Dear R users: I am using the package coda (the last verison in CRAN) to analyse the output from a MCMC Bayesian analysis. And I get unconsitented results. I have export the chain using the read.table function and after I have transformed this data frame to an mcmc object using the mcmc function. I am interested in three variables, when I use the function effectiveSize I have these figures: 403.3730 1854.4534 369.8643. But when I run the function codamenu to perform same convergence test I get this warning mensage:
Checking effective sample size ... ******************************************* WARNING !!! Some variables in your chain have an effective sample size of less than 200 This is too small, and may cause errors in the diagnostic tests HINT: Look at plots first to identify variables with slow mixing. (Choose menu Output Analysis then Plots) Re-run your chain with a larger sample size and thinning interval. If possible, reparameterize your model to improve mixing ******************************************* Some thing is wrong. Could someone explain to me what is happening? Thanks, Juan Pablo. =========================== Juan Pablo Sánchez Serrano Dep. Ciencia Animal, UPV. C/ Camino de Vera s/n 46022 Valencia (Spain) Telf. 963877007 Ext.74382 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
