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--- readme.aireml [2012/05/29 13:40] – shogo
+++ readme.aireml [2012/05/30 13:28] – shogo
@@ Line 10: / Line 10: @@
 OPTION conv_crit 1d-12
 </file>
-    convergence criterion (default 1d-10).
+Convergence criterion (default 1d-10).
 <file>
-OPTION maxrounds 500
+OPTION maxrounds 1000
 </file>
-    maximum rounds (default 5000). When it is negative, the program calculates BLUP without running REML.
+Maximum rounds (default 5000). When the number < 2, the program calculates BLUP without iterating REML.
 <file>
 OPTION EM-REML 10
 </file>
-    run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0).
+Run EM-REML (REMLF90) for first 10 rounds to get initial variances within the parameter space (default 0).
 <file>
 OPTION tol 1d-12
 </file>
-    tolerance (or precision) (default 1d-14) for positive definite matrix and g-inverse subroutines. Convergence may be much faster by changing this value.
+Tolerance (or precision) (default 1d-14) for positive definite matrix and g-inverse subroutines. Convergence may be much faster by changing this value.
 <file>
 OPTION sol se
 </file>
-    store solutions and s.e.
+Store solutions and those s.e.
 <file>
 OPTION missing -1
 </file>
-    set the missing value (default 0).
+Set the missing value (default 0).
 **Heterogeneous residual variances for a single trait**
@@ Line 36: / Line 36: @@
 OPTION hetres_pos 10 11
 </file>
-    specify the position of covariables.
+Specify the position of covariables.
 <file>
 OPTION hetres_pol 4.0 0.1 0.1
 </file>
-    initial values of coefficients for heterogeneous residual variances use ln(a0, a1, a2, ...) to make these values.
+Initial values of coefficients for heterogeneous residual variances use //ln//(a0, a1, a2, ...) to make these values.
 **Heterogeneous residual variances for multiple traits**
+Convergence will be very slow with multiple trait heterogeneous residual variances
 <file>
 OPTION hetres_pos 10 10 11 11
 </file>
-    specify the position of covariables (trait first).
+or
+<file>
+OPTION hetres_pos 10 11 12 13
+</file>
+Specify the position of covariables (trait first). "10 10" or "10 11" could be linear for first and second traits, and "11 11" or "12 13" could be quadratic.
 <file>
 OPTION hetres_pol 4.0 4.0 0.1 0.1 0.01 0.01
 </file>
-    initial values of coefficients for heterogeneous residual variances use //ln//(a0, a1, a2, ...) to make these values (trait first).
+Initial values of coefficients for heterogeneous residual variances use //ln//(a0, a1, a2, ...) to make these values (trait first). "4.0 4.0" are intercept for first and second traits. "0.1 0.1" could be linear and "0.01 0.01" could be quadratic.