean$last.1yr.growth [idx ] = old.datum$emean$last.1yr.growth [sel ]
new.datum$emean$last.2yr.growth [idx ] = old.datum$emean$last.2yr.growth [sel ]
new.datum$emean$last.3yr.growth [idx ] = old.datum$emean$last.3yr.growth [sel ]
new.datum$emean$last.1yr.mort [idx ] = old.datum$emean$last.1yr.mort [sel ]
new.datum$emean$last.2yr.mort [idx ] = old.datum$emean$last.2yr.mort [sel ]
new.datum$emean$last.3yr.mort [idx ] = old.datum$emean$last.3yr.mort [sel ]
new.datum$emean$last.1yr.dimort [idx ] = old.datum$emean$last.1yr.dimort [sel ]
new.datum$emean$last.2yr.dimort [idx ] = old.datum$emean$last.2yr.dimort [sel ]
new.datum$emean$last.3yr.dimort [idx ] = old.datum$emean$last.3yr.dimort [sel ]
new.datum$emean$last.1yr.ncbmort [idx ] = old.datum$emean$last.1yr.ncbmort [sel ]
new.datum$emean$last.2yr.ncbmort [idx ] = old.datum$emean$last.2yr.ncbmort [sel ]
new.datum$emean$last.3yr.ncbmort [idx ] = old.datum$emean$last.3yr.ncbmort [sel ]
new.datum$emean$agb.change [idx ] = old.datum$emean$agb.change [sel ]
new.datum$emean$acc.change [idx ] = old.datum$emean$acc.change [sel ]
new.datum$emean$acc.growth [idx ] = old.datum$emean$acc.growth [sel ]
new.datum$emean$acc.mort [idx ] = old.datum$emean$acc.mort [sel ]
new.datum$emean$acc.ncbmort [idx ] = old.datum$emean$acc.ncbmort [sel ]
new.datum$emean$acc.dimort [idx ] = old.datum$emean$acc.dimort [sel ]
new.datum$emean$acc.recr [idx ] = old.datum$emean$acc.recr [sel ]
new.datum$emean$last.1yr.change [idx ] = old.datum$emean$last.1yr.change [sel ]
new.datum$emean$last.2yr.change [idx ] = old.datum$emean$last.2yr.change [sel ]
new.datum$emean$last.3yr.change [idx ] = old.datum$emean$last.3yr.change [sel ]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# emsqu -- mean sum of squares of polygon-level variable. #
#---------------------------------------------------------------------------------------#
new.datum$emsqu$gpp [idx] = old.datum$emsqu$gpp [sel]
new.datum$emsqu$plant.resp [idx] = old.datum$emsqu$plant.resp [sel]
new.datum$emsqu$het.resp [idx] = old.datum$emsqu$het.resp [sel]
new.datum$emsqu$cwd.resp [idx] = old.datum$emsqu$cwd.resp [sel]
new.datum$emsqu$soil.resp [idx] = old.datum$emsqu$soil.resp [sel]
new.datum$emsqu$cflxca [idx] = old.datum$emsqu$cflxca [sel]
new.datum$emsqu$cflxst [idx] = old.datum$emsqu$cflxst [sel]
new.datum$emsqu$hflxca [idx] = old.datum$emsqu$hflxca [sel]
new.datum$emsqu$hflxlc [idx] = old.datum$emsqu$hflxlc [sel]
new.datum$emsqu$hflxwc [idx] = old.datum$emsqu$hflxwc [sel]
new.datum$emsqu$hflxgc [idx] = old.datum$emsqu$hflxgc [sel]
new.datum$emsqu$wflxca [idx] = old.datum$emsqu$wflxca [sel]
new.datum$emsqu$qwflxca [idx] = old.datum$emsqu$qwflxca [sel]
new.datum$emsqu$wflxlc [idx] = old.datum$emsqu$wflxlc [sel]
new.datum$emsqu$wflxwc [idx] = old.datum$emsqu$wflxwc [sel]
new.datum$emsqu$wflxgc [idx] = old.datum$emsqu$wflxgc [sel]
new.datum$emsqu$transp [idx] = old.datum$emsqu$transp [sel]
new.datum$emsqu$ustar [idx] = old.datum$emsqu$ustar [sel]
new.datum$emsqu$albedo [idx] = old.datum$emsqu$albedo [sel]
new.datum$emsqu$rshortup [idx] = old.datum$emsqu$rshortup [sel]
new.datum$emsqu$rlongup [idx] = old.datum$emsqu$rlongup [sel]
new.datum$emsqu$parup [idx] = old.datum$emsqu$parup [sel]
new.datum$emsqu$rnet [idx] = old.datum$emsqu$rnet [sel]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# SZPFT -- Size (DBH) and plant functional type (PFT) array. An extra level is #
# appended to the end, which will hold the sum of all categories. #
#---------------------------------------------------------------------------------------#
new.datum$szpft$agb [idx,,] = old.datum$szpft$agb [sel,,]
new.datum$szpft$biomass [idx,,] = old.datum$szpft$biomass [sel,,]
new.datum$szpft$lai [idx,,] = old.datum$szpft$lai [sel,,]
new.datum$szpft$wai [idx,,] = old.datum$szpft$wai [sel,,]
new.datum$szpft$tai [idx,,] = old.datum$szpft$tai [sel,,]
new.datum$szpft$ba [idx,,] = old.datum$szpft$ba [sel,,]
new.datum$szpft$gpp [idx,,] = old.datum$szpft$gpp [sel,,]
new.datum$szpft$npp [idx,,] = old.datum$szpft$npp [sel,,]
