R help - Jul 2006 - 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

	[[alternative HTML version deleted]]

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.
> 
> Ren? Eschen
> 
> CABI Bioscience Centre Switzerland
> Rue des Grillons 1
> 2800 Del?mont
> Switzerland
> 
> 	[[alternative HTML version deleted]]
> 
>