Include RH outputs

R/RcppExports.R

@@ -1,6 +1,9 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#' @rdname carboncycle
+NULL
+
 #' @describeIn msgtype Message type for retrieving data from a component
 #' @keywords internal
 GETDATA <- function() {
@@ -1292,6 +1295,10 @@ RH <- function() {
     .Call('_hector_RH', PACKAGE = 'hector')
 }
 
+RH_DETRITU <- function() {
+    .Call('_hector_RH_DETRITU', PACKAGE = 'hector')
+}
+
 #' @describeIn parameters Preindustrial CO2 concentration (\code{"ppmv CO2"})
 #' @export
 PREINDUSTRIAL_CO2 <- function() {

inst/include/simpleNbox.hpp

@@ -140,6 +140,8 @@ class SimpleNbox : public CarbonCycleModel {
       final_npp; //!< final NPP after any NBP constraint accounted for, Pg C/yr
   fluxpool_stringmap
       final_rh; //!< final RH after any NBP constraint accounted for, Pg C/yr
+  fluxpool_stringmap
+      final_rh_detritus; //!< final RH detritus after any NBP constraint accounted for, Pg C/yr
 
   // Other state variables
   unitval Ca_residual; //!< residual (when constraining [CO2]), Pg C
@@ -175,7 +177,10 @@ class SimpleNbox : public CarbonCycleModel {
       final_npp_tv; //!< Time series of biome-specific final NPP
   tvector<fluxpool_stringmap>
       final_rh_tv; //!< Time series of biome-specific final RH
-
+tvector<fluxpool_stringmap>
+        final_rh_detritus_tv; //!< Time series of biome-specific final detritus RH
+
+
   tseries<unitval> Ca_residual_ts; //!< Time series of residual flux values
 
   tvector<double_stringmap> tempfertd_tv,

src/RcppExports.cpp

@@ -2170,6 +2170,16 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// RH_DETRITU
+String RH_DETRITU();
+RcppExport SEXP _hector_RH_DETRITU() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(RH_DETRITU());
+    return rcpp_result_gen;
+END_RCPP
+}
 // PREINDUSTRIAL_CO2
 String PREINDUSTRIAL_CO2();
 RcppExport SEXP _hector_PREINDUSTRIAL_CO2() {
@@ -2971,6 +2981,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_hector_CONCENTRATIONS_CO2", (DL_FUNC) &_hector_CONCENTRATIONS_CO2, 0},
     {"_hector_NPP", (DL_FUNC) &_hector_NPP, 0},
     {"_hector_RH", (DL_FUNC) &_hector_RH, 0},
+    {"_hector_RH_DETRITU", (DL_FUNC) &_hector_RH_DETRITU, 0},
     {"_hector_PREINDUSTRIAL_CO2", (DL_FUNC) &_hector_PREINDUSTRIAL_CO2, 0},
     {"_hector_ATMOSPHERIC_CO2", (DL_FUNC) &_hector_ATMOSPHERIC_CO2, 0},
     {"_hector_FFI_EMISSIONS", (DL_FUNC) &_hector_FFI_EMISSIONS, 0},

src/csv_outputstream_visitor.cpp

@@ -174,6 +174,7 @@ void CSVOutputStreamVisitor::visit(SimpleNbox *c) {
   STREAM_UNITVAL(csvFile, c, D_NPP, c->final_npp[SNBOX_DEFAULT_BIOME]);
   STREAM_UNITVAL(csvFile, c, D_RH, c->final_rh[SNBOX_DEFAULT_BIOME]);
   STREAM_UNITVAL(csvFile, c, D_RH_CH4, c->final_rh[SNBOX_DEFAULT_BIOME]);
+  STREAM_UNITVAL(csvFile, c, D_RH_DETRITUS, c->final_rh_detritus[SNBOX_DEFAULT_BIOME]);
   STREAM_MESSAGE_DATE(csvFile, c, D_CO2_CONC, current_date);
   STREAM_MESSAGE(csvFile, c, D_ATMOSPHERIC_CO2);
   STREAM_MESSAGE(csvFile, c, D_ATMOSPHERIC_C_RESIDUAL);

src/rcpp_constants.cpp

@@ -1128,6 +1128,11 @@ String NPP() { return D_NPP; }
 // [[Rcpp::export]]
 String RH() { return D_RH; }
 
+//' @rdname carboncycle
+ //' @export
+ // [[Rcpp::export]]
+ String RH_DETRITU() { return D_RH_DETRITUS; }
+
 //' @describeIn parameters Preindustrial CO2 concentration (\code{"ppmv CO2"})
 //' @export
 // [[Rcpp::export]]

src/simpleNbox-runtime.cpp

@@ -478,6 +478,9 @@ void SimpleNbox::stashCValues(double t, const double c[]) {
     // issue, we track it and adjust in the mass balance check below
     cumulative_pf_ch4 += rh_fpa_ch4_flux.value(U_PGC);
 
+      final_rh_detritus[biome] = rh_fda_flux;
+
+
     // Permafrost thaw and refreeze
     if (!in_spinup) {
       // We pass in the annual fluxes here, because want annual thaw and

src/simpleNbox.cpp

@@ -685,6 +685,9 @@ unitval SimpleNbox::getData(const std::string &varName, const double date) {
   } else if (varNameParsed == D_RH) {
     returnval =
         sum_fluxpool_biome_ts(varName, date, biome, final_rh, final_rh_tv);
+  } else if (varNameParsed == D_RH_DETRITUS) {
+      returnval =
+        sum_fluxpool_biome_ts(varName, date, biome, final_rh_detritus, final_rh_detritus_tv);
   } else if (varNameParsed == D_RH_CH4) {
     returnval = sum_fluxpool_biome_ts(varName, date, biome, RH_ch4, RH_ch4_tv);
   } else {
@@ -709,6 +712,7 @@ void SimpleNbox::reset(double time) {
   thawed_permafrost_c = thawed_permafrost_c_tv.get(time);
   final_npp = final_npp_tv.get(time);
   final_rh = final_rh_tv.get(time);
+  final_rh_detritus = final_rh_detritus_tv.get(time);
   RH_thawed_permafrost = RH_thawed_permafrost_tv.get(time);
   RH_ch4 = RH_ch4_tv.get(time);