new.datum$szpft$dcbadt [idx,,] = old.datum$szpft$dcbadt [sel,,]
new.datum$szpft$wood.dens [idx,,] = old.datum$szpft$wood.dens [sel,,]
new.datum$szpft$leaf.resp [idx,,] = old.datum$szpft$leaf.resp [sel,,]
new.datum$szpft$root.resp [idx,,] = old.datum$szpft$root.resp [sel,,]
new.datum$szpft$froot.resp [idx,,] = old.datum$szpft$froot.resp [sel,,]
new.datum$szpft$croot.resp [idx,,] = old.datum$szpft$croot.resp [sel,,]
new.datum$szpft$stem.resp [idx,,] = old.datum$szpft$stem.resp [sel,,]
new.datum$szpft$growth.resp [idx,,] = old.datum$szpft$growth.resp [sel,,]
new.datum$szpft$storage.resp [idx,,] = old.datum$szpft$storage.resp [sel,,]
new.datum$szpft$plant.resp [idx,,] = old.datum$szpft$plant.resp [sel,,]
new.datum$szpft$assim.light [idx,,] = old.datum$szpft$assim.light [sel,,]
new.datum$szpft$assim.rubp [idx,,] = old.datum$szpft$assim.rubp [sel,,]
new.datum$szpft$assim.co2 [idx,,] = old.datum$szpft$assim.co2 [sel,,]
new.datum$szpft$mco [idx,,] = old.datum$szpft$mco [sel,,]
new.datum$szpft$cba [idx,,] = old.datum$szpft$cba [sel,,]
new.datum$szpft$cbamax [idx,,] = old.datum$szpft$cbamax [sel,,]
new.datum$szpft$cbalight [idx,,] = old.datum$szpft$cbalight [sel,,]
new.datum$szpft$cbamoist [idx,,] = old.datum$szpft$cbamoist [sel,,]
new.datum$szpft$cbarel [idx,,] = old.datum$szpft$cbarel [sel,,]
new.datum$szpft$ldrop [idx,,] = old.datum$szpft$ldrop [sel,,]
new.datum$szpft$sm.stress [idx,,] = old.datum$szpft$sm.stress [sel,,]
new.datum$szpft$phap.sms [idx,,] = old.datum$szpft$phap.sms [sel,,]
new.datum$szpft$leaf.gbw [idx,,] = old.datum$szpft$leaf.gbw [sel,,]
new.datum$szpft$phap.lgbw [idx,,] = old.datum$szpft$phap.lgbw [sel,,]
new.datum$szpft$leaf.gsw [idx,,] = old.datum$szpft$leaf.gsw [sel,,]
new.datum$szpft$phap.lgsw [idx,,] = old.datum$szpft$phap.lgsw [sel,,]
new.datum$szpft$wood.gbw [idx,,] = old.datum$szpft$wood.gbw [sel,,]
new.datum$szpft$leaf.temp [idx,,] = old.datum$szpft$leaf.temp [sel,,]
new.datum$szpft$phap.ltemp [idx,,] = old.datum$szpft$phap.ltemp [sel,,]
new.datum$szpft$leaf.water [idx,,] = old.datum$szpft$leaf.water [sel,,]
new.datum$szpft$phap.lwater [idx,,] = old.datum$szpft$phap.lwater [sel,,]
new.datum$szpft$wood.temp [idx,,] = old.datum$szpft$wood.temp [sel,,]
new.datum$szpft$leaf.vpd [idx,,] = old.datum$szpft$leaf.vpd [sel,,]
new.datum$szpft$phap.lvpd [idx,,] = old.datum$szpft$phap.lvpd [sel,,]
new.datum$szpft$demand [idx,,] = old.datum$szpft$demand [sel,,]
new.datum$szpft$supply [idx,,] = old.datum$szpft$supply [sel,,]
new.datum$szpft$nplant [idx,,] = old.datum$szpft$nplant [sel,,]
new.datum$szpft$mort [idx,,] = old.datum$szpft$mort [sel,,]
new.datum$szpft$dimort [idx,,] = old.datum$szpft$dimort [sel,,]
new.datum$szpft$ncbmort [idx,,] = old.datum$szpft$ncbmort [sel,,]
new.datum$szpft$growth [idx,,] = old.datum$szpft$growth [sel,,]
new.datum$szpft$recr [idx,,] = old.datum$szpft$recr [sel,,]
new.datum$szpft$change [idx,,] = old.datum$szpft$change [sel,,]
new.datum$szpft$agb.mort [idx,,] = old.datum$szpft$agb.mort [sel,,]
new.datum$szpft$agb.dimort [idx,,] = old.datum$szpft$agb.dimort [sel,,]
new.datum$szpft$agb.ncbmort [idx,,] = old.datum$szpft$agb.ncbmort [sel,,]
new.datum$szpft$agb.growth [idx,,] = old.datum$szpft$agb.growth [sel,,]
new.datum$szpft$agb.recr [idx,,] = old.datum$szpft$agb.recr [sel,,]
new.datum$szpft$agb.change [idx,,] = old.datum$szpft$agb.change [sel,,]
new.datum$szpft$acc.mort [idx,,] = old.datum$szpft$acc.mort [sel,,]
new.datum$szpft$acc.dimort [idx,,] = old.datum$szpft$acc.dimort [sel,,]
new.datum$szpft$acc.ncbmort [idx,,] = old.datum$szpft$acc.ncbmort [sel,,]
new.datum$szpft$acc.growth [idx,,] = old.datum$szpft$acc.growth [sel,,]
new.datum$szpft$acc.recr [idx,,] = old.datum$szpft$acc.recr [sel,,]
new.datum$szpft$acc.change [idx,,] = old.datum$szpft$acc.change [sel,,]
new.datum$szpft$bsa.mort [idx,,] = old.datum$szpft$bsa.mort [sel,,]
new.datum$szpft$bsa.dimort [idx,,] = old.datum$szpft$bsa.dimort [sel,,]
new.datum$szpft$bsa.ncbmort [idx,,] = old.datum$szpft$bsa.ncbmort [sel,,]
