no carbon storage across years for annual grasses in BioCro

CHANGELOG.md

@@ -9,6 +9,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ### Fixed
 
+- Use initial biomass pools for Sorghum and Setaria #2495, #2496
 - PEcAn.DB::betyConnect() is now smarter, and will try to use either config.php or environment variables to create a connection. It has switched to use db.open helper function (#2632).
 - PEcAn.utils::tranformstats() assumed the statistic names column of its input was a factor. It now accepts character too, and returns the same class given as input (#2545).
 - fixed and added tests for `get.rh` function in PEcAn.data.atmosphere 

models/biocro/R/call_biocro.R

@@ -10,7 +10,7 @@ call_biocro_0.9 <- function(WetDat, genus, year_in_run,
   # Check that all variables are present in the expected order --
   # BioGro < 1.0 accesses weather vars by position and DOES NOT check headers.
   expected_cols <- c("year", "doy", "hour", "[Ss]olar", "Temp", "RH", "WS|windspeed", "precip")
-  if(!all(mapply(grepl, expected_cols, colnames(WetDat)))){
+  if (!all(mapply(grepl, expected_cols, colnames(WetDat)))) {
     PEcAn.logger::logger.severe("Format error in weather file: Columns must be (", expected_cols, "), in that order.")
   }
   day1 <- min(WetDat$doy) # data already subset upstream, but BioCro 0.9 assumes a full year if day1/dayn are unset
@@ -26,52 +26,60 @@ call_biocro_0.9 <- function(WetDat, genus, year_in_run,
   # If not, rescale day1 and dayn to be relative to the start of the input.
   #   Scaling is derived by inverting Biocro's day->index equations.
   biocro_checks_doy <- tryCatch(
-    {m <- BioCro::BioGro(
-      WetDat = matrix(c(0,10,0,0,0,0,0,0), nrow = 1),
-      day1 = 10, dayn = 10, timestep = 24);
-    inherits(m, "BioGro") },
-    error = function(e){FALSE})
-  if (!biocro_checks_doy && min(WetDat[,"doy"])>1) {
-    if (!is.null(day1)){
+    {
+      m <- BioCro::BioGro(
+        WetDat = matrix(c(0, 10, 0, 0, 0, 0, 0, 0), nrow = 1),
+        day1 = 10, dayn = 10, timestep = 24
+      )
+      inherits(m, "BioGro")
+    },
+    error = function(e) {
+      FALSE
+    }
+  )
+  if (!biocro_checks_doy && min(WetDat[, "doy"]) > 1) {
+    if (!is.null(day1)) {
       # Biocro calculates line number as `indes1 <- (day1 - 1) * 24`
-      indes1 <- Position(function(x)x==day1, WetDat[,"doy"])
-      day1 <- indes1/24 + 1
+      indes1 <- Position(function(x) x == day1, WetDat[, "doy"])
+      day1 <- indes1 / 24 + 1
     }
-    if (!is.null(dayn)){
+    if (!is.null(dayn)) {
       # Biocro calculates line number as `indesn <- (dayn) * 24`
-      indesn <- Position(function(x)x==dayn, WetDat[,"doy"], right = TRUE)
-      dayn <- indesn/24
+      indesn <- Position(function(x) x == dayn, WetDat[, "doy"], right = TRUE)
+      dayn <- indesn / 24
     }
   }
 
-  coppice.interval = config$pft$coppice.interval
-  if(is.null(coppice.interval)) {
-     coppice.interval = 1 # i.e. harvest every year
+  coppice.interval <- config$pft$coppice.interval
+  if (is.null(coppice.interval)) {
+    coppice.interval <- 1 # i.e. harvest every year
   }
 
   if (genus == "Saccharum") {
+    # probably should be handled like coppice shrubs or perennial grasses
     tmp.result <- BioCro::caneGro(
       WetDat = WetDat,
       lat = lat,
-      soilControl = l2n(config$pft$soilControl))
-    # Addin Rhizome an Grain to avoid error in subsequent script processing results
+      soilControl = l2n(config$pft$soilControl)
+    )
+    # Addin Rhizome and Grain to avoid error in subsequent script processing results
     tmp.result$Rhizome <- 0
     tmp.result$Grain <- 0
-  } else if (genus %in% c("Salix", "Populus")) {
+  } else if (genus %in% c("Salix", "Populus")) { # coppice trees / shrubs
     if (year_in_run == 1) {
       iplant <- config$pft$iPlantControl
     } else {
       iplant$iRhizome <- data.table::last(tmp.result$Rhizome)
       iplant$iRoot <- data.table::last(tmp.result$Root)
       iplant$iStem <- data.table::last(tmp.result$Stem)
 
