[R-sig-ME] Model diagnostics show slope in residuals plot and slope on the observed vs fitted plot is different than y = x

Carlos Familia carlosfamilia at gmail.com
Mon Oct 3 10:34:50 CEST 2016


The image can be found here https://s18.postimg.org/rbx2vh2ex/Pasted_Graphic_4.png <https://s18.postimg.org/rbx2vh2ex/Pasted_Graphic_4.png>

Best regards,
Carlos Família

> On 3 Oct 2016, at 08:50, Thierry Onkelinx <thierry.onkelinx at inbo.be> wrote:
> Dear Carlos,
> Your plot got stripped from your mail. Try sending it as pdf or put it someone online and send us the URL.
> Best regards,
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest 
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance 
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner 
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
> 2016-10-02 17:57 GMT+02:00 Carlos Familia <carlosfamilia at gmail.com <mailto:carlosfamilia at gmail.com>>:
> Hello,
> I have in hands a quite large and unbalanced dataset, for which a Y continuous dependent variable was measured in 3 different conditions (C) for about 3000 subjects (ID) (although, not all subjects have Y values for the 3 conditions). Additionally, there is continuous measure W which was measured for all subjects.
> I am interested in testing the following:
> - Is the effect of W significant overall
> - Is the effect of W significant at each level of C
> - Is the effect of C significant
> In order to try to answer this, I have specified the following model with lmer:
> lmer( Y ~ W * C + (1 | ID), data = df)
> Which seems to proper reflect the structure of the data (I might be wrong here, any suggestions would be welcome).
> However when running the diagnostic plots I noticed a slope in the residuals plot and a slope different than y = x for the observed vs fitted plot (as shown bellow). Which made me question the validity of the model for inference.
> Could I still use this model for inference? Should I specify a different formula? Should I turn to lme and try to include different variances for each level of conditions (C)? Any ideas?
> I would be really appreciated if anyone could help me with this.
> Thanks in advance,
> Carlos Família
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