[R-meta] Calculating conditional and marginal r-squared values for rma.mv models in metafor

Sun Sep 24 20:27:45 CEST 2017

Hello,

Thanks to Wolfgang for pointing me in the direction of this list-serve!

I am currently revising a manuscript that uses metafor to investigate how
sea surface temperature stress affects coral bleaching and mortality during
El Niño events. We are using linear mixed effects models to take into
account within-study variance, with study (ACC) as a random factor in our
model. To do this, we are using rma.mv. In our simplest model, this looks
like this: 

> cover.rma <- rma.mv(yi, vi, random=~1|ACC, method="REML",
data=cover.hedges) 

> cover.rma

Multivariate Meta-Analysis Model (k = 192; method: REML)

Variance Components: 

            estim    sqrt  nlvls  fixed    factor

sigma^2    2.3650  1.5378     29     no        ACC

Test for Heterogeneity: 

Q(df = 191) = 1355.9701, p-val < .0001

Model Results:

estimate       se     zval     pval    ci.lb    ci.ub

 -1.5225   0.2946  -5.1682   <.0001  -2.1000  -0.9451      *** 

---

Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

We have also used glmulti (as explained here
http://www.metafor-project.org/doku.php/tips:model_selection_with_glmulti),
to conduct coefficient selection, which looks like this (output truncated
for brevity).

> cov <- glmulti(yi~DHWtodate+Timelagtodate+tmean+tvar,
random=list("~1|ACC"), # First try the full model with all 4 potential
moderators

+                 data=cover.hedges, fitfunction = rma.glmulti, level=2,
crit="aicc") # Level 2 looks at the interactions between all moderators.
AICc allows for correction of a small N

Initialization...

TASK: Exhaustive screening of candidate set.

Fitting...

After 50 models:

Best model: yi~1+tmean:DHWtodate+tvar:tmean Crit= 780.334181647103 Mean
crit= 806.821778458654 .

After 1050 models:

Best model: yi~1+DHWtodate+tmean+Timelagtodate:DHWtodate+tmean:DHWtodate

Crit= 773.219300469166

Mean crit= 776.66700421609

Completed.

> print(cov) # View summary of cov model

glmulti.analysis

Method: h / Fitting: rma.glmulti / IC used: aicc

Level: 2 / Marginality: FALSE

From 100 models:

Best IC: 773.219300469166

Best model:

[1] "yi ~ 1 + DHWtodate + tmean + Timelagtodate:DHWtodate + tmean:DHWtodate"

Evidence weight: 0.0488927941262297

Worst IC: 777.81840821166

8 models within 2 IC units.

90 models to reach 95% of evidence weight.

> tmp <- weightable(cov) # Save tmp weightable for cov2 tmp <- 

> tmp[tmp$aicc <= min(tmp$aicc) + 10000,] tmp # print AICc and weights for
all models

  model         aicc     weights

1 yi ~ 1 + DHWtodate + tmean + Timelagtodate:DHWtodate + tmean:DHWtodate
773.2193 0.048892794

2 yi ~ 1 + DHWtodate + tmean + tmean:DHWtodate + tvar:DHWtodate +
tvar:Timelagtodate         773.9826 0.033380831

3 yi ~ 1 + DHWtodate + tvar + tmean:DHWtodate + tvar:tmean
774.2527 0.029163932

4 yi ~ 1 + DHWtodate + tvar + tmean:DHWtodate
774.8099 0.022072363

5 yi ~ 1 + DHWtodate + tmean + tvar + Timelagtodate:DHWtodate +
tmean:DHWtodate                        774.9541 0.020537024

6 yi ~ 1 + DHWtodate + tmean + Timelagtodate:DHWtodate + tmean:DHWtodate +
tvar:tmean               775.0963 0.019127989

7 yi ~ 1 + DHWtodate + tmean + Timelagtodate:DHWtodate + tmean:DHWtodate +
tvar:DHWtodate               775.1307 0.018801511

