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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: examplesoptions, 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 SORFSPAK 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 blup90iod2blu90iod2r, 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>​
  
  
faq.1576223126.txt.gz · Last modified: 2019/12/13 07:45 by yutaka