Differences

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--- faq [2012/05/10 19:48] – created ignacy
+++ faq [2024/05/17 18:17] (current) – dani
@@ Line 1: / Line 1: @@
-FAQ for BLUPF90 programs
+======  FAQ: examples, options, and tips for BLUPF90 family programs and modeling ======
-Input files
-    data
+Download {{:blupf90_ALL.pdf|BLUPF90 manual}}
-    pedigree
-Data preparation program
+==== Technical problems and segmentation fault ====
-    renumf90 (ver 1.92) read me
+    * [[FAQ.segfault|Segmentation Fault]]: Received a message with "Segmentation fault"
-    examples
+    * [[FAQ.windows|System Error]]: Received a message like "The program can't start because libiomp5md.dll is missing..." in Windows.
+    * [[FAQ.openmp|Better settings for OpenMP]]: How should I define the number of threads used with a program?
+    * [[FAQ.intellibs|Installation of Intel Libraries]]: For users with customized programs
-Frequent mistakes in a parameter file for BLUPF90 programs
-    parameter files for various models
+==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs =====
-    examples
-REML
+    * [[[[FAQ.data|data]]
+    * [[[[FAQ.pedigree|pedigree]]
+    * [[[[FAQ.parameter|parameter]]
+    * [[[[FAQ.example|examples]]
-    remlf90 (ver 1.76) read me: EM algorithm - PDF
+=== Data preparation program ===
-    airemlf90 (ver 1.99) read me: Average Information REML + REMLF90 - Standard Errors (PDF)
-Gibbs sampling
+    * [[[[readme.renumf90|renumf90]]
-OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed variances
+    * [[[[FAQ.renum_example|examples]]
-    gibbs1f90 (ver 1.42) read me: Faster than GIBBS2F90 without missing traits
+=== REML ===
-    gibbs2f90 (ver 1.76) read me
-    gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances
-    thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model
-Post-Gibbs Analysis
+    * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90
-    postgibbsf90 (ver 3.02) read me: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs)
+    * [[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)]]
+    * [[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?]]
-BLUP
+=== 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
-    blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF
+    * [[readme.gibbsf90plus|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
-    blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions)
-    cblup90iod2 (ver 3.16) read me: Threshold model + linear model for a large number of equations (available only under some conditions)
-Accuracy
+    * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits
+    * [[readme.gibbs2|gibbs2f90]]: Useful with missing traits
+    * [[readme.gibbs3|gibbs3f90]]: With heterogeneous residual variances
+    * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model
+    * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances
-    accf90 : (ver 1.63) read me: Accuracy (reliability) for a large number of animals (available only under some conditions)
+    * [[faq.gibbs|General questions]]: Common to all Gibbs samplers
+=== 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.
+=== BLUP ===
+    * [[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.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.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)
+    * [[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) ===
+    * [[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.accgs2|accf90GS2]]: New accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options
+=== Genomic Analysis ===
+    * [[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.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>
-Genomic Analysis
-    preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs