[R] Random structure of nested design in lme

[Doran, Harold]

Can you provide an example of what you have done with lme so we might be able to evaluate the issue? 

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of ESCHEN Rene
> Sent: Wednesday, July 19, 2006 7:37 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Random structure of nested design in lme
> 
> All,
> 
> I'm trying to analyze the results of a reciprocal transplant 
> experiment using lme(). While I get the error-term right in 
> aov(), in lme() it appears impossible to get as expected. I 
> would be greatful for any help.
> 
> My experiment aimed to identify whether two fixed factors 
> (habitat type and soil type) affect the development of 
> plants. I took soil from six random sites each of two types 
> (arable and grassland) and transplanted them back into the 
> sites of origin in such way that in each of the sites there 
> were six pots containing arable soil and six pots of 
> grassland soil, each containing a seedling.
> 
> With aov(), I got the analysis as I expected, with habitat 
> type tested against destination site, and soil type tested 
> against origin site:
> 
> summary(aov(response~soiltype*habitat+Error(destination+origin)))
> #
> #Error: destination
> #          Df  Sum Sq Mean Sq F value Pr(>F)
> #habitat    1  1.0000  1.0000   0.699 0.4226
> #Residuals 10 14.3056  1.4306               
> #
> #Error: origin
> #          Df  Sum Sq Mean Sq F value   Pr(>F)   
> #soiltype   1 1.77778 1.77778  11.636 0.006645 **
> #Residuals 10 1.52778 0.15278                    
> #---
> #Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #
> #Error: Within
> #                  Df  Sum Sq Mean Sq F value Pr(>F)
> #soiltype:habitat   1  0.2500  0.2500  2.1774 0.1427
> #Residuals        120 13.7778  0.1148     
> 
> However, when I try to replicate this analysis in lme, I am 
> unable to get the structure of the random factors (origin and 
> destination) correct. Does anyone have a suggestion how to 
> resolve this problem?
> 
> Thanks in advance.
> 
> René Eschen
> 
> CABI Bioscience Centre Switzerland
> Rue des Grillons 1
> 2800 Delémont
> Switzerland
> 
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