Re: [R] Random structure of nested design in lme

From: ESCHEN Rene <rene.eschen_at_unifr.ch>
Date: Thu 20 Jul 2006 - 02:00:38 EST

Although I know it's not correct, this is what I tried in lme:

anova(lme(NA.1~soiltype*habitat,random=~1|destination/habitat/origin/soiltype))

#                 numDF denDF   F-value p-value
#(Intercept)          1   130 12.136195  0.0007
#soiltype             1   130 15.099792  0.0002
#habitat              1    10  0.699045  0.4226
#soiltype:habitat     1   130  2.123408  0.1475

René.

-----Original Message-----
From: Doran, Harold [mailto:HDoran@air.org] Sent: Wed 2006-07-19 13:53
To: ESCHEN Rene; r-help@stat.math.ethz.ch Subject: RE: [R] Random structure of nested design in lme  

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@stat.math.ethz.ch
> [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of ESCHEN Rene
> Sent: Wednesday, July 19, 2006 7:37 AM
> To: r-help@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
>
> [[alternative HTML version deleted]]
>
>

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