readme.blupf90
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readme.blupf90 [2012/05/29 16:56] – shogo | readme.blupf90 [2016/10/21 22:16] – [Options] shogo | ||
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====== BLUPF90 ====== | ====== BLUPF90 ====== | ||
- | The documentation for blupf90 is available separately as a PDF document. | + | ===== Summary ===== |
+ | The documentation for blupf90 is available separately as a {{: | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
Line 7: | Line 10: | ||
OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
</ | </ | ||
- | set convergence criteria (deault 1e-12). | + | Set convergence criteria (deault 1e-12). |
< | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
</ | </ | ||
- | set maximum number of rounds (default 1000). | + | Set maximum number of rounds (default 1000). |
< | < | ||
OPTION solv_method FSPAK | OPTION solv_method FSPAK | ||
</ | </ | ||
- | selection | + | Selection |
< | < | ||
OPTION r_factor 1.6 | OPTION r_factor 1.6 | ||
</ | </ | ||
- | set relaxation factor for SOR (default 1.4). | + | Set relaxation factor for SOR (default 1.4). |
< | < | ||
OPTION sol se | OPTION sol se | ||
</ | </ | ||
- | store solutions and s.e. | + | Store solutions and standard errors. |
+ | < | ||
+ | OPTION store_pev_pec 6 | ||
+ | </ | ||
+ | Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in " | ||
< | < | ||
OPTION missing -999 | OPTION missing -999 | ||
</ | </ | ||
- | missing | + | Specify |
< | < | ||
OPTION residual | OPTION residual | ||
</ | </ | ||
- | y-hat and residual will be shown in yhat_residual. | + | y-hat and residual will be included |
< | < | ||
OPTION blksize 3 | OPTION blksize 3 | ||
</ | </ | ||
- | set block size for preconditioner (default 1). | + | Set block size for preconditioner (default 1). |
+ | < | ||
+ | OPTION prior_solutions | ||
+ | </ | ||
+ | Using the previous solution file to start the iteration. An additional software is required to use this option. | ||
+ | < | ||
+ | OPTION stdresidual | ||
+ | </ | ||
+ | y-hat and student residuals will be included in " | ||
+ | < | ||
+ | OPTION check_levels 0 | ||
+ | </ | ||
+ | Check levels (default 1 = true). | ||
+ | < | ||
+ | OPTION use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). | ||
< | < | ||
OPTION SNP_file snp | OPTION SNP_file snp | ||
</ | </ | ||
- | specify | + | Specify |
readme.blupf90.txt · Last modified: 2024/05/15 19:00 by dani