process,variable,value,description,range_value
Basic,number_pops_phase2,1,Number of populations of phase 2 (must be the same as number of populations in phase 1),Dependent on computing resources
Basic,gen_number_phase2,10,Number of generations of phase 2,Dependent on computing resources
Genetic drift,population_size_phase2,"""50""","Census population size of each population of phase 2 (must be even, space delimited and in quotes)",Dependent on computing resources
Genetic drift,variance_offspring_phase2,1000000,Coefficient that determines the variance in the number of offspring per mating for phase 2,Defined by the user
Genetic drift,number_offspring_phase2,5,Mean number offspring per mating for phase 2,Dependent on computing resources
Genetic drift,replace_parents,TRUE,"Whether parents reproduce more than once, i.e. parents are sampled with replacement",TRUE or FALSE
Gene flow,dispersal_phase2,FALSE,Simulate dispersal in phase 2,TRUE or FALSE
Gene flow,dispersal_type_phase2,"""all_connected""",Type of dispersal in phase 2,"""line"",""circle"",""all_connected"""
Gene flow,number_transfers_phase2,1,Number of dispersing individuals in phase 2,< population size
Gene flow,transfer_each_gen_phase2,1,Interval of number of generations in which dispersal occurs in phase 2,< number of generations
Natural selection,selection_phase2,FALSE,Simulate selection in phase 2,TRUE or FALSE
Natural selection,natural_selection_model,"""relative""",Selection model to use,ÒrelativeÓ or ÒabsoluteÓ
Natural selection,genetic_load,0.8,Approximation of the genetic load of the proportion of the genome that is simulated. This parameter is used in the absolute fitness model,Defined by the user
Natural selection,local_adap,NULL,Populations in which local adaptation occurs (must be space delimited and in quotes),Defined by the user (must be character)
Natural selection,clinal_adap,NULL,"Starting and ending populations in which clinal adaptation occurs (two values must be provided, be space delimited and in quotes)",Defined by the user (must be character)
Natural selection,clinal_strength,10,Percentage of the decrease of the selection coefficient along the cline,0-100
Mutation,mutation,FALSE,Simulate mutation ,TRUE or FALSE
Mutation,mut_rate,0.1,Mutation rate,Defined by the user
Recombination,recombination,TRUE,Whether recombination occurs,TRUE or FALSE
Recombination,recombination_males,TRUE,Whether recombination occurs in males and females (or only females),TRUE or FALSE
phase1,phase1,FALSE,Simulate phase 1,TRUE or FALSE
phase1,number_pops_phase1,1,Number of populations of phase 1 (must be the same as number of populations in phase 2),Dependent on computing resources
phase1,gen_number_phase1,10,Number of generations of phase 1,Dependent on computing resources
phase1,population_size_phase1,"""100""","Census population size of each population of phase 1 (must be even, space delimited and in quotes)",Dependent on computing resources
phase1,same_line,FALSE,Sample phase 2 populations from the same phase 1 population or from different phase 1 populations,TRUE or FALSE
phase1,variance_offspring_phase1,1000000,Coefficient that determines the variance in the number of offspring per mating for phase 1,Defined by the user
phase1,number_offspring_phase1,5,Mean number offspring per mating for phase 1,Dependent on computing resources
phase1,dispersal_phase1,FALSE,Simulate dispersal in phase 1,TRUE or FALSE
phase1,dispersal_type_phase1,"""all_connected""",Type of dispersal in phase 1,"""line"",""circle"",""all_connected"""
phase1,number_transfers_phase1,1,Number of dispersing individuals in phase 1,< population size
phase1,transfer_each_gen_phase1,1,Interval of number of generations in which dispersal occurs in phase 1,< number of generations
phase1,selection_phase1,FALSE,Simulate selection in phase 1,TRUE or FALSE
Real information,real_pops,TRUE,Extract number of populations from genlight object,TRUE or FALSE
Real information,real_pop_size,TRUE,Extract census population sizes from genlight object,TRUE or FALSE
Real information,real_loc,TRUE,Extract location for neutral loci from genlight object,TRUE or FALSE
Real information,real_freq,TRUE,Extract allele frequencies for neutral loci from genlight object,TRUE or FALSE
Real information,chromosome_name,"""1""",Chromosome name from where to extract allele frequencies ,Defined by the user (must be character)