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[R-meta] Query model structure rma.mv

3 messages · Sybryn Maes, Wolfgang Viechtbauer

Original
Sybryn Maes
# 
Dear colleagues,

I have three questions regarding a meta-analysis multivariate model
structure I am using for my dataset that is complex in the following way:
There are multiple sites, and within those sites, multiple years of data
can occur. These years are not always the same, so one site can have data
for eg 2003 and 2004, whereas another site could have data only for 2005.
Another one can have data for 2001 to 2010 every year available.

I propose the following structure for my data :

*metamodel <- rma.mv
<http://rma.mv/>(Hedges_SMD, Hedges_SMD_VARIANCE, random=list(~ 1 |
Site_ID / Observation_ID , ~ Year |  Site_ID ),*

*struct="CAR", data=SMD_SITELEVEL)*


I am including the second part of the random structure list to account for
potential autocorrelation and non-independence between the different years
within a same site.

However, I have the following questions when looking at the output and when
trying to visualize the results (estimates + CIs) with a simple forest plot:


1) Does the "*forest*" command also work with complex rma.mv structures -
i.e. for making forest plots? I have an outcome and do not get errors, but
I cannot find anywhere

 whether it is appropriate to use for these multivariate objects.

2) When including my CAR structure, the *weights *change when I show them
in the forest plot (using "showweights=TRUE" to visualize them). This I
find strange as the sample

sizes are not changing in any way. Why could this be?
3) In order to *diagnostize *whether the non-independence and
autocorrelation is appropriately taken into account, I thought of running a
variogram with and without the CAR structure in the model, and an acf()
command. However, none of these two tools actually shows me that the
autocorrelation is reduced or removed. What could be the reason for this?
Could I find out in another way whether it is a "better" model with the CAR
structure included?

Thank you for any assistance/advice!

Cheers,
Sybryn
4 days later
Wolfgang Viechtbauer
# 
Dear Sybryn,

Please see below for my responses.

Best,
Wolfgang
Yes, you can use forest() in combination with rma.mv() objects. The function doesn't do anything special for 'rma.mv' objects, so it just shows the individual estimates (plus it adds the pooled estimate at the bottom if the model doesn't include any moderators). If you want to indicate some kind of grouping visually, you have to take some extra steps. See, for example, the last example at:

https://wviechtb.github.io/metafor/reference/forest.rma.html
Adding or changing the random effects structure impacts the weighting structure. This is to be expected.
I don't know what commands you ran, but if you looked at the ACF of the residuals within studies, then those will still be autocorrelated, even if the autocorrelation is accounted for in the model. Here is an example (not really a meta-analysis, so 'yi' are raw data, but this illustrates the principle and simplifies things since we don't have to worry about a nested structure of observations within studies):

############################

library(metafor)

sigma <- 0.5
rho   <- 0.6
n     <- 1000
time  <- 1:n
const <- rep(1, n)

yi <- arima.sim(model=list(ar=rho), n=n) * sqrt(1-rho^2) * sigma

# treat all observations as independent
res1 <- rma.mv(yi, 0, random = ~ 1 | time)
res1

# assume an AR1 structure for the observations
res2 <- rma.mv(yi, 0, random = ~ time | const, struct="AR")
res2

acf(resid(res1))
acf(resid(res2))

# both ACFs show the same autocorrelation in the residuals

############################

To 'get rid' of the autocorrelation in the residuals, one has to compute what are sometimes called 'normalized residuals' (see Pinheiro & Bates, 2000) or 'Choleksy residuals'. Continuing with the example:

acf(resid(res1, type="cholesky"))
acf(resid(res2, type="cholesky"))

The ACF for res2 shows no noteworthy autocorrelation.

For meta-analytic data, you would have to look at the residuals within studies. Also, there is the issue of how one should deal with any random effects that are 'higher' up in the hierarchy of your model, that is, when computing the residuals, should one compute them only around the fixed effects or should one remove/partial out the contributions of any additional random effects? This gets complicated quickly, so instead, I would just suggest to run a LRT comparing the two models:

anova(res1, res2)

This will tell you whether the model with the autocorrelation structure fits significantly better than the one without.
9 days later
Sybryn Maes
# 
Dear Wolfgang,

Thanks a lot for your reply and clarificaitons. About part 3): anova shows
there is a significant improvement in the model fit when including the CAR
structure and acf() now indeed shows reductions in AC. I now feel confident
of the final model.

All the best,
Sybryn




Op di 13 jul. 2021 om 14:17 schreef Viechtbauer, Wolfgang (SP) <
wolfgang.viechtbauer at maastrichtuniversity.nl>: