<html><head><base href="x-msg://13/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Charlotte,<div>I suspect that the pdf is not as up to date as the help file. I checked the help file ?do_admb and saw that there's a parameter called re, but not one called re_vectors.</div><div><br></div><div><table summary="R argblock" style="font-family: Times; position: static; z-index: auto; "><tbody><tr valign="top"><td><code>"re</code></td><td>a named list of the identities and dimensions of any random effects vectors or matrices used in the TPL file</td></tr></tbody></table>"<div>Try replacing "re_vectors" with "re" in your call to do_admb.</div><div>cheers,</div><div>Mollie</div><div><br></div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><br><br></span>
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<br><div><div>On 8 Sep 2011, at 5:26 PM, Charlotte Boyd wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-US" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">Hi</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">I would like to use R2admb with a random effects model. When I try the toy example in the vignette, I get the following error message:</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">Error in do_admb("test", data = tmpdat, re = TRUE, params = list(beta = rep(0, :</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> unused argument(s) (re_vectors = list(u_herd = ncol(Zherd)))</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">I’m using R version 2.13.1 (2011-07-08), and have tried this on other computers and got the same error message. I’ve copied all the code from R2admb.pdf (Bolker, 2011), but for completeness, the code I’m using and the ‘bare-bones’ .tpl file are below. It’s probably something simple I’m missing – I’d appreciate any suggestions on what that is.</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">With many thanks</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">Charlotte</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><i><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(49, 132, 155); ">Charlotte Boyd</span></i></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><i><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(49, 132, 155); ">School of Aquatic and Fishery Sciences</span></i></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><i><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(49, 132, 155); ">University of Washington</span></i></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><i><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(49, 132, 155); ">1122 NE Boat St Rm 116</span></i></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><i><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(49, 132, 155); ">Seattle WA 98105</span></i></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">library(R2admb)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">library(lme4)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), family = binomial, data = cbpp)</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">X <- model.matrix(~period,data=cbpp)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">Zherd <- model.matrix(~herd-1,data=cbpp)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">tmpdat <- list(X=X,Zherd=Zherd, incidence=cbpp$incidence,size=cbpp$size, nobs=nrow(cbpp))</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">d1 <- do_admb("test",data=tmpdat,re=TRUE,params=list(beta=rep(0,ncol(X)),sigma_herd=0.1),bounds=list(sigma_herd=c(0.0001,20)),re_vectors=list(u_herd=ncol(Zherd)),</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">run.opts=run.control(checkdata="write",checkparam="write"),mcmc=TRUE,mcmc.opts=mcmc.control(mcmcpars=c("beta","sigma_herd")))</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "># .tpl file</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">PARAMETER_SECTION</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> vector herdvec(1,nobs)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> vector eta(1,nobs)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> vector mu(1,nobs)</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); ">PROCEDURE_SECTION</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> herdvec = sigma_herd*(Zherd*u_herd);</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> eta = X*beta; // form linear predictor</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> eta += herdvec; // augment with random effects</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> mu = pow(1.0+exp(-eta),-1.0); // logistic transform</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> // binomial log-likelihood (unnormalized)</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> f -= sum(elem_prod(incidence,log(mu))+</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> elem_prod(size-incidence,log(1.0-mu)));</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> f+=0.5*norm2(u_herd); // log-prior (standard normal)</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Trebuchet MS', sans-serif; color: rgb(31, 73, 125); "> </span></p></div>_______________________________________________<br>Users mailing list<br><a href="mailto:Users@admb-project.org" style="color: blue; text-decoration: underline; ">Users@admb-project.org</a><br><a href="http://lists.admb-project.org/mailman/listinfo/users" style="color: blue; text-decoration: underline; ">http://lists.admb-project.org/mailman/listinfo/users</a><br></div></span></blockquote></div><br></div></body></html>