airemlf90

How do OPTIONs work? OPTION conv_crit1d-12 Convergence criterion (default 1d-10). OPTION maxrounds 500 Maximum rounds (default 5000). When it is negative, the program calculates BLUP without running REML. OPTION EM-REML 10 Run EM-REML for the first 10 rounds to get initial variances within the parameter space (default 0). OPTION tol 1d-12 Tolerance (or precision) for positive definite matrix and G-inverse subroutines (default 1d-14). OPTION sol se Store solutions and s.e. OPTION residual y-hat and residual will be shown in yhat_residual. OPTION missing -1 Set the missing observation (default 0). OPTION constant_var 5 1 2 The effect number (5), the first trait number (1), and the second trait number (2), implying the covariance between traits 1 and 2 for effect 5. OPTION SNP_file snp Specify the SNP file name to use genotype data. # Heterogeneous residual variances for a single trait OPTION hetres_pos 10 11 Specify positions of covariables. OPTION hetres_pol 4.0 0.1 0.1 Initial values of coefficients for heterogeneous residual variances. Use ln(a0, a1, a2, ...) to make these values. When the number of positions = the number of polynomials, the regressions do not include the intercept (e.g., linear spline). # Heterogeneous residual variances for multiple traits (the convergence will be very slow) OPTION hetres_pos 10 10 11 11 Specify positions of covariables (trait first). OPTION hetres_pol 4.0 4.0 0.1 0.1 0.01 0.01 Initial values of coefficients for heterogeneous residual variances. Use ln(a0, a1, a2, ...) to make these values (trait first). Why does the program sometimes run very slow? Your data and/or model is too large. Your covariance matrix is close to non-positive definite (variance is zero or close to zero). Need more examples?