Extracting stuff from objects has always been one of the most confusing aspects of R to me. I've fitted a bayesian linear regression model using rjags and have the following mcmc object:
summary(m_csim) Iterations = 1:150000 Thinning interval = 1 Number of chains = 1 Sample size per chain = 150000 1. Empirical mean and standard deviation for each variable, plus standard error of the mean: Mean SD Naive SE Time-series SE BR2 0.995805 0.0007474 1.930e-06 3.527e-06 BR2adj 0.995680 0.0007697 1.987e-06 3.633e-06 b -5.890842 0.1654755 4.273e-04 1.289e-02 b 1.941420 0.0390239 1.008e-04 1.991e-03 b 1.056599 0.0555885 1.435e-04 5.599e-03 sig2 0.004678 0.0008333 2.152e-06 3.933e-06 2. Quantiles for each variable: 2.5% 25% 50% 75% 97.5% BR2 0.994108 0.995365 0.995888 0.996339 0.99702 BR2adj 0.993932 0.995227 0.995765 0.996229 0.99693 b -6.210425 -6.000299 -5.894810 -5.784082 -5.55138 b 1.867453 1.914485 1.940372 1.967466 2.02041 b 0.942107 1.020846 1.057720 1.094442 1.16385 sig2 0.003321 0.004082 0.004585 0.005168 0.00657
In order to extract the coefficients' means I did
b = colMeans(mod_csim)[3:5]. I want to calculate credible intervals so I need to extract the 0.025 and 0.975 quantiles too. How do I do that programmatically ?
I hope I'm not overstepping my knowledge bounds, but I want to answer from the point of view of 'in general' rather than specifically for rjags. m_csim is an object and many methods can possibly be used on it. You've used the summary method to see something. As people have commented, probably there is a coef method. However as someone else has commented (while I was replying !), using str() to see what an object contains is the best way to see what information is in an object and how to address it. I'd be very surprised if using str() doesn't show how to find not only the coefficients but also enough information on the confidence intervals to allow you to find the desired CI.