Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with:
> CoastNear = subset(gel_data, Habitat != "I") The resulting data.frame has three levels for Habitat, but only two of those levels have any records. Then I run: > adonis(CoastNear[,5:118]~Habitat, data = CoastNear,permutations=1000, + method='jaccard') Call: adonis(formula = CoastNear[, 5:118] ~ Habitat, data = CoastNear, permutations = 1000, method = "jaccard") Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Habitat 2.0000000 0.0092966 0.0046483 2.0549327 0.0707 0.005 Residuals 54.0000000 0.1221491 0.0022620 0.9293 Total 56.0000000 0.1314457 1.0000 This appears to be wrong - with only two Habitat levels I should only have 1 Df, shouldn't I? I checked by forcibly excising the third factor level: > CoastNear$Habitat <- as.factor(as.character(CoastNear$Habitat)) > adonis(CoastNear[,5:118]~Habitat, data = CoastNear,permutations=1000, + method='jaccard') Call: adonis(formula = CoastNear[, 5:118] ~ Habitat, data = CoastNear, permutations = 1000, method = "jaccard") Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Habitat 1.0000000 0.0092966 0.0092966 4.1859740 0.0707 0.003 Residuals 55.0000000 0.1221491 0.0022209 0.9293 Total 56.0000000 0.1314457 1.0000 This appears to be correct. Subsetting factors is something I always struggle with in R, but, based on previous experience with lda(), it seems that R generally does the right thing. Am I doing something wrong here, or is there a problem in adonis? Thanks, Tyler ps. Sorry for not supplying a reproducible bit of code. The data.frame is quite large. The general layout is: > head(gel_data) # additional data columns trimmed for email Site Habitat Plot Concate A01 A02 A03 A04 A05 A06 A07 A08 A09 A10 1 PE C 1 PEC1 1 1 1 1 1 1 1 1 1 1 2 PE C 3 PEC3 1 1 1 1 0 1 1 1 1 1 3 PE C 4 PEC4 1 1 1 1 0 1 1 1 1 1 4 PE C 6 PEC6 1 1 1 1 0 1 1 1 1 1 5 PE C 12 PEC12 1 1 1 1 0 1 1 1 1 1 6 PE C 13 PEC13 1 1 1 1 0 1 1 1 1 1 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.