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@stineb
stineb committed Nov 8, 2019
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317 changes: 166 additions & 151 deletions R/prepare_input_sofun.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,22 @@
#' @param settings_input A list containging the model input settings. See vignette_rsofun.pdf for more information and examples.
#' @param settings_sims A list containing model simulation settings from \code{\link{prepare_setup_sofun}}. See vignette_rsofun.pdf for more information and examples.
#' @param overwrite_climate if \code{TRUE}, yearly climate input text files in the site-scale setup are overwritten.
#' @param overwrite_fapar if \code{TRUE}, yearly fAPAR input text files in the site-scale setup are overwritten.
#' @param overwrite_csv_climate if \code{TRUE}, climate input CSV files in the site-scale setup are overwritten.
#' @param overwrite_csv_climate_lev1 if \code{TRUE}, climate input CSV files created after collecting site-scale meteo data are overwritten.
#' @param overwrite_csv_climate_lev2 if \code{TRUE}, climate input CSV files created after collecting data from global field for all sites are overwritten.
#' @param overwrite_csv_climate_lev3 if \code{TRUE}, climate input CSV files created after deriving SOFUN-standard input (naming, units, and interpolation) are overwritten.
#' @param overwrite_csv_fapar if \code{TRUE}, fAPAR input CSV files in the site-scale setup are overwritten.
#' @param verbose if \code{TRUE}, additional messages are printed.
#'
#' @return A named list of data frames (tibbles) containing input data for each site is returned.
#' @export
#'
#' @examples inputdata <- prepare_input_sofun( settings_input = settings_input, settings_sims = settings_sims, overwrite_climate = FALSE, overwrite_fapar = TRUE, verbose = TRUE )
#' @examples inputdata <- prepare_input_sofun( settings_input = settings_input, settings_sims = settings_sims, overwrite_climate = FALSE, verbose = TRUE )
#'
prepare_input_sofun <- function( settings_input,
settings_sims,
overwrite_csv_climate_lev1=FALSE, overwrite_csv_climate_lev2=FALSE, overwrite_csv_climate_lev3=FALSE,
overwrite_rdata_climate=FALSE,
overwrite_fapar=FALSE, overwrite_csv_climate=FALSE, overwrite_csv_fapar=FALSE, verbose=FALSE ){
overwrite_csv_fapar=FALSE, verbose=FALSE ){

# # If FLUXNET 2015 data is required, make sure it's available locally
# #-----------------------------------------------------------
Expand Down Expand Up @@ -52,7 +54,7 @@ prepare_input_sofun <- function( settings_input,
~get_input_sofun_climate_bysite( .,
settings_input,
dplyr::filter(settings_sims, sitename == .),
overwrite_csv = overwrite_csv_climate,
overwrite_csv = overwrite_csv_climate_lev1,
verbose = verbose
)
)
Expand All @@ -64,8 +66,7 @@ prepare_input_sofun <- function( settings_input,
dplyr::select(ddf_climate, sitename, date),
settings_input,
settings_sims,
overwrite = overwrite_climate,
overwrite_csv = overwrite_csv_climate,
overwrite_csv = overwrite_csv_climate_lev2,
verbose = FALSE
)
ddf_climate <- ddf_climate %>%
Expand All @@ -74,6 +75,22 @@ prepare_input_sofun <- function( settings_input,
by = c("sitename", "date")
)

## Then, prepare climate input data files for sofun
ddf_climate <- purrr::map(
as.list(settings_sims$sitename),
~prepare_input_sofun_climate_bysite(
.,
dplyr::filter(ddf_climate, sitename == .),
settings_input,
settings_sims,
overwrite_csv = overwrite_csv_climate_lev3,
verbose = verbose
)
)
names(ddf_climate) <- settings_sims$sitename
ddf_climate <- ddf_climate %>%
bind_rows()

## write to file
save(ddf_climate, file = filnam_clim)

Expand All @@ -83,22 +100,6 @@ prepare_input_sofun <- function( settings_input,

}

## Then, prepare climate input data files for sofun
ddf_climate <- purrr::map(
as.list(settings_sims$sitename),
~prepare_input_sofun_climate_bysite(
.,
dplyr::filter(ddf_climate, sitename == .),
settings_input,
settings_sims,
overwrite_csv=overwrite_csv_climate,
verbose = verbose
)
)
names(ddf_climate) <- settings_sims$sitename
ddf_climate <- ddf_climate %>%
bind_rows()


##-----------------------------------------------------------
## Get fapar input
Expand Down Expand Up @@ -179,7 +180,7 @@ prepare_input_sofun <- function( settings_input,
##-----------------------------------------------------------
## Read climate data from files given by sites
##-----------------------------------------------------------
get_input_sofun_climate_bysite <- function( sitename, settings_input, settings_sims, overwrite_csv, verbose=FALSE ){
get_input_sofun_climate_bysite <- function( sitename, settings_input, settings_sims, overwrite_csv=FALSE, verbose=FALSE ){

# if (verbose) print(paste("Getting climate data for site", sitename ))

Expand Down Expand Up @@ -303,139 +304,153 @@ get_input_sofun_climate_bysite <- function( sitename, settings_input, settings_s
##-----------------------------------------------------------
## Read climate data from files as global fields
##-----------------------------------------------------------
get_input_sofun_climate_globalfields <- function( ddf, settings_input, settings_sims, overwrite=FALSE, overwrite_csv=FALSE, verbose=FALSE ){
get_input_sofun_climate_globalfields <- function( ddf, settings_input, settings_sims, overwrite_csv=FALSE, verbose=FALSE ){

if (verbose) print("Getting climate data from global fields...")

