parasite code and data update

Analysis/05-02-23-ParasitesLongSpatial/TaskComp.R

@@ -8,9 +8,12 @@ library(scales)
 #Read in the data
 initial_data <- read.table("05-02-23-ParasitesLongSpatial/munged_basic.dat", h=T)
 initial_data$task <- factor(initial_data$task, levels=c("NOT", "NAND", "AND", "ORN", "OR", "ANDN", "NOR", "XOR", "EQU"))
-initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid0", "Well-mixed", x)}))
-initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid1", "Structured", x)}))
-final_update <- subset(initial_data, update == "40000")
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid0", "SA", x)}))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("Grid1", "SP", x)}))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("MOI0.0", "PA", x)}))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("MOI1.0", "PP", x)}))
+initial_data[2] <- data.frame(lapply(initial_data[2], function(x) {gsub("_", " ", x)}))
+final_update <- subset(initial_data, update == "120000")
 
 host_data <- subset(final_update, partner == "Host")
 
@@ -20,7 +23,7 @@ host_data <- subset(final_update, partner == "Host")
 ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_violin() + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free") + geom_boxplot(alpha=0.5, outlier.size=0, width=0.1) 
 
 #regular box plot
-ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_boxplot(alpha=0.5, outlier.size=1) + ylab("Task Count Final Update") + xlab("Parasites Present or Absent") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Parasites", values=viridis(3)) + facet_wrap(~task, scales = "free")
+ggplot(data=host_data, aes(x=treatment, y=count, color=treatment)) + geom_boxplot(alpha=0.5, outlier.size=1) + ylab("Operation Count Final Update") + xlab("Structure and Parasites Absent or Present") + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) + scale_color_manual(name="Treatment", values=viridis(4), labels=c("\nStructure Absent,\nParasites Absent\n", "\nStructure Absent,\nParasites Present\n", "\nStructure Present,\nParasites Absent\n", "\nStructure Present,\nParasites Present\n")) + facet_wrap(~task, scales = "free")+ scale_x_discrete(guide = guide_axis(angle = -20))
 
 
 
@@ -38,7 +41,7 @@ median(subset(host_data, treatment=="Present" & task=="OR")$count)
 wilcox.test(subset(host_data, treatment=="Absent" & task=="ORN")$count, subset(host_data, treatment=="Present" & task=="ORN")$count)
 
 #All tasks over time
-ggplot(data=initial_data, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(3)) + scale_fill_manual(values=viridis(3)) + facet_grid(task ~ partner, scales='free')
+ggplot(data=initial_data, aes(x=update, y=count, group=treatment, colour=treatment)) + ylab("Task count") + xlab("Updates") + stat_summary(aes(color=treatment, fill=treatment),fun.data="mean_cl_boot", geom=c("smooth"), se=TRUE) + theme(panel.background = element_rect(fill='white', colour='black')) + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + guides(fill=FALSE) +scale_colour_manual(values=viridis(4)) + scale_fill_manual(values=viridis(4)) + facet_grid(task ~ partner, scales='free')
 
 # Specific host tasks over time
 host_over_time <- subset(initial_data, partner=="Host")

source/default_mode/Host.h

@@ -439,11 +439,12 @@ class Host: public Organism {
    * Purpose: To add a symbionts to a host's symbionts
    */
   int AddSymbiont(emp::Ptr<Organism> _in) {
-    if((int)syms.size() >= my_config->SYM_LIMIT()){
-      emp::Ptr<Organism> last_sym = syms.back();
-      syms.pop_back();
-      last_sym->SetDead();
-    }
+    // Ousting code:
+    // if((int)syms.size() >= my_config->SYM_LIMIT()){
+    //   emp::Ptr<Organism> last_sym = syms.back();
+    //   syms.pop_back();
+    //   last_sym->SetDead();
+    // }
 
     if((int)syms.size() < my_config->SYM_LIMIT() && SymAllowedIn()){
       syms.push_back(_in);

