SymSettings.cfg

### 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 100                  # How frequently, in updates, should data print?
set SYNERGY 5                     # Amount symbiont's returned resources should be multiplied by
set VERTICAL_TRANSMISSION 0.7     # 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 1001                  # 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 -1          # Number of total resources available over the entire run, -1 for unlimited
set HORIZ_TRANS 1                 # Should non-lytic horizontal transmission occur? 0 for no, 1 for yes
set HOST_REPRO_RES 1000           # How many resources required for host reproduction
set SYM_HORIZ_TRANS_RES 100       # 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 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 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

### 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

### 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          # whether the initialization of the donation rate is randomized
set PGG_DONATE_MAX 1.0           # Max value of the donation rate during initialization
set PGG_DONATE_MIN 0.0           # Min value of the donation rate during initialization
set PGG_DONATE_NORMAL 1          # whether the initialization of the donation rate is randomized using a normal distribution
set PGG_DONATE_NORMAL_MEAN 0.5   # Mean of the normal distribution used during the initialization of the donation rate
set PGG_DONATE_NORMAL_STD 0.167  # Standard deviation of the normal distribution used during the initialization of the 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)