Hello, all! So, as stated in the title, the Lme4 package used to output p-values for the fixed effects. What happened?! Literally 2 weeks ago, I ran code, got output with no errors, and had p-values listed for my fixed effects. Now, running THE SAME CODE with THE SAME DATASET (nothing at all has changed, not the data, not my computer, not R, nothing), I do not get p-values. I've tried other computers, I've tried resetting R. Any ideas? I'd really need to get some p-values. Thank you! D
Lme4 Package Help!
5 messages · Daniel Mello, Ben Bolker, Doran, Harold +1 more
Daniel Mello <dmello2 <at> ucmerced.edu> writes:
Hello, all! So, as stated in the title, the Lme4 package used to output p-values for the fixed effects. What happened?! Literally 2 weeks ago, I ran code, got output with no errors, and had p-values listed for my fixed effects. Now, running THE SAME CODE with THE SAME DATASET (nothing at all has changed, not the data, not my computer, not R, nothing), I do not get p-values. I've tried other computers, I've tried resetting R. Any ideas? I'd really need to get some p-values. Thank you! D
Applying my mind-reading skills, I'm going to guess that you are running anova() and that you had previously loaded the lmerTest package (which extends the anova() method from lme4 in several ways), and that now you are loading only the base lme4 package and not the lmerTest package. If my guess isn't right, then you're going to have to provide more information. Follow-ups to r-sig-mixed-models at r-project.org , please . Ben Bolker
Daniel Lmer has never returned p-values from a model summary; this is a well-known and discussed issue. You must have post-processed the data in some way to get the p-values. Our only way of helping is for you to provide sample code on what you did -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Daniel Mello Sent: Thursday, November 06, 2014 6:24 PM To: r-help at r-project.org Subject: [R] Lme4 Package Help! Hello, all! So, as stated in the title, the Lme4 package used to output p-values for the fixed effects. What happened?! Literally 2 weeks ago, I ran code, got output with no errors, and had p-values listed for my fixed effects. Now, running THE SAME CODE with THE SAME DATASET (nothing at all has changed, not the data, not my computer, not R, nothing), I do not get p-values. I've tried other computers, I've tried resetting R. Any ideas? I'd really need to get some p-values. Thank you! D ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
1 day later
Doran, Harold <HDoran <at> air.org> writes:
Daniel Lmer has never returned p-values from a model summary; this is a well-known and discussed issue. You must have post-processed the data in some way to get the p-values.
But it's worth noting that lmerTest does, and the way it works makes it pretty hard to see that the results are not coming from vanilla lme4. If this is what happened I wouldn't blame the OP for getting confused.
Actually, I believe that for a brief period (around 2006) lmer did return p-values (chisq-based), but then 2006 is a long time ago... If the question pertains p-values in the usual output of coef( summary( model ) ), I'll just mention that with doBy and pbkrtest you can do linest( model, diag(1, length(coef(model)) ) ) With the next release of doBy you do not need to specify the diag-stuff, but for now you have to. Cheers S?ren |-----Original Message----- |From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] |On Behalf Of Ben Bolker |Sent: 9. november 2014 03:48 |To: r-help at stat.math.ethz.ch |Subject: Re: [R] Lme4 Package Help! | |Doran, Harold <HDoran <at> air.org> writes: | |> |> Daniel |> |> Lmer has never returned p-values from a model summary; this is a |> well-known and discussed issue. You must have post-processed the data |> in some way to get the p-values. | | But it's worth noting that lmerTest does, and the way it works makes it |pretty hard to see that the results are not coming from vanilla lme4. If |this is what happened I wouldn't blame the OP for getting confused. | |______________________________________________ |R-help at r-project.org mailing list |https://stat.ethz.ch/mailman/listinfo/r-help |PLEASE do read the posting guide http://www.R-project.org/posting- |guide.html |and provide commented, minimal, self-contained, reproducible code.