new.datum$szpft$bsa.growth [idx,,] = old.datum$szpft$bsa.growth [sel,,]
new.datum$szpft$bsa.recr [idx,,] = old.datum$szpft$bsa.recr [sel,,]
new.datum$szpft$bsa.change [idx,,] = old.datum$szpft$bsa.change [sel,,]
new.datum$szpft$bdead [idx,,] = old.datum$szpft$bdead [sel,,]
new.datum$szpft$balive [idx,,] = old.datum$szpft$balive [sel,,]
new.datum$szpft$bleaf [idx,,] = old.datum$szpft$bleaf [sel,,]
new.datum$szpft$bstem [idx,,] = old.datum$szpft$bstem [sel,,]
new.datum$szpft$broot [idx,,] = old.datum$szpft$broot [sel,,]
new.datum$szpft$bfroot [idx,,] = old.datum$szpft$bfroot [sel,,]
new.datum$szpft$bcroot [idx,,] = old.datum$szpft$bcroot [sel,,]
new.datum$szpft$bsapwood [idx,,] = old.datum$szpft$bsapwood [sel,,]
new.datum$szpft$bstorage [idx,,] = old.datum$szpft$bstorage [sel,,]
new.datum$szpft$bseeds [idx,,] = old.datum$szpft$bseeds [sel,,]
new.datum$szpft$hflxlc [idx,,] = old.datum$szpft$hflxlc [sel,,]
new.datum$szpft$wflxlc [idx,,] = old.datum$szpft$wflxlc [sel,,]
new.datum$szpft$census.lai [idx,,] = old.datum$szpft$census.lai [sel,,]
new.datum$szpft$census.wai [idx,,] = old.datum$szpft$census.wai [sel,,]
new.datum$szpft$census.tai [idx,,] = old.datum$szpft$census.tai [sel,,]
new.datum$szpft$census.agb [idx,,] = old.datum$szpft$census.agb [sel,,]
new.datum$szpft$census.ba [idx,,] = old.datum$szpft$census.ba [sel,,]
new.datum$szpft$par.leaf [idx,,] = old.datum$szpft$par.leaf [sel,,]
new.datum$szpft$par.leaf.beam [idx,,] = old.datum$szpft$par.leaf.beam [sel,,]
new.datum$szpft$par.leaf.diff [idx,,] = old.datum$szpft$par.leaf.diff [sel,,]
new.datum$szpft$i.gpp [idx,,] = old.datum$szpft$i.gpp [sel,,]
new.datum$szpft$i.npp [idx,,] = old.datum$szpft$i.npp [sel,,]
new.datum$szpft$i.plant.resp [idx,,] = old.datum$szpft$i.plant.resp [sel,,]
new.datum$szpft$i.mco [idx,,] = old.datum$szpft$i.mco [sel,,]
new.datum$szpft$i.cba [idx,,] = old.datum$szpft$i.cba [sel,,]
new.datum$szpft$i.cbamax [idx,,] = old.datum$szpft$i.cbamax [sel,,]
new.datum$szpft$i.cbalight [idx,,] = old.datum$szpft$i.cbalight [sel,,]
new.datum$szpft$i.cbamoist [idx,,] = old.datum$szpft$i.cbamoist [sel,,]
new.datum$szpft$i.transp [idx,,] = old.datum$szpft$i.transp [sel,,]
new.datum$szpft$i.wflxlc [idx,,] = old.datum$szpft$i.wflxlc [sel,,]
new.datum$szpft$i.hflxlc [idx,,] = old.datum$szpft$i.hflxlc [sel,,]
new.datum$szpft$f.gpp [idx,,] = old.datum$szpft$f.gpp [sel,,]
new.datum$szpft$f.plant.resp [idx,,] = old.datum$szpft$f.plant.resp [sel,,]
new.datum$szpft$f.npp [idx,,] = old.datum$szpft$f.npp [sel,,]
new.datum$szpft$f.mco [idx,,] = old.datum$szpft$f.mco [sel,,]
new.datum$szpft$f.cba [idx,,] = old.datum$szpft$f.cba [sel,,]
new.datum$szpft$f.bstorage [idx,,] = old.datum$szpft$f.bstorage [sel,,]
new.datum$szpft$f.bleaf [idx,,] = old.datum$szpft$f.bleaf [sel,,]
new.datum$szpft$f.bstem [idx,,] = old.datum$szpft$f.bstem [sel,,]
new.datum$szpft$f.broot [idx,,] = old.datum$szpft$f.broot [sel,,]
new.datum$szpft$f.bseeds [idx,,] = old.datum$szpft$f.bseeds [sel,,]
new.datum$szpft$f.dcbadt [idx,,] = old.datum$szpft$f.dcbadt [sel,,]
new.datum$szpft$leaf.par [idx,,] = old.datum$szpft$leaf.par [sel,,]
new.datum$szpft$leaf.par.beam [idx,,] = old.datum$szpft$leaf.par.beam [sel,,]
new.datum$szpft$leaf.par.diff [idx,,] = old.datum$szpft$leaf.par.diff [sel,,]
new.datum$szpft$leaf.gpp [idx,,] = old.datum$szpft$leaf.gpp [sel,,]
new.datum$szpft$phap.lpar [idx,,] = old.datum$szpft$phap.lpar [sel,,]
new.datum$szpft$leaf.rshort [idx,,] = old.datum$szpft$leaf.rshort [sel,,]
new.datum$szpft$leaf.rlong [idx,,] = old.datum$szpft$leaf.rlong [sel,,]
new.datum$szpft$transp [idx,,] = old.datum$szpft$transp [sel,,]
new.datum$szpft$wue [idx,,] = old.datum$szpft$wue [sel,,]
new.datum$szpft$cue [idx,,] = old.datum$szpft$cue [sel,,]
new.datum$szpft$ecue [idx,,] = old.datum$szpft$ecue [sel,,]
new.datum$szpft$etue [idx,,] = old.datum$szpft$etue [sel,,]
new.datum$szpft$rue [idx,,] = old.datum$szpft$rue [sel,,]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# LU -- Polygon-level variables, split by land use type. One extra dimension is #
