Differences

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

--- readme.aireml [2014/07/09 12:16] – andres
+++ readme.aireml [2014/07/10 13:22] – shogo
@@ Line 78: / Line 78: @@
 <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.
+As an alternative of SE, 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\\
+''<label>''\\
-''<function>'' function of (co)variances to estimate SD, all elements of the function should be written with no spaces.\\
+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, …).\\
+''<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.\\
+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.
 \\
-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''
 Several functions could be added, with one OPTION line per function.
+\\
 Examples:\\
 \\
@@ Line 102: / Line 103: @@
 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 function the total heritability.
+The second function calculates the heritability for the direct component.
-The fourth function calculates the SD of the genetic correlation between traits 1 and 2, for the direct genetic effect (effect number 2)
+The third function the total heritability.
+The fourth function calculates the SD of the genetic correlation between traits 1 and 2 for the direct genetic effect (effect number 2)
 <file>OPTION samples_se_covar_function <n></file>
@@ Line 111: / Line 114: @@
 <file>OPTION out_se_covar_function</file>
 Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.)