[R-sig-ME] post hoc tests for glmmTMB

[Lenth, Russell V]

With emmeans/lsmeans, it turns out the mistake was in sourcing that obsolete lsmeans-methods.R code. Please  erase all functions in your workspace that begin with "recover.data" or "lsm.basis" -- then you can obtain EMMs without problems, because emmeans support is built-in to the cirrent glmmTMB package. For example:

    require(glmmTMB)
    require(emmeans)

    example("glmmTMB")
    # ... quite a few lines excluded here

    emmeans(m2, "spp")
#   spp        emmean        SE  df   lower.CL  upper.CL
#    GP     0.10429796 0.2629172 626 -0.4120086 0.6206045
#    PR    -0.85940395 0.6723753 626 -2.1797882 0.4609803
#    DM     0.27498137 0.2456147 626 -0.2073472 0.7573099
#    EC-A  -0.28275838 0.3610020 626 -0.9916800 0.4261633
#    EC-L   0.59224612 0.2581265 626  0.0853474 1.0991448
#    DES-L  0.69378481 0.2410053 626  0.2205080 1.1670616
#    DF    -0.00896838 0.2496003 626 -0.4991237 0.4811869

Russ

-----Original Message-----
From: Lenth, Russell V 
Sent: Friday, November 9, 2018 10:22 AM
To: r-sig-mixed-models using r-project.org; 'Aoibheann Gaughran' <gaughra using tcd.ie>
Subject: RE: 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 using tcd.ie>
To: r-sig-mixed-models using r-project.org
Subject: [R-sig-ME] post hoc tests for glmmTMB
Message-ID:
	<CAN=0SEmQE6f=OAofUeSg_e2f-O2tnfUepqUSRO28onLw_dgh1w using mail.gmail.com>
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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