Differences

This shows you the differences between two versions of the page.

--- faq [2023/09/04 20:32] – [Individual program] shogo
+++ faq [2023/12/20 23:25] – [Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs] shogo
@@ Line 10: / Line 10: @@
     * [[FAQ.intellibs|Installation of Intel Libraries]]: For users with customized programs
-==== Variance Components ====
-    * [[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?]]
 ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs =====
@@ Line 20: / Line 17: @@
     * [[[[FAQ.parameter|parameter]]
     * [[[[FAQ.example|examples]]
-==== Individual program ====
 === Data preparation program ===
@@ Line 30: / Line 25: @@
 === REML ===
+    * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90
     * [[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.blupf90plus|blupf90+]]: This is a combination of remlf90, 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 ===
 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.gibbs2|gibbs2f90]]: Useful with missing traits
@@ Line 42: / Line 39: @@
     * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model
     * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances
-    * [[readme.gibbsf90plus|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
     * [[faq.gibbs|General questions]]: Common to all Gibbs samplers
@@ Line 51: / Line 47: @@
 === BLUP ===
-    * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG
     * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90
+    * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, blu90iodrr, blup90iod2hr, and blup90mbe 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)
-    * [[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, ...
-    * [[blup90iod3]]: (G)BLUP for a large number of equations
 === Accuracy (approximation) ===