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Error fitting reduced model in bglmer for LRT

Josie Galbraith

Thu, Mar 12, 2015 4:39 PM

Thanks Vince.
So should I just use the Wald-Z output instead then? Or another method of
inference? Any ideas which is best in this situation?

The code for the temp fix didn't work for me (see below).  But that may not
be important if I use another method of inference...

Cheers,
Josie

getOption("digits"), ...) {
+   scaleString <- ""
+   scale <- crossprod(solve(x at R.scale.inv))
Error: unexpected symbol in:
"  scaleString <- ""
  scale <- crossprod(solve(x at"

+     scaleString <- paste("scale = c(", toString(round(scale[1:4],
digits)), ", ...)", sep = "")
+   } else if (nrow(scale) == 2) {
+     scaleString <- paste("scale = c(", toString(round(scale[1:4],
digits)), ")", sep = "")
+   } else {
+     scaleString <- paste("scale = ", toString(round(scale[1], digits)),
sep = "")
+   }
Error in if (nrow(scale) > 2) { : argument is of length zero

Error: unexpected symbol in "  paste("t(df = ", x at"

Error: unexpected ',' in "        ", common.scale = ","

Error: unexpected ',' in "        ")","

Error: unexpected '}' in "}"

Date: Tue, 10 Mar 2015 13:23:22 -0400

From: Vincent Dorie <vjd4 at nyu.edu>
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] Error fitting reduced model in bglmer for LRT
Message-ID: <9FBE19D0-EA83-4F5B-8333-0C52C18390D9 at nyu.edu>
Content-Type: text/plain; charset=utf-8

I don't know what exactly anova() does for glmms, but I wouldn't recommend
a likelihood ratio test to compare posterior modes unless you can be
certain the data swamp the prior.

The error you experienced is a copy/paste error on my part. You can run
the code below to fix it temporarily, until I can get a new release on CRAN.

assignInNamespace("toString.bmerTDist", function(x, digits =
getOption("digits"), ...) {
  scaleString <- ""
  scale <- crossprod(solve(x at R.scale.inv))

  if (nrow(scale) > 2) {
    scaleString <- paste("scale = c(", toString(round(scale[1:4],
digits)), ", ...)", sep = "")
  } else if (nrow(scale) == 2) {
    scaleString <- paste("scale = c(", toString(round(scale[1:4],
digits)), ")", sep = "")
  } else {
    scaleString <- paste("scale = ", toString(round(scale[1], digits)),
sep = "")
  }

  paste("t(df = ", x at df, ", ", scaleString,
        ", common.scale = ", x at commonScale,
        ")", sep="")
}, "blme")

Vince

On Mar 9, 2015, at 11:47 PM, Josie Galbraith <josie.galbraith at gmail.com>

wrote:

Hi all,

In following on from this post
<https://stat.ethz.ch/pipermail/r-sig-mixed-models/2015q1/023191.html>,
regarding using blme and fixed effect priors to address issues of

complete

separation in my data, I've come up against a problem trying to fit

reduced

models for testing the model terms using likelihood ratio tests (LRT).

Firstly, can I use LRTs (anova()) for testing the fixed effects of bglmer
models, as I would for glmer models?

If yes, then I need help understanding why I'm getting the following

error

fitting a reduced bglmer model:
"Error in if (nrow(cov) == 2) { : argument is of length zero"

This is my full model:
SE.les.mod = bglmer (LESION ~ FOOD*SEASON +(1|SITE), data = SEYE.df,

family

= binomial, fixef.prior = t(1,2.5), cov.prior = NULL)

I can fit a model without the interaction term ok:
SE.les.add = bglmer (LESION ~ FOOD+SEASON +(1|SITE), data = SEYE.df,

family

= binomial, fixef.prior = t(1,2.5), cov.prior = NULL)

But I get the error message with both of the single fixed effects models:
SE.les.FOOD = bglmer (LESION ~ SEASON +(1|SITE), data = SEYE.df, family =
binomial, fixef.prior = t(1,2.5), cov.prior = NULL)
SE.les.SEAS = bglmer (LESION ~ FOOD +(1|SITE), data = SEYE.df, family =
binomial, fixef.prior = t(1,2.5), cov.prior = NULL)

Thanks very much,
Josie



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*Josie Galbraith* MSc (hons)

PhD candidate
*University of Auckland *
Joint Graduate School in Biodiversity and Biosecurity ? School of
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*Josie Galbraith* MSc (hons)

PhD candidate
*University of Auckland *
Joint Graduate School in Biodiversity and Biosecurity ? School of
Biological Sciences ? Tamaki Campus ? Private Bag 92019 ? Auckland 1142* ?
P:* 09-373 7599 ext. 83132* ? E:* josie.galbraith at gmail.com* ? W: * UoA Web
Profile <https://unidirectory.auckland.ac.nz/profile/jgal026> and
*www.birdfeedingnz.weebly.com/* <http://birdfeedingnz.weebly.com/>

Thread (2 messages)

Josie Galbraith Error fitting reduced model in bglmer for LRT Mar 12 Vincent Dorie Error fitting reduced model in bglmer for LRT Mar 12