thrgibbs1f90

number of samples (excluding the previous run) and length of burn-in Give n to store every n-th sample? (1 means store all samples) How do OPTIONs work? OPTION cat 2 0 2 indicates that the first trait is binary (categorical with 2 categories) and 0 indicates that the second trait is linear (continuous). OPTION fixed_var all 1 2 3 All solutions and posterior means and SD for effects for effects1, 2, and 3 are stored in "all_solutions" and in "final_solutions" every round using fixed variances. Without numbers, all solutions for all effects are stored. OPTION fixed_var mean 1 2 3 Posterior means and SD for effects1, 2, and 3 in "final_solutions". OPTION solution all 1 2 3 All solutions and posterior means and SD for effects1, 2, and 3 are stored in "all_solutions" and in "final_solutions" every round. Without numbers, all solutions for all effects are stored. OPTION solution mean 1 2 3 Posterior means and SD for effects1, 2, and 3 in "final_solutions". OPTION cont 10000 10000 is the number of samples run previously when restarting the program from the last run. OPTION prior 5 5 is the degree of belief for the priors specified in the parameter file. OPTION seed 123 321 Two seeds for a random number generator can be specified. OPTION thresholds 0.0 1.0 2.0 Set the fixed thresholds. No need to set 0 for binary traits. OPTION residual 1 Set the residual variance = 1. OPTION censored xx Negative values of the last category in the data set indicate censored records. "xx" determines the lower and upper limit of the category + xx when sampling from the distribution. OPTION SNP_file snp Specify the SNP file name to use genotype data. OPTION missing -1 Change the missing value for a continuous trait (default 0). This option is not available yet. Fixed effects (with no or zero variance) should be placed before random effects (with (co)variance) in the parameter file for faster or more stable convergence. Need more examples?