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--- readme.aireml [2014/06/06 15:28] – [Options] ignacio
+++ readme.aireml [2014/06/06 15:37] – [Options] ignacio
@@ Line 81: / Line 81: @@
 ''label'' given name for a particular function\\
-''function'' function of (co)variances to estimate SD, all elements of the function should be written written with no spaces.\\
+''function'' function of (co)variances to estimate SD, all elements of the function should be written with no spaces.\\
 \\
 Each element of the function corresponds to (co)variances elements and could include any the random effects (G) and residual (R) (co)variances.\\
 Notation is with reference to the effect and trait number:\\
-''G_eff1_eff2_trt1_trt2'': indicate the element of the (co)variance matrix for random effect ''eff1'' and ''eff2'' and ''trt1'' and ''trt2'', where ''eff1'', ''eff2'' are the effect number of the random effect, and ''trt1'' and ''trt2'' the trait number\\
+''G_eff1_eff2_trt1_trt2'': indicate the element of the (co)variance matrix for random effect ''eff1'' and ''eff2'' and ''trt1'' and ''trt2'', where ''eff1'', ''eff2'' are the effect number, and ''trt1'' and ''trt2'' the trait number\\
 ''R_trt1_trt1'': indicate the element of the residual (co)variance matrix for traits ''trt1'' and ''trt2''
-OPTION se_covar_function P   G_2_2_1_1+G_2_3_1_1+G_3_3_1_1+G_4_4_1_1+R_1_1
+Examples:\\
+\\
+''OPTION se_covar_function P   G_2_2_1_1+G_2_3_1_1+G_3_3_1_1+G_4_4_1_1+R_1_1''\\
+''OPTION se_covar_function H2d   G_2_2_1_1/(G_2_2_1_1+G_2_3_1_1+G_3_3_1_1+G_4_4_1_1+R_1_1)''\\
+''OPTION se_covar_function H2t (G_2_2_1_1+1.5*G_2_3_1_1+0.5*G_3_3_1_1)/(G_2_2_1_1+G_2_3_1_1+G_3_3_1_1+G_4_4_1_1+R_1_1)''\\
+The first function calculates the SD for the total variance for a maternal model with permanent maternal effect, where 2 and 3 are the effect number for the direct and maternal additive genetic effects respectively, and 4 is the effect number for the maternal permanent random effect.
+The second function calculates the heritability for the direct component and the third the total heritability.
 <file>OPTION samples_se_covar_function <n></file>
 Set the number of samples to calculate SE for function of (co)variances.\\