R help - Jul 2007 - presence/absence matrix

I have a table such that:

sample #   species
1    a
1    b
2    a   
2    c
3    b     

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

See ?table  i.e.

 > x
   sample # species
1        1       a
2        1       b
3        2       a
4        2       c
5        3       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


rocchini at unisi.it wrote:
> I have a table such that:
> 
> sample #   species
> 1    a
> 1    b
> 2    a   
> 2    c
> 3    b     
> 
> 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 at 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.
>

What about

table(sample,species)

Stefano


On Fri, Jul 20, 2007 at 04:16:39PM +0200, rocchini a unisi.it wrote:
<rocchini>I have a table such that:
<rocchini>
<rocchini>sample #   species
<rocchini>1    a
<rocchini>1    b
<rocchini>2    a   
<rocchini>2    c
<rocchini>3    b     
<rocchini>
<rocchini>and i would like to build a matrix with species names (i.e. a b
and c)
<rocchini>as field names and samples (i.e. 1,2 and 3) as row names
<rocchini>and 1/0 as inner values
<rocchini>such as:
<rocchini>    a   b   c
<rocchini>1   1   1   0
<rocchini>2   1   0   1
<rocchini>3   0   1   0
<rocchini>
<rocchini>I am currently using Rcmdr package for managing datasets but
need a
<rocchini>function about.... I tried to use stack function but only with
worst results
<rocchini>
<rocchini>Thanks
<rocchini>Duccio
<rocchini>
<rocchini>______________________________________________
<rocchini>R-help a stat.math.ethz.ch mailing list
<rocchini>https://stat.ethz.ch/mailman/listinfo/r-help
<rocchini>PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
<rocchini>and provide commented, minimal, self-contained, reproducible
code.

On 20-Jul-07 14:16:39, rocchini at unisi.it wrote:
> I have a table such that:
> 
> sample #   species
> 1    a
> 1    b
> 2    a   
> 2    c
> 3    b     
> 
> 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.

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Date: 20-Jul-07                                       Time: 16:14:14
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