[R-sig-eco] Understanding the output from lme anova

[Dunbar, Michael J.]

Dear Petter

It is indeed difficult to read your model because you are converting to factors on-the-fly within the model.

Regarding the nesting, I have never ever seen explicit nesting in the fixed part of the model. Have you copied this format from someone else's model? If you have blocks in the model then they ought to be part of the random effects structure. This sets the structure of the data, and the fixed effects will match across to the relevant level in the random effects: i.e. lme knows which level the fixed effects correspond to, based on how the data are coded. 

To get some help from the list, it would be useful to have the details on what each variable represents. E.g. how many sites do you have - traditionally site identity would be the sort of thing that would be specified as a random effect unless there are very few levels, but it's impossible to help more without more information.

Regards
Mike


-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Hedberg Peter
Sent: 06 December 2010 14:46
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] Understanding the output from lme anova

Dear all.

I have a question regarding how to interpret the output from my lme.anova.

My model looks like this

lme_Cyperaceae<-lme(Cyperaceae~Site+Ditch_block+Tree_cut+as.factor(Dist_start)+((as.factor(Dist_start))*Tree_cut)+((as.factor(Dist_ditch))/Ditch_block),random=~1|Mainplot/Transect/Obsplot)

My question concerns that I use the divission sign to indicate nesting in ((as.factor(Dist_ditch))/Ditch_block), and I use * to indicate two-way interaction in ((as.factor(Dist_start))*Tree_cut), but in the output both terms are presented
with a colon (:) sign.

Tree_cut:as.factor(Dist_start)        3     6  0.259899  0.8520
Ditch_block:as.factor(Dist_ditch)     4    56  2.695738  0.0399

Is there something wrong in how I wrote the model, or is the colon sign  used for all interactions weather nested or the * type.

Would be greatly thankful for any help in understanding this.

The output mentioned above is from an analysis of lme.anova on the result of the lme model.

Best regards,

Petter Hedberg



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