I had to fix some things to convert from markdown to R code (add
* to the stan code for multiplication and replace curly quotes to straight ones), but every single one of the plots worked for me. The only weirdness is that when 6 parameters are plotted on a 2 x 2 grid via a for-loop the first plot will immediately be replaced in the viewer with the next set of plots.
This does have a typo though.
pairs should be
pars, but this doesn’t break any plots.
This should just be
mu = beta0 * com + beta1 * pri + ... rat ~ normal(mu, sigma);
You’ll need to make everything like
com a vector.
I’d also recommend declaring
beta as a vector, using
beta ~ normal(0, 1) and then replacing
beta and so on.
This can just be a one-liner
real<lower = 0> sigma = exp(-ln_sigma);
But then I wouldn’t call
ln_sigma that as it’s really the negation of log sigma if I’m reading this right. I have no idea why you’d negate here as
ln_sigma gets a
normal(0, 1) prior, which is symmetric around zero, so it doesn’t do anything other than add a little drag and reverse signs.