[R] nested anova<-R chrashing
joerg stephan
stephanj at rhrk.uni-kl.de
Mon Sep 12 20:05:43 CEST 2011
Hi,
I tried to do a nested Anova with the attached Data. My response
variable is "survivors" and I would like to know the effect of
(insect-egg clutch) "size", "position" (of clutch on twig) and "clone"
(/plant genotype) on the survival of eggs (due to predation). Each plant
was provided with three different sizes of clutches (45,15,5) and had
pseudo-replications of size 15 and 5 on it.
_Question 1: right code for nested Anova_
Here part of the code I used:
clone1<-as.factor(ifelse(clone=="Gudrun",1,ifelse(clone=="Loden",2,ifelse(clone=="021",3,4))))
plant1<-as.factor(ifelse(plant==1,1,ifelse(plant==2,2,ifelse(plant==3,3,ifelse(plant==4,4,ifelse(plant==5,5,ifelse(plant==6,6,
ifelse(plant==7,7,ifelse(plant==8,8,ifelse(plant==9,9,ifelse(plant==10,10,ifelse(plant==11,11,ifelse(plant==12,12,
ifelse(plant==13,13,ifelse(plant==14,14,ifelse(plant==15,15,ifelse(plant==16,16,ifelse(plant==17,17,ifelse(plant==18,18,
ifelse(plant==19,19,ifelse(plant==20,20,ifelse(plant==21,21,ifelse(plant==22,22,ifelse(plant==23,23,ifelse(plant==24,24,
ifelse(plant==25,25,ifelse(plant==26,26,ifelse(plant==27,27,ifelse(plant==28,28,ifelse(plant==29,29,ifelse(plant==30,30,
ifelse(plant==31,31,ifelse(plant==32,32,ifelse(plant==33,33,ifelse(plant==34,34,ifelse(plant==35,35,ifelse(plant==36,36,
ifelse(plant==37,37,ifelse(plant==38,38,ifelse(plant==39,39,ifelse(plant==40,40,ifelse(plant==41,41,ifelse(plant==42,42,43)))))))))))))))))))))))))))))))))))))))))))
size1<-as.factor(ifelse(size==5,1,ifelse(size==15,2,3)))
position1<-as.factor(ifelse(position==1,1,ifelse(position==2,2,ifelse(position==3,3,
ifelse(position==4,4,ifelse(position==5,5,ifelse(position==6,6,ifelse(position==7,7,
ifelse(position==8,8,ifelse(position==9,9,ifelse(position==10,10,ifelse(position==11,11,ifelse(position==12,12,13)))))))))))))
ANOVA<-aov(survivors~(clone1*size1*position1)+Error(plant1/(size1*position1)))
After that command it says: "Error() model is singular". Even after
googling (looks like many people had that problem) I am still uncertain
how to solve that, mainly because I am not sure if the used code for the
Anova meets my set up requirements. If I am using
"ANOVA<-aov(survivors~clone1*plant1/(size1*position1)))" R sometimes is
even crashing down.
_Question 2: normal distribution and homogeneity of variance_
So fare I tested "normal" Anovas by doing a linear model following
plotting and KS-test and Bartlett-test including Q-Q-plot.
fm<-lm(survivors~clone1*plant1*size1*position1)
Residuen<-resid(fm) Here R is crashing again!!!
ks.test(Residuen,mean(Residuen),sd(Residuen))
plot(density(Residuen))
qqnorm(Residuen)
par(mfrow=c(2,2))
plot(fm)
bartlett.test(survivors~clone1*plant1*position1*size1)
Is that too much to compute for R? Is it OK to look for the
preconditions for that nested Anova in that way, or do I have to use the
same code for the Bartlett also (or evaluate only by looking at the
Graphs (Zuur et al. 2010))??????
Thank you very much in advance
Jörg
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