F phenvar 1 + 2 # pheno variance F genvar 1 * 4 # geno var H heritability 4 3 # heritabilityThe .pin file specifies the functions to be calculated. The .pin file is run as an independent process either in the same run of ASReml (ASReml 3 only) or as a subsequent run of ASReml. In that process, ASReml reads the model information from the .asr and .vvp files and calculates the requested functions. These are reported in the .pvc file. Processing the .pin file as a subsequent run, the user re-runs ASReml with the -P command line option specifying the .pin file as the input file. If the .asr file filename does not match the .pin file filename, append the former to the -P option i.e. ASReml -Pcoopwwt coop.pin Processing the .pin file within the primary run, use the VPREDICT directive. The calculations are based on the estimated variance parameters and their variance matrix as represented by the inverse of the average information matrix. Note that this matrix has zero values for fixed variance parameters including those near the parameter space boundary. The algebraic expressions used are given in the ASReml User Guide.

F is for linear combinations of variance components,

H is for forming the ratio of two components (a heritability),

R is for forming the correlation based on three components,

F

Where matrices are to be combined the form F

F phenvar 1 + 2forms a third component which is the sum of components 1 and 2, that is, the phenotypic variance, and

F genvar 1 * 4forms a fourth component which is the sire variance component multiplied by 4, that is, the genotypic variance.

H heritability 4 3calculates the heritability by calculating component 4 (from second line of .pin) / component 3 (from first line of .pin), that is, genetic variance / phenotypic variance.

Alternatively, R

Components 1:3 constitute the residual matrix Components 4:6 constitute the genetic matrix F phenvar 1:3 + 4:6 R phencorr 7 8 9 R gencorr 4:6might be the .pin file used. Note the two leading comment lines

R phencor 7 8 9calculates the phenotypic correlation by dividing component 8 by the square roots of components 7 and 9 where components 7, 8 and 9 are created with the 'phenvar' line of the .pin file, and

R gencor 4:6calculates the genotypic covariance by dividing component 5 by the square roots of components 4 and 6 where components 4, 5 and 6 are variance components from the analysis.

Bivariate sire model sire !I ywt fat bsiremod.asd ywt fat ~ Trait !r Trait.sire 1 2 1 0 # ASReml will count units Trait 0 US 3*0 Trait.sire 2 Trait 0 US !GP 3*0 sireThe following sample .pin file is a little more complicated. It relates to the preceding bivariate sire model.

Residual UnStruct 1 26.2197 26.2197 18.01 0 U Residual UnStruct 1 2.85090 2.85090 9.55 0 U Residual UnStruct 2 1.71556 1.71556 18.00 0 U Tr.sire UnStruct 1 16.5262 16.5262 2.69 0 U Tr.sire UnStruct 1 1.14422 1.14422 1.94 0 U Tr.sire UnStruct 2 0.132847 0.132847 1.88 0 U F phenvar 1:3 + 4:6 F addvar 4:6 * 4 H heritA 10 7 H heritB 12 9 R phencorr 7 8 9 R gencor 4:6The first six lines displays variance component table from the {\tt.asr} on which the .pin file is based.

1 Residual UnStruct 1 26.2197 26.2197 18.01 0 U 2 Residual UnStruct 1 2.85090 2.85090 9.55 0 U 3 Residual UnStruct 2 1.71556 1.71556 18.00 0 U 4 Tr.sire UnStruct 1 16.5262 16.5262 2.69 0 U 5 Tr.sire UnStruct 1 1.14422 1.14422 1.94 0 U 6 Tr.sire UnStruct 2 0.132847 0.132847 1.88 0 U 7 phenvar 1 42.75 6.297 8 phenvar 2 3.995 0.6761 9 phenvar 3 1.848 0.1183 10 addvar 4 66.10 24.58 11 addvar 5 4.577 2.354 12 addvar 6 0.5314 0.2831 h2ywt = addvar 10/phenvar 7= 1.5465 0.3571 h2fat = addvar 12/phenvar 9= 0.2875 0.1430 phencorr = phenvar /SQR[phenvar *phenvar ]= 0.4495 0.0483 gencor 2 1 = Tr.si 5/SQR[Tr.si 4*Tr.si 6]= 0.7722 0.1537