Differences

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

--- readme.aireml [2013/07/17 16:27] – shogo
+++ readme.aireml [2014/06/04 13:17] – [Options] ignacio
@@ Line 21: / Line 21: @@
 </file>
 Run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0).
+<file>
+OPTION use_yams
+</file>
+Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved.
 <file>
 OPTION tol 1d-12
@@ Line 31: / 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 68: / 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 Meyer and Houle 2013.
+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
+<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.)