[R] Function for translation of a list into a matrix as used by ordination?

[John Kane]

I think you can do this fairly easily with the reshape
package. Is this basically what you want?

x <- "Plot1 Species1    Abundance1
 Plot1 Species2    Abundance2
 Plot2 Species1    Abundance1
 Plot2 Species3    Abundance3 "
 
 xx <- read.table(textConnection(x), header=TRUE,
as.is=TRUE); xx
 names(xx) <- c("plot", "species", "abon")
  
 ab <- melt(xx, id=c("plot", "species"),
measured=c("abon"))
 
 cast(ab, plot~  species + variable)



--- Billy_Schweiger at nps.gov wrote:

> 
> Hello.
> 
> Does anyone know of an existing function that takes
> a list in the form of:
> 
> Plot1 Species1    Abundance1
> Plot1 Species2    Abundance2
> Plot2 Species1    Abundance1
> Plot2 Species3    Abundance3
> .
> .
> .
> PlotN SpeciesN    AbundanceN
> 
> and translates into a matrix in the form of
> 
>       Species1    Species2....      SpeciesN
> Plot1 Abundance1  Abundance2...     AbundanceN
> Plot2 Abundance1  Abundance2...     AbundanceN
> .
> .
> 
> .
> PlotN AbundanceN  AbundanceN...     AbundanceN
> 
> 
> This is a basic operation used in the initial stages
> of ordination etc of
> ecological data (vegetation or other species) that
> is usually stored in a
> database or flatfile in the list format above. It is
> similar to a cross
> tabulation like the function xtabs(), however its
> useful to be able to
> control whether a measured abundance for a taxa is
> included or a boolean
> (presence/absence) for the taxa in a given plot.
> 
> Im new to such analyses in R, but before writing it
> myself hope or suspect
> that such a function or library is out there
> (although I dont see it after
> some quick searching in things like Vegan or
> BiodivesityR or labdsv).
> 
> 
> Thanks
> billy
> 
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