I'm currently translating existing code from SAS to R. I'm working on longitudinal data (CD4 count over time). I have the following SAS code :

Proc mixed data=df;
class NUM_PAT;
model CD4t=T /s ;
repeated / sub=NUM_PAT type=sp(pow)(T);

The SAS spatial power covariance structure is useful for unequally spaced longitudinal measurements where the correlations decline as a function of time (as shown by the picture below). Spatial Power Covariance Structure

I think I have to use gls( ) from {nlme} since I don't have any random effects. As R 'only' provides "spherical", "exponential", "gaussian", "linear", and "rational" as correlation spatial structures, my guess is that I need to use corSpatial plus a weights argument.

I tried the following code, but it doesn't work :

gls(CD4t~T, data=df, na.action = (na.omit), method = "ML",
corr=corCompSymm(form=~1|NUM_PAT), weighhts=varConstPower(form=~1|T))

What am I doing wrong ?

Thanks for any help.


The spatial power covariance structure is a generalization of the first-order autoregressive covariance structure. Where the first-order autoregressive structure assumes the time points are equally spaced, the spatial power structure can account for a continuous time point. In reality, we could just forget the first-order autoregressive structure entirely, because if we fit the spatial power structure when the data are equally spaced we'll get the same answer as when using the first-order autoregressive structure.

All that aside, the correlation function you're looking for is corCAR1(), which is the continuous first-order autoregressive structure. If you're looking to duplicate what you fit in SAS, then the code you're looking for is:

gls(CD4t~T, data=df, na.action = (na.omit), method = "REML",

Of course, you don't need to specify method = "REML", since, as in SAS, the default method in gls() is already restricted maximum likelihood.

| cite | improve this answer | |

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.