I’m referring to the paper “How to compare cross-lagged associations in a multilevel autoregressive model.” from Schuurman et al. (http://dx.doi.org/10.1037/met0000062). The authors show how they use Bayesian multivariate response multilevel models (using Bugs, code available here: http://supp.apa.org/psycarticles/supplemental/met0000062/met0000062_supp.html) to fit a cross-lagged panel model in a multilevel design.
My question is, how this would translate into brms, and if this is currently possible? I have no such comprehensive statistical background to understand the formulas in detail. What I find confusing is that the authors state at p. 208 that “The model as defined in Equations 1–3 forms level one of the multilevel model.” - which seems to me that level 1 includes all observations. However, some sentences later they say that “…whereas the model defined at level one is identical to an n=1 autoregressive time series model”. So is level 1 defined as a n=1 model, or does it include all observations, or am I confusing something here?
Let’s say, we have 3 time points and x and y were measured at each time point, while we have covariates that are constant accross all time points. From what I understood, the model would be written in brms like this:
Edited Code Example, this addresses Paul’s first comment
f1a <- bf(x2 ~ x1 + y1 + covariate + (1 |id1|subject))
f1b <- bf(y2 ~ x1 + y1 + covariate + (1 |id1|subject))
f2a <- bf(x3 ~ x2 + y2 + covariate + (1 |id1|subject))
f2b <- bf(y3 ~ x2 + y2 + covariate + (1 |id1|subject))
# maybe also set_rescor(TRUE)?
model <- brm(f1a + f1b + f2a + f2b + set_rescor(FALSE), data = data)
Is this correct? Would this describe a cross-lagged panel model with random intercept structure?
From quickly looking at the paper, I have two suggestions.
- You should use x1 and y1 as predictors of x2 and y2 (not the other way round). Same for the 2nd time point.
- You should set rescor to TRUE.
True, this is what I always do in SEM/lavaan - no idea, why I switched it in my notation above. Would you say that the above model represents a cross-lagged multilevel panel model? I’m not sure in which way the paper’s authors consider the n=1 autoregressive model… But maybe that’s already covered by using
subject as random intercept (and more complex nested strucures would be written as nested random intercepts then…).
I do think it represents a cross-lagged panel model. From my understanding, the autoregressive part is just that y3 is regressed on y2 which is in turn regressed on y1 (same for x). But I haven’t read the paper thoroughly enough to be sure they mean exactly that.
Ok, thanks! I consider this question as solved, but probably do not tag the thread als “solved”, so others may get in into this discussion as well.
Just running one of these models myself trying to replicate Lavaan findings in BRMS.
Typically in a CLPM you model covariance in outcomes and predictors. Setting
set_rescor(TRUE) addresses the former but do we need to do anything to capture the latter ?
CLPMs assume equal spacing between waves, but that isn’t always the case and I suspect that it isn’t necessary in a multilevel setting. Is it possible to extend the syntax to account for unequal spacings between waves? Maybe by including time as a covariate?
If you have covariates, you could include:
bf(x1 ~ covariate + (1 |id1|subject))
bf(y1 ~ covariate + (1 |id1|subject))
f1a <- bf(x1 ~ covariate + (1 |id1|subject))
f1b <- bf(y1 ~ covariate + (1 |id1|subject))
f2a <- bf(x2 ~ x1 + y1 + covariate + (1 |id1|subject))
f2b <- bf(y2 ~ x1 + y1 + covariate + (1 |id1|subject))
f3a <- bf(x3 ~ x2 + y2 + covariate + (1 |id1|subject))
f3b <- bf(y3 ~ x2 + y2 + covariate + (1 |id1|subject))
model <- brm(f1a + f1b + f2a + f2b + f3a + f3b + set_rescor(TRUE), data = data)
If I’m not mistaken, this should take care of the correlations for the initial predictors. The rest of the predictors are outcomes too so should be accounted for.
I guess we could indeed “weight” the autoregressive predictors according their distance or let the model find out itself (using an interaction or something similar) how the autoregressive effects change of distance between time points.
So normally, I think, one would fit a model like this using the “long” data in which one row represents one person at one time (so there are subjects * times rows in total).
You could generate the lagged variables prior to sending to
brms, like this
arrange(time, .by_group = TRUE) %>%
y_lag = lag(y),
x_lag = lag(x)
Assuming the long data had columns
covariate to begin with.
So in this case, we could adapt to this
f1 <- bf(y ~ y_lag + x_lag + covariates + (y_lag | id)
f2 <- bf(x ~ x_lag + y_lag + covariates + (x_lag | id)
model <- brm(f1 + f2 + set_rescor(TRUE), data = long_data)
Is that right? Note that I add a random slope for the autoregressive parameter because that’s what that research group normally does and it comes closest to have a time series model at the subject level while still applying shrinkage to those subject-level estimates.
Yes, this looks reasonable to me. What to do with the covariate exactly depends on the research question I guess, but for a main effect of a covariate that does not vary across time within the same person, your approach looks good.
Hey I was working on this a while ago, just got my revise and resubmit last week actually. Just to add some of the challenges I ran into as follows.
Typically with these models you want to model the residual correlations on the predictors and the residuals of their lagged effects.
You might try something as follows to get around this…
bf(y_lag ~ 1) +
bf(x_lag ~ 1) +
bf(y ~ y_lag + x_lag + covariates + (y_lag | id) +
bf(x ~ x_lag + y_lag + covariates + (x_lag | id) +
data = long_data
The problem here is that you then model residual correlations of
y, etc. which you might not want. To my knowledge there is no way to choose which residual correlations you want to model in
I drew this in a state of the art SEM plotter, MS Paint. The red arrow is the bit I think we would struggle with but everything else is quite easily achievable.
Hopefully this is of some interest to you, gotta start paying back the help I get on here !
@paul.buerkner, in line with your comments here, could we fit a model with correlated residuals without the problem @haututu mentions as follows?
bf(y_lag ~ 1 + (1 |a| obs)) +
bf(x_lag ~ 1 + (1 |a| obs)) +
bf(y ~ y_lag + x_lag + covariates + (y_lag | id) + (1 |b| obs)) +
bf(x ~ x_lag + y_lag + covariates + (x_lag | id) + (1 |b| obs)) +
data = long_data
obs is the observation/row number?
@jackbailey the problem with this approach when using normal response distributions is that we have two residual SDs battling for the same information, first the distributional parameter
sigma and second the SD of
obs. This will likely yield a badly sampling model.
Adding to what Paul said - I was suspicious that you could get this to converge and alas, I tried my best but couldnt get a decent enough sampling model.
Oh well. I guess we’ll just have to wait for brms 3.0 ;)