8 yi ~ 1 + DHWtodate + tmean + Timelagtodate:DHWtodate + tmean:DHWtodate +
tvar:Timelagtodate               775.1505 0.018616442

> cov.summ <- summary(cov at objects[[1]]) # create summary object for data 

> cov.summ

Multivariate Meta-Analysis Model (k = 192; method: ML)

   logLik   Deviance        AIC        BIC      AICc

-380.3826   588.5923   772.7652   792.3102 773.2193  

Variance Components: 

            estim    sqrt  nlvls  fixed            factor

sigma^2    2.2116  1.4872     29     no        ACC

Test for Residual Heterogeneity: 

QE(df = 187) = 1117.8900, p-val < .0001

Test of Moderators (coefficient(s) 2,3,4,5): 

QM(df = 4) = 82.9952, p-val < .0001

Model Results:

                         estimate      se intrcpt                   14.4108
3.0184 DHWtodate                 -0.6322  0.2191 tmean
-0.5737  0.1103 DHWtodate:Timelagtodate   -0.0001  0.0000 DHWtodate:tmean
0.0228  0.0086

                            zval    pval intrcpt                   4.7743
<.0001 DHWtodate                -2.8858  0.0039 tmean
-5.2030  <.0001 DHWtodate:Timelagtodate  -2.1840  0.0290 DHWtodate:tmean
2.6613  0.0078

                           ci.lb    ci.ub intrcpt                   8.4948
20.3268  *** DHWtodate                -1.0617  -0.2028   ** tmean
-0.7898  -0.3576  *** DHWtodate:Timelagtodate  -0.0001  -0.0000    *
DHWtodate:tmean           0.0060   0.0395   **

---

Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

We report the fsn for the model without coefficients, as well as the AICc
for the top models with coefficients (within 2AICc units of the best model).

Our reviewer has asked for a measure of model performance:

"I don't see a clear measure of model performance beyond AICc. This is
concerning as most readers will be looking for an R2, deviance explained or
something similar, particularly from linear models. Were the fits poor?
Either way you need to report these values, otherwise it's hard for the
reader to judge how much we should be interpreting the models."

I understand that it is not possible to calculate standard R2 values from
linear mixed effects models, and that pseudo-r2s are potentially
questionable (see Robert Long's paragraph here
https://stats.stackexchange.com/questions/111150/calculating-r2-in-mixed-mod
els-using-nakagawa-schielzeths-2013-r2glmm-me), but that conditional-r2 and
marginal-r2 (Nakagawa & Schielzeth 2012) are potential candidates for
demonstrating model fit. I see that these metrics are implemented in MuMIn
(https://ecologyforacrowdedplanet.wordpress.com/2013/08/27/r-squared-in-mixe
d-models-the-easy-way/, r.squaredGLMM(x)
https://cran.r-project.org/web/packages/MuMIn/MuMIn.pdf) and in piecewiseSEM
(sem.model.fits
https://jonlefcheck.net/2013/03/13/r2-for-linear-mixed-effects-models/),
however neither of  these packages/functions can utilize a rma (or rma.mv)
object. I have also looked at the original equations from Nakagawa and
Schielzeth, but am having trouble understanding how they and the output of
our models fit together, given that only one metric of variance is supplied
in the output (sigma^2).

Can anyone point me in the right direction of either a) why it isn't
possible to calculate conditional & marginal-r2 for an rma.mv object, b) how
to calculate conditional & marginal-r2 for our model, or c) if there is a
better metric to demonstrate model fit in this situation?

Please let me know if I have misunderstood anything, or if I can provide any
additional information that would assist with discussing my question.

Thanks in advance!

All the best,

Danielle

-- 

Danielle Claar

PhD Candidate - University of Victoria

PO Box 1700 STN CSC

Victoria, BC, V8W 2Y2 Canada

dclaar at uvic.ca

danielleclaar.weebly.com

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