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--- readme.aireml [2014/01/22 19:49] – shogo
+++ readme.aireml [2014/06/06 15:37] – [Options] ignacio
@@ Line 35: / Line 35: @@
 Store solutions and those s.e.
 <file>
-OPTION missing -1
+OPTION residual
 </file>
-Set the missing value (default 0).
+y-hat and residuals will be included in "yhat_residual".
+<file>
+OPTION missing -999
+</file>
+Specify the missing value (default 0).
 **Heterogeneous residual variances for a single trait**
@@ Line 72: / Line 76: @@
 </file>
 Specify the SNP file name to use genotype data.
+<file>OPTION se_covar_function <label> <function></file>
+Calculate SD for function of (co)variances by repeated sampling of parameters estimates from their asymptotic multivariate normal distribution, following idea presented by Meyer and Houle 2013.
+''label'' given name for a particular function\\
+''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, and ''trt1'' and ''trt2'' the trait number\\
+''R_trt1_trt1'': indicate the element of the residual (co)variance matrix for traits ''trt1'' and ''trt2''
+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.\\
+default value 5000
+<file>OPTION out_se_covar_function</file>
+Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.)