# appended to the end, which will hold the sum of all land use types. #
#---------------------------------------------------------------------------------------#
new.datum$lu$agb [idx, ] = old.datum$lu$agb [sel, ]
new.datum$lu$biomass [idx, ] = old.datum$lu$biomass [sel, ]
new.datum$lu$lai [idx, ] = old.datum$lu$lai [sel, ]
new.datum$lu$gpp [idx, ] = old.datum$lu$gpp [sel, ]
new.datum$lu$npp [idx, ] = old.datum$lu$npp [sel, ]
new.datum$lu$area [idx, ] = old.datum$lu$area [sel, ]
new.datum$lu$ba [idx, ] = old.datum$lu$ba [sel, ]
new.datum$lu$dist [idx,,] = old.datum$lu$dist [sel,,]
new.datum$lu$f.agb [idx, ] = old.datum$lu$f.agb [sel, ]
new.datum$lu$f.biomass [idx, ] = old.datum$lu$f.biomass [sel, ]
new.datum$lu$f.lai [idx, ] = old.datum$lu$f.lai [sel, ]
new.datum$lu$f.gpp [idx, ] = old.datum$lu$f.gpp [sel, ]
new.datum$lu$f.npp [idx, ] = old.datum$lu$f.npp [sel, ]
new.datum$lu$f.ba [idx, ] = old.datum$lu$f.ba [sel, ]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMEAN -- Polygon-level variables, containing the mean diel (diurnal cycle). #
#---------------------------------------------------------------------------------------#
new.datum$qmean$gpp [idx,] = old.datum$qmean$gpp [sel,]
new.datum$qmean$npp [idx,] = old.datum$qmean$npp [sel,]
new.datum$qmean$plant.resp [idx,] = old.datum$qmean$plant.resp [sel,]
new.datum$qmean$leaf.resp [idx,] = old.datum$qmean$leaf.resp [sel,]
new.datum$qmean$root.resp [idx,] = old.datum$qmean$root.resp [sel,]
new.datum$qmean$froot.resp [idx,] = old.datum$qmean$froot.resp [sel,]
new.datum$qmean$het.resp [idx,] = old.datum$qmean$het.resp [sel,]
new.datum$qmean$cwd.resp [idx,] = old.datum$qmean$cwd.resp [sel,]
new.datum$qmean$soil.resp [idx,] = old.datum$qmean$soil.resp [sel,]
new.datum$qmean$assim.light [idx,] = old.datum$qmean$assim.light [sel,]
new.datum$qmean$assim.rubp [idx,] = old.datum$qmean$assim.rubp [sel,]
new.datum$qmean$assim.co2 [idx,] = old.datum$qmean$assim.co2 [sel,]
new.datum$qmean$assim.ratio [idx,] = old.datum$qmean$assim.ratio [sel,]
new.datum$qmean$nep [idx,] = old.datum$qmean$nep [sel,]
new.datum$qmean$nee [idx,] = old.datum$qmean$nee [sel,]
new.datum$qmean$reco [idx,] = old.datum$qmean$reco [sel,]
new.datum$qmean$cflxca [idx,] = old.datum$qmean$cflxca [sel,]
new.datum$qmean$cflxst [idx,] = old.datum$qmean$cflxst [sel,]
new.datum$qmean$hflxca [idx,] = old.datum$qmean$hflxca [sel,]
new.datum$qmean$hflxlc [idx,] = old.datum$qmean$hflxlc [sel,]
new.datum$qmean$hflxwc [idx,] = old.datum$qmean$hflxwc [sel,]
new.datum$qmean$hflxgc [idx,] = old.datum$qmean$hflxgc [sel,]
new.datum$qmean$qwflxca [idx,] = old.datum$qmean$qwflxca [sel,]
new.datum$qmean$wflxca [idx,] = old.datum$qmean$wflxca [sel,]
new.datum$qmean$wflxlc [idx,] = old.datum$qmean$wflxlc [sel,]
new.datum$qmean$wflxwc [idx,] = old.datum$qmean$wflxwc [sel,]
new.datum$qmean$wflxgc [idx,] = old.datum$qmean$wflxgc [sel,]
new.datum$qmean$runoff [idx,] = old.datum$qmean$runoff [sel,]
new.datum$qmean$intercepted [idx,] = old.datum$qmean$intercepted [sel,]
new.datum$qmean$wshed [idx,] = old.datum$qmean$wshed [sel,]
new.datum$qmean$evap [idx,] = old.datum$qmean$evap [sel,]
new.datum$qmean$transp [idx,] = old.datum$qmean$transp [sel,]
new.datum$qmean$atm.temp [idx,] = old.datum$qmean$atm.temp [sel,]
new.datum$qmean$can.temp [idx,] = old.datum$qmean$can.temp [sel,]
new.datum$qmean$leaf.temp [idx,] = old.datum$qmean$leaf.temp [sel,]
new.datum$qmean$leaf.water [idx,] = old.datum$qmean$leaf.water [sel,]
new.datum$qmean$wood.temp [idx,] = old.datum$qmean$wood.temp [sel,]
new.datum$qmean$gnd.temp [idx,] = old.datum$qmean$gnd.temp [sel,]
new.datum$qmean$atm.shv [idx,] = old.datum$qmean$atm.shv [sel,]
new.datum$qmean$can.shv [idx,] = old.datum$qmean$can.shv [sel,]
new.datum$qmean$gnd.shv [idx,] = old.datum$qmean$gnd.shv [sel,]
new.datum$qmean$atm.vpd [idx,] = old.datum$qmean$atm.vpd [sel,]
new.datum$qmean$can.vpd [idx,] = old.datum$qmean$can.vpd [sel,]
new.datum$qmean$leaf.vpd [idx,] = old.datum$qmean$leaf.vpd [sel,]
