<p>I'm going to go ahead and promote my comment to an answer.</p>

<ul>
<li><p>there may be a terminology issue about exactly what you mean by "latent trait scores", but I'm 99% certain that you want <code>ranef()</code>: see <code>?ranef.merMod</code>.  (In the linear mixed model world these are called BLUPs; Doug Bates prefers to call them <em>conditional modes</em> so that the terminology extends to GLMMs (where they are no longer necessarily best, linear, or unbiased).)</p></li>
<li><p>I'm sorry to give you a link rather than an explicit answer, but the best source to find out about the guts of <code>merMod</code> objects is probably <a href="http://arxiv.org/abs/1406.5823" rel="nofollow">this ArXiv preprint</a>, in press at <em>Journal of Statistical Software</em> (hopefully, out any day now). <code>?getME</code> may be useful, too -- it has the advantage that anything you find there can be safely used without worrying that the guts of <code>merMod</code> objects will change in future releases. (Once you use the <code>@</code>-accessor, all bets are off.)</p></li>
</ul>
How do I obtain latent trait scores from a merMod object in R?
<p>this is probably a "stupid" question, but I need to obtain the <strong>latent trait scores</strong> from a <em>merMod</em> object (<em>lme4</em> package). Also, I don't seem to find any explanation of the values in the merMod object. It would be helpful for me to know what the mu, wtres, eta, u, LUtx, Utx, Utr, V, and Xwts are supposed to be (generally).</p>

<p>I guess(ed) that the latent trait scores are not in the object, but need to be computed. Irtoys offers a function that does that (e.g., dpv), but requires me to have a matrix of responses that can only be 0 or 1 with no NAs. My data includes NA by design though. Also, I will be working with models that have values other than 0 and 1. Any ideas on workarounds? The Irtoys package seems to offer all I need, but if I'm not able to use it because of these limitations, that would be a pity.</p>

<p>Thank you in advance,
KH</p>