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faq [2019/12/13 07:45] yutaka [Gibbs sampler] |
faq [2024/01/09 03:25] (current) shogo [Modeling] |
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- | ====== FAQ: examples and options for BLUPF90 family programs ====== | + | ====== FAQ: examples, options, and tips for BLUPF90 family programs and modeling ====== |
- | Download {{:blupf90_ALL7.pdf|BLUPF90 manual}} | + | Download {{:blupf90_ALL8.pdf|BLUPF90 manual}} |
==== Technical problems and segmentation fault ==== | ==== Technical problems and segmentation fault ==== | ||
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* [[FAQ.intellibs|Installation of Intel Libraries]]: For users with customized programs | * [[FAQ.intellibs|Installation of Intel Libraries]]: For users with customized programs | ||
- | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ==== | + | |
+ | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ===== | ||
* [[[[FAQ.data|data]] | * [[[[FAQ.data|data]] | ||
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* [[[[FAQ.example|examples]] | * [[[[FAQ.example|examples]] | ||
- | ==== Data preparation program ==== | + | === Data preparation program === |
* [[[[readme.renumf90|renumf90]] | * [[[[readme.renumf90|renumf90]] | ||
* [[[[FAQ.renum_example|examples]] | * [[[[FAQ.renum_example|examples]] | ||
- | ==== REML ==== | + | === REML === |
+ | |||
+ | * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 | ||
* [[readme.reml|remlf90]]: EM algorithm | * [[readme.reml|remlf90]]: EM algorithm | ||
* [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 including heterogeneous residual variances [[http://nce.ads.uga.edu/html/projects/AI_SE_revised.pdf|Standard Errors (PDF)]] | * [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 including heterogeneous residual variances [[http://nce.ads.uga.edu/html/projects/AI_SE_revised.pdf|Standard Errors (PDF)]] | ||
- | * [[readme.blupf90new|blupf90test]]: This is a beta version for a combined program of airemlf90 and blupf90 | + | * [[FAQ.vc#I got weird messages and nonsense estimates in AI REML. What is it?|I got weird messages and nonsense estimates in AI REML. What is it?]] |
- | ==== Gibbs sampler ==== | + | === Gibbs Sampler === |
OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed (known) variances | OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed (known) variances | ||
+ | |||
+ | * [[readme.gibbsf90plus|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 | ||
* [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits | * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits | ||
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* [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model | * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model | ||
* [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances | * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances | ||
- | * [[readme.gibbsf90new|gibbsf90test]]: This is a beta version for a combined Gibbs program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 | + | |
* [[faq.gibbs|General questions]]: Common to all Gibbs samplers | * [[faq.gibbs|General questions]]: Common to all Gibbs samplers | ||
- | ==== Post-Gibbs Analysis ==== | + | === Post-Gibbs Analysis === |
* [[readme.postgibbs|postgibbsf90]]: Statistics and graphics for convergence diagnosis and post-Gibbs analysis (use postgibbsold for old Gibbs sampler programs). The graphs are created with gnuplot, which must be pre-installed. | * [[readme.postgibbs|postgibbsf90]]: Statistics and graphics for convergence diagnosis and post-Gibbs analysis (use postgibbsold for old Gibbs sampler programs). The graphs are created with gnuplot, which must be pre-installed. | ||
- | ==== BLUP ==== | ||
- | * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG | + | === BLUP === |
- | * [[readme.blupf90new|blupf90test]]: This is a beta version for a combined program of airemlf90 and blupf90 | + | |
+ | * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 | ||
+ | * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, blu90iod2r, blup90iod2hr, and blup90mbe2 with new features | ||
+ | * [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions) | ||
* [[readme.predictf90|predictf90]]: Calculates y-hat | * [[readme.predictf90|predictf90]]: Calculates y-hat | ||
+ | |||
+ | * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG | ||
* [[readme.pcg2|blup90iod2]]: (G)BLUP for a large number of equations (available only under some conditions) | * [[readme.pcg2|blup90iod2]]: (G)BLUP for a large number of equations (available only under some conditions) | ||
* [[readme.pcg2r|blup90iod2r]]: (G)BLUP with GIBBS3F90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | * [[readme.pcg2r|blup90iod2r]]: (G)BLUP with GIBBS3F90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | ||
* [[readme.pcg2hr|blup90iod2hr]]: (G)BLUP with AIREMLF90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | * [[readme.pcg2hr|blup90iod2hr]]: (G)BLUP with AIREMLF90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | ||
- | * [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions) | ||
* [[blup90mbe2]]: (G)BLUP for a large number of equations for multi-breed evaluations (available only under some conditions). The prior external EBV can be from other breeds, lines, foreign origins, ... | * [[blup90mbe2]]: (G)BLUP for a large number of equations for multi-breed evaluations (available only under some conditions). The prior external EBV can be from other breeds, lines, foreign origins, ... | ||
- | ==== Accuracy (approximation) ==== | + | |
+ | === Accuracy (approximation) === | ||
* [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | * [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | ||
* [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options | * [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options | ||
+ | * [[readme.accgs2|accf90GS2]]: New accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options | ||
- | ==== Genomic Analysis ==== | + | === Genomic Analysis === |
* [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS) | * [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS) | ||
* [[readme.pregsf90|postGSf90]]: Post-analysis of genomic programs with options (GWAS) | * [[readme.pregsf90|postGSf90]]: Post-analysis of genomic programs with options (GWAS) | ||
* [[readme.predf90|predf90]]: Prediction of EBV using only SNP | * [[readme.predf90|predf90]]: Prediction of EBV using only SNP | ||
+ | * [[readme.qcf90|qcf90]] - a quality-control tool on genotypes and pedigree information | ||
+ | |||
+ | === Additional programs === | ||
+ | |||
+ | * [[Readme.Inbupgf90|inbupgf90]] - a program to calculate inbreeding coefficients with incomplete pedigree | ||
+ | * [[Readme.SeekParentf90|seekparentf90]] - a program to verify paternity and parent discovery using SNP markers | ||
+ | |||
+ | |||
+ | ===== Modeling ===== | ||
+ | <file> | ||
+ | |||
+ | * Sire model (cg: contemporary group) | ||
+ | y = μ + cg + ... + sire + e | ||
+ | y = μ + cg + ... + sire + MGS + e | ||
+ | where cg = common environment (farm, year, season, management, ...) | ||
+ | * Animal model (pe: permanent environment) | ||
+ | * Single record / animal | ||
+ | y = μ + cg + ... + animal + e | ||
+ | * Multiple records / animal | ||
+ | y = μ + cg + ... + animal + pe + e | ||
+ | * Random regressions f(t) | ||
+ | y = μ + cg + ... + f(t1) + f(t2)*animal + f(t3)*pe + e | ||
+ | where f(t) = a function of t (t: continuous variable) | ||
+ | * Maternal effect model (mpe: maternal permanent environment) | ||
+ | y = μ + cg + ... + animal + maternal + mpe + e | ||
+ | |||
+ | </file> | ||