I think you can still read as a table, just use argument fill=TRUE.
Reading from Excel in general: you can save data as 'csv' or tab-delimited
file and then use read.csv or read.delim, respectively, or use one of the
packages listed in the following post (for some reason lines breaks are
messed up but hope you can extract the content):
http://tolstoy.newcastle.edu.au/R/e2/help/07/06/19925.html
## read in data
x <-
read.table(textConnection(
"spl_A spl_B spl_C
spcs1 spcs1 spcs2
spcs2 spcs3 spcs3
spcs4 spcs5
spcs5"
),fill=TRUE,header=TRUE,na.string="")
Then,
## 1. find unique
spcs <- sort(na.omit(unique(unlist(x))))
## 2. create matrix of zeros
mat <- matrix(0,ncol=ncol(x),nrow=length(spcs),
dimnames=list(spcs,names(x)))
## 3. assign zeros to matches
for( i in 1:ncol(mat) ) mat[match(x[,i],rownames(mat)),i] <- 1
Alternatively,
## find unique
spcs <- sort(na.omit(unique(unlist(x))))
## return the matrix you want (combine steps 2 and 3 from above)
sapply(x,function(.x,spcs)
"names<-"(ifelse(!is.na(match(spcs,.x)),1,0),spcs),spcs)
Hope this helps.
ST
--- Patrick Zimmermann <[EMAIL PROTECTED]> 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?
>
> Thanks for any help,
> Patrick Zimmermann
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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