new.datum$qmean$atm.co2 [idx,] = old.datum$qmean$atm.co2 [sel,]
new.datum$qmean$can.co2 [idx,] = old.datum$qmean$can.co2 [sel,]
new.datum$qmean$atm.prss [idx,] = old.datum$qmean$atm.prss [sel,]
new.datum$qmean$can.prss [idx,] = old.datum$qmean$can.prss [sel,]
new.datum$qmean$atm.vels [idx,] = old.datum$qmean$atm.vels [sel,]
new.datum$qmean$ustar [idx,] = old.datum$qmean$ustar [sel,]
new.datum$qmean$sm.stress [idx,] = old.datum$qmean$sm.stress [sel,]
new.datum$qmean$rain [idx,] = old.datum$qmean$rain [sel,]
new.datum$qmean$rshort [idx,] = old.datum$qmean$rshort [sel,]
new.datum$qmean$rshort.beam [idx,] = old.datum$qmean$rshort.beam [sel,]
new.datum$qmean$rshort.diff [idx,] = old.datum$qmean$rshort.diff [sel,]
new.datum$qmean$rshort.gnd [idx,] = old.datum$qmean$rshort.gnd [sel,]
new.datum$qmean$rshortup [idx,] = old.datum$qmean$rshortup [sel,]
new.datum$qmean$rlong [idx,] = old.datum$qmean$rlong [sel,]
new.datum$qmean$rlong.gnd [idx,] = old.datum$qmean$rlong.gnd [sel,]
new.datum$qmean$rlongup [idx,] = old.datum$qmean$rlongup [sel,]
new.datum$qmean$par.tot [idx,] = old.datum$qmean$par.tot [sel,]
new.datum$qmean$par.beam [idx,] = old.datum$qmean$par.beam [sel,]
new.datum$qmean$par.diff [idx,] = old.datum$qmean$par.diff [sel,]
new.datum$qmean$par.gnd [idx,] = old.datum$qmean$par.gnd [sel,]
new.datum$qmean$parup [idx,] = old.datum$qmean$parup [sel,]
new.datum$qmean$par.leaf [idx,] = old.datum$qmean$par.leaf [sel,]
new.datum$qmean$par.leaf.beam [idx,] = old.datum$qmean$par.leaf.beam [sel,]
new.datum$qmean$par.leaf.diff [idx,] = old.datum$qmean$par.leaf.diff [sel,]
new.datum$qmean$rnet [idx,] = old.datum$qmean$rnet [sel,]
new.datum$qmean$albedo [idx,] = old.datum$qmean$albedo [sel,]
new.datum$qmean$albedo.par [idx,] = old.datum$qmean$albedo.par [sel,]
new.datum$qmean$albedo.nir [idx,] = old.datum$qmean$albedo.nir [sel,]
new.datum$qmean$rlong.albedo [idx,] = old.datum$qmean$rlong.albedo [sel,]
new.datum$qmean$leaf.gsw [idx,] = old.datum$qmean$leaf.gsw [sel,]
new.datum$qmean$leaf.gbw [idx,] = old.datum$qmean$leaf.gbw [sel,]
new.datum$qmean$wood.gbw [idx,] = old.datum$qmean$wood.gbw [sel,]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QMSQU -- Polygon-level variables, containing the mean sum of squares for the diel #
# (diurnal cycle). #
#---------------------------------------------------------------------------------------#
new.datum$qmsqu$gpp [idx,] = old.datum$qmsqu$gpp [sel,]
new.datum$qmsqu$npp [idx,] = old.datum$qmsqu$npp [sel,]
new.datum$qmsqu$plant.resp [idx,] = old.datum$qmsqu$plant.resp [sel,]
new.datum$qmsqu$leaf.resp [idx,] = old.datum$qmsqu$leaf.resp [sel,]
new.datum$qmsqu$root.resp [idx,] = old.datum$qmsqu$root.resp [sel,]
new.datum$qmsqu$froot.resp [idx,] = old.datum$qmsqu$froot.resp [sel,]
new.datum$qmsqu$het.resp [idx,] = old.datum$qmsqu$het.resp [sel,]
new.datum$qmsqu$cwd.resp [idx,] = old.datum$qmsqu$cwd.resp [sel,]
new.datum$qmsqu$soil.resp [idx,] = old.datum$qmsqu$soil.resp [sel,]
new.datum$qmsqu$nep [idx,] = old.datum$qmsqu$nep [sel,]
new.datum$qmsqu$cflxca [idx,] = old.datum$qmsqu$cflxca [sel,]
new.datum$qmsqu$cflxst [idx,] = old.datum$qmsqu$cflxst [sel,]
new.datum$qmsqu$hflxca [idx,] = old.datum$qmsqu$hflxca [sel,]
new.datum$qmsqu$hflxlc [idx,] = old.datum$qmsqu$hflxlc [sel,]
new.datum$qmsqu$hflxwc [idx,] = old.datum$qmsqu$hflxwc [sel,]
new.datum$qmsqu$hflxgc [idx,] = old.datum$qmsqu$hflxgc [sel,]
new.datum$qmsqu$qwflxca [idx,] = old.datum$qmsqu$qwflxca [sel,]
new.datum$qmsqu$wflxca [idx,] = old.datum$qmsqu$wflxca [sel,]
new.datum$qmsqu$wflxlc [idx,] = old.datum$qmsqu$wflxlc [sel,]
new.datum$qmsqu$wflxwc [idx,] = old.datum$qmsqu$wflxwc [sel,]
new.datum$qmsqu$wflxgc [idx,] = old.datum$qmsqu$wflxgc [sel,]
new.datum$qmsqu$transp [idx,] = old.datum$qmsqu$transp [sel,]
new.datum$qmsqu$ustar [idx,] = old.datum$qmsqu$ustar [sel,]
new.datum$qmsqu$albedo [idx,] = old.datum$qmsqu$albedo [sel,]
new.datum$qmsqu$rshortup [idx,] = old.datum$qmsqu$rshortup [sel,]
new.datum$qmsqu$rlongup [idx,] = old.datum$qmsqu$rlongup [sel,]
new.datum$qmsqu$parup [idx,] = old.datum$qmsqu$parup [sel,]
