Release version 1.1.2

CHANGELOG.md

@@ -12,6 +12,15 @@ The format is based on [Keep a Changelog][] by Olivier Lacan, and this project a
 [Keep a Changelog]: <https://keepachangelog.com/en/1.0.0/>
 [Semantic Versioning]: <https://semver.org/spec/v2.0.0.html>
 
+## [1.1.2] - 2021-07-27
+
+### Added
+- `demo_results.Rmd` now only tries to plot those files that are available [#39]
+
+### Fixed
+- Allow `simulation.one_hft_per_habitat` only for `herbivore_type = "Cohort"`
+- Issue that only one HFT got created and outputted if `simulation.one_hft_per_habitat = true`
+
 ## [1.1.1] - 2021-07-26
 
 ### Fixed
@@ -239,8 +248,9 @@ The format is based on [Keep a Changelog][] by Olivier Lacan, and this project a
 [Illius & O’Connor (2000)]: <https://doi.org/10.2307/3800911>
 [Taylor et al. (1981)]: <https://doi.org/10.1017/S0003356100040617>
 
-[Unreleased]: https://github.com/wtraylor/modular_megafauna_model/compare/1.1.0...develop
-[1.1.1]: https://github.com/wtraylor/modular_megafauna_model/compare/1.1.0...1.1.0
+[Unreleased]: https://github.com/wtraylor/modular_megafauna_model/compare/1.1.2...develop
+[1.1.2]: https://github.com/wtraylor/modular_megafauna_model/compare/1.1.1...1.1.2
+[1.1.1]: https://github.com/wtraylor/modular_megafauna_model/compare/1.1.0...1.1.1
 [1.1.0]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.3...1.1.0
 [1.0.3]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.2...1.0.3
 [1.0.2]: https://github.com/wtraylor/modular_megafauna_model/compare/1.0.1...1.0.2
@@ -280,6 +290,7 @@ The format is based on [Keep a Changelog][] by Olivier Lacan, and this project a
 [#31]: https://github.com/wtraylor/modular_megafauna_model/issues/31
 [#32]: https://github.com/wtraylor/modular_megafauna_model/issues/32
 [#34]: https://github.com/wtraylor/modular_megafauna_model/issues/34
+[#39]: https://github.com/wtraylor/modular_megafauna_model/issues/39
 [#41]: https://github.com/wtraylor/modular_megafauna_model/issues/41
 [#43]: https://github.com/wtraylor/modular_megafauna_model/issues/43
 [#44]: https://github.com/wtraylor/modular_megafauna_model/issues/44

CITATION.cff

@@ -10,9 +10,9 @@ authors:
     affiliation: Senckenberg Biodiversity and Climate Research Centre
     orcid: https://orcid.org/0000-0003-4925-7248
 title: "Modular Megafauna Model"
-version: 1.1.1
+version: 1.1.2
 # This DOI represents all versions, and will always resolve to the latest one.
 doi: 10.5281/zenodo.4710254
-date-released: 2021-07-26
+date-released: 2021-07-27
 license: LGPL-3.0-or-later
 repository-code: https://github.com/wtraylor/modular_megafauna_model

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required (VERSION 3.10)
 project ("Modular Megafauna Model"
   # This version must match exactly the Git tag!
   # Compare the "check_version" job in ".gitlab-ci.yml".
-  VERSION 1.1.1
+  VERSION 1.1.2
   DESCRIPTION "A physiological, dynamic herbivore simulator in C++."
   LANGUAGES CXX
   )

codemeta.json

@@ -5,10 +5,10 @@
     "codeRepository": "git+https://github.com/wtraylor/modular_megafauna_model.git",
     "contIntegration": "https://gitlab.com/wtraylor/modular_megafauna_model/pipelines",
     "datePublished": "2021-04-26",
-    "dateModified": "2021-07-26",
+    "dateModified": "2021-07-27",
     "issueTracker": "https://github.com/wtraylor/modular_megafauna_model/issues/",
     "name": "Modular Megafauna Model (MMM)",
-    "version": "1.1.1",
+    "version": "1.1.2",
     "identifier": "10.5281/zenodo.4710254. ",
     "description": "Extendable, dynamic, process-based herbivore simulator that can be integrated into a dynamic vegetation model. Written as a C++ library.\n",
     "applicationCategory": "Ecological Modeling",

include/Fauna/world.h

@@ -70,14 +70,6 @@ class World {
   World(const std::shared_ptr<const Parameters> params,
         const std::shared_ptr<const HftList> hftlist);
 
-  /// Constructor: Create deactivated `World` object.
-  /**
-   * Even if the megafauna model should be completely deactivated, there might
-   * be a need to create a "dummy" \ref World instance. An object created with
-   * this constructor will not simulate anything.
-   */
-  World();
-
   /// Default destructor.
   ~World();
 