source/sgp_mode/GenomeLibrary.h

@@ -15,14 +15,15 @@ using Library = sgpl::OpLibrary<
     inst::ShiftLeft, inst::ShiftRight, inst::Increment, inst::Decrement,
     // biological operations
     // no copy or alloc
-    inst::Reproduce, inst::PrivateIO, 
-    //inst::SharedIO,
+    inst::Reproduce, 
+    //inst::PrivateIO, 
+    inst::SharedIO,
     // double argument math
     inst::Add, inst::Subtract, inst::Nand,
     // Stack manipulation
     inst::Push, inst::Pop, inst::SwapStack, inst::Swap,
     // no h-search
-    //inst::Donate, 
+    inst::Donate, 
     inst::JumpIfNEq, inst::JumpIfLess, 
     //inst::Reuptake,
     //fls basics
@@ -72,6 +73,24 @@ class ProgramBuilder : emp::vector<sgpl::Instruction<Spec>> {
     return program;
   }
 
+  sgpl::Program<Spec> BuildNoRepro(size_t length) {
+    Add("Donate");
+    Add("Donate");
+    Add("Donate");
+    Add("Donate");
+    Add("Donate");
+    sgpl::Program<Spec> program;
+    // Set everything to 0 - this makes them no-ops since that's the first
+    // inst in the library
+    program.resize(length - size());
+    program[0].op_code = Library::GetOpCode("Global Anchor");
+    program[0].tag = START_TAG;
+
+    program.insert(program.end(), begin(), end());
+
+    return program;
+  }
+
   void AddNot() {
     // sharedio   r0
     // nand       r0, r0, r0
@@ -289,6 +308,12 @@ sgpl::Program<Spec> CreateSquareProgram(size_t length) {
   return program.Build(length);
 }
 
+sgpl::Program<Spec> CreateMutualistStart(size_t length) {
+  ProgramBuilder program;
+  program.AddNand();
+  return program.BuildNoRepro(length);
+}
+
 /**
  * Picks what type of starting program should be created based on the config and
  * creates it. It will be either random, a program that does NOT, or a program
@@ -298,7 +323,7 @@ sgpl::Program<Spec> CreateStartProgram(emp::Ptr<SymConfigBase> config) {
   if (config->RANDOM_ANCESTOR()) {
     return CreateRandomProgram(PROGRAM_LENGTH);
   } else if (config->TASK_TYPE() == 1) {
-    return CreatePrivateNotProgram(PROGRAM_LENGTH);
+    return CreateNotProgram(PROGRAM_LENGTH);
   } else {
     return CreateSquareProgram(PROGRAM_LENGTH);
   }

source/sgp_mode/Instructions.h

@@ -124,7 +124,6 @@ void AddOrganismPoints(CPUState state, uint32_t output) {
 }
 // Set output to value of register and set register to new input
 INST(SharedIO, {
-  std::cout << "shared io" << std::endl;
   AddOrganismPoints(state, *a);
   uint32_t next;
   if (state.world->GetConfig()->RANDOM_IO_INPUT()) {

source/sgp_mode/SGPWorldSetup.cc

@@ -9,10 +9,10 @@
 void SGPWorld::SetupHosts(unsigned long *POP_SIZE) {
   for (size_t i = 0; i < *POP_SIZE; i++) {
     emp::Ptr<SGPHost> new_org = emp::NewPtr<SGPHost>(
-        &GetRandom(), this, my_config, CreatePrivateNotProgram(100), my_config->HOST_INT());
+        &GetRandom(), this, my_config, CreateNotProgram(100), my_config->HOST_INT());
     if(my_config->START_MOI()==1){
       emp::Ptr<SGPSymbiont> new_sym = emp::NewPtr<SGPSymbiont>(
-          &GetRandom(), this, my_config, my_config->SYM_INT());
+          &GetRandom(), this, my_config, CreateMutualistStart(100), my_config->SYM_INT());
       new_org->AddSymbiont(new_sym);
     }
     InjectHost(new_org);