[R] Tukey Test, lme, error: less than two groups
Lilith
sweelith at gmx.de
Thu Dec 2 18:39:10 CET 2010
Dear R-group,
I am trying desperately to get this Tukey test working. Its my first time
here so I hope my question is not too stupid, but I couldn't find anything
helpful in the help or in the forum.
I am analysing a dataset of treated grasses. I want to find out, if the
grasses from different Provenances react differently.
In the aov test I found a significance for the combination Treatment and
provenance:
summary(PAMaov<-aov(PAMval~Treatmentf*Pretreatmentf*Provenancef+Error(Datef/Code)))
Treatmentf:Provenancef p-value: 0.008023 **
In the Linear fixed effects model lme, I can see that there is a
significance for two provenances (HU and ES)
summary(PAM.lme<-lme(PAMval~Treatmentf*Provenancef*Pretreatmentf, random=
~1|Datef/Code,na.action=na.omit))
Value Std.Error DF t-value
p-value
(Intercept) 0.6890317 0.06117401 994 11.263473
0.0000
TreatmentfF -0.2897619 0.05484590 467 -5.283201
0.0000
ProvenancefDE 0.0105873 0.05484590 467 0.193037
0.8470
TreatmentfF:ProvenancefES 0.1647302 0.08226884 467 2.002340
0.0458
TreatmentfF:ProvenancefHU 0.1569524 0.07756381 467 2.023526
0.0436
No the big mystery is the Tukey test. I just can't find the mistake, it
keeps telling me, that there are " less than two groups"
summary(glht(PAM.lme, linfct = mcp(Provenancef = "Tukey")))
Fehler in contrMat(table(mf[[nm]]), type = types[pm]) :
less than two groups
I guess its important to know that I made factors out of some of the data.
Here is the code:
PAMdata$provenance[PAMdata$provenance == "5"] = "ES"
PAMdata$provenance[PAMdata$provenance == "6"] = "HU"
# etc.
Treatmentf <- factor(PAMdata$treatment, levels=c("C","F"))
Datef <- factor(PAMdata$Date, levels=c( "25.05.10 14:00","26.05.10
19:00","27.05.2010 7:30","27.05.10 14:00","01.06.10 14:00","02.06.10
19:00","23.06.10 12:30"),ordered=TRUE)
Pretreatmentf <- as.factor(PAMdata$pretreatment)
Provenancef <- as.factor(PAMdata$provenance)
Greenhousef <- as.factor(PAMdata$greenhouse)
Individualf <- as.factor(PAMdata$individual)
PAMval <- (PAMdata$DataPAM)
Code<-(PAMdata$code)
Thank you for any hint! That Tukey test seems so easy, I just can't find the
mistake....
Thank you very much fpr your help and greetings from Tanzania,
Lilith
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