[R] denominator degrees of freedom and F-values in nlme

From: M R Robinson <matthew.r.robinson_at_ed.ac.uk>
Date: Sun 09 Jul 2006 - 08:41:51 EST


I am struggling to understand how denominator degrees of freedom and subsequent significance testing based upon them works in nlme models.

I have a data set of 736 measurements (weight), taken within 3 different age groups, on 497 individuals who fall into two morphological catagories (horn types).

My model is: Y ~ weight + horn type / age group, random=~1|individual

I am modeling this using glmm.PQL function with family=neg.bin (negative binomial distribution, estimating theta based upon a glm without individual as a random effect). My data set will not be balanced, with varying numbers of measurements taken on different individuals and some individuals have no weight measures just a morphological type.

My output:

              denDF    numberdf
Intercept     495
weight        232       1
horn type     495       1
horn type:age 232       4

So my question is where do these denDF come from and how are they calculated? I wish to then test significane of these fixed effects and can get F-ratio's and P-values but are these appropriate?

Thank-you for your time.
Kind regards

Matt Robinson

Institute of Evolutionary Biology
Room 413, Ashworth Labs,
King's Buildings,
University of Edinburgh

Tel: 0131 650 5990

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