new.datum$qmsqu$rnet [idx,] = old.datum$qmsqu$rnet [sel,]
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# PATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
new.datum$patch$ipa = old.datum$patch$ipa
new.datum$patch$age = old.datum$patch$age
new.datum$patch$area = old.datum$patch$area
new.datum$patch$lu = old.datum$patch$lu
new.datum$patch$nep = old.datum$patch$nep
new.datum$patch$het.resp = old.datum$patch$het.resp
new.datum$patch$soil.resp = old.datum$patch$soil.resp
new.datum$patch$can.temp = old.datum$patch$can.temp
new.datum$patch$gnd.temp = old.datum$patch$gnd.temp
new.datum$patch$can.shv = old.datum$patch$can.shv
new.datum$patch$gnd.shv = old.datum$patch$gnd.shv
new.datum$patch$can.vpd = old.datum$patch$can.vpd
new.datum$patch$can.co2 = old.datum$patch$can.co2
new.datum$patch$can.prss = old.datum$patch$can.prss
new.datum$patch$cflxca = old.datum$patch$cflxca
new.datum$patch$cflxst = old.datum$patch$cflxst
new.datum$patch$nee = old.datum$patch$nee
new.datum$patch$hflxca = old.datum$patch$hflxca
new.datum$patch$hflxgc = old.datum$patch$hflxgc
new.datum$patch$qwflxca = old.datum$patch$qwflxca
new.datum$patch$wflxca = old.datum$patch$wflxca
new.datum$patch$wflxgc = old.datum$patch$wflxgc
new.datum$patch$ustar = old.datum$patch$ustar
new.datum$patch$albedo = old.datum$patch$albedo
new.datum$patch$rshortup = old.datum$patch$rshortup
new.datum$patch$rlongup = old.datum$patch$rlongup
new.datum$patch$parup = old.datum$patch$parup
new.datum$patch$rshort.gnd = old.datum$patch$rshort.gnd
new.datum$patch$par.gnd = old.datum$patch$par.gnd
new.datum$patch$par.leaf = old.datum$patch$par.leaf
new.datum$patch$par.leaf.beam = old.datum$patch$par.leaf.beam
new.datum$patch$par.leaf.diff = old.datum$patch$par.leaf.diff
new.datum$patch$rnet = old.datum$patch$rnet
new.datum$patch$lai = old.datum$patch$lai
new.datum$patch$wai = old.datum$patch$wai
new.datum$patch$tai = old.datum$patch$tai
new.datum$patch$agb = old.datum$patch$agb
new.datum$patch$ba = old.datum$patch$ba
new.datum$patch$wood.dens = old.datum$patch$wood.dens
new.datum$patch$can.depth = old.datum$patch$can.depth
new.datum$patch$can.area = old.datum$patch$can.area
new.datum$patch$phap.lpar = old.datum$patch$phap.lpar
new.datum$patch$phap.ltemp = old.datum$patch$phap.ltemp
new.datum$patch$phap.lwater = old.datum$patch$phap.lwater
new.datum$patch$phap.lvpd = old.datum$patch$phap.lvpd
new.datum$patch$phap.sms = old.datum$patch$phap.sms
new.datum$patch$phap.lgbw = old.datum$patch$phap.lgbw
new.datum$patch$phap.lgsw = old.datum$patch$phap.lgsw
new.datum$patch$sm.stress = old.datum$patch$sm.stress
new.datum$patch$leaf.temp = old.datum$patch$leaf.temp
new.datum$patch$leaf.water = old.datum$patch$leaf.water
new.datum$patch$leaf.vpd = old.datum$patch$leaf.vpd
new.datum$patch$leaf.gpp = old.datum$patch$leaf.gpp
new.datum$patch$leaf.gsw = old.datum$patch$leaf.gsw
new.datum$patch$leaf.par = old.datum$patch$leaf.par
new.datum$patch$leaf.par.beam = old.datum$patch$leaf.par.beam
new.datum$patch$leaf.par.diff = old.datum$patch$leaf.par.diff
new.datum$patch$assim.light = old.datum$patch$assim.light
new.datum$patch$assim.rubp = old.datum$patch$assim.rubp
new.datum$patch$assim.co2 = old.datum$patch$assim.co2
new.datum$patch$wood.temp = old.datum$patch$wood.temp
new.datum$patch$gpp = old.datum$patch$gpp
new.datum$patch$npp = old.datum$patch$npp
new.datum$patch$cba = old.datum$patch$cba
new.datum$patch$plant.resp = old.datum$patch$plant.resp
new.datum$patch$reco = old.datum$patch$reco
new.datum$patch$hflxlc = old.datum$patch$hflxlc
new.datum$patch$hflxwc = old.datum$patch$hflxwc
new.datum$patch$wflxlc = old.datum$patch$wflxlc
new.datum$patch$wflxwc = old.datum$patch$wflxwc
new.datum$patch$transp = old.datum$patch$transp
new.datum$patch$fast.soil.c = old.datum$patch$fast.soil.c
new.datum$patch$slow.soil.c = old.datum$patch$slow.soil.c
new.datum$patch$struct.soil.c = old.datum$patch$struct.soil.c
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# QPATCH -- patch level variables, we save as lists because the dimensions vary. #
