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--- readme.aireml [2014/07/10 13:28] – shogo
+++ readme.aireml [2014/09/05 16:16] – shogo
@@ Line 16: / Line 16: @@
 OPTION maxrounds 1000
 </file>
-Maximum rounds (default 5000). When the number < 2, the program calculates BLUP without iterating REML.
+Maximum rounds (default 5000). When the number = 0, the program calculates BLUP without iterating REML and some statistics (-2logL, AIC, SE for (co)variances, ...).
 <file>
 OPTION EM-REML 10
@@ Line 33: / Line 33: @@
 OPTION sol se
 </file>
-Store solutions and those s.e.
+Store solutions and those standard errors.
+<file>
+OPTION store_pev_pec 6
+</file>
+Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in "pev_pec_bf90".
 <file>
 OPTION residual
@@ Line 42: / Line 46: @@
 </file>
 Specify the missing value (default 0).
+<file>
+OPTION constant_var 5 1 2 ...
+</file>
+: effect number\\
+: first trait number\\
+: second trait number\\
+implying the covariance between traits 1 and 2 for effect 5.
 **Heterogeneous residual variances for a single trait**
@@ Line 102: / Line 113: @@
 ''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)''\\
-''OPTION se_covar_function  rg12  G_2_2_1_2/((G_2_2_1_1*G_2_2_2_2)**0.5)''\\
+''OPTION se_covar_function  rg12  G_2_2_1_2/(G_2_2_1_1*G_2_2_2_2)**0.5''\\
 \\
 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.