process,variable,value,description,range_value
Basic,chunk_number,100,Number of chromosome chunks,Defined by the user
Basic,chunk_bp,100000,Number of basepairs (bp) per chromosome chunk,Defined by the user
Basic,chunk_cM,10,Number of centiMorgans (cM) per chromosome chunk,Defined by the user
Basic,chunk_neutral_loci,1,Number of loci with neutral alleles per chromosome chunk,Defined by the user
Basic,q_neutral,0.5,Initial frequency of all neutral alleles,0-1
Basic,loci_deleterious,0,Number of loci with deleterious alleles,Dependent on computing resources
Basic,loci_advantageous,0,Number of loci with advantageous alleles,Dependent on computing resources
Selection coefficient,s_distribution_del,"""gamma""",Distribution to sample selection coefficients for deleterious alleles,"""equal"" or ""gamma"" or ""log_normal"""
Selection coefficient,s_del,0.001,Selection coefficient for all deleterious alleles,0-1
Selection coefficient,gamma_scale,0.03,Scale of the gamma distribution from where s values are sampled,Defined by the user
Selection coefficient,gamma_shape,0.4,Shape of the gamma distribution from where s values are sampled,Defined by the user
Selection coefficient,log_mean,0.002,Mean of the log normal distribution from where s values are sampled,0-1
Selection coefficient,log_sd,4,Standard deviation of the log normal distribution from where s values are sampled,Defined by the user
Selection coefficient,s_distribution_adv,"""exponential""",Distribution to sample selection coefficients of advantageous alleles,"""equal"" or ""exponential"""
Selection coefficient,s_adv,0.001,Selection coefficient for all advantageous alleles,0-1
Selection coefficient,exp_rate,16,Mean of the exponential distribution for advantageous alleles,Defined by the user
Dominance,h_distribution_del,"""normal""",Distribution to sample dominance for deleterious alleles,"""equal"" or ""normal"" or ""equation"""
Dominance,h_del,0.25,Dominance for all deleterious alleles,0-1
Dominance,h_mean_del,0.25,Mean of the normal distribution from where h values are sampled,0-1
Dominance,h_sd_del,sqrt(0.001),Standard deviation of the normal distribution from where h values are sampled,Defined by the user
Dominance,h_intercept_del,0.5,Value for the intercept of the equation to determine h (maximum value of h when s = 0)Ê,Defined by the user
Dominance,h_rate_del,500,Value for the variable rate of the dominance equation to calculateÊh,Defined by the user
Dominance,h_distribution_adv,"""normal""",Distribution to sample dominance for advantageous alleles,"""equal"" or ""normal"" or ""equation"""
Dominance,h_adv,0.25,Dominance for all advantageous alleles,0-1
Dominance,h_mean_adv,0.25,Mean of the normal distribution from where h values are sampled,0-1
Dominance,h_sd_adv,sqrt(0.001),Standard deviation of the normal distribution from where h values are sampled,Defined by the user
Dominance,h_intercept_adv,0.5,Value for the intercept of the equation to determine h (maximum value of h when s = 0)Ê,Defined by the user
Dominance,h_rate_adv,500,Value for the variable rate of the dominance equation to calculateÊh,Defined by the user
Initial frequency,q_distribution_del,"""equation""",Method to determine initial allele frequency of deleterious alleles,"""equal"" or ""equation"""
Initial frequency,q_del,0.05,Initial frequency of all deleterious alleles,0-1
Initial frequency,q_equation_del,5*10^-5,Mutation rate per generation per site for deleterious alleles,Defined by the user
Initial frequency,q_distribution_adv,"""equation""",Method to determine initial allele frequency of advantageous alleles,"""equal"" or ""equation"""
Initial frequency,q_adv,0.05,Initial frequency of all advantageous alleles,0-1
Initial frequency,q_equation_adv,5*10^-5,Mutation rate per generation per site for advantageous alleles,Defined by the user
Mutation,loci_mut_neu,0,Number of loci with neutral alleles available to mutation ,Dependent on computing resources
Mutation,loci_mut_del,0,Number of loci with deleterious alleles available to mutation ,Dependent on computing resources
Mutation,loci_mut_adv,0,Number of loci with advantageous alleles available to mutation ,Dependent on computing resources
Real information,real_loc,FALSE,Extract location of neutral loci from genlight object,TRUE or FALSE
Real information,real_freq,FALSE,Extract allele frequencies of neutral loci from genlight object,TRUE or FALSE
Real information,chromosome_name,"""1""","Chromosome name from where to extract location, alllele frequency, recombination map and targets of selection (if provided).",Defined by the user
Real information,deleterious_factor,10,Percentage of the number targets from the input file 'targets_of_selection.csv' to use for deleterious alleles,Defined by the user
Real information,mutations_factor,10,Percentage of the number targets from the input file 'targets_of_selection.csv' to use for mutations of deleterious alelles,Defined by the user