chris, it seems like you need the plyr package, esp ddply. for example:
stems353 <- data.frame(Time = rep(c("Modern", "Old"), 4),
SizeClass = rep(c("class1","class2"), each = 4),
Species = rep(c("a","b"), each = 4),
Stems = seq(1,8,1))
ddply(stems353, .(Species, SizeClass, Time), summarise,
mean = mean(Stems)
)
On Friday, February 25, 2011 at 2:09 PM, Christopher R. Dolanc wrote:
> I'm trying to use tapply to output means and SD or SE for my data but
> seem to be limited by how many times I can subset it. Here's a snippet
> of my data
>
> > stems353[1:10,]
> Time DataSource Plot Elevation Aspect Slope Type Species
> SizeClass Stems
> 1 Modern Cameron 70F221 1730 ESE 20 Conifer ABCO
> Class1 3
> 2 Modern Cameron 70F221 1730 ESE 20 Conifer ABMA
> Class1 0
> 3 Modern Cameron 70F221 1730 ESE 20 Hardwood ACMA
> Class1 0
> 4 Modern Cameron 70F221 1730 ESE 20 Hardwood AECA
> Class1 0
> 5 Modern Cameron 70F221 1730 ESE 20 Hardwood ARME
> Class1 0
> 6 Modern Cameron 70F221 1730 ESE 20 Conifer CADE
> Class1 15
> 7 Modern Cameron 70F221 1730 ESE 20 Hardwood CELE
> Class1 0
> 8 Modern Cameron 70F221 1730 ESE 20 Hardwood CONU
> Class1 0
> 9 Modern Cameron 70F221 1730 ESE 20 Conifer JUCA
> Class1 0
> 10 Modern Cameron 70F221 1730 ESE 20 Conifer JUOC
> Class1 0
>
> I'd like to see means/SD of "Stems" stratified by "Species", "Time" and
> "SizeClass". I can get R to give me this for means by species:
>
> > tapply(stems353$Stems, stems353$Species, mean)
> ABCO ABMA ACMA AECA
> ARME CADE CELE
> 0.7305240793 0.8569405099 0.0003541076 0.0010623229 0.0017705382
> 0.4684844193 0.0063739377
> CONU JUCA JUOC LIDE
> PIAL PICO PIJE
> 0.0017705382 0.0003541076 0.0959631728 0.0138101983 0.3905807365
> 1.5651558074 0.2315864023
> PILA PIMO PIMO2 PIPO
> PISA POTR PSME
> 0.1774079320 0.1880311615 0.0311614731 0.6735127479 0.0237252125
> 0.0506373938 0.2000708215
> QUCH QUDO QUDU QUKE
> QULO QUWI Salix
> 0.0474504249 0.1203966006 0.0000000000 0.2071529745 0.0003541076
> 0.0548866856 0.0003541076
> SEGI TSME
> 0.0021246459 0.5017705382
> >
>
> but I really need to see each species by SizeClass and Time so that each
> value would be labeled something like "ABCOSizeClass1TimeModern".
> Adding 2 variables to the function doesn't seem to work
>
> > tapply(stems353$Stems, stems353$Species, stems353$SizeClass,
> stems353$Time, mean)
> Error in match.fun(FUN) :
> 'stems353$SizeClass' is not a function, character or symbol
>
> I've already created proper subsets for each of these groups, e.g. one
> subset is called "stems353ABCO1" and I can run analyses on this. But,
> trying to extract means straight from those subsets doesn't seem to work
>
> > mean(stems353ABCO1)
> [1] NA
> Warning message:
> In mean.default(stems353ABCO1) :
> argument is not numeric or logical: returning NA
> >
>
> Thanks,
> Chris Dolanc
>
> --
> Christopher R. Dolanc
> PhD Candidate
> Ecology Graduate Group
> University of California, Davis
> Lab Phone: (530) 752-2644 (Barbour lab)
>
>
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>
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>
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