Merge branch 'master' into pkgdown

ashiklom · web-flow · commit 78a733e3da6c · 2019-04-06T19:51:48.000-04:00
diff --git a/NAMESPACE b/NAMESPACE
@@ -54,6 +54,11 @@ export(EMISSIONS_SO2)
 export(FFI_EMISSIONS)
 export(FLUX_INTERIOR)
 export(FLUX_MIXED)
+export(F_LITTERD)
+export(F_LUCD)
+export(F_LUCV)
+export(F_NPPD)
+export(F_NPPV)
 export(GETDATA)
 export(GLOBAL_TEMP)
 export(GLOBAL_TEMPEQ)
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -706,6 +706,36 @@ BETA <- function() {
     .Call('_hector_BETA', PACKAGE = 'hector')
 }
 
+#' @describeIn parameters NPP fraction to vegetation (\code{"(unitless)"})
+#' @export
+F_NPPV <- function() {
+    .Call('_hector_F_NPPV', PACKAGE = 'hector')
+}
+
+#' @describeIn parameters NPP fraction to detritus (\code{"(unitless)"})
+#' @export
+F_NPPD <- function() {
+    .Call('_hector_F_NPPD', PACKAGE = 'hector')
+}
+
+#' @describeIn parameters Litter fraction to detritus (\code{"(unitless)"})
+#' @export
+F_LITTERD <- function() {
+    .Call('_hector_F_LITTERD', PACKAGE = 'hector')
+}
+
+#' @describeIn parameters LUC fraction to vegetation (\code{"(unitless)"})
+#' @export
+F_LUCV <- function() {
+    .Call('_hector_F_LUCV', PACKAGE = 'hector')
+}
+
+#' @describeIn parameters LUC fraction to detritus (\code{"(unitless)"})
+#' @export
+F_LUCD <- function() {
+    .Call('_hector_F_LUCD', PACKAGE = 'hector')
+}
+
 #' @rdname so2
 #' @export
 NATURAL_SO2 <- function() {
diff --git a/man/parameters.Rd b/man/parameters.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -1175,6 +1175,56 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// F_NPPV
+String F_NPPV();
+RcppExport SEXP _hector_F_NPPV() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(F_NPPV());
+    return rcpp_result_gen;
+END_RCPP
+}
+// F_NPPD
+String F_NPPD();
+RcppExport SEXP _hector_F_NPPD() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(F_NPPD());
+    return rcpp_result_gen;
+END_RCPP
+}
+// F_LITTERD
+String F_LITTERD();
+RcppExport SEXP _hector_F_LITTERD() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(F_LITTERD());
+    return rcpp_result_gen;
+END_RCPP
+}
+// F_LUCV
+String F_LUCV();
+RcppExport SEXP _hector_F_LUCV() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(F_LUCV());
+    return rcpp_result_gen;
+END_RCPP
+}
+// F_LUCD
+String F_LUCD();
+RcppExport SEXP _hector_F_LUCD() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(F_LUCD());
+    return rcpp_result_gen;
+END_RCPP
+}
 // NATURAL_SO2
 String NATURAL_SO2();
 RcppExport SEXP _hector_NATURAL_SO2() {
@@ -1511,6 +1561,11 @@ static const R_CallMethodDef CallEntries[] = {
     {"_hector_LUC_EMISSIONS", (DL_FUNC) &_hector_LUC_EMISSIONS, 0},
     {"_hector_Q10_RH", (DL_FUNC) &_hector_Q10_RH, 0},
     {"_hector_BETA", (DL_FUNC) &_hector_BETA, 0},
+    {"_hector_F_NPPV", (DL_FUNC) &_hector_F_NPPV, 0},
+    {"_hector_F_NPPD", (DL_FUNC) &_hector_F_NPPD, 0},
+    {"_hector_F_LITTERD", (DL_FUNC) &_hector_F_LITTERD, 0},
+    {"_hector_F_LUCV", (DL_FUNC) &_hector_F_LUCV, 0},
+    {"_hector_F_LUCD", (DL_FUNC) &_hector_F_LUCD, 0},
     {"_hector_NATURAL_SO2", (DL_FUNC) &_hector_NATURAL_SO2, 0},
     {"_hector_Y2000_SO2", (DL_FUNC) &_hector_Y2000_SO2, 0},
     {"_hector_EMISSIONS_SO2", (DL_FUNC) &_hector_EMISSIONS_SO2, 0},
diff --git a/src/rcpp_constants.cpp b/src/rcpp_constants.cpp
@@ -872,6 +872,40 @@ String BETA() {
 return D_BETA;
 }
 
