13
$\begingroup$

I am fitting the following model in "mgcv" package in R using option family=betar to predict a percentage cover response variable (cyano %):

    g6 = gam(cyano/100 ~ s(SEGLOWFLOW) + s(SEGJANAIRT) + 
             s(LOCHAB) + s(LOCSED) + s(T2PastoralHeavy) + 
             s(SEDO) + s(USDAYSRAIN) + s(USAVGSLOPE) + 
             s(USHARDNESS), data=nati1, 
             family = betar(link='logit'))

I get the following warning message:

    Warning message:
    In object$family$saturated.ll(G$y, wts, theta) :
      saturated likelihood may be inaccurate

The summary output gives me negative explained deviance values:

    R-sq.(adj) =  0.0871   Deviance explained = -29.9%
    -REML = -2370.5  Scale est. = 1         n = 463

Although the diagnostics plots (gam.check) look fine and the predictions make sense, I am worried about the warning message and the negative deviance explained value.

Any thoughts will be appreciated.

Improve this question
$\endgroup$
5
  • 1
    $\begingroup$ I tried fixing some mistakes, but I am not sure whether you are using betareg anywhere. You do use family=betar, though. Please check the accuracy of your post and pardon if my edit might have introduced any new mistakes. $\endgroup$
    – Richard Hardy
    Jul 15, 2016 at 17:18
  • 1
    $\begingroup$ Great, thanks heaps. I only used betar family in the mgcv library. $\endgroup$
    – jatalah
    Jul 18, 2016 at 0:23
  • 1
    $\begingroup$ I'm running into the same question. Is it just that REML and dev.explained don't give sensible values with betar ? $\endgroup$
    – puslet88
    Feb 23, 2019 at 14:26
  • 1
    $\begingroup$ Does your response variable contain 0's or 1's? If so, you likely need to increase eps within betar(). $\endgroup$
    – cpp
    Aug 3, 2020 at 16:35
  • $\begingroup$ @jatalah did you end up sorting out what was causing this warning message? I'm running into the same thing. $\endgroup$
    – tnt
    Mar 15 at 19:19

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Browse other questions tagged or ask your own question.