##----------------------------------------------------------------------
## Read WATCH-WFDEI data (extracting from NetCDF files for this site)
##----------------------------------------------------------------------
## temperature
if ("watch_wfdei" %in% settings_input$temperature){
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "Tair_daily", settings_input, settings_sims ) %>%
dplyr::rename(temp_watch = myvar) %>%
dplyr::mutate(temp_watch = temp_watch - 273.15) %>%
dplyr::right_join(ddf, by = c("sitename", "date"))
}

## precipitation
if ("watch_wfdei" %in% settings_input$precipitation){
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "Rainf_daily", settings_input, settings_sims ) %>%
dplyr::mutate( rain = myvar ) %>%
left_join(
get_input_sofun_climate_globalfields_watch_byvar( "Snowf_daily", settings_input, settings_sims ) %>%
dplyr::mutate( snow = myvar ),
by = c("sitename", "date")
) %>%
dplyr::rename(prec_watch = (rain + snow) * 60 * 60 * 24 ) %>% # kg/m2/s -> mm/day
dplyr::right_join(ddf_prec, by = c("sitename", "date"))
}

## humidity
if ("watch_wfdei" %in% settings_input$vpd){
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "Qair_daily", settings_input, settings_sims ) %>%
dplyr::rename(qair_watch = myvar) %>%
dplyr::right_join(ddf_qair, by = c("sitename", "date"))
}

## PPFD
if ("watch_wfdei" %in% settings_input$ppfd){
kfFEC <- 2.04
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "SWdown_daily", settings_input, settings_sims ) %>%
dplyr::rename(ppfd_watch = myvar * kfFEC * 1.0e-6 * 60 * 60 * 24 ) %>% # umol m-2 s-1 -> mol m-2 d-1
dplyr::right_join(ddf_ppfd, by = c("sitename", "date"))
}


##----------------------------------------------------------------------
## Fill missing variables
##----------------------------------------------------------------------
if (is.na(settings_input$cloudcover)){
rlang::warn("Filling column ccov_dummy with value 50 (%).")
ddf <- ddf %>% mutate( ccov_dummy = 50 )
}

##----------------------------------------------------------------------
## Read CRU monthly data (extracting from NetCDF files for this site)
##----------------------------------------------------------------------
cruvars <- c()
mdf <- ddf %>%
dplyr::select(sitename, date) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(sitename, year, moy) %>%
dplyr::distinct()
## path of CSV file with data for this site
dir <- paste0( settings_input$path_input, "/sitedata/climate/" )
if (!dir.exists(dir)) system( paste0( "mkdir -p ", dir ) )
csvfiln <- paste0( dir, "/clim_daily_lev2.csv" )

## temperature
if ("cru" %in% settings_input$temperature){
cruvars <- c(cruvars, "temp")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "tmp", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(temp_cru = myvar) %>%
if (overwrite_csv || !file.exists(csvfiln)){
##----------------------------------------------------------------------
## Read WATCH-WFDEI data (extracting from NetCDF files for this site)
##----------------------------------------------------------------------
## temperature
if ("watch_wfdei" %in% settings_input$temperature){
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "Tair_daily", settings_input, settings_sims ) %>%
dplyr::rename(temp_watch = myvar) %>%
dplyr::mutate(temp_watch = temp_watch - 273.15) %>%
dplyr::right_join(ddf, by = c("sitename", "date"))
}

## precipitation
if ("watch_wfdei" %in% settings_input$precipitation){
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "Rainf_daily", settings_input, settings_sims ) %>%
dplyr::mutate( rain = myvar ) %>%
left_join(
get_input_sofun_climate_globalfields_watch_byvar( "Snowf_daily", settings_input, settings_sims ) %>%
dplyr::mutate( snow = myvar ),
by = c("sitename", "date")
) %>%
dplyr::rename(prec_watch = (rain + snow) * 60 * 60 * 24 ) %>% # kg/m2/s -> mm/day
dplyr::right_join(ddf_prec, by = c("sitename", "date"))
}

## humidity
if ("watch_wfdei" %in% settings_input$vpd){
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "Qair_daily", settings_input, settings_sims ) %>%
dplyr::rename(qair_watch = myvar) %>%
dplyr::right_join(ddf_qair, by = c("sitename", "date"))
}

## PPFD
if ("watch_wfdei" %in% settings_input$ppfd){
kfFEC <- 2.04
ddf <- get_input_sofun_climate_globalfields_watch_byvar( "SWdown_daily", settings_input, settings_sims ) %>%
dplyr::rename(ppfd_watch = myvar * kfFEC * 1.0e-6 * 60 * 60 * 24 ) %>% # umol m-2 s-1 -> mol m-2 d-1
dplyr::right_join(ddf_ppfd, by = c("sitename", "date"))
}