+//' @describeIn parameters NPP fraction to vegetation (\code{"(unitless)"})
+//' @export
+// [[Rcpp::export]]
+String F_NPPV() {
+return D_F_NPPV;
+}
+
+//' @describeIn parameters NPP fraction to detritus (\code{"(unitless)"})
+//' @export
+// [[Rcpp::export]]
+String F_NPPD() {
+return D_F_NPPD;
+}
+
+//' @describeIn parameters Litter fraction to detritus (\code{"(unitless)"})
+//' @export
+// [[Rcpp::export]]
+String F_LITTERD() {
+return D_F_LITTERD;
+}
+
+//' @describeIn parameters LUC fraction to vegetation (\code{"(unitless)"})
+//' @export
+// [[Rcpp::export]]
+String F_LUCV() {
+return D_F_LUCV;
+}
+
+//' @describeIn parameters LUC fraction to detritus (\code{"(unitless)"})
+//' @export
+// [[Rcpp::export]]
+String F_LUCD() {
+return D_F_LUCD;
+}
 
 /* SLR component */
 // // Apparently not yet implemented
diff --git a/src/simpleNbox.cpp b/src/simpleNbox.cpp
@@ -70,6 +70,11 @@ void SimpleNbox::init( Core* coreptr ) {
     core->registerInput(D_PREINDUSTRIAL_CO2, getComponentName()); 
     core->registerInput(D_BETA, getComponentName());
     core->registerInput(D_Q10_RH, getComponentName());
+    core->registerInput(D_F_NPPV, getComponentName());
+    core->registerInput(D_F_NPPD, getComponentName());
+    core->registerInput(D_F_LITTERD, getComponentName());
+    core->registerInput(D_F_LUCV, getComponentName());
+    core->registerInput(D_F_LUCD, getComponentName());
 }
 
 //------------------------------------------------------------------------------
@@ -159,23 +164,23 @@ void SimpleNbox::setData( const std::string &varName,
         // Partitioning
         else if( varNameParsed == D_F_NPPV ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
-            f_nppv = data.getUnitval(U_UNDEFINED);
+            f_nppv = data.getUnitval(U_UNITLESS);
         }
         else if( varNameParsed == D_F_NPPD ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
-            f_nppd = data.getUnitval(U_UNDEFINED);
+            f_nppd = data.getUnitval(U_UNITLESS);
         }
         else if( varNameParsed == D_F_LITTERD ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
-            f_litterd = data.getUnitval(U_UNDEFINED);
+            f_litterd = data.getUnitval(U_UNITLESS);
         }
         else if( varNameParsed == D_F_LUCV ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
-            f_lucv = data.getUnitval(U_UNDEFINED);
+            f_lucv = data.getUnitval(U_UNITLESS);
         }
         else if( varNameParsed == D_F_LUCD ) {
             H_ASSERT( data.date == Core::undefinedIndex() , "date not allowed" );
-            f_lucd = data.getUnitval(U_UNDEFINED);
+            f_lucd = data.getUnitval(U_UNITLESS);
         }
         
         // Initial fluxes
@@ -436,6 +441,25 @@ unitval SimpleNbox::getData(const std::string& varName,
     } else if( varName == D_RF_T_ALBEDO ) {
         H_ASSERT( date != Core::undefinedIndex(), "Date required for albedo forcing" );
         returnval = Ftalbedo.get( date );
+
+        // Partitioning parameters.
+        // For now, only global values are supported.
+        // TODO Biome-specific versions of all of these
+    } else if(varName == D_F_NPPV) {
+        H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for vegetation NPP fraction");
+        returnval = unitval(f_nppv, U_UNITLESS);
+    } else if(varName == D_F_NPPD) {
+        H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for detritus NPP fraction");
+        returnval = unitval(f_nppd, U_UNITLESS);
+    } else if(varName == D_F_LITTERD) {
+        H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for litter-detritus fraction");
+        returnval = unitval(f_litterd, U_UNITLESS);
+    } else if(varName == D_F_LUCV) {
+        H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for LUC vegetation fraction");
+        returnval = unitval(f_lucv, U_UNITLESS);
+    } else if(varName == D_F_LUCD) {
+        H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for LUC detritus fraction");
+        returnval = unitval(f_lucd, U_UNITLESS);
         
     } else if( varName == D_EARTHC ) {
         if(date == Core::undefinedIndex())
diff --git a/tests/testthat/test_parameters.R b/tests/testthat/test_parameters.R
