[R] means, SD's and tapply

[David Winsemius]

On Feb 25, 2011, at 3:09 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)

Some functions let you put an arbitrary number of items after the  
first (aggregate() always confuses me because it _does_ this)  but  
tapply expects them to be in a list or vector, so try:

with( stems353, tapply(Stems, list(Species, SizeClass, Time) , mean) )

with() improves readability

> Error in match.fun(FUN) :
>   'stems353$SizeClass' is not a function, character or symbol

The third item in your arguments got matched to what tapply was  
expecting to be a function name.

>
> 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
>>
>


David Winsemius, MD
West Hartford, CT