Patrick Zimmermann wrote:
> Problem: I have a Set of samples each with a list of observed species
> (presence only).
> Data is stored in a excel spreadsheet and the columns (spl) have
> different numbers of observations (spcs).
> Now I want to organize the data in a species by sample matrix with
> presence/absence style in R.
>
> data style (in excel):
>
> spl_A spl_B spl_C
> spcs1 spcs1 spcs2
> spcs2 spcs3 spcs3
> spcs4 spcs5
> spcs5
>
> desired style:
>
> spl_A spl_B spl_C
> spcs1 1 1 0
> spcs2 1 0 1
> spcs3 0 1 1
> .
> .
> .
>
> How and in which form do I import the data to R?
> (read.table() seems not to be appropriate, as data is not organized as a
> table)
>
> How can I create the species by sample matrix?
I'm not going to tackle how to read in the Excel data, but assuming
you had several vectors of species names gather together in a list, you
could construct a presence/absence data frame or matrix as follows:
spl_A <- c("spcs1","spcs2","spcs4","spcs5")
spl_B <- c("spcs1","spcs3")
spl_C <- c("spcs2","spcs3","spcs5")
mylist <- list(spl_A = spl_A, spl_B = spl_B, spl_C = spl_C)
mymat <- sapply(mylist,
function(x){as.numeric(sort(unique(unlist(mylist))) %in% x)})
rownames(mymat) <- sort(unique(unlist(mylist)))
mymat
spl_A spl_B spl_C
spcs1 1 1 0
spcs2 1 0 1
spcs3 0 1 1
spcs4 1 0 0
spcs5 1 0 1
> Thanks for any help,
> Patrick Zimmermann
>
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--
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
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