-----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
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