-      if ((year_in_run - 1)%%coppice.interval == 0) {
+      if ((year_in_run - 1) %% coppice.interval == 0) {
         # coppice when remainder = 0
         HarvestedYield <- round(data.table::last(tmp.result$Stem) * 0.95, 2)
-      } else if ((year_in_run - 1)%%coppice.interval == 1) {
+      } else if ((year_in_run - 1) %% coppice.interval == 1) {
         # year after coppice
         iplant$iStem <- iplant$iStem * 0.05
-      }  # else { # do nothing if neither coppice year nor year following
+      } # else { # do nothing if neither coppice year nor year following
     }
     ## run willowGro
     tmp.result <- BioCro::willowGro(
@@ -85,9 +93,9 @@ call_biocro_0.9 <- function(WetDat, genus, year_in_run,
       canopyControl = l2n(config$pft$canopyControl),
       willowphenoControl = l2n(config$pft$phenoParms),
       seneControl = l2n(config$pft$seneControl),
-      photoControl = l2n(config$pft$photoParms))
-
-  } else if (genus %in% c("Miscanthus", "Panicum")) {
+      photoControl = l2n(config$pft$photoParms)
+    )
+  } else if (genus %in% c("Miscanthus", "Panicum")) { # perennial grasses
     if (year_in_run == 1) {
       iRhizome <- config$pft$iPlantControl$iRhizome
     } else {
@@ -104,35 +112,33 @@ call_biocro_0.9 <- function(WetDat, genus, year_in_run,
       phenoControl = l2n(config$pft$phenoParms),
       seneControl = l2n(config$pft$seneControl),
       iRhizome = as.numeric(iRhizome),
-      photoControl = config$pft$photoParms)
-
-  } else if (genus %in% c("Sorghum", "Setaria")) {
-    if (year_in_run == 1) {
-      iplant <- config$pft$iPlantControl
-    } else {
-      iplant$iRhizome <- data.table::last(tmp.result$Rhizome)
-      iplant$iRoot <- data.table::last(tmp.result$Root)
-      iplant$iStem <- data.table::last(tmp.result$Stem)
-    }
+      photoControl = config$pft$photoParms
+    )
+  } else if (genus %in% c("Sorghum", "Setaria")) { # annual grasses
+    # Perennial Sorghum exists but is not a major crop
+    # assume these are replanted from seed each year
+    # https://landinstitute.org/our-work/perennial-crops/perennial-sorghum/
+    iplant <- config$pft$iPlantControl
     ## run BioGro
     tmp.result <- BioCro::BioGro(
       WetDat = WetDat,
       iRhizome = as.numeric(iplant$iRhizome),
       iRoot = as.numeric(iplant$iRoot),
       iStem = as.numeric(iplant$iStem),
-      iLeaf = as.numeric(iplant$iLeaf), 
+      iLeaf = as.numeric(iplant$iLeaf),
       day1 = day1,
       dayn = dayn,
       soilControl = l2n(config$pft$soilControl),
       canopyControl = l2n(config$pft$canopyControl),
       phenoControl = l2n(config$pft$phenoParms),
       seneControl = l2n(config$pft$seneControl),
-      photoControl = l2n(config$pft$photoParms))
-
+      photoControl = l2n(config$pft$photoParms)
+    )
   } else {
     PEcAn.logger::logger.severe(
       "Genus '", genus, "' is not supported by PEcAn.BIOCRO when using BioCro 0.9x.",
-      "Supported genera: Saccharum, Salix, Populus, Sorghum, Miscanthus, Panicum, Setaria")
+      "Supported genera: Saccharum, Salix, Populus, Sorghum, Miscanthus, Panicum, Setaria"
+    )
   }
   names(tmp.result) <- sub("DayofYear", "doy", names(tmp.result))
   names(tmp.result) <- sub("Hour", "hour", names(tmp.result))
@@ -148,7 +154,6 @@ call_biocro_0.9 <- function(WetDat, genus, year_in_run,
 call_biocro_1 <- function(WetDat, genus, year_in_run,
                           config, lat, lon,
                           tmp.result, HarvestedYield) {
-
   if (year_in_run == 1) {
     initial_values <- config$pft$initial_values
   } else {
@@ -162,13 +167,15 @@ call_biocro_1 <- function(WetDat, genus, year_in_run,
     initial_values = initial_values,
     parameters = config$pft$parameters,
     varying_parameters = WetDat,
-    modules = config$pft$modules)
+    modules = config$pft$modules
+  )
 
   tmp.result <- dplyr::rename(tmp.result,
     ThermalT = "TTc",
     LAI = "lai",
     SoilEvaporation = "soil_evaporation",
-    CanopyTrans = "canopy_transpiration")
+    CanopyTrans = "canopy_transpiration"
+  )
   tmp.result$AboveLitter <- tmp.result$LeafLitter + tmp.result$StemLitter
   tmp.result$BelowLitter <- tmp.result$RootLitter + tmp.result$RhizomeLitter