#---------------------------------------------------------------------------------------#
new.datum$qpatch$nep = old.datum$qpatch$nep
new.datum$qpatch$het.resp = old.datum$qpatch$het.resp
new.datum$qpatch$can.temp = old.datum$qpatch$can.temp
new.datum$qpatch$gnd.temp = old.datum$qpatch$gnd.temp
new.datum$qpatch$can.shv = old.datum$qpatch$can.shv
new.datum$qpatch$gnd.shv = old.datum$qpatch$gnd.shv
new.datum$qpatch$can.vpd = old.datum$qpatch$can.vpd
new.datum$qpatch$can.co2 = old.datum$qpatch$can.co2
new.datum$qpatch$can.prss = old.datum$qpatch$can.prss
new.datum$qpatch$cflxca = old.datum$qpatch$cflxca
new.datum$qpatch$cflxst = old.datum$qpatch$cflxst
new.datum$qpatch$nee = old.datum$qpatch$nee
new.datum$qpatch$hflxca = old.datum$qpatch$hflxca
new.datum$qpatch$hflxgc = old.datum$qpatch$hflxgc
new.datum$qpatch$qwflxca = old.datum$qpatch$qwflxca
new.datum$qpatch$wflxca = old.datum$qpatch$wflxca
new.datum$qpatch$wflxgc = old.datum$qpatch$wflxgc
new.datum$qpatch$ustar = old.datum$qpatch$ustar
new.datum$qpatch$albedo = old.datum$qpatch$albedo
new.datum$qpatch$rshortup = old.datum$qpatch$rshortup
new.datum$qpatch$rlongup = old.datum$qpatch$rlongup
new.datum$qpatch$parup = old.datum$qpatch$parup
new.datum$qpatch$rshort.gnd = old.datum$qpatch$rshort.gnd
new.datum$qpatch$par.gnd = old.datum$qpatch$par.gnd
new.datum$qpatch$rnet = old.datum$qpatch$rnet
new.datum$qpatch$sm.stress = old.datum$qpatch$sm.stress
new.datum$qpatch$leaf.temp = old.datum$qpatch$leaf.temp
new.datum$qpatch$leaf.water = old.datum$qpatch$leaf.water
new.datum$qpatch$leaf.vpd = old.datum$qpatch$leaf.vpd
new.datum$qpatch$wood.temp = old.datum$qpatch$wood.temp
new.datum$qpatch$par.leaf = old.datum$qpatch$par.leaf
new.datum$qpatch$par.leaf.beam = old.datum$qpatch$par.leaf.beam
new.datum$qpatch$par.leaf.diff = old.datum$qpatch$par.leaf.diff
new.datum$qpatch$leaf.gpp = old.datum$qpatch$leaf.gpp
new.datum$qpatch$leaf.gsw = old.datum$qpatch$leaf.gsw
new.datum$qpatch$leaf.par = old.datum$qpatch$leaf.par
new.datum$qpatch$leaf.par.beam = old.datum$qpatch$leaf.par.beam
new.datum$qpatch$leaf.par.diff = old.datum$qpatch$leaf.par.diff
new.datum$qpatch$assim.light = old.datum$qpatch$assim.light
new.datum$qpatch$assim.rubp = old.datum$qpatch$assim.rubp
new.datum$qpatch$assim.co2 = old.datum$qpatch$assim.co2
new.datum$qpatch$gpp = old.datum$qpatch$gpp
new.datum$qpatch$npp = old.datum$qpatch$npp
new.datum$qpatch$plant.resp = old.datum$qpatch$plant.resp
new.datum$qpatch$hflxlc = old.datum$qpatch$hflxlc
new.datum$qpatch$hflxwc = old.datum$qpatch$hflxwc
new.datum$qpatch$wflxlc = old.datum$qpatch$wflxlc
new.datum$qpatch$wflxwc = old.datum$qpatch$wflxwc
new.datum$qpatch$transp = old.datum$qpatch$transp
new.datum$qpatch$soil.resp = old.datum$qpatch$soil.resp
#---------------------------------------------------------------------------------------#
#----- Cohort level, we save as lists because the dimensions vary. ---------------------#
new.datum$cohort$ipa = old.datum$cohort$ipa
new.datum$cohort$ico = old.datum$cohort$ico
new.datum$cohort$area = old.datum$cohort$area
new.datum$cohort$lu = old.datum$cohort$lu
new.datum$cohort$dbh = old.datum$cohort$dbh
new.datum$cohort$age = old.datum$cohort$age
new.datum$cohort$pft = old.datum$cohort$pft
new.datum$cohort$nplant = old.datum$cohort$nplant
new.datum$cohort$height = old.datum$cohort$height
new.datum$cohort$ba = old.datum$cohort$ba
new.datum$cohort$agb = old.datum$cohort$agb
new.datum$cohort$biomass = old.datum$cohort$biomass
new.datum$cohort$lai = old.datum$cohort$lai
new.datum$cohort$wai = old.datum$cohort$wai
new.datum$cohort$tai = old.datum$cohort$tai
new.datum$cohort$gpp = old.datum$cohort$gpp
new.datum$cohort$leaf.resp = old.datum$cohort$leaf.resp
new.datum$cohort$root.resp = old.datum$cohort$root.resp
new.datum$cohort$froot.resp = old.datum$cohort$froot.resp
new.datum$cohort$croot.resp = old.datum$cohort$croot.resp
new.datum$cohort$stem.resp = old.datum$cohort$stem.resp
new.datum$cohort$storage.resp = old.datum$cohort$storage.resp
