readme.aireml
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readme.aireml [2012/05/28 14:10] – created shogo | readme.aireml [2014/06/06 15:39] – [Options] ignacio | ||
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- | AIREMLF90 | + | ====== |
- | + | ||
- | A modification of REMLF90 with computing by the Average-Information | + | |
- | Algorithm. | + | |
- | + | ||
- | Initially written by Shogo Tsuruta, University of Georgia, 03/ | + | |
- | + | ||
- | + | ||
- | AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is | + | |
- | described in Jensen et al. (1996-7). For most problems, it converges in far | + | |
- | fewer rounds than EM REML as implemented in REMLF90. While typically REMLF90 | + | |
- | takes 50-300 rounds to converge, AIREMLF90 converges in 5-15 rounds and to a | + | |
- | higher accuracy. For selected problems, AI REML fails to converge when the | + | |
- | covariance matrix is close to non-positive definite. Adjust sensitivity of the | + | |
- | program by setting the appropriate tolerance. | + | |
- | + | ||
- | + | ||
- | Several options are avaiable: | + | |
+ | ===== Summary ===== | ||
+ | A modification of REMLF90 for estimating variances with the Average-Information algorithm. Initially written by Shogo Tsuruta in 03/ | ||
+ | \\ | ||
+ | AIREMLF90 uses a second derivative REML algrithm with extra heuristics, as is described in Jensen et al. (1996-7). For most models, it converges in far fewer rounds than EM-REML as implemented in REMLF90. While typically REMLF90 takes 50-300 rounds to converge, AIREMLF90 converges in 5-15 rounds and to a higher accuracy. For selected models, AI-REML may fail to converge when the covariance matrix is close to non-positive definite. Adjust sensitivity of the program by setting the appropriate tolerance or setting good starting values. The final results will be saved in " | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
+ | ===== Options ===== | ||
+ | < | ||
OPTION conv_crit 1d-12 | OPTION conv_crit 1d-12 | ||
- | + | </ | |
- | | + | Convergence |
- | + | < | |
- | OPTION maxrounds | + | OPTION maxrounds |
- | + | </ | |
- | | + | Maximum |
- | when it is negative, the program calculates BLUP without | + | < |
OPTION EM-REML 10 | OPTION EM-REML 10 | ||
- | + | </ | |
- | | + | Run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0). |
- | | + | < |
+ | OPTION use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved. | ||
+ | < | ||
OPTION tol 1d-12 | OPTION tol 1d-12 | ||
- | + | </ | |
- | | + | Tolerance |
- | | + | Convergence may be much faster by changing this value. |
- | | + | < |
OPTION sol se | OPTION sol se | ||
+ | </ | ||
+ | Store solutions and those s.e. | ||
+ | < | ||
+ | OPTION residual | ||
+ | </ | ||
+ | y-hat and residuals will be included in " | ||
+ | < | ||
+ | OPTION missing -999 | ||
+ | </ | ||
+ | Specify the missing value (default 0). | ||
- | store solutions and s.e. | + | **Heterogeneous residual variances for a single trait** |
- | + | < | |
- | OPTION missing -1 | + | |
- | + | ||
- | set the missing value (default 0). | + | |
- | + | ||
- | + | ||
- | # Heterogeneous residual variances for a single trait | + | |
OPTION hetres_pos 10 11 | OPTION hetres_pos 10 11 | ||
+ | </ | ||
+ | Specify the position of covariables. | ||
+ | < | ||
+ | OPTION hetres_pol 4.0 0.1 0.1 | ||
+ | </ | ||
+ | Initial values of coefficients for heterogeneous residual variances using //ln//(a0, a1, a2, ...) to make these values. | ||
- | specify | + | **Heterogeneous residual variances for multiple traits**\\ |
+ | Convergence will be very slow with multiple trait heterogeneous residual variances | ||
+ | < | ||
+ | OPTION hetres_pos 10 10 11 11 | ||
+ | </ | ||
+ | or | ||
+ | < | ||
+ | OPTION hetres_pos 10 11 12 13 | ||
+ | </ | ||
+ | Specify | ||
+ | "10 10" or "10 11" could be linear for first and second traits.\\ | ||
+ | "11 11" or "12 13" could be quadratic. | ||
+ | < | ||
+ | OPTION hetres_pol 4.0 4.0 0.1 0.1 0.01 0.01 | ||
+ | </ | ||
+ | Initial values of coefficients for heterogeneous residual variances using //ln//(a0, a1, a2, ...) to make these values (trait first).\\ | ||
+ | "4.0 4.0" are intercept for first and second traits.\\ | ||
+ | "0.1 0.1" could be linear and "0.01 0.01" could be quadratic.\\ | ||
+ | To transform back to the original scale, use exp(a0+a1*X1+a2*X2). | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. | ||
- | OPTION | + | < |
+ | Calculate SD for function of (co)variances by repeated sampling of parameters estimates from their asymptotic multivariate normal distribution, | ||
- | initial values of coefficients | + | '' |
- | use ln(a0, a1, a2, ...) to make these values. | + | '' |
+ | \\ | ||
+ | Each element of the function corresponds to (co)variances elements and could include any the random effects (G) and residual | ||
+ | Notation is with reference to the effect and trait number:\\ | ||
+ | '' | ||
+ | '' | ||
+ | Several functions could be added, with one OPTION line per function. | ||
- | # Heterogeneous residual variances for mutiple traits | + | Examples: |
+ | \\ | ||
+ | '' | ||
- | OPTION | + | '' |
- | specify the position of covariables | + | '' |
- | + | ||
- | OPTION hetres_pol 4.0 4.0 0.1 0.1 0.01 0.01 | + | |
- | initial values of coefficients | + | The first function calculates the SD for the total variance for a maternal model with permanent maternal effect, where 2 and 3 are the effect number for the direct and maternal additive genetic effects respectively, and 4 is the effect number for the maternal permanent random effect. |
- | use ln(a0, a1, a2, ...) to make these values (trait first). | + | |
+ | The second function calculates the heritability for the direct component and the third function the total heritability. | ||
+ | < | ||
+ | Set the number of samples to calculate SE for function of (co)variances.\\ | ||
+ | default value 5000 | ||
+ | < | ||
+ | Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) | ||
readme.aireml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1