Update examples, arguments of var_update() and names of dimensions

PecanProject · Jul 10, 2024 · b419a4c · b419a4c
1 parent f1825d2
commit b419a4c
Showing 1 changed file with 9 additions and 5 deletions.
diff --git a/models/fates/R/model2netcdf.FATES.R b/models/fates/R/model2netcdf.FATES.R
@@ -21,7 +21,7 @@
 ##' @examples  
 ##' \dontrun{
 ##' example.output <- system.file("case.clm2.h0.2004-01-01-00000.nc",package="PEcAn.FATES")
-##' model2netcdf.FATES(outdir="~/")
+##' model2netcdf.FATES(outdir="~/",sitelat, sitelon, start_date, end_date, pfts)
 ##' }
 ##'
 ##' @author Michael Dietze, Shawn Serbin
@@ -41,7 +41,7 @@ model2netcdf.FATES <- function(outdir, sitelat, sitelon, start_date, end_date, p
                       c("Qle","Evap","Evap","kgC m-2 s-1","Total evaporation"),
                       c("QVEGT","Transp","kg m-2 s-1","Canopy transpiration")) 
 
-  var_update <- function(out,oldname,newname,newunits=NULL,long_name=NULL){
+  var_update <- function(out,oldname,newname,nc_month,nc_month_names,newunits=NULL,long_name=NULL){
     if (oldname %in% nc_month_names) {
       ## define units of variables
       oldunits <- ncdf4::ncatt_get(nc_month,oldname,"units")$value
@@ -50,14 +50,18 @@ model2netcdf.FATES <- function(outdir, sitelat, sitelon, start_date, end_date, p
       if (is.null(newunits)) newunits = oldunits
 
       ## check pft dimensions
-      if (any(grepl('pft',easyNCDF::NcReadDims(nc_month, oldname)))){
+      d_name <- c()
+      for (i in (nc_month$var[[oldname]]$dim)){
+          d_name <- append(d_name, i$name)
+      }
+      if (any(grepl('pft',d_name))){
         dimension <- xypt # include fates_levpft
       }else{ 
         dimension <- xyt 
       } # only xyt
 
       ## transpose dimensions into (,t)
-      if (easyNCDF::NcReadDims(nc_month, oldname)[length(easyNCDF::NcReadDims(nc_month, oldname))]=='time'){
+      if (d_name[length(d_name)]=='time'){
             dat_0 <- ncdf4::ncvar_get(nc_month,oldname) # time at the tail of dims
             dat.new <- PEcAn.utils::misc.convert(dat_0,oldunits,newunits) # convert data units
           }
@@ -112,7 +116,7 @@ model2netcdf.FATES <- function(outdir, sitelat, sitelon, start_date, end_date, p
 
         ## write monthly files with start(1,1,i)
         for (name_param in matched_var){
-          out  <- var_update(out,name_param[1],name_param[2],name_param[3],name_param[4]) # convert monthly fates output into one variable
+          out  <- var_update(out,name_param[1],name_param[2],name_param[3],name_param[4],nc_month,nc_month_names) # convert monthly fates output into one variable
         }
         out$var[[length(out$var) + 1]] <- ncdf4::ncvar_def(name="time_bounds", units='', 
                                           longname = "history time interval endpoints", dim=list(time_interval,t), prec = "double")