CODEWITHSUNDEEP
routputcorrelationmixed-models
Jens
Jens

Reputation: 2439

How to suppress correlation table in LME?

In the standard example of the lme() function in the nlme package of R:

fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
summary(fm2)

there appears a correlation table:

Correlation: 
          (Intr) age   
age       -0.813       
SexFemale -0.372  0.000

which can be huge if there are many factor combinations involved.

Is there any way to suppress the output in the summary command? I know that I can use 

   print(fm2, cor=F)

but this does not show me the rest of the usual output for example no p-value calculation.

Upvotes: 6

Views: 2192

Answers (3)

Wolfgang
Wolfgang

Reputation: 3395

I just recently ran into the same issue when fitting models with lots of fixed effects and the correlation table was huge and really cluttered up the output. Looking at print.summary.lme() (which isn't exported, so you have to use nlme:::print.summary.lme) shows that the part comes from these lines:

if (nrow(x$tTable) > 1) {
    corr <- x$corFixed
    class(corr) <- "correlation"
    print(corr, title = " Correlation:", ...)
}

as already pointed out by Ben. Instead of rewriting/replacing the entire function, we can also use a simple trick, replacing nlme:::print.correlation (which is what is actually doing the printing of the correlation matrix) with our own print method for objects of class correlation. This can be done with:

assignInNamespace("print.correlation", function(x, title) return(), ns="nlme")

Now the correlation matrix will be omitted, but you get the remaining output.

Upvotes: 3

bokov
bokov

Reputation: 3534

Or, more concisely, summary(fm2)$tTable

Upvotes: 3

Ben Bolker
Ben Bolker

Reputation: 226192

Looking at nlme:::print.summary.lme I don't see a way to suppress the correlation matrix printing (although you could create a hacked version of that function removing the if clause beginning if (nrow(x$tTable)>1) ...)

Perhaps it would be useful to you to be able to print just the summary of the fixed-effect parameters ... ?

 printCoefmat(summary(fm2)$tTable)

Upvotes: 4

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