[R] Nested ANOVA with a random nested factor (how to use the lme function?)

From: Addison, Prue <paddison_at_museum.vic.gov.au>
Date: Mon 18 Jul 2005 - 13:59:58 EST


I am having trouble using the lme function to perform a nested ANOVA with a random nested factor.  

My design is as follows:  

Location (n=6) (Random)

Site nested within each Location (n=12) (2 Sites nested within each Location) (Random)

Dependent variable: sp (species abundance)    

By using the aov function I can generate a nested ANOVA, however this assumes that my nested factor is fixed.  

> summary(aov(sp~Location/Site, data=mavric))

Df Sum Sq Mean Sq F value Pr(>F)

Location 4 112366 28092 1.2742 0.2962

Location:Transect 5 121690 24338 1.1039 0.3736

Residuals 40 881875 22047    

I have tried the following lme function to specify that Site is random:  

> lme1 <- lme(sp~Location, random=~1|Site, data=mavric)

> lme2 <- lme(sp~Location, random=~1|Location/Site, data=mavric)

> anova(lme1)

            numDF denDF F-value p-value

(Intercept) 1 40 3.418077 0.0719

Location 4 5 1.152505 0.4294  

This gives me the correct F-value for Location from MSLocation/MSLocation:Transect, but the p-value doesn't seem to be correct (by my calculations in Microsoft Excel it should be 0.345)  

> anova(lme2)

Warning in pf(q, df1, df2, lower.tail, log.p) :

         NaNs produced

Warning: NAs introduced by coercion

            numDF denDF F-value p-value

(Intercept) 1 40 0.459966 0.5015

Location 4 0 0.155091 NaN  

? I don't know what this output means  

> anova(lme1,lme2)

     Model df AIC BIC logLik Test L.Ratio p-value

lme1 1 7 603.7534 616.4000 -294.8767

lme2 2 8 605.7534 620.2067 -294.8767 1 vs 2 1.815674e-05 0.9966  

? I also don't know what this output means.  

Can anyone tell me if there is a way to use the lme() function in order to obtain the same output as the aov() function (above), but so it correctly calculates the MS, F and p values for my main Location factor?  



This e-mail is solely for the named addressee and may be confidential. You should only read, disclose, transmit, copy, distribute, act in reliance on or commercialise the contents if you are authorised to do so. If you are not the intended recipient of this e-mail, please notify postmaster@museum.vic.gov.au by e-mail immediately, or notify the sender and then destroy any copy of this message. Views expressed in this e-mail are those of the individual sender, except where specifically stated to be those of an officer of Museum Victoria. Museum Victoria does not represent, warrant or guarantee that the integrity of this communication has been maintained nor that it is free from errors, virus or interference.  

Museum Victoria
+61 3 8341 7777
11 Nicholson St

        [[alternative HTML version deleted]]

R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Jul 18 14:07:44 2005

This archive was generated by hypermail 2.1.8 : Fri 03 Mar 2006 - 03:33:46 EST