Merge branch 'K-Johnson-Horrigan-main'

source/Organism.h

@@ -150,7 +150,7 @@ class Organism {
   virtual void SetSymbionts(emp::vector<emp::Ptr<Organism>> _in) {
     std::cout << "SetSymbionts called from Organism" << std::endl;
     throw "Organism method called!";}
-  virtual void AddSymbiont(emp::Ptr<Organism> _in)
+  virtual int AddSymbiont(emp::Ptr<Organism> _in)
    {std::cout << "AddSymbiont called from Organism" << std::endl;
      throw "Organism method called!";}
   virtual void AddReproSym(emp::Ptr<Organism> _in) {

source/default_mode/DataNodes.h

@@ -16,6 +16,7 @@ void SymWorld::CreateDateFiles(){
 
   SetupHostIntValFile(my_config->FILE_PATH()+"HostVals"+my_config->FILE_NAME()+file_ending).SetTimingRepeat(TIMING_REPEAT);
   SetupSymIntValFile(my_config->FILE_PATH()+"SymVals"+my_config->FILE_NAME()+file_ending).SetTimingRepeat(TIMING_REPEAT);
+  SetUpTransmissionFile(my_config->FILE_PATH()+"TransmissionRates"+my_config->FILE_NAME()+file_ending).SetTimingRepeat(TIMING_REPEAT);
 
   if(my_config->FREE_LIVING_SYMS() == 1){
     SetUpFreeLivingSymFile(my_config->FILE_PATH()+"FreeLivingSyms_"+my_config->FILE_NAME()+file_ending).SetTimingRepeat(TIMING_REPEAT);
@@ -193,6 +194,36 @@ void SymWorld::WritePhylogenyFile(const std::string & filename) {
 }
 
 
+/**
+ * Input: The address of the string representing the suffixes for the files to be created.
+ *
+ * Output: None.
+ *
+ * Purpose: To setup and write to the files that track the counts of attempted
+ * tranmissions.
+ */
+
+emp::DataFile & SymWorld::SetUpTransmissionFile(const std::string & filename){
+  auto & file = SetupFile(filename);
+  auto & node1 = GetHorizontalTransmissionAttemptCount();
+  auto & node2 = GetHorizontalTransmissionSuccessCount();
+  auto & node3 = GetVerticalTransmissionAttemptCount();
+
+  file.AddVar(update, "update", "Update");
+
+  //horizontal transmission
+  file.AddTotal(node1, "attempts_horiztrans", "Total number of horizontal transmission attempts", true);
+  file.AddTotal(node2, "successes_horiztrans", "Total number of horizontal transmission successes", true);
+
+  //vertical transmission
+  file.AddTotal(node3, "attempts_verttrans", "Total number of horizontal transmission attempts", true);
+
+  file.PrintHeaderKeys();
+
+  return file;
+}
+
+
 /**
  * Input: None
  *
@@ -521,4 +552,56 @@ emp::DataMonitor<double,emp::data::Histogram>& SymWorld::GetHostedSymInfectChanc
   data_node_hostedsyminfectchance->SetupBins(0, 1.1, 11);
   return *data_node_hostedsyminfectchance;
 }
+
+
+/**
+ * Input: None
+ *
+ * Output: The DataMonitor<int>& that has the information representing
+ * how many attempts were made to horizontally transmit.
+ *
+ * Purpose: To retrieve the data nodes that is tracking the
+ * number of attempted horizontal transmissions.
+ */
+emp::DataMonitor<int>& SymWorld::GetHorizontalTransmissionAttemptCount() {
+  if (!data_node_attempts_horiztrans) {
+    data_node_attempts_horiztrans.New();
+  }
+  return *data_node_attempts_horiztrans;
+}
+
+
+/**
+ * Input: None
+ *
+ * Output: The DataMonitor<int>& that has the information representing
+ * how many successful attempts were made to horizontally transmit.
+ *
+ * Purpose: To retrieve the data nodes that is tracking the
+ * number of successful horizontal transmissions.
+ */
+emp::DataMonitor<int>& SymWorld::GetHorizontalTransmissionSuccessCount() {
+  if (!data_node_successes_horiztrans) {
+    data_node_successes_horiztrans.New();
+  }
+  return *data_node_successes_horiztrans;
+}
+
+
+/**
+ * Input: None
+ *
+ * Output: The DataMonitor<int>& that has the information representing
+ * how many attempts were made to vertically transmit.
+ *
+ * Purpose: To retrieve the data nodes that is tracking the
+ * number of attempted vertical transmissions.
+ */
+emp::DataMonitor<int>& SymWorld::GetVerticalTransmissionAttemptCount() {
+  if (!data_node_attempts_verttrans) {
+    data_node_attempts_verttrans.New();
+  }
+  return *data_node_attempts_verttrans;
+}
+
 #endif

source/default_mode/Host.h

@@ -430,17 +430,20 @@ class Host: public Organism {
   /**
    * Input: The pointer to the organism that is to be added to the host's symbionts.
    *
-   * Output: None
+   * Output: The int describing the symbiont's position ID, or 0 if it did not successfully
+   * get added to the host's list of symbionts.
    *
    * Purpose: To add a symbionts to a host's symbionts
    */
-  void AddSymbiont(emp::Ptr<Organism> _in) {
+  int AddSymbiont(emp::Ptr<Organism> _in) {
     if((int)syms.size() < my_config->SYM_LIMIT() && SymAllowedIn()){
       syms.push_back(_in);
       _in->SetHost(this);
       _in->UponInjection();
+      return syms.size();
     } else {
       _in.Delete();
+      return 0;
     }
   }