Merge pull request #3071 from DongchenZ/develop

Change from g to kg for SIPNET IC.process
PecanProject · Dec 21, 2022 · ab55731 · ab55731
2 parents 8335ea5 + ab5a366
commit ab55731
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Showing 3 changed files with 9 additions and 7 deletions.
diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R
@@ -502,7 +502,7 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
       IC.nc <- ncdf4::nc_open(IC.path) #for additional variables specific to SIPNET
       ## plantWoodInit gC/m2
       if ("wood" %in% names(IC.pools)) {
-        param[which(param[, 1] == "plantWoodInit"), 2] <- PEcAn.utils::ud_convert(IC.pools$wood, "g m-2", "g m-2")
+        param[which(param[, 1] == "plantWoodInit"), 2] <- PEcAn.utils::ud_convert(IC.pools$wood, "kg m-2", "g m-2")
       }
       ## laiInit m2/m2
       lai <- IC.pools$LAI
@@ -520,7 +520,7 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
       }
       ## soilInit gC/m2
       if ("soil" %in% names(IC.pools)) {
-        param[which(param[, 1] == "soilInit"), 2] <- PEcAn.utils::ud_convert(sum(IC.pools$soil), 'g m-2', 'g m-2') # BETY: kgC m-2
+        param[which(param[, 1] == "soilInit"), 2] <- PEcAn.utils::ud_convert(sum(IC.pools$soil), 'kg m-2', 'g m-2') # BETY: kgC m-2
       }
       ## soilWFracInit fraction
       soilWFrac <- try(ncdf4::ncvar_get(IC.nc,"SoilMoistFrac"),silent = TRUE)

diff --git a/modules/data.land/R/cohort2pool.R b/modules/data.land/R/cohort2pool.R
@@ -70,7 +70,7 @@ cohort2pool <- function(dat, allom_param = NULL, dbh_name="DBH") {
       return(AGB)
     }
   }
-  #calculate total herbaceous biomass, already in gC
+  #calculate total herbaceous biomass, already in kgC
   tot_herb <- sum(dat[[1]][,"dryMass"])/(herb_plot*herb_num)
 
   #Calculate AGB
@@ -83,12 +83,12 @@ cohort2pool <- function(dat, allom_param = NULL, dbh_name="DBH") {
   tot_leaf <- sum(leaf,na.rm = TRUE)
 
   #Divide by plot area, divide by 2 to convert from kg to kgC
-  leaf_biomass = ((tot_leaf/(total_area))/2 + tot_herb/1000)*1000#convert from kg to g
+  leaf_biomass = ((tot_leaf/(total_area))/2 + tot_herb)#in kg
 
   if(tot_biomass == 0){
     AGB <- leaf_biomass
   }else{
-    AGB <- ((tot_biomass/(total_area))/2 + tot_herb/1000)*1000#in gram
+    AGB <- ((tot_biomass/(total_area))/2 + tot_herb)#in kg
   }
   wood_biomass = AGB - leaf_biomass
 

diff --git a/modules/data.land/R/extract_NEON_veg.R b/modules/data.land/R/extract_NEON_veg.R
@@ -90,6 +90,7 @@ extract_NEON_veg <- function(lon, lat, start_date, end_date, store_dir, neonsite
     filter.herb$year <- format(as.Date(filter.herb$collectDate.y, format="%Y-%m-%d"),"%Y")
     #Rename NEON column names to match pecan functions
     colnames(filter.herb) <- c("site_name", "plot", "Subplot", "plotType", "clipArea", "dryMass", "date", "year")
+    filter.herb$dryMass <- PEcAn.utils::ud_convert(filter.herb$dryMass, 'g m-2', 'kg m-2')#convert from g to kg.
     filter.herb <- Grab_First_Measurements_of_Each_Plot(filter.herb)
   }
 
@@ -162,8 +163,9 @@ extract_NEON_veg <- function(lon, lat, start_date, end_date, store_dir, neonsite
         #calculate soil carbon
         joined.soil$bulkDensity <- bulkDensity
 
-        #convert from g/cm2 to g/m2, note that we have to divide by 100 because of percentage
-        joined.soil$SoilCarbon <- (joined.soil$organicCPercent * joined.soil$bulkDensity)*30*100 
+        #here we multiply bulkdensity (in kg/m3) with soil depth (in m) to calculate the soil biomass (in kg/m2) at the top 30 cm depth of soil.
+        #note that we have to divide by 100 because of percentage for the organicCPercent variable.
+        joined.soil$SoilCarbon <- joined.soil$organicCPercent/100 * PEcAn.utils::ud_convert(joined.soil$bulkDensity, "g cm-3", "kg m-3") * PEcAn.utils::ud_convert(30, "cm", "m")
       }
     }
   }