@@ -115,9 +107,6 @@ class World {
    */
   const std::list<SimulationUnit>& get_sim_units() const { return sim_units; }
 
-  /// Whether this \ref World object has been created with parameters and HFTs.
-  const bool is_activated() const { return activated; }
-
   /// Iterate through all simulation units and perform simulation for this day.
   /**
    * This is the central access point to start the perform the herbivore
@@ -166,8 +155,8 @@ class World {
    */
   Output::WriterInterface* construct_output_writer() const;
 
-  /// Whether the whole model is active or not.
-  const bool activated;
+  /// Whether this object is going to simulate or just lint an instruction file.
+  const SimMode mode = SimMode::Simulate;
 
   /// Whether the habitat counts per aggregation unit have been checked.
   /**

src/Fauna/Output/combined_data.cpp

@@ -33,23 +33,25 @@ CombinedData& CombinedData::merge(const CombinedData& other) {
   // HERBIVORE DATA
   // Merge herbivore data for each output group.
 
+  // Groups can be for instance HFTs.
   typedef std::map<const std::string, HerbivoreData> GroupMap;
 
-  // First, create empty HerbivoreData objects for all groups that are not
-  // yet present in this object.
-  for (const auto& itr : hft_data) {
-    // create new object if group not found.
+  // First, create empty HerbivoreData objects for all HFTs/groups from the
+  // *other* object that are not yet present in *this* object.
+  for (const auto& itr : other.hft_data) {
+    // Create new, empty object if the group is new to this object.
     if (!hft_data.count(itr.first)) hft_data[itr.first] = HerbivoreData();
   }
 
-  // Second, merge all herbivore data.
+  // Now we have all groups in this->hft_data, and we can merge for each
+  // group/HFT.
   for (auto& itr : hft_data) {
-    // try to find this group in the other object
-    GroupMap::const_iterator found = other.hft_data.find(itr.first);
-
-    // If the other object doesn’t contain this HFT, we use an empty
-    // object.
-    HerbivoreData other_herbi_data;
+    // If an HFT/group in this->hft_data is not in other.hft_data, we create a
+    // temporary empty HerbivoreData object.
+    const auto& found = other.hft_data.find(itr.first);
+    HerbivoreData other_herbi_data;  // Temporary empty object for now.
+    // If we did find the HFT/group in the other object, we use that for
+    // merging.
     if (found != other.hft_data.end()) other_herbi_data = found->second;
 
     // Let the class HerbivoreData do the actual merge.

src/Fauna/Output/combined_data.test.cpp

@@ -69,6 +69,7 @@ TEST_CASE("Fauna::Output::CombinedData") {
     // merge with equal weight
     c1.datapoint_count = c2.datapoint_count = 3;
 
+    // Merge c2 into c1. The HFTs in c2 are a *subset* of those in c1.
     c1.merge(c2);
 
     CHECK(c1.datapoint_count == 6);
@@ -90,6 +91,33 @@ TEST_CASE("Fauna::Output::CombinedData") {
           Approx(3.0));  // weighted by inddens, but only one data point
   }
 
+  // This is the same as before, but merging the other way round.
+  SECTION("merge() and create new HFT record") {
+    // merge with equal weight
+    c1.datapoint_count = c2.datapoint_count = 3;
+
+    // Merge c1 into c2. Now there is one new HFT coming from c1.
+    c2.merge(c1);
+
+    CHECK(c2.datapoint_count == 6);
+
+    CHECK(c2.habitat_data.available_forage.grass.get_mass() == Approx(1.5));
+    // c1 now has data for both HFTs
+    REQUIRE(c2.hft_data.size() == 2);
+    // in HFT 0, two datapoints are merged
+    CHECK(c2.hft_data[hfts[0].get()->name].inddens ==
+          Approx((1.0 + 2.0) / 2.0));  // normal average
+    CHECK(
+        c2.hft_data[hfts[0].get()->name].expenditure ==
+        Approx((1.0 * 1.0 + 2.0 * 2.0) / (1.0 + 2.0)));  // weighted by inddens
+
+    // in HFT 1, one datapoint is merged with zero values
+    CHECK(c2.hft_data[hfts[1].get()->name].inddens ==
+          Approx((0.0 + 3.0) / 2.0));  // normal average
+    CHECK(c2.hft_data[hfts[1].get()->name].expenditure ==
+          Approx(3.0));  // weighted by inddens, but only one data point
+  }
+
   SECTION("merge() with different data point counts") {
     c1.datapoint_count = 1;
     c2.datapoint_count = 2;

src/Fauna/parameters.cpp

@@ -22,6 +22,13 @@ bool Parameters::is_valid(std::string& messages) const {
   //------------------------------------------------------------
   // add new checks in alphabetical order
 
