[R] About matrix manipulation

[Rui Barradas]

Hello,

Try the following.


library(reshape2)

# Don't need 'cbind'
mat <- data.frame(sp1=c(rep(0, 5), rep(1, 5)),
         sp2=sample(c(rep(0, 6),rep(1, 4))),
         fac=c(rep("a", 3), rep("b", 3), rep("c", 4)))

mat.new <- matrix (c(0, 1, 1, 1, 1, 1), nrow=2, ncol=3)
rownames(mat.new) <- c("sp1", "sp2")
colnames(mat.new) <- c("a", "b", "c")

m <- melt(mat, id.vars = "fac")
result <- xtabs(value ~ variable + fac, data = m)
result <- apply(result, 2, function(x) ifelse(x == 0, 0, 1))

Hope this helps,

Rui Barradas

Em 21-08-2012 20:29, Thiago Gonçalves-Souza escreveu:
> Dear list,
>
> I'm trying to create a matrix by combining the sites that species occur in
> a new matrix with species as rows and sites as columns.
>
> The main matrix is "mat":
>
> mat <- as.data.frame(cbind(sp1=c(rep(0, 5), rep(1, 5)),sp2=sample(c(rep(0,
> 6),rep(1, 4))),
> fac=c(rep("a", 3), rep("b", 3),rep("c", 4))))
>
> The first two columns are species and the third one is the site that
> species occur (value 1) or not (value 0).
>
> The resulting matrix ("mat.new") should be like this one:
>
> mat.new <- matrix (c(0, 1, 1, 1, 1, 1), nrow=2, ncol=3)
> rownames(mat.new) <- c("sp1", "sp2")
> colnames(mat.new) <- c("a", "b", "c")
> mat.new
>
> So, species are now the rownames and sites are colnames and the values
> within this matrix are the presence/absence of each species. I've tried
> aggregate, tapply, sapply functions but I wasn't able to re-create that
> matrix.
>
> Thanks in advance,
>
> Thiago.
>
> 	[[alternative HTML version deleted]]
>
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