setting up long runs with and without parasites and spatial structure

Data/05-02-23-ParasitesLongSpatial/SymSettings.cfg

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+### MAIN ###
+# Global Settings
+
+set SEED 10                       # What value should the random seed be? If seed <= 0, then it is randomly re-chosen.
+set DATA_INT 500                  # How frequently, in updates, should data print?
+set SYNERGY 5                     # Amount symbiont's returned resources should be multiplied by
+set VERTICAL_TRANSMISSION 0.0     # Value 0 to 1 of probability of symbiont vertically transmitting when host reproduces
+set HOST_INT -2                   # Interaction value from -1 to 1 that hosts should have initially, -2 for random
+set SYM_INT -2                    # Interaction value from -1 to 1 that symbionts should have initially, -2 for random
+set GRID_X 100                    # Width of the world, just multiplied by the height to get total size
+set GRID_Y 100                    # Height of world, just multiplied by width to get total size
+set POP_SIZE -1                   # Starting size of the host population, -1 for full starting population
+set SYM_LIMIT 1                   # Number of symbiont allowed to infect a single host
+set START_MOI 1                   # Ratio of symbionts to hosts that experiment should start with
+set UPDATES 120001                  # Number of updates to run before quitting
+set RES_DISTRIBUTE 100            # Number of resources to give to each host each update if they are available
+set LIMITED_RES_TOTAL 10          # Starting number of total resources available over the entire run, -1 for unlimited
+set LIMITED_RES_INFLOW 500          # Number of resources to add to the total every update, only used if LIMITED_RES_TOTAL is not -1
+set HORIZ_TRANS 1                 # Should non-lytic horizontal transmission occur? 0 for no, 1 for yes
+set HOST_REPRO_RES 100           # How many resources required for host reproduction
+set SYM_HORIZ_TRANS_RES 10       # How many resources required for symbiont non-lytic horizontal transmission
+set SYM_VERT_TRANS_RES 0          # How many resources required for symbiont vertical transmission
+set GRID 0                        # Do offspring get placed immediately next to parents on grid, same for symbiont spreading
+set SYM_INFECTION_CHANCE 1        # The chance (between 0 and 1) that a sym will infect a parallel host on process
+set SYM_INFECTION_FAILURE_RATE 0  # The chance (between 0 and 1) that a sym will be killed by the world while trying to infect a host
+set HOST_AGE_MAX -1               # The maximum number of updates hosts are allowed to live, -1 for infinite
+set SYM_AGE_MAX -1                # The maximum updates symbionts are allowed to live, -1 for infinite
+set PHYLOGENY 0                   # Should the world keep track of host and symbiont phylogenies? (0 for no, 1 for yes)
+set NUM_PHYLO_BINS 5              # How many bins should organisms be sepeated into if phylogeny is on?
+set NO_MUT_UPDATES 0              # How many updates should be run after the end of UPDATES with all mutation turned off?
+set FILE_PATH                     # Output file path
+set FILE_NAME _data               # Root output file name
+set DOMINANT_COUNT 10             # Number of dominant hosts to select
+
+### MUTATION ###
+# Mutation
+
+set MUTATION_SIZE 0.002        # Standard deviation of the distribution to mutate by
+set HOST_MUTATION_SIZE -1      # Standard deviation of the distribution to mutate by for hosts, if -1 MUTATION_SIZE used
+set MUTATION_RATE 1            # Value 0 to 1 of probability of mutation
+set HOST_MUTATION_RATE -1      # Value 0 to 1 of probability of mutation for hosts, if -1 MUTATION_RATE used
+set MUTATE_LYSIS_CHANCE 0      # Should the chance of lysis mutate? 0 for no, 1 for yes
+set MUTATE_INDUCTION_CHANCE 0  # Should the chance of Induction mutate? 0 for no, 1 for yes
+set MUTATE_INC_VAL 0           # Whether the incorporation vals mutate or not, 0 or 1
+set EFFICIENCY_MUT_RATE -1     # The overall mutation rate of the efficiency trait in symbionts, -1 makes it same as mutation rate as determined by transmission mode
+set INT_VAL_MUT_RATE -1        # The overall mutation rate of the interaction value trait in symbionts, -1 makes it same as mutation rate as determined by tranmission mode
+set HORIZ_MUTATION_SIZE -1     # Standard deviation of the distribution to mutate by for horizontal transmission, if -1 MUTATION_SIZE used
+set HORIZ_MUTATION_RATE -1     # Value 0 to 1 of probability of mutation for horizontal transmission, if -1 MUTATION_RATE used
+
+### ECTOSYMBIOSIS ###
+# Settings for ectosymbiosis and free-living symbionts
+
+set FREE_LIVING_SYMS 0         # Are symbionts able to live outside of the host?
+set MOVE_FREE_SYMS 0           # Should the free living syms move around in the world? 0 for no, 1 for yes
+set ECTOSYMBIOSIS 0            # Do free-living syms and parallel hosts interact? (0 for no, 1 for yes)
+set ECTOSYMBIOTIC_IMMUNITY 0   # Does a hosted sym confer immunity to ectosymbiosis? (0 for no, 1 for yes)
+set FREE_SYM_RES_DISTRIBUTE 0  # Number of resources to give to each free-living symbiont each update if they are available
+set FREE_SYM_REPRO_RES -1      # How many resources required for free living symbiont reproduction. If -1, use the horizontal transmission required point value.
+
+### LYSIS ###
+# Lysis Settings, coming soon to the GUI!
+
+set LYSIS_CHANCE -1        # Chance of lysis vs. lysogeny for starting population of phage, -1 for random distribution
+set CHANCE_OF_INDUCTION 0  # Chance of induction for starting lysogenic phage, -1 for random distribution
+set LYSIS 0                # Should lysis occur? 0 for no, 1 for yes
+set BURST_SIZE 10          # If there is lysis, this is how many symbionts should be produced during lysis. This will be divided by burst_time and that many symbionts will be produced every update
+set BURST_TIME 10          # If lysis enabled, this is how many updates will pass before lysis occurs
+set PROPHAGE_LOSS_RATE 0   # Rate at which infected lysogens become re-susceptible to new phage
+set BENEFIT_TO_HOST 0      # Should lysogenic phage give a benefit to their hosts? 0 for no, 1 for yes
+set PHAGE_INC_VAL 0        # The compatibility of the prophage to its placement within the bacterium's genome, from 0 to 1, -1 for random distribution
+set HOST_INC_VAL 0         # The compatibility of the bacterium for the phage's placement in its genome, from 0 to 1, -1 for random distribution
+set SYM_LYSIS_RES 1        # How many resources required for symbiont to create offspring for lysis each update
+set PHAGE_EXCLUDE 0        # Do phage have a decreased chance of getting into the host if there is already a lytic phage?
+
+### PGG ###
+# Public Goods Game Settings
+
+set PGG_DONATE 0                 # Ratio of symbionts‘ energy to PGG pool that experiment should start with
+set PGG 0                        # whether have social goods game among syms
+set PGG_SYNERGY 1.1              # Amount symbiont's returned resources should be multiplied by when doing PGG
+set PGG_DONATE_RANDOM 0          # Make the ratio of symbionts' energy to PGG pool be random for each organism at the start of the experiment
+set PGG_DONATE_MIN 0             # The minimum value of the symbionts' donation rate, if randomly selected, at initialization
+set PGG_DONATE_MAX 1             # The maximum value of the symbionts' donation rate, if randomly selected, at initialization
+set PGG_DONATE_NORMAL 0          # Make the random initialization of the symbionts' donation rate be initialized using a normal distribution
+set PGG_DONATE_NORMAL_MEAN 0.5   # The mean of the normal distribution of the initialization of the symbionts' donation rate
+set PGG_DONATE_NORMAL_STD 0.167  # The standard deviation of the normal distribution of the initialization of the symbionts' donation rate
+
+### DTH ###
+# Settings for the Dirty Transmission Hypothesis
+
+set EFFICIENT_SYM 0     # Do you want symbionts that also have an efficiency value that evolves
+set COMPETITION_MODE 0  # Should a competition between two types be conducted? (Which is specified in the code)
+
+### SGP ###
+# Complex Genomes Settings
+
+set CYCLES_PER_UPDATE 4            # Number of CPU cycles that organisms run every update
+set THREAD_COUNT 1                # Number of threads used to process organisms in parallel
+set RANDOM_ANCESTOR 0              # Randomize ancestor genomes instead of using the blank genome with just NOT and reproduction
+set TASK_TYPE 1                    # 0 for squaring tasks, 1 for logic tasks
+set DONATION_STEAL_INST 0          # 1 if you want donate and steal instructions in the instruction set, 0 if not
+set RANDOM_IO_INPUT 1              # 1 to give organisms random input when they IO, 0 to give them only ones
+set LIMITED_TASK_RESET_INTERVAL 20  # Number of updates before an org is allowed to complete a non-unlimited task again
+set STEAL_PENALTY 0.1              # Proportion of resources that are lost when stealing from a host
+set DONATE_PENALTY 0.1             # Proportion of resources that are lost when donating to a host
+

