Not  reproducible.
Could you please attach the dataset

QInflAvgbyPlot

Otherwise I don't see anything obviously wrong here.
Ciao!
                                mario

On 30-Sep-11 01:37, kelseyann wrote:
SiteSpp<-
c("ADHALP","ADLCON","ADLARC","BDALAT","BDPARC","BDLCON","BDLARC","AWCAQU","AWERUS","AWEANG","AWDPSI","BWCSTA","BWHPAU","BWETRI","BWERUS","BWDFIS","BWPARC","BWLCON","BWLARC","BWJBIG")

n.SiteSpp<- length(SiteSpp)

   for (i in (1:n.SiteSpp)) {
       QInfl.aov<- aov(AvgOfnumResponse ~ strTrea*strYear,
data=QInflAvgbyPlot, subset=(SiteSpp == SiteSpp[i]))
       print(summary(QInfl.aov))
   }

--
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82

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