Re: [R] presence/absence matrix
On 20-Jul-07 14:16:39, [EMAIL PROTECTED] wrote:
> I have a table such that:
>
> sample # species
> 1a
> 1b
> 2a
> 2c
> 3b
>
> and i would like to build a matrix with species names (i.e. a b and c)
> as field names and samples (i.e. 1,2 and 3) as row names
> and 1/0 as inner values
> such as:
> a b c
> 1 1 1 0
> 2 1 0 1
> 3 0 1 0
>
> I am currently using Rcmdr package for managing datasets but need a
> function about I tried to use stack function but only with worst
> results
The following generates the sort of thing you show above:
## Identities of possible species and samples
Species<-c("a","b","c","d")
Samples<-c(1,2,3,4,5,6)
## Generate a set of samples and corresponding species:
species<-sample(Species,20,replace=TRUE)
samples=sample(Samples,20,replace=TRUE)
## Have a look:
cbind(samples,species)
samples species
[1,] "5" "c"
[2,] "2" "c"
[3,] "4" "a"
[4,] "5" "b"
[5,] "5" "d"
[6,] "1" "d"
[7,] "2" "b"
[8,] "2" "b"
[9,] "3" "b"
[10,] "2" "d"
[11,] "4" "d"
[12,] "1" "b"
[13,] "3" "b"
[14,] "2" "c"
[15,] "2" "d"
[16,] "6" "b"
[17,] "5" "a"
[18,] "4" "a"
[19,] "2" "b"
[20,] "5" "a"
## Now generate a table:
T<-table(samples,species)
T
species
samples a b c d
1 0 1 0 1
2 0 3 2 2
3 0 2 0 0
4 2 0 0 1
5 2 1 1 1
6 0 1 0 0
Now this is a "table" structure, and also gives counts of
occurrences and not merely presence/absence. So we need to
get these out as a matrix.
U<-as.matrix(T)
U
species
samples a b c d
1 0 1 0 1
2 0 3 2 2
3 0 2 0 0
4 2 0 0 1
5 2 1 1 1
6 0 1 0 0
U<-1*(U>0)
U
species
samples a b c d
1 0 1 0 1
2 0 1 1 1
3 0 1 0 0
4 1 0 0 1
5 1 1 1 1
6 0 1 0 0
Is that what you want?
Best wishes,
Ted.
E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 20-Jul-07 Time: 16:14:14
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Re: [R] presence/absence matrix
What about table(sample,species) Stefano On Fri, Jul 20, 2007 at 04:16:39PM +0200, [EMAIL PROTECTED] wrote: I have a table such that: sample # species 1a 1b 2a 2c 3b and i would like to build a matrix with species names (i.e. a b and c) as field names and samples (i.e. 1,2 and 3) as row names and 1/0 as inner values such as: a b c 1 1 1 0 2 1 0 1 3 0 1 0 I am currently using Rcmdr package for managing datasets but need a function about I tried to use stack function but only with worst results Thanks Duccio __ 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. __ 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.
Re: [R] presence/absence matrix
See ?table i.e. > x sample # species 11 a 21 b 32 a 42 c 53 b > table(x) species sample # a b c 1 1 1 0 2 1 0 1 3 0 1 0 Regards, Francisco Francisco J. Zagmutt [EMAIL PROTECTED] wrote: > I have a table such that: > > sample # species > 1a > 1b > 2a > 2c > 3b > > and i would like to build a matrix with species names (i.e. a b and c) > as field names and samples (i.e. 1,2 and 3) as row names > and 1/0 as inner values > such as: > a b c > 1 1 1 0 > 2 1 0 1 > 3 0 1 0 > > I am currently using Rcmdr package for managing datasets but need a > function about I tried to use stack function but only with worst results > > Thanks > Duccio > > __ > 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. > __ 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.
