Add "body_fat_by_hft" as new output table

Compare gh-43

examples/megafauna.toml

@@ -28,6 +28,7 @@ directory = "."
 precision = 4
 tables = [
   "available_forage",
+  "body_fat_by_hft",
   "digestibility",
   "eaten_forage_per_ind",
   "eaten_nitrogen_per_ind",

src/Fauna/Output/text_table_writer.cpp

@@ -28,12 +28,19 @@ TextTableWriter::TextTableWriter(const OutputInterval interval,
   create_directories(dir);
 
   // Add all selected output files to list of file streams.
+  // -> Add new output files here in alphabetical order.
   if (options.available_forage) {
     const std::string path = dir + "/available_forage" + FILE_EXTENSION;
     check_file_exists(path);
     file_streams.push_back(&available_forage);
     available_forage.open(path);
   }
+  if (options.body_fat_by_hft) {
+    const std::string path = dir + "/body_fat_by_hft" + FILE_EXTENSION;
+    check_file_exists(path);
+    file_streams.push_back(&body_fat_by_hft);
+    body_fat_by_hft.open(path);
+  }
   if (options.digestibility) {
     const std::string path = dir + "/digestibility" + FILE_EXTENSION;
     check_file_exists(path);
@@ -58,7 +65,6 @@ TextTableWriter::TextTableWriter(const OutputInterval interval,
     file_streams.push_back(&mass_density_per_hft);
     mass_density_per_hft.open(path);
   }
-  // -> Add new output files here.
 
   for (auto& s : file_streams) {
     // Set precision for all output streams.
@@ -184,13 +190,14 @@ void TextTableWriter::write_datapoint(const Datapoint& datapoint) {
       else
         digestibility << FIELD_SEPARATOR << NA_VALUE;
     }
-    // Add more tables here.
+    // -> Add more tables here in alphabetical order.
   }
   if (available_forage.is_open()) available_forage << std::endl;
   if (digestibility.is_open()) digestibility << std::endl;
-  // Add more tables here.
+  // -> Add more tables here in alphabetical order.
 
   // Per-HFT Tables
+  if (body_fat_by_hft.is_open()) start_row(datapoint, body_fat_by_hft);
   if (eaten_nitrogen_per_ind.is_open())
     start_row(datapoint, eaten_nitrogen_per_ind);
   if (mass_density_per_hft.is_open())
@@ -200,15 +207,18 @@ void TextTableWriter::write_datapoint(const Datapoint& datapoint) {
     const HerbivoreData* d = get_hft_data(&datapoint, hft_name);
     assert(d);
     // Add datum for this HFT.
+    if (body_fat_by_hft.is_open())
+      body_fat_by_hft << FIELD_SEPARATOR << d->bodyfat;
     if (eaten_nitrogen_per_ind.is_open())
       eaten_nitrogen_per_ind << FIELD_SEPARATOR << d->eaten_nitrogen_per_ind;
     if (mass_density_per_hft.is_open())
       mass_density_per_hft << FIELD_SEPARATOR << d->massdens;
     // -> Add more per-HFT tables here in alphabetical order.
   }
+  if (body_fat_by_hft.is_open()) body_fat_by_hft << std::endl;
   if (eaten_nitrogen_per_ind.is_open()) eaten_nitrogen_per_ind << std::endl;
   if (mass_density_per_hft.is_open()) mass_density_per_hft << std::endl;
-  // Add more tables here.
+  // -> Add more tables here in alphabetical order.
 
   // Per-HFT/Per-Forage Tables
   // There is one new row for each forage type.
@@ -283,6 +293,9 @@ void TextTableWriter::write_captions(const Datapoint& datapoint) {
           hft_name + "' contains the field delimiter '" + FIELD_SEPARATOR +
           "'");
 
+    // -> Add new output files here in alphabetical order.
+    if (body_fat_by_hft.is_open())
+      body_fat_by_hft << FIELD_SEPARATOR << hft_name;
     if (eaten_forage_per_ind.is_open())
       eaten_forage_per_ind << FIELD_SEPARATOR << hft_name;
     if (eaten_nitrogen_per_ind.is_open())

src/Fauna/Output/text_table_writer.h

@@ -136,6 +136,7 @@ class TextTableWriter : public WriterInterface {
 
   /** @{ \name File Streams */
   std::ofstream available_forage;
+  std::ofstream body_fat_by_hft;
   std::ofstream digestibility;
   std::ofstream eaten_forage_per_ind;
   std::ofstream eaten_nitrogen_per_ind;

src/Fauna/Output/text_table_writer_options.h

@@ -45,7 +45,11 @@ struct TextTableWriterOptions {
 
   /** @} */
 
-  /** @{ \name Per-HFT tables: one column per HFT. */
+  /** @{ \name By-HFT tables: one column per HFT. */
+
+  /// Proportional body fat, i.e. fat mass per total body mass [kg/kg].
+  /** \see \ref Fauna::HerbivoreBase::get_bodyfat() */
+  bool body_fat_by_hft = false;
 
   /// Daily consumption of nitrogen by herbivore individuals [mgDM/day/ind].
   /**

src/Fauna/insfile_reader.cpp

@@ -835,6 +835,8 @@ void InsfileReader::read_table_output_text_tables() {
       for (const auto& s : *value)
         if (lowercase(s) == "available_forage")
           params.output_text_tables.available_forage = true;
+        else if (lowercase(s) == "body_fat_by_hft")
+          params.output_text_tables.body_fat_by_hft = true;
         else if (lowercase(s) == "digestibility")
           params.output_text_tables.digestibility = true;
         else if (lowercase(s) == "eaten_forage_per_ind")
@@ -847,8 +849,9 @@ void InsfileReader::read_table_output_text_tables() {
         else
           throw invalid_option(
               key, s,
-              {"available_forage", "digestibility", "eaten_forage_per_ind",
-               "eaten_nitrogen_per_ind", "mass_density_per_hft"});
+              {"available_forage", "body_fat_by_hft", "digestibility",
+               "eaten_forage_per_ind", "eaten_nitrogen_per_ind",
+               "mass_density_per_hft"});
     }
   }
   // Remove the table "output" in order to indicate that it’s been parsed.