Data/05-02-23-ParasitesLongSpatial/simple_repeat.py

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+#a script to run several replicates of several treatments locally
+#You should create a directory for your result files and run this script from within that directory
+# usage: python3 simple_repeat.py <start_seed> <end_seed>
+# Assumes that symbulation executable and SymSettings.cfg already in the folder
+
+import subprocess
+import sys
+
+spatial = [0,1]
+MOI = [0.0,1.0]
+
+def cmd(command):
+    '''This wait causes all executions to run in sieries.                          
+    For parralelization, remove .wait() and instead delay the                      
+    R script calls unitl all neccesary data is created.'''
+    return subprocess.Popen(command, shell=True).wait()
+
+def silent_cmd(command):
+    '''This wait causes all executions to run in sieries.                          
+    For parralelization, remove .wait() and instead delay the                      
+    R script calls unitl all neccesary data is created.'''
+    return subprocess.Popen(command, shell=True, stdout=subprocess.PIPE).wait()
+
+start_range = 10
+end_range = 21
+
+#collect optional command line arguments
+if(len(sys.argv) > 1):
+    #first argument is the starting range for seeds
+    start_range = int(sys.argv[1])
+    if(len(sys.argv) > 2):
+        #if the user provides a second argument, use it
+        #as the inclusive end of the seed range
+        end_range = int(sys.argv[2]) + 1
+    else:
+        #if the user does not provide a second argument,
+        #set the seed range as just the single seed 
+        #indicated by the first argument
+        end_range = start_range + 1
+
+seeds = range(start_range, end_range)
+
+#Tell the user the inclusive range of seeds
+print("Using seeds", start_range, "through", end_range-1)
+
+for a in seeds:
+    for b in spatial:
+        for c in MOI:
+            command_str = './symbulation_parasite -SEED '+str(a)+ ' -GRID ' +str(b)+ ' -START_MOI ' +str(c) + ' -FILE_NAME _Grid'+str(b)+'_MOI'+str(c)
+            settings_filename = "Output_Grid"+str(b)+'_MOI'+str(c)+"_SEED"+str(a)+".data"
+
+            print(command_str)
+            print(settings_filename)
+            #cmd(command_str+" > "+settings_filename)