data-raw/DETha.R

In bgctw/etpart: Partitioning evapotranspiration into transpiration and evaporation

library(REddyProc)
library(dplyr)
library(bigleaf)
library(ncdfTools) # https://github.com/bgctw/ncdfTools



# repeat 1 month of 1998 to span more years
df <- bind_rows(
  Example_DETha98,
  Example_DETha98 %>% head(48*31) %>% mutate(Year = 1999)
) %>%
  fConvertTimeToPosix('YDH',Year = 'Year',Day = 'DoY', Hour = 'Hour') %>%
  filterLongRuns("NEE")

# load precip from MDIData
ncfile = file.path("/Net/Groups/BGI"
                   ,"data/DataStructureMDI/DATA"
                   , "site/Fluxnet/halfhourly/level5/Data/single_sites"
                   , "DE-Tha.1996.2006.hourly.nc"
)
infoNcdfVars(ncfile, order.var = 'id')$name # precip_f
#readNcdfVarName(ncfile)
dfprecip <- readNcdfDataframe(ncfile, "precip") %>%
  filter(between(time, min(df$DateTime), max(df$DateTime)+1))

df <- df %>%
  mutate(
    ET = LE.to.ET(LE, Tair) * 60*30 # from bigleaf convert from mm/s to mm/half-hour
    , precip = dfprecip$precip
  )

# partition GPP
EProc <- sEddyProc$new('DE-Tha', df,
                       c('NEE','Rg','Tair','VPD', 'Ustar','ET'))
EProc$sMDSGapFillAfterUstar('NEE', uStarTh = 0.45, uStarSuffix = "")
EProc$sSetLocationInfo(LatDeg = 51.0, LongDeg = 13.6, TimeZoneHour = 1)
EProc$sMDSGapFill('Tair', FillAll = FALSE,  minNWarnRunLength = NA)
EProc$sMDSGapFill('VPD', FillAll = FALSE,  minNWarnRunLength = NA)
EProc$sMRFluxPartition()
EProc$sMDSGapFill('ET') # gapfill ET to get model, errors, and sd
tmp <- EProc$sExportResults()
df <- df %>% mutate(
  GPP = tmp$GPP_f
  ,GPP_sd = tmp$NEE_fsd # use the uncertainty of NEE for GPP_sd
  ,NEE_fall = tmp$NEE_fall
  ,Rg_pot = tmp$PotRad
  ,ET_fall = tmp$ET_fall
  ,ET_sd = tmp$ET_fsd
  ,Tair_f = tmp$Tair_f # use gap-filled versions
  ,VPD_f = tmp$VPD_f
)

DETha <- df %>% select(
  timestamp = DateTime, precip, ET, NEE, GPP, Tair = Tair_f, rH, VPD = VPD_f,
  Rg, Rg_pot, u = Ustar,
  GPP_sd, NEE_fall, ET_fall, ET_sd)

usethis::use_data(DETha, overwrite = TRUE)