R-sig-mixed-models Digest, Vol 143, Issue 12

I screwed up -- in a kind of brown-paper-bag way...

I think it may work with emmeans if you do this:

    recover.data <- function(object, ...) UseMethod("recover.data")
    lsm.basis <- function(object, ...) UseMethod("lsm.basis")
    recover.data.default <- function(object, ...) emmeans::recover_data(object, ...)
    lsm.basis.default <- function(object, ...) emmeans::emm_basis(object, ...)

Hope this helps.

Russ Lenth

Russell V. Lenth? -? Professor Emeritus
Department of Statistics and Actuarial Science?? 
The University of Iowa ?-? Iowa City, IA 52242? USA?? 
Voice (319)335-0712 (Dept. office)? -? FAX (319)335-3017



-----Original Message-----

Message: 1
Date: Fri, 9 Nov 2018 12:24:47 +0000
From: Aoibheann Gaughran <gaughra at tcd.ie>
To: r-sig-mixed-models at r-project.org
Subject: [R-sig-ME] post hoc tests for glmmTMB
Message-ID:
	<CAN=0SEmQE6f=OAofUeSg_e2f-O2tnfUepqUSRO28onLw_dgh1w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear list,

I am trying to perform post hoc tests on a glmmTMB model. I would normally use car::Anova and mulgcomp::glht on my glmms (lmers). However, these functions do not appear to be working for glmmTMB (when I run the model as an lmer they work fine). I have also tried lsmeans and emmeans but they do not appear to support glmmTMB either (although it appears they used to). I have found various treads online suggesting that these functions should work with TMB but they date back a few months.

I am using the most up to date versions of R (3.5.1) and have updated all of my packages e.g. glmmTMB 0.2.2.0, lsmeans 2.30-0

The following are the error messages that I receive:

Anova(topmodTRFETE, type = 2)Error in I.p[c(subs.relatives, subs.term), , drop = FALSE] :

subscript out of bound

summary(glht(topmodTRFETE, linfct = mcp(roadworks = "Tukey")), test = adjusted("holm"))Error in modelparm.default(model, ...) :

dimensions of coefficients and covariance matrix don't match

source(system.file("other_methods","lsmeans_methods.R",package="glmmTMB"))> lsmeans(topmodTRFETE, pairwise ~ roadworks, adjustSigma = TRUE, adjust = "holm")Error in ref_grid(object, ...) :

Can't handle an object of class  ?glmmTMB?
 Use help("models", package = "emmeans") for information on supported models.> rw.emm.s <- emmeans(topmodTRFETE, "roadworks")Error in ref_grid(object, ...) :
  Can't handle an object of class  ?glmmTMB?
 Use help("models", package = "emmeans") for information on supported models.


Can any point me in the direction of a workaround for performing posthocs on my glmmTMB model?

Many thanks,

--
Aoibheann Gaughran

Behavioural and Evolutionary Ecology Research Group Zoology Building School of Natural Sciences Trinity College Dublin Dublin 2 Ireland
Phone: +353 (86) 3812615