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--- readme.gibbs2 [2017/03/09 23:40] – [Running] shogo
+++ readme.gibbs2 [2020/08/28 22:20] – [Running] shogo
@@ Line 11: / Line 11: @@
 You can run as
-<file>gibbs2f90 parameter_file --rounds 1000000 --burnin 10000 - -thin 10 --thinprint 10 </file>
+<file>gibbs2f90 parameter_file --rounds 1000000 --burnin 10000 --thin 10 --thinprint 10 </file>
 in which case you give the number of rounds, the burn-in, the storage of samples in the file ''gibbs_samples'', and the interval between printouts in the screen. Otherwise you can simply type ''gibbs1f90'' and you will be asked the parameter file and the questions below:
@@ Line 37: / Line 37: @@
 OPTION solution all 1 2 3
 </file>
+Caution: this option will create a huge output solution file when you run many rounds and/or use a large model.
 All solutions and posterior means and SD for effects1, 2, and 3 are stored in "all_solutions" and in "final_solutions" every round. Without numbers, all solutions for all effects are stored.
 <file>
 OPTION solution mean 1 2 3
 </file>
+Caution: this option will create a huge output solution file when you run many rounds and/or use a large model.
 Posterior means and SD for effects1, 2, and 3 in "final_solutions".
 <file>
@@ Line 53: / Line 55: @@
 OPTION prior eff1 db1    eff2 db2 ...    effn dbn    -1 dbres\\
 effx correspond to the effect number and dbx to the degree of belief for this random effect, -1 corresponds to the degree of belief of the residual variance.\\
-In this example 2 is the degree of belief for the 5th effect, and 5 is the degree of belief for the residual.\\
+In this example, 2 is the degree of belief for the 5th effect, and 5 is the degree of belief for the residual.
+If the model has correlated random effects, specify only the first effect.\\
 <file>
 OPTION seed 123 321