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--- readme.aireml [2014/07/10 13:23] – shogo
+++ readme.aireml [2014/07/10 13:24] – shogo
@@ Line 82: / Line 82: @@
 ''<label>''\\
 A name for a particular function (e.g., P1 for phenotypic variance of trait 1, H2_1 for heritability for trait 1, rg12 for genetic correlation between traits 1 and 2, …).\\
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 ''<function>''\\
 A formula to calculate a function of (co)variances to estimate SD. All terms of the function should be written with no spaces.\\
 \\
 Each term of the function corresponds to (co)variance elements and could include any random effects (G, PE, ...) and residual (R) (co)variances.\\
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 Notation is with reference to the effect number and the trait number (G_eff1_eff2_trt1_trt2) that indicate the element of the (co)variance matrix for random effect ''eff1'' and ''eff2'' and ''trt1'' and ''trt2'', where ''eff1'' and ''eff2'' are effect numbers 1 and 2, and ''trt1'' and ''trt2'' are trait numbers 1 and 2.\\
 ''R_trt1_trt1'' indicates the element of the residual (co)variance matrix for traits 1 and 2.\\
 Several functions could be added, with one OPTION line per function.\\
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 Examples:\\
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 ''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''\\
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 ''OPTION se_covar_function rg12 G_2_2_1_2/((G_2_2_1_1*G_2_2_2_2)**0.5)''\\
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 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.