+  if (one_hft_per_habitat && (herbivore_type != HerbivoreType::Cohort)) {
+    stream << "'simulation.one_hft_per_habitat' is only defined for "
+              "'simulation.herbivore_type = \"cohort\"'."
+           << std::endl;
+    is_valid = false;
+  }
+
   if (herbivore_establish_interval < 0) {
     stream << "herbivore_establish_interval must be >=0" << std::endl;
     is_valid = false;

src/Fauna/world.cpp

@@ -45,23 +45,27 @@ Output::WriterInterface* World::construct_output_writer() const {
 }
 
 World::World(const std::string instruction_filename, const SimMode mode)
-    : activated(true),
+    : mode(mode),
       insfile(read_instruction_file(instruction_filename)),
       days_since_last_establishment(get_params().herbivore_establish_interval),
       output_aggregator(new Output::Aggregator()),
       output_writer(mode == SimMode::Lint ? NULL : construct_output_writer()),
       world_constructor(new WorldConstructor(insfile.params, get_hfts())) {}
 
-World::World() : activated(false) {}
-
 World::World(const std::shared_ptr<const Parameters> params,
              const std::shared_ptr<const HftList> hftlist)
-    : activated(true),
-      insfile({hftlist, params}),
+    : insfile({hftlist, params}),
       days_since_last_establishment(get_params().herbivore_establish_interval),
       output_aggregator(new Output::Aggregator()),
       output_writer(construct_output_writer()),
-      world_constructor(new WorldConstructor(insfile.params, get_hfts())) {}
+      world_constructor(new WorldConstructor(insfile.params, get_hfts())) {
+  if (params.get() == NULL)
+    throw std::invalid_argument(
+        "Fauna::World::World() The argument 'params' is NULL.");
+  if (hftlist.get() == NULL)
+    throw std::invalid_argument(
+        "Fauna::World::World() The argument 'hftlist' is NULL.");
+}
 
 // The destructor must be implemented here in the source file, where the
 // forward-declared types are complete.
@@ -71,14 +75,16 @@ void World::create_simulation_unit(std::shared_ptr<Habitat> habitat) {
   if (habitat == NULL)
     throw std::invalid_argument(
         "World::create_simulation_unit(): Pointer to habitat is NULL.");
-  if (!activated) return;
+  if (mode != SimMode::Simulate) return;
 
   int habitat_ctr = 0;
   // Find the number of habitats already created in this aggregation unit.
-  for (const auto& sim_unit : sim_units)
-    if (sim_unit.get_habitat().get_aggregation_unit() ==
-        habitat->get_aggregation_unit())
-      habitat_ctr++;
+  const std::string this_agg_unit(habitat->get_aggregation_unit());
+  for (const auto& sim_unit : sim_units) {
+    const std::string existing_agg_unit(
+        sim_unit.get_habitat().get_aggregation_unit());
+    if (this_agg_unit == existing_agg_unit) habitat_ctr++;
+  }
   PopulationList* populations =
       world_constructor->create_populations(habitat_ctr);
   assert(populations);
@@ -100,11 +106,6 @@ const HftList& World::get_hfts() const {
 }
 
 const Parameters& World::get_params() const {
-  if (!activated)
-    throw std::logic_error(
-        "Fauna::World::get_params() "
-        "The megafauna model was created without an instruction file. "
-        "Parameters are not available.");
   if (!insfile.params)
     throw std::logic_error(
         "Fauna::World::get_params() "
@@ -164,14 +165,15 @@ World::InsfileContent World::read_instruction_file(
 }
 
 void World::simulate_day(const Date& date, const bool do_herbivores) {
-  if (!activated) return;
+  if (mode != SimMode::Simulate) return;
 
   // Sanity checks for simulation units
   if (!simulation_units_checked) {
     // Count the number of habitats in any case to throw an exception if they
     // differ. Compare the habitat count against HFT count only if necessary.
     const int habitat_count = get_habitat_count_per_agg_unit();
     if (get_params().one_hft_per_habitat &&
+        (get_params().herbivore_type == HerbivoreType::Cohort) &&
         (habitat_count % get_hfts().size() != 0))
       throw std::logic_error(
           "Fauna::World::simulate_day() "
@@ -230,8 +232,6 @@ void World::simulate_day(const Date& date, const bool do_herbivores) {
     if (do_herbivores) days_since_last_establishment++;
 
     // Create function object to delegate all simulations for this day to.
-    // TODO: Create function object only once per day and for all simulation
-    //       units.
     SimulateDay simulate_day(date.get_julian_day(), sim_unit, feed_herbivores);
 
     // Call the function object.