new.datum$cohort$plant.resp = old.datum$cohort$plant.resp
new.datum$cohort$assim.light = old.datum$cohort$assim.light
new.datum$cohort$assim.rubp = old.datum$cohort$assim.rubp
new.datum$cohort$assim.co2 = old.datum$cohort$assim.co2
new.datum$cohort$assim.ratio = old.datum$cohort$assim.ratio
new.datum$cohort$npp = old.datum$cohort$npp
new.datum$cohort$cba = old.datum$cohort$cba
new.datum$cohort$cbamax = old.datum$cohort$cbamax
new.datum$cohort$cbalight = old.datum$cohort$cbalight
new.datum$cohort$cbamoist = old.datum$cohort$cbamoist
new.datum$cohort$cbarel = old.datum$cohort$cbarel
new.datum$cohort$dcbadt = old.datum$cohort$dcbadt
new.datum$cohort$mcost = old.datum$cohort$mcost
new.datum$cohort$ldrop = old.datum$cohort$ldrop
new.datum$cohort$sm.stress = old.datum$cohort$sm.stress
new.datum$cohort$phap.sms = old.datum$cohort$phap.sms
new.datum$cohort$light = old.datum$cohort$light
new.datum$cohort$lightbeam = old.datum$cohort$lightbeam
new.datum$cohort$lightdiff = old.datum$cohort$lightdiff
new.datum$cohort$balive = old.datum$cohort$balive
new.datum$cohort$bdead = old.datum$cohort$bdead
new.datum$cohort$bleaf = old.datum$cohort$bleaf
new.datum$cohort$bstem = old.datum$cohort$bstem
new.datum$cohort$broot = old.datum$cohort$broot
new.datum$cohort$bfroot = old.datum$cohort$bfroot
new.datum$cohort$bcroot = old.datum$cohort$bcroot
new.datum$cohort$bsapwood = old.datum$cohort$bsapwood
new.datum$cohort$bstorage = old.datum$cohort$bstorage
new.datum$cohort$bseeds = old.datum$cohort$bseeds
new.datum$cohort$hflxlc = old.datum$cohort$hflxlc
new.datum$cohort$wflxlc = old.datum$cohort$wflxlc
new.datum$cohort$transp = old.datum$cohort$transp
new.datum$cohort$wue = old.datum$cohort$wue
new.datum$cohort$cue = old.datum$cohort$cue
new.datum$cohort$ecue = old.datum$cohort$ecue
new.datum$cohort$etue = old.datum$cohort$etue
new.datum$cohort$demand = old.datum$cohort$demand
new.datum$cohort$supply = old.datum$cohort$supply
new.datum$cohort$mort = old.datum$cohort$mort
new.datum$cohort$dimort = old.datum$cohort$dimort
new.datum$cohort$ncbmort = old.datum$cohort$ncbmort
new.datum$cohort$recruit = old.datum$cohort$recruit
new.datum$cohort$growth = old.datum$cohort$growth
new.datum$cohort$agb.growth = old.datum$cohort$agb.growth
new.datum$cohort$bsa.growth = old.datum$cohort$bsa.growth
new.datum$cohort$f.gpp = old.datum$cohort$f.gpp
new.datum$cohort$f.plant.resp = old.datum$cohort$f.plant.resp
new.datum$cohort$f.npp = old.datum$cohort$f.npp
new.datum$cohort$f.mco = old.datum$cohort$f.mco
new.datum$cohort$f.cba = old.datum$cohort$f.cba
new.datum$cohort$f.bstorage = old.datum$cohort$f.bstorage
new.datum$cohort$f.bleaf = old.datum$cohort$f.bleaf
new.datum$cohort$f.bstem = old.datum$cohort$f.bstem
new.datum$cohort$f.broot = old.datum$cohort$f.broot
new.datum$cohort$f.bseeds = old.datum$cohort$f.bseeds
new.datum$cohort$f.dcbadt = old.datum$cohort$f.dcbadt
new.datum$cohort$leaf.par = old.datum$cohort$leaf.par
new.datum$cohort$leaf.par.beam = old.datum$cohort$leaf.par.beam
new.datum$cohort$leaf.par.diff = old.datum$cohort$leaf.par.diff
new.datum$cohort$leaf.gpp = old.datum$cohort$leaf.gpp
new.datum$cohort$phap.lpar = old.datum$cohort$phap.lpar
new.datum$cohort$leaf.rshort = old.datum$cohort$leaf.rshort
new.datum$cohort$leaf.rlong = old.datum$cohort$leaf.rlong
new.datum$cohort$rue = old.datum$cohort$rue
#---------------------------------------------------------------------------------------#
#---------------------------------------------------------------------------------------#
# Send the data back. #
#---------------------------------------------------------------------------------------#
return(new.datum)
#---------------------------------------------------------------------------------------#
}#end update
#==========================================================================================#
#==========================================================================================#
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