##----------------------------------------------------------------------
## Fill missing variables
##----------------------------------------------------------------------
if (is.na(settings_input$cloudcover)){
rlang::warn("Filling column ccov_dummy with value 50 (%).")
ddf <- ddf %>% mutate( ccov_dummy = 50 )
}

##----------------------------------------------------------------------
## Read CRU monthly data (extracting from NetCDF files for this site)
##----------------------------------------------------------------------
cruvars <- c()
mdf <- ddf %>%
dplyr::select(sitename, date) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
dplyr::select(sitename, year, moy) %>%
dplyr::distinct()

## temperature
if ("cru" %in% settings_input$temperature){
cruvars <- c(cruvars, "temp")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "tmp", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(temp_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))

}

## precipitation
if ("cru" %in% settings_input$precipitation){
cruvars <- c(cruvars, "prec")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "pre", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(prec_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## vpd from vapour pressure
if ("cru" %in% settings_input$temperature){
cruvars <- c(cruvars, "vap")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "vap", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(vap_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## cloud cover
if ("cru" %in% settings_input$cloudcover){
cruvars <- c(cruvars, "ccov")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "cld", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(ccov_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
# dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## wet days
if ("cru" %in% settings_input$wetdays){
cruvars <- c(cruvars, "wetd")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "wet", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(wetd_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## VPD
## calculated as a function of vapour pressure and temperature, vapour
## pressure is given by CRU data.
if ("vap" %in% cruvars){
## calculate VPD (vap is in hPa)
mdf <- mdf %>%
mutate( vpd_vap_cru_temp_cru = calc_vpd( eact = 1e2 * vap_cru, tc = temp_cru ) )
}
}

## precipitation
if ("cru" %in% settings_input$precipitation){
cruvars <- c(cruvars, "prec")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "pre", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(prec_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## vpd from vapour pressure
if ("cru" %in% settings_input$temperature){
cruvars <- c(cruvars, "vap")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "vap", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(vap_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## cloud cover
if ("cru" %in% settings_input$cloudcover){
cruvars <- c(cruvars, "ccov")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "cld", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(ccov_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
# dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## wet days
if ("cru" %in% settings_input$wetdays){
cruvars <- c(cruvars, "wetd")
mdf <- get_input_sofun_climate_globalfields_cru_byvar( "wet", settings_input, settings_sims ) %>%
dplyr::select(sitename, date, myvar) %>%
dplyr::rename(wetd_cru = myvar) %>%
dplyr::mutate(year = lubridate::year(date), moy = lubridate::month(date)) %>%
dplyr::select(-date) %>%
dplyr::right_join(mdf, by = c("sitename", "year", "moy"))
}

## VPD
## calculated as a function of vapour pressure and temperature, vapour
## pressure is given by CRU data.
if ("vap" %in% cruvars){
## calculate VPD (vap is in hPa)
mdf <- mdf %>%
mutate( vpd_vap_cru_temp_cru = calc_vpd( eact = 1e2 * vap_cru, tc = temp_cru ) )
}

## expand monthly to daily data
if (length(cruvars)>0){
ddf <- expand_clim_cru_monthly( mdf, cruvars ) %>%
right_join( ddf, by = "date" )
}

## expand monthly to daily data
if (length(cruvars)>0){
ddf <- expand_clim_cru_monthly( mdf, cruvars ) %>%
right_join( ddf, by = "date" )
## Write to file
readr::write_csv(ddf, path = csvfiln)

} else {
## Read from file
ddf <- readr::read_csv( csvfiln )

}

return( ddf )

}
Expand Down Expand Up @@ -534,7 +549,7 @@ prepare_input_sofun_climate_bysite <- function( sitename, ddf, settings_input, s
## path of CSV file with data for this site
dir <- paste0( settings_input$path_input, "/sitedata/climate/", sitename )
if (!dir.exists(dir)) system( paste0( "mkdir -p ", dir ) )
csvfiln <- paste0( dir, "/clim_daily_lev2_", sitename, ".csv" )
csvfiln <- paste0( dir, "/clim_daily_lev3_", sitename, ".csv" )

# ## Add site name to dataframe (is merged by rows with ddf of other sites)
# ddf <- ddf %>% dplyr::select( -(starts_with("year_dec")) ) %>% mutate( sitename = sitename )
Expand Down Expand Up @@ -813,7 +828,7 @@ prepare_input_sofun_fapar_bysite_GEE <- function( df_siteinfo, start_date,
##---------------------------------------------
sitename <- df_siteinfo$sitename[1]
df_siteinfo <- slice(df_siteinfo, 1)
print(paste("getting fapar for site", sitename))
#print(paste("getting fapar for site", sitename))

dirnam_daily_csv <- paste0(settings_input$path_input, "sitedata/fapar/", sitename)
dirnam_nice_csv <- settings_input[paste0("path_", stringr::str_replace(productnam ,"_gee", ""))] %>% unlist() %>% unname()
Expand Down
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