[R-meta] multi-model prediction with rma.mv ?
Kelly Gravuer
kelly.gravuer at gmail.com
Wed Jan 3 19:21:09 CET 2018
Dear Wolfgang,
Thank you so much - this was exactly what I needed!
Best,
Kelly
On Tue, Jan 2, 2018 at 12:46 PM, Viechtbauer Wolfgang (SP) <
wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
> Dear Kelly,
>
> If I understand you correctly, you want to obtain multimodel predicted
> values and corresponding CIs.
>
> See, for example, Anderson (2008; Model Based Inference in the Life
> Sciences: A Primer on Evidence), Chapter 5.
>
> I don't see a way to get this to work 'out of the box', but you can make
> this work with predict() from metafor and glmulti with a bit of code. To
> illustrate, I will use the same example that you linked to (i.e.,
> http://www.metafor-project.org/doku.php/tips:model_selection_with_glmulti).
> So, to start:
>
> library(metafor)
> library(glmulti)
>
> dat <- get(data(dat.bangertdrowns2004))
> dat <- dat[!apply(dat[,c("length", "wic", "feedback", "info", "pers",
> "imag", "meta")], 1, anyNA),]
>
> rma.glmulti <- function(formula, data, ...)
> rma(formula, vi, data=data, method="ML", ...)
>
> res <- glmulti(yi ~ length + wic + feedback + info + pers + imag + meta,
> data=dat,
> level=1, fitfunction=rma.glmulti, crit="aicc",
> confsetsize=128)
>
> ### get model weights
> weights <- weightable(res)$weights
>
> ### vector with the values for which you want to make a prediction
> x <- c("length"=15, "wic"=1, "feedback"=1, "info"=0, "pers"=0, "imag"=1,
> "meta"=1)
>
> ### get predicted values based on all models
>
> preds <- list()
>
> for (j in 1:length(weights)) {
>
> model <- res at objects[[j]]
> vars <- names(coef(model))[-1]
>
> ### need special handling for the intercept-only model
> if (length(vars) == 0) {
> preds[[j]] <- predict(model)
> } else {
> preds[[j]] <- predict(model, newmods=x[vars])
> }
>
> }
>
> ### multimodel prediction
> yhat <- sum(weights * sapply(preds, function(x) x$pred))
> yhat
>
> ### multimodel SE (based on the unconditional variance)
> se <- sqrt(sum(weights * sapply(preds, function(x) x$se^2 + (x$pred -
> yhat)^2)))
> se
>
> ### multimodel 95% CI
> yhat + c(-1,1)*qnorm(.975)*se
>
> That's basically it. You should be able to adapt this to your case.
>
> Best,
> Wolfgang
>
> -----Original Message-----
> From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-
> bounces at r-project.org] On Behalf Of Kelly Gravuer
> Sent: Tuesday, 02 January, 2018 19:43
> To: r-sig-meta-analysis at r-project.org
> Subject: [R-meta] multi-model prediction with rma.mv ?
>
> Hello all,
> Using the rma.mv() function in metafor, I'm running models with two
> random effects and four moderator variables. The format of the model
> is:
>
> m1 <- rma.mv(yi ~ mod1 + mod2 + mod3 + mod4, vi, random = list(~ 1 |
> rand1, ~1 | rand2), tdist=TRUE, method="ML", data=d)
>
> I would like to do two things: (1) understand the relationship of each
> of the four moderator variables to the effect size; (2) predict an
> effect size with confidence interval (CI) for some new suites of
> values of the moderators.
>
> I have found multi-model inference using glmulti() to be a very useful
> approach to my first objective, using the methods described here:
> http://www.metafor-project.org/doku.php/tips:model_selection_with_glmulti.
> I would now like to use this multi-model suite to make predictions
> with CIs.
>
> I realize I can run the model as specified above (including all four
> moderators as main effects) and then use predict.rma() to generate
> estimated effect sizes + CIs. I realize I can also calculate an
> effect size estimate that is informed by the multiple model fits using
> the coefficient estimates in the multi-model coefficient table.
> However, I don't know how to get CIs for these effect size estimates
> that are informed by the multiple model fits.
>
> I think one way to do this would be to write a predict function that
> links rma.mv with glmulti. I don't feel up to this task myself, but
> wanted to inquire whether anyone on this list has written such a
> function? Or alternatively, does anyone have other suggestions for
> how to use the information from the multiple model fits to inform the
> predicted CIs?
>
> Thanks so much for any thoughts,
> Kelly
>
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